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Compiled by Amit Yadav. amityadav8@gmail.com Last Updated on 30th July 2008.

THE GLOSSARY OF GE ETICS, CELL & MOLECULAR BIOLOGY


free 5' C at the other. The free 3' C normally carries a - OH group and the 5' C a phosphate group. 5' untranslated region: A region of a gene which IS transcribed into mRNA, becoming the 5' end of the message, but which does not contain protein coding sequence. The 5'untranslated region is the portion of the DNA starting from the cap site and extending to the base just before the ATG translation initiation codon. While not itself translated, this region may have sequences which alter the translation efficiency of the mRNA, or which affect the stability of the mRNA. # The short sequence between the transcription initiation site and the start of translation that is retained in mRNA but not translated. It contains the ribosomal binding site (leader sequence) and signal sequence. 5 end: The end of a DNA or RNA strand with a free 5 phosphate group corresponding to the transcription initiation (see also three-prime end).

3' end/5' end: A nucleic acid strand is inherently directional, and the "5 prime end" has a free hydroxyl (or phosphate) on a 5' carbon and the "3 prime end" has a free hydroxyl (or phosphate) on a 3' carbon (carbon atoms in the sugar ring are numbered from 1' to 5'. That's simple enough for an RNA strand or for single-stranded (ss) DNA. However, for doublestranded (ds) DNA it's not so obvious - each strand has a 5' end and a 3' end, and the 5' end of one strand is paired with the 3' end of the other strand (it is "antiparallel". One would talk about the 5' end of ds DNA only if there was some reason to emphasize one strand over the other - for example if one strand is the sense strand of a gene. In that case, the orientation of the sense strand establishes the direction. 3' flanking region: A region of DNA which is NOT copied into the mature mRNA, but which is present adjacent to 3' end of the gene. It was originally thought that the 3' flanking DNA was not transcribed at all, but it was discovered to be transcribed into RNA, but quickly removed during processing of the primary transcript to form the mature mRNA. The 3' flanking region often contains sequences that affect the formation of the 3' end of the message. It may also contain enhancers or other sites to which proteins may bind. 3' untranslated region: A region of the DNA which IS transcribed into mRNA and becomes the 3' end or the message, but which does not contain protein coding sequence. Everything between the stop codon and the polyA tail is considered to be 3' untranslated. The 3' untranslated region may affect the translation efficiency of the mRNA or the stability of the mRNA. It also has sequences which are required for the addition of the poly (A) tail to the message (including one known as the "hexanucleotide", AAUAAA). 3 end: The end of a DNA or RNA strand with a free 3 hydroxyl group corresponding to the end of transcription (see also five-prime end). 5' flanking region: A region of DNA which is NOT transcribed into RNA, but rather is adjacent to 5' end of the gene. The 5'-flanking region contains the promoter, and may also contain enhancers or other protein binding sites. 5' or 3' end The nucleoside residues which form nucleic acids are joined by phosphodiester linkages between the 3' C atom of one ribose moiety and the 5' C atom of the next. Therefore each strand of DNA or RNA has a free 3' C at one end and a

A
A form. A duplex DNA structure with right-handed twisting in which the planes of the base pairs are tilted about 70 with respect to the helix axis. A site: holds the incoming tRNA molecule charged with the next amino acid; the tRNA are held so that the anticodons form base pairs with adjacent complementary codons of the mRNA moving through the ribosome. Abdomen -- region of the body furthest from the mouth. In insects, the third body region behind the head and thorax. Abiotic stress. Outside (nonliving) factors which can cause harmful effects to plants, such as soil conditions, drought, and extreme temperatures. Ablation experiment: An experiment designed to produce an animal deficient in one or a few cell types, in order to study cell lineage or cell function. The idea is to make a transgenic mouse with a toxin gene (often diphtheria toxin) under control of a specialized promoter which activates only in the target cell type. When embryo development progresses to the point where it starts to form the target tissue, the toxin gene is activated, and that specific tissue dies. Other tissues are unaffected. Absorption - the taking in of water and dissolved minerals and nutrients across cell membranes. Contrast with ingestion. Abyssal plain -- the ocean floor offshore from the continental margin, usually very flat with a slight slope. Abzyme. See Catalytic antibody. Acentric fragment: a portion of a chromatid or chromosome that lacks a centromere. Acetal. The product formed by the successive condensation of two alcohols with a single aldehyde. It contains two ether-linked oxygen attached to a central carbon atom. Acetyl-CoA. Acetyl-coenzyme A, a high-energy ester of acetic acid that is important both in the tricarboxylic acid cycle and in fatty acid biosynthesis.

Acrocentric chromosome: A chromosome with its centromere towards one end. Human chromosomes 13,14,15,21,22 are Acrocentric. Acrylamide gels: A polymer gel used for electrophoresis of DNA or protein to measure their sizes (in daltons for proteins, or in base pairs for DNA). See "Gel Electrophoresis". Acrylamide gels are especially useful for high-resolution separations of DNA in the range of tens to hundreds of nucleotides in length. Actin. A protein found in combination with myosin in muscle and also found as filaments constituting an important part of the cytoskeleton in many eukaryotic cells. Actinomycin D pulse experiments The application of actinomycin D to actively metabolizing cells results in the cessation of new RNA transcription. Consequently, serial determinations of specific RNA levels will allow one to calculate the mRNA half-life. Should this vary between control and stimulated conditions, evidence is garnered that a gene of interest is regulated at the level of mRNA stability. Actinomycin D. An antibiotic that binds to DNA and inhibits RNA chain elongation. Activated complex. The highest free energy state of a complex in going from reactants to products. Active site. The region of an enzyme molecule that contains the substrate binding site and the catalytic site for converting the substrate(s) into product(s). Active transport. The energy-dependent transport of a substance across a membrane. Adaptation change in a organism resulting from natural selection; a structure which is the result of such selection. # Adjustment to environmental demands through the long-term process of natural selection acting on genotypes. Adaptive immunity: A collective term for the long-lasting and specific response of lymphocytes to antigens. Requires the MHC, T-cell receptors (TCR) and immunoglobulins (Ig) as well as enzymes with a recombinase activity (for the rearrangements at TCR and Ig gene loci). Present in all vertebrates except jawless fish (see innate immunity). Adaptive radiation. The evolution of new species or sub species to fill unoccupied ecological niches. Additive and non-additive components: In studies of heredity, the portions of the genetic component that are passed and not passed to offspring, respectively. Additive genetic variance: genetic variance atributed to the average effects of substituting one allele for another at a iven locus, or at the multiple loci governing a polygenic trait. Adenine. A purine base found in DNA or RNA. Adenosine Triphosphate ATP: Adenosine 5'- (tetrahydrogen triphosphate). An adenine nucleotide containing three phosphate groups esterified to the sugar moiety. In addition to its crucial roles in metabolism adenosine triphosphate is a neurotransmitter. [MeSH] # The nucleotide formed by adding a pyrophosphate group to the 5'-OH group of adenosine. Adenosine. A purine nucleoside found in DNA, RNA, and many cofactors. Adenylate cyclase. The enzyme that catalyzes the formation of cyclic 3',5' adenosine monophosphate (cAMP) from ATP. Adipocyte. A specialized cell that functions as a storage depot for lipid. Adult - the mature stage of an organism, usually recognized by the organism's attaining the ability to reproduce.

Advanced (synonym: derived; opposite: primitive): In phylogenic studies, an organism or character further removed from an evolutionary divergence than a more primitive one. Aerobe. A microorganism that grows in the presence of oxygen. See Anaerobe. Aerobic -- aerobic organisms require oxygen for their life processes. Affinity Chromatography This separation method depends on using any molecule that can preferentially bind to a protein of interest. Typical methodologies include using lectins (such as wheat germ or concanavalin A) to bind glycoproteins or using covalently coupled monoclonal antibodies to bind specific protein ligands. # A column chromatographic technique that employs attached functional groups that have a specific affinity for sites on particular proteins. Agarose Gel Electrophoresis - A method for separating nucleic acids (DNA or RNA) within a gel made of agarose in a suitable buffer under the influence of an electrical field. Suitable for separation of large fragments of nucleic acid, separation is based primarily upon the size of the nucleic acid. # A matrix composed of a highly purified form of agar that is used to separate larger DNA and RNA molecules ranging 20,000 nucleotides. (See Electrophoresis.) Agarose gels: A polysaccharide gel used to measure the size of nucleic acids (in bases or base pairs). See "Gel Electrophoresis". This is the gel of choice for DNA or RNA in the range of thousands of bases in length, or even up to 1 megabase if you are using pulsed field gel electrophoresis. Agnatha (means jawless): The Class Agnatha represents the most primitive jawless vertebrates. MHC genes have been cloned from all vertebrate classes except Agnatha. Agrobacterium tumefaciens: A soil bacterium that causes a cancer-like plant disease (crown gall) in dicotyledenous plants (all agricultural crops except cereals). It contains the Ti plasmid. The tumor induction ability of the bacterium spreads to neighboring cells via the plasmid. a-helix: Common secondary structure of proteins in which the linear sequence of amino acids is folded into a spiral that is stabilized by hydrogen bonds between the carboxyl oxygen of each peptide bond. Alcohol. A molecule with a hydroxyl group attached to a carbon atom. Aldehyde. A molecule containing a doubly bonded oxygen and a hydrogen attached to the same carbon atom. Algae: A heterogeneous group of aquatic, unicellular, colonial or multicellular, eukaryotic and photosynthetic organisms. They belong to the Kingdom Protista and include the multicellular red (rhodophyte), green and brown (kelp) algae. They are not plants but all land plants evolved from the green algae (see also Chromista). Alginate -- component of the cell walls of many rhodophytes and kelps. Alginates have an affinity for water, and so help to slow dessication when the algae are exposed to the air; they are commercially important in the production of paper, toothpaste, beer, and frozen foods. Alkaline -- term pertaining to a highly basic, as opposed to acidic, subtance. For example, hydroxide or carbonate of sodium or potassium. Allee effect: The benefit individuals gain from the presence of conspecifics. Link to a brief explanation of Allee effect. Allele - One of two or more alternative forms of a gene that may occupy the same locus on a particular chromosome #Alternate

forms of a gene or DNA sequence, which occur on either of two homologous chromosomes in a diploid organism. (See DNA polymorphism.) # A known variation (version) of a particular gene. Formerly called allelomorph. # One of a series of possible alternative forms of a given gene, differing in DNA sequence and affecting the functioning of a single product (RNA or protein Allele frequencies (or gene frequencies) - the proportions of different alleles present at a particular locus in a population of organisms. # The percentage of all alleles at a given locus in a population gene pool represented by a particular allele. Allele-specific hybridization If the nucleotide basis for a specific genetic abnormality is known, oligonucleotides specific for wild type and for mutant sequence can be designed and used to probe Southern blots of an individuals genomic DNA. The pattern of hybridization thus gives specific information regarding which alleles are present. In a polymorphic disease such as thalassemia (in which multiple mutations can give rise to the same disease phenotype), multiple probes might be required to detect all possible causes. In addition, new mutations causing the same disease would be missed. However, should a specific probe prove useful for one population group or be positive in one family member, that probe becomes very useful for the individual under study. Allele-specific PCR By using generic PCR primers flanking the immunoglobulin or T cell receptor genes, the precise rearranged gene characteristic of a B or T cell neoplasm can be amplified and sequenced. Once so obtained, new PCR primers can then be designed that are unique to the patients tumor. Such allele-specific PCR can then be used to detect blood cell contamination by tumor and to detect minimal residual disease following therapy. Allelic exclusion: Expression of only one of the two homologous alleles at a locus in the case of heterozygosity. This usually occurs at loci such as immunoglobulin or T cell receptor (TCR) genes where a functional rearrangement among genes takes place. One of the alleles is either nonfunctionally or incompletely rearranged and not expressed. This way, each T-cell expresses only one set of TCR genes. Allelopathy: The influence exerted by a living plant on other plants nearby or microorganisms through production of a chemical. Allens Rule: Within species of warm-blooded animals (birds + mammals) those populations living in colder environments will tend to have shorter appendages than populations in warmer areas. Alliance for Cellular Signaling AfCS: The overall goal of the Alliance for Cellular Signaling is to understand as completely as possible the relationships between sets of inputs and outputs in signaling cells that vary both temporally and spatially. The same goal, stated from a slightly different perspective, is to understand fully how cells interpret signals in a context-dependent manner. This will involve identification of all the proteins that comprise the various signaling systems, the assessment of time- dependent information flow through the systems in both normal and pathological states, and finally the reduction of the mass of detailed data into a set of interacting theoretical models that describe cellular signaling. http://www.afcs.org/ Allochthonous refers to something formed elswhere than its present location. Antonym of autochthonous.

Allogeneic: Two genetically dissimilar individuals of the same species like any two human beings except monozygotic twins. Allometry Equation: Most lines of relative growth conform to y = bxa where y and x are the two variates being compared, b and a are constants. The value of a, the allometric exponent, is 1 one the growth is isometric; allometry is said to be positive when a>1 and negative when a<1. Allophenic: Chimeric, i.e., composed of cells of two different genotypes (also called hybrid). Allopolyploidy: the combination of genetically distinct chromosome sets that results in a polyploid organism. Allorecognition: Recognition by T cells of the MHC molecules on an allogeneic individuals antigen-presenting cells which results in allograft rejection in vivo and mixed lymphocyte reaction (MLR) in vitro. Allosteric enzyme. An enzyme whose active site can be altered by the binding of a small molecule at a nonoverlapping site. Allosteric protein: a protein that may change its shape as a consequence of interaction with another molecule. Allozygosity: having two homologous genes at one locus that are of independent origin, as far as can be determined from a pedigree. Allozymes - Alternative enzyme forms found in a population, encoded by different alleles at the same locus. Altered self: A term used to describe the MHC molecule associated with a peptide rather than in its native form. Thus, a native MHC molecule does not induce an immune reaction except when it is presenting a peptide. Alternation of generations: An alternation of sexual (haploid) and asexual (diploid) form of generations in a life cycle (example: aphids). The relative dominance of each phase is variable in each organism (mosses have a dominant haploid phase whereas angiosperms have a dominant diploid phase). Besides aphids, Daphnia (water flea), rotifers, Hydra have alternation of generations in response to environmental conditions. # Life cycle in which haploid and diploid generations alternate with each other. Alternative mR A splicing. The inclusion or exclusion of different exons to form different mRNA transcripts. (See RNA.) Alternative splicing: Formation of diverse mRNAs through differential splicing of the same RNA precursor. Altruism: Helping others without direct benefit, and sometimes harm, to oneself. Ambulacra -- row of tube feet of an echinoderm. Amino acid. unit molecule from which proteins are constructed by polymerization. # Any of 20 basic building blocks of proteins composed of a free amino (NH2) end, a free carboxyl (COOH) end, and a side group (R). # The 20 basic building blocks of proteins, consisting of the basic formula NH2-CHR-COOH, where "R" is the side chain which defines the amino acid: Amino Terminus - Refers to the NH2 end of a peptide chain. Amino-acyl trna synthetase: an enzyme that activates amino acids and attaches each activated amino acid to its own species of tRNA. Amp resistance: See "Antibiotic resistance". Amphiesma -- the outer covering of a dinoflagellate, consisting of several membrane layers. Amphipathic: A molecule that has both a hydrophobic and a hydrophilic part.

Amphotropic viruses Retroviruses whose coat proteins bind to a receptor found throughout multiple species, usually including man, making these vectors suitable for human use. Ampicillin (beta-lactamase). An antibiotic derived from penicillin that prevents bacterial growth by interfering with cell wall synthesis. Amplification - Refers to the production of additional copies of a chromosomal sequence, found either as intrachromosomal or extrachromosomal DNA. Also refers to the in vitro process in the polymerase chain reaction. Amplify. To increase the number of copies of a DNA sequence, in vivo by inserting into a cloning vector that replicates within a host cell, or in vitro by polymerase chain reaction (PCR). Amplimer - Region of DNA sequence which is amplified during a PCR reaction and which is defined by a pair of PCR primers (these primer pairs are sometimes called amplimers). Anaerobe. An organism that grows in the absence of oxygen. See Aerobe. Anaerobic -- anaerobic organisms do not require oxygen for their life processes, in fact oxygen is toxic to many of them. Most anaerobic organisms are bacteria or archaeans. Anagensis -- evolutionary change along an unbranching lineage; change without speciation. Analogy: A similarity due to convergent evolution (common function) but not inheritance from a common ancestor (bats wings and birds wings). See also homology. Ancestor -- any organism, population, or species from which some other organism, population, or species is descended by reproduction. Anchor Sequence - A hydrophobic amino acid sequence which fixes a segment of a newly synthesized, translocating protein within the lipid bilayer membrane of the endoplasmic reticulum. Andesite -- igneous volcanic rock, less mafic than basalt, but more mafic than dacite; rough volcanic equivalent of diorite. Anemophily -- seed plants which are pollinated by wind are said to be anemophilous. Aneuploidy: a condition in which the chromosome number of an individual is not an exact multiple of the typical haploid set for the species. Angiogenesis: The growth of new blood vessels - is an important natural process occurring in the body, both in health and in disease. The healthy body controls angiogenesis through a series of "on" and "off" switches: When angiogenic growth factors are produced in excess of angiogenesis inhibitors, the balance is tipped in favor of blood vessel growth. When inhibitors are present in excess of stimulators, angiogenesis is stopped. The normal, healthy body maintains a perfect balance of angiogenesis modulators. In many serious diseases states, the body loses control over angiogenesis. Angiogenesis- dependent diseases result when new blood vessels either grow excessively or insufficiently. Angiogenesis therapies - designed to "turn on" or "turn off" - are revolutionizing medicine by providing a unified approach for treating crippling and life-threatening conditions. Currently, more than 200 biotechnology, genomics, and medical device companies and every major pharmaceutical company is racing to develop new angiogenesis- based medicines. Angiosperm: common name for flowering plants. The term refers to the fact that the seeds are enclosed within an ovary which matures into a fruit. # The most recently evolved and

the largest group of plants whose reproductive organs are in their flowers (flowering plants). A superclass in the sperm plants (Spermatophyta) division belonging to the vascular plants (Tracheophyta) phylum of the plant kingdom. They are divided into two subclasses: Dicots (Magnoliopsida such as magnolia, dandelion, roses, violet) and Monocots (Liliopsida such as lilly, iris, orchid, grasses). Their ovules are enclosed in the carpel and pollen travels through the pollen tube to reach it. Angiosperms evolved in the Cretaceous era together with the Mammals. Angiosperms in Tree of Life. Angstrom (). A unit of length equal to 10-10 m. Anisogamy: Sexual reproduction in which one sex produces sex cells much larger (egg) than those of the other (sperm). Anneal. Generally synonymous with "hybridize". # The pairing of complementary DNA or RNA sequences, via hydrogen bonding, to form a double-stranded polynucleotide. Most often used to describe the binding of a short primer or probe. Annealing Formation of double-stranded molecules from two single strands of nucleic acid by base pairing of complementary sequence. Usually achieved incubation at a favourable temperature. Anomers. The sugar isomers that differ in configuration about the carbonyl carbon atom. This carbon atom is called the anomeric carbon atom of the sugar. Antagonistic pleiotropy: The effects of a gene which are beneficial early in life (i.e., increasing fitness) but deleterious later in life (no change in fitness after the reproductive age). Such genes will be maintained by selection, because by the time the gene exerts its damage, its bearers will already have had more offspring than other individuals. Anther -- the pollen producing tip of a stamen; part of a flower. More info? Antheridium -- the organ on a gametophyte plant which produces the sperm cells. Anthophyte -- a flowering plant, or any of its closest relatives, such as the bennettitales, gnetales, or pentoxylales. Anthropology: The study of human kind. Antibiotic resistance. The ability of a microorganism to produce a protein that disables an antibiotic or prevents transport of the antibiotic into the cell. #Plasmids generally contain genes which confer on the host bacterium the ability to survive a given antibiotic. If the plasmid pBR322 is present in a host, that host will not be killed by (moderate levels of) ampicillin or tetracycline. By using plasmids containing antibiotic resistance genes, the researcher can kill off all the bacteria which have not taken up his plasmid, thus ensuring that the plasmid will be propagated as the surviving cells divide. Antibiotic. A class of natural and synthetic compounds that inhibit the growth of or kill other microorganisms. (See Antibiotic resistance, Bacteriocide, Bacteriostat.) Antibody. A specific protein that interacts with a foreign substance (antigen) in a specific way. # An immunoglobulin protein produced by B-lymphocytes of the immune system that binds to a specific antigen molecule. (See monoclonal antibodies, polyclonal antibodies.) Anticline a fold of rock layers that is convex upwards. Antonym of syncline. Anticodon. A nucleotide base triplet in a transfer RNA molecule that pairs with a complementary base triplet, or codon, in a messenger RNA molecule. See Codon, mRNA, RNA. # A sequence of three bases on the transfer RNA that pair with the bases in the corresponding codon on the messenger RNA.# The

triplet of nucleotides in a transfer RNA molecule which associates by complementary base pairing with a specific triplet codon in the messenger RNA molecule during its translation in the ribosome Antigen. Any foreign substance, such as a virus, bacterium, or protein, that elicits an immune response by stimulating the production of antibodies. (See Antigenic determinant, antigenic switching.) # Any macromolecule that triggers an immune response. Antigenicity depends on the ability of the peptide fragments to be presented by the MHC molecules Antigenic determinant. A surface feature of a microorganism or macromolecule, such as a glycoprotein, that elicits an immune response. Antigenic switching. The altering of a microorganism's surface antigens through genetic rearrangement, to elude detection by the host's immune system. Antimicrobial agent. Any chemical or biological agent that harms the growth of microorganisms. Anti-oncogene. See Recessive oncogene. Antiparallel b-pleated sheet (b-sheet). A hydrogen bonded secondary structure formed between two or more extended polypeptide chains. Anti-parallel: the opposite strand orientations with which all nucleic acid duplexes associate; if one strand is oriented left to right 5' to 3', the complementary strand is oriented left to right 3' to 5'. Antisense oligonucleotides By introducing short single stranded deoxyribonucleic acids (ODN) into a cell, specific gene expression can be interrupted. Several mechanisms have been postulated to account for these results including interruption of ribosome binding to mRNA, enhanced degradation of mRNA mediated by the double-strand specific RNAseH, DNA triplex formation, and impairment of translation efficiency. Most successful attempts using antisense ODN have targeted sequences surrounding and including the initiation codon. To reduce nuclease attack, the antisense ODN are often synthesized using an altered chemistry involving thiol rather than phosphodiester linkages. Antisense strand (or primer) - refers to the RNA or DNA strand of a duplex molecule which is complementary to that encoding a polypeptide. More specifically, the DNA strand which serves as template for the synthesis of RNA and which is complementary to it. "antisense oligonucleotides" hybridize to mRNA, and are used to prime cDNA synthesis. AP-1 site: The binding site on DNA at which the transcription "factor" AP-1 binds, thereby altering the rate of transcription for the adjacent gene. AP-1 is actually a complex between cfos protein and c-jun protein, or sometimes is just c-jun dimers. The AP-1 site consensus sequence is (C/G)TGACT(C/A)A. Also known as the TPA-response element (TRE). [TPA is a phorbol ester, tetradecanoyl phorbol acetate, which is a chemical tumor promoter] Aperture small opening, for example the opening in the test of a foram. Apes: Species belonging to the Family Pongidae of the Order Primates: Gibbon (genus Hylobates), Orangutan (genus Pongo), Chimpanzee (genus Pan), and Gorilla (genus Gorilla). They have no tails. Apical meristem -- group of cells at the growing tip of a branch or root. It divides cells to create new tissues.

Apo activator. A regulatory protein that stimulates transcription from one or more genes in the presence of a coactivator molecule. Apoptosis: The genetically programmed death of cells at specific times during embryonic morphogenesis and development, metamorphosis, and during cell turnover in adults including the maturation of T and B cells of the immune system. Defects in apoptosis are associated with maintenance of the transformed state and cancer. Anti-apoptotic proteins include Bcl-2 and HSP families (see also caspase). Apoptosis is often induced by activation of death receptors (DR) belonging to the tumor necrosis factor receptor (TNFR) family. Examples are Fas (CD95), TNFR-1 and TNFR-related apoptosis-mediated protein (TRAMP). Death signals are conducted through a cytoplasmic motif (death domain - DD) - death-inducing signaling complex (DISC) and caspase-8 that leads to the activation of caspase cascade and eventual death of the cell. Apoptosis: The molecular and morphological processes leading to controlled cellular self- destruction was first introduced in a publication by Kerr, Wyllie and Currie (Br. J. Cancer, 1972, 26: 239). 'Apoptosis' is of Greek origin, having the meaning "falling off or dropping off", in analogy to leaves falling from trees or petals from flowers. By choosing this term, the authors might have intended to stress that this form of cell death is a natural phenomenon, an active and defined process which plays an important role in the regulation of the cell population in tissues upon physiological and pathological conditions. Apoptotic cell death can be induced by a variety of stimuli, such as ligation of cell surface receptors, starvation, growth factor/ survival factor deprivation, heat shock, hypoxia, DNA damage, viral infection, and cytotoxic/ chemotherapeutical agents. The apoptotic process is of widespread biological significance, and it was reported to be involved in embryogenesis, differentiation, proliferation/ homoeostasis, removal of defect and therefore harmful cells, and especially in the regulation and function of the immune system. Thus, dysfunction or disregulation of the apoptotic program is implicated in a variety of pathological conditions, such as immunodeficiency, auto- immune diseases, neurodegenerative diseases, and cancer. One of the two mechanisms by which CELL DEATH occurs (the other being the pathological process of NECROSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic D A (DNA FRAGMENTATION) at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth. [MeSH, 1993] Aposematic coloring: Coloration that warns the predators about poisonous or distasteful nature of the organism. Usually black and yellow stripes in animal. Aposematic coloring of poisonous organisms is sometimes mimicked by others to gain advantage against predators (mimicry). (Link to an interesting article by Lev-Yadun on aposematic coloring in plants.) Arabidopsis thaliana: A small member of the mustard family (kitchen cress). It has a very small genome (130-140 Mbp), five chromosomes and contains almost no repetitive DNA. Its genome will be completely sequenced by the end of 2000. It is a plant model system of choice because of the additional advantages of short generation time (about five weeks), high

seed production (up to 40,000 seeds per plant) and natural self-pollination (as opposed to natural cross-pollination in maize). It has five small chromosomes. Link to Arabidopsis website. Arboreal: Tree-living (like monkeys). Archaea: A prokaryote kingdom that has not diverged much from the ancestral prokaryote stock. Contemporary species of Archeabacteria live in extreme conditions. The three major groups are halobacteria, sulphobacteria and methanogens. All other prokaryotes are grouped in Eubacteria. Archegonium -- the organ on a gametophyte plant which produces the egg cell, and nurtures the young sporophyte. Archezoa: One of the kingdom level taxa proposed by Cavallier-Smith which consists of the most ancient unicellular eukaryotes with a nucleus and rod shaped chromosome but no mitochondria or plastid, thus believed to be the intermediate stage between prokaryotes and eukaryotes. They are also used as evidence for the evolution of nucleus before the organelles. The intestinal parasite Giardia lamblia (a protist) is an example. ARS: Autonomously replicating sequence. ARS is the origin of replication in yeast. Artificial cells: Artificial cells designed for specific applications combine properties of biological systems such as nanoscale efficiency, self- organization and adaptability at relatively low cost. Individual components needed for such structures have already been developed, and now the main challenge is to integrate them in functional microscopic compartments. [Andrew Pohorille, "Artificial cells, prospects for biotechnology" Trends in Biotechnology, 20 (3): 123- 128, Mar. 2002] Artificial chromosome DNA constructs that are composed of, at least, elements such as a REPLICATION ORIGIN; TELOMERE; and CENTROMERE, that are required for successful replication, propagation to and maintenance in progeny cells. In addition, they are constructed to carry other sequences for analysis or gene transfer. [MeSH, 2001] # A vector constructed from host cell chromosomal elements such as origin of replication, telomeres and centromere (in eukaryotes). So that it replicates and is segregated during cell division in the same way as a normal chromosome. The main uses are in preparation of genomic libraries since very large inserts (in the Mbp range) can be integrated. Has also been used in expression studies. Yeast artificial chromosomes (YACs) are the most commonly used form. Artificial selection: Selective evolutionary pressure imposed by humans to obtain breeds with certain features (such as breeding cows, dogs, chicken). Asexual reproduction - Growth and cell duplication that does not involve the union of nuclei from cells of opposite mating types. # A type of reproduction involving only one parent that usually produces genetically identical offspring. Asexual reproduction occurs without meiosis or syngamy, and may happen though budding, by the division of a single cell, or the breakup of an entire organism into two or more parts. Assembled epitope - see conformational epitope. Association (genetic): Association refers to a concurrence greater than predicted by chance between a specific allele and another trait (for example, a disease) that may or may not have a genetic basis. Evaluation of association requires the study of unrelated individuals. Association studies may prove useful in identifying a genetic factor in a disease. Except when linkage

disequilibrium exists, association is not due to genetic linkage and should not be confused with it. Assortative matings: sexual reproduction in which there is a tendency for males of a particular kind to mate with females of a particular kind # Reproduction in which mate selection is not random but is based on physical, cultural, or religious grounds (see negative and positive assortative mating). Asymmetric carbon. A carbon that is covalently bonded to four different groups. ATG or AUG: The codon for methionine; the translation initiation codon. Usually, protein translation can only start at a methionine codon (although this codon may be found elsewhere within the protein sequence as well). In eukaryotic DNA, the sequence is ATG; in RNA it is AUG. Usually, the first AUG in the mRNA is the point at which translation starts, and an open reading frame follows. i.e. the nucleotides taken three at a time will code for the amino acids of the protein, and a stop codon will be found only when the protein coding region is complete. Atomic mass unit (amu or dalton): The basic unit of mass on an atomic scale. One amu or dalton is one-twelfth the mass of a carbon 12 atom (in other words, the mass of a hydrogen atom, 1.66 x 10-24 g). Therefore, there are 6.023 x 1023 amu in one gram (Avogadro number). ATP -- "adenosine triphosphate". A relatively stable, highenergy molecule used to fuel chemical reactions within cells. See adenosine triphosphate. Attenuator: A provisional transcription stop signal. # a nucleotide sequence that is located upstream of those bacterial operons which encode the enzymes that are involved in the synthesis of amino acids; controls transcription of operons. Australopithecus: The extinct genus of Plio-Pleistocene hominids found in South and East Africa. The evolutionary link between apes and humans. Autochthonous -- refers to something formed in its present location. Antonym of allochthonous. Automorphy: Unique derived characteristic; a trait present in only one member of a lineage or in only one lineage among many. Autopolyploid: a polyploid that originates by the multiplication of one basic set of chromosomes. Autoradiograph: a photographic picture showing the position of radioactive substances in tissues, obtained by coating a squash preparation or a section with a photographic emulsion in the dark, and subsequently developing the latent image produced by the decay radiations. Autoradiography - The technique of exposing film in the presence of disintegrating radioactive particles. Used to obtain information on the distribution of radioactivity in a gel or a thin cell section. # A process to detect radioactively labeled molecules (which usually have been separated in an sds-page or agarose gel) based on their ability to create an image on photographic or x-ray film. This process does not result in a linear relationship between the intensity of the signal and the amount of radioactivity unless special steps are taken. There is now increasing use of phosphorimagers and other modern devices to detect and quantitate radioactive molecules which have been separated in gels. Autoregulation. The process in which a gene regulates its own expression. Autosome: A chromosome other than a sex chromosome. An autosomal gene is a gene on any chromosome other than the sex chromosomes. # A chromosome that is not involved in sex de-

termination. # A chromosome not involved in sex determination. The diploid human genome consists of 46 chromosomes, 22 pairs of autosomes, and 1 pair of sex chromosomes (the X and Y chromosomes). [DOE] Autotroph -- An organism that can form its organic constituents from CO2. # Any organism that is able to manufacture its own food. Most plants are autotrophs, as are many protists and bacteria. Contrast with consumer. Autotrophs may be photoautotrophic, using light energy to manufacture food, or chemoautotrophic, using chemical energy. Autozygosity: having two homologous genes at a given locus that are identical by descent; both genes are derived from the same ancestor. Auxin. A plant growth hormone usually concentrated in the apical bud. Auxotroph. A mutant that cannot grow on the minimal medium on which a wild-type member of the same species can grow. # A mutant microorganism that can be grown only upon minimal medium that has been supplemented with growth factors not required by wildtype strains. Auxotrophic mutant A bacterial strain which has a mutation in at least one of the enzymes in a biochemical pathway responsible for synthesising an essential substance, for example an amino acid. The mutant strain will be unable to grow on minimal salts medium with glucose as sole carbon source unless this is supplemented with the substance which is deficient in synthesis. The mutant phenotype can therefore be easily detected. Avidin - a glycoprotein which binds to biotin with very high affinity (kd = 10-15). Avirulent: having lost the ability to produce disease. Avogadro's number. The number of molecules in a gram molecular weight of any compound (6.023 x 1023). Axil -- the angle formed between a leaf stalk and the stem to which it is attached. In flowering plants, buds develop in the axils of leaves. Axolot l (Ambystoma mexicanum): Literally meaning water monster (in Aztec), axolotl is a salamander (amphibian) extensively used in the evolutionary immunogenetic studies.

B
B cells: One of the major types of cells in the immune system. B cells can differentiate to form memory cells or antibodyforming cells # A major family of small lymphocytes that are responsible for antigen-specific humoral immunity as part of the adaptive immunity. Their antigen receptors are surface immunoglobulins (antibodies). They recognize peptides directly and secrete antibodies by differentiating into plasma cells. They also exist as long-lived memory cells. B Factor: A fungal incompatibility factor. It operates in the Basidiomycetes species Schizophyllum commune (not to be confused with Factor B of the immune system). B form. The most common form of duplex DNA, containing a right-handed helix and about 10 (10.5 exactly) base pairs per turn of the helix axis. BAC: Bacterial artificial chromosome A vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. Based on naturally occurring F-factor plasmid found in the bacterium E. coli. Compare cloning vector. [DOE]. DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for

successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes. [MeSH, 2002] # A cloning vector capable of carrying between 100 and 300 kilobases of target sequence. They are propagated as a mini-chromosome in a bacterial host. The size of the typical BAC is ideal for use as an intermediate in large-scale genome sequencing projects. Entire genomes can be cloned into BAC libraries, and entire BAC clones can be shotgun-sequenced fairly rapidly. Bacillus thuringiensis (Bt). A bacterium that kills insects; a major component of the microbial pesticide industry. # This bacteria is pathogenic to insects and the gene for its toxin is used to create transgenic plants with their own insecticide. Bacillus. A rod-shaped bacterium. Back mutation - reverse the effect of a point or frame-shift mutation that had altered a gene; thus it restores the wild-type phenotype (see revertant). Back translation Use of the experimentally determined amino acid sequence of part or all of a polypeptide to determine the theoretical nucleic acid base sequence(s) which could code for it. This is normally done using a computer programme. Backcross - The cross of an F1 heterozygote with an individual having the genotype of one of its parents. # Crossing an organism with one of its parent organisms. Background extinction: The normal constant occurrence of extinctions. See extinction files in BBC Education. Bacteriocide. A class of antibiotics that kills bacterial cells. Bacteriophage - a virus that infects bacteria; often simply called a phage. The phages which are most often used in molecular biology are the e. Coli viruses lambda, m13 and t7. # A virus that in-fects bacteria. Altered forms are used as vectors for cloning DNA. # Virus which infects and destroys a bacterial host. Some phages, however, will incorporate their DNA into that of their host, and remain dormant for an extended period. For this reason, they have become essential tools of genetic engineers. # Bacterial virus. Lambda bacteriophage is the basis of many E. coli vectors which are used for cDNA and genomic DNA libraries. Filamentous bacteriophages are used to produce single-stranded DNA for sequencing or in vitro mutagenesis (eg. M13), and as vectors for Phage display expression screening systems Bacteriophage lambda: A virus which infects E. coli, and which is often used in molecular genetics experiments as a vector, or cloning vehicle. Recombinant phages can be made in which certain non-essential DNA is removed and replaced with the DNA of interest. The phage can accommodate a DNA "insert" of about 15-20 kb. Replication of that virus will thus replicate the investigator's DNA. One would use phage rather than a plasmid if the desired piece of DNA is rather large. Bacteriostat. A class of antibiotics that prevents growth of bacterial cells. Bacterium. A single-celled, microscopic prokaryotic organism: a single cell organism without a distinct nucleus. Balanced lethal: Lethal mutations in different genes on the same pair of chromosomes that remain in repulsion because of close linkage or crossover suppression. In a closed population, only the trans-heterozygotes (l1 + / + l2) for the lethal mutations survive. Balanced polymorphism: The maintenance of two or more alleles in a population due to a selective advantage of the heterozygote.

Balancing selection: Selection involving opposing forces in which selective advantages and disadvantages cancel each other out. Heterozygote advantage (or overdominant selection) is an example in which an allele selected against in the homozygous state is retained because of the superiority of heterozygotes. Other balanced states may occur including when: an allele is favored at one developmental stage and is selected against at another (antagonistic pleiotropy); an allele is favored in one sex and selected against in another (sexual antagonism); an allele is favored when it is rare and selected against when it is common (negative frequency dependent selection). Band shift assay: see Gel shift assay. Barr body: Also called sex-chromatin body which represents the inactivated X chromosome in the nucleus of somatic mammalian cells. Normally only seen in female cells and not in male cells. # The condensed single x chromosome seen in the nuclei of somatic cells of female mammals. Basal group -- the earliest diverging group within a clade; for instance, to hypothesize that sponges are basal animals is to suggest that the lineage(s) leading to sponges diverged from the lineage that gave rise to all other animals. Basalt -- highly mafic igneous volcanic rock, typically finegrained and dark in color; rough volcanic equivalent of gabbro. Base analog. A compound, usually a purine or a pyrimidine, that differs somewhat from a normal nucleic acid base. Base pair - one pair of complementary nucleotides within a duplex strand of a nucleic acid. Under watson-crick rules, these pairs consist of one pyrimidine and one purine: i.e., C-g, a-t (dna) or a-u (rna). However, "noncanonical" base pairs (e.g., G-u) are common in rna secondary structure. Base stacking. The close packing of the planes of base pairs, commonly found in DNA and RNA structures. Base The adenine, guanine, cytosine or thymine group attached to a nucleotide or nucleoside. Also may be used to refer to a nucleic acid unit within a polynucleotide chain, as when a gene is said to be 2000 bases long. # the purine or pyrimidine component of a nucleotide; often used to refer to a nucleotide residue within a nucleic acid chain. # A compound, usually containing nitrogen, that can accept a H+. It is used to describe the non-sugar components of nucleotides (despite the basic nature of nucleotides, nucleic acids are acidic due to the phosphate atoms they contain). The five bases that form the nucleic acids are adenine (A), guanine (G), cytosine (C), tymine (T) and uracil (U). Basic helix-loop-helix proteins These transcriptional proteins are characterized by two alpha helical regions separated by a loop structure; this domain is involved in protein dimerization. Examples of this family of transcription factors include E12/E47 of the immunoglobulin promoter or Myo D of muscle cell regulation. Bcl-1 This gene, located on chromosome 11 q13, was first identified at the site of translocation p(11;14)(q13;q32), has a strong association with central acinar/mantle cell lym Bedrock -- general term referring to the rock underlying other unconsolidated material, i.e. Soil. Benthic -- organisms that live on the bottom of the ocean are called benthic organisms. They are not free-floating like pelagic organisms are. Bergmanns Rule: Northern races of mammals and birds tend to be larger than Southern races of the same species.

Beta-bend (b-bend) or turn. A characteristic way of turning an extended polypeptide chain in a different direction, involving the minimum number of residues, and held together by hydrogen bonding. beta-D A. The normal form of DNA found in biological systems, which exists as a right-handed helix. beta-Lactamase. Ampicillin resistance gene. (See Selectable marker.) Beta-oxidation (b-oxidation). Oxidative degradation of fatty acids that occurs by the successive oxidation of the b-carbon atom. Beta-sheet (b-sheet). A sheetlike structure formed by the interaction between two or more extended polypeptide chains. Bidirectional replication. Replication in both directions away from the origin, as opposed to replication in one direction only (unidirectional replication). Biejerniks Principle (of microbial ecology): Everything is everywhere; the environment selects. Bilayer. A double layer of lipid molecules with the hydrophilic ends oriented outward, in contact with water, and the hydrophobic parts oriented inward. Bile salts. Derivatives of cholesterol with detergent properties that aid in the solubilization of lipid molecules in the digestive tract. Binary fission: Mode of reproduction not involving any sex but division of a parent cell into two equally sized offspring. Binding site: A place on cellular DNA to which a protein (such as a transcription factor) can bind. Typically, binding sites might be found in the vicinity of genes, and would be involved in activating transcription of that gene (promoter elements), in enhancing the transcription of that gene (enhancer elements), or in reducing the transcription of that gene (silencers). NOTE that whether the protein in fact performs these functions may depend on some condition, such as the presence of a hormone, or the tissue in which the gene is being examined. Binding sites could also be involved in the regulation of chromosome structure or of DNA replication. Binomial theorem: the theorem that gives the terms of the expansion of a binomial expression raised a particular power. Bioaugmentation. Increasing the activity of bacteria that decompose pollutants; a technique used in bioremediation. Biochemical pathway. A series of enzyme-catalyzed reactions that results in the conversion of a precursor molecule into a product molecule. Biochemistry -- the study of those molecules used and manufactured by living things. Biodiversity. The wide diversity and interrelatedness of earth organisms based on genetic and environmental factors. Bioenrichment. Adding nutrients or oxygen to increase microbial breakdown of pollutants. Biofilms. See Microbial mats. Biologics. Agents, such as vaccines, that give immunity to diseases or harmful biotic stresses. Bioluminescence -- the production of light by a chemical reaction within an organism. The process occurs in many bacteria and protists, as well as certain animals and fungi. Bioluminescence. The production of light by a biochemical system. Biomass. The total dry weight of all organisms in a particular sample, population, or area.

Biome: A grouping of plant ecosystems into a large distinct group occupying a major terrestrial region. They are created and maintained by climate. See examples of biomes. Bioremediation. The use of microorganisms to remedy environmental problems. See Bioaugmentation, Bioenrichment. Biosphere: The geographical region of the Earth where life is found. Biostratinomy -- the study of what happens between the death of an organism and burial. Part of taphonomy. Biotechnology. The scientific manipulation of living organisms, especially at the molecular genetic level, to produce useful products. Gene splicing and use of recombinant DNA (rDNA) are major techniques used. Biotic stress. Living organisms which can harm plants ,such as viruses, fungi, and bacteria, and harmful insects. See Abiotic stress. Biotin - a coenzyme which is essential for carboxylation reactions (see avidin). Bipedal: Two-footed posture and locomotion like a human standing upright on the hindlimbs. Biramous -- arthropod appendages that are biramous have two branches, an outer branch and an inner branch. These branches may have separate functions; in crustaceans, for instance, the inner branch of a leg is used for walking, while the outer branch may be paddle-shaped or feathery and often functions as a gill. Contrast with uniramous. Bisporangiate -- when a flower or cone produces both megaspores and microspores, it is said to be bisporangiate. Most flowers are bisporangiate. Bivalent: a pair of homologous, synapsed chromosomes. Blastoderm. The stage in embryogenesis when a unicellular layer at the surface surrounds the yolk mass. Blood -- fluid which circulates throughout the body of an animal, distributing nutrients, and often oxygen as well. Blotting The process of transferring nucleic acids or proteins from an unstable medium eg electrophoresis gel or agar plate onto nylon or nitrocellulose membrane. This allows the blotted material to be analysed by interaction with a specific, labelled probe to test for the presence of a specific molecular structure. For example a particular nucleic acid base sequence can be recognised by base pairing with a nucleic acid probe of complementary sequence # A technique for detecting one RNA within a mixture of RNAs (a Northern blot) or one type of DNA within of a mixture of DNAs (a Southern blot). A blot can prove whether that one species of RNA or DNA is present, how much is there, and its approximate size. Basically, blotting involves gel electrophoresis, transfer to a blotting membrane (typically nitrocellulose or activated nylon), and incubating with a radioactive probe. Exposing the membrane to X-ray film produces darkening at a spot correlating with the position of the DNA or RNA of interest. The darker the spot, the more nucleic acid was present there. (see figure, below) Blueschist -- metamorphic rock formed under great pressures, but not so great temperatures. Blunt end - a terminus of a duplex dna molecule which ends precisely at a base pair, with no overhang (unpaired nucleotide) in either strand. Some but not all restriction endonucleases leave blunt ends after cleaving dna. Bluntended dna can be ligated nonspecifically to other blunt-ended dna molecules (compare with sticky end).

Blunt end End of a DNA fragment produced by a restriction enzyme which cuts both strands of DNA at the same point, leaving no single-stranded sections. DNA with this type of end is more difficult to ligate cD A DNA which has been synthesised using an RNA template (cDNA = copy or complementary DNA). Most frequently used to describe double-stranded DNA copies of mRNA sequences eg. cDNA libraries. May be single or double stranded. Bond energy. The energy required to break a bond. Bony fish (class Osteichthyes): The vertebrate Class evolved after jawless and cartilaginous fishes. They have jaws, their skeleton is made up of bone and their body is covered with overlapping scales. Most familiar freshwater and sea water fishes belong to this group. The living fossil Coelacanth is a bony fish whose relatives (lobe-finned fishes) can be traced back to the Devonian geological period (363-409 Mya). Book lung -- a set of soft overlapping flaps, covered up by a plate on the abdomen, through which oxygen is taken up and carbon dioxide given off. Characteristic of many terrestrial arachnids such as scorpions and spiders. Botryllus schlosseri: A clonal hermaphrodite (Phylum Chordata, Subphylum Tunicata, Class Ascidian=sea squirts). It grows fast, reproduces weekly, and thus, a good model for genetic studies of protochordates. It also has a wellcharacterized allorecognition system called Fu/HC whose functions are prevention of fusion with non-kin and selective fertilization by sperm bearing Fu/HC alleles different from that of the egg. See a webpage about Botryllus. Bottleneck: A drastic reduction in the population size followed by an expansion. This often results in altered gene pool as a result of genetic drift. # A large population passes through a contracted stage and then expands again with an altered gene pool as a consequence of genetic drift; causes fluctuations in gene frequencies. Box - refers to a short nucleic acid consensus sequence or motif that is universal within kingdoms of organisms. Examples of dna boxes are the pribow box (tataat) for rna polymerase, the hogness box (tata) that has a similar function in eukaryotic organisms, and the homeo box. Rna boxes have also been described, such as pilipenko's box-a motif that may be involved in ribosome binding in some viral rnas. bp: Abbreviation for base pair(s). Double stranded DNA is usually measured in bp rather than nucleotides. b-pleated sheet: A planar secondary structure element of proteins. It is created by hydrogen bonding between the backbone atoms in two different polypeptide chains or segments of a single folded chain. Bract -- any reduced leaf-like structure associated with a cone or flower. Brain -- collection of nerve cells usually located at the anterior end of an animal, when present at all. The nerves coordinate information gathered by sense organs, locomotion, and most internal body activities. Branched chain D A (b-D A) A method that exploits the formation of branched DNA to provide a sensitive and specific assay for viral RNA or DNA. The assay is performed in a microtiter format, in which partially homologous oligodeoxynucleotides bind to target to create a branched DNA. Enzyme-labeled probes are then bound to the branched DNA, and light output from a chemiluminescence substrate is directly proportional to the amount of starting target RNA. Standards

provide quantitation. The assay displays a 4 log dynamic range of detection, with greater sensitivity to changes in viral load than RT-PCR based assays. It has been employed to quantitate levels of HIV, HCV, and HBV. Branchpoint. An intermediate in a biochemical pathway that can follow more than one route in following steps. Brevitoxin -- neurotoxin produced by the dinoflagellate ptychodiscus brevis. Bryophyte -- plants in which the gametophyte generation is the larger, persistent phase; they generally lack conducting tissues. Bryophytes include the hepaticophyta (liverworts), anthocerotophyta (hornworts), and bryophyta (mosses). Buffer. A conjugate acid-base pair that is capable of resisting changes in pH when acid or base is added to the system. This tendency will be maximal when the conjugate forms are present in equal amounts.

C
C terminus - see carboxyl terminus. C value: The amount of DNA comprising the haploid genome for a given species (picograms per cell; 2-3 pg in mammals). The C value paradox is the lack of correlation between the C values of species and their evolutionary complexity. For example, some amphibians have 30 times as much DNA as we have but not more complex than humans. CAAT box: A highly conserved DNA sequence found about 75 bp 5 to the site of transcription in eukaryotic genes. Its specific (trans-acting) transcription factor is CTF-1 (NF-1) (see also TATA / Goldberg-Hogness box).# part of a dna sequence possibly involved in binding rna polymerase. c-abl This gene, present on human chromosome 9, encodes a tyrosine kinase whose role in normal hematopoiesis is unclear; however, its fusion to the BCR gene on human chromosome 22, the functional counterpart of the Ph1 chromosome strongly associated with the disease chronic myelogenous leukemia, eliminates the first two or three exons of c-abl and results in unregulated tyrosine kinase activity. The resultant fusion protein is either 210 kDa or 195 kDa. The latter version is more acutely transforming in experimental settings; it is also associated with acute lymphoblastic leukemia and with a worse prognosis in both disease settings. One of the ways in which the unregulated kinase activity may be manifest is through phosphorylation of SHC and/or GRB-2, adopter proteins necessary for coupling growth factor signals to ras. Caenorhabditis elegans: A normally self-fertilizing hermaphrodite soil nematode whose developmental genetics has been extensively studied. It is no more than 1 mm long. Loss of an X chromosome by meiotic disjunction leads to the production of males. The genetic basis of apoptosis was first shown in C.elegans in 1986. It has five equally sized chromosomes and it is the first animal whose whole genome has been sequenced (in 1998). The 97 Mbp genome contains 19,000 genes on 6 chromosomes. About 74% of human genes have their homologues in the C.elegans genome. Links to the C.elegans website and an introduction to C.elegans. Calcareous -- refers to substances containing or composed of calcium carbonate. Calcium carbonate -- a "salt" used by many marine invertebrates, such as corals and echinoderms, and by protists, such as coccolithophorids, to construct their exoskeletons. Calcium phosphate This method relies on the production of a calcium/phosphate/DNA microprecipitate, which is then taken

up by cells by pinocytosis. The method is very effective for a number of commonly used mammalian cell expression systems including COS, BHK, 293, and CHO cells. Cambrian: Cambria is the old name for Wales (UK) where the first skeletalized animal fossils were found. The first period in the Palaeozoic era marked by the occurrence of many forms of invertebrate life (540-500 Mya). The sudden appearance of the major animal phyla in the fossil record during the Cambrian period is called Cambrian explosion. cAMP. 3',5' cyclic adenosine monophosphate. The cAMP molecule plays a key role in metabolic regulation. Camp-cap complex: composed of cyclic amp and catabolite activator protein, this complex binds to a part of the promoter and enhances the affinity of rna polymerase for the promoter. Canopy -- layer of vegetation elevated above the ground, usually of tree braches and epiphytes. In tropical forests, the canopy may be more than 100 feet above the ground. Cap site: The initiation site of transcription in a eukaryotic gene. The initiation of translation of most eukaryotic mRNAs involves recognition of the cap followed by either the first downstream AUG or by a 5 proximal AUG with a consensus sequence surrounding it (like the bacterial Shine-Dalgarno or the viral Kozak sequence). Such a consensus sequence has not been recognized in eukaryotes yet. # Two usages: In eukaryotes, the cap site is the position in the gene at which transcription starts, and really should be called the "transcription initiation site". The first nucleotide is transcribed from this site to start the nascent RNA chain. That nucleotide becomes the 5' end of the chain, and thus the nucleotide to which the cap structure is attached (see "Cap"). In bacteria, the CAP site (note the capital letters) is a site on the DNA to which a protein factor (the Catabolite Activated Protein) binds.. CAP. A 7-methyl guanosine residue linked 5' to 5' through a triphosphate bridge to the 5' end of eukaryotic mrnas; facilitates initiation of translation. # All eukaryotes have at the 5' end of their messages a structure called a "cap", consisting of a 7methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of the mRNA. It is added post-transcriptionally, and is not encoded in the DNA#The catabolite gene activator protein, sometimes incorrectly referred to as the CRP protein. The latter term, in small letters (crp), should be used to refer to the gene but not to the protein. Capping. Covalent modification involving the addition of a modified guanidine group in a 5'-5" linkage. It occurs only in eukaryotes, primarily on mRNA molecules. Capsid -- the protein "shell" of a free virus particle. Carbohydrates -- A polyhydroxy aldehyde or ketone. Class of biochemical compounds which includes sugars, starch, chitin, and steroids. Carbon film -- thin layer of carbon remains of past life found in sedimentary rocks. Carbonate -- sediment, or rocks formed by sediment, derived from the precipitation of calcium, magnesium, or iron carbonates, (caco3, mgco3, or feco3) either from inorganic or oganic sources. For example, limestone or dolomite. Carboxyl terminus - refers to the cooh end of a peptide chain (by custom drawn at the right of a protein sequence) Carboxylic acid. A molecule containing a carbon atom attached to a hydroxyl group and to an oxygen atom by a double bond. Carcinogen. A substance that induces cancer. Carcinoma. A malignant tumor derived from epithelial tissue, which forms the skin and outer cell layers of internalorgans.

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Carnivore -- literally, an organism that eats meat. Most carnivores are animals, but a few fungi, plants, and protists are as well. Carotenoids. Lipid-soluble pigments that are made from isoprene units. Carpel -- a unit of the pistil; it is evolutionarily a modified leaf. Cartilaginous fish (Class Chondrichthyes): The most primitive jawed vertebrates evolved about 400 Mya. Their skeleton is composed of entirely cartilage. The Class includes the sharks, rays and skates (subclass Elasmobranchii) and the ratfish (subclass Holocephali). The earliest taxon which has both MHC class I and class II genes. The next step in the evolutionary ladder is the bony fish. Caspase: Cysteine-containing aspartic acid-specific proteases involved in the execution phase of apoptosis. Fas/Fas ligand system is one activator of caspase-dependent apoptotic cell death. CAT (chloramphenicol acetyl transferase) The bacterial gene for chloramphenicol resistance, chloramphenicol acetyl transferase (CAT) is commonly used as a reporter gene for investigating physiologic gene regulation. The assay depends on the ability of transfected cellular cytoplasm to convert 14C chloramphenicol to its acetylated form in the presence of acetyl CoA. The acetylated forms are separated from the 14C substrate using thin layer chromatography. #An enzyme assay. CAT stands for chloramphenicol acetyl transferase, a bacterial enzyme which inactivates chloramphenicol by acetylating it. CAT assays are often performed to test the function of a promoter. The gene coding for CAT is linked onto a promoter (transcription control region) from another gene, and the construct is "transfected" into cultured cells. The amount of CAT enzyme produced is taken to indicate the transcriptional activity of the promoter (relative to other promoters which must be tested in parallel). It is easier to perform a CAT assay than it is to do a Northern blot, so CAT assays were a common method for testing the effects of sequence changes on promoter function. Largely supplanted by the reporter gene luciferase. Catabolism. That part of metabolism that is concerned with degradation reactions. Catabolite repression. The general repression of transcription of genes associated with catabolism that is seen in the presence of glucose. Catalyst. A compound that lowers the activation energy of a reaction without itself being consumed. # A substance that promotes a chemical reaction by lowering the activation energy of a chemical reaction, but which itself remains unaltered at the end of the reaction. (See Catalytic antibody, Catalytic RNA.) Catalytic antibody (abzyme). An antibody selected for its ability to catalyze a chemical reaction by binding to and stabilizing the transition state intermediate. Catalytic R A (ribozyme). A natural or synthetic RNA molecule that cuts an RNA substrate. Catalytic site. The site of an enzyme involved in the catalytic process. Cataphyll -- in cycads, a scale-like modified leaf which protects the developing true leaves. Catarrhini: One of the two divisions (suborder) of Primates containing the old world monkeys and apes (extinct and

extant). The other division is Platyrrhini (new world monkeys). Catenane. An interlocked pair of circular structures, such as covalently closed DNA molecules. Catenation. The linking of molecules without any direct covalent bonding between them, as when two circular DNA molecules interlock like the links in a chain. Cation. A positively charged ion. CCAAT box: (CAT box, CAAT box, other variants) A sequence found in the 5' flanking region of certain genes which is necessary for efficient expression. A transcription factor (CCAAT-binding protein, CBP) binds to this site. Cdk (cyclin-dependent kinase) A related group of cellular kinases, present in virtually all cells, that are regulated both positively and negatively by specific phosphorylation events and negatively by association with other proteins, and are dependent on cyclins, present only during certain phases of the cell cycle (cdk1activated during G2/M phase, cdk2G1/S phases, cdk4G1/S phases, cdk6G1 phase, cdk7throughout the cell cycle). CdkI (cdk inhibitors) Proteins that inhibit the cdks by stoicheometric combination, arresting cells in G1 phase, and include p27, p21 and the p16 Ink 4A family of proteins. The latter are implicated as tumor suppressor genes, as their deficiency in mice leads to rapid cellular proliferation and a high rate of spontaneous tumor development. Moreover, deficiency of p16 family members has been associated with numerous types of human tumors, including a fraction of cases of B cell ALL and T cell leukemia. cD A - complementary dna. A dna molecule which was originally copied from an rna molecule by reverse transcription. The term "cdna" is commonly used to describe double-stranded dna which originated from a single-stranded rna molecule, even though only one strand of the dna is truly complementary to the rna. #A complementary copy of a stretch of DNA produced by recombinant DNA technology. Usually, cDNA represents the mRNA of a given gene of interest. cD A blunting First and second strand synthesis usually results in nonflush ends. To prepare the cDNA for insertion into a cloning vector, the ends must be made flush with one another. Such blunting reactions can be conducted with a DNA polymerase, such as the Klenow fragment of DNA polymerase I or T4 DNA polymerase. cD A clone: "complementary DNA"; a piece of DNA copied from an mRNA. The term "clone" indicates that this cDNA has been spliced into a plasmid or other vector in order to propagate it. A cDNA clone may contain DNA copies of such typical mRNA regions as coding sequence, 5'-untranslated region, 3' untranslated region or poly(A) tail. No introns will be present, nor any promoter sequences (or other 5' or 3' flanking regions). A "full-length" cDNA clone is one which contains all of the mRNA sequence from nucleotide #1 through to the poly(A) tail. Cdna Library is usually just a mixture of bacteria, where each bacteria carries a different plasmid. Inserted into the plasmids (one per plasmid) are thousands of different pieces of cDNA (each typ. 500-5000 bp) copied from some source of mRNA, for example, total liver mRNA. The basic idea is that if you have a large enough number of different liver-derived cDNAs carried in those bacteria, there is a 99% probability that a cDNA copy of any given liver mRNA exists somewhere in the tube. The real trick is to find the one you want out of that mess - a process called screening (see "Screening"). # A collection of cdna

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fragments, each of which has been cloned into a separate vector molecule. cD A library preparation Once the cDNA has been prepared and sticky ends generated, the library is inserted into a convenient cloning vector. Because of high cloning efficiency, most cDNA libraries are constructed in a phage vector. Typically, if screening is to be performed using a monoclonal antibody, gt 11 is used. If screening is to be performed using oligonucleotide probes, gt 10 can be used. If larger DNA fragments are to be prepared, such as from genomic fragments of DNA, vectors that can accommodate up to 20 kb are available (e.g., Charon 4A). Cell -- fundamental structural unit of all life. The cell consists primarily of an outer plasma membrane, which separates it from the environment; the genetic material (dna), which encodes heritable information for the maintainance of life; and the cytoplasm, a heterogeneous assemblage of ions, molecules, and fluid. Cell commitment. That stage in a cell's life when it be comes committed to a certain line of development. Cell culture: The in vitro propagation of animal of plant cells, in an artificial nutrient medium. [IUPAC Biotech] Cell cycle -- complete sequence of steps which must be performed by a cell in order to replicate itself, as seen from mitotic event to mitotic event. Most of the cycle consists of a growth period in which the cell takes on mass and replicates its dna. Arrest of the cell cycle is an important feature in the reproduction of many organisms, including humans. # All of those stages that a cell passes through from one cell generation to the next. # The growth cycle of a cell from one division to the next. In eukaryotic cells the growth cycle is divided into the following 4 phases: G1- phase: the period of the cycle beginning after mitosis and preceding the initiation of DNA synthesis. S-phase: discrete period of cell cycle when most DNA synthesis occurs. G2- phase: period of cell cycle when cells contain twice the G1 complement of DNA. M-phase: division of the cell into two (cf. mitosis), each with one complete genome. [IUPAC Biotech]. The complex series of phenomena, occurring between the end of one cell division and the end of the next, by which cellular material is divided between daughter cells. [MeSH, 1978] Cell differentiation: Progressive restriction of the developmental potential and increasing specialization of function which takes place during the development of the embryo and leads to the formation of specialized cells, tissues, and organs. [MeSH, 1966] Cell function: The level at which we wish to understand the function of the cell determines to a large extent the degree of experimental reductionism required. The smallest building block required to understand the function of the cell appears to be the protein. While the genetic sequence provides the basic informational foundation of the cell, it is the network of protein- gene, protein- protein, and protein- metabolite interactions - the fluxes and flows of material and information - which result in cell function. Studies of whole cell dynamics currently employ optical imaging of diffusion, generally through the use of steady state or dynamic photobleaching recovery methods. Associated with such studies is the need to label specific intracellular entities. Expansion of these approaches to include the wealth of protein species in the cell will involve development of new labeling methods, new dyes and means of introducing them; widely scaling imaging

techniques permitting examination of the whole cell or of intracellular compartments; MR micro- imaging techniques, particularly those sensitive to chemical species; environmental EM techniques, which may provide the capability of rapid single cell microprobe analysis; creative evanescent wave approaches to characterizing the cell membrane; and new tools capable of mechanical assessment of global (and local) mechanical properties of the cell. ... Ultimately, the systematic characterization of cell biology will be the result of the efforts of a great many laboratories integrated over many years. Archiving and interpreting (understanding) these results will require coordination at all levels. Whether or not the paradigm of the Human Genome Project is appropriate for integrating such celllevel studies was discussed at length with the full realization that overriding clinical, pharmaceutical, and cell biology questions may ultimately focus the effort more effectively than a central coordinating agency. Whatever organizational paradigm is employed, there are fundamental and overriding infrastructural issues which must be addressed at the outset, the most urgent of which are the development of enabling technologies and the creation of highly defined panels of cell types for the use of the research community [National Center for Research Resources "Integrated Genomics Technologies Workshop Report" Jan 1999] Cell fusion: Fusion of somatic cells in vitro or in vivo, which results in somatic cell hybridization. [MeSH] Cell genotype: Genetic makeup of cells. Cell line. An established clone originally derived from a whole organism through a long process of cultivation. # Defined unique population of cells obtained by culture from a primary implant through numerous generations. [IUPAC Tox] Often mammalian. Cell lineage. The pedigree of cells resulting from binary fission. Cell membrane -- the outer membrane of a cell, which separates it from the environment. Also called a plasma membrane or plasmalemma. Cell patterning: The shape of a cell can tell us much about its status. The fate of a cell, whether it will divide, differentiate, or undergo apoptosis, is closely dependent on whether it is spread or rounded. However it is still unclear how cell shape is sensed and how the signal is transduced. In recent years, various forms of photolithography and micro- fabrication technology have made it possible to precisely control the shape of a cell. These technologies involve creating micron scale patterns of cell adhesive islands on a non- adhesive background. Cells seeded on patterned surfaces are only able to attach to the adhesive areas and consequently adopt the shape of the adhesive island. However, the current microfabrication technology only allows patterning on rigid surfaces. Thus after the cell has attached, the experimenter cannot change the shape of the cell nor control the rate of cell spreading. Our goal is to develop a simple patterning technique on flexible polymer surfaces. Though stretching the polymer substrate which cells are attached to, we can control the time as well as the magnitude of cell shape changes. By fully taking advantage of this capability, experiments designed to elucidate the shape signaling pathway can be performed more elegantly and in a more controlled manner. For example, we can now allow cells to fully attach before changing the shape of the cell. This way, biochemical signals that result from the seeding and initial attachment of the cell from solution will no longer add noise to the data. A better understanding of the pathway cell use to sense and respond to shape changes may lead to new

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treatments for various diseases. This talk describes patterning of proteins at surfaces via colloidal assembly, and effects of specific protein patterns on cell organization and behavior. Protein coated colloidal particles are used to pattern proteins on two length scales: the size of individual particles (500 nm 2 microns), and of micropatterns of particle arrays produced via self-assembly and soft lithography (10 100 microns). Interfaces produced in this way show that the organization of cell adhesion proteins on sub-cellular length scales can directly affect cell adhesion, shape and spreading. In particular, by varying the density of particles coated with fibronectin we switched fibroblast cells from a morphology consistent with a static, adhesive state to a morphology consistent with a dynamic, migratory state. In the past, such changes had been seen only in response to changes in protein composition on surfaces. We show that these changes can be directed through protein organization on surfaces. Cell phenotype: Organisms express their genomes in a cellspecific manner, resulting in a variety of cellular phenotypes or phenomes. Mapping cell phenomes under a variety of experimental conditions is necessary to understand the responses of organisms to stimuli. Representing such data requires an integrated view of experimental, computational, and informatic infrastructure. A system, named BioSig, provides the foundation for cataloging cellular responses as a function of specific conditioning, treatment, or staining for either fixed or living cell studies. A data model has been developed to link laboratory notebooks to images and their detailed quantitative analysis in terms of cell morphology, protein expression, or physiomics. The quantitative information constructs a hierarchical representation at tissue, cell, and organelle scales. Several examples of protein expression studies and physiomics will be presented. The informatics architecture is distributed and enables database content to be shared among multiple researchers. Is defined by all of the genes expressed by a given cell under a specific biological circumstance. Until recently, it has been impossible to know how various stimuli alter cell phenotype or the pattern of gene expression to any degree of completion. However, recent advances in genome research make it now possible to embark on an unprecedented, genomic- scale approach to defining and understanding cell phenotype. Cell physiology: While it [prediction of the threedimensional structure and function of proteins from their linear sequence information] would be a remarkable accomplishment, the future achievement of a satisfactory protein structure/ function predictive capability will simply provide a second important substratum upon which to begin the exploration of the intricacies of the operation of the living cell, since it is the interactions among cell proteins which, in large part, define cell physiology. Biologists understand a great deal about the protein constituents of cells, their roles in metabolism, the signaling roles of small molecules and selective modifications of intracellular proteins, and how cellular structures assemble themselves and transduce energy, but it is unlikely that a useful understanding of the cell will be possible until a quantitative appreciation of both rates and equilibria of molecular processes in the living cell is achieved. Cell sorting A very powerful feature of flow cytometry. The ability to use multiparameter analysis to provide the criteria for sorting allows exquisite selection of cell populations for enrichment. Modern commercial cell sorters are able to sort

cells at speeds exceeding 20,000 per second with purities of over 99%. In addition to cells, organelles and in particular chromosomes are also readily purified, flow sorted chromosomes providing the raw material for DNA libraries and chromosome paints. Cell strain: Cells having specific properties or markers derived from a primary culture or cell line. [IUPAC Tox] Cell wall -- any tough layer which surrounds a cell and its cell membrane. In plants, this wall is composed of cellulose. # Rigid structure deposited outside the cell membrane. Plants are known for their cell walls of cellulose, as are the green algae and certain protists, while fungi have cell walls of chitin. # A tough outer coating found in many plant, fungal, and bacterial cells that accounts for their ability to withstand mechanical stress or abrupt changes in osmotic pressure. Cell walls always contain a carbohydrate component and frequently also a peptide and a lipid component. Cellular component: The place in the cell where a gene product is active. Cellular oncogene (proto-oncogene). A normal gene that when mutated or improperly expressed contributes to the development of cancer. (See Oncogene.) Cellular processes: In some cases the machinery that cells use to make decisions is reasonably well understood at a qualitative level. However, in no case do we possess a corresponding quantitative understanding of cellular workings. A reflection of this ignorance is that biology is insufficiently predictive, and that biologists are not very good at predicting the outcomes of perturbations to the genome, the internal workings of the cell, or its external environment. One path to understanding the behavior of these ensembles of components clearly lies in construction of mechanism- based quantitative models that represent cellular processes. Building such models requires solution of numerous computational and even more numerous experimental biological challenges. I will detail some of these, and progress toward surmounting them, in the context of our ongoing work to gain a quantitative predictive understanding of the response of individual yeast cells to an outside stimulus, the mating pheromone. Progress on this work would have positive impacts on scientific understanding, on therapies, and on the development of a design based engineering of biological systems. Cellular resolution: Molecular analysis at the resolution of pure cell populations is proving to be much more informative than data based on mixed cell samples, and is clearly the direction where more research is headed. This conference brings together, for the first time, experts in the technology and applications of molecular analysis at the resolution of pure cell populations. This data is proving to be much more informative than data based on mixed cell samples, and is clearly the direction where more research is headed. Cellular signaling: Cell signaling is at the core of most biological processes and represents a vibrant area of research. Signaling Update provides a one- stop overview of what's happening in cell signaling for the specialist researcher and the interested non- specialist alike. Cellular systems: Cellular systems are organized into networks of modules. A network- clustering method was developed to show this emergent level of biological organization. Abstraction of modular network- structure identifies network elements occupying important positions within and between modules.

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The functions of these elements suggest that they are important for module function and intermodule communication. Cellulose -- carbohydrate polymer of the simple sugar glucose. It is found in the cell walls of plants and green algae, as well as dinoflagellates. Cellulose is the most abundant compound on earth that is manufactured by living things. Centers of origin. Usually the location in the world where the oldest cultivation of a particular crop has been identified. Central dogma. Francis Crick's seminal concept that in nature genetic information generally flows from DNA to RNA to protein. # The concept describing the functional interrelations between dna, rna, and protein; the direction of transmission is dna-->rna-->protein. Centric fusion: breakage in the very short arms of two acrocentric chromosomes, followed by fusion of the long parts into a single chromosome; the two small fragments are usually lost; also known as a robertsonian event or translocation # Fusion of the long arms of two acrocentric chromosomes [13,14,15,21,22] into a single chromosome having lost the short arms at the same time. Most often occurs as 21/21, 13/14, and 14/21 translocations. Apart from being an important cause of uniparental disomy, it may cause trisomy 21 (Downs syndrome) in the offspring. Human chromosome 2 is a result of a centric fusion between two ancestral ape chromosomes (gorillas have 24 pairs of chromosomes). Centrifugation. Separating molecules by size or density using centrifugal forces generated by a spinning rotor. G forces of several hundred thousand times gravity are generated in ultracentrifugation. (See Density gradient centrifugation.) Centrifuge: an apparatus used for the separation of substances by the application of centrifugal force generated by whirling at a high rate of rotation a vessel containing a fluid in which the substances are suspended. Centrioles: - Microtubules which serve as the organization centre of spindle fibres. # a cylindrical cellular organelle that is found in eukaryotes; they migrate to the polar regions of the cell during mitosis and meiosis Centromere - A constricted chromosomal region that is associated with the spindle fibres during mitosis and meiosis. # The central portion of the chromosome to which the spindle fibers attach during mitotic and meiotic division. # a constricted region in eukaryotic chromosomes on which the kinetochore lies. #Constricted region where sister chromatids are attached in mitotic chromosomes. The centromere is generally flanked by repetitive DNA sequences and it is late to replicate. The centromere is an A-T region of about 130 bp. It binds several proteins with high affinity to form the kinetochore which is the anchor for the mitotic spindle. # The clear constricted portion of the chromosome at which the chromatids are joined and by which the chromosome is attached to the spindle during cell division. [MeSH, 1991] Cephalon -- in trilobites, the head shield bearing the eyes, antennae, and mouth. More info? Cetacea: An Order of marine mammals. The suborder Odontocetti includes dolphins, killer whales and toothed whales. Many of the great whales (such as the blue whale) belong to a different suborder (baleen whales or Mysticetti). c-fos This ~62 kDa leucine zipper protein cannot homodimerize but rather functions in heterodimeric complex with c-jun and other members of the AP1 family of transcription factors.

CGH (comparative genome hybridization) In CGH, DNA is extracted from tumor and from normal tissues and differentially labeled with fluorescent dyes. Once the DNA samples are mixed and hybridized to normal metaphase chromosome spreads, chromosomal regions that are underrepresented or overrepresented in the tumor sample can be identified. This method can be applied to extremely small tumor samples (by using PCR methods) of formalin-fixed or frozen tissue. It has been applied to detect loss of chromosome 18q or 17p in colon cancer and is likely to be applied to hematologic malignancies. The sensitivity of the technique approaches 1 cell in 100. Chaetae -- stiff bristles characteristic of annelids. Chain terminator - see dideoxynucleotide. Chaperone proteins - a series of proteins present in the endoplasmic reticulum which guide the proper folding of secreted proteins through a complex series of binding and release reactions.# Any cellular protein that binds to an unfolded or partially folded target protein to prevent misfolding, aggregation, and/or degradation of it. Chaperones also facilitate the target proteins proper folding, translocation and assembly within cells, preventing inappropriate interactions with other proteins. Character -- heritable trait possessed by an organism; characters are usually described in terms of their states, for example: "hair present" vs. "hair absent," where "hair" is the character, and "present" and "absent" are its states. Character displacement: Forced evolution of dissimilar characters in related species where their ranges overlap. Elsewhere, where they exist on their own, their similarities are maintained. Character release: This is the opposite of character displacement. Two closely related species become more alike in regions where their ranges do not overlap than in regions where they do. Chelate. A molecule that contains more than one binding site and frequently binds to another molecule through more than one binding site at the same time. Chelicera -- the first pair of appendages of a chelicerate arthropod. Originally a short clawed appendage, the chelicerae of many arachnids are highly modified for feeding; in spiders, for instance, they are modified into poisonous fangs. Chemiosmotic coupling. The coupling of ATP synthesis to an electrochemical potential gradient across a membrane. Chemotherapy. A treatment for cancers that involves administering chemicals toxic to malignant cells. Chert -- hard, dense sedimentary rock, composed of interlocking quartz crystals and possibly amorphous silica (opal). The origin of the silica is normally biological, from diatoms, radiolaria or sponge spicules. Synonymous with flint. Chiasma (plural chiasmata): The points of physical overlap of nonsister chromatids crossing-over in meiosis. # a point where non-sister chromatids exchanged genetic material during pachynema. # The places at which pairs of homologous chromatids are in contact during meiosis and at which exchanges of homologous parts between chromatids take place by crossing ov Chi-like Sequence: An octamer nucleotide sequence (A/G C/T - A/T - A/G - G - A/T - G - G) that creates a recombinational hotspot in the genome (originally discovered in coliphage lambda). MHC class I transmembrane domain length variation, frequent gene conversions and deletions in the MHClinked 21-hydroxylase gene (CYP21), gene conversions within

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the MHC class II genes in mice and humans, many oncogene translocations (BCL2 for example) are attributed to chi-like sequences at the breakpoint region. It acts like a restriction site for recombinase. Chimeric D A. Recombinant DNA whose components originate from two or more different sources. Chinese hamster ovary cells: See CHO cells. Chiral compound. A compound that can exist in two forms that are non-superimposable images of one another. Chi-square: a statistical procedure that enables the investigator to determine how closely an experimentally obtained set of values fits a given theoretical expectation. Chitin -- carbohydrate polymer found in the cell walls of fungi, and in the exoskeletons of arthropods. It is the compound which makes cockroaches "crunchy". Chlamydomonas: The unicellular green alga that is probably the closest living organism to the ancestor of green plants. It reproduces both asexually and sexually (two mating types). When reproduces sexually, the mitochondria are inherited from the (-) mating type and chloroplasts from the (+) mating type. Chloramphenicol acetyl transferase : see CAT Chloramphenicol. An antibiotic that interferes with protein synthesis. Chlorophyll -- photosynthetic pigment. It includes a magnesium atom surrounded by a porphyrin ring, and often has a long hydrophobic tail # photosynthetic pigment. It includes a porphyrin ring, and often has a long hydrophobic tail. # green photosynthetic pigment that is made of a magnesium dihydroporphyrin complex. CHO cells: Cell line derived from the ovary of the Chinese hamster, Cricetulus griseus. The species is a favorite for cytogenetic studies because of its small chromosome number. The cell line has provided model systems for the study of genetic alterations in cultured mammalian cells. [MeSH, 1992] Chordata: A major phylum in the Kingdom Animalia. A chordate is characterized by the presence of a dorsal notochord at some stage of development and a dorsal hollow nerve chord. Chromatid - In all duplicated chromosomes, the two longitudinal subunits which become visible during mitosis. #Each of the two daughter strands of a duplicated chromosome joined at the centromere during mitosis and meiosis #The structural material of eukaryotic chromosomes, composed of of DNA, proteins, and some RNA, identifiable in cell nuclei because it has special staining properties. # One of two copies of a replicated chromosome during mitosis. Together they are called sister chromatids. Each one becomes a daughter chromosome at anaphase of mitosis and at the second meiotic division. Chromatin. The nucleoprotein fibers of eukaryotic chromosomes. # The complex of DNA and associated histone and non-histone proteins that represents the normal state of genes in the nucleus. It exists in two forms: euchromatin can be transcribed, and heterochromatin is highly condensed and cannot be transcribed. # The material of CHROMOSOMES. It is a complex of DNA, HISTONES, and nonhistone proteins (CHROMOSOMAL PROTEINS, NON- HISTONE) found within the nucleus of a cell. [MeSH, 1972] Chromatography. A procedure for separating chemically similar molecules. Segregation is usually carried out on paper or in glass or metal columns with the help of different

solvents. The paper or glass columns contain porous solids with functional groups that have limited affinities for the molecules being separated. Chromista: A major taxon in the Kingdom Protoctista (also called Heterokonta). They are mostly photosynthetic algae but distinct from the rest of the algae. They have genetic material derived from four different ancestors (purple bacteria, cyanobacteria, red alga and green alga). Link to Chromista. Chromosome arms - The two main segments of the chromosome, separated by the centromere. Cloning development of a whole plant or animal from a single somatic cell OR production of multiple copies of a DNA segment. Chromosome mapping: the process of determining the locations of genes on chromosomes. Chromosome puff. A swollen region of a giant chromosome; the swelling reflects a high degree of transcription activity. Chromosome walking - the sequential isolation of clones carrying overlapping sequences of dna which span large regions of a chromosome. Overlapping regions of clones can be identified by hybridization. #Working from a flanking DNA marker,overlapping clones are successively identified that span a chromosomal region of interest. (See Chromosome.) #A technique for cloning everything in the genome around a known piece of DNA (the starting probe). You screen a genomic library for all clones hybridizing with the probe, and then figure out which one extends furthest into the surrounding DNA. The most distal piece of this most distal clone is then used as a probe, so that ever more distal regions can be cloned. This has been used to move as much as 200 kb away from a given starting point (an immense undertaking). Typically used to "walk" from a starting point towards some nearby gene in order to clone that gene. Also used to obtain the remainder of a gene when you have isolated a part of it Chromosome. A single DNA molecule, a tightly coiled strant of DNA, condensed into a compact structure in vivo by complexing with accessory histones or histone-like proteins. Chromosomes exist in pairs in higher eukaryotes. (See Chromosome walking.) # A thread-like structure, visible in the cell nucleus during metaphase, that carries the hereditary information. # A self-replicating structure consisting of DNA complexed with various proteins and involved in the storage and transmission of genetic information; the physical structure that contains genes. Eukaryotic cells have a characteristic number of chromosomes per cell ( ploidy [haploid or diploid]) and contain DNA as linear duplexes ... The chromosomes of bacteria consist of double- stranded, circular DNA molecules. [MeSH] . One of the threadlike "packages" of genes and other DNA in the nucleus of a cell. Different kinds of organisms have different numbers of chromosomes. Humans have 23 pairs of chromosomes, 46 in all: 44 autosomes and two sex chromosomes. Each parent contributes one chromosome to each pair, so children get half of their chromosomes from their mothers and half from their fathers. [NHGRI]. All human chromosomes should be sequenced to a "finished" state no later than 2003. # Structure in a cell nucleus that carries the genes. Each chromosome consists of one very long strand of DNA, coiled and folded to produce a compact body. They become more compact and visible during metaphase of cell division. In interphase chromosomes, chromatin fibers are organized into 30 to 100 kb loops anchored in a supporting matrix within the nucleus. The length of each DNA molecule must be compressed

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about 8000-fold to generate the structure of a condensed metaphase chromosome. Ciliates: This group of protists are most like animals in their behavior and complexity. The Paramecium is the representative of the Ciliates. Cis - as used in molecular biology, an interaction between two sites which are located within the same molecule. However, a cis-acting protein can either be one which acts only on the molecule of dna from which it was expressed, or a protein which acts on itself (e.g., Self-proteolysis). Cis configuration: the situation in which both mutant alleles of different genes are located on the same homologue; the wildtype alleles are located on the other homologue. Cis dominance. Property of a sequence or a gene that exerts a dominant effect on a gene to which it is linked. Cis-acting factors These are regions at a gene either upstream, within, or downstream of the coding sequence that contains sites to which transcriptionally important proteins may bind. Sequences that contain 5 to 25 nucleotides are present in a typical cis-acting element. Cis-acting gene: A gene acting on or co-operating with another gene on the same chromosome (see trans-acting gene). Cistron - A gene: ie a DNA sequence coding for a single polypeptide #a nucleic acid segment corresponding to a polypeptide chain, including the relevant translational start (initiation) and stop (termination) codons. # A DNA sequence that codes for a specific polypeptide; a gene. See DNA, Gene. #A genetic unit that encodes a single polypeptide chain. # A DNA segment coding for a specific polypeptide, and includes its own start and stop codons. When an mRNA encodes two or more proteins, it is called polycistronic. Citric acid cycle. See tricarboxylic acid (TCA) cycle. c-jun This proto-oncogene encodes a ~45 kDa transcription factor that is a member of AP1 family of transcriptional proteins. c-jun must form dimers to function and does so through the leucine zipper motif. Although c-jun c-jun homodimers do form, they do so with low affinity and are not thought to be critical in gene transcription. Rather, a second partner, usually c-fos, generates the transcriptionally active heterodimer. Clade -- a monophyletic taxon; a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. From the greek word "klados", meaning branch or twig. #All descendants of any given species. A single whole branch of a phylogeny. Cladogenesis -- the development of a new clade; the splitting of a single lineage into two distinct lineages; speciation. Cladogram -- a diagram, resulting from a cladistic analysis, which depicts a hypothetical branching sequence of lineages leading to the taxa under consideration. The points of branching within a cladogram are called nodes. All taxa occur at the endpoints of the cladogram. Class switching: The process by which a IgM or IgD producing B lymphocyte switches to produce one of the secondary immunoglobulins (IgG, IgA or IgE) with the same antigen binding specificity. Class: A category of classification (taxon); a subdivision of subphylum. The classes in the Subphylum Vertebrata are: Pisces (Fishes), Amphibia, Reptilia, Avis (Birds) and Mammalia. Clast -- an individual grain or constituent of a rock.

Clitellum -- in annelids, a swelling of the body towards the head of the animal, where the gonads are located. Both oligochaetes and leeches have a clitellum. Clone - an identical copy of an organism. Most plants, fungi, algae, and many other organisms naturally reproduce by making clones of themselves as a form of asexual reproduction. # describes a large number of cells, viruses, or molecules which are identical and which are derived from a single ancenstral cell, virus or molecule. The term can be used to refer to the process of isolating single cells or viruses and letting them proliferate (as in a hybridoma clone, which is a "biological clone"), or the process of isolating and replicating a piece of dna by recombinant dna techniques ("molecular clone"). The use of the word as a verb is acceptable for the former meaning, but not necessarily the latter meaning.# The term "clone" can refer either to a bacterium carrying a cloned DNA, or to the cloned DNA itself. If you receive a clone from a collaborator, you should first figure out if they send you DNA or bacteria. If it is DNA, your first job is to introduce it ("transform" it) into bacteria [see "Transformation (with respect to bacteria)"]. Occasionally, someone might send just the "insert", rather than the whole plasmid. "You assignment, Jim, if you decide to accept it", is to splice that DNA into a convenient vector, and only then can you transform it into bacteria. Clone (verb): To "clone" something is to produce copies of it. To clone a piece of DNA, one would insert it into some type of vector (say, a plasmid) and put the resultant construct into a host (usually a bacterium) so that the plasmid and insert replicate with the host. An individual bacterium is isolated and grown and the plasmid containing the "cloned" DNA is re-isolated from the bacteria, at which point there will be many millions of copies of the DNA - essentially an unlimited supply. Actually, an investigator wishing to clone some gene or cDNA rarely has that DNA in a purified form, so practically speaking, to "clone" something involves screening a cDNA or genomic library for the desired clone. See also "Probe" for a description of how one might start a cloning project, and "Screening" for how the probe in used. Cloning and Library Screening Obtaining cDNA representing a protein of interest is usuallythe first step in the process of applying the techniques of recombinant DNA research to an important physiologic question. A suitable cDNA library must first be constructed starting with RNA abundant (or as abundant as possible) in the transcripts for the gene of interest. Following library construction a probe must be developed that can specifically recognize the gene or cDNA of interest, or the expressed protein product of the specific cDNA. Cloning. The mitotic division of a progenitor cell to give rise to a population of identical daughter cells or clones. (See Directional cloning, Megabase cloning, Molecularcloning, Subcloning.) c-myb This gene encodes a transcription factor not belonging to any other class previously described and is expressed primarily in immature hematopoietic cells anddeclines as cells differentiate. Forced expression of c-myb tends to block hematopoietic differentiation. Clinically, high levels of myb are noted in acute leukemia, and such patients are less likely to enter remission or tend to have a short remission duration. c-myc This proto-oncogene plays a critical role in hematopoietic cell proliferation. Like the leucine zipper protein, it too functions as a heterodimer. One of its partners is termed Max. The myc-related protein, Mad, also dimerizes with Max; the

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myc/Max complex stimulates proliferation, the Mad/Max complex inhibits myc-function. The importance of dysregulated myc function can be seen in Burkitt lymphoma in which a t(8;14) brings myc, on chromosome 8, into juxtaposition with the immunoglobulin enhancer on chromosome 14. Such upregulation of myc in a B lymphocyte setting results in a proliferative advantage and represents one important step in the genesis of this lymphoma. Myc has both leucine zipper and helix-loop-helix domains. Cnidaria: See Coelamata. Cnidocyst -- the "stinging cell" of a cnidarian. Coadaptation: Interaction of genes at the genotypic level. Natural selection acts on the complex product of such interactions rather than on individual locus. The correlated variation and adaptation present in two mutually dependent organisms. Coalescence theory: The evolutionary theory that estimates the time for divergence from the last common ancestor. A lecture on Coalescent Theory. Coalescence: Growing into each other, uniting into one whole. Link to a lecture on coalescence. Coat protein (capsid). The coating of a protein that enclosed the nucleic acid core of a virus. Coding sequence: The portion of a gene or an mRNA which actually codes for a protein. Introns are not coding sequences; nor are the 5' or 3' untranslated regions (or the flanking regions, for that matter - they are not even transcribed into mRNA). The coding sequence in a cDNA or mature mRNA includes everything from the AUG (or ATG) initiation codon through to the stop codon, inclusive. Coding strand: an ambiguous term intended to refer to one specific strand in a double-stranded gene. See "Sense strand". # the strand of duplex DNA that has the same nucleotide sequence as mrna except that t substitutes in DNA for u in RNA Codominance: Equal effect on the phenotype of two alleles of the same locus (as opposed to recessive and dominant). Codominant alleles - two alleles at a locus which can both be detected phenotypically in a heterozygote individual Codominant: designating genes when both alleles of a pair are fully expressed in the heterozygote. Codon - a nucleotide triplet (sequence of three nucleotides) which specifies a specific amino acid, or a translational start or stop.# A three-base unit of mRNA coded for by a nucleotide sequence in the complementary DNA: code for a specific amino acid NB that most amino acids are specified by more than one codon # Three successive nucleotides on an mRNA that encode a specific amino acid in the polypeptide. Sixty-one codons encode the 20 amino acids, leading to codon redundancy, and three codons signal termination of polypeptide synthesis. # In an mRNA, a codon is a sequence of three nucleotides which codes for the incorporation of a specific amino acid into the growing protein. The sequence of codons in the mRNA unambiguously defines the primary structure of the final protein. Of course, the codons in the mRNA were also present in the genomic DNA, but the sequence may be interrupted by introns Codon bias - the tendency for an organism or virus to use certain codons more than others to encode a particular amino acid. An important detrminant of codon bias is the guanosinecytosine (gc) content of the genome. An organism that has a relatively low g+c content of 30% will be less likely to have a

g or c at the third position of a codon (wobble position) than a a or t to specify an amino acid that can be represented by more than one codon.# Although several codons code for a single amino acid, an organism may have a preferred codon for each amino acid. This is called codon bias. Coefficient of coincidence: an experimental value equal to the observed number of double crossovers divided by the expected number. Coefficient of relatedness: r = n(0.5)L where n is the alternative routes between the related individuals along which a particular allele can be inherited; L is the number of meiosis or generation links. Coefficient of Relatedness: r = n(0.5)L where n is the alternative routes between the related individuals along which a particular allele can be inherited; L is the number of meiosis or generation links. Coelacanth: Any member of a zoological family of largely extinct lobe-finned fish (like the living genus Latimeria). Coelom -- fluid-filled cavity within the body of an animal; usually refers to a cavity lined with specialized tissue peritoneum in which the gut is suspended. The structure and development of the coelom is an important character for recognizing major groups of animals. Coelomata (Cnidaria): A phylum in the Animal Kingdom. They are invertebrate aquatic animals showing radial or biradial symmetry. Examples are corals, sea anemones, jelly fish. See also Cnidaria in the Shape of Life (PBS). Coenocytic -- condition in which an organism consists of filamentous cells with large central vacuoles, and whose nuclei are not partitioned into separate compartments. The result is a long tube containing many nuclei, with all the cytoplasm at the periphery. Coenzyme (cofactor). An organic molecule, such as a vitamin, that binds to an enzyme and is required for its catalytic activity. Co-evolution: Joint evolution of two unrelated species that have a close ecological relationship resulting in reciprocal adaptations as happens between host and parasite, and plant and insect. Cognate molecule: A relative descended from a common ancestor. Usually used to describe the corresponding partner in a receptor-ligand complex. Cohesive end: Also known as sticky end. Overhanging ends of a double-stranded DNA molecule that are capable of hybridizing with complementary ends. Colchicine: an alkaloid that inhibits the formation of the spindle and delays the division of centromeres; used to produce polyploid varieties of horticulturally important species; also used to stop mitosis at metaphase for preparation of karyotypes. Collagen -- long proteins whose structure is wound into a triple helix. The resulting fibers have a high tensile strength. Collagen is a primary component of mammalian hair. Colonial -- condition in which many unicellular organisms live together in a somewhat coordinated group. Unlike true multicellular organisms, the individual cells retain their spearate identities, and usually, their own membranes and cell walls. Colony lift Blot taken from colonies (normally bacterial) growing on an agar plate. Normally used for detection of a colony containing a plasmid with a specific inserted sequence (screening). Colony. A group of identical cells (clones) derived from a single progenitor cell. Color complementation assay This method is an advancement over competitive oligonucleotide hybridization in that the wild

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type and mutation specific PCR primers are labeled with different color fluorescent tags, and both are used in a PCR reaction with genomic DNA. Using highly stringent conditions, the fluorescent colors of the resultant PCR product indicate whether wild type, mutant, or both specific alleles were present in the original DNA sample. Columella -- a small column of tissue which runs up through the center of a spore capsule. It is present in hornworts, mosses, and some rhyniophytes. Commensalism. The close association of two or more dissimilar organisms where the association is advantageous to one and doesn't affect the other(s). See Parasitism, Symbiosis. Competency. An ephemeral state, induced by treatment withcold cations, during which bacterial cells are capable of uptaking foreign DNA. Competent - bacterial cells which are capable of accepting foreign extra-chromosomal dna. There are a variety of processes by which cells may be made competent. Competitive oligonucleotide hybridization Mutant or wild type-specific oligonucleotide primers are used in a PCR reaction with genomic DNA. The primers and stringency of PCR are chosen so that single-based mismatches between genomic DNA and PCR primer fail to yield an amplified product. Thus, the PCR detection of a locus-specific product allows the genotyping of the individual. Complementary (copy) DNA (cDNA): Single-stranded DNA produced from an RNA template (usually mRNA) by reverse transcriptase in vitro. It lacks the introns present in corresponding genomic DNA. It is most commonly made to use in PCR to amplify RNA (RT-PCR). Complementary D A or R A. The matching strand of a DNA or RNA molecule to which its bases pair. (See DNA, RNA.) Complementary nucleotides. Members of the pairs adeninethymine, adenine-uracil, and guaninecytosine that have the ability to hydrogen bond to one another. (See nucleotide.) Compound eye -- found in many but not all arthropods, a compound eye is composed of a large number of small, closely packed simple eyes (ommatidia), each with its own lens and nerve receptors. Compound heterozygote: An individual who is affected with an autosomal recessive disorder having two different mutations in homologous alleles. Compression -- the decrease in volume of a rock, rock unit or fossil caused by forces oriented in opposite directions. Concatemer. A DNA segment composed of repeated sequences linked end to end. Conformational epitope - an epitope which is dependent upon folding of a protein; amino acid residues present in the antibody binding site are often located at sites in the primary sequence of the protein which are at some distance from each other. The vast majority of b-cell (antibody binding) epitopes are conformational. Congenic: Animals which have been bred to be genetically identical except for a single gene locus. This is achieved by superimposing the locus of interest on the genetic background of another by first crossing two inbred lines followed by extensive (about 20 generations) backcrossing hybrids to one parental line (the background strain) while selecting for the alleles of the locus of interest of the other. The result is an inbred strain uniquely identified by a difference at a single locus.

Congenital: existing at birth; may or may not be of genetic origin. Conglomerate -- a coarse-grained sedimentary rock, with clasts larger than 2 mm. Conifers: Cone bearing trees. A Class of the Gymnospermae which includes needle-leaved trees such as pines and cypresses. Their flowers are in cones, and male and flower cones are separate. The oldest (britlecone pine) and the largest (sequoia) extant organisms belong to this Class. Their unique feature is the inheritance of cytoplasmic DNA (chloroplasts) via pollens. Conjugation. The joining of two bacteria cells when genetic material is transferred from one bacterium to another. # a temporary union of two single-celled organisms with at least one of them receiving genetic material from the other; in bacteria the exchange is unidirectional with the donor cell extruding all or a portion of one of its chromosomes into the recipient cell. # In unicellular organisms, temporary cell contact between complementary genders and exchange of genetic material, as in the ciliate Paramecium aurelia, or one-way transfer of genes as in bacteria (see F Factor) and green alga Spirogyra Consanguineous matings: Matings between two individuals who share a common ancestor in the preceding two or three generations. Consensus sequence: The nucleotides or amino acids most commonly found at each positions of the sequences of related molecules # a linear series of nucleotides, commonly with gaps and some degeneracy, that define common features of homologous sequences or recognition sites for proteins that act on or bind to nucleic acids. # A nominal sequence inferred from multiple, imperfect examples. Multiple lanes of shotgun sequence can me merged to show a consensus sequence. The optimal sequence of nucleotides recognized by some factor. A DNA binding site for a protein may vary substantially, but one can infer the consensus sequence for the binding site by comparing numerous examples. For example, the (fictitious) transcription factor ZQ1 usually binds to the sequences AAAGTT, AAGGTT or AAGATT. The consensus sequence for that factor is said to be AARRTT (where R is any purine, i.e. A or G). ZQ1 may also be able to weakly bind to ACAGTT (which differs by one base from the consensus). Conservative replication: a postulated mode of dna replication in which an intact double helix acts as a template for a new double helix; known to be incorrect. Conservative substitution - a nucleotide mutation which alters the amino acid sequence of the protein, but which causes the substitution of one amino acid with another which has a side chain with similar charge/polarity characteristics (see amino acid). The size of the side chain may also be an important consideration. Conservative mutations are generally considered unlikely to profoundly alter the structure or function of a protein, but there are many exceptions (see nonconservative substitution). Constitutive promoter. An unregulated promoter that allowsfor continual transcription of its associated gene. (See Promoter.) Consumer -- any organism which must consume other organisms (living or dead) to satisfy its energy needs. Contrast with autotroph. Contig - a series of two or more individual dna sequence determinations that overlap. In a sequencing project the contigs get larger and larger until the gaps between the contigs are filled in # The jargon term used to describe the assembly of clones

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necessary to include all of the DNA in a specific stretch of chromosome. Such maps are usually assembled from overlapping YAC (yeast artificial chromosome) or BAC (bacterial artificial chromosome) clones. Once the genome project is complete, it will consist of 24 (very large) contigs (22 autosomal, an X and a Y).# Several uses, all nouns. The term comes from a shortening of the word contiguous. A contig may refer to a map showing placement of a set of clones that completely, contiguously cover some segment of DNA in which you are interested. Also called the minimal tiling path. More often, the term contig is used to refer to the final product of a shotgun sequencing project. When individual lanes of sequence information are merged to infer the sequence of the larger DNA piece, the product consensus sequence is called a contig. Contiguous (contig) map. The alignment of sequence data from large, adjacent regions of the genome to produce a continuous nucleotide sequence across a chromosomal region. (See Mapping.) Contractile vacuole -- in many protists, a specialized vacuole with associated channels designed to collect excess water in the cell. Microtubules periodically contract to force this excess water out of the cell, regulating the cell's osmotic balance. Convergence -- similarities which have arisen independently in two or more organisms that are not closely related. Contrast with homology. Convergent evolution: Evolution of two or more different lineages towards similar morphology due to similar adaptive pressures. Examples of convergence are: fins or fin-like structures in fish, cuttlefish and whales; extreme similarity in alarm calls by five small birds; endothermy in dogs and ducks, wings of butterflies and birds. Copes law of the unspecialized: The evolutionary novelties associated with new major taxa are more likely to originate from a generalized member of an ancestral taxon rather than a specialized member. # Animals tend to get larger during the course of their phyletic evolution Cosmid - a genetically-engineered plasmid containing bacteriophage lambda packaging signals and potentially very large pieces of inserted foreign dna (up to 50 kb) which can be replicated in bacterial cells. Cosmid cloning allows for isolation of dna fragments which are larger than those which can be cloned in conventional plasmids. # An artificial hybrid vector into which large (~40kbp) DNA fragments can be inserted; this makes it useful in genomic library preparation. Cosmids replicate as plasmids in the host cell, but are inserted into the bacterium from lambda phage infectious particles, since transformation would be extremely inefficient with plasmids of this size. The cosmids carry cos sequences from lambda phage so that they can be packaged into phage heads (in vitro ), and circularise once in the cell. # A type of vector used for cloning 35-45 kb of DNA. These are plasmids carrying a phage cos site (which allows packaging into capsids), an origin of replication and an antibiotic resistance gene. A plasmid of 40 kb is very difficult to put into bacteria, but can replicate once there. Cosmids, however, have a cos site, and thus can be packaged into phage heads (a reaction which can be performed in vitro ) to allow efficient introduction into bacteria (you'll have to look up the cos site elsewhere Cotyledon -- the "seed leaves" produced by a seed plant embryo. They serve to absorb nutrients packaged in the seed,

until the seedling is able to produce its first true leaves and begin photosynthesis. The number of cotyledons is a key feature for the identification of the two major groups of flowering plants. Coupling (cis-arrangement): The condition in which a double heterozygote has received two linked mutations from one parent and their wild-type alleles from the other parent, e.g., a b / + + (as opposed to a + / + b; see also repulsion). Covalent bonds Links between atoms formed by sharing of two electrons, one from each atom. These bonds are strong, requiring significant energy for breakage. They are the bonds between the atoms forming the basic structures of biological molecules.# a valence bond formed by a shared electron between the atoms in a covalent compound. CpG island: Repetitive CpG doublets creating a region of DNA greater than 200 bp in length with a G+C content of more than 0.5 and an observed/expected presence of CpG more than 0.6. Usually associated with transcription-initiation regions of (housekeeping) genes transcribed at low rates that do not contain a TATA box. The CpG-rich stretch of 20-50 nucleotides occurs within the first 100-200 bases upstream of the start site region (where promoter-proximal elements reside). A transacting transcription factor called SP1 recognizes the CpG islands (see also Htf islands). In vertebrates, many of the nontranscribed genes (and the genes on the inactivated X chromosome) have a 5-methyl group on the C residue in CpG dinucleotides in transcription-control regions. On the other hand, many genes with restricted expression patterns have (methylated) CpG islands located downstream of transcription initiation does not block elongation of the transcript (see also Methylation paradox). CpG This under-represented (i.e., <1/16 frequency) dinucleotide pair is a hotspot for point mutation. CpG dinucleotides are often methylated on cytosine. Should Me- C undergo spontaneous deamination, uracil arises, which is then repaired by cellular surveillance mechanisms and altered to thymidine. The net result is a C to T mutation. c-rel This gene belongs to the NF- B family of transcription factors and can act to enhance or repress transcription from selected genes. This family of proteins includes p50 and its precursor p105, p65, p49 and its precursor p100, and Bcl-3, one of the I B family. Cross - mating of parents from different genetic lines or strains Cross-hybridization. The hydrogen bonding of a singlestranded DNA sequence that is partially but not entirely complementary to a singlestranded substrate. Often, this involves hybridizing a DNA probe for a specific DNA sequence to the homologous sequences of different species. Crossing-over - reciprocal exchange of chromosome segments during meiosis by symmetrical breaking and rejoining of the segments # The exchange of genetic material between non-sister chromatids of homologous chromosomes (i.e., between maternal and paternal chromosomes) during meiosis. This results in a new and unique combination of genes on the daughter chromosome which will be passed on to the offspring (if that particular gamete is involved in fertilization). Cross-pollination. Fertilization of a plant from a plant with a different genetic makeup. Crown group -- all the taxa descended from a major cladogenesis event, recognized by possessing the clade's synapomorphy. See: stem group.

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Cryptic female choice: Besides precopulatory female sexual selection, there are also postcopulatory selection processes going on in the female reproductive system. This less appreciated mechanism is the basis for differential fertilization which includes sperm selection as opposed to pollen selection in plants. This should not be confused with sperm competition / pollen tube competition (link to a book by Tim Birkhead on Sperm Selection). Culture. A particular kind of organism growing in a laboratory medium. Cuticle -- in animals, a multilayered, extracellular, external body covering, usually composed of fibrous molecules such as chitin or collagen, and sometimes strengthened by the deposition of minerals such as calcium carbonate. # waxy layer which seals the outer surface of land plants, helping to retain moisture. Cyanobacteria: Unicellular, photosynthetic (photo-autotroph) prokaryote (in the Kingdom Monera). Formerly known as blue-green algae. It contains chlorophyll a but not chloroplast. They reproduce by fission and never sexually. Cyclic AMP (cyclic adenosine monophosphate). A second messenger that regulates many intracellular reactions by transducing signals from extracellular growth factors to cellular metabolic pathways. Cyclins A group of proteins that vary in expression throughout the cell cycle. Once a threshold level is attained, interaction with specific cellular kinases results in phosphorylationof critical components of the mitotic machinery. Several classes of cyclins (A through E) exist that regulate different aspects of the cell cycle (G0, G1, S, G2, M). Altered expression of some cyclins is associated with hematologic malignancy, e.g., t(11;14) in mantle cell lymphoma leads to over-expression of cyclin D1, a G1 phase cyclin. Cytogenetics - Branch of genetics which correlates the structure and number of chromosomes as seen in isolated cells with variation in genotype and phenotype. [MeSH, 1967] # aspects of genetics which concentrate on the analysis of chromosomes in mitosis and meiosis. # Study that relates the appearance and behavior of chromosomes to genetic phenomenon. Cytoplasm -- all the contents of a cell, including the plasma membrane,but not including the nucleus. Cytoskeleton -- integrated system of molecules within eukaryotic cells which provides them with shape, internal spatial organization, motility, and may assist in communication with other cells and the environment. Red blood cells, for instance, would be spherical instead of flat if it were not for their cytoskeleton.

D
Dalton. A unit of measurement equal to the mass of a hydrogen atom, 1.67 x 10E-24 gram/L (Avogadro's number). Database search - once an open reading frame or a partial amino acid sequence has been determined, the investigator compares the sequence with others in the databases using a computer and a search algorithm. This is usually done in a protein database such as pir or swiss-prot. Nucleic acid sequences are in genbank and embl databases. The search algorithms most commonly used are blast and fasta. De novo: Literally, from new as opposed to inherited.

DEAE dextran This method depends on the formation of a complex between the insoluble positively charged dextran and the DNA to be transfected. Like calcium phosphate, this method is highly successful with many cell types. Death phase. The final growth phase, during which nutrients have been depleted and cell number decreases. (See Growth phase.) Decomposition -- the breakdown of dead organic material by detrivores or saprophytes. Degeneracy refers to the fact that multiple different codons in mrna can specify the same amino acid in an encoded protein.# Backtranslation of amino acid sequences usually leads to a collection of possible base sequences which can code for the amino acid sequence, due to the degeneracy of the genetic code. In practice, when synthesising an oligonucleotide primer or probe based on this information a mixture of all the possible sequences is made, and referred to as a degenerate oligonucleotide. # A feature of the genetic code that more than one nucleotide triplet codes for the same amino acid. The same applies to the termination signal which is encoded by three different stop codons. Deletion - mutation in which a segment of a chromosome is lost. # The loss of a segment of the genetic material from a chromosome. Denaturation - with respect to nucleic acids, refers to the conversion from double-stranded to the single-stranded state, often achieved by heating or alkaline conditions. This is also called "melting" dna. With respect to proteins, refers to the disruption of tertiary and secondary structure, often achieved by heat, detergents, chaotropes, and sulfhydryl-reducing agents. # Separation of two complementary strands of nucleic acid by breakage of the hydrogen bonds involved in base pairing. This is necessary prior to probe hybridisation and most methods involving enzymic DNA synthesis on a DNA template e.g. sequencing, PCR, some labelling methods. Denaturation may be achieved by heating or treatment with NaOH.. # Reversible disruption of hydrogen bonds between nucleotides converting a double-stranded DNA molecule to single-stranded molecules. Heating or strong alkali treatment result in denaturation of DNA. Denaturing gel - an agarose or acrylamide gel run under conditions which destroy secondary or tertiary protein or rna structure. For protein, this usually means the inclusion of 2-me (which reduces disulfide bonds between cysteine residues) and sds and/or urea in an acrylamide gel. For rna, this usually means the inclusion of formaldehyde or glyoxal to destroy higher ordered rna structures. In dna sequencing gels, urea is included to denature dsdna to ssdna strands. In denaturing gels, macromolecules tend to be separated on the basis of size and (to some extent) charge, while shape and oligomerization of molecules are not important. Contrast with native gel. Dendritic cells. A set of antigen- presenting cells present in lymph nodes, spleen and at low levels in blood, which are particularly active in stimulating T cells. Density gradient centrifugation. High-speed centrifugation in which molecules "float" at a point where their density equals that in a gradient of cesium chloride or sucrose. (See Centrifugation.) # a technique of separation using a gradient of densities established by adding a high molecular weight salt such as cesium chloride; the mixture to be separated is layered in the gradient and then centrifuged until each molecule reaches the layer in the gradient with a density equal to its own.

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Deoxyribonuclease (D Ase) - an enzyme which specifically catalyzes the hydrolysis of DNA. Deoxyribonucleotide - nucleotides which are the building blocks of DNA and which lack the 2' hydroxyl moiety present in the ribonucleotides of RNA. Deposition -- any accumulation of material, by mechanical settling from water or air, chemical precipitation, evaporation from solution, etc. Derived -- describes a character state that is present in one or more subclades, but not all, of a clade under consideration. A derived character state is inferred to be a modified version of the primitive condition of that character, and to have arisen later in the evolution of the clade. For example, "presence of hair" is a primitive character state for all mammals, whereas the "hairlessness" of whales is a derived state for one subclade within the mammalia. Detritus -- accumulated organic debris from dead organisms, often an important source of nutrients in a food web. Detrivore -- any organism which obtains most of its nutrients from the detritus in an ecosystem. Developmental biology: The field of biology which deals with the process of the growth and differentiation of an organism. [MeSH, 1990] Diabetes. A disease associated with the absence or reduced levels of insulin, a hormone essential for the transport of glucose to cells. Diagenesis -- all of the changes that occur to a fossil (or more generally any sediment) after initial burial; includes changes that result from chemical, physical as well as biological processes. The study of diagenesis is part of taphonomy. Diatomite -- diatomite, or diatomaceous earth, is a siliceous sedimaentary rock formed from the accumulations of diatoms or other nanoplankton. Dicentric chromosome: One chromosome having two centromeres. Dicentric fragment: a chromosome or chromatid that has two centromeres. Dideoxy sequencing - enzymatic determination of DNA or RNA sequence by the method of sanger and colleagues, based on the incorporation of chain terminating dideoxynucleotides in a growing nucleic acid strand copied by dna polymerase or reverse transcriptase from a dna or rna template. Separate reactions include dideoxynucleotides containing a,c, g, or t bases. The reaction products represent a collection of new. Labeled dna strands of varying lengths, all terminating with a dideoxynucleotide at the 3' end (at the site of a complementary base in the template nucleic acid), and are separated in a polyacrylamide/urea gel to generate a sequence "ladder". This method is more commonly used than "maxam-gilbert" (chemical) sequencing. # Dideoxynucleotide (dd ) chain termination sequencing Also termed Sanger sequencing, this method relies on the random incorporation of dideoxynucleotides into a growing enzyme-catalyzed DNA chain. As no 3' hydroxyl group is present on the ddN, chain synthesis halts following its incorporation into the chain. If 32P or 35S nucleotides are also incorporated into the reaction, a family of DNA fragments will be generated that can be visualized on a polyacrylamide gel. This method is presently the most commonly used chemistry to determine the sequence of DNA. Dideoxynucleotide (did ). A deoxynucleotide that lacks a 3 hydroxyl group, and is thus unable to form a 3'-5'

phosphodiester bond necessary for chain elongation. Dideoxynucleotides are used in DNA sequencing and the treatment of viral diseases. (See Nucleotide.) Dideoxyribonucleotide - a nucleotide which lacks both 3' and 2' hydroxyl groups. Such dideoxynucleotides can be added to a growing nucleic acid chain, but do not then present a 3' -oh group which can support further propagation of the nucleic acid chain. Thus such compounds are also called "chain terminators", and are useful in dna and rna sequencing reactions (see deoxyribo-nucleotide). Differential display A form of RT-PCR in which primers are used to select a subset of the total mRNA population. This allows comparison of mRNAs from different cells. leading to identification of those mRNAs which are expressed only in certain situations e.g. after stimulation. Differentiation: The process by which cells become structurally and functionally specialized during embryonic development. In cancer, refers to how mature (developed) the cancer cells are in a tumor. Differentiated tumor cells resemble normal cells and tend to grow and spread at a slower rate than undifferentiated or poorly- differentiated tumor cells, which lack the structure and function of normal cells and grow uncontrollably. Digest. To cut DNA molecules with one or more restriction endonucleases. Dihybrid cross - mating which considers differences at 2 loci: normally a cross between two double heterozygotes. Dikaryotic -- a dikaryotic cell contains two separate haploid nuclei. This condition is limited to certain fungi. having two different and distinct nuclei per cell; found in the fungi. # A dikaryotic individual is called a dikaryon. # A cell that contains two separate haploid nuclei (n+n) which is different from being haploid (n) or diploid (2n). Naturally seen in fungal heterokaryons. Dikaryosis is a significant genetic peculiarity of the fungi. Dinosteranes / dinosteroids -- chemicals found in dinoflagellates, which have been useful in documenting their existence early in the fossil record. Diorite -- igneous plutonic rock, less mafic than gabbro, but more mafic than granite and granodiorite; rough plutonic equivalent of andesite. Dip -- the angle that a bedding plane or fault makes with the horizontal when measured perpendicular to the strike of the bedding plane or fault. Diploblast: A lower invertebrate such as jelly fish that are composed of two tissue layers (ectoderm and endoderm) and lacking the third layer (mesoderm) present in higher invertebrates and vertebrates. Diploid - a diploid cell contains a nucleus with two complete sets of chromosomes, one set inherited from each parent. The diploid condition is often abbreviated as 2n. Most plants and animals are diploid. Contrast with haploid. # having two different sets of chromosomes in the same nucleus of each cell. Most metazoans and plants are diploid. Diploid cell. A cell which contains two copies of each chromosome. See Haploid cell. Diploid life cycle - occurs when the only multicellular stage in an organism's life cycle is diploid. Diploid number (2n): The full complement of chromosomes in a somatic cell (or a sex cell before meiosis). In humans, the diploid number is 46.

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Direct repeats - identical or related sequences present in two or more copies in the same orientation in the same molecule of DNA; they are not necessarily adjacent. Directional cloning To improve efficiency when screening functional expression libraries, many investigators construct cDNA libraries in which the proper coding orientation of the scDNA is maintained in the library. In conventional library preparation, the 5' and 3' ends of the DNA are identical; thus, cDNA can be inserted into the cloning vector in either orientation. If screening is dependent on the production of a functional protein, one-half of the library will be useless, as those cDNA inserted in an inverse orientation will not produce functional protein. Directional cloning is dependent on producing sticky ends that differ on the 5' and 3' termini. The cloning vector has the appropriate pair of complementary cloning sites. # DNA insert and vector molecules are digested with two different restriction enzymes to create noncomplementary sticky ends at either end of each restriction fragment. This allows the insert to be ligated to the vector in a specific orientation and prevents the vector from recircularizing. (See Cloning.) Directional selection: selection resulting in a shift in the population mean in the direction desired by the breeder or in the direction of greater adaptation by nature. Disassortative mating: the mating of two individuals with dissimilar phenotypes. Disease -- organisms suffer from disease when their normal function is impaired by some genetic disorder, or more often from the activity of a parasite or other organism living within them. Many diseases are caused by viruses, bacteria, or fungi. Disjunction: Separation of homologous chromosomes during anaphase of mitotic or meiotic divisions (see also nondisjunction). Dispersal -- spread of a species to a new location. In many organisms, this happens at a particular stage in the life cycle, and is often crucial to the survival of the species. Organisms may disperse as spores, seeds, eggs, larvae, or adults. Dispersive replication: an obsolete model of dna replication in which parental and newly synthesized daughter molecules are interspersed in an essentially random fashion. Disposable soma theory: A theory on the evolution of ageing and death suggesting that organisms derive little benefit from investing resources in increasing their lifespan beyond a certain point. It originated from the economic phenomenon that manufacturers invest minimum in durability. Disruptive selection: Selection against the middle range of variation causing an increase in the frequency of a trait showing the extreme ranges of its variation. Disruptive selection might cause one species to evolve into two. # the selection of divergent phenotypic extremes in a population until, after several generations of selection, two discontinuous strains are obtained. Disulfide bond (-S-S-): A covalent linkage between two cysteine residues in different parts of a protein or between two different proteins. Insulin (a small protein having two polypeptide chains) and immunoglobulin molecules, for example, have interchain and intrachain disulfide bonds. HLA molecules also have disulfide bonds. The C282Y mutation removes one of the disulfide bonds in the HLA class I-like HFE protein and abolishes its surface expression.

Divergent evolution: A kind of evolutionary change that results in increasing morphological difference between initially more similar lineages. Diversity -- term used to describe numbers of taxa, or variation in morphology. Dizygotic twins: arise when two eggs are released and fertilized; no more genetically similar than ordinary siblings. dn/ds ratio: In molecular phylogenetic studies, the ratio of the number of non-synonymous nucleotide substitutions to the number of synonymous nucleotide substitutions. In the case of functionally important (or otherwise constrained) genes, ds is expected to exceed dn (dn/ds <1). Because most amino acid changes will disrupt protein structure and those nonsynonymous substitutions (dn) causing them will not be maintained. In a non-functional pseudogene, there will be no discrimination between them and equal numbers of dn and ds are expected (dn/ds=1). When natural selection is acting to favor changes at the amino acid level, it is predicted that dn will exceed ds, hence a high dn/ds ratio. In classical MHC loci, in the peptide binding regions (allele-specific sequences) because of heterozygote advantage/frequency-dependent selection, there is always a high dn/ds ratio (>1) whereas in the remainder of the gene dn/ds <1 (due to functional constrains). This suggests balancing selection is acting on peptide binding regions. D A -- "deoxyribonucleic acid". The nucleic acid which carries the genetic code of an organism. It is the primary component of chromosomes. #An organic acid and polymer composed of four nitrogenous bases--adenine, thymine, cytosine, and guanine linked via intervening units of phosphate and the pentose sugar deoxyribose. DNA is the genetic material of most organisms and usually exists as a double-stranded molecule in which two antiparallel strands are held together by hydrogen bonds between adeninethymine and cytosine-guanine. (See b-DNA, cDNA, Complementary DNA or RNA, DNA polymorphism, DNA sequencing, Double-stranded complementary DNA, Duplex DNA, Z-DNA.) # The polymer constructed of successive nucleotides linked by phosphodiester bonds. Some 3 109 nucleotides are contained in the human haploid genome. During interphase, DNA exists in a nucleoprotein complex containing roughly equal amounts of histones and DNA, which interacts with nuclear matrix proteins. This complex is folded into a basic structure termed a nucleosome containing approximately 150 base pairs. From this highly ordered structure, DNA replication requires a complex process of nicking, unfolding, replication, and splicing. In contrast, gene transcription requires nucleosomal reorganization such that sites critical for the binding of transcriptional machinery reside at internucleosomal junctions. D A fingerprint. The unique pattern of DNA fragments identified by Southern hybridization (using a probe that binds to a polymorphic region of DNA) or by polymerase chain reaction (using primers flanking the polymorphic region). D A binding motif: Common sites on different proteins which facilitate their binding to DNA. Examples are leucine zipper and zinc finger proteins. Any such protein is called DNA-binding protein. D A diagnosis. The use of DNA polymorphisms to detect the presence of a disease gene. Dna ligase - an enzyme (usually from the t4 bacteriophage) which catalyzes formation of a phosphodiester bond between two adjacent bases from double-stranded dna fragments. Rna ligases also exist, but are rarely used in molecular biology.

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D A methylases These enzymes are normally part of a bacterial host defense against invasion by foreign DNA. The enzyme normally methylates endogenous (host) DNA and thereby renders it resistant to a series of endogenous restriction endonucleases. In recombinant DNA work, methylation finds use in cDNA cloning to prevent subsequent digestion by the analogous restriction endonuclease. D A polymerase - a polymerase which synthesizes dna (see polymerase). # The enzyme that synthesizes DNA from a DNA template. The intact enzyme purified from bacteria (termed the holoenzyme) has both synthetic and editing functions. The editing function results from nuclease activity. # A group of enzymes mainly involved in copying a singlestranded DNA molecule to make its complementary strand. Eukaryotic DNA polymerases participate in chromosomal replication, repair, crossing-over and mitochondrial replication. To initiate replication, DNA polymerases require a priming RNA molecule. They extend the DNA using deoxyribonucleotide triphosphates (dNTP) as substrates and releasing pyrophosphates. The dNMPs are added to the 3 OH end of the growing strand (thus, DNA replication proceeds from 5 to 3 end). D A polymorphism. One of two or more alternate forms (alleles) of a chromosomal locus that differ in nucleotide sequence or have variable numbers of repeated nucleotide units. (See Allele.) D A repair: Restoration of the correct nucleotide sequence of a DNA molecule that has acquired a mutation or modification. It includes proofreading by DNA polymerase (see helicase). D A sequencing. Procedures for determining the nucleotide sequence of a DNA fragment. D A/D A, D A/R A, and R A/R A hybrids. At high stringency, duplexes form only between strands with perfect one-to-one complementarity; lower stringency allows annealing between strands with some degree of mismatch between bases. D Ase footprinting This technique depends on the ability of protein specifically bound to DNA to block the activity of the endonuclease DNAse I. 32P-labeled DNA is mixed with nuclear proteins, which potentially contain specific DNAbinding proteins, and the reaction is then subjected to limited DNAse digestion. If a given site of DNA is free of protein, it will be cleaved by the DNAse. In contrast, regions of DNAse specifically bound by proteins (transcription factors or enhancers) will be protected from digestion. The resultant mixture of DNA fragments from control and proteincontaining reactions are then separated on a polyacrylamide gel. As the site of 32P labeling of the original DNA fragment is known, sites that were protected from DNAse digestion will be represented on the gel as a region devoid of that length fragment. Therefore, in comparison to naked DNA, regions that bind specific proteins will be represented as a footprint. D Ase hypersensitivity site mapping This technique is designed to uncover regions of DNA that are in an active transcriptional state. It depends on the hypersensitivity of such sites (because of the lack of the highly compact nucleosome structure) to limited digestion with DNAse. Intact nuclei are subjected to limited DNAse digestion. The resultant large DNA fragments are then extracted, electrophoretically separated, and hybridized with a 32P-labeled probe from a known site within the gene of interest. If, for example, the

probe were located at the site of transcription initiation, and should DNA fragments of 2 kb and 5 kb be detected with this probe, hypersensitive sites would thereby be mapped to 2kb and 5 kb upstream of the start of transcription initiation. By extrapolation, these sites would then be assumed important in the transcriptional regulation of the gene of interest, especially if such a footprint were only detected using cells that express that gene. D ase: Deoxyribonuclease, a class of enzymes which digest DNA. The most common is DNase I, an endonuclease which digests both single and double-stranded DNA. d TP deoxyribonucleoside triphosphate. Domain: Region of a protein with a distinct tertiary structure and characteristic activity (for example, the membrane distal and membrane proximal domains of an MHC molecule). Dominance/dominant allele - a dominant allele is one in which only one copy is required to produce a particular phenotype in a diploid organism (cf recessive, which requires that two copies of the allele, one on each homologous chromosome, be present in a diploid in order to produce its particular phenotype.) # The property possessed by some alleles of determining the phenotype for any particular gene by masking the effects of the other allele (when heterozygous). Thus, homozygosity or heterozygosity for the dominant allele result in the same genotype in complete dominance (if red is dominant over white, the petals of a flower heterozygous for red and white would be red). Incomplete dominance appears as a blend of the phenotypes corresponding to the two alleles (like pink petals as opposed to red or white). In co-dominance, both alleles equally contribute to the phenotype (red and white petals occur together). Dominant allele: An allele that masks an alternative allele when both are present (in heterozygous form) in an organisms (see recessive). Dominant gene. A gene whose phenotype is when it is present in a single copy. Dominant trait: a trait controlled by an allele that expresses itself even when heterozygous. Dominant(-acting) oncogene. A gene that stimulates cell proliferation and contributes to oncogenesis when present in a single copy. (See Oncogene.) Dominant-negative mutation: A (heterozygous) dominant mutation on one allele blocking the activity of wild-type protein still encoded by the normal allele causing a loss-of-function phenotype. The phenotype is indistinguishable from that of homozygous dominant mutation. p53 mutations may act as dominant-negative (see also haploinsufficiency). Dormancy - a period of suspended growth and metabolic activity. Many plants, seeds, spores, and some invertebrates become dormant during unfavorable conditions. #A period in which a plant does not grow, awaiting necessary environmental conditions such as temperature,moisture, nutrient availability. Dosage compensation: The phenomenon in women, who have two copies of genes on the X chromosome, of having the same level of the products of those genes as males (who have a single X chromosome). This is due to the process of inactivation of one of the X chromosomes in females (Lyonization). See Lyons hypothesis. Dot blot - dna or rna is simply spotted onto nitrocellulose or nylon membranes, denatured and hybridized with a probe. Unlike southern or northern blots, there is no separation of the target dna or rna by electrophoresis (size), and thus potentially

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much less specificity. # The simplest form of blot. Prepared by pipetting known volumes of DNA or RNA mixtures onto a blotting membrane. The blot is probed in the normal way, allowing detection and quantitation of molecules carrying specific sequence in the original mixtures. # A technique for measuring the amount of one specific DNA or RNA in a complex mixture. The samples are spotted onto a hybridization membrane (such as nitrocellulose or activated nylon, etc.), fixed and hybridized with a radioactive probe. The extent of labeling (as determined by autoradiography and densitometry) is proportional to the concentration of the target molecule in the sample. Standards provide a means of calibrating the results. Double cross-over: breakage and interchange occurring twice within a tetrad involving two, three, or four of the chromatids. Double fertilization: The union of one male gametophyte nucleus with the ovum nucleus and another male gametophyte nucleus with the polar nuclei to form the endosperm in seed plants. See also pollen grain. Double helix: the watson-crick model of dna structure, involving coiling of two hydrogen-bonded polynucleotide, antiparallel strands wound into a right-handed spiral configuration. Describes the coiling of the antiparallel strands of the DNA molecule, resembling a spiral staircase in which the paired bases form the steps and the sugar-phosphate backbones form the rails. Double heterozygote: An individual who is heterozygous at two loci under investigation. Double membrane -- in mitochondria and plastids, there is a two-layered membrane which surrounds the organelle. This is believed to be the result of endosymbiosis, with the outer membrane coming from the eukaryotic cell, and the inner membrane belonging to the original prokaryote which was "swallowed". Double stranded R A (dsR A): In eukaryotes, it is an accidental byproduct of transcriptional process. It may occur as the genome of certain viruses (such as reovirus) or may be produced during viral replication as a general marker for viral infection. It is believed that dsRNA is the toxic substance responsible for general symptoms of viral infection as it induces cytokine production. dsRNA is the major activator of the PKR enzyme which is the major agent of anti-viral innate immunity. Double transformant: a bacteria that has simultaneously transformed two or more genes; the genes cotransformed are inferred to be closely linked because transforming dna fragments are usually small. Double-stranded complementary D A (dscD A). A duplex DNA molecule copied from a cDNA template. Downstream - identifies sequences proceeding farther in the direction of expression; for example, the coding region is downstream from the initiation codon, toward the 3' end of an mrna molecule. Sometimes used to refer to a position within a protein sequence, in which case downstream is toward the carboxyl end which is synthesized after the amino end during translation. # The region extending in a 3' direction from a gene. # The direction which RNA polymerase moves during transcription (5 to 3) and ribosomes moves during translation. By convention, the +1 position of a gene is the first transcribed nucleotide, nucleotides downstream from the +1 position are designated +2, +3, etc.

Drift evolution: A high rate of immunologically significant mutations in certain viruses. This results in drifting away from recognition by the immune system by antigenic change. Influenza virus, HIV and HCV constantly change their antigenic structure through drift evolution. Drosophila melanogester: Common fruit fly. It contributed heavily to the study of genetics because of its ease and speed to breed. It contains only four pairs of chromosomes. Link to Drosophila website. dscD A. See double-stranded complementary DNA. Duplex - a nucleic acid molecule in which two strands are base paired with each other. Duplex D A. Double-stranded DNA.

E
E. coli: A common Gram-negative bacterium useful for cloning experiments. Present in human intestinal tract. Hundreds of strains of E. coli exist. One strain, K-12, has been completely sequenced. Ecogenetics: The branch of genetics that studies how (inherited or acquired) genetic factors influence human susceptibility to environmental health risks. It studies the genetic basis of environmental toxicity to develop methods for the detection, prevention and control of environment-related disease. Ecogenetics interacts with ecology, molecular genetics, toxicology, public health medicine and environmental epidemiology. Ecological genetics: The analysis of genetics of natural populations and of the adaptations of them to the environment. Ecology: The study of the interrelationships among living organisms and their environment. Human ecology means the study of human groups as influenced by environmental factors, including social and behavioral ones. Ecosystem -- all the organisms in a particular region and the environment in which they live. The elements of an ecosystem interact with each other in some way, and so depend on each other either directly or indirectly. # The organisms in a plant population and the biotic and abiotic factors which impact on them. See abiotic factors; Biotic factors. Ecotropic viruses Murine retroviruses that contain coat proteins that can only bind to murine cellular receptors. Ectoderm -- the outer basic layer of tissue in those animals with true tissues. In vertebrates, for instance, the embryonic ectoderm differentiates into the skin and also the nervous system. Ediacaran fauna: E Vendian age assemblage of soft-bodied multicellular animals. The oldest fauna known. Effective population size (N or Ne): number of individuals contributing alleles to the next generation (Nf= number of mothers in a population; relevant in the calculation of number of generations for the fixation of a mitochondrial allele). Egg - (1) a large gamete without flagellae that is fertilized by a sperm cell. An egg cell is also called an ovum. (2) a complex multicellular structure in which an animal embryo develops. Elater -- a cell or part of a cell which assists in dispersing spores. The elaters change shape as they lose or acquire water, and they will then push against surrounding spores. # a cell or part of a cell which assists in dispersing spores. The elaters change shape as they lose or acquire water, and they will then push against surrounding materials. Elaters are found in liverworts and sphenophytes. Electrophoresis - method of separating closely-related proteins by differences in size and electrical charge. The technique of

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separating charged molecules in a matrix to which is applied an electrical field. (See Agarose gel electrophoresis, Polycrylamide gel electrophoresis.) also See "Gel electrophoresis". Electroporation - a method for introducing foreign nucleic acid into bacterial or eukaryotic cells that uses a brief, high voltage dc charge which renders the cells permeable to the nucleic acid. Also useful for introducing synthetic peptides into eucaryotic cells.# When cells are suspended in buffer between two electrodes, discharge of an electrical impulse momentarily creates pores in the cell membrane. During this time, DNA in solution is free to diffuse into the cells. This method is highly successful in transfecting a large number of cell types, including cells previously thought to be difficult to transfect with other methods, such as endothelial cells and fibroblasts.# A method for transforrning DNA, especially useful for plant cells, in which high voltage pulses of electricity are used to open pores in cell membranes, through which foreign DNA can pass. Elongation factor: a protein that complexes with ribosomes to promote elongation of polypeptide chains. Embryo - once a zygote begins to undergo cellular divisions, it becomes an embryo. # A developing offspring during the period when most of its internal organs are forming. It is called fetus in the next stage of development. Embryonic stem cells ES: Cultured cells derived from the pluripotent inner cell mass of blastocyst- stage embryos. [NHLBI] . Use of stem cells has a number of promising research applications. The British government has recently approved proposals for allowing stem cell research [Nature 409 (6819): 445, 25 Jan. 2001 and Nature 409:5, 2001] although the rest of Europe was predicted to continue to outlaw this research. Embryophyte -- synonym for the plantae, as here defined. It includes all green photosynthetic organisms which begin the development of the sporophyte generation within the archegonium. Enations -- flaps of tissue such as those found on psilophytes. Encapsidation. Process by which a virus' nucleic acid is enclosed in a capsid. See Coat protein. End labeling - the technique of adding a radioactively labeled group to one end (5' or 3' end) of a dna strand. End-labelling Transfer of 32P to the 5' end(s) of a DNA or RNA molecule, using polynucleotide kinase. Endoderm -- the innermost basic layer of tissue in those animals with true tissues. Forms the gut and its derivatives: in vertebrates, these include the liver, trachea, and lungs. Endodermis -- literally "inner skin", this is a layer of cells which surrounds the central core of vascular tissue, and which helps to regulate the flow of water and dissolved substances. Endonuclease - cleaves bonds within a nucleic acid chain; they may b especific for rna or for single-stranded or doublestranded dna. A restriction enzyme is a type of endonuclease.# An enzyme that digests nucleic acids from within the sequence. Usually, specific sequences are recognized at the site where digestion begins. #A nuclease which cuts a nucleic acid molecule by cleaving the phosphodiester bonds between two internal residues. Best known examples are restriction endonucleases. Endophyte. An organism that lives inside another.

Endoplasmic reticulum -- (er) network of membranes in eukaryotic cells which helps in control of protein synthesis and cellular organization. Endosymbiosis -- when one organism takes up permanent residence within another, such that the two become a single functional organism. Mitochondria and plastids are believed to have resulted from endosymbiosis. Enhancer - a eukaryotic transcriptional control element which is a dna sequence which acts at some distance to enhance the activity of a specific promoter sequence. Unlike promoter sequences, the position and orientation of the enhancer sequence is generally not important to its activity.# An enhancer is a segment of DNA that lies either upstream, within, or downstream of a structural gene that serves to increase transcription initiation from that gene. A classical enhancer element can operate in either orientation and can operate up to 50 kb or more from the gene of interest. Enhancers are cisacting in that they must lie on the same chromatin strand as the structural gene undergoing transcription. These cis-acting sequences function by binding specific proteins, which then interact with the RNA polymerase complex. # A cis-acting (on either side of a gene) enhancer of promoter function. They are located 10 to 50 kb downstream or upstream of a gene. They may be tissue-specific. The enhancer effect is mediated through sequence-specific DNA-binding proteins (see also silencer).# An enhancer is a nucleotide sequence to which transcription factor(s) bind, and which increases the transcription of a gene. It is NOT part of a promoter; the basic difference being that an enhancer can be moved around anywhere in the general vicinity of the gene (within several thousand nucleotides on either side or even within an intron), and it will still function. It can even be clipped out and spliced back in backwards, and will still operate. A promoter, on the other hand, is position- and orientationdependent. Some enhancers are "conditional" - in other words, they enhance transcription only under certain conditions, for example in the presence of a hormone. Entomophily -- seed plants which are pollinated by insects are said to be entomophilous. Environment -- the place in which an organism lives, and the circumstances under which it lives. Environment includes measures like moisture and temperature, as much as it refers to the actual physical place where an organism is found. Environmental Protection Agency (EPA). The U.S. regulatory agency for biotechnology of microbes. The major laws under which the agency has regulatory powers are the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA); and the Toxic Substances Control Act (TSCA). Enzyme -- complex protein which helps to speed biochemical reactions. Enzymes are important in the construction and degradation of other molecules. # Proteins that control the various steps in all chemical reactions. Eocene epoch: A temporal subdivision (epoch) of the Tertiary period (58 to 37 Mya). EPA. See Environmental Protection Agency. Epicenter -- point on the earth's surface directly above the focus of an earthquake. Epidemiology: The study of the distribution and determinants of health-related events (including but not only disease epidemics) aiming to trace down their cause and subsequently to control health problems.

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Epidermis -- the outermost layer of cells; the "skin" of a plant, covering the leaves, stem, and roots. This tissue often contains specialized cells for defense, gas exchange, or secretion. Epigenesis: The theory that the development of an embryo consists of the gradual production and organization of parts.# The study of heritable changes in gene expression that occur without a change in DNA sequence. Epigenetic phenomena such as imprinting and paramutation violate Mendelian principles of heredity. Epigenetic studies link genotype to phenotype working out the chain of processes (mainly in developmental biology) (see Epigenetics: Special Issue of Science, 2001). Epiphyte -- a plant which grows upon another plant. The epiphyte does not "eat" the plant on which it grows, but merely uses the plant for structural support, or as a way to get off the ground and into the canopy environment. # A plant which grows upon another plant. The epiphyte does not "eat" the plant on which it grows, but merely uses the plant for structural support, or as a way to get off the ground and into the canopy environment. Episome: a class of genetic elements; f factor is an example; compare with plasmid. Epistasis - when a gene at one locus affects the phenotypic expression of a gene at another locus. Eugenics - deliberate attempt to improve future generations of human beings through selective breeding schemes. # The nonreciprocal interaction between nonallelic genes. This may result in masking of one and in this case, the masked gene is said to be hypostatic. An epistatic-hypostatic relationship between two loci is similar to a dominant-recessive relationship between alleles at a particular locus.# the nonreciprocal interaction of nonallelic genes; the situation in which one gene masks the expression of another. Epithelium -- layer of cells which lines a body cavity; cells may be ciliated or unciliated, and may be squamous (flat, scale-shaped), cuboidal (cube-shaped), or columnar (columnshaped). Your stomach and cheeks are lined with epithelium. Epitope - as related to protein antigens, b-cell epitopes consist of the amino acid residues of a protein molecule which interact directly through noncovalent bonds with the amino acid residues of a particular antibody molecule (complementarity determining region). The average epitope probably involves about 15-20 contact amino acid residues, but one or two of these may be critical to the epitope's specificity and the avidity of the antibody-antigen reaction. Bcell epitopes may be either linear or conformational in nature. T-cell epitopes represent the small, processed peptides which bind to mhc class i and ii molecules on the surface of t cells. Equilibrium population: a population in which the allelic frequencies of its gene pool do not change through successive generations. ERE: Estrogen Response Element. A binding site in a promoter to which the activated estrogen receptor can bind. The estrogen receptor is essentially a transcription factor which is activated only in the presence of estrogens. The activated receptor will bind to an ERE, and transcription of the adjacent gene will be altered. See also "Response element". Erosion -- processes (mechanical and chemical) responsible for the wearing away, loosening, and dissolving of materials of the earth's crust.

Escherichia coli. A commensal bacterium inhabiting the human colon that is widely used in biology, both as a simple model of cell biochemical function and as a host for molecular cloning experiments. # A gram-negative bacterium whose genome has been sequenced in its entirety. It is model organisms for the study of the prokaryotes. Link to the E.coli genome project website. Esophagus -- that portion of the gut which connects the pharynx to the stomach. Ethidium bromide - A fluorescent dye used to stain DNA and RNA. The dye fluoresces when exposed to UV light. # Intercalates within the structure of nucleic acids in such a way that they fluoresce under uv light. Ethidium bromide staining is commonly used to visualize rna or dna in agarose gels placed on uv light boxes. Proper precautions are required, because the ethidium bromide is highly mutagenic and the uv light damaging to the eyes. Ethidium bromide is also included in cesium chloride gradients during ultracentrifugation, to separate supercoiled circular dna from linear and relaxed circular dna. Ethology: Study of animal behavior under normal conditions. Link to animal behavior resources. Euchromatin: Chromosome regions that are loosely packaged and more accessible to RNA polymerases than HETEROCHROMATIN. These regions also stain differentially in CHROMOSOME BANDING preparations. [MeSH, 2001] . In humans are particularly rich in genes. # regions of eukaryotic chromosomes that are diffuse during interphase; presumably the actively transcribing dna of the chromosomes. Eugenics: The idea of improving the quality of human species by selective breeding. Encouraging breeding of those with supposedly good genes is positive eugenics, whereas discouraging those with genes for undesirable traits is negative eugenics. Eukaryote. An organism whose cells possess a nucleus and other membrane-bound vesicles, including all members of the protist, fungi, plant and animal kingdoms; and excluding viruses, bacteria, and blue-green algae. See Prokaryote. # Organisms whose cells have their genetic material packed in a membrane- surrounded, structurally discrete nucleus and with well- developed cell organelles. Eukaryotes include all organisms except archaebacteria and eubacteria (cg. prokaryotes). [IUPAC Biotech] # literally "true nucleus", the term applies to all protists, plants, animals, and fungi. Eukaryotic cells have internal membranes which partition them into regions for different functions, such as mitochondria, plastids, the er, golgi apparatus, etc. They also possess a cytoskeleton which helps them control their shape. Eukaryotic cell: The DNA lies within a true nucleus (eukaryon). May be unicellular (protist, some fungi) or multicellular (most fungi, plants, animals). Among eukaryotes, most fungi are haploid.# Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane [MeSH, 1991] Euploidy: a polyploid cell or organism whose chromosome number is an exact multiple of the basic number of the species from which it originated. Eustele -- when a plant's vascular tissue develops in discrete bundles, it is said to have a eustele. See also protostele and siphonostele. Eutheria: Placental mammals. A subclass of the Class Mammalia (others are monotremes and marsupials). Embryo and fetus are nourished by a placenta. They are viviparous

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(producing young alive rather than lying eggs), have a long period of gestation and the young is born immature. Evolution -- darwin's definition: descent with modification. The term has been variously used and abused since darwin to include everything from the origin of man to the origin of life. # The long-term process through which a population of organisms accumulats genetic changes that enable its members to successfully adapt to environmental conditions and to better exploit food resources. # The process that results in heritable changes in a population spread over many generations (change in allele frequencies over time). Biological evolution refers to populations and not to individuals and that the changes must be passed on to the next generations. Genes mutate, individuals are selected, and populations evolve. Link to evolution-related links. Evolutionarily stable strategy (ESS): A strategy such that, if most members of a population adopt it, would give a reproductive fitness higher than any mutant strategy. Evolutionary clock - defined by the rate at which mutations accumulate within a given gene. Evolutionary tree -- a diagram which depicts the hypothetical phylogeny of the taxa under consideration. The points at which lineages split represent ancestor taxa to the descendant taxa appearing at the terminal points of the cladogram. Ewens-Watterson eutrality Test: Also called E-W homozygosity statistics. Described by Ewens (1972) and Watterson (1978). A widely used test in population genetics to estimate the selection acting on a locus. It compares the sum of observed homozygosity for each allele of a given locus (Fo) with the expected Fe value based on the number of alleles in the locus of interest, neutrality expectations and random mating assumption. A test of comparison yields an F value. Values close to zero mean that the locus is evolving under neutrality (genetic drift only) and there is no selection. Values of F significantly different from zero suggest selection. When Fo > Fe, the locus is undergoing purifying selection, and when Fe > Fo, the locus is under balancing selection (very common for HLA loci). Alternative tests for neutrality are Tajimas D (Tajima F: Genetics 1989;123:585) and Slatkins Exact Test for Neutrality (Slatkin M: Genet Res 1996;68:259). See also Slatkin & Muirhead: Genetics 2000:156:2119). Excinuclease: The excision nuclease involved in nucleotide exchange repair of DNA. Exon - intron boundary: Introns end with the dinucleotide ApG [3 splice site / acceptor] and start with the dinucleotide GpT [5 splice site / donor]. Exon the portion of a gene that is actually translated into protein (see intron, splicing).# A DNA sequence that is ultimately translated into protein. See DNA. # a portion of the split gene that is included in the transcript of a gene and survives processing of the rna in the cell nucleus to become part of a spliced messenger of a structural rna in the cell cytoplasm.# The coding sequence of a eukaryotic gene (see also open reading frame).# Those portions of a genomic DNA sequence which WILL be represented in the final, mature mRNA. The term "exon" can also be used for the equivalent segments in the final RNA. Exons may include coding sequences, the 5' untranslated region or the 3' untranslated region.# The coding sections of eukarotic genes, separated by introns. # These are the regions of the primary RNA transcript that, following splicing, form the mature mRNA species, which encodes polypeptide sequence.

Exonuclease - an enzyme which hydroylzes dna beginning at one end of a strand, releasing nucleotides one at a time (thus, there are 3' or 5' exonucleases) # An enzyme that digests nucleic acids starting from the 5' or 3' terminus and extending inward. # A nuclease which degrades a double-stranded DNA molecule by removing nucleotides from its two ends.# an enzyme that digests dna, beginning at the ends of the strands.# An enzyme which digests nucleic acids starting at one end. An example is Exonuclease III, which digests only double-stranded DNA starting from the 3' end. Express. To translate a gene's message into a molecular product. Expression - usually used to refer to the entire process of producing a protein from a gene, which includes transcription, translation, post-translational modification and possibly transport reactions. Expression clone: This is a clone (plasmid in a bacteria, or maybe a phage in bacteria) which is designed to produce a protein from the DNA insert. Mammalian genes do not function in bacteria, so to get bacterial expression from your mammalian cDNA, you would place its coding region (i.e. no introns) immediately adjacent to bacterial transcription/translation control sequences. That artificial construct (the "expression clone") will produce a pseudo-mammalian protein if put back into bacteria. Often, that protein can be recognized by antibodies raised against the authentic mammalian protein, and vice versa. Expression of a gene - the effect of a gene on its phenotype Expression of Recombinant Proteins In order to exploit the techniques of recombinant DNA research, one must possess a system to manufacture the protein of interest. After identifying the gene encoding the protein and obtaining a cDNA representation of it (cloning), the cDNA must be placed in a vector capable of driving high levels of RNA transcription in a host system capable of translating and appropriately modifying the polypeptide to produce fully functional protein. And just like obtaining a protein of interest from natural sources, one must purify protein from the final expression system. Because of the nature of the highly engineered systems and high levels of expression, this latter task is usually considerably easier using recombinant methods than from natural sources. The methods used to generate expression vectors are described in Section IV, but the methods to purify proteins are discussed in only a rudimentary way and are beyond the scope of this glossary. Expression vector - a plasmid or phage designed for production of a polypeptide from inserted foreign DNA under specific controls. Often an inducer is used. The vector always provides a promoter and often the transcriptional start site, ribosomal binding sequence, and initiation codon. In some cases the product is a fusion protein. # A plasmid that contains all of the elements necessary to express an inserted cDNA in the host of interest. For a mammalian cell host, such a vector typically contains a powerful promoter coupled to an enhancer, a cloning site, and a polyadenylation signal. In addition, several expression vectors also contain a selectable marker gene such as DHFR or NeoR, which aids in the generation of stable cell lines. The plasmid also requires a bacterial origin of replication and an antibiotic resistance gene (AmpR) to allow propagation and expansion in a bacterial host. # A vector which is designed to allow expression (transcription and translation) of the inserted section of DNA. The vector carries a promoter (normally inducible) on one side of the cloning site, and a transcription terminator on the other side. These must be recognisable by the

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intended host cell. The vector may also carry a ribosome binding sequence (for bacterial expression) and a start codon, depending on the nature of the inserted DNA. Some expression vectors produce fusion proteins. Expression: To "express" a gene is to cause it to function. A gene which encodes a protein will, when expressed, be transcribed and translated to produce that protein. A gene which encodes an RNA rather than a protein (for example, a rRNA gene) will produce that RNA when expressed. Expressivity - a measure of the extent to which a gene is expressed in the phenotype. Expressivity: the range of phenotypes expressed by a given genotype under any given set of environmental conditions, or over a range of environmental conditions. #The range of phenotypes resulting from a given genotype (cystic fibrosis, for example, may have a variable degree of severity). This is different from pleiotropy which refers to a variety of different phenotypes resulting from the same genotype. Extended phenotype: All effects of a gene upon the world where the effects influence the survival chance of a gene [Richard Dawkins]. Extinction -- when all the members of a clade or taxon die, the group is said to be extinct. Extracellular matrix -- (ecm) region outside of metazoan cells which includes compounds attached to the plasma membrane, as well as dissolved substances attracted to the surface charge of the cells. The ecm functions both to keep animal cells adhered together, and well as buffering them from their environment. # A meshwork- like substance found within the extracellular space and in association with the basement membrane of the cell surface. It promotes cellular proliferation and provides a supporting structure to which cells or cell lysates in culture dishes adhere. [MeSH, 1984] Extrachromosomal genes - DNA found outside the cell nucleus in eukaryotes - eg mitochondrial DNA F-1 - the offspring of a cross between two different homozygous genotypes. Extra-chromosomal inheritance: Non-Mendelian inheritance due to extra-nuclear DNA (mitochondrial DNA in animals). The transmission of the trait only occurs from mothers. Extrusive -- igneous. Antonym of intrusive. Eyespot -- light-sensitive organelle found in many groups of protists, and in some metazoans.

F
F- cell: a bacterial cell devoid of an f factor and that therefore can act only as a recipient during conjugation. F Factor (Fertility Factor): Transmissible plasmid (episome) in bacteria (such as E. coli) that acts as a sex factor. It is a circular DNA about 94 kb long. Conjugation and chromosomal gene transfer occur from F+ (male) to F(female) bacterium. F- strain: E.coli strain behaving as recipients during conjugation (female). It lacks the F factor. F (F-prime) factor: Normally, the F factor contains genes related to conjugation/mating. The F factor contains an additional portion of the bacterial genome. F+ cell: a bacterial cell possessing a fertility factor in a plasmid; this cell can act as a donor during conjugation. F+ strain: E.coli strain behaving as donors during conjugation (male). It has the F factor.

F1: First filial (son or daughter) hybrids arising from a first cross. Subsequent generations are denoted by F2, F3 etc. FACS: Fluorescence activated cell sorter. Farnesyl protein transferase (FTPase) FTPase adds 15 carbon farnesyl groups to CAAX motifs, such as onepresent in ras, allowing their insertion into cellular membranes. Fault -- a fracture or zone of fractures in rocks of mappable size along which there has been displacement of one side relative to the other. Fauna: A certain species of animals occurring in a particular region or period. Fecundity: potential fertility or the capability of repeated fertilization; specifically refers to the quantity of gametes produced per individual over a period of time. Felsic -- term used to describe the amount of light-colored feldspar and silica minerals in an igneous rock. Complement of mafic. Female - in organisms with separate sexes, the one which produces eggs. Fertility factor: a supernumerary sex chromosome that determines the sex of e. Coli; in the presence of the f episome, the bacterium functions as a male. Fertilization - the process by which an egg is made capable of generating offspring. It is often synonymous with syngamy. # Fusion of female and male haploid gametes to form a diploid zygote from which a new individual develops. Fiber -- elongated and thickened cell found in xylem tissue. It strengthens and supports the surrounding cells. Fibroblasts Connective tissue cells which secrete an extracellular matrix rich in collagen and other macromolecules. [MeSH, 1965] Filament -- long chain of proteins, such as found in hair, muscle, or in flagella. Filling-in In vitro synthesis of DNA (by DNA polymerase) to convert an overhanging end of a double-stranded DNA fragment to a blunt end. Fingerprinting: The use of RFLPs or repeat sequence DNA to establish a unique individual-specific pattern of DNA fragments. First strand synthesis The retroviral enzyme reverse transcriptase is used along with an antisense primer to produce a complementary DNA strand of mRNA extracted from a cellular source known to express the gene of interest. Two types of primers are used, either oligo dT, in which the poly A tail begins the cDNA synthesis, or random primers, in which a whole range of start sites will be used. FISH (fluorescence in situ hybridization) A general method to assign chromosomal location, gene copy number (both increased and decreased), or chromosomal rearrangements. Biotin-containing nucleotides are incorporated into specific cDNA probes by nick-translation. Alternatively, digoxigenin or fluorescent dyes can be incorporated by enzymatic or chemical methods. The probes are then hybridized with solubilized, fixed metaphase cells, and the copy number of specific chromosomes or genes are determined by counter-staining with fluorescein isothiocyanate (FITC)- labeled avidin or other detector reagents. The number and location of detected fluorescent spots correlates with gene copy number and chromosomal location. The method also allows chromosomal analysis in interphase cells, allowing extension to conditions of low cell proliferation. AAA RNA Fishers Fundamental Theorem: The rate of increase in fitness is equal to the additive genetic variance in fitness. This

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means that if there is a lot of variation in the population the value of S will be large. Fishers Theorem of the Sex Ratio: In a population where individuals mate at random, the rarity of either sex will automatically set up selection pressure favoring production of the rarer sex. Once the rare sex is favored, the sex ratio gradually moves back toward equality. Fission -- division of single-celled organisms, especially prokaryotes, in which mitosis does not occur. Also used to refer to mitosis in certain unicellular fungi. Fitness - in population genetics, the ability of a particular genotype to reproduce itself compared to all other genotypes. # Lifetime reproductive success of an individual (i.e., the total number of offspring who themselves survive to reproduce). It can be seen as the extent to which an individual successfully passes on its genes to the next generation. It has two components: survival (viability) and reproductive success (fecundity). Variation in fitness is the major driving force in biological evolution. # The relative ability of an organism to survive and transmit its genes to the next generation. Fixation: the status of a locus in which all members of a population are homozygous; the frequency of the fixed allele is 1.0. Fixed: The establishment of a single allelic variant at a locus as a result random genetic drift. Flagellin -- protein which is the primary component of prokaryotic flagella. Flagellum -- hair-like structure attached to a cell, used for locomotion in many protists and prokaryotes. The prokaryotic flagellum differs from the eukaryotic flagellum in that the prokaryotic flagellum is a solid unit composed primarily of the protein flagellin, while the eukaryotic flagellum is composed of several protein strands bound by a membrane, and does not contain flagellin. The eukaryotic flagellum is sometimes referred to as an undulipodium. Flanking region. The DNA sequences extending on either side of a specific locus or gene. Flow cytometry: Technique for characterizing or separating particles such as beads or cells, usually on the basis of their relative fluorescence. Technique using an instrument system for making, processing, and displaying one or more measurements on individual cells obtained from a cell suspension. Cells are usually stained with one or more fluorescent dyes specific to cell components of interest, e.g., DNA, and fluorescence of each cell is measured as it rapidly transverses the excitation beam (laser or mercury arc lamp). Fluorescence provides a quantitative measure of various biochemical and biophysical properties of the cell, as well as a basis for cell sorting. Other measurable optical parameters include light absorption and light scattering, the latter being applicable to the measurement of cell size, shape, density, granularity, and stain uptake. [MeSH, 1982] Flow sorting: Employs flow cytometry to separate, according to size, chromosomes isolated from cells during cell division when they are condensed and stable. As the chromosomes flow singly past a laser beam, they are differentiated by analyzing the amount of DNA present, and individual chromosomes are directed to specific collection tubes. Flower -- collection of reproductive structures found in flowering plants. # The part of an angiosperm containing the organs of reproduction (male stamen and female stigma as well as the ovary).

Focus -- the initial point within the earth that ruptures in an earthquake, directly below the epicenter. Fold -- bent rock strata. Food chain / food web -- all the interactions of predator and prey, included along with the exchange of nutrients into and out of the soil. These interactions connect the various members of an ecosystem, and describe how energy passes from one organism to another. Footprinting - a technique for identifying the site on a dna (or rna) molecule which is bound by some protein by virtue of the protection afforded phosphodiester bonds in this region against attack by nuclease or nucleolytic compounds.# DNA with protein bound is resistant to digestion by DNAase. When a sequencing reaction is performed using such DNA, a protected area representing the footprint of the bound protein will be detected. This permits identification of the protein binding regions of the DNA. # A technique by which one identifies a protein binding site on cellular DNA. The presence of a bound protein prevents DNase from "nicking" that region, which can be detected by an appropriately designed gel. Fossil -- any evidence of past life, including remains, traces, imprints as well as life history artifacts. Examples of artifacts include fossilized bird's nests, bee hives, etc. Founder effect (Sewall Wright effect): A type of genetic drift in which allele frequencies are altered in a small population which is a nonrandom sample of a larger (main) population. # the principle that when a small sample of a larger population establishes itself as a newly isolated entity, its gene pool carries only a fraction of the genetic diversity represented in the parental population. Frameshift mutation - a mutation (deletion or insertion, never a simple substitution) of one or more nucleotides but never a multiple of 3 nucleotides, which shortens or lengthens a trinucleotide sequence representing a codon; the result is a shift from one reading frame to another reading frame. The amino acid sequence of the protein downstream of the mutation is completely altered, and may even be much shorter or longer due to a change in the location of the first termination (stop) codon. # Mutations, usually deletions or insertions, that change the reading frame of the codon triplets. Frugivore -- animal which primarily eats fruit. Many bats and birds are frugivores. Fruit -- in flowering plants, the structure which encloses the seeds. True fruits develop from the ovary wall, such as bananas and tomatoes, though not all fruits are edible, such as the dry pods of milkweed or the winged fruits of the maple. # Mature ovary with seeds inside. Its function is seed protection and dispersal. Fruits are a development of the ovary wall and sometimes the other flower parts as well. Its formation is induced by the plant hormone auxin which is released by the maturing seeds. Frustule -- the mineral "skeleton" of a diatom or other unicellular organism. Fu/HC: The fusion/histocompatibility system of the Ascidians. It is involved in self - nonself recognition regulating the fusion between compatible organisms and prevention of selffertilization. Link to an abstract on Fu/HC research (see also Bottryllus and protochordates). Fucoxanthin -- yellowish-brown pigment found in some members of the chromista, including kelps and diatoms. Fugu: The puffer fish, Fugu rubripes, has essentially the same number of genes as the human genome, but its genome is eight

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times more compact than human genome (about 400 Mb as opposed to 3 Gb). A project to sequence the whole Fugu genome is underway. Link to Fugu Website which has the draft sequence (Oct 25, 2001). Fundamental number: the number of chromosome arms in a somatic cell of a particular species. Fungi/Fungus: A Kingdom made up of a diverse group of unicellular or multicellular, eukaryotic organisms which are not plants or animals. Many are parasitic or saprophytic. Both asexual and sexual reproductions are possible. The Kingdom includes five phyla: Zygomycetes (conjugating fungi, black bread molds), Deuteromycetes (reproduce only asexually, Aspergillus brown mold and Penicillium), Basidiomycetes (incl. mushrooms), Ascomycetes (incl. Neurospora bread mold and Saccharomyces bakers yeast) and Mycophycophyta (incl. lichens). Some of them (Basidiomycetes) have one of the most ancient pheromonebased mating-type recognition systems. See Fungi in Kimballs Biology Pages and Fungus in Tree of Life. See also dikaryosis, heterokaryon and mating types. Fusion gene. A hybrid gene created by joining portions of two different genes (to produce a new protein) or by joining a gene to a different promoter (to alter or regulate gene transcription). Fusion protein - a product of recombinant dna in which the foreign gene product is juxtaposed ("fused") to either the carboxyl-terminal or amino-terminal portion of a polypeptide encoded by the vector itself. Use of fusion proteins often facilitates expression of otherwise lethal products and the purification of recombinant proteins. # A recombinant protein which is composed of amino acid sequences derived from more than one gene. Produced by insertion of coding DNA sequence "in frame" within a gene, followed by expression from the promoter of the original gene.. Fusion: The amalgamation of two distinct cells or macromolecules into a single integrated unit.

G
Gabbro -- highly mafic igneous plutonic rock, typically dark in color; rough plutonic equivalent of basalt. Gaia hypothesis: A hypothesis developed by Lovelock, Watson, Margulis and others. In its form, -based on a mathematical model- this theory proposes that the physical and chemical condition of the surface of the Earth, of the atmosphere, and of the oceans has been and is actively made fit and comfortable by the presence of life itself. This is in contrast to the conventional wisdom which held that life adapted to the planetary conditions and they evolved their separate ways. Lovelock and Watson developed the Daisyworld model - an imaginary planet, which maintains conditions for its survival simply by following its own natural processes. This simple model has since become an integral part of the debate about the Gaia Hypothesis. The Daisyworld planet contains only two species of life: light daisies and dark daisies and an example of a self-regulating system. Galactosidase The presence of galactosidase activity in the cytoplasm of transfected cells can be readily detected by its ability to convert a colorless substrate to a blue-colored product. This is usually assayed using a fluorimeter. Galtons Regression Law: Individuals differing from the average character of the population produce offspring which,

on the average, differ to a lesser degree but in the same direction from the average as their parents. Gamete - Haploid germ cell produced during meiosis - an ovum (egg) in females, sperm in males. Gamete - reproductive cells which fuse to form a zygote. Gametes are haploid, and may be differentiated into egg and sperm. # A haploid sex cell, egg or sperm, that contains a single copy of each chromosome. # A haploid reproductive cell such as sperm (or pollen) and egg (oocyte). # Mature male or female reproductive cell (sperm or ovum) with a haploid set of chromosomes (23 for humans). Gametic association: see linkage disequilibrium. Gametic selection: the forces acting to cause differential reproductive success of one allele over another in a heterozygote. Gametophyte - the haploid stage in the life cycle of an organism undergoing alternations of generations. The gametophyte is multicellular and mitotically produces gametes. In plants, the gametophyte nourishes the zygote and young sporophyte. # The haploid, gamete-forming (sexual) generation in plants with alternation of generations. Typically it is produced from a haploid spore. See also sporophyte. Gastrodermis -- in cnidarians, the endodermis which lines the gut cavity. The term is often used instead of endodermis since cnidarians only have two tissue layers instead of three. Gauses Rule (competitive exclusion principle): Two species cannot live the same way in the same place at the same time (ecologically identical species cannot coexist in the same habitat). This is only possible through evolution of niche differentiation (difference in beak size, root depths, etc.). Gel electrophoresis: A method to analyze the size of DNA (or RNA) fragments. In the presence of an electric field, larger fragments of DNA move through a gel slower than smaller ones. If a sample contains fragments at four different discrete sizes, those four size classes will, when subjected to electrophoresis, all migrate in groups, producing four migrating "bands". Usually, these are visualized by soaking the gel in a dye (ethidium bromide) which makes the DNA fluoresce under UV light. Gel filtration Chromatography This technique is designed to separate proteins based on their molecular weight. It is dependent on the exclusion of proteins from a matrix of specific size. Proteins that are too large to fit into the matrix of the gel bed run to the bottom of the column more quickly than smaller proteins, which are included in the volume of the matrix. Therefore, using appropriate size markers, the approximate molecular weight of a given protein can be determined and it can be separated from proteins of dissimilar size. Typical separation media for gel filtration chromatography include Sephadex and Ultragel. Gel shift - a method by which the interaction of a nucleic acid (dna or rna) with a protein is detected. The mobility of the nucleic acid is monitored in an agarose gel in the presence and absence of the protein: if the protein binds to the nucleic acid, the complex migrates more slowly in the gel (hence "gel shift"). A "supershift" allows determination of the specific protein, by virtue of a second shift in mobility that accompanies binding of a specific antibody to the nucleic acid-protein complex. Gel shift assay: (aka gel mobility shift assay (GMSA), band shift assay (BSA), electrophoretic mobility shift assay (EMSA)) A method by which one can determine whether a particular protein preparation contains factors which bind to a particular

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DNA fragment. When a radiolabeled DNA fragment is run on a gel, it shows a characteristic mobility. If it is first incubated with a cellular extract of proteins (or with purified protein), any protein-DNA complexes will migrate slower than the naked DNA - a shifted band. GEM. A genetically engineered microorganism. Gender: Differences between any two complementary organisms of the same species that render them capable of mating (see mating types). Gene - generally speaking, the genomic nucleotide sequence that codes for a particular polypeptide chain, including relevant transcriptional control sequences and introns (if a eukaryote). However, the term is often loosely used to refer to only the relevant coding sequence. Gene amplification. The presence of multiple genes. Amplification is one mechanism through which protooncogenes are activated in malignant cells. Gene cloning. The process of synthesizing multiple copies of a particular DNA sequence using a bacteria cell or another organism as a host. See DNA, Host. Gene conversion - the alteration of all or part of a gene by a homologous donor dna that is itself not altered in the process. # Partial sequence transfer from one allele to another (interallelic recombination) converting one gene or allele to another one. It is the most common mechanism, especially for the HLA-B locus, in the generation of new MHC alleles. Less common are conversions between alleles of different MHC loci (intergenic conversion). Gene expression. The process of producing a protein from its DNA- and mRNA-coding sequences. Gene flow - the movement of genes from one population to another as a result of the migration of the individuals who carry them. Gene flow. The exchange of genes between different but (usually) related populations.# The movement of genes within a population or between two populations following genetic admixture. Gene flow creates new combinations of genes or alleles in individuals that can be tested against the environment. This way it is one of the sources of variation in the process of natural selection. Gene frequency - see allele frequency. # The percentage of a given allele in a population of organisms. See Allele. Gene fusion: Fusion of structural genes to analyze protein behavior or fusion of regulatory sequences with structural genes to determine mechanisms of regulation. [MeSH, 1998] Gene insertion. The addition of one or more copies of a normal gene into a defective chromosome. Gene knock-in experiments A similar technology to knockout strategy, but rather than simply obliterating function of the targeted gene, the knock-in is designed to replace the locus with a specific mutation of interest. Gene knock-out experiments Specific genes in the mammalian genome can now be targeted for interruption or correction based on the technique of homologous recombination. By generating DNA constructs that contain an interrupted gene of interest, or a corrected gene, in the setting of adequate flanking sequences to allow for targeting to the genetic locus of interest, the endogenous gene can be replaced or corrected. The methods involve introduction of the gene into an embryonic stem (ES) cell line, selection for subclones of cells that have had successful homologous recombination events, and then introduction of the ES subclone into the

blastocyst of a developing embryo. A chimeric animal results, and should the newly introduced gene become part of the germline, it can be bred to the homozygous state. Using these techniques, investigators can now determine whether a single genetic locus is responsible for a given disease, determine the significance of specific cytokines or growth factors, and generate model systems useful investigation of human disease. Gene linkage. The hereditary association of genes located on the same chromosome. Gene mapping - procedures used to determine the linear sequence of genetic loci on a chromosome. Gene modification. The chemical repair of a gene's defective DNA sequence. See DNA. Gene pool - the total of all the genes in all the individuals in an interbreeding population. # The totality of all alleles of all genes of all individuals in a particular population. Gene splicing. Combining genes from different organisms into one organism. See recombinant DNA. Gene therapy Gene therapy takes many forms. To treat malignancy, it may involve the insertion of an adjuvant substance (such as GMCSF) into tumor cells to generate a tumor vaccine, transfer of a gene that renders tumor cells susceptible to eradication with an antitumor agent (e.g., herpes thymidine kinase), or insertion of a gene that makes bystander cells resistant to the effects of chemotherapy (e.g., MDR). For gene deficiencies, insertion of the wild type allele is the therapeutic goal. Obtaining cDNA for desired genes has become common. Insertion of the gene into target cells and high (adequate) level expression is more problematic. Several types of transfer vehicles have found use, including viral vectors and chemical agents. Gene translocation. The movement of a gene fragment from one chromosomal location to another, which often alters or abolishes expression. Gene. A locus on a chromosome that encodes a specific protein or several related proteins. It is considered the functional unit of heredity. (See Dominant gene, Fusion gene, Gene amplification, Gene expression, Gene flow, Gene pool, Gene splicing, Gene translocation, Recessive gene, Regulatory gene.) # A hereditary unit that occupies a specific position within the genome; it has one or more specific effects upon the phenotype of the organism; it can mutate to various allelic forms. # A unit of DNA which performs one function. Usually, this is equated with the production of one RNA or one protein. A gene contains coding regions, introns, untranslated regions and control regions. # Physical and functional unit of heredity that carries information from one generation to the next. The entire DNA sequence necessary for the synthesis of a functional polypeptide or RNA molecule. In addition to the coding regions (exons), a gene may have non-coding intervening sequences (introns) and transcription-control regions. Generalist -- organism which can survive under a wide variety of conditions, and does not specialize to live under any particular set of circumstances. Genetic anticipation: The progressive shift of the age of onset of a hereditary disease to earlier ages in successive generations. It may occur because a parent is a mosaic, and the child has the full mutation in all cells. Triplet repeat expansion may demonstrate anticipation when the number of repeats increases with each generation.

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Genetic assimilation. Eventual extinction of a natural species as massive pollen flow occurs from another related species and the older crop becomes more like the new crop. See Gene flow. Genetic code - the system which specifies the information contained in the DNA sequence - for structural genes, triplet nucleotide units each specifying an amino acid in a polypeptide. # The three-letter code that translates nucleic acid sequence into protein sequence. The relationships between the nucleotide base-pair triplets of a messenger RNA molecule and the 20 amino acids that are the building blocks of proteins. See Base pair, Nucleic acid, Nucleotide. # the consecutive nucleotide triplets of dna and rna that specify the sequence of amino acids for protein synthesis. Genetic counseling: the analysis of risk of producing genetically defective offspring within a family, and the presentation to family members of available options to avoid or ameliorate possible risks. Genetic disease. A disease that has its origin in changes to the genetic material, DNA. Usually refers to diseases that are inherited in a Mendelian fashion, although noninherited forms of cancer also result from DNA mutation. Genetic Distance Estimation by PHYLIP: The most popular (and free) phylogenetics program PHYLIP can be used to estimate genetic distance between populations. Most components of PHYLIP can be run online. One component of the package GENDST estimates genetic distance from allele frequencies using one of the three methods: Neis, CavalliSforzas or Reynolds (see papers by Nei et al, 1983, Nei M, 1996 and a lecture note for more information on these methods). GENDST can be run online using the default options (Neis genetic distance) to obtain genetic distance matrix data. The PHYLIP program CONTML estimates phylogenies from gene frequency data by maximum likelihood under a model in which all divergence is due to genetic drift in the absence of new mutations (Cavalli-Sforzas method) and draws a tree. The program comes as a freeware as part of PHYLIP or this program can be run online with default options. If new mutations are contributing to allele frequency changes, Neis method should be selected on GENDST to estimate genetic distances first. Then a tree can be obtained using one of the following components of PHYLIP: NEIGHBOR also draws a phylogenetic tree using the genetic distance matrix data (from GENDST). It uses either Neis Neighbor Joining Method, or the UPGMA (unweighted pair group method with arithmetic mean; average linkage clustering) method. Neighbor Joining is a distance matrix method producing an unrooted tree without the assumption of a clock (UPGMA does assume a clock). NEIGHBOR can be run online. Other components of PHYLIP that draw phylogenetic trees from genetic distance matrix data are FITCH / online (does not assume evolutionary clock) and KITSCH / online (assumes evolutionary clock). Genetic distance: A measurement of genetic relatedness of populations. The estimate is based on the number of allelic substitutions per locus that have occurred during the separate evolution of two populations. Link to a lecture on Estimating Genetic Distance and GeneDist: Online Calculator of Genetic Distance. The software Arlequin, PHYLIP, GDA, PopGene, Populations and SGS are suitable to calculate population-topopulation genetic distance from allele frequencies. GenAlEx can be used to calculate genetic distance on Excel.

Genetic drift - changes in the gene frequencies present in a population due to chance fluctuations from one generation to the next, and occurring when successful parents are (by chance) not representative of the whole gene pool; pronounced in small populations but trivial in large populations. # Random variation in gene frequency from one generation to another. # Evolutionary change over generations due to random events in small populations (not to be mixed with sampling error due to a small sample size). It operates unless overcome by strong selective forces. Wildly different HLA allele frequencies among South AmerIndian tribes are believed to be result of probable genetic drift in each small tribe. Link to a lecture on genetic drift and a simulation. # the random fluctuations of gene frequencies due to sampling errors; while drift occurs in all populations, its effects are most evident in very small populations. Genetic engineering. The manipulation of an organism's genetic endowment by introducing or eliminating specific genes through modern molecular biology techniques. A broad definition of genetic engineering also includes selective breeding and other means of artificial selection. Genetic heterogeneity: Presence of several different genotypes contributing to the genetic component of a disease on their own. Genetic linkage map. A linear map of the relative positions of genes along a chromosome. Distances are established by linkage analysis, which determines the frequency at which two gene loci become separated during chromosomal recombination. (See Mapping.) Genetic linkage: The situation referring to segregation of two or more genes together as a unit. Genetic linkage is thought to arise to accommodate genes that function best in each others company, i.e., to provide a necessary cooperative effect that enhances survival. Genetic linkage reflects a lack of meiotic crossovers between two genes. Genetic load: The average number of lethal equivalents (or any recessive mutant lowering fitness) per individual in a population which are propagated by heterozygotes in a masked state. Genetic marker. A gene or group of genes used to "mark" or track the action of microbes. # A known site on the chromosome. It might for example be the site of a locus with some recognizable phenotype, or it may be the site of a polymorphism that can be experimentally discerned. Genetics: Study of variation and heredity and their physical basis in DNA. Genocopy: The same phenotype due to different genetic causes. Genome - the complete set of genetic information defining a particular animal, plant, organism or virus. # the sum total of all the genes in an organism # The genetic complement contained in the chromosomes of a given organism, usually the haploid chromosome state. # a term used to refer to all of the genes carried by a single gamete. # The total DNA contained in each cell of an organism. Mammalian genomic DNA (including that of humans) contains 6x109 base pairs of DNA per diploid cell. There are somewhere in the order of a hundred thousand genes, including coding regions, 5' and 3' untranslated regions, introns, 5' and 3' flanking DNA. Also present in the genome are structural segments such as telomeric and centromeric DNAs and replication origins, and intergenic DNA. # Total genetic material in a set of haploid chromosomes as in a germ cell. The human genome contains 3,000 Mbp whereas the E.coli genome has 4.6 Mbp (see also C value). Link to the Genome Catalogue. Genomic blot: A type of Southern blot specifically used to analyze a mixture of DNA fragments derived from total

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genomic DNA. Because genomic DNA is very complicated, when it has been digested with restriction enzymes, it produces a complex set of fragments ranging from tens of bp to tens of thousands of bp. However, any specific gene will be reproducibly found on only one or a few specific fragments. A million identical cells will produce a million identical restriction fragments for any given gene, so probing a genomic Southern with a gene-specific probe will produce a pattern of perhaps one or just a few bands. Genomic clone: A piece of DNA taken from the genome of a cell or animal, and spliced into a bacteriophage or other cloning vector. A genomic clone may contain coding regions, exons, introns, 5' flanking regions, 5' untranslated regions, 3' flanking regions, 3' untranslated regions, or it may contain none of these...it may only contain intergenic DNA (usually not a desired outcome of a cloning experiment!). Genomic D A The DNA contained in the chromosomes of a cell. Genomic imprinting: Differing expression of genetic material dependent on the parent-of-origin. This is due to methylation of one of the alleles depending of its origin. A very illustrative example is the inherited neck tumor paraganglioma for which the susceptibility gene is only active if inherited from the father. Genomic imprinting must be considered in disorders that appear to have skipped a generation. Link to a genomic imprinting website. Genomic library - a dna library which contains dna fragments hopefully representing each region of the genome of an organism, virus, etc, cloned into individual vector molecules for subsequent selection and amplification. The dna fragments are usually very small in size compared with the genome. Such libraries are cdna libraries when prepared from rna viruses. # It is similar in concept to a cDNA library, but differs in three major ways - 1) the library carries pieces of genomic DNA (and so contains introns and flanking regions, as well as coding and untranslated); 2) you need bacteriophage or cosmids, rather than plasmids, because... 3) the inserts are usually 5-15 kb long (in a library) or 20-40 kb (in a cosmid library). Therefore, a genomic library is most commonly a tube containing a mixture of phages. Enough different phages must be present in the library so that any given piece of DNA from the source genome has a 99% probability of being present. # A library composed of fragments of genomic DNA. (See Library.) Genotype - the genetic constitution of an individual with respect to a specified locus or loci # the genetic constitution of an organism; determined by its nucleic acid sequence. As applied to viruses, the term implies a group of evolutionarily related viruses possessing a defined degree of nucleotide sequence relatedness. #The structure of DNA that determines the expression of a trait. See Phenotype. # The diploid genetic formula at one or more loci. # the genetic constitution of an organism, as distinguished from its physical appearance. Genotype-environment interaction - occurs when a particular genotype produces different phenotypes in different environments. Genotypic frequency: - the proportions of different genotypes in a population. # the proportion of individuals in a population that possess a given genotype. Genotypic value - the average value for a particular characteristic of all the phenotypes in a population which have a particular genotype.

Genus. A category including closely related species. Interbreeding between organisms within the same category can occur. GEO. Genetically engineered organism. Geological time-scale: The period between the origin of earth (4,500 Mya) and the beginning of the Cambrian period (540 Mya) is called the Precambrian Eon. The last 540 million years (Phanerozoic Eon) are divided into three eras: Palaeozoic (540245 Mya); Mesozoic (245-65 Mya); Cainozoic. The geological periods (included in an era, longer than en epoch) are as follows: Vendian (immediately before the Cambrian; 610-540 Mya); Cambrian (540-510 Mya); Ordovician; Silurian; Devonian; Carboniferous; Permian; Triassic / Jurassic / Cretaceous (altogether the Mesozoic Era); Tertiary (65-1.64 Mya) and Quaternary. An epoch is a subdivision of a period. See the geological table in BBC Education. Germ cell (germ line) gene therapy. The repair or replacement of a defective gene within the gamete-forming tissues, which produces a heritable change in an organism's genetic constitution. # The reproductive cells in multicellular organisms. Includes Ovum (Oocytes, Oogonia, Zona Pellucida , Zygote) and Spermatozoa (Sperm Head + , Sperm Tail, Spermatids, Spermatocytes, Spermatogonia Germ line: Genetic material transmitted from one generation to the next through the gametes. A germ line mutation exists in all cells of the offspring formed from that gamete. Germination - the process by which a seedling emerges and develops from a seed, or by which a sporeling emerges and develops from a spore. Gill -- in aquatic animals, highly vascularized tissues with large surface area; these are extended out of the body and into the surrounding water for gas exchange. Gill arches -- stiffenings which support the flesh between the gill slits of chordates. In most vertebrates, the first gill arches have been modified to form the jaw, and in tetrapods, the inner ear bones. Gill slit -- a slitlike or porelike opening connecting the pharynx of a chordate with the outside of the body. Gill slits may contain the gills and be used for gas exchange, as in most fish, but may also be used for filter-feeding, or may be highly modified in land-dwelling vertebrates. Glass -- a non-crystaline rock that results from very rapid cooling of magma. Glucose -- simple sugar, and the primary product of photosynthesis. It is polymerized to make cellulose and chitin. Glycoprotein -- a glycosylated protein # a membrane-bound protein which has attached branching carbohydrates. These may function in cell-cell recognition, such as in human blood groups and immune system response, as well as in resisting compression of cells. Glycosylation - the covalent addition of sugar moities to n or o atoms present in the side chains of certain amino acids of certain proteins, generally occuring within the golgi apparatus during secretion of a protein. Glycosylation sites are only partially predictable by current computer searches for relevant motifs in protein sequence. Glycosylation may have profound but very unpredictable effects on the folding, stability, and antigenicity of secreted proteins. Glycosylation is a property of eukaryotic cells, and differs among different cell types (i.e., It may be very different in yeast or insect cells used for protein expression, when compared with chinese hamster ovary (cho) cells). GMO. Genetically modified organism.

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Gnathastomata: Jawed vertebrates, evolved following the jawless vertebrates (Class Agnatha). The oldest extant branch of jawed vertebrates is the cartilaginous fish. Gnathobase -- the expanded and hardened base of the appendage of many arthropods, notably trilobites, crustaceans, and marine cheliceramorphs. Used to macerate food items before ingestion. Golgi apparatus - a membranous, vesicular structure which is in continuity with the endoplasmic reticulum of eukaryotic cells and generally in close proximity to the nucleus, the golgi plays an important role in the posttranslational processing and transport of secreted proteins. # eukaryotic organelle which package cell products, such as enzymes and hormones, and coordinate their transport to the outside of the cell. Gradualism -- a model of evolution that assumes slow, steady rates of change. Charles darwin's original concept of evolution by natural selection assumed gradualism. Contrast with punctuated equilibrium. Grain -- (1) the texture of wood, produced by the kinds of xylem cells present. (2) the fruit of a member of the grasses. GRE: Glucocorticoid Response Element: A binding site in a promoter to which the activated glucocorticoid receptor can bind. The glucocorticoid receptor is essentially a transcription factor which is activated only in the presence of glucocorticoids. The activated receptor will bind to a GRE, and transcription of the adjacent gene will be altered. See also "Response element". Great Ape: Chimpanzees (including bonobos), gorillas, and orangutans. Green revolution. Advances in genetics, petrochemicals, and machinery that culminated in a dramatic increase in crop productivity during the third quarter of the 20th century. Growth curve. See Growth phase. Growth factor. A serum protein that stimulates cell division when it binds to its cell-surface receptor. Growth phase (curve). The characteristic periods in the growth of a bacterial culture, as indicated by the shape of a graph of viable cell number versus time. (See Death phase, Lag phase, Logarithmic phase, Stationary phase.) GTP (guanosine 5-triphosphate): A nucleotide that is a precursor in RNA synthesis which plays a role in protein synthesis (as well as in signal transduction and microtubule assembly). See also cap. # an energy-rich molecule analogous to atp that is required for the synthesis of all peptide bonds during translation. Guard cells -- pair of cells which surround a stomate and regulate its size by altering their shape. Gut (enteron) -- body cavity formed between the mouth and anus in which food is digested and nutrients absorbed; it consists of the mouth, pharynx, esophagus, stomach, intestine, and anus, though some animals do not have all these regions. Gymnosperm -- generally any seed plant which does not produce flowers. The term may or may not exclude the pteridosperms. # (Gr. gymnos=naked; sperm=seed): Woody plants whose life histories include alternation of generations and ovules are not enclosed in a carpel. The pollen typically germinates on the surface of the ovule. A superclass in the sperm plants (Spermatophyta) division. Examples are cycad, conifer and gingko. Cycads are the most primitive ones evolved in the Devonian period about 400 Mya. There are

about 700 extant species in Gymnosperms. Link to a lecture on Gymnosperms. Gynostemium -- the central reproductive stalk of an orchid, which consists of a stamen and pistil fused together. Gyrase: One of the bacterial DNA topoisomerases that functions during DNA replication to reduce molecular tension caused by supercoiling (supertwisting). DNA gyrase produces, then seals, double-stranded breaks.

H
h2 = genetic variance / total phenotypic variance H-2 complex: The major histocompatibility complex (MHC) of the mouse. It is the first MHC discovered in 1937 by Peter Gorer. Habit -- the general growth pattern of a plant. A plant's habit may be described as creeping, trees, shrubs, vines, etc. Habitat -- the place and conditions in which an organism lives. Haeckels Biogenetic Law: Proposed by Ernst Haeckel in 1874 as an attempt to explain the relationship between ontogeny and phylogeny. It claimed that ontogeny recapitulates phylogeny, i.e., an embryo repeats in its development the evolutionary history of its species as it passes through stages in which it resembles its remote ancestors (embryos, however, do not pas through the adult stages of their ancestors; ontogeny does not recapitulate phylogeny. Rather, ontogeny repeats some ontogeny - some embryonic features of ancestors are present in embryonic development (L. Wolpert: The Triumph of Embryo. Oxford University Press, 1991). Also discussed in detail with original pictures by Haeckel in D Bainbridge: Making Babies. Harvard University Press, 2001). Hair pin loop: Binding of complementary sequences to each other to form a hair pin loop (also called stem loop). If happens in a PCR primer, it will not function. # a helical (duplex) region formed by base pairing between adjacent (inverted) complementary sequences within a single strand of rna or dna. Haldanes Hypothesis (on recombination and sex): Selection to lower recombination on the Y-chromosome causes a pleiotropic reduction in recombination rates on other chromosomes [hence, the recombination rate is lower in heterogametic sex such as males in humans, females in butterflies]. Halophile -- organism which lives in areas of high salt concentration. These organisms must have special adaptations to permit them to survive under these conditions. Hamiltons Altruism Theory: If selection favored the evolution of altruistic acts between parents and offspring, then similar behavior might occur between other close relatives possessing the same altruistic genes which were identical by descent. In other words, individual may behave altruistically not only to their own immediate offspring but to others such as siblings, grandchildren and cousins (as happens in the bee society). Hamiltons Rule (theory of kin selection): In an altruistic act, if the donor sustains cost C, and the receiver gains a benefit B as a result of the altruism, then an allele that promotes an altruistic act in the donor will spread in the population if B/C >1/r or rBC>0 (where r is the relatedness coefficient). Haploid - a haploid cell contains a nucleus with a single complete set of chromosomes. The haploid condition is often abbreviated as n. Most fungi, protists, and algae are haploid, as are some insects, bryophytes, and the gametes of all organisms. Contrast with diploid. # having a single set of chromosomes in the nucleus of each cell. Mosses, and many protists and fungi,

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are haploid. # the genetic chromosome number; the state in which each type of chromosome is represented only once (n). # The number of chromosomes in a sperm or egg cell, half the diploid number. [NHGRI]. A single set of chromosomes (half the full set of genetic material), present in the egg and sperm cells of animals and in the egg and pollen cells of plants. Human beings have 23 chromosomes in their reproductive cells. Haploid cell. A cell containing only one set, or half the usual (diploid) number, of chromosomes. Haploid life cycle - occurs when the only multicellular stage in an organism's life cycle is haploid. Haploid number (n): The number of chromosomes in the gamete after meiosis. In humans, the haploid number is 23. Haploid-diploid life cycle - occurs when a multicellular diploid phase, or sporophyte, alternates with a multicellular haploid phase, or gametophyte. Only plants and certain algae possess this kind of life cycle, which is also called "alternation of generations". Haploinsufficiency: Situation where one normal copy of a gene alone is not sufficient to maintain normal function. It is observed as a dominant mutation on one allele (or deletion of it) resulting in total loss-of-function in a diploid cell because of the insufficient amount of the wild-type protein encoded by the normal allele on the other haplotype (see also dominant negative). A recent example of haploinsufficiency by Kurotaki et al, 2002 in Sotos syndrome. Haplotype: The particular combination of alleles in a linked group encoded by genes in close vicinity on the same chromosome. Haptonema -- peg-like structure unique to the prymnesiophyta; its function is not known. Hardy-Weinberg equilibrium (HWE): In an infinitely large population, gene and genotype frequencies remain stable as long as there is no selection, mutation, or migration. For a biallelic locus where the gene frequencies are p and q: p2+2pq+q2 = 1 (Online HWE Analysis; lectures on HWE: 1 & 2). Hardy-Weinberg law - a rule for predicting genotype frequencies from a knowledge of allele frequencies in a panmictic population. A corollary of the Hardy-Weinberg law is that in the absence of selection, mutation, and gene flow, allele and genotype frequencies will remain the same from generation to generation. # In an infinitely large population, gene and genotype frequencies remain stable as long as there is no selection, mutation, or migration. In a panmictic population in infinite size, the genotype frequencies will remain constant in this population. For a biallelic locus where the allele frequencies are p and q # the concept that both gene frequencies and genotype frequencies will remain constant from generation to generation in an infinitely large, interbreeding population in which mating is at random and there is no selection, migration, or mutation. Head -- that part of the body at the "front" end, where the brain, mouth, and most sensory organs are located. Heart -- muscular pump which circulates the blood. Heat Shock Response: Heat shock response is ubiquitous and highly conserved defense mechanism for protection of cells from harmful conditions such as heat shock, UV irradiation, toxic chemicals, infection, transformation and appearance of mutant and misfolded proteins. Heat Shock Proteins (HSPs) also function as accessory molecules in antigen presentation.

HSP70 genes are within the MHC in most vertebrates. High levels of HSP70 prevent stress-induced apoptosis, and may have a transforming potential. Helicase: an enzyme that unwinds a dna double helix molecule ahead of dna polymerase iii. # An enzyme that unwinds the double DNA helix near the replication fork before DNA polymerase acts on it. Replication fork moves from 3 to 5 of the leading strand. Unwinding is also necessary for DNA repair. Mutations in the helicase genes on chromosome 2q and 19q are one group of causes of the DNA repair defect xeroderma pigmentosum (an autosomal recessive disease). See also primosome. Helix-loop-helix: A protein structural motif characteristic of certain DNA-binding proteins. Helix-turn-helix This family of transcriptionally active proteins depends on the helix-turn-helix motif for dimerization. Examples include the homeodomain genes such as the Hox family. Hematopoiesis: The development and formation of various types of blood cells. [MeSH] Hematopoietic stem cells: Progenitor cells from which all blood cells derive. [MeSH, 1984]. An unspecialized precursor cell that will develop into a mature blood cell. [NHGRI] Hemizygous: As in any X-linked trait in males, absence of a homologous counterpart for an allele. It may also result from deletion. # The condition of loci on the x chromosome of the heterogametic sex of a diploid species. Hemoglobin -- protein complex found in the blood of most chordates and the roots of certain legumes. It binds oxgen molecules, and in chordates serves as the means by which the oxygen is supplied to the cells of the body. Hemophilia. An X-linked recessive genetic disease, caused by a mutation in the gene for clotting factor VIII (hemophilia A) or clotting factor IX (hemophilia B), which leads toabnormal blood clotting. Herb -- generally any plant which does not produce wood, and is therefore not as large as a tree or shrub, is considered to be an herb. Herbicde. Any substance that is toxic to plants; usually used to kill specific unwanted plants. Herbivore -- literally, an organism that eats plants or other autotrophic organisms. The term is used primarily to describe animals. Heritability - "In the broad sense" - a measure of the proportion of variation between phenotypes which can be attributed to genetic differences between them. "In the narrow sense" - a measure of the extent to which offspring tend to resemble their parents (or technically, the ratio of additive genetic variance to the total phenotypic variance). # an attribute of a quantitative trait in a population that expresses how much of the total phenotypic variation is due to genetic variation. # The proportion of the total phenotypic variance that is attributable to genetic causes (h2= genetic variance / total phenotypic variance). # the proportion of the total phenotypic variance that is attributable to genetic causes: Hermaphroditic: having both male and female reproductive organs. Hermaphroditism: Having both male and female sexual organs in one individual. Most invertebrates and plants are hermaphrodites. Union of the gametes of the same individual (self-fertilization) is the most extreme example of inbreeding.

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Heterochromatin. Dark-stained regions of chromosomes thought to be for the most part genetically inactive. # chromatin that remains tightly coiled and darkly staining throughout the cell cycle. # The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE. [MeSH, 1972]. Highly repetitive lengths of DNA with little genetic information. Heteroduplex D A - generated by base pairing between complementary single strands derived from different parental duplex molecules; heteroduplex DNA molecules occur during genetic recombination in vivo and during hydridization of different but related DNA strands in vitro. Since the sequences of the two strands in a heteroduplex differ, the molecule is not perfectly base-paired; the melting temperature of a heteroduplex dna is dependent upon the number of mismatched base pairs. # A double-stranded DNA molecule or DNA-RNA hybrid, where each strand is of a different origin. Heterogametic - possessing two different sorts of sex chromosomes -- in humans, the male is the heterogametic sex and the female is the homogametic sex; this is not true of all species. # the sex that produces gametes containing unlike sex chromosomes. Heterogametic sex: The sex which has the two different sex chromosomes (XY). Human and Drosophila males are the heterogametic sex, whereas, in birds, moths, some fish and amphibians, females are the heterogametic sex (ZW). Heterogeneous nuclear R A (hnR A). The name originally given to large RNA molecules found in the nucleus, which are now known to be unedited mRNA transcripts, or premRNAs. (See RNA.) # RNA products immediately synthesized from the DNA template in the nucleus (sometimes called DNA-like RNA or dRNA). This RNA species has a short half-life, is very heterogeneous and very large (molecular weight in excess of 107). hnRNA molecules are processed to generate the mRNA molecules (molecular weight generally less than 2x106) before leaving the nucleus. Heterokaryon: A cell containing more than one genetically different nuclei. Naturally occurs in fungi as long as their fungal (heterokaryon) incompatibility types are identical (see also dikaryotic). Heteromorphic: the state of having homologous chromosomes that differ morphologically. Heterosis - the situation in which the heterozygous phenotype is greater in some measure than either of the homozygous phenotypes; eg "hybrid vigour" Heterosporangiate -- producing two different kinds of sporangia, specifically microsporangia and megasporangia. Compare with heterosporous. Heterosporous -- producing two different sizes or kinds of spores. These may come from the same or different sporangia, and may produce similar or different gametophytes. Contrast with homosporous, and compare with heterosporangiate. # producing two kinds of spores. Heterothallic: Organisms (fungi, algae, plants) which can only undergo sexual reproduction with another bearing a different mating/compatibility type (self-incompatible). See also homothallic. Heterozygosity: Presence of two different alleles at a locus in a diploid organism (see homozygosity). It is the result of inheritance of different alleles from parents. Heterozygote advantage: the situation where the heterozygote has a greater fitness than either homozygote.

Heterozygous - a genotype at a diploid locus with two different alleles present; cf homozygous, in which the genotype has two identical alleles at the locus. # having different alleles in the corresponding loci of homologous chromosomes. Hfr: A male bacterial cell that has the F factor integrated into its chromosome is an Hfr (high frequency of recombination) cell. Crosses between Hfr cells and F- females produce far more recombinant progeny than do crosses between F+ males and Ffemales. High performance liquid (HPLC Chromatography) A general methodology to improve the separation of complexprotein mixtures. The types of HPLC columns available are the same as for conventional chromatography, such as those based on size exclusion, hydrophobicity, and ionic interaction, but the improved flow rates resulting from the high pressure system provide enhanced separation capacity and improved speed. Histones -- proteins attached to the dna of eukaryotes which allows it to be packaged into chromosomes. # Basic proteins that are involved in the packing of DNA. They bind to the phosphate groups of DNA. There are five major types of histone proteins. HLA complex: The human major histocompatibility complex (MHC). An HLA haplotype has been totally sequenced in 1999. hnR A: Heterogeneous nuclear RNA; refers collectively to the variety of RNAs found in the nucleus, including primary transcripts, partially processed RNAs and snRNA. The term hnRNA is often used just for the unprocessed primary transcripts, however. Holandric gene: A gene carried on the Y chromosome and therefore transmitted from father to son. Holdfast -- anchoring base of an alga. Homeobox: Conserved protein sequence which forms a DNAbinding domain in a class of transcription factors. Hominid: A member of the Hominidae family. Homogametic: the sex with homomorphic sex chromosomes; it produces only one kind of gamete in regard to the sex chromosomes. Homologous - refers to the chromosomes in diploid cells which have similar genetic content and which pair at meiosis. # Chromosomes that have the same linear arrangement of genes-a pair of matching chromosomes in a diploid organism. See Chromosomes. # A pair of chromosomes containing the same linear gene sequences, each derived from one parent. [DOE] # Chromosomes that occur in pairs one having come from the male parent and the other from the female parent. They pair participate in crossing-over during meiosis. Homologous chromosomes contain the same array of genes but may contain different alleles at those loci. Homologous recombination - the exchange of sequence between two related but different dna (or rna) molecules, with the result that a new "chimeric" molecule is created. Several mechanisms may result in recombination, but an essential requirement is the existence of a region of homology in the recombination partners. In dna recombination, breakage of single strands of dna in the two recombination partners is followed by joining of strands present in opposing molecules, and may involve specific enzymes. Recombination of rna molecules may occur by other mechanisms. # When a manipulated gene is introduced into a cell, it can be incorporated into the genome either randomly or at a specific locus. By incorporating sequences that normally flank the desired locus, a

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manipulated gene can be specifically (albeit rarely) introduced into the genome. Selection for this unlikely event can be enhanced by introduction of the herpes thymidine kinase (TK) gene into the original targeting construct. Should the construct be randomly incorporated into the genome, the TK gene will also be introduced, rendering the cell sensitive to gancyclovir. If homologous recombination occurs, the TK gene will be eliminated, as there are no homologous sequences at the specific genetic locus of interest and the resultant cell will be resistant to the antibiotic. #. The exchange of DNA fragments between two DNA molecules or chromatids of paired chromosomes (during crossing over) at the site of identical nucleotide sequences. Homology - indicates similarity between two different nucleotide or amino acid sequences, often with potential evolutionary significance. It is probably better to use more quantitative and descriptive terms such as nucleotide "identity" or, in the case of proteins, amino acid "identity" or "relatedness" (the latter refers to the presence of amino acids residues with similar polarity/charge characteristics at the same position within a protein). # two structures are considered homologous when they are inherited from a common ancestor which possessed the structure. This may be difficult to determine when the structure has been modified through descent. Homomorphic: morphologically identical members of a homologous pair of chromosomes. Homopolymer tailing Extension of the 3' ends of a piece of double-stranded DNA using the enzyme terminal transferase and a single deoxynucleoside triphosphate as substrate, resulting in a 3' overhang composed of a single base repeat. If DNA which is to be annealed to this is tailed with the complementary base, mutually cohesive ends are produced. The tailed molecules are unable to circularise because their ends are not cohesive. Sometimes used for insertion of DNA into vectors. Homosporous - producing one kind of spore; all spores are identical. # producing only one size or kind of spore. Contrast with heterosporous. Homothallic: Organisms (fungi, algae, plants) which can undergo sexual reproduction with a similar strain including the self (self-compatible) (see also heterothallic). Homozygosity: Presence of two identical alleles at a locus in a diploid organism (see heterozygosity). It is the result of inheritance of identical alleles from both parents. # having identical alleles in the corresponding loci of homologous chromosomes and therefore breeding true. Homozygote. An organism whose genotype is characterized by two identical alleles of a gene. See Allele, Genotype. Host -- organism which serves as the habitat for a parasite, or possibly for a symbiont. A host may provide nutrition to the parasite or symbiont, or simply a place in which to live. Host strain (bacterial): The bacterium used to harbor a plasmid. Typical host strains include HB101 (general purpose E. coli strain), DH5 (ditto), JM101 and JM109 (suitable for growing M13 phages), XL1-Blue (general-purpose, good for blue/white lacZ screening). Note that the host strain is available in a form with no plasmids (hence you can put one of your own into it), or it may have plasmids present (especially if you put them there). Hundreds, perhaps thousands, of host strains are available.

House-keeping genes: Genes which are constitutively expressed in most cells because they provide basic functions. Htf island: Hpa Tiny Fragment island which are unmethylated CpG-rich regions in the genome. Eighty percent of these occur at or near genes, particularly housekeeping genes. Many of the MHC genes discovered were not near Htf islands. Human Genome Project. A project coordinated by the National Institutes of Health (NIH) and the Department of Energy (DOE) to determine the entire nucleotide sequence of the human chromosomes. (See NIH.) Human growth hormone (HGH, somatotrophin). A protein produced in the pituitary gland that stimulates the liver to produce somatomedins, which stimulate growth of bone and muscle. Hybrid vigor (heterosis): Unusual growth, strength, and health of heterozygous offspring from two less vigorous homozygous parents. Hybrid. The offspring of two parents differing in at least one genetic characteristic (trait). Also, a heteroduplex DNA or DNA-RNA molecule.# a heterozygote; an offspring from genetically dissimilar parents, even different species. # The offspring of two distinct species. Hybridisation Formation of a double-stranded nucleic acid molecule by complementary base pairing of two single strands from different sources. DNA-RNA hybrids are possible. Describes the process in which a nucleic acid probe is allowed to bind to and detect a complementary sequence on a blot. # the process of base pairing leading to formation of duplex rna or dna or rna-dna molecules. #. The hydrogen bonding of complementary DNA and/or RNA sequences to form a duplex molecule. (See Northern hybridization, Southern hybridization.) # The reaction by which the pairing of complementary strands of nucleic acid occurs. DNA is usually double-stranded, and when the strands are separated they will re-hybridize under the appropriate conditions. Hybrids can form between DNA-DNA, DNA-RNA or RNA-RNA. They can form between a short strand and a long strand containing a region complementary to the short one. Imperfect hybrids can also form, but the more imperfect they are, the less stable they will be (and the less likely to form). To "anneal" two strands is the same as to "hybridize" them. Hybridoma - a clone of plasmacytoma cells which secrete a monoclonal antibody; usually produced by fusion of peripheral or splenic plasma cells taken from an immunized mouse with an immortalized murine plasmacytoma cell line (fusion partner), followed by cloning and selection of appropriate antibodyproducing cells. # A hybrid cell, composed of a B Lymphocyte fused to a tumor cell, which grows indefinitely in tissue culture and is selected for the secretion of a specific antibody of interest. Hydrogen bond A weak bond between molecules, or different parts of the same molecule, formed by a restricted form of sharing of electrons between atoms. Readily formed between OH (hydroxyl) and NH2 (amino) groups and oxygen or nitrogen atoms. They are important in proteins and are the mechanism for base-pairing in nucleic acids. They are easily disrupted by heat. They are responsible for base-pairing in nucleic acids and for the maintenance of 3D structure in proteins. # A relatively weak bond formed between n y. a hydrogen atom (which is covalently bound to a nitrogen or oxygen atom) and a nitrogen or oxygen with an unshared electron pair. # the weak electrostatic attraction that exists between a hydrogen atom that is covalently

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bonded to an o or n atom and an atom containing an unshared electron pair. Hydrolysis. A reaction in which a molecule of water is added at the site of cleavage of a molecule to two products. Hydrophilic -- "water loving". Hydrophilic compounds dissolve easily in water, and are usually polar. Hydrophilicity plot - a computer plot which examines the relative summed hyrophobicity/hydrophilicity of adjacent amino acid sidechains (usually within a moving window of about 6 amino acid residues) along the primary sequence of a polypeptide chain. Values for the contribution of sidechains of each the 20 common amino acids to hydrophobicity/hydrophilicity have been developed by hopp & woods, and kyte & doolittle, and these plots are often named after these workers. Generally, hydrophobic regions of proteins are considered likely to be in the interior of the native protein, while hydrophilic domains are likely to be exposed on the surface and thus possibly antigenic sites (epitopes). At best, these are crude predictions. Hydrophobic -- "water fearing". Hydrophobic compounds do not dissolve easily in water, and are usually non-polar. Oils and other long hydrocarbons are hydrophobic. Hydrophobic Chromatography This methodology separates proteins based on their hydrophobicity. Proteins preferentially bind to the matrix based on the strength of this interaction; proteins are then eluted off using solvents of increasing hydrophobicity. Separation media include phenyl-sepharose and octyl-sepharose. Hypothesis -- a concept or idea that can be falsified by various scientific methods. # An unproven but testable scientific proposition. A theory is a statement with some confirmation. Hypotrich: A protozoan of the Ciliate order which reproduces sexually or by asexual binary division. Sexual reproduction can be via conjugation (nuclear exchange) or gamete fusion. In the former, multiple mating types are involved. In gametic fusion there are only two types one of which is the only source of intracellular organelles (see also mating type).

I
Ichthyosaur: An extinct group of marine fish-like or porpoise-like reptiles abundant in Mesozoic seas. Idiomorph: This term is used to describe the fungal mating types which are extremely dissimilar from each other and do not show homology between strains of the opposite sex (as opposed to the allelic relationship in most polymorphic systems). Also used as ideomorph. Immortalizing oncogene. A gene that upon transfection enables a primary cell to grow indefinitely in culture. (See Oncogene.) Immunoblot - see western blot. Immunoprecipitation - a process whereby a particular protein of interest is isolated by the addition of a specific antibody, followed by centrifugation to pellet the resulting immune complexes. Often, staphylococcal proteins a or g, bound to sepharose or some other type of macroscopic particle, is added to the reaction mix to increase the size and ease collection of the complexes. Usually, the precipitated protein is subsequently examined by sds-page. Imprinting: See genomic imprinting. In situ hybridization This technique is designed to detect specific RNA present in histological samples. Tissue is

prepared with particular care not to degrade RNA. The cells are fixed on a microscope slide, allowed to hybridize to probe, and then washed and overlaid with photographic emulsion. Following exposure for one to four weeks, the emulsion is developed and silver grains overlying cells that contain specific RNA are detected. The most useful probes for this purpose are metabolically 35S-labeled riboprobes generated by in vitro transcription of a cDNA using viral RNA polymerase. These probes give the lowest background and are preferable to using terminal deoxynucleotidyl transferase or alternative methods using 32P as an isotope. In situ. Refers to performing assays or manipulations with intact tissues. In vitro translation - see reticulocyte lysate. In vitro: Literally, in glass meaning in the laboratory. In vivo. Refers to biological processes that take place within a living organism or cell. # Literally, in the living organism. Inbreeding - matings between relatives - ie between individuals who are genetically similar because they share a recent common ancestor. Inbreeding coefficient: the probability that two allelic genes united in a zygote are both descended from a gene found in an ancestor common to both parents; also the proportion of loci at which an individual is homozygous. Inbreeding depression: Reduction in offspring fitness resulting from mating between blood relatives. Inbreeding: Production of offspring by (blood) related parents. Its most extreme form is self-fertilization in hermaphrodites (most invertebrates and plants).# the crossing of closely related plants or animals. Incest: Sexual relationships between parents and children, or between brothers and sisters. Incomplete dominance - when the phenotype of the heterozygote is intermediate between that of the two homozygotes. # A condition where a heterozygous off spring has a phenotype that is distinctly different from, and intermediate to, the parental phenotypes. See Heterozygote, Phenotype. # failure of a dominant phenotype to be fully expressed in an organism carrying a dominant and a recessive allele; the result is usually an intermediate between the homozygous dominant and the recessive forms. #: One allele is not expressed, but the other allele expresses itself normally so that the phenotype gets half the dose of the effect. Independent assortment - when non-alleles of unlinked genes segregate independently of each other. Inducer - a small molecule, such as iptg, that triggers gene transcription by binding to a regulator protein, such as lacz. Inducible system: a regulatory system in which the product of a regulator gene is active and blocks transcription of the operon. Inflorescence -- a cluster of flowers. Ingestion -- the intake of water or food particles by "swallowing" them, taking them into the body cavity or into a vacuole. Contrast with absorption. Ingroup -- in a cladistic analysis, the set of taxa which are hypothesized to be more closely related to each other than any are to the outgroup. Initiation codon - the codon at which translation of a polypeptide chain is initiated. This is usually the first aug triplet in the mrna molecule from the 5' end, where the ribosome binds to the cap and begins to scan in a 3' direction. However, the surrounding sequence context is important and may lead to the first aug being bypassed by the scanning ribosome in favor of an

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alternative, downstream aug. Also called a "start codon". Occasionally other codons may serve as initiation codons, e.g. Uug. # The ATG triplet is used to begin polypeptide synthesis. This is usually the first ATG codon, located approximately 30 nucleotides downstream of the site of transcription initiation (cap site). However, the context in which the ATG resides is also important (see KOZAK sequence). # The mRNA sequence AUG, coding for methionine, which initiates translation of mRNA. Initiation complex This multi-protein complex forms at the site of transcription initiation and is composed of RNA polymerase, a series of ubiquitous transcription factors (TF II family), and specific enhancers and/or silencers. The proteins are brought together by the looping of DNA strands so that protein binding sites, which may range up to tens of kb apart, can be brought into close juxtaposition. Specific proteinprotein interactions then allow assembly of the complex. # A multi-protein complex that forms at the site of transcription initiation and is composed of RNA polymerase II, ubiquitous or general transcription or initiation factors (TFII or IF/eIF) and gene-specific enhancers/silencers. Initiation factor: a protein required for the initiation of protein synthesis. Innate immunity: Pre-existing and non-specific defense immunity with a very low memory component if any. As the primitive immune response against bacteria, it is present in invertebrates and vertebrates. Inositol lipid. A membrane-anchored phospholipid that transduces hormonal signals by stimulating the release of any of several chemical messengers. (See Phospholipid.) Insert: In a complete plasmid clone, there are two types of DNA - the "vector" sequences and the "insert". The vector sequences are those regions necessary for propagation, antibiotic resistance, and all those mundane functions necessary for useful cloning. In contrast, however, the insert is the piece of DNA in which you are really interested. Insertion mutations. Changes in the base sequence of a DNA molecule resulting from the random integration of DNA from another source. See DNA, Mutation. Insertion sequence - a small bacterial transposon carrying only the genetic functions involved in transposition. There are usually inverted repeats at the ends of the insertion sequence. Insulin. A peptide hormone secreted by the islets of Langerhans of the pancreas that regulates the level of sugar in the blood. Integrase: An enzyme that catalyzes a site-specific recombination (integration or excision) involving a prophage and a bacterial chromosome. Integrin -- adhesive protein of the extracellular matrix in animals. Interference The mechanisms by which infection of a cell by one virus excludes infection by others. Interference is often due to the cellular production of coat proteins, which bind to and block the cells remaining viral receptors. Interferon. A family of small proteins that stimulate viral resistance in cells. Intergenic regions. DNA sequences located between genes that comprise a large percentage of the human genome with no known function. Intergenic: Between two genes; e.g. intergenic DNA is the DNA found between two genes. The term is often used to mean non-functional DNA (or at least DNA with no known

importance to the two genes flanking it). Alternatively, one might speak of the "intergenic distance" between two genes as the number of base pairs from the polyA site of the first gene to the cap site of the second. This usage might therefore include the promoter region of the second gene. Internode -- the region of a stem between two nodes, when there is no branching of the vascular tissue. Intestine -- the portion of the digestive tract between the stomach and anus; it is the region where most of the nutrients and absorbed. Intracellular infections: Several microorganisms considered as potential biological warfare agents are capable of surviving intracellularly. Treating such intracellular infections poses a great challenge to the medical community since these infections may be lethal and their intracellular habitat renders these microbes relatively inaccessible. Our ongoing project aims to characterize host cell response to the prototypic intracellular infections tularemia and plague. Characterization of the host cell responses is performed by large-scale cDNA microarray analysis. These studies will elucidate interactions and identify genes regulated by eukaryotic cells in response to intracellular infections. "Characterizing Host Cell Response to the Prototypic Intracellular Infections: Tularemia and Plague" Dr. Anders Sjstedt, Defense Research Establishment; and Professor, Department of Clinical Microbiology, Division of Clinical Bacteriology, Ume University Introgression. Backcrossing of hybrids of two plant populations to introduce new genes into a wild population. Intron - intervening sequences in eukaryotic genes which do not encode protein but which are transcribed into rna. Removed from pre-mrna during nuclear splicing reactions. #. A noncoding DNA sequence within a gene that is initially transcribed into messenger RNA but is later snipped out. See Coding, DNA, Messenger RNA, Transcription. # A non-coding section of DNA within a gene that is not translated to a peptide. Intervening sequences between exons. Introns are featured in the primary transcript (pre-mRNA) but removed by splicing during nuclear RNA processing/editing. # in split genes, a segment that is transcribed into nuclear rna, but is subsequently removed from within the transcript and rapidly degraded. # Introns are portions of genomic DNA which ARE transcribed (and thus present in the primary transcript) but which are later spliced out. They thus are not present in the mature mRNA. Note that although the 3' flanking region is often transcribed, it is removed by endonucleolytic cleavage and not by splicing. It is not an intron. # Sequences of non-coding bases found in eukaryotic genes. They may make up a large proportion of the total gene length. Introns are spliced out of the RNA transcript during its processing to mRNA. # These are the regions of the primary RNA transcript that are eliminated during splicing. Their precise function is uncertain. However, several transcriptional regulatory regions have been mapped to introns, and they are postulated to play an important role in the generation of genetic diversity (exon shuffling mechanism). Intrusive -- plutonic. Antonym of extrusive. Invasiveness. Ability of a plant to spread beyond its introduction site and become established in new locations where it may provide a deliterious effect on organisms already existing there. Inversion - situation in which a chromosomal segment has been broken and turned end-to-end before being rejoined: this

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produces chromosomal loops ("inversion loops") when meiosis occurs in a cell which is heterozygous for an inversion. Inversion: chromosome segments that have been turned through 180 degrees with the result that the gene sequence for the segment is reversed with respect to that of the rest of the chromosome. Invertebrate: All animals other than those in the phylum Chordata; lower metazoans. They do not possess a notochord or vertebral column. Examples are worms, corals, sponges, etc. The protochordates are sometimes called higher invertebrates. Inverted repeats - two copies of the same or related sequence of dna repeated in opposite orientation on the same molecule (contrast with direct repeats). Adjacent inverted repeats constitute a palindrome. Ion an atom or small molecule which carries a positive or negative charge. Ion exchange Chromatography This separation methodology depends on the preferential binding of positively charged proteins to a matrix containing negatively charged groups or a negatively charged protein binding to a matrix containing positively charged groups. Increases in the buffer concentration of sodium chloride are then used to break the ionic interaction between protein and matrix and elute offbound proteins. Examples of such separation media include DEAE and CM cellulose. IRF-1 (interferon regulatory factor-1) Interferon regulatory factor-1 is a transcription factor that activates the expression of IFN and and maps to chromosome 5q31.1. As it is thought to act as a tumor suppressor gene, its role in the pathologic consequences of the 5q- syndrome is under active investigation. IRF-2 (interferon regulatory factor-2) Interferon regulatory factor-2 is a gene which binds to a promoter element shared by IFN and and many IFN-inducible genes; unlike IRF-1, which stimulates such genes, IRF-2 represses transcription at the site. It is felt that the ratio of IRF-1 to IRF- 2 might be a critical event in the regulation of cellular proliferation. Iso schizomer Restriction endonucleases that contain an identical recognition site but are derived from different species of bacteria (and hence have different names). Isotope -- one of two or more variations of the same chemical element, differing in the number of neutrons not the number of protons. # One of two or more forms of an element that have the same number of protons (atomic number) but differing numbers of neutrons (mass numbers). Radioactive isotopes are commonly used to make DNA probes and metabolic tracers. Isozymes - families of related enzymes separated by some technique - often by electrophoresis. Iterative evolution: Repeated origination of lineages with generally similar morphology at different times in the history of a clade.

Jawless vertebrates (Class Agnatha): The most primitive Vertebrates evolved about 500 Mya. The extant species hagfish and lampreys in the order Cyclostomata belong to this group. Joining (J) segment. A small DNA segment that links genes to yield a functional gene encoding an immunogobulin. Jointed when stiff body parts are connected by a soft flexible region, the body is said to be jointed.

K
Kanamycin. An antibiotic of the aminoglycoside family that poisons translation by binding to the ribosomes. See Kanamycin. kanr. Kanamycin resistance gene. (See Selectable marker.) Karyogamy - a process of fusion of the nuclei of two cells; the second step in syngamy. Karyotype - the chromosome complement of an individual. # All of the chromosomes in a cell or an individual organism, visible through a microsope during cell division. # A photomicrograph of an individuals chromosomes arranged in a standard format showing the number, size, and shape of each chromosome type; used in low- resolution physical mapping to correlate gross chromosomal abnormalities with the characteristics of specific diseases. [DOE] # the number, size, and morphology of the chromosome set of a cell, individual, or species. Kb - 'kilobase" unit of 1000 nucleotide bases, either RNA or DNA. KB: abbreviation for kilobase, one thousand bases. kbp kilobase pairs. A measure of size of double-stranded DNA. Kelp forest -- marine ecosystem dominated by large kelps. These forests are restricted to cold and temperate waters, and are most common along the western coasts of continents. Kelp forests first appeared in the miocene. Kin recognition: Ability to distinguish the incest from unrelated members of a species. Kin selection: Natural selection for behaviors that lowers an individuals own chance of survival but raises that of a relative. Kinase - A kinase is in general an enzyme that catalyzes the transfer of a phosphate group from ATP to something else. In molecular biology, it has acquired the more specific verbal usage for the transfer onto DNA of a radiolabeled phosphate group. This would be done in order to use the resultant "hot" DNA as a probe. # These enzymes transfer the -phosphate group from ATP to the 5' hydroxyl group of a nucleic acid chain. see phosphorylation. Kinasing = phosphorylation. Addition of a phosphate group to the 5' ends of DNA or RNA molecules, using polynucleotide kinase. Kinetochore: the chromosomal point of attachment for spindle fibers during mitosis and meiosis; located on the centromere. Kingdom: The major taxonomic group in the current classification of living organisms with the exception of informal division of prokaryotic and eukaryotic empires. The five Kingdoms are Monera, Protoctista, Fungi, Plants and Animals. In the late 1980s Cavalier-Smith proposed that within the Eukaryota there are six kingdoms: Archezoa, Protozoa, Chromista, Plants, Fungi, and Animals (see also taxonomy). Klenow fragment - the large fragment of e. Coli dna polymerase i which lacks 5' -> 3' exonuclease activity. Very useful for sequencing reactions, which proceed in a 5' -> 3' fashion (addition of nucleotides to templated free 3' ends of primers). # A modified version of bacterial DNA polymerase

J
Jacobsons organ: In some vertebrates, an accessory olfactory organ developed in connection with the roof of the mouth. Jaw -- often loosely applied to any movable, toothed structures at or near the mouth of an animal, such as the scolecodonts of annelids. In vertebrates, the jaw is derived from the first gill arch.

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that has been modified so that only the polymerase function remains; the 5' 3' exonuclease activity has been eliminated. Knock-out - the excision or inactivation of a gene within an intact organism or even animal (e.g., "knock-out mice"), usually carried out by a method involving homologous recombination. Knock-out experiment: A technique for deleting, mutating or otherwise inactivating a gene in a mouse. This laborious method involves transfecting a crippled gene into cultured embryonic stem cells, searching through the thousands of resulting clones for one in which the crippled gene exactly replaced the normal one (by homologous recombination), and inserting that cell back into a mouse blastocyst. The resulting mouse will be chimaeric but, if you are lucky (and if you've gotten this far, you obviously are), its germ cells will carry the deleted gene. A few rounds of careful breeding can then produce progeny in which both copies of the gene are inactivated. KOZAK sequence This five-nucleotide sequence resides just prior to the initiation codon and is thought to represent a ribosomal-binding site. The most consistent position is located three nucleotides upstream from the initiation ATG and is almost always an adenine nucleotide. When multiple potential initiation codons are present in an open reading frame, the ATG codon, which contains a strong consensus KOZAK sequence, is likely the true initiation codon. # In some viral mRNAs, the consensus sequence surrounding the initiating AUG 5 ACCAUGG 3 . It facilitates ribosomal binding and therefore, protein synthesis. The most consistent position is located three nucleotides before the initiation codon (ATG) and is almost always an adenine nucleotide (see also ShineDalgarno sequence).

L
Lac operon: A structural unit in the E.coli genome that consists of three structural genes (encoding different enzymes involved in sugar metabolism) transcribed together and their common promoter and operator genes. Provides a good model for studying the interactions between promoters and repressors. Lag phase. The initial growth phase, during which cell number remains relatively constant prior to rapid growth. See growth phase. Lagging strand: the discontinuously synthesized strand of dna containing ligated okazaki fragments. Lambda: see Bacteriophage Lambda. Lamina -- any broad and flattened region of a plant or alga, which allows for increased photosynthetic surface area. Laminarin -- a beta-glucan polysaccharide produced by many chromists through photosynthesis. Larva - among invertebrates, an immature stage in the life cycle which usually is much smaller than, and morphologically different from, the adult. In insects with metamorphosis, the larva must become a pupa before reaching adulthood. Laser Capture Microdissection LCM: A method for procuring pure cells from specific microscopic regions of tissue sections. These tissue sections may contain many cell types (for example connective, blood vessel, muscle, adipose and immune cells) interspersed and effectively locked together by adhesive interactions. Cancer cells, such as those in prostate cancer, are usually found in such heterogeneous

environments. LCM permits one to "put a bead" on these cells to isolate them and obtain high levels of signal in gene expression and protein expression analysis. The procedure is simple in practice, with the technician placing the cells of interest from a tissue section in the center of the microscope field, and pushing a button that activates an integral laser. The laser activates an area of the film immediately above the center of view and the film bonds with the targeted cells. When the film is lifted, the cells are carried with it, leaving behind the unwanted material. The method was developed at NIH and is being developed commercially with Arcturus Engineering, Inc. It is highly reproducible and accurate, and amenable to automation. Last male sperm precedence: A situation that results in fertilization of the ovum by the sperm of the last male in multiply inseminated female. This is due to sperm incapacitation by the semen and sperm displacement. This well-documented form of sperm competition is best known in Drosophila. Latency (viral): The state of viral infection in which the virus exists in host cells without reproducing itself. This is slightly different from viral persistence when basal replication continues. Lava -- any molten material that is extrusive or volcanic, or the rock that forms from a molten extrusive. Lawn. A uniform and uninterrupted laver of bacterial growth, in which individual colonies cannot be observed. LCM: see Laser Capture Microdissection LCR (locus control region) Cis-acting sites are occasionally organized into a region removed from the structural gene(s) they control. Such locus control regions (LCRs) are best described for the globin and globin loci. First recognized by virtue of clustering of multiple DNAse hypersensitive sites, the globin LCR is required for high level expression from all of the genes and appears to be critical for their stage-specific developmental pattern of expression. Leader sequence: A sequence at the 5 (N-terminal) of the DNA and mRNA which leads the newly synthesized mRNA to the ribosome (it is not translated). It is also used to mean the signal sequence which is translated but is subject to posttranslation cleavage when the final destination is reached or following secretion. Leading strand: the dna strand synthesized with few or no interruptions; synthesized 5' to 3' toward the replication fork. Leaf -- an organ found in most vascular plants; it consists of a flat lamina (blade) and a petiole (stalk). Many flowering plants have additionally a pair of small stipules near the base of the petiole. Leaf trace -- the strand of vascular tissue which connects the leaf veins to the central vascular system of the stem. Leaflet -- in a compound leaf, the individual blades are called leaflets. Legume. A member of the pea family that possesses root nodules containing nitrogen-fixing bacteria. Lek: A special site where communal courtship display takes place by swarms of animals. Lekking is best known in male birds to attract female mates. Rare form of lekking by females is seen in the African butterfly (Acraea encedon), the Dance fly (Empis borealis) and the European dotterel bird (Eudromias morinellus). Leucine zipper proteins A family of DNA-binding proteins that require a dimeric state for activity and that dimerize by virtue of an alpha helical region that contains leucine at every

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seventh position. Because 3.4 amino acids reside in each turn of an alpha helix, the occurrence of leucine at every seventh position results in a strip of highly hydrophobic residues on one surface of the alpha helix. Such a domain on one polypeptide can intercollate with a similar domain on a second polypeptide, resulting in the formation of a stable homodimer or heterodimer. Examples of the leucine zipper family include the proto-oncogenes c-jun and c-fos. # A motif found in certain proteins in which Leu residues are evenly spaced through an -helical region, such that they would end up on the same face of the helix. Dimers can form between two such proteins. The Leu zipper is important in the function of transcription factors such as Fos and Jun and related proteins. Library - a set of cloned fragments together representing with some degree of redundancy the entire genetic complement of an organism (see cdna library, genomic library). # A collection of clones or DNA fragments which contains all of the sequences present in the source. Thus a genomic library contains all of the sequences present in the genome and a cDNA library contains copies of all the mRNA molecules present in the extracted cells. # A collection of cells, usually bacteria or yeast, that have been transformed with recombinant vectors carrying DNA inserts from a single species. (See cDNA library, Expression library, Genomic library.) # A library might be either a genomic library, or a cDNA library. In either case, the library is just a tube carrying a mixture of thousands of different clones - bacteria or phages. Each clone carries an "insert" - the cloned DNA. Library screening Three major methods are available to obtain cDNA of interest. The classic technique utilizes DNA probes (such as oligonucleotides or intact cDNA from a homologous gene) to screen cDNA libraries. An oligonucleotide probe is usually derived from a reverse translation of known protein sequence. By expressing cDNA as a fusion protein with galactosidase, various antisera can be used to screen for fusion proteins encoded by the cDNA of interest. Finally, cDNA libraries may be constructed in cloning vectors that allow for expression of the cDNA insert in E. coli or a mammalian cell host. If a highly sensitive assay for the desired proteins function can be developed, pools of cDNA clones can be expressed and then assayed together; a positive assay from a pool would allow one to subdivide into smaller pools and eventually at clonal density. Librigenae -- the "free cheeks"; separate, detachable portions of the trilobite cephalon. Ligase (D A ligase). An enzyme that catalyzes a condensation reaction that links two DNA molecules via the formation of a phosphodiester bond between the 3' hydroxyl and 5' phosphate of adjacent nucleotides. # an enzyme that catalyzes the formation of a phosphodiester bond between adjacent 3'-oh and 5'-p atoms in DNA. # An enzyme which is of vital importance in recombinant DNA technology. It joins nucleotides together by a phosphodiester bond between the 5P end of a polynucleotide chain and the 3-OH end of another one. # An enzyme, T4 DNA ligase, which can link pieces of DNA together. The pieces must have compatible ends (both of them blunt, or else mutually compatible sticky ends), and the ligation reaction requires ATP. # These enzymes utilize the -phosphate group of ATP for energy to form a phosphodiester linkage between two pieces of DNA. The nucleotide contributing the 5' hydroxyl group to the linkage

must contain a phosphate, which is then linked to the 3' hydroxyl group of the growing chain. Ligate. The process of joining two or more DNA fragments. Ligation - see DNA ligase. Ligation In vitro reaction used to make the covalent phosphodiester linkage between two double stranded DNA ends. The reaction requires the presence of a phosphate group on the free 5' end and a -OH group on the free 3' end of the strands to be joined. The reaction is catalysed by the enzyme DNA ligase.# The process of splicing two pieces of DNA together. In practice, a pool of DNA fragments are treated with ligase (see "Ligase") in the presence of ATP, and all possible splicing products are produced, including circularized forms and end-to-end ligation of 2, 3 or more pieces. Usually, only some of these products are useful, and the investigator must have some way of selecting the desirable ones. Limestone -- a carbonate sedimentary rock composed of more than 50 percent of the mineral calcium carbonate (caco3). Limnology -- the study of river system ecology and life. Lineage -- any continuous line of descent; any series of organisms connected by reproduction by parent of offspring. # A chart that traces the flow of genetic information from generation to generation. Linear epitope - an epitope formed by a series of amino acids which are adjacent to each other within the primary structure of the protein. Such epitopes can be successfully modelled by synthetic peptides, but comprise only a small proportion of all epitopes. The minimal epitope size is about 5 amino acid residues. Also called a sequential epitope. LI ES (long interspersed elements): One of the abundant intermediate (6 to 7 kb) repeat DNA sequences in mammals (see also SINES). Linkage - the tendency of genes to be inherited together as a result of their relatively close proximity on the same chromosome, or location on the same plasmid. # the greater association in inheritance of two or more nonallelic genes than is to be expected from independent assortment; genes are linked because they reside on the same chromosome. # The tendency of genes on the same chromosome to segregate together. This means that linked genes are transmitted to the same gamete more than 50% of the time. Genetic linkage reflects a lack of meiotic crossovers between two genes. Linkage disequilibrium (LD): The tendency for two alleles to be present on the same chromosome (positive LD), or not to segregate together (negative LD). As a result, specific alleles at two different loci are found together more or less than expected by chance. The same situation may exist for more than two alleles. Its magnitude is expressed as the delta (D) value and corresponds to the difference between the expected and the observed haplotype frequency. It can have positive or negative values. LD is decreased by recombination. Thus, it decreases every generation of random mating unless some process opposing the approach to linkage equilibrium. Permanent LD may result from natural selection if some gametic combinations result in higher fitness than other combinations. Link to a lecture on linkage disequilibrium; online linkage disequilibrium analysis. Linkage group - Genes that are physically linked to each other by being on the same chromosome. Locus - the site of a gene on a chromosome Linkage map. See Genetic linkage map.

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Linkage. The frequency of coinheritance of a pair of genes and/or genetic markers, which provides a measure of their physical proximity to one another on a chromosome. Linked genes/markers. Genes and/or markers that are so closely associated on the chromosome that they are coinherited in 80% or more of cases. Linker - a short oligodeoxyribonucleotide, usually representing a specific restriction endonuclease recognition sequence, which may be ligated onto the termini of a dna molecule to facilitate cloning. Following the ligation reaction, the product is digested with the endonuclease, generating a dna fragment with the desired sticky or blunt ends.# A short, double-stranded oligonucleotide containing a restriction endonuclease recognition site, which is ligated to the ends of a DNA fragment. # A small piece of synthetic double-stranded DNA which contains something useful, such as a restriction site. A linker might be ligated onto the end of another piece of DNA to provide a desired restriction site. Linkering To efficiently insert the cDNA library into a cloning vector, synthetic duplex oligonucleotides that contain a restriction endonuclease site are attached to the blunted ends of the cDNA. A restriction endonuclease is chosen that rarely cuts DNA (such as the 8 bp recognition sequence for Not I, or if a more common restriction site is used such as Eco RI, the cDNA should first be methylated in order to prevent subsequent cDNA digestion with the enzyme) and is used to generate sticky ends on the cDNA. Lipids -- a class of biochemical compounds which includes fats, oils, and waxes. Lipofectin - a commercially marketed liposome suspension which is mixed with dna or rna to facilitate uptake of the nucleic acid by eukaryotic cells (see transfection). Liposome: Small spheres of phospholipid bilayers (just like cell membranes). They are used for gene transfer into cells. The DNA to be transferred is attached to them. The DNAliposome complex fuses with the cell membrane to enter the cell and releases the DNA into the cell. # By encapsulating the DNA to be transfected in an artificial lipid carrier, foreign DNA can be introduced into the cell. This method, like electroporation, has been successful in transfecting cells previously thought difficult to manipulate. Its only drawback is its expense # Membrane-bound vesicles constructed in the laboratory to transport biological molecules. Litter -- leaf litter, or forest litter, is the detritus of fallen leaves and bark which accumulate in forests. Living fossil: An extant species which is morphologically very similar to a species from the ancient past. Despite apparent lack of change, they seem to have escaped extinction. Coelacanth (a 350 million-years-old lobe-finned fish), Horseshoe Crab (a 510 million-years-old marine arthropod), Amazon River Dolphin, Gingko (maidenhair tree, a gymnosperm), and Metasequoia (Metasequoia glyptostrobodes, a conifer) are examples. Lobe-finned fish: A group of fish that have bone and muscle in their limbs as opposed to simple fins as in most teleosts. The group includes coelacanth and lungfish. Locus (plural = loci). A specific location or site on a chromosome. # (plural: loci) the position that a gene occupies in a chromosome or within a segment of genomic DNA. # The position on a chromosome occupied by a particular gene (plural: loci).

Lod score: a technique for determining the most likely recombination frequency between two loci from pedigree analysis. # Logarithm of the odds favoring linkage obtained from the statistical analysis of linkage. The lod score (Z) of +3 is considered evidence for linkage. Log phase. See Logarithmic phase. Logarithmic phase (log or exponential growth phase). The steepest slope of the growth curve--the phase of vigorous growth during which cell number doubles every 20-30 minutes. (See Growth phase.) Lophophore -- complex ring of hollow tentacles used as a feeding organ. The tentacles are covered by cilia, which generate a current to bring food particles into the mouth. The structure is only found in the brachiopods, phoronids, and bryozoans. More info? Lorica -- a vase-shaped or cup-shaped outer covering. Found in many protists, including some flagellates, ciliates, chrysophytes, and choanoflagellates, as well as in some animal cells. Loss-of-heterozygosity (LOH): Refers to the disappearance of polymorphic marker alleles when constitutional DNA and tumor DNA from cancer patients are compared. The consequence is usually genomic deletion discarding the normal copies of tumor suppressor genes. Such deletion (or functional deletion through methylation) may uncover existing mutations in the homologue copy. Luciferase -- enzyme which activates luciferin to produce bioluminescence. # This gene, which is the most recent reporter gene to be used, has gained increasing acceptance because of its ease of assay and extreme sensitivity. The assay is based on the ability of the protein to undergo chemiluminescence and transmit light, detected with a luminometer. Luciferin -- compound whose activated form emits light. Lyon hypothesis: the hypothesis that dosage compensation in mammals is accomplished by the random inactivation of one of the two x chromosomes in the somatic cells of females. Lyon hypothesis: The proposition by Mary F Lyon that random inactivation of one X chromosome in the somatic cells of mammalian females is responsible for dosage compensation and mosaicism. Lysis. The destruction of the cell membrane.# Cell rupture caused by physical or chemical means, or by phage infection and propagation leading to the release of the cell content; also the death of microorganisms after the stationary phase of a batch fermentation. [IUPAC Biotech] Lysogen Bacterial cell or strain which carries a copy of a bacteriophage genome in its chromosome. Genes within the prophage will be expressed providing their promoters are active.# A bacterial cell whose chromosome contains integrated viral DNA. Lysogenic. A type or phase of the virus life cycle during which the virus integrates into the host chromosome of the infected cell, often remaining essentially dormant for some period of time. See Lysogen. Lysosome -- eukaryotic organelle which carries digestive enzymes. The lyzosome fuses with a vacuolar membrane containing ingested particles, which are then acted upon by the enzymes. Lytic. A phase of the virus life cycle during which the virus replicates within the host cell, releasing a newgeneration of viruses when the infected cell lyses.

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M
M13: A bacteriophage which infects certain strains of E. coli . The salient feature of this phage is that it packages only a single strand of DNA into its capsid. If the investigator has inserted some heterologous DNA into the M13 genome, copious quantities of single-stranded DNA can subsequently be isolated from the phage capsids. M13 is often used to generate templates for DNA sequencing. Mafic -- term used to describe the amount of dark-colored iron and magnesium minerals in an igneous rock. Complement of felsic. Magma -- molten rock generated within the earth. Magnoliid -- any member of the basal assemblage of flowering plants. Maize (Zea mays): A crop plant used as animal and human food. It features frequently in scientific literature because it is the only diploid plant among economically important food crops such as oats and wheat (which are polyploids). Its disadvantages are that it has a relatively long generation time (a maximum of three generations per year), and a very large and complex genome with a lot of repetitive sequences. Natural cross-pollination ability of maize is another problem. Its meiotic chromosomes are, however, excellent subjects for cytogenetic studies. At present, the model system in plant genetics is Arabidopsis thaliana. Link to Maize website. Major Histocompatibility Complex (MHC): A genetic complex of vertebrates consisting of around 100 genes including the extremely polymorphic cell surface molecules called HLA in humans and H-2 in mice. These molecules provide an immunological marker for selfness and a genetic self-identity to the individual. This information is used in mate choice, union of gametes, maintenance of pregnancy, and immune response against nonself (including a transplanted graft). These molecules are the most polymorphic ones in vertebrates. The polymorphism arises from point mutations not at an unusually higher rate than other genes, and mainly from interallelic gene conversion events. The polymorphism is maintained through pathogen and non-pathogen driven mechanisms via heterozygous advantage (overdominant selection) and negative frequency dependent selection. A 3.6 Mb long human MHC haplotype and the 92 kb chicken MHC have been totally sequenced (see Nature 1999(Oct 28);401:921-925). Male - in organisms with separate sexes, the one which produces sperm. Malignant. Having the properties of cancerous growth. Mammalian protein kinases These enzymes transfer phosphate groups from ATP to either tyrosine, threonine, or serine residues of proteins. These enzymes are among the most important signaling molecules present in mammalian cell biology. Mammals: One of the eight Classes in the Phylum Chordata which contains approximately 4500 species in 15 Orders. In mammals, the fertilization of the egg is internal, the young develops within the body of the mother, and is fed by milk produced by the mammary glands. The mammals are warmblooded and the body is covered with hair. In Mammals, female is the heterogametic sex (XY) and thus male-to-male competition is the predominant form of sexual selection. Mannoxylic -- wood in which there is a great deal of parenchyma tissue among the xylem is called mannoxylic.

Cycads and pteridosperms have mannoxylic wood. Contrast with pycnoxylic. Mantle -- that portion of the interior of the earth that lies between the crust and the core. Map distance: the distance between genes expressed as map units or centimorgans (cm). Map unit (or centi-Morgan) - unit for measuring the distance between linked genes - based on the frequency with which recombination occurs between them: one map unit corresponds to a recombination frequency of 0.01. Mapping. Determining the physical location of a gene or genetic marker on a chromosome. (See Continuous map,Genetic map, Physical map.) Marine -- refers to the ocean. Marker A gene which, on expression, allows easy identification of cells which carry it. Normally used to describe genes carried by a vector which are used to detect vector presence or state in a host cell. Marker gene - a gene whose position on the chromosome is known, and hence can be used in recombination analyses to locate other genes. Master switch genes These polypeptide products are thought to regulate a whole family of genes and result in a cell undergoing a new program of differentiation. An example of such a system is Myo D, in which activation is thought to lead to differentiation along the muscle cell lineage. Mastigoneme -- small hair-like filaments found on the "hairy" flagellum of the chromista. Maternal effect lethals: One form of selfish/parasitic DNA that facilitates its own propagation. They are post-zygotic distorters that kill progeny lacking the factor. Medea in beetles and Scat in mice are the known examples. Progeny of the heterozygous mothers that are homozygous for wild-type are killed. Progeny carrying a copy of the lethal are actually protected. Maternal inheritance: Diseases due to mutations in mtDNA are transmitted only by mothers because all mitochondria are inherited via the egg. Thus, all offspring of an affected female are at risk of inheriting the abnormality, whereas no offspring of an affected male are at risk. Clinical manifestations are variable and may be due to variable mixtures of mutant and normal mitochondrial genomes (heteroplasmy) within cells and tissues. Mating type: Genetically determined characteristics of bacteria, ciliates, fungi and algae, determining their ability to conjugate and undergo sexual reproduction with other members of the species. In yeasts (S.cerevisiae) which have only two types, only cells of opposite types can conjugate. The common mushroom Schizophyllum has more than 50,000 mating types (genders) encoded in two separate loci. In species where the organelles are inherited uniparentally and reproduction is by the union of gametes, there are only two mating types. In species reproducing via sexual conjugation (nuclear exchange) so that each cell preserves its own organelles, there can be multiple types. Maxam-Gilbert sequencing A method to determine the sequence of a stretch of DNA based on its differential cleavage pattern in the presence of different chemical exposures. A nucleic acid chain can be cleaved following G, A, C, or C and T by exposure of 32P-labeled DNA to neutral dimethylsulfate, dimethylsulfate-acid, hydrazine-NaCl-piperidine or hydrazinepiperidine alone, respectively. Megabase cloning. The cloning of very large DNA fragments.(See Cloning.)

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Megaspore -- in plants which are heterosporous, the larger kind of spore is called a megaspore; it usually germinates into a female (egg-producing) gametophyte. Contrast with microspore. Meiosis - a two-stage type of cell division in sexually reproducing organisms. In meiosis, a diploid cell divides to produce four haploid cells, each with half the original chromosome content. For this reason, meiosis is often called a "reduction division". In organisms with a diploid life cycles, the products of meiosis are usually called gametes. In organisms with an alternation of generations, the products of meiosis are caled spores. # Nuclear divisions that give rise to haploid gametes in eukaryotes. # The reduction division process by which haploid gametes and spores are formed, consisting of a single duplication of the genetic material followed by two mitotic divisions. #: Cell division with two phases resulting four haploid cells (gametes) from a diploid cell. In meiosis I, the already doubled chromosome number reduces to half to create two diploid cells each containing one set of replicated chromosomes. Genetic recombination between homologous chromosome pairs occurs during meiosis I. In meiosis II, each diploid cell creates two haploid cells resulting in four gametes from one diploid cell. # the nuclear process in diploid eukaryotes that results in gametes or spores with only one member of each original homologous pair of chromosomes per nucleus. # The reductive cell division which results in daughter cells containing one copy of each of the chromosomes of the parent. The entire meiotic process involves two separate divisions (meiosis I and meiosis II). The first division is a true reductive division with the chromosome number being halved, whereas the second division resembles mitosis in many ways. Thus, a diploid parental cell will give rise to haploid daughter cells (cf. ploidy). IUPAC Biotech].A special method of cell division, occurring in maturation of the germ cells, by means of which each daughter nucleus receives half the number of chromosomes characteristic of the somatic cells of the species. [MeSH, 1968] Melange -- a body of rocks consisting of large blocks (mappable size) of different rocks jumbled together with little continuity of contacts. Melting - the dissociation of a duplex nucleic acid molecule into single strands, usually by increasing temperature. See denaturation. Melting temperature The temperature at which the two strands of a double-stranded DNA molecule come apart. A short (<18 nucleotides) oligonucleotides Tm value (0C) is estimated by the formula: Tm = (number of A + T)x2 + (number of G + C)x4. Membrane -- semi-fluid structure which bounds all cells, and partitions the interior of eukaryotic cells. It consists primarily of two lipid layers, with proteins "dissolved" in the lipids. Mendels first law (law of segregation): The two alleles received one from each parent segregate independently in gamete formation, so that each gamete receives one or the other with equal probability. Mendels second law (law of recombination): Two characters determined by two unlinked genes are recombined at random in gametic formation, so that they segregate independently of each other, each according to the first law (note that recombination here is not used to mean crossingover in meiosis).

Mendelian inheritance: Inheritance of traits mediated by nuclear genes (as opposed to mitochondrial DNA) according to the laws defined by Gregor Mendel. Meristem -- group of undifferentiated cells from which new tissues are produced. Most plants have apical meristems which give rise to the primary tissues of plants, and some have secondary meristems which add wood or bark. Merodiploid/merozygote: a partially diploid bacterial zygote containing an exogenotic chromosomal fragment donated by the f+ mate; the exogenote may also be introduced during transduction or sexduction. Merophytes -- group of cells which have all been produced from the same initial cell. Leaves and stems in particular are often built from specific patterns of merophytes. Mesenchymal Stem Cells MSCs The body's storehouse of potential spare parts, pockets of unspecialized cells, tucked into a variety of places, that can migrate to an injury and, responding to signals in the milieu, embark on a normal developmental pathway to become what's needed. They are not totipotent, as are ES cells, but pluripotent, capable of differentiating into connective tissue and its derivatives. Neither are they as far along the developmental trajectory as hematopoietic stem cells used to replenish bone marrow,3 or the neural stem cells that researchers recently rerouted to produce hematopoietic cells.4 # Refers to cells that develop into connective tissue, blood vessels, and lymphatic tissue. [Cancernet] Part of the embryonic mesoderm. Mesoderm -- in animals with three tissue layers (i.e. All except sponges and cnidarians), the middle layer of tissue, between the ectoderm and the endoderm. In vertebrates, for instance, the mesoderm forms the skeleton, muscles, heart, spleen, and many other internal organs. Mesogloea -- jellylike material between the outer ectoderm and the inner endoderm of cnidarians. May be very thin or may form a thick layer (as in many jellyfish) Mesokaryotic -- nuclear condition unique to the dinoflagellates in which the chromosomes remain permanently condensed. Messenger R A (mR A) - Ribose nucleic acid molecules made by transcription from DNA and used as a template for polypeptide synthesis. # The class of RNA molecules that copies the genetic information from DNA, in the nucleus, and carries it to ribosomes, in the cytoplasm, where it is translated into protein. (See RNA.) Metacentric chromosome: A chromosome with its centromere near the center. If the centromere is slightly off-center, the chromosome is said to be submetacentric (see also acrocentric and telocentric). Metallothionein. A protective protein that binds heavy metals, such as cadmium and lead. Metamorphic rock -- any rock derived from other rocks by chemical, mineralogical and structural changes resulting from pressure, temperature or shearing stress. Metamorphosis - a process of developmental change in insects whereby a larva reaches adulthood only after a radical change in morphology, often involving a pupa stage. Metaphase: Mitotic phase at which replicated chromosomes are fully condensed and become visible under the light microscope. Metazoa: A major division in the Animal Kingdom consisting of multicellular animals. Methylation paradox: Methylation of the CpG islands in the transcribed region is often correlated with transcription but an inverse correlation is seen at the CpG islands at the transcription

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initiation site (link to a review on Methylation Paradox by PA Jones). Methylation: The addition of a methyl group (-CH3) to DNA. Methylated DNA is inactivated and not transcribed. Most frequently occurs at CpG doublets (see genomic imprinting and CpG islands). MHC restriction: The phenomenon that a T cell can only recognize a peptide when it is (processed and) presented by another cell sharing the same MHC type. The only exception is that a foreign MHC antigen itself does not have to be presented by a cell but is able to induce a reaction directly (as happens in MHC - mismatched transplantation). MHC: Major Histocompatibility Complex. H-2 complex in mice, HLA complex in humans. MHC: see Major Histocompatibility Complex Microbial mats (biofilms). Layered groups or communities of microbial populations. Microinjection. A means to introduce a solution of DNA, protein, or other soluble material into a cell using a fine microcapillary pipet. Microlymphocytotoxicity (MLC) assay: An assay used in the typing of HLA molecules (serological typing). Microphyll -- a kind of leaf, specifically one which has a single, unbranched vein in it. Microphylls are only found in the lycophytes. Microsatellite repeat sequences: Sequences of 2 to 5 bp repeated up to 50 times such as a TA dinucleotide repeat polymorphism. The variable number of repeats creates the polymorphism. They may occur at 50 - 100 thousand locations in the human genome. Microsatellites mutate faster than nonrepeat polymorphisms and can be used to estimate evolutionary relationships over shorter time scales (see the abstract of a study by Goldstein et al). Microspore -- in plants which are heterosporous, the smaller kind of spore is called a microspore; it usually germinates into a male (sperm-producing) gametophyte. Contrast with megaspore. Microtubules -- type of filament in eukaryotic cells composed of units of the protein tubulin. Among other functions, it is the primary structural component of the eukaryotic flagellum. Microvilli -- thin fingerlike protrusions from the surface of a cell, often used to increase absorptive capacity or to trap food particles. The "collar" of choanoflagellates is actually composed of closely spaced microvilli. Mid-oceanic ridges -- elongated rises on the ocean floor where basalt periodically erupts, forming new oceanic crust; similar to continental rift zones. Migration: in population genetics, the movement of individuals between different populations of a species, resulting in gene flow. Mimicry: the resemblance of one kind of organism to another to make the organism difficult to find, to discourage the potential predators, or to attract potential prey. The common kinds of mimicry are Batesian and Mullerian mimicry (see Evolutionary Biology Notes). See also molecular mimicry. # the similarity in appearance of one species of animal to another that affords one or both protection; mimic: the organism that imitates the phenotype of another species. Missense mutation - a nucleotide mutation which results in a change in the amino acid sequence of the encoded protein (contrast with silent mutation). # Mutation of the mRNA sequence to generate an altered codon, which results in an

amino acid change, is termed a missense mutation. # A mutation that causes the substitution of one amino acid for another (nonsynonymous change). An example is the major HFE mutation C282Y in which results in an amino acid change at position 282. Missing link: An absent member needed to complete an evolutionary lineage. Mitochondria: Organelles appearing in all eukaryotic cells which produce ATP as useful energy for the cell by oxidative phosphorylation. The proteins for the adenoseine 5triphosphate (ATP)- generating electron transport of the respiration chain are located in the inner mitochondrial membrane. Mitochondria contain many enzymes of the citric acid cycle and for fatty acid [beta]- oxidation. Many of them are coded for by nuclear DNA. [IUPAC Biotech] Mitochondrial D A Mitochondria, and chloroplasts in plants, carry their own small chromosomes, usually in multiple copies per organelle. These carry a limited number of genes which code for rRNA, tRNA and a few organelle proteins. This DNA is maternally inherited. # The maternally inherited nucleic acid found in cytoplasm whose homologue in plants is chloroplastic DNA. This small circular DNA codes for tRNAs, rRNAs and some mitochondrial DNAs. It is more closely related to bacterial DNA than to eukaryotic nuclear DNA. Mitochondrial DNA mutates 10-20 times faster than nuclear DNA. Mitosis - Nuclear divisions giving rise to daughter cells which are genetically identical to each other and to the parent. # the process of nuclear division in eukaryotes. It is one step in cytokinesis, or cellular division. # The replication of a cell to form two daughter cells with identical sets of chromosomes. # Cell division into two identical daughter cells with the same chromosome number as the mother cell (see also meiosis). Replicated chromosomes separate and each chromatid goes to a daughter cell. # the nuclear division producing two daughter nuclei identical to the original nucleus; divided into four stages of prophase, metaphase, anaphase, and telophase. # The process whereby a cell nucleus divides into two daughter nuclei, each having the same genetic component as the parent cell. [IUPAC Biotech]. A method of indirect cell division by means of which the two daughter nuclei normally receive identical complements of the number of chromosomes of the somatic cells of the species [MeSH] Mitotic recombination: During mitosis sister chromatids freely exchange material without changing anything in genetic material because they are identical. Very rarely, and by chance, homologous chromosomes come very close to each other and exchange material as in meiosis which results in a recombinant chromosome. Mitotic spindle - group of fibres visible during nuclear division which pull the two daughter sets of chromosomes apart toward the cell poles. Mixed lymphocyte reaction (MLR): The activation of T cells in vitro by other (allogeneic) lymphocytes due to differences in their MHC molecules. Mobility shift - see gel shift. Mobility shift (or band shift) assays Like DNAse footprinting, this technique is also utilized to determine whetherafragment of DNA bindsspecific proteins. 32Plabeled DNA (either duplex oligonucleotides or small restriction fragments) are incubated with nuclear protein extracts and subjected to native acrylamide gel electrophoresis. Should specific DNA-binding proteins that recognize the oligonucleotide or restriction fragment probe be present in the nuclear extracts, a DNA-protein complex will be

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formed and its migration through the native gel will be retarded compared to the unbound DNA. Hence, the labeled band will be shifted to a more slowly migrating position. The specificity of their reaction can be demonstrated by also incubating, in separate reactions, competitor DNA that contains the presumed binding site or irrelevant DNA sequence. Model: the organism whose phenotype is imitated by a mimic. Molecular cloning. The biological amplification of a specific DNA sequence through mitotic division of a host cell into which it has been transformed or transfected. (See Cloning.) Molecular genetics. The study of the flow and regulation of genetic information between DNA, RNA, and protein molecules. Molecular mimicry: Resemblance of a DNA sequence or a polypeptide by an unrelated sequence at the nucleotide or amino acid level, respectively. Mimicry of MHC proteins is an immunoevasion mechanism used by pathogens. Molecular Weight Size Marker: a piece of DNA of known size, or a mixture of pieces with known size, used on electrophoresis gels to determine the size of unknown DNAs by comparison. Monera: One of the five Kingdoms which contains all prokaryotes. It contains archaebacteria, eubacteria and cyanobacteria. The first life form emerged over 3,500 Mya were the members of this Kingdom from which eukaryotes evolved. Monocistronic: coding for a single polypeptide chain; typical of eukaryotic cells. Monoclonal antibodies. Immunoglobulin molecules of single-epitope specificity that are secreted by a clone of B cells. # an antibody with very specific and often unique binding specificity which is secreted by a biologically cloned line of plasmacytoma cells in the absence of other related antibodies with different binding specificities. Differs from polyclonal antibodies, which are mixed populations of antibody molecules such as may be present in a serum specimen, within which many different individual antibodies have different binding specificities. Monoculture. The agricultural practice of cultivating crops consisting of genetically similar organisms. Monogenic. Controlled by or associated with a single gene. Monohybrid Cross - Mating between individuals who are genetically different at a specified locus. Monophyletic -- term applied to a group of organisms which includes the most recent common ancestor of all of its members and all of the descendants of that most recent common ancestor. A monophyletic group is called a clade. More? Monosomic: having only one chromosome of a homologous chromosome. Monotreme: A subclass of the Class Mammalia consisting of animals that lay eggs. Monozygotic twins: result from a separation of a fertilized egg; genetically identical.. Morphometry: Measurement of shape, structure and form. Used in a variety of disciplines, including environmental studies, geology, imaging and cell biology. Mosaicism: Mosaicism is the presence of more than one cell lines differing in genotype or karyotype but derived from one zygote. Post-zygotic new mutations result in mosaic individuals who may not be clinically affected themselves, but

are at risk of bearing multiple affected offspring. Mosaicism is well recognized in Duchenne muscular dystrophy and in autosomal dominant disorders with high new mutation rates. Motif - a recurring pattern of short sequence of dna, rna, or protein, that usually serves as a recognition site or active site. The same motif can be found in a variety of types of organisms. Motile - able to move oneself about, capable of self-locomotion. Mouth -- front opening of the digestive tract, into which food is taken for digestion. In flatworms, the mouth is the only opening into the digestive cavity, and is located on the "belly" of the worm. mR A - a cytoplasmic rna which serves directly as the source of code for protein synthesis. See translation. # "messenger RNA" or sometimes just "message"; an RNA which contains sequences coding for a protein. The term mRNA is used only for a mature transcript with polyA tail and with all introns removed, rather than the primary transcript in the nucleus. As such, an mRNA will have a 5' untranslated region, a coding region, a 3' untranslated region and (almost always) a poly(A) tail. Typically about 2% of the total cellular RNA is mRNA. # Messenger RNA. It is the first product of the DNA transcription by RNA polymerase. mRNA forms 1-5% of the total cellular RNA. Its molecular weight is generally less than 2x106. At any time, there are about 105 species of mRNA in a cell. # messenger rna; an rna molecule that functions during translation to specify the sequence of amino acids in a nascent polypeptide. Mtoc -- (microtubule organizing center) mtocs are bundles of protein tubes which may be found at the base of a eukaryotic flagellum. In animals, they also function in creating the arrays of microtubules that pull the chromosomes apart during mitosis. Mucus -- sticky secretion used variously for locomotion, lubication, or protection from foreign particles. Mullers ratchet: The continual decrease in fitness due to accumulation of (usually deleterious) mutations without compensating mutations and recombination in an asexual lineage. Recombination (sexual reproduction) is much more common than mutation, so it can take care of mutations as they arise. This is one of the reasons why sex is believed to have evolved. # The continual decrease in fitness due to accumulation of (usually deleterious) mutations without compensating mutations and recombination in an asexual lineage (HJ Muller, 1964). Recombination (sexual reproduction) is much more common than mutation, so it can take care of mutations as they arise. This is one of the reasons why sex is believed to have evolved. Multicellular: Practically speaking, few processes peculiar to multicellular organisms have meaning when abstracted from anatomy, a particularly good example being developmental processes. The general consensus is that 'when it gets multicellular, it gets complicated'. Multicistronic message - an mrna transcript with more than one cistron and thus encoding more than one polypeptide. These generally do not occur in eukaryotic organisms, due to differences in the mechanism of translation initiation. Multicopy plasmids - present in bacteria at amounts greater than one per chromosome. Vectors for cloning dna are usually multicopy; there are sometimes advantages in using a single copy plasmid. Multi-locus probe. A probe that hybridizes to a number of different sites in the genome of an organism. (See Probe.) Multiple cloning site - an artificially constructed region within a vector molecule which contains a number of closely spaced

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recognition sequences for restriction endonucleases. This serves as a convenient site into which foreign dna may be inserted. Multivariate analysis: A statistical analysis of several variables assessed simultaneously. Should be preferred over individual analyses of pairs of variables. Muscle -- bundle of contractile cells which allow animals to move. Muscles must act against a skeleton to effect movement. Mutagen. Any agent or process that can cause mutations. See Mutation. Mutagenesis, site-specific Several methods are now available to intentionally introduce specific mutations into a cDNA sequence of interest. Most are based on designing an oligonucleotide that contains the desired mutation in the context of normal sequence. This oligonucleotide is then incorporated into the cDNA using DNA polymerase, either using a single-stranded DNA template (phage M13) or in a PCR format to produce a heteroduplex DNA containing both wild type and mutant sequences. Using M13, recombinant phage are then produced and mutant cDNA are screened for on the basis of the difference in wild type and mutant sequences; using the PCR format, the exponential amplification of the mutant sequence results in its overwhelming numerical advantage over wild type sequence, resulting in nearly all clones containing mutant sequence. Both of these methods require that the entire cDNA insert synthesized in vitro be sequenced in its entirety to guarantee the fidelity of mutagenesis and synthesis of the remaining wild type sequences. Mutation - change in the genetic material of an organism that is detectable and inherited by offspring and is not caused by recombination or segregation. Includes a variety of changes, such as base substitutions, insertions, and deletions, as well as larger changes such as translocations, inversions, and aneuploidy. # An alteration in DNA structure or sequence of a gene. (See Point mutation.) # Any heritable change (not only point mutation) brought about by an alteration in the genetic material. Includes gene conversion, deletion, duplication, insertion and so forth. Link to Human Gene Mutation Database (Cardiff, UK). # the process by which a gene undergoes structural changes. Mutation pressure: Evolution by different mutation rates alone. Mutation rate: The number of mutations at a particular locus which occur per gene per cell generation. This is the only source of variation in asexual organisms. The mutation rate is the likelihood of parentage when findings suggest otherwise. Beware of the different units in different mutation rates. In humans, the mutation rate is 1 bp per 109 bp per cell division. This corresponds to 10-6 mutations per gene per cell division and because there are 1016 divisions in a lifetime, 1010 mutations per gene per lifetime. Mya: Million years ago. Mycorrhizae -- symbiotic association between a fungus and the roots or rhizoids of a plant. # symbiotic association between a fungus and the roots or rhizoids of a plant. # Fungi that form symbiotic relationships with roots of more developed plants. Myotome -- segment of the body formed by a region of muscle. The myotomes are an important feature for recognizing early chordates.

- or C-terminal The amino acids which form polypeptides are joined by peptide bonds between the amino group of one amino acid and the carboxy group of the next. Therefore each polypeptide has a free amino group at one end (N-terminal) and a free carboxy group at the other (C-terminal). ative gel - an electrophoresis gel run under conditions which do not denature proteins (i.e., In the absence of SDS, urea, 2mercaptoethanol, etc.). atural killer ( K) cell: Bone marrow-derived, mononuclear white blood cells (large granular lymphocytes) that are able to kill invading microorganisms without activation by cells of the immune system. They are, therefore, part of the innate immune system. They are specialized in killing virus-infected cells and cells transformed to develop cancer. atural selection - see selection atural selection (Darwins definition, 1859): As many more individuals of each species are born than can possibly survive; and as, consequently, there is a frequent recurrent struggle for existence, it follows that any being, if it varies however slightly in any manner profitable to itself, under the complex and sometimes varying conditions of life, will have a better chance of surviving, and thus be naturally selected. Link to a simulation on natural selection. Natural selection tends to reduce heritability because strong (directional or stabilizing) selection leads to reduced variation. # The differential survival and reproduction of organisms with genetic characteristics that enable them to better utilize environmental resources. ature-nurture debate: The debate on the relative contributions of genetics (nature) and environment (nurture) to the characteristics of an organism. An example is the debate on whether gene(s) and/or environmental factors determine the sexual orientation of an individual. Finding a gene playing a role in the development of a condition does not necessarily mean it is a purely genetic trait. avigated Laser Capture Microdissection: A major issue in proteomic analysis is the ability to profile protein expression in specific cell groups or cells expressing specific markers. We have developed techniques to permit accurate protein profiling of cells from specific brain regions using Laser Capture Microdissection (LCM) coupled to two- dimensional gel electrophoresis (2DE). Unlike the situation for mRNA expression, conventional tissue staining (and several unconventional stains) greatly reduces protein recovery from samples. We have refined the technique of "navigated" LCM, in which an adjacent stained section is used to guide the capture of specific cells from an unstained section, so there is minimal loss of protein expression using this technique. We have also modified conventional immunostaining protocols such that proteins from cells expressing specific markers can be recovered with approximately 90% fidelity. These techniques are currently being applied in our laboratory to address questions of interest in the field of drug addiction. These methods should also have broad applicability to questions of biological and pharmacological interest. egative assortative mating: A type of nonrandom mating in which individuals of unlike phenotype mate more often than predicted under random mating conditions. ematocyst -- older name for a cnidocyst. eo-darwinism: the post-darwinian concept that species evolve by the natural selection of adaptive phenotypes caused by mutant genes.

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eoteny: Retention of juvenile features in sexually mature adult animals. Neoteny frequently correlates with recent evolution of the species (like Homo sapiens). erve -- a bundle of neurons, or nerve cells. More properly, it is a bundle of axons. erve cord -- primary bundle of nerves in chordates, which connects the brain to the major muscles and organs of the body. ervous system: The nervous system presents an enormous challenge for drug discovery as it contains more than twice the level of cellular complexity than the rest of the body combined. Renovis enables drug discovery in the nervous system through technologies that give access to the "neurons that matter" the neuronal cell types and circuits that control particular behaviors and underlie specific neurological or psychiatric diseases and disorders. Our research engine permits the identification, manipulation, and isolation of key neurons and brain cells for both target discovery, systematic validation, and subsequent drug development. As an illustration of our approach, we will discuss data highlights from our neuropathic pain program. In nuclear transfer the DNA is removed from an unfertilised egg and the nucleus of a specially prepared body cell is introduced and the combination or "couplet" is triggered either by an electrical pulse, or the introduction of a chemical, to fuse them together and begin the process of development. Much is still to be known about what happens in this process and most attempts fail at the start. At Roslin this has been achieved by inserting a treated cell inside the outer shell of the "empty" egg. Other groups report success in extracting the nucleus of the cell and inserting it into the egg. ested PCR - a very sensitive method for amplfication of dna, which takes part of the product of a single pcr reaction (after 30-35 cycles), and subjects it to a new round of pcr using a different set of pcr primers which are nested within the region flanked by the original primer pair (see polymerase chain reaction). # By using an independent set of PCR primers located within the sequence amplified by the primary set, the specificity of a PCR reaction can be greatly enhanced. In Figure 1, should the first PCR reaction yield a product of 600 nucleotides, a second PCR reaction using the first product as template and a different set of primers will produce a smaller, nested PCR product, the presence of which acts to confirm the identity of the primary product. euron -- a specialized cell that can react to stimuli and transmit impulses. A neuron consists of a body which contains the nucleus; dendrites, which are short branches off the body that receive incoming impulses; and a long axon which carries impulses away from the body and to the next neuron. eurospora crassa: Haploid, heterothallic, filamentous Ascomycete fungus (bread mold). It has two mating types (A and a) operating as sexual compatibility system, and 11 het loci operating as heterokaryon compatibility system in vegetative phase. Link to Neurospora website. eurotoxin -- poison which interferes with nerve function, usually by affecting the flow of ions through the cell membrane. eutral alleles - alternative alleles at a locus which give equally fit genotypes. eutral theory: Link to a lecture on neutral theory of evolutionary change.

F-1 The gene responsible for neurofibromatosis. The normal protein functions to negatively regulate ras proteins, key intermediates in cytokine-induced cellular proliferation. iche -- the portion of the environment which a species occupies. A niche is defined in terms of the conditions under which an organism can survive, and may be affected by the presence of other competing organisms. ick - in duplex dna, this refers to the absence of a phosphodiester bond between two adjacent nucleotides on one strand. ick translation - a method for introducing labeled nucleotides into a double-stranded dna molecule which involves making small nicks in one strand with dnase, and then repairing with dna polymerase i.# A procedure for making a DNA probe in which a DNA fragment is treated with DNase to produce singlestranded nicks, followed by incorporation of radioactive nucleotides from the nicked sites by DNA polymerase I. # A method for incorporating radioactive isotopes (typically 32P) into a piece of DNA. The DNA is randomly nicked by DNase I, and then starting from those nicks DNA polymerase I digests and then replaces a stretch of DNA. Radiolabeled precursor nucleotide triphosphates can thus be incorporated. # This technique is used to label cDNA to high specific activity for the purpose of probing Southern and Northern blots and screening cDNA libraries. The cDNA fragment is first nicked with a limiting concentration of DNAse, then DNA polymerase is used to both digest and fill in the resulting gaps with labeled nucleotides. icked circle (relaxed circle). During extraction of plasmid DNA from the bacterial cell, one strand of the DNA becomes nicked. This relaxes the torsional strain needed to maintain supercoiling, producing the familiar form of plasmid. (See Plasmid.) itrocellulose. A membrane used to immobilize DNA, RNA, or protein, which can then be probed with a labeled sequence or antibody. itrogen fixation -- the conversion of gaseous nitrogen into a form usable by plants. Ususally by bacteria. itrogenous bases. The purines (adenine and guanine) and pyrimidines (thymine, cytosine, and uracil) that comprise DNA and RNA molecules. octurnal -- active only at night. ode -- the region of a stem between two internodes, where there is branching of the vascular tissue into leaves or other appendages. odule. The enlargement or swelling on roots of nitrogenfixing plants. The nodules contain symbitic nitrogen-fixing bacteria. on penetrance - the situation in which an individual possesses a certain genotype but does not express the phenotype normally associated with the genotype. on-coding region: Parts of a gene that include sequences which are not translated. Both 5 and 3 untranslated regions (UTRs), upstream promoter region and introns are classified as non-coding regions. on-coding strand: Anti-sense strand. See "Sense strand" for a discussion of sense strand vs. anti-sense strand. onconservative substitution - a mutation which results in the substitution of one amino acid within a polypeptide chain with an amino acid belonging to a different polarity/charge group (see amino acids, conservative mutation)

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on-disjunction: Due to failure in pairing of homologous chromosomes in meiosis, the two members of one pair migrate to the same pole, giving rise to unbalanced gametes, one of which contain both homologous chromosomes, and the other none (most frequent in sex chromosomes). The nondisjunction event is much more frequent in maternal meiosis I. This may be due to the fact that in a mature woman, oocytes have been held in the ovary for a very long time at prophase I of meiosis from before her birth to shortly before ovulation of the oocyte in question. # The failure of homologous chromosomes in meiosis i or sister chromatids in meiosis ii to separate properly and to move to opposite poles; results in one daughter cell receiving both and the other daughter receiving none of the chromosomes in question. on-parental: see recombinant. Nonpolar side chains (hydrophobic) Glycine, Alanine Valine Isoleucine Leucine Phenylalanine Proline Methionine Tryptophan Cysteine Noncharged polar side chains (hydrophilic) Serine Threonine Tyrosine Asparagine Glutamine Acidic side chains (very polar, hydrophilic) Aspartic Acid Glutamic Acid Basic side chains (very polar, hydrophilic) Lysine Arginine Histidine on-recombinant: in mapping studies, offspring that have alleles arranged as in the original parents. onsence codon - a ribonucleotide triplet signaling the termination of the translation of a protein chain. # see stop codon. onsense mutation - a change in the sequence of a nucleic acid that causes a nonsense (stop or termination) codon to replace a codon representing an amino acid. # This type of mutation results in the generation of a premature termination codon and hence creates a truncated polypeptide. # A mutation that changes an amino acid specifying codon to one of the three termination (stop) codons. ontarget organism. An organism which is affected by an interaction for which it was not the intended recipient. ontranslated R A (ntr) - the segments located at the 5' and 3' ends of a mrna molecule which do not encode any part of the polyprotein; may contain important translational control elements. onviral transduction methods Nonviral methods include polylysine-ligand DNA complexes, where the ligand (e.g., transferrin) allows access to the cell through normal receptormediated uptake, and phospholipid vesicles. Both methods suffer from not providing a mechanism for genomic integration, precluding long-term expression. orthern blot: A technique for analyzing mixtures of RNA, whereby the presence and rough size of one particular type of RNA (usually an mRNA) can be ascertained. See "Blotting" for more information. After Dr. E. M. Southern invented the Southern blot, it was adapted to RNA and named the "Northern" blot. # RNA molecules are separated by electrophoresis (usually in an agarose gel) on the basis of size, then transferred to a solid-phase support (nitrocellulose paper or suitable other membrane) and detected by hybridization with a labeled probe (see southern blot, western blot). # RNA blot taken from an electrophoresis gel. orthern blotting This modification of a Southern blot is used to detect specific RNA. The sample to be sizefractionated in this case is RNA and, with the exception of

denaturation conditions (alkali treatment of the Southern blot versus formamide/formaldehyde treatment of the RNA sample for Northern blot), the techniques are essentially identical. The probe for Northern blotting must be antisense. orthern hybridization. (Northern blotting). A procedure in which RNA fragments are transferred from an agarose gel to a nitrocellulose filter, where the RNA is then hybridized to a radioactive probe. (See Hybridization.) otochord -- characteristic of chordates, the notochord is a stiff rod of tissue along the back of the body. In vertebrates, the backbone is deposited around the notochord and nerve cord. # A rod that forms in the embryonic mesoderm and which establishes the front-to-back orientation of vertebrate embryos. It also initiates the formation of the nervous system, the skeleton and most muscles. T: Abbreviation for nucleotide; i.e. the monomeric unit from which DNA or RNA are built. One can express the size of a nucleic acid strand in terms of the number of nucleotides in its chain; hence nt can be a measure of chain length. uclear membrane -- the double membrane which surrounds the eukaryotic nucleus. It has many pores in its surface which regulate the flow of large compounds into and out of the nucleus. uclear run-on: A method used to estimate the relative rate of transcription of a given gene, as opposed to the steady-state level of the mRNA transcript (which is influenced not just by transcription rates, but by the stability of the RNA). This technique is based on the assumption that a highly-transcribed gene should have more molecules of RNA polymerase bound to it than will the same gene in a less-active state. If properly prepared, isolated nuclei will continue to transcribe genes and incorporate 32P into RNA, but only in those transcripts that were in progress at the time the nuclei were isolated. Once the polymerase molecules complete the transcript they have in progress, they should not be able to re-initiate transcription. If that is true, then the amount of radiolabel incorporated into a specific type of mRNA is theoretically proportional to the number of RNA polymerase complexes present on that gene at the time of isolation. A very difficult technique, rarely applied appropriately from what I understand. uclease protection assay: See "RNase protection assay". uclease. A class of enzymes that degrades DNA and/or RNA molecules by cleaving the phosphodiester bonds that link adjacent nucleotides. In deoxyribonuclease (DNase), the substrate is DNA. In endonuclease, it cleaves at internal sites in the substrate molecule. Exonuclease progressivelycleaves from the end of the substrate molecule. In ribonuclease (RNase), the substrate is RNA. In the S1 nuclease, the substrate is singlestranded DNA or RNA. # An enzyme that breaks bonds in nucleic acids. Deoxyribonuclease (DNAase) and ribonuclease (RNAase).# An enzyme which degrades nucleic acids. A nuclease can be DNA-specific (a DNase), RNA-specific (RNase) or non-specific. It may act only on single stranded nucleic acids, or only on double-stranded nucleic acids, or it may be non-specific with respect to strandedness. A nuclease may degrade only from an end (an exonuclease), or may be able to start in the middle of a strand (an endonuclease). To further complicate matters, many enzymes have multiple functions; for example, Bal31 has a 3'-exonuclease activity on double-stranded DNA, and an endonuclease activity specific for single-stranded DNA or RNA.# A number of common tools of recombinant DNA technology have been developed from the study of the

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basic enzymology of bacteria and bacteriophage. For example, most unicellular organisms have defense systems to protect against the invasion of foreign DNA. Usually, they specifically methylate their own DNA and then express restriction endonucleases to degrade any DNA not appropriately modified. From such systems come very useful tools. Today, most restriction endonucleases (and most other enzymes of commercial use) are highly purified from either natural or recombinant sources and are highly reliable. Using these tools, the manipulation of DNA and RNA has become routine practice in multiple disciplines of science. ucleic acid -- class of biochemical compounds which includes dna and rna. They are among the largest molecules known. # A polymeric molecule composed of nucleotide monomers joined by phosphodiester bonds. These link the 5' ribose carbon atom of one nucleotide residue with the 3' ribose carbon atom of the neighbouring nucleotide residue, through a phosphate group. Each phosphate group ionises by losing a hydrogen ion thus becoming negatively charged, and giving the molecule its acidic character. The negative charge of nucleic acids is made use of in electrophoretic separations. # The two nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are made up of long chains of molecules called nucleotides. uclein. The term used by Friedrich Miescher to describe the nuclear material he discovered in 1869, which today is known as DNA. ucleoid -- region in prokaryotes where the dna is concentrated. Unlike a nucleus, it is not bound by a membrane. # The loosely tangled clump of DNA within the cytoplasm of a prokaryotic cell. ucleolar organizer: A region on a chromosome that is associated with formation of a new nucleolus following cell division. It contains the genes for several species of ribosomal RNA (rRNA), i.e., 18S, 5.8S, 5S and 28S in eukaryotes # the chromosomal region around which the nucleolus forms; site of tandem repeats of the major ribosomal RNA gene ucleolus: The site of synthesis of rRNA within the nucleus of a eukaryotic cell. ucleoside analog. A synthetic molecule that resembles a naturally occuring nucleoside, but that lacks a bond site needed to link it to an adjacent nucleotide. (See Nucleoside.) nucleoside: a purine or pyrimidine base attached to ribose or deoxyribose. # the composite sugar and purine or pyrimidine base which are present in nucleotides which are the basic building blocks of dna and rna. Compare with nucleotide: nucleoside = base + sugar # In molecular biology; a molecule composed of a sugar (2' deoxyribose in DNA; ribose in RNA) which is linked to a purine (adenine or guanine) or a pyrimidine (thymine (DNA), cytidine or uridine (RNA)). The link is through the 1' carbone atom in ribose or deoxyribose. # A building block of DNA and RNA, consisting of a nitrogenous base linked to a five carbon sugar. (See Nucleoside analog.) # A small molecule composed of a purine or pyrimidine base linked to a five-carbon sugar (pentose: ribose or deoxyribose). With the addition of a phosphate group, it becomes a nucleotide. Nucleosides in RNA are adenosine, guanosine, cytidine and uridine; in DNA, they are (d)adenosine, (d)guanosine, (d)cytidine and (d)thymidine. ucleosome: A beadlike structure of eukaryotic chromosomes. It consists of a core of eight histone molecules and a DNA segment of about 150 base pairs. Each nucleosome

is separated from another by a linker DNA sequence of about 50 base pairs. Nucleosome structure helps to fold DNA into a compact form in the interphase nucleus. Otherwise the length of a chromosome, when linear, is many orders of magnitude greater than the diameter of the nucleus. # When linear, the length of a specific chromosome is many orders of magnitude greater than the diameter of the nucleus. Therefore, a mechanism must exist for folding DNA into a compact form in the interphase nucleus. Nucleosomes are complex DNA protein polymers in which the protein acts as a scaffold around which DNA is folded. The mature chromosomal structure then appears as beads on a string; within each bead (nucleosome) are folded DNA and protein. Nucleosome structure is quite fluid, and internucleosomal stretches of DNA are thought to be sites that are important for active gene transcription. ucleotide - a nucleic acid building block consisting of a purine or pyrimidine base, a sugar (deoxyribose in DNA and ribose in RNA) and a phosphate group # the composite phosphate, sugar, and purine or pyrimidine base which are the basic building blocks of the nucleic acids dna and rna. The five nucleotides are adenylic acid, guanylic acid (contain purine bases), and cytidylic acid, thymidylic acid, and uridylic acid (contain pyrimidine bases). Nucleotide = base + sugar + phosphate (1, 2, or 3) # unit from which nucleic acids are constructed by polymerization. It contains a sugar, a phosphate group, and an organic base. Atp is a nucleotide.# In molecular biology; the phosphate ester of a nucleoside, it may carry one, two or three phosphates linked to each other e.g. adenosine mono-, di- and triphosphates (AMP, ADP and ATP). The phosphates are carried on the 5' carbon atom of the ribose or deoxyribose part of the molecule. See also nucleic acid and oligonucleotide. #. A building block of DNA and RNA, consisting of a nitrogenous base, a five-carbon sugar, and a phosphate group. Together, the nucleotides form codons, which when strung together form genes, which in turn link to form chromosomes. (See Chromosome, Codon, Complementary nucleotides, Dideoxynucleotide, DNA, Gene, Oligonucleotide, RNA.) # one of the monomeric units from which dna or rna polymers are constructed, consisting of a purine or pyrimidine base, a pentose, and a phosphoric acid group. # The monomeric unit that makes up the DNA or RNA, formed by a phosphate group, a pentose and one of the nitrogenous bases (A, T/U, C, G). Nucleotides in RNA are adenylate, guanylate, cytidylate and uridylate; in DNA, they are (d)adenylate, (d)guanylate, (d)cytidylate and thymidylate. ucleus -- membrane-bound organelle which contains the dna in the form of chromosomes. It is the site of dna replication, and the site of rna synthesis. # The central cell structure that houses the chromosomes. [NHGRI] utrient -- any element or simple compound necessary for the health and survival of an organism. This includes air and water, as well as food. utrient cycling -- all the processes by which nutrients are transferred from one organism to another. For instance, the carbon cycle includes uptake of carbon dioxide by plants, ingestion by animals, and respiration and decay of the animal. ymph - in aquatic insects, the larval stage.

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O
Oceanic crust -- the earth's crust which is formed at midoceanic ridges, typically 5 to 10 kilometers thick with a density of 3.0 grams per centimeter cubed. Oceanic trench -- deep steep-sided depression in the ocean floor caused by the subduction of oceanic crust beneath either other oceanic crust or continental crust. Okazaki fragment: the short pieces of replicated DNA along the lagging strand that are later rejoined by DNA ligase. # The small (<1 kb), discontinuous strands of DNA produced using the lagging strand as template during DNA synthesis. DNA ligase links the Okazaki fragments to give rise to a continuous strand. Olfactory: Related to smell. Oligodeoxyribonucleotide - a short, single-stranded dna molecule, generally l5-50 nucleotides in length, which may be used as a primer or a hybridization probe. Oligodeoxyribonucleotides are synthesized chemically under automated conditions. Oligonucleotide A short nucleic acid molecule; normally refers to molecules between 5 and 200 nucleotide residues(bases) long. see oligodeoxyribonucleotide. # A DNA polymer composed of only a few nucleotides. (See Nucleotide.) # A short, synthetic DNA string used as a probe (as in SSOP) or primer (as in SSP) in molecular genetic studies. Oligonucleotide ligation assay (OLA): A PCR-based method for SNP typing. It is a ligase mediated gene detection system which uses exact 3 matching of a primer to one of the SNP allele. If this happens the other labeled oligonucleotide which binds to the nucleotide immediately next to the SNP on the other side would be joined to the primer by ligase. The resulting sample can then be tested for the presence of the label (for example biotin). Unless controls are included, false positives are possible (link to a book chapter explaining OLA). Omnivore -- literally, an organism that will eat anything. Refers to animals who do not restrict their diet to just plants or other animals. Oncogene - one of a number of genes believed to be associated with the malignant transformation of cells; originally identified in certain oncogenic retroviruses (v-onc) but also present in cells (c-onc). See proto-oncogene. # A gene that contributes to cancer formation when mutated or inappropriately expressed. (See Cellular oncogene, Dominant oncogene, Immortalizing oncogene, Recessive oncogene.) #A gene capable of causing malignant transformation. Link to an overview of oncogenes. # A gene in a tumor virus or in cancerous cells which, when transferred into other cells, can cause transformation (note that only certain cells are susceptible to transformation by any one oncogene). Functional oncogenes are not present in normal cells. A normal cell has many "proto-oncogenes" which serve normal functions, and which under the right circumstances can be activated to become oncogenes. The prefix "v-" indicates that a gene is derived from a virus, and is generally an oncogene (like v-src , v-ras, v-myb , etc). See also "Transformation (with respect to cultured cells)". Oncogenesis and Anti-Oncogenes Oncogenes have usually been identified in the context of a tumor-inducing virus. Such viral oncogenes (v-onc) are thought to be derived from host cells, but have been altered such that abnormal regulation of

production or function has ensued during the transfer process. Subsequent reintroduction of the altered gene into a host cell leads to transformation. Proto-oncogenes, the normal cellular counterpart of viral oncogenes, can contribute to cellular transformation by mechanisms that disturb normal gene function. Such mechanisms include mutation (resulting in abnormal function), amplification (resulting in abnormal levels of expression), rearrangement (resulting in a new function), or promoter mutation (again resulting in abnormal levels of expression). Most or all proto-oncogenes are involved in normal cellular processes such as growth factor signal transduction, mitogenic signaling, or regulation of DNA transcription or cellular proliferation. The nomenclature convention is to indicate the cellular version of the protooncogene as c-onc and the viral version, which is transforming, as v-onc. Most altered proto-oncogenes act in a dominant genetic fashion. Antioncogenes, or tumor suppressor genes, usually act in a recessive genetic fashion and function to slow processes involved in cellular proliferation. Most of the identified anti-oncogenes have been involved in gene transcription, presumably acting to enhanced differentiation. One can also clone more complex organisms, with considerable difficulty. The much-publicized Scottish research that resulted in the sheep Dolly exemplifies this approach. # The progression of cytological, genetic, and cellular changes that culminate in a malignant tumor. One gene - one (enzyme) polypeptide hypothesis: The hypothesis that each gene controls the synthesis of a single polypeptide which may be a subunit of a complex protein. Oocyte: Female sex cell which undergoes meiosis and produces an egg (ovum). Open pollination. Pollination by wind, insects, or other natural mechanisms. Open reading frame - a region within a reading frame of an mrna molecule that potentially encodes a polypeptide; and which does not contain a translational stop codon (see reading frame). # A nucleotide sequence encoding a polypeptide starting with a start and ending with a stop codon. # A long DNA sequence that is uninterrupted by a stop codon and encodes part or all of a protein. (See Reading frame.) # Any region of DNA or RNA where a protein could be encoded. In other words, there must be a string of nucleotides (possibly starting with a Met codon) in which one of the three reading frames has no stop codons. See "Reading frame" for a simple example. # The term given to any stretch of a chromosome that could encode a polypeptide sequence, i.e., the region between a methionine codon (ATG) that could serve to initiate proteins translation, and the inframe stop codon downstream of it. Several features of the ORF can be used to judge whether it actually encodes an expressed protein, including its length, the presence of a Kozak sequence upstream of the ATG (implying a ribosome might actually bind there and initiate protein translation), whether the ORF exists within the coding region of another gene, the presence of exon/intron boundary sequences and their splicing signals, and the presence of upstream sequences that could regulate expression of the putative gene. Operator - the site on dna at which a repressor protein binds to prevent transcription from initiating at the adjacent promoter. # A prokaryotic regulatory element that interacts with a repressor to control the transcription of adjacent structural genes. # a chromosomal region capable of interacting with a specific repressor, controlling the functioning of adjacent cistrons.

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Operon - a complete unit of bacterial gene expression and regulation, including the structural gene or genes, regulator gene(s), and control elements in dna recognized by regulator gene products(s). # A type of genetic unit which consists of one or more transcription units that are transcribed together into a polycistronic mRNA. The transcription of each operon is initiated at a promoter region and controlled by a neighboring regulatory gene (an operator which binds to a repressor or an apoinducer, to repress or induce the transcription, respectively). An example is the lac operon of E.coli. # a unit consisting of one or more cistrons that function coordinately under the control of an operator gene. Ordered spores: a linear sequence of four haploid meiotic spores (or pairs of spores produced by a post-meiotic division) within a fungi ascus; this arrangement allows identification of chromatids participating in crossover events. ORF: see Open reading frame Organ -- collection of tissues which performs a particular function or set of functions in an animal's body. The heart, brain, and skin are three organs found in most animals. Organs are composed of tissues, and may be organized into larger organ systems. #collection of tissues which performs a particular function or set of functions in an plant's body. The leaf, stem, and root are three organs found in many plants. Organs are composed of tissues. Organ system -- collection of organs which have related roles in an organism's functioning. The nervous system, vascular system, and muscle system are all organ systems. Organelle -- membrane-bound structure in a eukaryotic cell. Organelles partition the cell into regions which carry out different cellular functions. Mitochondria, the er, and lysosomes are examples of organelles. Organelles: Separated components within a cell with specialized functions, e.g. nuclei (containing most of the genetic material), mitochondria (respiratory energy supply for the cell), chloroplasts (location of photosynthesis) etc. [IUPAC Biotech]. Specific, usually subcellular, particles of membrane- bound organized living substances present in practically all eukaryotic cells, including mitochondria, the Golgi complex, endoplasmic reticulum, lysosomes, centrioles and the cell center, as well as the plastids of plant cells. Includes also the minute organs of protozoa concerned with such functions as locomotion and metabolism. [MeSH, 1989] Organic -- generally refers to those substances produced by the metabolism of a living organism, especially carboncontaining compounds. Ori: The origin of replication in prokaryotes. Origin - a site within a dna sequence of a chromosome, plasmid, or non-integrated virus at which replication of the dna is initiated. Origin of replication (ori ) Section of DNA sequence which is recognised by a cell's DNA replication proteins, allowing initiation of new DNA synthesis. DNA molecules which do not carry an ori recognised by the host cell will be eventually lost from a growing population unless they are incorporated into the cell's genome. # The nucleotide sequence at which DNAsynthesis is initiated. # Nucleotide sequences present in a plasmid which are necessary for that plasmid to replicate in the bacterial host. (Abbr. "ori") Orthology: Being homologous by descent. In other words, descendants from a common ancestor. An example is the

MHC class II genes in different species that all descended from a common ancestral class I gene. Osculum -- the main opening through which filtered water is discharged. Found in sponges. Outbreeding: the crossing of genetically unrelated plants or animals. Outcrop -- any place where bedrock is visible on the surface of the earth. Outgroup -- in a cladistic analysis, any taxon used to help resolve the polarity of characters, and which is hypothesized to be less closely related to each of the taxa under consideration than any are to each other. Ovary -- in flowering plants, the part of the flower which encloses the ovules. When the ovary matures, it becomes the fruit. Overdominance: See balancing selection. See also underdominance. Overhang - a terminus of a duplex dna molecule which has one or more unpaired nucleotides in one of the two strands (hence either a 3' or 5' overhang). Cleavage of dna with many restriction endonucleases leaves such overhangs (see sticky end). # Single-stranded section of DNA at the end of a doublestranded fragment, for example in a sticky end. Overhangs may be 3' or 5' i.e. the end of the single-stranded section may carry a free 3' or 5' end. This will depend on how the overhang was created. Overlapping reading frames. Start codons in different reading frames generate different polypeptides from the same DNA sequence. (See Reading frame.) Oviparity: Egg birth as opposed to live birth (viviparity). Ovule -- in seed plants, the structure which gives rise to the seed. Ovum. A female gamete.

P
p site: holds the trna molecule that is attached to the growing end of the nascent polypeptide.. p2 + 2pq + q2 = 1 (see otes on Population Genetics for more). Package - in recombinant dna procedures, refers to the step of incorporation of cosmid or other lambda vector dna with an insert into a phage head for transduction of dna into host. PAGE: see Polyacralamide gel Erlectrophoresis. Paleoherb -- any member of a group of basal flowering herbs which may be the closest relatives of the monocots. They include the water lilies, piperales, and aristolochiales. Paleontology. The study of the fossil record of past geological periods and of the phylogenetic relationships between ancient and contemporary plant and animal species. Paleosol -- soil horizon from the geologic past. Palindrome. See Palindromic sequence. Palindromic sequence - a nucleotide sequence which is the same when read in either direction, usually consisting of adjacent inverted repeats. Restriction endonuclease recognition sites are palindromes. pAMP. Ampicillin-resistant plasmid developed for this laboratory course. (See Plasmid.) Panmictic - mating behaviour which results in the random union of gametes from different individuals (i.e. behaviour resulting in random mating). Papilla(e) -- cellular outgrowths. These look like little bumps or fingers on the surface of cells.

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Paracentric inversion: an inversion that excludes the centromere. Parallel evolution: Evolution of roughly similar changes in two or more closely related lineages. Paralogy: Being homologous due to a recent or past duplication in the same species. An example is the chromosomal regions 1q22-q23;6p21.31; and 9q33-q34 in humans. These regions contain very similar genes including some of the MHC class III genes. Paramecium: A unicellular Protoctist belonging to the group Ciliates. Although normally reproduces asexually, they also undergo sexual conjugation in which mating types play a role. Paramecium aurelia has 34 hereditary mating types that form 16 distinct mating groups (link to Paramecium in Encyclopedia Britannica). Paramutation: In paramutation, two alleles of a gene interact so that one of the alleles is epigenetically silenced. The silenced state is then genetically transmissible for many generations. Parapatric speciation: Speciation that occurs as a result of two populations diverging in adjacent geographical areas. Paraphyletic -- term applied to a group of organisms which includes the most recent common ancestor of all of its members, but not all of the descendants of that most recent common ancestor. More? Parapodia -- a sort of "false foot" formed by extension of the body cavity. Polychaetes and some insect larvae have parapodia in addition to their legs, and these provide extra help in locomotion. Parasexual: an offspring formed from more than a single parent, bypassing standard meiosis and fertilization; often occurs as a result of the fusion of two genetically unlike cells or nuclei. Parasite -- organism which lives on or within another organism, on which it feeds. Parasitism. The closee association of two or more dissimilar organisms where the association is harmful to at least one. See Commensalism, Parasitism, Symbiosis. Parenchyma -- a generalized cell or tissue in a plant. These cells may manufacture or store food, and can often divide or differentiate into other kinds of cells. Parental imprinting: see genomic imprinting. Parental: see non-recombinant. Parsimony -- refers to a rule used to choose among possible cladograms, which states that the cladogram implying the least number of changes in character states is the best. Parsimony: The scientific convention whereby the simplest explanation is preferred over the others. This is usually a phylogenetic tree requiring the fewest evolutionary steps. Parthenogenesis (virgin birth): Reproduction involving unfertilized eggs. The offspring of parthenogenetic parents are less diverse than those of sexual parents. Parthenogenesis often alternates with sexual reproduction. Two examples are the desert grassland whiptail lizard (Cnemidophorus uniparens) and Caucasian rock lizard. Never seen in birds and mammals. Parthenogenetic: the ability to reproduce offspring without fertilization of the egg. Patch clamping: A technique for studying the electrical currents involved in the movement of ions across cell membranes. With this technique, an electrode is affixed to the membrane so that a small patch of membrane is electrically

isolated, allowing currents through it can be determined. Patch clamping is a high-resolution technique, meaning that movements through one ion channel can be recorded. Patch clamping can also involve the use of very fine pipette to measure what is going on in or on an individual cell. [ Path diagram: a modified pedigree showing only the direct line of descent from common ancestors. Pathogen. Organism which can cause disease in another organism. Pathogenic -- organism which causes a disease within another organism. pBR322: A derivation of ColE1, one of the first plasmid vectors widely used. (See Plasmid.) #A common plasmid. Along with the obligatory origin of replication, this plasmid has genes which make the E. coli host resistant to ampicillin and tetracycline. It also has several restriction sites (BamHI, PstI, EcoRI, HindIII etc.) into which DNA fragments could be spliced in order to clone them. PCR See Polymerase chain reaction. Pedigree - a graphical summary of the interrelationships among members of related nuclear families, normally including information about the distribution among them of a specific trait. #A diagram mapping the genetic history of a particular family. #: a diagram setting forth the ancestral history or genealogical register; may be used to determine the inheritance pattern of a particular trait. Pedipalps -- the second pair of appendages of cheliceromorphs. In many arachnids, such as spiders, the pedipalps are enlarged in the male and used for copulation. Pedomorphosis: The retention of infantile, fetal or embryonic characteristics into the adult. Pelagic -- pelagic organisms swim through the ocean, and may rise to the surface, or sink to the bottom. They are not confined to live on the bottom as benthic organisms do. Penetrance - realization of a given phenotype associated with a specific phenotype.# the proportion of individuals of a specified genotype that show the expected phenotype under a defined set of environmental conditions. # The proportion of individuals with a given genotype (heterozygotes for a dominant gene) who express an expected trait, even if mildly. If a disease gene is not causing the disease in all its carriers, its penetrance is low [not to be mixed with variable expression]. BRCA1 mutations show both age-dependent penetrance and overall reduced penetrance, the lifetime risk for a female mutation carrier being estimated at around 70%. Breast cancer is also an example of an autosomal condition where penetrance is sex-dependent. While male mutation carriers can develop breast cancer (particularly with BRCA2 mutations), females are at much greater risk. Peptide - a chain formed by two or more amino acids linked through peptide bonds: dipeptide = two amino acids, oligopeptide = small number of amino acids, etc. Peptide - a molecule formed by peptide bonds covalently linking two or more amino acids. Short peptides (generally less than 60 amino acid residues, and usually only half that length) can be chemically synthesized by one of several different methods; larger peptides (more correctly, polypeptides) are usually expressed from recombinant dna. Peptide bond - a covalent bond between two amino acids, in which the carboxyl group of one amino acid (x1--cooh) and the amino group of an adjacent amino acid (nh2--x2) react to form x1-co-nh-x2 plus h2o.

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Peptidoglycan -- carbohydrate polymer cross-linked by proteins. It is found in the cell wall of gram positive bacteria, where it stains with the dye crystal-violet. Peptidyl transferase: an enzyme that catalyzes the transfer of the bond between trna and the amino acid to a new bond between amino acids. Perennial -- a plant which continues to grow after it has reproduced, usually meaning that it lives for several years. Perianth -- the sepals and petals of a flower are together called the perianth; literally "around the anthers". More info? Pericentric inversion: an inversion that includes the centromere. Peridinin -- carotenoid pigment found in dinoflagellates. Periphyton -- dense strands of algal growth that cover the water surface between the emergant aquatic plants. Spirogyra is commonly responsible for this growth. Peristome -- a set of cells or cell parts which surround the opening of a moss sporangium. In many mosses, they are sensitive to humidity, and will alter their shape to aid in spore dispersal. Persistence. Ability of an organism to remain in a particular setting for a period of time after it is introduced. Pesticide. A substance that kills harmful organisms (for example, an insecticide or fungicide). Petal -- one of the outer appendages of a flower, located between the outer sepals and the stamens. Petals often display bright colors that serve to attract pollinators. More info? Phage (particle). See Bacteriophage. # A virus of bacteria, phage such as lambda have been used to introduce foreign DNA into bacteria. Because of its infectious nature, the transfection (introduction) efficiency into the bacterial host is usually two orders of magnitude greater for phage over that of plasmids. Phage display Phage display vectors express the inserted DNA as a protein at a prominent position on their capsid. This allows capture and isolation of recombinant phage clones by immobilised interacting proteins (eg. antibodies). This screening method is called biopanning. Phagemid A plasmid-based vector which carries a filamentous phage ori , leading to production of singlestranded copies of the phagemid when the cell is infected with the relevant helper phage. Under normal circumstances the phagemid behaves in exactly the same way as a plasmid. # A type of plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with "helper" phage, the phagemid is replicated along with the phage DNA and packaged into phage capsids. Pharyngeal slits -- characteristic of chordates, pharyngeal slits are openings through which water is taken into the pharynx, or throat. In primitive chordates the pharyngeal slits are used to strain water and filter out food particles; in fishes they are modified for respiration. Most terrestrial vertebrates have pharyngeal slits only in the embryonic stage. Pharynx -- cavity in the digestive tract just past the mouth itself. May be muscularized for sucking or swallowing in various animals. Phenocopy: A condition which is due to environmental factors but resembles one which is genetic. Phenotype - a characteristic possessed by an organism. # the appearance of other characteristics of an organism resulting from the interaction of its genetic constitution with the environment. # The observable characteristics of an organism,

the expression of gene alleles (genotype) as an observable physical or biochemical trait. See Genotype. # the observable properties of an organism, produced by the genotype in conjunction with the environment. # The visible or measurable (i.e., expressed) characteristics of an organism (see genotype). Phenotypic value - a measurement of a specified phenotypic characteristic. Phenylketonuria (pku): a hereditary disorder of amino acid metabolism in humans, inherited as an autosomal recessive. Pheromone (formerly called mating-type factors, sex factors or gamones): Species- or mating-type-specific chemical produced by an animal to communicate with an effect on their behavior without being consciously perceived as smell. Probably the most ancient communication system in living organisms. It has been noted in bacteria (Streptomyces faecalis); protists such as ciliates (Euplotes raikovi); amoeba (Dictyostelium); algae (Fucus vesiculosus); and in fungi (for example Basidiomycetous). It is mainly used to attract opposite sex in insects (in cockroaches, moths, beetles and bees) but social insects use them for communication other than reproduction, and mammals use them for territory marking. In vertebrates, they are also used for kin recognition and mate selection. Specific examples of pheromones include a substance produced by male cockroaches that orients females in the correct mating positions and a desert locust pheromone that accelerates sexual maturation in adults of both sexes. Maleattracting pheromones are produced by the females of many species of beetles, bees, and moths. The polyphemus moth needs red oak leaves for mating as the leaves release a volatile aldehyde that stimulates the female to produce her maleattracting pheromone. Links to an essay on pheromones, Human Pheromone Research and pheromone-related links. # A hormone-like substance that is secreted into the environment. Phloem -- nutrient-conducting tissue of vascular plants. Phosphatase, alkaline - an enzyme which catalyzes the hydrolysis of phosphomonoesters of the 5' nucleotides. Used to dephosphorylate (remove phosphate groups from) the 5' ends of dna or rna molecules, to facilitate 5' end-labeling with 32p added back by t4 polynucleotide kinase; or to dephosphorylate the 5' ends of dna molecules to prevent unwanted ligation reactions during cloning. Phosphatase. An enzyme that hydrolyzes esters of phosphoric acid, removing a phosphate group. Phosphatasing = dephosphorylating. Removal of 5' phosphate from an RNA or DNA molecule, using alkaline phosphatase. Phosphate -- an ion consisting of a phosphorus atom and four oxygen atoms. Among other things, it is used in the constuction of nucleic acids. Phosphodiester bond - the covalent bond between the 3' hydroxyl in the sugar ring of one nucleotide and the 5' phosphate group of the sugar ring of the adjacent nucleotide residue within nucleic acid: 5'-ribose- 3' - o - p(o)2 - o - 5' -ribose - 3' - etc. # A bond in which a phosphate group joins adjacent carbons through ester linkages. A condensation reaction between adjacent nucleotides results in a phosphodiester bond between 3' and 5' carbons in DNA and RNA. Phospholipid. A class of lipid molecules in which a phosphate group is linked to glycerol and two fatty acyl groups. A chief component of biological membranes. (See Inositol phospholipid.)

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Phosphorylation - the addition of a phosphate monoester to a macromolecule, catalyzed by a specific kinase enzyme. With respect to proteins, certain amino acid side chains (serine, threonine, tyrosine) are subject to phosphorylation catalyzed by protein kinases; altering the phosphorylation status of a protein may have dramatic effects on its biologic properties, and is a common cellular control mechanism. With respect to dna, 5' ends must be phosphorylated for ligation. # The addition of a phosphate group to a compound. Photic zone -- region of the ocean through which light penetrates; and the place where photosynthetic marine organisms live. Photosynthesis -- biochemical process in which light energy is absorbed by chlorophyll, and is used to fuel the building of sugar molecules. # biochemical process in which light energy is absorbed by chlorophyll, and is used to fuel the building of sugar molecules. Phycocyanin -- blue, water-soluble pigment found in the cyanobacteria and the red algae. Phycoerythrin -- red, water-soluble pigment found in the cyanobacteria and red algae. Phyletic gradualism: A model of evolutionary mode characterized by slow and gradual modifications of biological structures leading to speciation. This is the opposite of punctuated equilibrium. PHYLIP: see Genetic Distance Estimation by PHYLIP. Phylogenetic footprinting: The use of phylogenetic comparisons to reveal conserved functional elements. Phylogenetics -- field of biology that deals with the relationships between organisms. It includes the discovery of these relationships, and the study of the causes behind this pattern. # Study of reconstructing evolutionary genealogical ties between taxa and line of descent of species or higher taxon. Phylogeny -- the evolutionary relationships among organisms; the patterns of lineage branching produced by the true evolutionary history of the organisms being considered. # An evolutionary tree showing the inferred relationships of descent and common ancestry of any given taxa. Link to the Tree of Life, Spectrum of Life, Lecture on Tree Construction, Freeware Phylogenetic Data Analysis Download Pages: Phylogenetics Software, Phylogeny Programs Physical map. A map showing physical locations on a DNA molecule, such as restriction sites, and sequence-tagged sites. (See Mapping.) Physiologic Gene Regulation The regulation of gene expression is central to physiology. Complex organisms have evolved multiple mechanisms to accomplish this task. The first step in protein expression is the transcription of a specified gene. The rate of initiation and elongation of this process is the most commonly used mechanism for regulating gene expression. Once formed, the primary transcript must be spliced, polyadenylated, and transported to the cytoplasm. These mechanisms are also possible points of regulation. In the cytoplasm, mRNA can be rapidly degraded or retained, another potential site of control. Protein translation next occurs on the ribosome, which can be free or membraneassociated. Secreted proteins take the latter course, and the trafficking of the protein through these membranes and ultimately to storage or release makes up another important point of potential regulation. Individual gene expression is

often controlled at multiple levels, making investigation and intervention a complex task. Phytomelanin -- a papery "sooty" black layer over the seed of plants in the asparagales, which includes agaves, aloes, onions and hyacinths. It is an important character for defining the group. Phytoplankton -- tiny, free-floating, photosynthetic organisms in aquatic systems. They include diatoms, desmids, and dinoflagellates. Pigment -- any colorful compound, used by living things to absorb or block sunlight, and in sexual displays. More info? Pillow lava -- lava extruded beneath water characterised by pillow-type shapes. Pinnately compound -- leaves which are divided up like a feather are said to be pinnately compound. Pistil -- the central set of organs in a flower; it is composed of one or more carpels. More info? Pith to severely damage the brain of a frog, also any central region of parenchyma tissue within a plant stem. Pits thin regions of the cell wall in xylem conducting cells. Their structure is an important characteristic for recognizing different kinds of wood. Plankton -- tiny, free-floating organisms of the ocean or other aquatic systems. They may be phytoplankton or zooplankton. Plaque lift Blot taken from plaques (usually bacteriophage on a bacterial lawn) growing on an agar plate. Normally used for detection of a plaque containing a phage with a specific inserted sequence (screening). Plaque. A clear spot on a lawn of bacteria or cultured cells where cells have been Iysed by viral infection. Plasma membrane -- outer membrane of a cell, sometimes called the cell membrane. The term plasma membrane is used more frequently when discussing prokaryotes. Plasmid - an extrachromosomal,usually circular, doublestranded dna which is capable of replication within a cell, and which usually contains and expresses genes encoding resistance to antibiotics. By strict definition, a plasmid is not essential to the life of the cell. # circular loop of dna in prokaryotes. Eukaryotic dna is organized into chromosomes. # A circular DNA molecule, capable of autonomous replication, which typically carries one or more genes encoding antibiotic resistance proteins. Plasmids can transfer genes between bacteria and are important tools of transformation for genetic engineers. (See Nicked circle, pAMP, Relaxed plasmid, Stringent plasmid, Supercoiled plasmid.) # Double stranded, circular DNA molecule found in bacteria and some fungi. Size range from ~5 - 200kbp, contains genes which may be useful to host, but are not essential. Plasmids can be eliminated from bacterial populations by growth under selective conditions ("curing"). Carry an origin of replication (ori ) which allows replication in a specific host species. Plasmids used in recombinant DNA work are generally smaller than 10kbp in size and have a copy number of up to 500/cell depending on plasmid type. # A circular piece of DNA present in bacteria or isolated from bacteria. Escherichia coli, the usual bacteria in molecular genetics experiments, has a large circular genome, but it will also replicate smaller circular DNAs as long as they have an "origin of replication". Plasmids may also have other DNA inserted by the investigator. A bacterium carrying a plasmid and replicating a million-fold will produce a million identical copies of that plasmid. Common plasmids are pBR322, pGEM, pUC18. # A transferable extrachromosomal genetic element

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found in some bacteria. They are 1 to 200 kb long, doublestranded, circular DNA molecules. They replicate independently of the bacterial chromosomes and usually confer an advantage to the bacteria (such as antibiotic or heavy metal resistance). Plasmids are popular vectors in recombinant DNA technology. They can carry up to 10 kb foreign DNA. # Autonomously replicating circular DNA that are passed epigenetically between bacteria or yeast. In order to propagate, plasmids must contain an origin of replication. Naturally occurring plasmids transfer genetic information between hosts; of these, the genes encoding resistance to a number of antibiotics are the most important clinically. The essential components of plasmids are used by investigators to introduce genes into bacteria and yeast and to generate large amounts of DNA for manipulation. Plasmodesmata -- cytoplasmic connections between neighboring cells in plant tissues. Plasmogamy - a process of fusion of the cytoplasm of two cells; the first step in syngamy. Plastid: Chloroplast and related organelles in the cells of eukaryotic algae and green plants. Together with mitochondria they are responsible for energy production. Plate -- rigid parts of the earth's crust and part of the earth's upper mantle that move and adjoin eachother along zones of seismic activity. Platyrrhini: New world monkeys found in South America with widely spaced nostrils. They last had a common ancestor with the old world monkeys (Catarrhini) about 55 million years ago. Platyspermic -- having seeds which are flattened and disclike. Contrast with radiospermic. Pleiotrophy. The effect of a particular gene on several different traits. # More than one effect of a gene on the phenotype. The effects may occur simultaneously or sequentially. An example is the determination of the color pattern and the shape of the eyes by a single allele in Siamese cats. Another example is the DNA repair enzymes which have several other functions (transcription, cell cycle regulation, regulation of gene rearrangements). # the phenomenon where a single gene is responsible for a number of distinct and seemingly unrelated phenotypic effects. Pleiotropism - Multiple phenotypic effects resulting from a single gene Plesiomorphy -- a primitive character state for the taxa under consideration. Pleurae -- in trilobites and other arthropods, pleurae are elongated flat outgrowths from each body segment, that overlie and protect the appendages. Plicate -- folded like a paper fan, as in the leaves of palms, cyclanthoids, and some orchids. Ploidies: The degree of replication of the chromosome set in the karyotype. [MeSH, 1976] Ploidy: Indicates the number of sets of chromosomes present in an organism, e.g. haploid (one) or diploid (two). [IUPAC Biotech] Pluripotent stem cell research - human: Because pluripotent stem cells give rise to almost all of the cells types of the body, such as muscle, nerve, heart, and blood, they hold great promise for both research and health care. This advance in human biology continues to generate enthusiasm among scientists, patients suffering from a broad range of diseases,

including cancer, heart disease and diabetes, and their families. Pluripotent: Cells able to develop into most specialized types of cells. Plutonic -- applies to igneous rocks formed beneath the surface of the earth; typically with large crystals due to the slowness of cooling. Synonym of intrusive. Antonym of volcanic. Point mutation - a single nucleotide substitution within a gene; there may be several point mutations within a single gene. Point mutations do not lead to a shift in reading frames, thus at most cause only a single amino acid substitution (see frameshift mutation).# mutation occurring at a specific genetic locus # A change in a single base pair of a DNA sequence in a gene. (See Mutation.) # A single nucleotide change in the DNA sequence. Even if it is in the coding region of a gene, it may or may not change the amino acid sequence. The rates of point mutation for MHC genes are not unusually high. The extensive polymorphism results from their accumulation over many millions of years of transspecies evolution. Polar body - a small cell containing one of the three extra sets of chromosomes produced during oogenesis which do not become eggs. Polarity of characters -- the states of characters used in a cladistic analysis, either original or derived. Original characters are those acquired by an ancestor deeper in the phylogeny than the most recent common ancestor of the taxa under consideration. Derived characters are those acquired by the most recent common ancestor of the taxa under consideration. Polishing In vitro digestion of the single-stranded section of an overhanging end (by exonuclease) to produce a blunt end. Pollen -- the microspore of seed plants. Pollen (tube) competition: The plant equivalent of sperm competition (see also cryptic female selection). A type of sexual selection. Pollen grain: The microspores of seed plants. It germinates to form the male gametophyte. The male gametophyte contains three haploid nuclei. One of these fertilizes the ovum, a second fuses with the two polar nuclei to form the triploid endosperm, and the third degenerates once double fertilization occurs. Pollen tube -- in seed plants, the extension of the male gametophyte as it emerges from the pollen grain in search of the female gametophyte. Pollination -- process of transferring the pollen from its place of production to the place where the egg cell is produced. This may be accomplished by the use of wind, water, insects, birds, bats, or other means. Pollination is usually followed by fertilization, in which sperm are released from the pollen grain to unite with the egg cell. Pollinator -- animal which carries pollen from one seed plant to another, unwittingly aiding the plant in its reproduction. Common pollinators include insects, especially bees, butterflies, and moths, birds, and bats. Pollinia -- a mass of fused pollen produced by many orchids. Poly (A) tail: A sequence of 20 - 200 adenylic acid residues which is added to the 3 end of most eukaryotic mRNAs. It increases their stability by making them resistant to nuclease digestion. # After an mRNA is transcribed from a gene, the cell adds a stretch of A residues (typically 50-200) to its 3' end. It is thought that the presence of this "polyA tail" increases the stability of the mRNA (possibly by protecting it from nucleases). Note that not all mRNAs have a polyA tail; the histone mRNAs in particular do not

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Poly(A) polymerase. Catalyzes the addition of adenine residues to the 3' end of pre-mRNAs to form the poly(A) tail. (See Polymerase.) Poly-a track - a lengthy adenylic acid polymer (rna) which is covalently linked to the 3' end of newly synthesized mrna molecules in the nucleus. Function not polymerase chain reaction (pcr) - a dna amplification reaction involving multiple (30 or more) cycles of primer annealing, extension, and denaturation, usually using a heat-stable dna polymerase such as taq polymerase. Paired primers are used, which are complementary to opposing strands of the dna and which flank the area to be amplified. Under optimal conditions, single dna sequence can be amplified a million-fold. Polyacrylamide gel (page) - used to separate proteins and smaller dna fragments and oligonucleotides by electrophoresis. When run under conditions which denature proteins (i.e., In the presence of 2-mercaptoethanol, sds, and possibly urea), molecules are separated primarily on the basis of size. #. Electrophoresis through a matrix composed of a synthetic polymer, used to separate proteins, small DNA, or RNA molecules of up to 1000 nucleotides. Used in DNA sequencing. (See Electrophoresis.) Polyadenylation Following transcription of a gene, a specific signal near the 3' end of the primary transcript (AATAAA) signals that a polyadenine tail be added to the newly formed transcript. The tail may be up to several hundred nucleotides long. The precise function of the poly A tail is uncertain but it seems to play a role in stability of the mRNA and perhaps in its metabolism through the nuclear membrane to the ribosome. Polycistronic: coding for two or more proteins. Polyclonal antibodies. A mixture of immunoglobulin molecules secreted against a specific antigen, each recognizing a different epitope. Also see monoclonal antibody. Polygene - One of many genes which contribute to a particular phenotypic effect, and which are not normally individually distinguishable. # one of a group of genes that together control a quantitative character. Polygenic inheritance - inheritance of characters controlled by several genes, each with a small effect on the phenotype Polygenic. Controlled by or associated with more than one gene. Polygenic: Traits controlled by two or more genetic loci. They are usually influenced by environment as well (multifactorial). Polylinker. A short DNA sequence containing several restriction enzyme recognition sites that is contained in cloning vectors. Polymer -- a large molecule constructed from many smaller identical units. These include proeins, nucleic acids, and starches. # A molecule composed of repeated subunits. # a macromolecule composed of a covalently bonded collection of repeating subunits or monomers linked together during a repetitive series of similar chemical reactions. Polymerase (D A). Synthesizes a double-stranded DNA molecule using a primer and DNA as a template. (See Poly(A) polymerase, Polymerase chain reaction, RNA polymerase, Taq polymerase.) Polymerase - an enzyme which catalyzes the addition of a nucleotide to a nucleic acid molecule. There are a wide variety of rna and dna polymerases which have a wide range of specific activities and which operate optimally under different conditions. In general, all polymerases require templates upon which to build a new strand of dna or rna; however, dna

polymerases also require a primer to initiate the new strand, while rna polymerases start synthesis at a specific promoter sequence. # An enzyme which links individual nucleotides together into a long strand, using another strand as a template. There are two general types of polymerase DNA polymerases (which synthesize DNA) and RNA polymerase (which makes RNA). Within these two classes, there are numerous sub-types of polymerase, depending on what type of nucleic acid can function as template and what type of nucleic acid is formed. A DNA-dependant DNA polymerase will copy one DNA strand starting from a primer, and the product will be the complementary DNA strand. A DNA-dependant RNA polymerase will use DNA as a template to synthesize an RNA strand Polymerase Chain Reaction (PCR) is the basis for a number of extremely important methods in molecular biology. It can be used to detect and measure vanishingly small amounts of DNA and to create customized pieces of DNA. It has been applied to clinical diagnosis and therapy, to forensics and to vast numbers of research applications. It would be difficult to overstate the importance of PCR to science. # This technique finds use in several arenas of recombinant DNA technology. It is based on the ability of sense and antisense DNA primers to hybridize to a cDNA of interest. Following extension from the primers on the cDNA template by DNA polymerase, the reaction is heatdenatured and allowed to anneal with the primers once again. Another round of extension leads to a multiplicative increase in DNA products. Therefore, a minute amount of cDNA can be efficiently amplified in an exponential fashion to result in easily manipulable amounts of cDNA. By including critical controls, the technique can be made quantitative. Important clinical examples of the use of PCR or reverse transcription PCR (see below) include (1) detection of diagnostic chromosomal rearrangements [e.g., bcr/abl in CML, t(15;17) in AMLM3, t(8;21) in AML-M2, or bcl-2 in follicular small cleaved cell lymphoma], or (2) detection of minimal residual disease following treatment. The level of sensitivity is one in104 to 105 cells. #. An in vitro technique to produce many copies of a specific section of DNA sequence. PCR is normally used to amplify sections up to ~2kbp in length, although routine PCR of sections up to 20kbp is becoming possible. PCR amplification is possible from complex sequence background e.g. a short sequence from an entire chromosome, and from impure DNA. The technique is widely used in many applications. # A procedure that enzymatically amplifies a DNA polymerase. (See Polymerase.) # A technique for replicating a specific piece of DNA in-vitro , even in the presence of excess non-specific DNA. Primers are added (which initiate the copying of each strand) along with nucleotides and Taq polymerase. By cycling the temperature, the target DNA is repetitively denatured and copied. A single copy of the target DNA, even if mixed in with other undesirable DNA, can be amplified to obtain billions of replicates. PCR can be used to amplify RNA sequences if they are first converted to DNA via reverse transcriptase. This twophase procedure is known as RT-PCR.. Polymorphic: having two or more genetically different classes in the same interbreeding population. Polymorphism - occurrence of two or more alleles in a population at a given locus, with the lower-frequency allele having a frequency of 1% or more. # variation within a DNA or RNA sequence.

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Polymorphism: Presence of discreetly different forms of a gene or a character. It is defined as a Mendelian trait that exists in the population in at least two phenotypes, neither of which occurs at a frequency of less than 1%. Polymorphism at a genetic locus is due to either balanced polymorphism (heterozygous advantage, frequency-dependent selection) or unequilibrium states (temporary polymorphism) as occurs during frequency-dependent selection and genetic drift (alleles becoming fixed or extinct). Polymorphisms. Variant forms of a particular gene that occur simultaneously in a population. Polynucleotide kinase - enzyme which catalyzes the transfer of the terminal phosphate of atp to 5' hydroxyl termini of polynucleotides, either dnaor rna. Usually derived from t4 bacteriophage. Polynucleotide. A DNA polymer composed of multiple nucleotides. (See Nucleotide.) Polypeptide - chain of amino acids held together by peptide bonds. One or more polypeptide chains forms a protein. # A polymer composed of multiple amino acid units linked by peptide bonds. Polyphyletic -- term applied to a group of organisms which does not include the most recent common ancestor of those organisms; the ancestor does not possess the character shared by members of the group. Polyploid - 3N or more. # A multiple of the haploid chromosome number that results from chromosome replication without nuclear division. Polyploidy: having more than two sets of chromosomes. # The situation in which the organism has more than two (2n) sets of chromosomes. It could be 3n, 4n or more. A common situation in earthworms and plants. About half of angiosperms are polyploid. It arises as a result of meiotic irregularities and gives rise to sterile progeny which can still reproduce asexually. The original South American potato is a tetraploid (4n). Many of the common food plants are polyploid as this results in larger flowers and fruits (as well as larger cells, thicker and fleshier leaves). The wheat now grown for bread T. aestivum is hexaploid (6n = 42 chromosomes). Polyploidy is a common mechanism for sympatric speciation which played a role in angiosperm evolution. Link to a mini-essay on polyploidy. Polysaccharide. A polymer composed of multiple units of monosaccharide (simple sugar). Polyvalent vaccine. A recombinant organism into which has been cloned antigenic determinants from a number of different disease-causing organisms. (See Vaccine.) Polytene chromosome: a giant cablelike chromosome consisting of many identical chromatids lying in parallel.. Population biology: The study of the patterns in which organisms are related in time and space. It is a combination of disciplines such as population genetics, ecology, taxonomy, ethology and others. Link to a population biology website. Population genetics: The branch of genetics that deals with frequencies of alleles and genotypes in breeding populations. It also deals with selective influences on the genetic composition of the population (links to freeware population genetic data analysis software: Arlequin 2000, PopGene, GDA, Genetix, Tools for Population Genetic Analysis, GenePop, GeneStrut, SGS, GenAlEx; features of data analysis software; lectures on population genetics and population biology). See also Basic Population Genetics.

Population. A local group of organisms belonging to the same species and capable of interbreeding. # a geographically defined group of specific organisms sharing a common gene pool. Pore -- any opening into or through a tissue or body structure. Position effect: A difference in phenotype that is dependent on the position of a gene or a group of genes, often caused by heterochromatin nearby. Thus, the change in a genes location may cause a change in its expression (a problem that has to be overcome in gene therapy). # the change in the expression of a gene accompanying a change in the position of the gene with respect to neighboring genes; the change in position may result from crossing over or from a chromosomal aberration. Positive assortative mating: A type of nonrandom mating in which individuals of similar phenotype mate more often than predicted under random mating conditions. Post-transcriptional regulation Mechanisms of gene regulation that do not involve transcriptional enhancement or silencing and include altering the rate of mRNA degradation, the efficiency of translation or post-translational modification, or transportation of the polypeptide out of the cell. Post-transcriptional regulation: Any process occurring after transcription which affects the amount of protein a gene produces. Includes RNA processing efficiency, RNA stability, translation efficiency, protein stability. For example, the rapid degradation of an mRNA will reduce the amount of protein arising from it. Increasing the rate at which an mRNA is translated will increase the amount of protein product. Post-translational modification - modifications made to a polypeptide molecule after its initial synthesis, this includes proteolytic cleavages, phosphorylation, glycosylation, carboxylation, addition of fatty acid moieties, etc. # Cleavage of amino terminal peptide, hydroxylation and oxidation of amino acids in the polypeptide chain for cross-linking, covalent modifications by acetylation, phosphorylation and glycosylation. Post-translational processing: The reactions which alter a protein's covalent structure, such as phosphorylation, glycosylation or proteolytic cleavage. # Any process which affects the amount of protein produced from a gene, and which occurs AFTER translation in the grand scheme of genetic expression. Actually, this is often just a buzz-word for regulation of the stability of the protein. The more stable a protein is, the more it will accumulate. PRE: Progesterone Response Element: A binding site in a promoter to which the activated progesterone receptor can bind. The progesterone receptor is essentially a transcription factor which is activated only in the presence of progesterone . The activated receptor will bind to a PRE, and transcription of the adjacent gene will be altered. See also "Response element". Pre-Cambrian Eon: The whole of geological time before the Cambrian period (< 540 Mya). Predator -- organism which hunts and eats other organisms. This includes both carnivores, which eat animals, and herbivores, which eat plants. Pre-mrna - an rna molecule which is transcribed from chromosomal dna in the nucleus of eukaryotic cells, and subsequently processed through splicing reactions to generate the mrna which directs protein synthesis in the cytoplasm. Pre-mR A (precursor mR A): The primary transcript and intermediates in RNA processing that yield functional (mature) mRNA.

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Pribnow box: a segment upstream from the start-point of prokaryotic structural genes to which the sigma subunit of the rna polymerase binds; the nucleotides most commonly found are TATAAT. Primary cell. A cell or cell line taken directly from a living organism, which is not immortalized. Primary structure -refers to the sequence of amino acid residues or nucleotides within protein or nucleic acid molecules, respectively (also see secondary and tertiary structure). Primary transcript: When a gene is transcribed in the nucleus, the initial product is the primary transcript, an RNA containing copies of all exons and introns. This primary transcript is then processed by the cell to remove the introns, to cleave off unwanted 3' sequence, and to polyadenylate the 5' end. The mature message thus formed is then exported to the cytoplasm for translation. Primase: An enzyme that makes the RNA primer required by DNA polymerase in DNA replication. See also primosome. Primates: One of the Mammalian Orders which includes Lemurs (suborder Prosimii), old world and new world Monkeys, Apes and Humans. The suborder Anthropoidea covers all Primates except Prosimii. Prosimians and Anthropoids diverged from each other 65 Mya; Apes and Old World Monkeys 35 Mya. The separation of the two groups of Anthropoids (Platyrrhini and Catarrhini) occurred about 55 Mya. Primer - an oligonucleotide which is complementary to a specific region within a dna or rna molecule, and which is used to prime (initiate) synthesis of a new strand of complementary dna at that specific site, in a reaction or series of reactions catalyzed by a dna polymerase. The newly synthesized dna strand will contain the primer at its 5' end. Typically, primers are chemically synthesized oligonucleotides 15-50 nucleotides in length, selected on the basis of a known sequence. However, "random primers" (shorter oligonucleotides, about 6 nucleotides in length, and comprising all possible sequences) may be used to prime dna synthesis from dna or rna of unknown sequence.completely known, but probably serves to enhance stability of the rna. Is frequently used to select mrna for cloning purposes by annealing to a column containing a matrix bound to polyuridylic acid. # A short DNA or RNA fragment annealed to single-stranded DNA, from which DNA polymerase extends a new DNA strand to produce a duplex molecule. # A short nucleic acid molecule which, when annealed to a complementary template strand, provides a 3 terminus suitable for copying by a DNA polymerase. # A small oligonucleotide (anywhere from 6 to 50 nt long) used to prime DNA synthesis. The DNA polymerases are only able to extend a pre-existing strand along a template; they are not able to take a naked single strand and produce a complementary copy of it de-novo. A primer which sticks to the template is therefore used to initiate the replication. Primers are necessary for DNA sequencing and PCR. Primer extension - a reaction in which dna is reverse transcribed from an rna template to which a specific oligonucleotide primer has been annealed. The new cdna product is an extension of the primer, which is synthesized at the 3' end of the primer in a direction extending toward the 5' end of the rna. This reaction is useful for exploring the extreme 5' end of rna molecules. # This is a method used to

figure out how far upstream from a fixed site the start of an mRNA is. For example, perhaps you have isolated a cDNA clone, but you don't think that the clone has all of the 5' untranslated region. To find out how much is missing, you would first sequence the part you have, and figure out which strand is coding strand (usually the coding strand will have a large open reading frame). Next, you ask the DNA Synthesis Facility to make an oligonucleotide complementary to the 5'most region of the coding strand (and thus complementary to the mRNA). This "primer" is hybridized to mRNA (say, a mixture of mRNA containing the one in which you are interested), and reverse transcriptase is added to copy the mRNA from the primer out to the 5' end. The size of the resulting DNA fragment shows how far away from the 5' end your primer is. Primitive -- describes a character state that is present in the common ancestor of a clade. A primitive character state is inferred to be the original condition of that character within the clade under consideration. For example, "presence of hair" is a primitive character state for all mammals, whereas the "hairlessness" of whales is a derived state for one subclade within the mammalia. Primosome: The mobile complex of helicase and primase that is involved in DNA replication. Prion. See Proteinaceous infectious particle. #An infectious agent which does not have any nucleic acid (but just protein). Responsible for scrapie in sheep, kuru and Creutzfeldt-Jakob disease in humans. Probability: the long-term frequency of an event relative to all alternative events, and usually expressed as a decimal fraction. Probe - usually refers to a dna or rna molecule which has been labeled with 32p or with biotin, to facilitate its detection after it has specifically hybridized with a target dna or rna sequence. However, the term may also refer to antibody probes used in western blots. # A labelled molecule which will recognise and bind to a specific target molecule, thus allowing detection of the target. DNA probes are used to locate and quantitate DNA (or RNA) of complementary sequence. Antibody probes may also be used in aspects of recombinant DNA work, e.g. screening an expression library. The label may be radioactive (32P), biotin or digoxygenin (DIG). # A sequence of DNA or RNA, labeled or marked with a radioactive isotope, used to detect the presence of complementary nucleotide sequences. See Nucleotide. # A single-stranded DNA that has been radioactively labeled and is used to identify complementary sequences in genes or DNA fragments of interest. (See Multilocus probe.) #: A fragment of DNA or RNA which is labeled in some way (often incorporating 32P or 35S), and which is used to hybridize with the nucleic acid in which you are interested. For example, if you want to quantitate the levels of alpha subunit mRNA in a preparation of pituitary RNA, you might make a radiolabeled RNA in-vitro which is complementary to the mRNA, and then use it to probe a Northern blot of the pit RNA. A probe can be radiolabeled, or tagged with another functional group such as biotin. A probe can be cloned DNA, or might be a synthetic DNA strand. As an example of the latter, perhaps you have isolated a protein for which you wish to obtain a cDNA or genomic clone. You might (pay to) microsequence a portion of the protein, deduce the nucleic acid sequence, (pay to) synthesize an oligonucleotide carrying that sequence, radiolabel it and use it as a probe to screen a cDNA library or genomic library. A better way is to call up someone who already has the clone.

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Proboscis -- elongated organ, usually associated with the mouth. The proboscis is an important feeding appendage in echiurans. Processed pseudogene: A pseudogene, derived from a retrotranscript of mRNA of any expressed gene and inserted back into the genome. A processed pseudogene is intronless, usually flanked by the repeat sequence (GC/AGCTCTCC), and rich in multiple genetic lesions including substitution, deletion and/or insertion events that modify the reading frames. Because of the lack of its original promoter and the genetic lesions it has accumulated, a processed pseudogene is not normally expressed. Processing - with respect to proteins, generally used to refer to proteolytic post-translational modifications of a polypeptide. In the case of rna, processing may involve the addition of a 5' cap and 3' poly-a tracks as well as splicing reactions in the nucleus. # The reactions occurring in the nucleus which convert the primary RNA transcript to a mature mRNA. Processing reactions include capping, splicing and polyadenylation. The term can also refer to the processing of the protein product, including proteolytic cleavages, glycosylation, etc. Processivity - the extent to which an rna or dna polymerase adhers to a template before dissociating, determines the average length (in kilobases) of the newly synthesized nucleic acid strands. Also applies to the action of exonucleases in digesting from the ends to the middle of a nucleic acid. Producer -- any organism which brings energy into an ecosystem from inorganic sources. Most plants and many protists are producers. Product rule: the rule that states that the probability of the occurrence of independent events is the product of their separate probabilities. Programmed cell death: Frequently, the terms 'apoptosis' and 'programmed cell death' are used as synonyms. Programmed cell death was originally used in order to describe the locally and temporally defined cell death during embryogenesis. It was already in the middle of our century that cell death was recognized as a natural process in the development of organisms. Prokaryote - an organism without a nuclear membrane and which does not undergo recognizable mitosis or meiosis. Viruses, bacteria, and blue-green algae. # A bacterial cell lacking a true nucleus; its DNA is usually in one long strand. See Eukaryote. # A unicellular organism characterized by the absence of a membrane- bound nucleus.. Includes bacteria, blue- green algae (Cyanobacteria) and mycoplasmas. [IUPAC Biotech] # microorganisms that lack a membrane-bound nucleus containing chromosomes; other organelles are also absent. # literally "before the nucleus", the term applies to all bacteria and archaea. Prokaryotic cells have no internal membranes or cytoskeleton. Their dna is circular, not linear. Prokaryotic cell: The cell type in which the DNA is not enclosed in a nucleus. Consists of Eubacteria and Archaebacteria. Always unicellular. When the cell has a proper nucleus (eu-karyon), it is eukaryotic. Link to Prokaryotes website. Promoter - a specific sequence within a double-stranded dna molecule that is recognized by an RNA polymerase, which binds to it and uses it to begin transcribing the dna template into a new RNA. The location and orientation of the promoter within a DNA molecule determines the start site of the new

rna. Other proteins (e.g. Transcriptional activators such as sigma factor) are usually required for an rna polymerase to recognize a promoter (see transcription). # A short base sequence which is positioned close to the 5" end of a gene and acts as a recognition and binding site for the RNA polymerase complex prior to transcription of the gene. # A region of DNA extending 150-300 bp upstream from the transcription start site that contains binding sites for RNA polymerase and a number of proteins that regulate the rate of transcription of the adjacent gene. (SeeConstitutive promoter.) # a region on a dna molecule to which an rna polymerase binds and initiates transcription. # Initial binding site for RNA polymerase in the process of gene expression. First transcription factors bind to the promoter which is located 5 to the transcription initiation site in a gene. General and tissue/cell-specific promoters stimulate the expression of a gene under the control of enhancers. # The first few hundred nucleotides of DNA "upstream" (on the 5' side) of a gene, which control the transcription of that gene. The promoter is part of the 5' flanking DNA, i.e. it is not transcribed into RNA, but without the promoter, the gene is not functional. Note that the definition is a bit hazy as far as the size of the region encompassed, but the "promoter" of a gene starts with the nucleotide immediately upstream from the cap site, and includes binding sites for one or more transcription factors which can not work if moved farther away from the gene. Promoter-proximal element: Any regulatory sequence in eukaryotic DNA that is located within 200 bp of a promoter and binds a specific protein to modulate transcription of the associated gene. Pronucleus. Either of the two haploid gamete nuclei just prior to their fusion in the fertilized ovum. Proofreading: In DNA synthesis, the ability of DNA polymerase to recognize mismatched bases. DNA polymerase corrects mistakes with its exonuclease activity. RNA editing is also possible at the mRNA level in some simple organisms. Prophage: The phage DNA inserted into a bacterial chromosome. Prosimians (Prosimii): The suborder of Primates including Lemurs, Lorises and Tarsiers. Protease. An enzyme that cleaves peptide bonds that link amino acids in protein molecules. Protein -- class of biochemical compounds constructed from amino acids. Proteins may be structural, such as those that make up hair and cartilage, or they may be reactive, such as the enzymes. Protein clock hypothesis: The idea that amino acid replacements occur at a constant rate in a given protein family (ribosomal proteins, cytochromes, etc) and the degree of divergence between two species can be used to estimate the time elapsed since their divergence. Protein translation This term is applied to the assembly of a polypeptide sequence from mRNA. Protein. A polymer of amino acids linked via peptide bonds and which may be composed of two or more polypeptide chains.(See Polypeptide.) # a molecule composed of one or more polypeptide chains, each composed of a linear chain of amino acids covalently linked by peptide bonds. Proteinaceous -- describes any structure which is composed of protein. Proteinaceous infectious particle (prion). A proposedpathogen 40composed only of protein with no

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detectable nucleic acid and which is responsible for Creutzfeldt-Jakob disease and kuru in humans and scrapie in sheep. Proteolytic. The ability to break down protein molecules. Proteomic analysis - cells and tissue: A component to understanding biological processes involves identifying the proteins expressed in cells as well as their modifications. A recent approach to identifying protein mixtures is direct analysis of the proteolytically digested proteins using liquid separation techniques and tandem mass spectrometry/ database searching. As peptide mixtures become more complex better separation techniques are required to resolve the peptide components for tandem mass spectrometry. We have an approach to separate complex peptide mixtures using microcolumn LC/LC in conjunction with tandem mass spectrometry. We are able to identify proteins, identify modifications, and in membrane enriched fractions identify proteins and determine protein folding topology. Results on studies of yeast protein complexes, human lens tissue, and rat golgi will be discussed. Protochordata: A division of chordata phylum including subphylum hemichordata, urochordata (tunicates) and cephalochordata (lancelets). Immediate ancestors of vertebrates. Protoctista: The modern name for the Kingdom Protista. Probably the first double-chromosomed beings. Well-known members are: seaweeds (algae), amoebas, ciliates, mastigotes, water molds, slime molds and slime nets. Proto-Oncogene - A cellular oncogene-like sequence which is thought to play a role in controlling normal cellular growth and differentiation. # A gene present in a normal cell which carries out a normal cellular function, but which can become an oncogene under certain circumstances. The prefix "c-" indicates a cellular gene, and is generally used for protooncogenes (examples: c-myb , c-myc , c-fos , c-jun , etc). Protoplasm -- all the contents of a cell, including the nucleus. (see: cytoplasm) Protostele -- when a plant's vascular tissue develops in a solid central bundle, it is said to have a protostele. See also siphonostele and eustele. Prototroph: an organism that is capable of growing on a defined minimal medium; often this is usually regarded as the wildtype strain. Protozoa (meaning first animals): A collective name for several phyla of unicellular and eukaryotic, the most animallike, mainly parasitic organisms belonging to the Kingdom Protista (modern name: Protoctista meaning first beings). This Kingdom includes Protozoa and other not necessarily single-celled but eukaryotic organisms (algae and others formerly known as fungi) except fungi. They reproduce by fission or conjugation, and move by cilia, flagella or pseudopodia. The taxonomic Kingdom Protista is thought to be the ancestor of the other eukaryotic kingdoms Fungi, Plants and Animals. Familiar examples of protozoa are flagellates (incl. Chlamydomonas), Amoeba, Plasmodium, Ciliates (incl. Paramecium). Link to a discussion of the Protists. Pseudoalleles: Genes that behave like alleles but can be separated by crossing over. The eye color genes on the X chromosome of Drosophila are for example closely adjacent but separable loci and not alleles of a single gene. Pseudoautosomal inheritance: The X and Y chromosomes share a common ancestor. There is a part of X chromosome

which has its homologous counterpart on the Y chromosome. The pattern of inheritance for a gene located on both the X and Y chromosomes may appear to be autosomal. Pseudoelaters -- moisture-sensitive cells produced in the sporangium of hornworts. Pseudoextinction -- the apparent disappearance of a taxon. In cases of pseudoextinction, this disappearance is not due to the death of all members, but the evolution of novel features in one or more lineages, so that the new clades are not recognized as belonging to the paraphyletic ancestral group, whose members have ceased to exist. The dinosauria, if defined so as to exclude the birds, is an example of a group that has undergone pseudoextinction. Pseudogene - Inactive but stable components of the genome which derived by duplication and mutation of an ancestral, active gene. Pseudogenes can serve as the donor sequence in gene conversion events. # A gene which has acquired a nonsense mutation and lost its transcription ability. Pseudoknot - A feature of RNA tertiary structure; best visualized as two overlapping stem-loops in which the loop of the first stem-loop participates as half of the stem in the second stem-loop. Pseudomonas syringae: The genetically engineered strain of this bacteria lack a cell-surface protein that helps ice crystals to form. Spraying these bacteria on crops may prevent freezingrelated damages. Pseudopodia -- fingerlike extensions from an amoeboid cell; literally "false feet". Pseudorevertant - A mutant virus or organism which has recovered a wildtype phenotype due to a second-site mutation (potentially located in a different region of the genome, or involving a different polypeptide) which has eliminated the effect of the initial mutation. Pseudotype virus Engineering an ecotropic virus to express amphytropic coat proteins. Pteridophyte -- plant in which the sporophyte generation is the larger phase and in which the gametophyte lives an existence independent of its parent sporophyte. Pteridophytes are almost all vascular plants, and include the lycophytes, trimerophytes, sphenophytes, and ferns. Pteridosperm -- an extinct group of seed plants which bore fern-like leaves. pUC. A widely used expression plasmid containing agalactosidase gene. (See Plasmid.) Pulse field gel electrophoresis (PFGE): A form of gel electrophoresis that allows extremely long DNA molecules to be separated from one another. # A gel technique which allows size-separation of very large fragments of DNA, in the range of hundreds of kb to thousands of kb. As in other gel electrophoresis techniques, populations of molecules migrate through the gel at a speed related to their size, producing discrete bands. In normal electrophoresis, DNA fragments greater than a certain size limit all migrate at the same rate through the gel. In PFGE, the electrophoretic voltage is applied alternately along two perpendicular axes, which forces even the larger DNA fragments to separate by size.# Separation of large (>50 kb) pieces of DNA, including complete chromosomes and genomes, by rapidly alternating the direction of electrophoretic migration in agarose gels. Punctuated equilibrium -- a model of evolution in which change occurs in relatively rapid bursts, followed by longer periods of stasis. # Put forward by Niles Eldredge and Stephen

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Jay Gould in 1972 as a counter theory to Darwins gradualism in speciation (see phyletic gradualism). It suggests that new species may have arisen rapidly over a few thousand years and then remained unchanged (stasis) for many millions of years. Punctuated equilibrium postulates that change occurred in only a small part of the population (rather than the whole population is evolving gradually). The most plausible explanation for a sudden and drastic change would be mutations in regulatory sequences that affect a whole operon (see Gould SJ & N Eldredge. Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiology 1977;3:115-51). Link to an essay on punctuated equilibrium. Punnett square: the checkerboard method commonly used to determine the types of zygotes produced by a fusion of gametes from the parents; the results allow the computation of genotypic and phenotypic ratios. Pupa - in metamorphozing insects, a stage between the larva and adult during which the organism undergoes major developmental changes. Pure line - a highly inbred strain of organisms whose members are genetically identical. Purine Bases - Adenine (A) or Guanine (G) (see NUCLEOTIDE). PVA. The Plant Variety Act. See U.S. Department of Agriculture. Pycnoxylic -- wood in which there is little or no parenchyma tissue among the xylem is called pycnoxylic. Conifers and flowering plants have pycnoxylic wood. Contrast with mannoxylic. Pygidium -- in trilobites, the posterior division of the body, formed by fusion of the telson with one or more posterior pleurae. Pyrimidine Bases - Cytosine (C), Thymine (T) or Uracil (U) (see NUCLEOTIDE).

developing this concept [as described on this webpage] and initial studies show the technology has broad applicability for the quantitation of protein molecules in pure populations of cells. Quasidominance: Direct transmission, generation to generation, of a recessive trait giving the impression of dominance. It happens if the recessive gene is frequent or inbreeding is intense. Quasispecies: The whole population of phylogenetically related (virus) variants observed within a single (infected) individual. Viruses with high mutation rates such as human immunodeficiency virus (HIV) and hepatitis C virus (HCV) occur like this. As a comparison, HIV variation within a single infected individual can be as great as the variation of influenza throughout the worldwide-infected population in a flu season. A review on quasispecies by DB Smith (1997).

R
Race: Described in population genetics as a geographic subdivision of a species distinguished from others by the allele frequencies of a number of genes. A beautiful discussion that there are no genetically defined races within Homo sapiens can be found in Cavalli-Sforzas book Genes, Peoples, and Languages (2000). Radiation -- event of rapid cladogenesis, believed to occur under conditions where a new feature permits a lineage to move into a new niche or new habitat, and is then called an adaptive radiation. Radicle -- the end of a plant embryo which gives rise to the first root. Radio-carbon dating - method for determining the age of an organic substance by measuring the amount of the carbon isotope, carbon-14, remaining in the substance; useful for determining ages in the range of 500 to 70,000 years. Radiospermic -- having seeds which are round or ovoid. Contrast with platyspermic. Random mating: a population mating system in which every male gamete has an equal opportunity to join in fertilization with every female gamete, including those gametes derived from the same individuals. # Mating without any preference for mates. One of the assumptions of Hardy-Weinberg equilibrium (nonrandom mating may be due to assortative or disassortative mating). Random primed synthesis: If you have a DNA clone and you want to produce radioactive copies of it, one way is to denature it (separate the strands), then hybridize to that template a mixture of all possible 6-mer oligonucleotides. Those oligos will act as primers for the synthesis of labeled strands by DNA polymerase (in the presence of radiolabeled precursors). Random priming This technique is also used to produce labeled cDNA probes and is dependent on using random 6- to 10-base oligonucleotides to sit down on a singlestranded cDNA and then using DNA polymerase to synthesize the complementary strand using labeled nucleotides. This technique usually produces more favorable results than nicktranslation. Rank -- in traditional taxonomy, taxa are ranked according to their level of inclusiveness. Thus a genus contains one or more species, a family includes one or more genera, and so on. RAPD Random amplification of polymorphic DNA. A method for identifying differences between genomes of different individuals by PCR with a single short (usually 10-base) primer, which will anneal with complementary sequence at

Q
Quantitative character: A character displaying a continuous phenotypic range rather than discrete classes (characters taking any value within a limit; characters measured rather than counted such as metabolic activity, height, length, width, body fat content, growth rate, milk production). The genetic variation underlying a continuous character distribution may be the result of segregation at a single genetic locus or more frequently, at numerous interacting loci which produce cumulative effect on the phenotype. A gene affecting a quantitative character is a quantitative trait locus, or QTL. Quantitative genetics: The statistical study of the genetics of quantitative characters (biometrical genetics) as opposed to Mendelian (discrete) characters. Quantitative genetic characters are those that do not assort in a simple way in crosses. Examples are physiological activity, reproductive rate, behavior, size, and height. A major task of quantitative genetics is to determine the ways in which genes interact with the environment to contribute to the formation of a given quantitative trait distribution (and the estimation of genetic and environmental variance). Link to a lecture on quantitative genetics. Quantitative Laser Capture Microdissection: In the field of proteomics, coupling laser capture microdissection (LCM) with sensitive quantitative chemiluminescent immunoassays has broad applicability when applied to normal, diseased, or genetically modified tissue. The NCI Prostate Group is

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undetermined positions in the genome. The products form a type of "genetic fingerprint". Rb The prototypical tumor suppressor gene Rb behaves in a genetically recessive fashion. Elimination or inactivation of both Rb gene copies is required for manifestation of the tumorgenic phenotype, first recognized in children with retinoblastoma. Such children inherit only a single functional copy; subsequent mutagenic inactivation of the remaining allele results in tumor susceptibility. Rb acts to sequester a group of transcription factors, termed E2F, which regulate genes critical for DNA synthesis. Alterations of Rb alleles are found in approximately 30% of human acute leukemias. Rbcl -- a gene which is located in the chloroplast of photosynthetic organisms. It codes for the large subunit of the protein rubisco, and its sequence has been useful in plant phylogenies. RDA (representational difference analysis) A molecular method to amplify genes that are expressed in an RNA sample of interest, that are not present, or present at very reduced levels, in a comparison RNA sample (e.g. cytokine induced and control cells). The method relies on RTPCR amplification of the RNA that does not contain the gene(s) of interest to produce a driver cDNA, and RTPCR to produce tester cDNA from the RNA population in which you hope to find new genes. After ligation of different oligonucleotides to the ends of each population, both are denatured and an excess of the driver is hybridized to the tester and PCR performed with primers that will amplify only sequences present in the tester that are not in the driver, thereby removing cDNA common to both populations. The resultant cDNA are enriched in uniquely expressed genes. Reading Frame - Refers to a polypeptide sequence potentially encoded by a single-stranded mR A. Because codons are nucleotide triplets, each mRNA has 3 reading frames (each nucleotide can participate in 3 codons, at the 1st, 2nd, and 3rd base position). Duplex DNA strands have 6 reading frames, 3 in each strand (see OPEN READING FRAME): AlaSerProLeuVal . . 1st reading frame ProAlaProTERTrp . . 2nd reading frame: TER = Stop GlnProProSerGly . . 3rd reading frame GCCAGCCCCCUAGTGGG... Nucleotide sequence of mRNA Reading frame. A series of triplet codons beginning from a specific nucleotide. Depending on where one begins, each DNA strand contains three different reading frames. (See Open reading frame, Overlapping reading frames.) Reading frame: When mRNA is translated by the cell, the nucleotides are read three at a time. By starting at different positions, the groupings of three that are produced can be entirely different. The following example shows a DNA sequence and the three reading frames in which it could be read. Not only is an entirely different amino acid sequence specified by the different reading frames, but two of the three frames have stop codons, and thus are not open reading frames. If we shift the grouping again, we will just get the first reading frame again. The reading frame that is actually used is determined by the first methionine codon (the initiation codon). Once that first AUG is recognized, the pattern of triplet groupings follows unambiguously. Real-time automated PCR During PCR, a fluorogenic probe, consisting of an oligodeoxynucleotide with both reporter and

quencher dyes attached, anneals between the two standard PCR primers. When the probe is cleaved during the next PCR cycle, the reporter is separated from the quencher so that the fluorescence at the end of PCR is a direct measure of the amplicons generated throughout the reaction. Such a system is amenable to automation and gives precise quantitative information. Recessive gene. Characterized as having a phenotype expressed only when both copies of the gene are mutated or missing. Recessive trait: a trait controlled by an allele that does not express itself in the heterozygous condition. Recessive(-acting) oncogene, (anti-oncogene). A single copy of this gene is sufficient to suppress cell proliferation; the loss of both copies of the gene contributes to cancer formation.(See Oncogene.) Recessive: A trait that is not expressed in heterozygotes (i.e., that can only be expressed in the homozygous state). Reciprocal cross: a cross with the phenotype of each sex reversed as compared with the original cross; made to test the role of parental sex on inheritance patterns. Recognition Sequence - A specific palindromic sequence within a double-stranded DNA molecule which is recognized by a restriction endonuclease, and at which the restriction endonuclease specifically cleaves the DNA molecule. Recognition sequence (site). A nucleotide sequence composed typically of 4, 6, or 8 nucleotides--that is recognized by a restriction endonuclease. Type II enzyrnes cut (and their corresponding modification enzymes methylate) within or very near the recognition sequence. Recombinant - An arrangement of alleles unlike that in either parent, resulting from either independent assortment or from crossing-over. # A DNA or protein molecule produced as a result of assembling and joining DNA sequences from different sources. Sometimes used to refer to an organism carrying such a gene. # A cell that results from recombination of genes. # the new individuals arising as a result of recombination. Recombinant D A. The process of cutting and recombining DNA fragments from different sources as a means to isolate genes or to alter their structure and function. Recombinase: A group of enzymes that catalyze the joining of two DNA molecules after recognizing the recombination sites. See also integrase and transposase. Recombination - See HOMOLOGOUS RECOMBINATION. Recombination (crossing-over): The exchange (reshuffling) of genetic material between a homologous pair of chromosomes during meiosis (see also somatic recombination; sister chromatid exchange). # the genetic result of crossing over, which results in new linkages between the alleles of different genes. # A natural cellular process through which DNA molecules of similar or identical sequence can be exchanged. This process is the molecular basis of crossing over during meiosis and some DNA repair mechanisms. Another form of recombination, site-specific recombination, is found where transfer, rearrangement or insertion of specific sections of DNA occurs e.g. insertion of viral DNA into chromosomes, gene switching etc. # the occurrence of progeny with combinations of genes other than those that occurred in the parents, due to independent assortment or crossing over. # A mode of filling a gap in one strand of duplex DNA by retrieving a homologous single strand from another duplex. Usually the underlying mechanism behind homologous recombination and gene conversion.

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Recombination frequency. The frequency at which crossing over occurs between two chromosomal loci--the probability that two loci will become unlinked during meiosis. Red Queen theory: An organisms biotic environment consistently evolves to the detriment of the organism. Sex and recombination result in progeny genetically different from the previous generations and thus less susceptible to the antagonistic advances made during the previous generations, particularly by their parasites. Regulator gene: a gene whose primary function is to control the rate of synthesis of the products of other distant genes. Regulators of Complement Activation (RCA): Membrane proteins that inhibit formation of and promote decay of C3activating convertases, and prevent formation of membrane attack complex. Their main role is to prevent host cells from complement attack. Regulatory gene - a gene that controls the activity of another gene. # A gene whose protein controls the activity of other genes or metabolic pathways. Relatedness -- two clades are more closely related when they share a more recent common ancestor between them than they do with any other clade. Relaxed Dna - See SUPERCOIL. Relaxed plasmid. A plasmid that replicates independently of the main bacterial chromosome and is present in 10-500 copies per cell. (See Plasmid.) Release factor: specific proteins that read termination codons and cause the release of the finished polypeptide. Renature. The reannealing (hydrogen bonding) of singlestranded DNA and/or RNA to form a duplex molecule. Repeat (repetitive) sequence D A Sections of DNA in which short base sequences are repeated from several to many times. Repetitive D A: A surprising portion of any genome consists not of genes or structural elements, but of frequently repeated simple sequences. These may be short repeats just a few nt long, like CACACA etc. They can also range up to a few hundred nt long. Examples of the latter include Alu repeats, LINEs, SINEs. The function of these elements is often unknown. In shorter repeats like di- and tri-nucleotide repeats, the number of repeating units can occasionally change during evolution and descent. They are thus useful markers for familial relationships and have been used in paternity testing, forensic science and in the identification of human remains. # Non-coding DNA which consists of nucleotide sequences repeatedly occurring in chromosomal DNA. They do not normally have any function but those capping the chromosomes prevent the loss of genetic information after each replication (as this would cause a 3 overhang). In human genome, at least 20% of the DNA consists of repetitive sequences. Replication - a duplication process requiring copying from a template # The copying of a nucleic acid molecule into a new nucleic acid molecule of similar type (i.e., DNA --> DNA, or RNA --> RNA). Replicon. A chromosomal region containing the DNA sequences necessary to initiate DNA replication processes. # a genetic element that behaves as an autonomous unit during dna replication; contains a segment to which a specific rna polymerase binds and a replicator locus at which dna replication commences. # A unit of genetic material which behaves autonomously during replication of DNA. In bacteria,

a whole chromosome is a replicon. In eukaryotes, chromosomes are divided into hundreds of replicons. Each replicon contains a segment beginning with a binding site for RNA polymerase. Reporter Gene - The use of a functional enzyme, such as betagalactosidase, luciferase, or chloramphenicol acetyltransderase, downstream of a gene, promoter, or translational control element of interest, to more easily identify successful introduction of the gene into a host and to measure transcription and/or translation. # Gene coding for an easily assayed protein which is used to detect expression of the gene under different conditions; usually to test the activity of a promoter. The galactosidase, luciferase and Green Fluorescent Protein genes are examples of reporter genes. # In order to determine how a gene promoter or enhancer works in vitro, that genetic element is often linked to a gene for which a simple assay is readily available and whose regulation is not affected by posttranscriptional processes. Such reporter genes include chloramphenicol acetyl transferase, galactosidase, and firefly luciferase. The first is the most commonly used reporter; however, more recent studies have emphasized the use of the latter two reporters, as these are more sensitive to minimal changes in promoter or enhancer activity. Repressible system: a regulatory system in which the product of a regulator gene blocks transcription of the operon only if it first reacts with an effector molecule; thus, transcription only occurs in the absence of the effector. Repression - Inhibition of transcription (or translation) by the binding of a repressor protein to a specific site on DNA (or mR A). # A DNA-binding protein in prokaryotes that blocksgene transcription by binding to the operator. # a protein synthesized by a regulator gene that binds to an operator locus and blocks transcription of that operon. Reproduction -- process by which new organisms are generated. Reproduction may be sexual, involving the fusion of gametes, or asexual. # the manufacture of offspring as part of an organism's life cycle. This is not the same as dispersal. Repulsion (trans-arrangement): The condition in which a double heterozygote has received a mutant and a wild-type allele from each parent, e.g., a + / + b (see also coupling). Residue - As applied to proteins, what remains of an amino acid after its incorporation into a peptide chain, with subsequent loss of a water molecule (see PEPTIDE BOND). #A compound such as an amino acid or a nucleotide when it is part of a larger molecule. Response element: By definition, a "response element" is a portion of a gene which must be present in order for that gene to respond to some hormone or other stimulus. Response elements are binding sites for transcription factors. Certain transcription factors are activated by stimuli such as hormones or heat shock. A gene may respond to the presence of that hormone because the gene has in its promoter region a binding site for hormoneactivated transcription factor. Example: the glucocorticoid response element (GRE). Restriction endonuclease (enzyme). A class of endonucleases that cleaves DNA after recognizing a specific sequence, such as BamH1 (GGATCC), EcoRI (GAATTC), and HindIII (AAGCTT). Type I. Cuts nonspecifically a distance greater than 1000 bp from its recognition sequence and contains bothrestriction and methylation activities. Type II. Cuts at or near a short, and often symmetrical, recognition sequence. A separate enzyme methylates the same recognition sequence. Type III. Cuts 24-26 bp downstream from a short, asymmetrical

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recognition sequence. Requires ATP and contains both restriction and methylation activities. # A bacterial enzyme which recognizes a specific palindromic sequence (recognition sequence) within a double-stranded DNA molecule and then catalyzes the cleavage of both strands at that site. Also called a restriction enzyme. Restriction endonucleases may generate either blunt or sticky ends at the site of cleavage. # These enzymes are among the most useful in recombinant DNA technology, capable of introducing a single cleavage site into a nucleic acid. The site of cleavage is dependent on sequence; recognition sites contain from 4 to 10 specific nucleotides. The resultant digested ends of the nucleic acid chain may either be blunt or contain a 5' or 3' overhang ranging from 1 to 8 nucleotides. # More correctly called a Type II Restriction Endonuclease. A bacterial enzyme which forms part of a system to protect the cell against infection by bacteriophage, and unregulated influx of foreign DNA. Binds to DNA at a short specific base sequence, and cuts both strands between specific bases in this sequence. # A class of enzymes ("restriction endonucleases") generally isolated from bacteria, which are able to recognize and cut specific sequences ("restriction sites") in DNA. Note that both strands contain the sequence GGATCC, but in antiparallel orientation. The recognition site is thus said to be palindromic, which is typical of restriction sites. Every copy of a plasmid is identical in sequence, so if BamHI cuts a particular circular plasmid at three sites producing three "restriction fragments", then a million copies of that plasmid will produce those same restriction fragments a million times over. There are more than six hundred known restriction enzymes. Bacteria produce restriction enzymes for protection against invasion by foreign DNA such as phages. The bacteria's own DNA is modified in such a way as to prevent it from being clipped. Restriction fragment: The piece of DNA released after restriction digestion of plasmids or genomic DNA. See "Restriction enzyme". One can digest a plasmid and isolate one particular restriction fragment (actually a set of identical fragments). The term also describes the fragments detected on a genomic blot which carry the gene of interest. # DNA fragments generated by digestion of a DNA preparation with one or more restriction endonucleases; usually separated by agarose gel electrophoresis and visualized by ethidium bromide staining under UV light (or alternatively subjected to Southern blot analysis). Restriction Map - A linear array of sites on a particular DNA which are cleaved by various selected restriction endonucleases. # A diagram of all or part of a dsDNA molecule which indicates the positions (in base pairs) of restriction enzyme recognition/cutting sites. Used extensively in identification of DNA fragments and in developing procedures for manipulating cloned DNA. # A "cartoon" depiction of the locations within a stretch of known DNA where restriction enzymes will cut. The map usually indicates the approximate length of the entire piece (scale on the bottom), as well as the position within the piece at which designated enzymes will cut. This map happens to be of a plasmid, and the two ends are joined together with about 25 nt between the EcoRI and HindIII sites. Restriction site: See Restriction enzyme. Reticulate -- interconnecting, like a network. Reticulation -- joining of separate lineages on a phylogenetic tree, generally through hybridization or through lateral gene

transfer. Fairly common in certain land plant clades; reticulation is thought to be rare among metazoans. Reticulocyte Lysate - A lysate of rabbit reticulocytes, which has been extensively digested with micrococcal nuclease to destroy the reticulocyte mR As. With the addition of an exogenous, usually synthetic, mRNA, amino acids and a source of energy (ATP), the translational machinery of the reticulocyte (ribosomes, eukaryotic translation factors, etc.) will permit in vitro translation of the added mRNA with production of a new polypeptide. This is only one of several available in vitro translation systems. Reticulopodia -- long thread-like pseudopodia that branch apart and rejoin, forming a fine network. They are characteristic of forams. Retrovirus. A member of a class of RNA viruses that utilizes the enzyme reverse transcriptase to reverse copy its genome into a DNA intermediate, which integrates into the hostcell chromosome. Many naturally occurring cancers of vertebrate animals are caused by retroviruses. Reverse allele-specific hybridization This automated variant of allele-specific hybridization couples unlabeled synthetic oligonucleotides specific for a wild type or mutant sequence to a solid support that is then allowed to bind genomic sequences of the locus of interest, which have been amplified by PCR. The use of highly stringent conditions of hybridization allows differential binding of the amplified DNA to the wild type or mutant specific oligonucleotide and thereby allows genotypic determination of the individual. Reverse genetics Often, large families of homologous proteins exist and multiple previously unknown members of the family can be obtained by screening cDNA libraries under low stringency using cDNA or oligonucleotide probes from regions highly conserved amongst members of the family. In this case, genes are identified before their function is known, a situation referred to as reverse genetics. Examples in hematology include identifying members of the tyrosine kinase family of receptor proteins using a probe derived from the conserved kinase domain of the cytoplasmic region of src or other tyrosine kinase proto-oncogenes, or the identification of transcription factors important in hematopoiesis using conserved motifs present in zinc finger or homeodomain proteins. #. Using linkage analysis and polymorphic markers to isolate a disease gene in the absence of a known metabolic defect, then using the DNA sequence of the cloned gene to predict the amino acid sequence of its encoded protein. Reverse Transcriptase - A D A polymerase which copies an RNA molecule into single-stranded cDNA; usually purified from retroviruses. # An enzyme isolated from retrovirusinfected cells that synthesizes a complementary (c)DNA strand from an RNA template. # This enzyme, first purified from retrovirus-infected cells, produces a cDNA copy from an mRNA molecule if first provided with an antisense primer (oligo dT or a random primer). This enzyme is critical for converting mRNA into cDNA for purposes of cloning, PCR amplification, or the production of specific probes. # an enzyme that synthesizes a single strand of dna using rna molecules as templates; occur in oncogenic rna viruses. # An enzyme which will make a DNA copy of an RNA template - a DNA-dependant RNA polymerase. RT is used to make cDNA; one begins by isolating polyadenylated mRNA, providing oligo-dT as a primer, and adding nucleotide triphosphates and RT to copy the RNA into cDNA

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Reverse Transcription - Copying of an RNA molecule into a DNA molecule. Revertant - See BACK MUTATION. RFLP (restriction fragment length polymorphism) If a mutation of one allele of a genetic locus either generates or destroys a restriction endonuclease site, the heterogeneity present within or very close to a gene of interest can be used to track which allele an individual has inherited from each parent. When genomic DNA is digested with a restriction enzyme that recognizes a polymorphic site and then hybridized with a probe specific for the gene of interest, the allelic pattern can be compared to that of a similar assessment of both parents. The presence of multiple family members allows a complete genetic pedigree to be constructed. For example, globin gene mutations such as sickle hemoglobin can be analyzed. The 6 mutation in hemoglobin, which results in Hgb S, destroys an Mst II site. Therefore, a larger than normal DNA fragment is generated by digestion of genomic DNA with Mst II, which can be easily detected by Southern blot hybridization. In this specific case, the Mst II polymorphism is absolutely specific for the mutant gene and family studies are not necessary. If the RFLP had not been specific for the mutation, but only existed close to the specific diseaseproducing mutation, then family studies would have been required to determine which pattern (presence or absence of restriction site) tracks with the mutant (disease) allele. # (restriction fragment length polymorphism): Genetic polymorphism as revealed by the sizes of fragments generated with a particular restriction endonuclease enzyme (such as EcoRI, PstI, BglII). # Restriction fragment length polymorphism. A difference in restriction fragment length between individuals due to loss or gain of a restriction enzyme site due to point mutation, or insertion or deletion between consecutive sites. Normally detected by Southern blotting and probing. Used in detection of genetic disease alleles etc. # Variations in the lengths of fragments of DNA generated by digestion of different DNAs with a specific restriction endonuclease, reflecting genetic variation (polymorphism) in the DNAs. # Differences in nucleotide sequence between alleles at a chromosomal locus result in restriction fragments of varying lengths detected by Southern analysis. # Restriction fragment length polymorphism; the acronym is pronounced "riflip". Although two individuals of the same species have almost identical genomes, they will always differ at a few nucleotides. Some of these differences will produce new restriction sites (or remove them), and thus the banding pattern seen on a genomic Southern will thus be affected. For any given probe (or gene), it is often possible to test different restriction enzymes until you find one which gives a pattern difference between two individuals - a RFLP. The less related the individuals, the more divergent their DNA sequences are and the more likely you are to find a RFLP. RFLP: See Restriction fragment length polymorphism: Rhizobia. Bacteria in a symbiotic relationship with leguminous plants that results in nitrogen fixation. See Nitrogen fixation. Rhizoid -- cellular outgrowth which usually aids in anchoring and to increase surface area for acquiring water or nutrients. Rhizome -- a horizontal underground stem, such as found in many ferns, where only the leaves may stick up into the air. Sphenophytes spread via rhizomes, but also produce erect stems.

Rhizosphere. The soils region on and around plant roots. Rhyolite -- highly felsic igneous volcanic rock, typically light in color; rough volcanic equivalent of granite. Ribonuclease (RNase) - An enzyme which catalyzes the hydrolysis of RNA. There are many different RNases, some of the more important include: RNase A Cleaves ssRNA 3' of pyrimidines RNase T1 Cleaves ssRNA at guanasine nucleotides RNase V1 Cleaves dsRNA (helical regions) RNase H Degrades the RNA part of RNA:DNA hybrids. # These enzymes degrade RNA and existas either exonucleases or endonucleases. The three mostcommonly used ribonucleases are termed RNase A, Rnase T1, and RNAse H (which degrades duplex RNA or the RNA portion of DNARNA hybrids). Riboprobe: A strand of RNA synthesized in-vitro (usually radiolabeled) and used as a probe for hybridization reactions. An RNA probe can be synthesized at very high specific activity, is single stranded (and therefore will not self anneal), and can be used for very sensitive detection of DNA or RNA. # These labeled RNA molecules are produced by first cloning the cDNA of interest into a plasmid vector that contains promoters for viral RNA polymerases. Following cloning, the viral RNA polymerase is added, and labeled nucleotides are incorporated into the resulting RNA transcript. This molecule is then purified and used in probing reactions. Many such cloning vectors (for example, pGEM) have different RNA polymerase promoters on either side of the cloning site, allowing the generation of both sense and antisense probes from the same construct. Ribosomal Binding Sequence (Shine-Dalgarno sequence) - In prokaryotic organisms, part or all of the polypurine sequence AGGAGG located on mR A just upstream of an AUG initiation codon; it is complementary to the sequence at the 3' end of 16S rRNA; and involved in binding of the ribosome to mR A. The internal ribosomal entry site found in some viruses may be an analogous eukaryotic genetic element. Ribosomal R A (rR A). The RNA component of the ribosome. (See RNA.) # One of the four types of RNA that exist in a eukaryotic cell. It has a very slow mutation rate which is useful in phylogenetic analysis of kingdoms and phyla. Ribosome-binding site. The region of an mRNA molecule that binds the ribosome to initiate translation. Ribosomes: Ribosomes are a complex consisting of ribosomal RNAs (rRNA) and several proteins # a cell organelle where mRNA is translated into polypeptide chains. # A complex ribonucleoprotein particle (eukaryotic ribosomes contain 4 RNAs and at least 82 proteins) which is the "machine" which translates mR A into protein molecules. In eukaryotic cells, ribosomes are often in close proximity to the endoplasmic reticulum. # A cellular particle which is involved in the translation of mRNAs to make proteins # Subcellular unit composed of specific rR A molecules and a large number of proteins that are responsible for protein synthesis. [IUPAC Compendium]. Cellular organelle that is the site of protein synthesis. [NHGRI]. Early in 1958, a three-day symposium on microsomal particles in protein synthesis met at MIT, sponsored by the Biophysical Society, organized by Richard Roberts, who was head of a group at the Carnegie Institution in Washington... The most important development at the meeting was semantic. Roberts suggested that for clear and handy distinction between the particles and the amorphous cellular fraction of protein and fat in which they were found, the particles themselves should be called "ribosomes" - short for "ribonucleoprotein particles of the

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microsome fraction." The new term quickly spread into general use #an organelle that is the site of translation. Ribosyme: RNA molecules with enzymatic activity. Its presence in organelles from plants, yeast, viruses and eukaryotic cells revolutionized the ideas about the origin of life. #A catalytically active RNA. A good example is the hepatitis delta virus RNA which is capable of self-cleavage and self-ligation in the absence of protein enzymes. # A complex RNA molecule that possesses endoribonuclease activity. A highly specific RNA sequence can generate secondary structure by virtue of intrachain base pairing. Hairpin loops and hammer head structures serve as examples of such phenomena. When the proper secondary structure forms, such RNA molecules can bind a second RNA molecule (e.g., an mRNA) at a specific location (dependent on an approximately 20-nucleotide recognition sequence) and cleave at a specific GUX triplet (where X = C, A, or U). These molecules will likely find widespread use as tools for specific gene regulation or as antiviral agents but are evolutionarily related to RNA splicing, which in its simplest form is autocatalytic. See Catalytic RNA. Rift zone -- elongate zones on continents that are in the form of a trough bounded by normal faults; the site of crustal extension, similar to that which occurs at mid-oceanic ridges. Riparian -- having to do with the edges of streams or rivers. R A (ribonucleic acid) Three varieties of RNA are easily identified in the mammalian cell. Most abundant is ribosomal RNA (rRNA), which occurs in two sizes, 28S (approximately 4600 nucleotides) and 18S (approximately 1800 nucleotides); together they form the basic core of the eukaryotic ribosome. Messenger RNA (mR A) is the term used to describe the mature form of the primary RNA transcript of the individual gene once it has been processed to eliminate introns and to contain a polyadenylated tail. MRNA links the coding sequence present in the gene to the ribosome, where it is translated into a polypeptide sequence. Transfer RNA (tR A) is the form of RNA used to shuttle successive amino acids to the growing polypeptide chain. A tRNA molecule contains an anti-codon, a three-nucleotide sequence by which the tRNA molecule recognizes the codon contained in the mRNA template, and an adapter onto which the amino acid is attached. # The nucleic acid which carries the dna message into parts of the cell where it is interpreted and used. The 18s ribosomal rna sequence has been used in many groups of organisms to reconstruct phylogeny # An organic acid composed of re-peating nucleotide units of adenine, guanine, cytosine, and uracil, whose ribose components are linked by phosphodiester bonds. (See Antisense RNA, Heterogeneous nuclear RNA, Messenger RNA, Ribosomal RNA, RNA polymerase, Small nuclear RNA, Transfer RNA.) # A singlestranded nucleic acid that is found both in nucleus and cytoplasm. Other differences from DNA are: it contains uracil instead of thymine, it is single-stranded, and its sugar molecule is ribose. Total cellular RNA is made up of ribosomal RNA (rRNA, 80-85%), transfer RNA (tRNA, 1520%) and messenger RNA (mRNA, 1-5%). See also small nuclear RNA and heterogeneous nuclear RNA. R A Polymerase - A polymerase which synthesizes RNA (see POLYMERASE). #: An enzyme that transcribes an RNA molecule from the template strand of a DNA molecule. It adds to the 3 end of the growing RNA molecule one nucleotide at a time using ribonucleotide triphosphates (rNTPs) as

substrates (this reaction releases pyrophosphates). RNA polymerase I is dedicated to the synthesis of only one type of RNA molecule (pre-rRNA). RNA polymerase II is required for general transcription reactions. RNA polymerase III produces small RNAs such as tRNAs and 5S rRNA. # an enzyme that transcribes an rna molecule from the antisense strand of a dna molecule. R A polymerase II This enzyme is used by mammalian cells to transcribe structural genes that result in mRNA. The enzyme interacts with a number of other proteins to correctly initiate transcription, including a number of general factors, and tissuespecific and induction-specific enhancing proteins. R A polymerase III This enzyme is used by the cell to transcribe ribosomal RNA genes. R A Splicing - A complex and incompletly understood series of reactions occuring in the nucleus of eukaryotic cells in which pre-mR A transcribed from chromosomal DNA is processed such that noncoding regions of the pre-mRNA (introns) are excised, and coding regions (exons) are covalently linked to produce an mR A molecule ready for transport to the cytoplasm. Because of splicing, eukaryotic DNA representing a gene encoding any given protein is usually much larger than the mRNA from which the protein is actually translated. R Ase - see RIBONUCLEASE R Ase protection assay This assay is in many ways similar to the S1 nuclease analysis. In this case, a 35S- or 32Plabeled antisense RNA probe is synthesized and hybridized with mRNA of interest. The duplex RNA is then subjected to digestion with RNAse A and T1, both of which will cleave only singlestranded RNA. Following digestion, the remaining labeled RNA is size-fractionated, and the size of the protected RNA probe then gives an indication of the size of the mRNA present in the original sample. This assay can also be used to quantitate the amount of specific RNA in the original sample. # This is a sensitive method to determine (1) the amount of a specific mRNA present in a complex mixture of mRNA and/or (2) the sizes of exons which comprise the mRNA of interest. A radioactive DNA or RNA probe (in excess) is allowed to hybridize with a sample of mRNA (for example, total mRNA isolated from tissue), after which the mixture is digested with single-strand specific nuclease. Only the probe that is hybridized to the specific mRNA will escape the nuclease treatment, and can be detected on a gel. The amount of radioactivity that was protected from nuclease is proportional to the amount of mRNA to which it hybridized. If the probe included both intron and exons, only the exons will be protected from nuclease and their sizes can be ascertained on the gel. R ase: Ribonuclease; an enzyme which degrades RNA. It is ubiquitous in living organisms and is exceptionally stable. The prevention of RNase activity is the primary problem in handling RNA. Robertsonian translocation: see centric fusion. Root -- usually the below ground portion of a plant. Contrast with shoot. Rosette -- a series of whorls of leaves or leaf-like structure produced at the base of the stem, just above the ground. Rotifer: Microscopic aquatic organisms (pseudocoelomates). Their peculiar features are ancient asexuality, parthenogenetic reproduction and dormancy. Despite being diploid, they dont have homologous chromosomes (see Aydin Orstans Bdelloid Rotifers website, and Rotifera by UCMP).

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rR A - Ribosomal RNA (four sizes in humans: 5S, 5.8S, 18S, and 28S); RNA component of the ribosome, which may play catalytic roles in translation. # Any of several RNAs which become part of the ribosome, and thus are involved in translating mRNA and synthesizing proteins. They are the most abundant RNA in the cell (on a mass basis). RT/PCR Reaction (reverse transcription PCR) - A series of reactions which result in RNA being copied into DNA and then amplified. A single primer is used to make singlestranded cD A copies from an RNA template under direction of reverse transcriptase. A second primer complementary to this "first strand" cDNA is added to the reaction mix along with Taq polymerase, resulting in synthesis of double-stranded DNA. The reaction mix is then cycled (denaturation, annealing of primers, extension) to amplify the DNA by conventional PCR. # This technique allows the rapid amplification of cDNA starting with RNA. The first step of the reaction is to reverse-transcribe the RNA into a first strand cDNA copy using the enzyme reverse transcriptase. The primer for the reverse transcription can either be oligo dT, to hybridize to the polyadenylation tail, or the antisense primer that will be used in the subsequent PCR reaction. Following this first step, standard PCR is then performed to rapidly amplify large amounts of cDNA from the reverse transcribed RNA. # PCR amplification from an RNA template. The first step involves synthesis of a single strand of cDNA on the RNA template using reverse transcriptase. The cDNA is then used as the template for PCR to produce a DNA product. Rubisco -- protein which fixes carbon in photosynthetic organisms. It binds molecules of carbon dioxide to a fivecarbon molcule. Rubisco is the most common protein on earth. Rule of independent assortment: mendels second rule, describing the independent segregation of alleles at different loci; the alleles of one gene can segregate independently of the alleles of other genes. Rule of segregation: mendels first principle describing how genes are passed from one generation to the next; a gamete receives only one allele from the pair of alleles possessed by an organism; fertilization (the union of two gametes) reestablishes the double number. Runoff Transcript - RNA which has been synthesized from plasmid DNA (usually by a bacteriophage R A polymerase such as T7 or SP6) and which terminates at a specific 3' site because of prior cleavage of the plasmid DNA with a restriction endonuclease. Run-off: see Nuclear run-on. Run-on: see Nuclear run-on. S1 end mapping: A technique to determine where the end of an RNA transcript lies with respect to its template DNA (the gene). Can't be described in a short paragraph. See "RNAse Protection assay" for a closely related technique.

S
S1 uclease - An enzyme which digests single-stranded DNA or RNA S1 nuclease analysis This technique is used to identify the start of RNA transcription. The DNAse enzyme S1 cleaves only at sites of single-stranded DNA. Therefore, if 32Plabeled DNA is hybridized with mRNA, the resulting heteroduplex can be digested with S1, and the resulting DNA fragment will be of length equivalent to the site at which the piece of DNA begins through the mature 5' end of the RNA.

S1 nuclease: An enzyme which digests only single-stranded nucleic acids. Saccharomycetes cerevisiae: Unicellular Ascomycete yeast known as the bakers or brewers yeast. Widely used as a simple eukaryotic model, particularly in recombinant DNA and cell cycle studies as well as in mating type and heterokaryon compatibility studies. It has most advantages of a prokaryotic system but is a true eukaryote. It is considered as the E.coli of the eukaryotes. S.cerevisiae can reproduce both asexually and sexually, and can be cultured in either the haploid or the diploid state. One major advantage of yeast is the ease with which specific gene disruptions, gene replacements, and gene retrievals can be accomplished. Its complete genome was sequenced in 1997 and contains 12,057,500 bp, 6,000 genes in 16 chromosomes. It is used in the creation of YACs. Link to S.cerevisiae website. SAGE (serial analysis of gene expression): A high-throughput method that uses 10-14 bp-long tags from each cDNA expressed in a cell. The concentration of each tag sequence is proportional to the level of its mRNA in the original sample. This method is used to explore gene regulation in cell populations. Link to the NCBI SAGE website. Salinity -- a measure of the salt concentration of water. Higher salinity means more dissolved salts. Salmonella. A genus of rod-shaped, gram-negative bacteria that are a common cause of food poisoning. Sampling distribution: the distribution of frequencies with which various possible events could occur or a probability distribution defined by a particular mathematical expression. Sandstone -- sedimentary rock composed of sand-sized clasts. Saprophyte -- organism which feeds on dead and decaying organisms, allowing the nutrients to be recycled into the ecosystem. Fungi and bacteria are two groups with many important saprophytes. Satellite D A A genomic DNA fraction which has a different density to the main body of genomic DNA and therefore forms a separate band (satellite) during density gradient ultracentrifugation. The difference in density is due to a bias in base content caused by the presence of repeat sequence DNA. Satellite R A (viroids). A small, self-splicing RNA molecule that accompanies several plant viruses, including tobacco ringspot virus. Saxitoxin -- neurotoxin found in a variety of dinoflagellates. If ingested, it may cause respiratory failure and cardiac arrest. Schizophyllum commune: A fungus species of Basidiomycetes group. It has thousands of mating types in a multiallelic locus, a pheromone receptor system and a pheromone system. Because of this, it has the maximal outbreeding rates (98.8%) in nature. SCL This proto-oncogene, first identified in a stem cell leukemia at the site of t(1;14), is a member of the helixloophelix group of transcriptionally active proteins. The gene, also termed Tal 1, is expressed in erythroid and mast cell lineages but not in T cells. The association of t(1;14) with up to 25% of T cell ALL suggests that its ectopic expression is associated with transformation. Screening: To screen a library (see "Library") is to select and isolate individual clones out of the mixture of clones. For example, if you needed a cDNA clone of the pituitary glycoprotein hormone alpha subunit, you would need to make (or buy) a pituitary cDNA library, then screen that library in order to detect and isolate those few bacteria carrying alpha subunit cDNA. There are two methods of screening which are

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particularly worth describing: screening by hybridization, and screening by antibody. Screening by hybridization involves spreading the mixture of bacteria out on a dozen or so agar plates to grow several ten thousand isolated colonies. Membranes are laid onto each plate, and some of the bacteria from each colony stick, producing replicas of each colony in their original growth position). The membranes are lifted and the adherent bacteria are lysed, then hybridized to a radioactive piece of alpha DNA (the source of which is a story in itself - see "Probe"). When X-ray film is laid on the filter, only colonies carrying alpha sequences will "light up". Their position on the membranes show where they grew on the original plates, so you now can go back to the original plate (where the remnants of the colonies are still alive), pick the colony off the plate and grow it up. You now have an unlimited source of alpha cDNA. Screening by antibody is an option if the bacteria and plasmid are designed to express proteins from the cDNA inserts (see "Expression clones"). The principle is similar to hybridization, in that you lift replica filters from bacterial plates, but then you use the antibody (perhaps generated after olde tyme protein purification rituals) to show which colony expresses the desired protein. SDS-Page - Denaturing protein gel electrophoresis (see Polyacrylamide Gel Electrophoresis). Sea Urchin: A small spiny marine invertebrate belonging to the phylum Echinodermata. It is a model animal for the study of fertilization and development. Because it is a spawner, its gametes can be obtained in large quantities. Simple mixing of sperms and eggs causes synchronous mitosis and cytokinesis. Furthermore, its eggs are large and clear. Links to Sea Urchin Embryology (Stanford) and Sea Urchin Genome Project (CalTech) websites. Seaweed -- any large photosynthetic protist, including rhodophytes and kelps. Seaweeds are not true plants, but like plants they can make their own food. Second messenger systems: Systems in which an intracellular signal is generated in response to an intercellular primary messenger such as a hormone or neurotransmitter. They are intermediate signals in cellular processes such as metabolism, secretion, contraction, phototransduction, and cell growth. Examples of second messenger systems are the adenyl cyclase- cyclic AMP system, the phosphatidylinositol diphosphate- inositol triphosphate system, and the cyclic GMP system. [MeSH, 1989]. A multi-step signal amplification process used by the cell to transmit, for example, signals from many hormones that cannot enter the cell directly. [NIGMS] Second messenger: An intracellular metabolite or ion increasing or decreasing as a response to the stimulation of receptors by agonists, considered as the "first messenger". This generic term usually does not prejudge the rank order of intracellular biochemical events. [IUPAC Medicinal Chemistry] Second strand synthesis The enzyme DNA polymerase is used to generate the sense strand of cDNA. Priming of the second strand can occur spontaneously, as the antisense first cDNA strand can form a hairpin loop at its 3' end bending back to prime second strand synthesis. Alternatively, a polynucleotide tail can be added to the first strand synthesis using terminal deoxynucleotide transferase, then second strand priming can occur using a synthetic oligonucleotide complementary to the TdT tail. Should the former technique be used, an extra step to nick the hairpin loop using the

enzyme S1 nuclease would be required prior to inserting the cDNA into its vector. Secondary growth -- growth in a plant which does not occur at the tips of the stems or roots. Secondary growth produces wood and bark in seed plants. Secondary Structure - (also see PRIMARY and TERTIARY STRUCTURE) Local structure within a protein which is conferred by the nature of the side chains of adjacent amino acids (e.g., alpha helix, beta sheet, random coil); local structure within an RNA molecule which is conferred by base pairing of nucleotides which are relatively closely positioned within the sequence (e.g., hairpins, stem-loop structures). Sedentary - living in a fixed location, as with most plants, tunicates, sponges, etc. Contrast with motile. # not moving. Many organisms, both plants and animals, spend the majority of their lives in one place. Sediment -- any solid material that has settled out of a state of suspension in liquid. Sedimentary rock -- any rock resulting from the consolidation of sediment. Seed - a structure produced by seed plants which encapsulates the embryo. The seed often provides nourishment during germination, but may lie dormant for many years first. # A fertilized and mature ovule which will develop into a new plant if sown. It contains usually one fertilized ovum (embryo) and endosperm (or perisperm) which is the nutritive cell surrounding the embryo. Segmentation -- in many animals, the body is divided into repeated subunits called segments, such as those in centipedes, insects, and annelids. Segmentation is the state of having or developing a body plan in this way. Segregation - in genetics, the appearance of offspring phenotypes different to those of their parents as a result of the separation and random distribution to cells of allele pairs during meiosis. Segregation distortion: Violation of Mendels first law which results in unequal segregation of a pair of alleles. Selectable marker A gene which is usually constitutively expressed and allows the selection of cells which carry it through growth on a selective medium. The most common example is the use of the -lactamase gene in plasmid vectors to confer ampicillin resistance on the host cell. # A gene whose expression allows one to identify cells that have been transforrned or transfected with a vector containing the marker gene. (See B-Lactamase, Kanr.) Selection - in evolutionary genetics, the differential survival or reproduction of different genotypes as a result of differences between their phenotypes. # process which favors one feature of organisms in a population over another feature found in the population. This occurs through differential reproduction -those with the favored feature produce more offspring than those with the other feature, such that they become a greater percentage of the population in the next generation. # The use of particular conditions, such as the presence of ampicillin, to allow survival only of cells with a particular phenotype, such as production of beta-lactamase. Selection Coefficient (s): s = 1 - W where W is relative fitness. This coefficient represents the relative penalty incurred by selection to those genotypes that are less fit than others. When the genotype is the one most strongly favored by selection its s value is 0.

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Selection Differential (S) and Response to Selection : Following a change in the environment, in the parental (first) generation, the mean value for the character among those individuals that survive to reproduce differs from the mean value for the whole population by a value of (S). In the second, offspring generation, the mean value for the character differs from that in the parental population by a value of R which is smaller than S. Thus, strong selection of this kind (directional) leads to reduced variability in the population Selection differential: the difference between the average value of a quantitative character in the whole population and the average value of those selected to be parents of the next generation. Selection: the process in nature whereby one genotype leaves more offspring than another genotype because of superior life history attributes such as survival or fecundity. Self-fertilization - the union of a sperm and an egg from the same individual -- the ultimate in inbreeding. Self-fertilization (also selfing, self-pollination): The fusion of male and female gametes produced by the same (hermaphrodite or bisexual) individual. Self-fertilization allows an individual to create a local population, but it fails to provide variability within a population and limits the possibilities for adaptation to environmental change. Some plants reproduce by self-fertilization but most hermaphroditic animals rarely use self-fertilization, since many of them have adaptations encouraging cross-fertilization. Self-incompatibility system (SI system): The genetic complex of plants that prevents self-fertilization. See also MHC and mating types. Self-pollination. Pollen of one plant is transferred to the female part of the same plant or another plant with the same genetic makeup. Semi conservative replication. During DNA duplication, each strand of a parent DNA molecule is a template for the synthesis of its new complementary strand. Thus, one half of a preexisting DNA molecule is conserved during each round of replication. # the method of replication of dna in which the molecule divides longitudinally, each half being conserved and acting as a template for the formation of a new strand. Sense mutation: A mutation that changes a termination (stop) codon into one that codes for an amino acid. Such a mutation results in an elongated protein. Sense strand: A gene has two strands: the sense strand and the anti-sense strand. The Sense strand is, by definition, the same 'sense' as the mR A; that is it can be translated exactly as the mR A sequence can. Note however that when the RNA is transcribed from this sequence, the ANTI-SENSE strand is used as the template for RNA polymerization. After all, the RNA must base-pair with its template strand (see Figure 3), so the process of transcription produces the complement of the anti-sense strand. This introduces some confusion about terminology: Some people use the term coding strand and non-coding strand to refer to the sense and antisense strands, respectively. Unfortunately, many people interpret these terms in exactly the opposite way. I consider the terms coding strand and non-coding strand to be too ambiguous. Some people use the exact opposite definition for sense and anti-sense that I have given here. Be aware of the possibility of a discrepancy. Textbooks I have consulted generally agree with the nomenclature given herein, albeit some avoid defining these terms at all.

Sepal -- the outermost structures of a flower. More info? Septum -- partition which divides up a larger region into smaller ones, such as in the central body cavity of some anthozoa. Sequence database A computer-based collection of nucleic acid or amino acid sequences containing all published and some unpublished sequences. These can be searched to check for similarities with newly determined sequences. Examples are Genbank and Swissprot. Sequence hypothesis. Francis Crick's seminal concept that genetic information exists as a linear DNA code; DNA and protein sequence are colinear. Sequence Polymorphism - See POLYMORPHISM. Sequence: As a noun, the sequence of a DNA is a buzz word for the structure of a DNA molecule, in terms of the sequence of bases it contains. As a verb, "to sequence" is to determine the structure of a piece of DNA; i.e. the sequence of nucleotides it contains. Sequence-tagged site (STS). A unique (single-copy) DNA sequence used as a mapping landmark on a chromosome. Sequential Epitope - See LINEAR EPITOPE. Serological typing: Identification of MHC molecules expressed on cells using either naturally occurring antibodies in multiparous women or by alloantiserum raised in animals. Sex chromosome: heteromorphic chromosomes whose distribution in a zygote determines the sex of the organism. Sex: Formation of new organism containing genetic material from more than a single parent. Sexduction: the process whereby a fragment of genetic material from one bacterium is carried with the sex factor f to a second bacterium. Sex-influenced dominance: A dominant expression that depends on the sex of the individual. For example horns in sheep are dominant in males and recessive in females. Sex-influenced trait: a phenotype that is conditioned by the sex of the individual; a gene may be dominant in males and recessive in females, or vice versa; the trait may be expressed only to a lesser degree in one sex. Sex-limited - a type of autosomal inheritance in which the expression of a gene is seen in only one sex. Sex-limited trait: a phenotype expressed in only one sex, although it may be due to a sex-linked or autosomal gene. Sex-linkage - the linkage of genes on the sex chromosome. Sex-linked inheritance: a special inheritance pattern for genes located on the x chromosome; the trait in question may be observed only in heterogametic individuals, and much less frequently in homogametic individuals. Sexual dimorphism: The existence, within a species, of differences in morphology between the sexes. Examples are greater size in males of gorilla, baboon and elephant seals. Sexual reproduction - a type of reproduction in which two parents give rise to offspring that have unique combinations of genes inherited through the gametes of the two parents. Sexual reproduction involves meiosis and syngamy. # The process where two cells (gametes) fuse to form one hybrid, fertilized cell. See Asexual reproduction, Gamete, Hybrid. # Reproduction requiring the union of sex cells (gametes) which are themselves products of meiotic division. Each offspring has a unique genetic composition due to independent assortment of chromosomes during meiosis, recombination and union of gametes.

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Sexual selection: a theory that in certain species there occurs a struggle between males for mated and that characteristics enhancing the success of those bearing them would have value and be perpetuated irrespective of their general value in the struggle for existence. # Natural selection operating on factors that contribute to an organisms mating success. Described by Darwin as natural selection in relation to sex. Links to an essay and a lecture note on sexual selection. Sexually antagonistic: Having opposite effects in the two sexes. Shine-Dalgarno (S-D) sequence: An eight nucleotide consensus sequence 5 UAAGGAGG 3 found in bacterial mRNAs five to ten bases before the translation initiation codon (AUG). It is thought to be involved in initiation of translation by helping the mRNA bind to the ribosome (16S rRNA), thus it can be called the ribosomal binding site (see also Kozak sequence). In eukaryotic DNA, there is no such sequence. The 5 cap present on all eukaryotic mRNAs seems to be the first signal to start protein synthesis. Shoot -- usually, the above ground portion of a plant, bearing the leaves. Contrast with root. Shotgun Cloning Or Sequencing - Cloning of an entire genome or large piece of DNA in the form of randomly generated small fragments. The individual sequences obtained from the clones will be used to construct contigs. # The practice of randomly clipping a larger DNA fragment into various smaller pieces, cloning everything, and then studying the resulting individual clones to figure out what happened. For example, if one was studying a 50 kb gene, it "may" be a bit difficult to figure out the restriction map. By randomly breaking it into smaller fragments and mapping those, a master restriction map could be deduced. See also Shotgun sequencing. # A way of determining the sequence of a large DNA fragment which requires little brainpower but lots of late nights. The large fragment is shotgun cloned (see above), and then each of the resulting smaller clones ("subclones") is sequenced. By finding out where the subclones overlap, the sequence of the larger piece becomes apparent. Note that some of the regions will get sequenced several times just by chance. Shuttle Vector - A small plasmid capable of transfection into both prokaryotic and eukaryotic cells. Sibling species: Two species evolved from a common ancestor and are genetically distinct but morphologically similar. Side Chain - See AMINO ACID. Siderite -- also called ironstone, that is a concretion of iron carbonate. Common in the mazon creek fossil beds. Sigma Factor - Certain small ancillary proteins in bacteria that increase the binding affinity of RNA polymerase to a promoter. Different sigma factors recognize different promoter sequences. # a polypeptide subunit of the RNA polymerase of e. Coli; serves to recognize specific binding sites on DNA molecules for initiation of RNA transcription. Signal Peptidase - An enzyme present within the lumen of the endoplasmic reticulum which proteolytically cleaves a secreted protein at the site of a signal sequence. Signal Sequence - A hydrophobic amino acid sequence which directs a growing peptide chain to be secreted into the endoplasmic reticulum. #: A stretch of hydrophobic amino acids at the amino-terminal of a protein that guides protein translocation through cellular membranes such as lysosomal membrane. It helps the protein to pass through the membrane

via interaction with its receptor on the membrane and is usually cleaved off at the final destination by an endopeptidase. Sometimes used interchangeably with leader sequence. Signal transduction. The biochemical events that conduct the signal of a hormone or growth factor from the cell exterior, through the cell membrane, and into the cytoplasm. This involves a number of molecules, including receptors, proteins, and messengers. # A complex multistep pathway from the cell membrane through the cytoplasm to the nucleus involved in cell proliferation and differentiation. The components are growth factors, growth factor receptors, membrane and cytoplasmic tyrosine kinases, GTP-binding (G) proteins, nuclear binding proteins and transcription factors. Silencer These elements are very similar to enhancers except that they have the function of binding proteins and inhibiting transcription. # A DNA sequence which acts in the opposite direction of an enhancer to inhibit the transcription of a gene. Silent Mutation - A nucleotide substitution (never a single deletion or insertion) which does not alter the amino acid sequence of an encoded protein due to the degeneracy of the genetic code. Such mutations usually involve the third base (wobble position) of codons. # Base-pair substitution which alters a codon but does not result in altered phenotype due to the degeneracy of the genetic code (synonymous mutation). Silica -- amorphous silicon dioxide (glass). It is a structural component in many organisms, such as diatoms and horsetails. Silicification -- process whereby silica replaces the original material of a substance. For example, silicified wood. SI ES (short interspersed elements): An abundant intermediate DNA sequence in mammals about 300 bp long (see also LINES). Single cell studies: Recent developments in optical imaging, particularly quantitative fluorescence microscopy; ultra- small volume sampling and analysis; incorporation of optically useful probes, such as green fluorescent protein into cellular constituents; combinations of photobleaching and imaging; and optical approaches to determining the rates and equilibria of intracellular processes clearly indicate the enormous potential of in vivo single cell studies for our understanding of cell physiology, as well as the remaining substantial difficulties. Biologists need tools capable of analyzing the genomic and proteomic information of the living single cell. The quantitation, localization, and identification of proteins within the cell, as well as full characterization of intracellular interactions involving proteins in their structural, catalytic, and control roles, will be essential for development of a comprehensive and integrative view of cell physiology. Furthermore, development of highly specific drugs must ultimately involve screening against in vivo cellular processes. Thus, the envisioned technology development will enable the application of profoundly powerful combinatorial approaches to understanding and regulating the interior world of the cell, as well as characterizing the cell- physiological consequences of rare phenotypes - particularly those associated with disease. Single ucleotide Polymorphism (S P): A single nucleotide change in the DNA code. It is the most common type of stable genetic variation and usually bi-allelic. SNPs may be silent -no change in phenotype- (sSNP), may cause a change in phenotype (cSNP) or may be in a regulatory region (rSNP) with potential to change phenotype. Anonymous SNPs are the most common ones. These are in non-coding regions and used as genetic markers. On average, each 1 kb of human genome contains 2-10

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SNPs, i.e., one in every 100-500 nucleotides is polymorphic most frequently a C to T substitution (links to a lecture and SNP Consortium Website). Single-stranded binding protein: a protein that binds to the single-stranded dna generated when a helicase opens the double helix; this stabilizes the molecule and prevents reannealing or formation of intrastrand hydrogen bonds. Siphon -- opening in molluscs or in urochordates which draws water into the body cavity. In many molluscs, the siphon may be used to expel water forcibly, providing a means of propulsion. Siphonostele -- when a plant's vascular tissue develops as a central cylinder, it is said to have a siphonostele. See also protostele and eustele. Sister chromatid exchange: An exchange (crossing-over) of genetic material between the two (identical) chromatids of a chromosome in mitosis (mitotic recombination). Normally, genetic recombination takes place between homologous chromosomes in meiosis I. Sister chromatid exchange may be a sign of chromosomal instability but has no genetic consequences as long as the exchange is the result of an equal crossover. Sister group -- the two clades resulting from the splitting of a single lineage. Site-Directed Mutagenesis - The introduction of a mutation, usually a point mutation or an insertion, into a particular location in a cloned DNA fragment. This mutated fragment may be used to "knock out" a gene in the organism of interest by homologous recombination. # The process of introducing specific base-pair mutations into a gene. Site-Specific Recombination - Occurs between two specific but not necessarily homologous sequences. Usually catalyzed by enzymes not involved in general or homologous recombination. Skeleton -- support structure in animals, against which the force of muscles acts. Vertebrates have a skeleton of bone or cartilage; arthropods have one made of chitin; while many other invertebrates use a hydrostatic skeleton, which is merely an incompressible fluid-filled region of their body. Slot blot: Similar to a dot blot, but the analyte is put onto the membrane using a slot-shaped template. The template produces a consistently shaped spot, thus decreasing errors and improving the accuracy of the analysis. See Dot blot. Small nuclear R A (snR A). Short RNA transcripts of 100300 bp that associate with proteins to form small nuclear ribonucleoprotein particles (snRNPs), which participate in RNA processing. (See RNA.) # Small (90 to 300 nucleotides) RNA molecules that are not directly involved in protein synthesis but may have roles in RNA processing (splicing) and the cellular architecture. # Small nuclear RNA; forms complexes with proteins to form snRNPs; involved in RNA splicing, polyadenylation reactions, other unknown functions (probably). # "snerps", Small Nuclear RiboNucleoProtein particles, which are complexes between small nuclear RNAs and proteins, and which are involved in RNA splicing and polyadenylation reactions. Soil -- unconsolidated materials above bedrock. Solution hybridization: A method closely related to RNase protection (see "RNase protection assay"). Solution hybridization is designed to measure the levels of a specific mRNA species in a complex population of RNA. An excess of radioactive probe is allowed to hybridize to the RNA, then

single-strand specific nuclease is used to destroy the remaining unhybridized probe and RNA. The "protected" probe is separated from the degraded fragments, and the amount of radioactivity in it is proportional to the amount of mRNA in the sample which was capable of hybridization. This can be a very sensitive detection method. Somatic cell gene therapy. The repair or replacement of a defective gene within somatic tissue. (See Somatic cell.) Somatic cell. Any nongerm cell that composes the body of an organism and which possesses a set of multiploid chromosomes (diploid in most organisms). (See Gamete, Somatic cell gene therapy.) # Any cell in the body except gametes and their precursors. [DOE] Are the precursors stem cells? All body cells, except the reproductive cells. [NHGRI] Somatic mutation - a mutation in any cell except a sperm or an egg. ] Somatic recombination: Rearrangement of genes in cells other than germ cells which happens to generate the extreme diversity of T-cell receptors and immunoglobulins (see adaptive immunity). Somatotrophin. See Human growth hormone. Southern Blot - DNA is separated by electrophoresis (usually in agarose gels), then transferred to nitrocellulose paper or other suitable solid-phase matrix (e.g., nylon membrane), and denatured into single strands so that it can be hybridized with a specific probe. The Southern blot was developed by E.M. Southern, a molecular biologist in Edinburgh. orthern and western blots were given contrasting names to reflect the different target substances (RNA and proteins, respectively) that are subjected in these procedures to electrophoresis, blotting and subsequent detection with specific probes. # DNA blot taken from an electrophoresis gel. The original blot type named after its originator Ed Southern. # A technique for analyzing mixtures of DNA, whereby the presence and rough size of one particular fragment of DNA can be ascertained. See "Blotting". Named for its inventor, Dr E. M. Southern. # The binding of protein to a nucleic acid on a matrix similar to what is done for western, northern, and southern blots. This technique is used to identify DNA binding proteins and the recognition sites for these proteins. Southern blotting This technique is used to detect specific sequences within mixtures of DNA. DNA is size-fractionated by gel electrophoresis and then transferred by capillary action to nitrocellulose or another suitable synthetic membrane. Following blocking of nonspecific binding sites, the nitrocellulose replica of the original gel electrophoresis experiment is then allowed to hybridize with a cDNA or oligonucleotide probe representing the specific DNA sequence of interest. Should specific DNA be present on the blot, it will combine with the labeled probe and be detectable by autoradiography. By co-electrophoresing DNA fragments of known molecular weight, the size(s) of the hybridizing band(s) can then be determined. For gene rearrangement studies, Southern blotting is capable of detecting clonal populations that represent approximately 1% of the total cellular sample. # A procedure in which DNA restriction fragments are transferred from an agarose gel to a nitrocellulose filter, where the denatured DNA is then hybridized to a radioactive probe (blotting). (See Hybridization.) # This technique is designed to detect specific DNA-binding proteins. Like the Western blot, proteins are size-fractionated and transferred to nitrocellulose. The probe in this case, however, is a double-stranded labeled

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DNA that contains a putative protein-binding site. Should the DNA probe hybridize to a specific protein on the blot, that protein can be subsequently identified by autoradiography. This technique often suffers from nonspecificity, so that a number of critical controls must be included in the experiment for the results to be considered rigorous. Sp6 R A Polymerase - A bacteriophage R A polymerase which is commonly used to transcribe plasmid DNA into RNA. The plasmid must contain an SP6 promoter upstream of the relevant sequence. Specialist -- organism which has adopted a lifestyle specific to a particular set of conditions. Contrast with generalist. Speciation: It is now almost universally agreed that the prevailing process of speciation is geographical (allopatric) speciation. (There are also parapatric and sympatric speciation concepts.) According to biological species concept, however, species are defined as aggregation of populations that are reproductively isolated from one another. Link to a lecture on speciation. Species. A classification of related organisms that can freely interbreed. # A group of individuals which can successfully breed with each other to produce offspring which can still breed with each other. There are evolutionary, biological, and recognition species concepts. Specific bands are detected by hybridization. The filter membrane is incubated with radioactive probe, which hybridizes to some bands. After the filter is washed (to remove unused probe), an X-ray film exposed to the filter will show which bands have hybridized Sperm competition: Competition not for access to females but for fertilization of egg. Equivalent to pollen tube competition in plants and a type of sexual selection. See Birkheads book Promiscuity (2000) for a detailed study of sperm competition in nature. Spermatocyte: A male germ cell that undergoes meiosis and produces a haploid spermatid and subsequently a sperm. Spermatophyta (sperm plants; Gr. sperm=seed; phyton=plant): A major subdivision within the vascular plants division of the plant Kingdom characterized by reproduction by seeds. Sperm plants include angiosperms and gymnosperms. Spicule -- crystalline or mineral deposits found in sponges, sea cucumbers, or urochordates. They are structural components in many sponges, and may serve a protective function in other organisms. Spindle fibers: a collection of microtubules responsible for the movement of eukaryotic chromosomes during mitosis and meiosis. # a microtubule within a cell which shortens to pull separated chromatids to opposite ends of the cell during anaphase of mitosis and meiosis. Spiracle -- in insects and some other terrestrial arthropods, a small opening through which air is taken into the tracheae. Insects have several spiracles, arranged along the sides of the abdomen. Spliceosomes: Organelles in which the splicing and excision reactions that remove introns from precursor messenger RNA molecules occur. One component of a spliceosome is five small nuclear R A molecules (U1, U2, U4, U5, U6) that, working in conjunction with proteins, help to fold pieces of RNA into the right shapes and later splice them into the message. [MeSH, 1993] # the organelle in which the excision

and splicing reactions that remove introns from premessenger rnas occur. Splicing see RNA SPLICING The primary RNA transcript contains a number of sequences that are not part of the mature mRNA. These regions are called introns and are removed from the primary RNA transcript by a process termed splicing. A complex tertiary structure termed a lariat is formed and the intron sequence is eliminated bringing the coding sequences (exons) together. Specific sequences within the primary transcript dictate the sites of intron removal. # An event which takes place within the nucleus whereby introns are removed from the precursor mRNA and the exons are joined together as a post-transcriptional modification. Spongin -- proteinacous compound of which the spicules in demospongiae are composed. Spongocoel -- central body cavity of sponges. More info? Spontaneous reversion: the naturally occurring reverse of a mutation. Sporangiophore -- a stalk to which sporangia are attached. Sporangium -- a chamber inside of which spores are produced through meiosis. Spore - a single cell that is dispersed as a reproductive unit, or which encapsulates a cell during unfavorable environmental conditions. In organisms with an alternation of generations, the products of meiosis are spores. # in plants, a reproductive cell that is capable of developing into a multicellular adult without fusion with another cell; spores are usually formed as the products of meiosis. In land plants the spore is covered by a hard shell. # A form taken by certain microbes that enables them to exist in a dormant stage. It is an asexual reproductive cell. See Asexual reproduction, Dormant. # In plants with alternation of generations, small reproductive bodies capable of giving rise to a new offspring either immediately or after a period of dormancy. It can be produced asexually or sexually. It usually germinates without fusing with another cell. Sexual spores of plants are haploid cells produced by meiosis. Sporophyll -- any leaf which bears sporangia is called a sporophyll. Sporophyte - the diploid stage in the life cycle of an organism undergoing an alternation of generations. The sporophyte is multicellular and develops from a zygote. The mature sporophyte meiotically produces haploid spores that later generate the gametophyte generation. # The diploid (asexual) spore-producing generation in plants with alternation of generations. A sporophyta is typically formed by the union of sexual cells produced by the gametophyta. In higher plants, the sporophyte is the conspicuous plant. In lower plants (such as mosses), the gametophyte is the dominant generation. SSOP: Sequence-specific oligonucleotide probe. Together with PCR-SSP, commonly used to type classical MHC genes following amplification by PCR reaction (see also serological typing). SSP: Sequence-specific primer. PCR-SSP is a common method to type classical MHC genes. Stabilizing selection: Natural selection against extreme deviations from the average (like low and high birth weight). # The removal of those alleles that produce deviations from the average population phenotype by selection against all deviant individuals. Stable equilibrium - occurs when the allele frequencies within a population stay the same through many generations.

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Stable transfection: A form of transfection experiment designed to produce permanent lines of cultured cells with a new gene inserted into their genome. Usually this is done by linking the desired gene with a "selectable" gene, i.e. a gene which confers resistance to a toxin (like G418, aka Geneticin). Upon putting the toxin into the culture medium, only those cells which incorporate the resistance gene will survive, and essentially all of those will also have incorporated the experimenter's gene. Stamen -- part of a flower, the tip of which produces pollen and is called the anther. Starch -- a complex polymer of glucose, used by plants and green algae to store surplus sugar for later use. Start Codon - See INITIATION CODON. # a group of three adjacent ribonucleotides (aug) in an mrna that initiates polypeptide formation. Stasis -- a period of little or no discernible change in a lineage. Stationary phase. The plateau of the growth curve after log growth, during which cell number remains constant. New cells are produced at the same rate as older cells die. (See Growth phase.) Stem cells: Relatively undifferentiated cells of the same lineage (family type) that retain the ability to divide and cycle throughout postnatal life to provide cells that can become specialized and take the place of those that die or are lost. Stem group -- all the taxa in a clade preceding a major cladogenesis event. They are often difficult to recognize because they may not possess synapomorpies found in the crown group. # A feature of RNA secondary structure, in which two complementary, inverted sequences which are separated by a short-intervening sequence within a single strand of RNA base pair to form a '"stem" with a "loop" at one end. Similar to a hairpin, but these usually have very small loops and longer stems. Sticky End - The terminus of a DNA molecule which has either a 3' or 5' overhang, and which typically results from a cut by a restriction endonuclease. Such termini are capable of specific ligation reactions with other termini which have complementary overhangs. A sticky end can be "blunt ended" either by the removal of an overhang, or a "filling in" reaction which adds additional nucleotides complementary to the overhang (see BLUNT END). # Short section of singlestranded DNA produced at the end of a double-stranded DNA fragment produced by DNA digestion with certain restriction enzymes. The single- stranded section will base-pair and "stick" loosely to another sticky end produced by the same enzyme, facilitating ligation. # A protruding, single-stranded nucleotide sequence produced when a restriction endonuclease cleaves off center in its recognition sequence. # After digestion of a DNA with certain restriction enzymes, the ends left have one strand overhanging the other to form a short (typically 4 nt) single-stranded segment. This overhang will easily re-attach to other ends like it, and are thus known as "sticky ends". For example, the enzyme BamHI recognizes the sequence GGATCC, and clips after the first G in each strand: Stigma -- dense region of pigments found in many photosynthetic protists which is sensitive to light, and thus functions somewhat like a miniature eye. Stipe -- a scientific term for "stalk". Stipules -- paired appendages found at the base of the leaves of many flowering plants.

Stomata -- openings in the epidermis of a stem or leaf of a plant which permit gas exchange with the air. In general, all plants except liverworts have stomata in their sporophyte stage. Stop (termination) codon: Codons that signal the end of a growing polypeptide chain. These are UAA, UGA and UAG. # A codon (UAA, UAG, UGA) which terminates translation. See Termination codon. Stratum -- a layer of sedimentary rock; plural is strata. Streptavidin - A bacterial analog of egg white avidin. Streptophytes -- the clade consisting of the plants plus their closest relatives, the charophytes. Strike -- the direction or trend of a bedding plane or fault, as it intersects the horizontal. Stringency - The conditions employed for hybridization which determine the specificity of the annealing reaction between two single-stranded nucleic acid molecules. Increasingly stringent conditions may be reached by raising temperature or lowering ionic strength, resulting in greater specificity (but lower sensitivity) of the hybridization reaction. # Reaction conditions-notably temperature, salt, and pH--that dictate the annealing of single-stranded. # A term used to describe the conditions of hybridization. By varying the conditions (especially salt concentration and temperature) a given probe sequence may be allowed to hybridize only with its exact complement (high stringency), or with any somewhat related sequences (relaxed or low stringency). Increasing the temperature or decreasing the salt concentration will tend to increase the selectivity of a hybridization reaction, and thus will raise the stringency. Stringent plasmid. A plasmid that only replicates along with the main bacterial chromosome and is present as a single copy, or at most several copies, per cell. (See plasmid.) Strobilus -- a tightly clustered group of sporophylls arranged on a central stalk; commonly termed a "cone" or "flower". Structure-functionalism. The scientific tradition that stresses the relationship between a physical structure and its function, for example, the related disciplines of anatomy and physiology. STS. See Sequence-tagged site. Style -- the narrow stalk of the pistil, located above the ovary but below the stigma. Subcellular fractionation: Concentrating a sample by separating out certain compartments of the cell. Allows study of cellular compartments and can provide greater resolution and sensitivity. Subcloning. The process of tranferring a cloned DNA fragment from one vector to another. (See Cloning.) # If you have a cloned piece of DNA (say, inserted into a plasmid) and you need unlimited copies of only a part of it, you might "sub-clone" it. This involves starting with several million copies of the original plasmid, cutting with restriction enzymes, and purifying the desired fragment out of the mixture. That fragment can then be inserted into a new plasmid for replication. It has now been subcloned. Subduction -- the process of one plate descending beneath another. Substrate -- "supporting surface" on which an organism grows. The substrate may simply provide structural support, or may provide water and nutrients. A substrate may be inorganic, such as rock or soil, or it may be organic, such as wood. Subtractive library The purpose of generating a subtractive library is to enrich for cDNA that are expressed under one condition but are not expressed under a second condition. This facilitates screening for the cDNA of interest in that the

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complexity of the library is much reduced, requiring one to screen far fewer clones. At its extreme, investigators have used subtractive libraries to generate a very highly select group of clones (in the range of 100) and then have sequenced all of the resulting cDNA. The principle behind a subtractive library is the elimination of cDNA common to induced and control conditions. By eliminating such clones, only cDNA that are present under the induced conditions will remain in the library. Those techniques depend on the differential elimination of duplex mRNA/cDNA or cDNA/cDNA hybrids, which form between genes expressed under both conditions, leaving the single-stranded mRNA or cDNA of interest. Subunit vaccine. A vaccine composed of a purified antigenic determinant that is separated from the virulent organism. (See Vaccine, Enzyme.) Sugar -- any of several small carbohydrates, such as glucose, which are "sweet" to the taste. Sum rule: the rule that states that the probability of the occurrence of mutually exclusive events is the sum of the probabilities of the individual events. Superantigen: An antigen of a virus or bacteria which bind to non-polymorphic parts (outside of the antigen-binding cleft) of MHC class II molecules and interact with the Vb domain of the T-cell receptor. This way, they activate an entire subgroup of T cells (rather than a specific clone) expressing the appropriate Vb and this is followed by deletion of the activated T cells upon exposure to the superantigen. One superantigen can activate up to 20% of the helper T cell repertoire. The prototype bacterial superantigen is the staphylococcal enterotoxins. Supercoil - Double-stranded circular DNA which is twisted about itself. Commonly observed with plasmids and circular viral DNA genomes (such as that of hepatitis B virus). A nick in one strand of the plasmid may remove the twist, resulting in a relaxed, circular DNA molecule. A complete break in the DNA puts the plasmid in a linear form. Supercoils, relaxed circular DNA, and linear DNA all have different migration properties in agarose gels, even though they contain the same number of base pairs. Supercoiled plasmid. The predominant in vivo form of plasmid, in which the plasmid is coiled around histone-like proteins. Supporting proteins are stripped away during extraction from the bacterial cell, causing the plasmid molecule to supercoil around itself in vitro. (See Plasmid.) Supercoiled/supertwisted D A: A closed circular DNA molecule in which the DNA molecule is further twisted on itself to form a more compact molecule. Left-handed (negative) supercoiling leads to a loosening of the strands of the double helix (underwinding). Positive supercoiling is not seen in vivo. Supergene. A group of neighboring genes on a chromosome that tend to be inherited together and sometimes are functionally related. # a chromosomal segment protected from crossing over and so transmitted from generation to generation as if it were a single recon. Supernatant. The soluble liquid &action of a sample after centrifugation or precipitation of insoluble solids. # the fluid lying above a precipitate in a centrifuge following the centrifugation of a suspension. Swedberg unit: the rate at which a given solute molecule suspended in a less dense solvent sediments in a field of centrifugal force.

Symbiosis -- literally, "living together". Many cases of symbiosis are mutual, in which both organisms rely on each other for survival. Other types of symbiosis include parasitism, in which one organism benefits at its host's expense, and commensalisms, in which one partner benefits and the other is neither benefitted nor harmed. # The close association of two or more dissimilar organisms where both receive an advantage from the association. See Commensalism, Parasitism. Sympatric speciation: Speciation that occurs as a result of divergence of two populations occupying the same geographical area. It is due to reproductive isolation of subpopulations of a species without physical isolation. One well-established mechanism is polyploidy. Synangium -- a cluster of sporangia which have become fused in development. Synapomorphy -- a character which is derived, and because it is shared by the taxa under consideration, is used to infer common ancestry. Synapsis. The pairing of homologous chromosome pairs during prophase of the first meiotic division, when crossing over occurs. Synaptonemal complex: a proteinaceous complex that mediates synapsis during zygote stage and then disintegrates. Syncline -- a fold of rock layers that is convex downwards. Antonym of anticline. Syncytic -- see hexactinellida Syngamy - the process of union of two gametes; sometimes called fertilization. It encompasses both plasmogamy and karyogamy. # The union of the (haploid) nuclei of two gametes following fertilization to form a single (diploid) nucleus for the zygote. Syngeneic: Genetically identical (isogeneic) members of the same species like monozygotic twins. Synonymous (silent) base change: A change in the nucleotide sequence that does not cause an amino acid change. Nonsynonymous changes replace the amino acid and are called replacement change. Synteny: Refers to two genomes in which certain groups of genes are conserved in similar regional maps. Parts of mouse chromosome 17 and human chromosome 6 are syntenic. Synthetic oligonucleotide A single strand of DNA made by machine and used for priming DNA synthesis in sequencing or PCR, or as a probe. The maximum achievable length is around 50 bases, but longer molecules can be constructed using oligonucleotides as building blocks. Synthetic theory of evolution: Proposed to explain the transformation of a species by natural selection and for the splitting of a species into reproductively isolated subgroups. Systematics -- field of biology that deals with the diversity of life. Systematics is usually divided into the two areas of phylogenetics and taxonomy. # Classification of living things with regard to their evolutionary relationship. Link to a lecture on systematics.

T
T cells: A subgroup of T lymphocytes characterized by having T-cell receptor (TCR) complex and CD3 surface marker. T cells are roughly subdivided into CD4+ helper t cells and CD8+ cytotoxic and suppressor T cells. T7 R A Polymerase - A bacteriophage R A polymerase which is commonly used to transcribe plasmid DNA into RNA. The

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plasmid must contain a T7 promoter upstream of the relevant sequence. Tandem repeat: an aberration in which two identical chromosomal segments lie one behind the other. Tangled Bank Theory: An alternative theory to the Red Queen theory of sex and reproduction. This one states that sex and recombination function to diversify the progeny from each other to reduce competition among them (link to an abstract by Burt & Bell on the Tangled Bank Theory). Taphonomy -- the study of what happens to a fossil, from the time of its initial creation (e.g. The death of an organism or the imprint left by the movement of an organism) and the time that the fossil is discovered by a paleontologist. For example, shells or bones can be moved my running water, and later be compressed by overlying sediment. Taphonomy is often broken into two parts, biostratinomy and the study of diagenesis. taq Polymerase - A D A polymerase which is very stable at high temperatures, isolated from the thermophilic bacterium Thermus aquaticus. Very useful in PCR reactions which must cycle repetitively through high temperatures during the denaturation step. # A heat-stable DNA polymerase isolated from the bacterium Therrnus aquaticus, used in PCR. (See Polymerase.) # A DNA polymerase isolated from the bacterium Thermophilis aquaticus and which is very stable to high temperatures. It is used in PCR procedures and high temperature sequencing. TATA box (Goldberg-Hogness box): A short nucleotide sequence in the promoter 25 to 35 bp upstream to the transcription initiation (cap) site of eukaryotic genes to which RNA polymerase II binds. The consensus sequence is TATAA/TA. The TATA box binds the general transcription factor TFIID (see also CAAT box). # An adenine- and thymine-rich promoter sequence located 25-30 bp upstream of a gene, which is the binding site of RNA polymerase. # a segment from the startpoint of eukaryotic structural genes to which rna polymerase binds; the nucleotides most commonly found are TATAAAA. #: A sequence found in the promoter (part of the 5' flanking region) of many genes. Deletion of this site (the binding site of transcription factor TFIID) causes a marked reduction in transcription, and gives rise to heterogeneous transcription initiation sites. # Many genes have a sequence that includes this tetranucleotide close to the beginning of gene transcription. RNA polymerase binds to the sequence and begins transcription at the cap site, usually located approximately 30 nucleotides downstream. Taxon: Any group of organisms to which any rank of taxonomic name (classification) is applied. Plural: taxa. Taxonomic hierarchy: All taxa are classified within the following groups (starting from the most inclusive): kingdom, (division in plants), phylum, class, order, family, genus, species, subspecies (race). See taxonomy in BBC Education. Taxonomy -- the science of naming and classifying organisms. TCA cycle: The tricarboxylic acid cycle (also known as the Krebs cycle). A major metabolic pathway involved in aerobic cellular respiration (energy production) which takes place in the mitochondria of animal and plant cells. Pyruvic acid produced during glycolysis is converted to acetyl CoA which is then oxidized to CO2. The reducing power of the end products NADH and FADH2 are used in the synthesis of ATP by oxidative phosphorylation.

T-D A (transfer D A, tumor-D A). The transforming region of DNA in the Ti plasmid of Agrobacterium tumefaciens. Teleology: Teleology, from the Greek word telos (purpose), asserts that there is an element of purpose or design behind the workings of nature. Attributing any purposeful direction to evolutionary change would be called teleological. Teleost: Bony fishes with well-developed bone structure. Teleostei in Tree of Life. Telocentric: A chromosome with a terminal centromere (like chromosome 21 in humans). Telomerase A specialized DNA polymerase that protects the length of the terminal segment of a chromosome. Should the telomere become sufficiently shortened (by repeated rounds of cell division), the cell undergoes apoptosis. The holoenzyme contains both a polymerase and an RNA template; only the latter has been characterized, although the gene for the enzymatic activity has recently been cloned. #: A reverse transcriptase (hTERT) containing an RNA molecule (hTR) that functions as the template for the tandem repeat at telomere. It synthesizes telomere to maintain its length after each cell division. It is active in embryonic cells and gametes, inactive in differentiated somatic cells, and reactivated in malignant cells. Telomerase can add one base at a time to the telomeric end of a chromosome. This maintenance work is required for cells to escape from replicative senescence. Telomerase activity is the most general molecular marker for identification of human cancer. Telomere A repeating structure found at the end of chromosomes, serving to prevent recombination with freeended DNA. Telomeres of sufficient length are required to maintain genetic integrity, and they are maintained by telomerase. # A terminal section of a chromosome which has a specialized structure and which is involved in chromosomal replication and stability. Its length is believed to be a few hundred base pairs. Involved in aging and senescence. # The end of eukaryotic chromosome consisting of tandemly repeated sequences. Chromosomes lose about 100 bp from telomere every time the cell divides. The enzyme telomerase can add the lost bases. Telson -- the last segment of the abdomen in many arthropods. May be flat and paddlelike, buttonlike, or long and spiny, as in the horseshoe crabs. Temperate -- region in which the climate undergoes seasonal change in temperature and moisture. Temperate regions of the earth lie primarily between 30 and 60 degrees latitude in both hemispheres. # A nucleic acid strand, upon which a primer has annealed and a nascent RNA stand is being extended. #. An RNA or single-stranded DNA molecule upon which a complementary nucleotide strand is synthesized. Tentacles -- appendages which are flexible, because they have no rigid skeleton. Cnidarians and molluscs are two kinds of orgnaisms which may have tentacles. Tepal -- when the sepals and petals of a flower are indistinguishable, they are referred to as tepals. Tepals are common in many groups of monocots. Terminal deoxynucleotidyl This lymphocyte-specific enzyme normally transfers available (random) nucleotides to the 3' end of a growing nucleic acid chain. In recombinant DNA technology, these enzymes can be used to add a homogeneous tail to a piece of DNA, thereby allowing its specific recognition in PCR reactions or in cloning efforts. Termination codon. See STOP CODON Any of three mRNA sequences (UGA, UAG,UAA) that do not code for an amino

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acid and thus signal the end of protein synthesis. Also known as stop codon. (See Codon.) Terminator - A sequence downstream from the 3' end of an open reading frame that serves to halt transcription by the RNA polymerase. In bacteria these are commonly sequences that are palindromic and thus capable of forming hairpins. Sometimes termination requires the action of a protein, such as Rho factor in E. coli. Terminator region. A DNA sequence that signals the end of transcription. Terrestrial -- living on land, as opposed to marine or aquatic. Tertiary Structure - (also see PRIMARY and SECONDARY STRUCTURE) Refers to higher ordered structures conferred on proteins or nucleic acids by interactions between amino acid residues or nucleotides which are not closely positioned within the sequence (primary structure) of the molecule. Test -- hard shell of certain unicellular protists. Test cross: a mating between an individual of unknown genotype with an individual known to carry only the recessive alleles of the genes in question. Testicular feminization: An X-linked trait that causes XY individuals to develop into phenotypic females. A mutation causes loss of sensitivity to testosterone. Testis-determining factor: general term for the gene determining maleness in the human being. Tet resistance: See "Antibiotic resistance". Tetracycline. An antibiotic that interferes with protein synthesis in prokaryotes. Tetrad: four homologous chromatids (two in each chromosome of a bivalent) synapsed during first meiotic prophase and metaphase. Tetrapods: Vertebrate animals other than fishes (amphibians, reptiles, birds, and mammals). Tetrapolar: Used for the mating types of Basidiomycete to describe four distinct ways of interactions between haploid mycelia. These fungi have two mating type loci and there are four degrees of matching: fully compatible at both loci, fully incompatible at both loci, semicompatible (compatible only at locus 1), and semicompatible (compatible only at locus 2). In Ascomycete, the mating type locus is biallelic and mating types are bipolar. Thalloid -- plants which have no roots, stems, or leaves are called thalloid, such as liverworts and hornworts. Theca -- general term for any stiff outer covering of a unicellular protist, and usually made up of interlocking plates. Dinoflagellates and diatoms are examples of protists with thecae. Thermostabile polymerases The prototype polymerase, Taq, and newer versions such as Vent and Tth polymerase are derived from microorganisms that normally reside at high temperature. Consequently, their DNA polymerase enzymes are quite stable to heat denaturation, making them ideal enzymes for use in the polymerase chain reaction. Thorax -- in insects, the second body region, between the head and thorax. It is the region where the legs and wings are attached. Three-point cross: a series of crosses designed to determine the order of three, nonallelic, linked genes upon a single chromosome on the basis of their crossover behavior. Thymidine kinase (tk). An enzyme that allows a cell to utilize an alternate metabolic pathway for incorporating

thymidine into DNA. Used as a selectable marker to identify transfected eukaryotic cells. Ti (tumor-inducing) plasmid. A giant plasmid of Agrobacterium tumefaciens that is responsible for tumor formation in infected plants. Ti plasmids are used as vectors to introduce foreign DNA into plant cells. # A plasmid of Agrobacterium tumefaciens that is often used as a vector in genetic engineering of plants. During tumor induction, a transposon of the plasmid (T-DNA) integrates into the host chromosome. Tissue -- a group of cells with a specific function in the body of an organism. Lung tissue, vascular tissues, and muscle tissue are all kinds of tissues found in some animals. Tissues are usually composed of nearly identical cells, and are often organized into larger units called organs. Tissue Microdissection: A laboratory method that is used to procure specific cells or cell populations from a histology slide under direct microscopic visualization. The recovered cells can be studied with a variety of DNA, messenger RNA, and protein analysis methods, including new high- throughput gene expression and proteomics technologies. This approach is permitting investigators to comprehensively examine the molecular anatomy of cells in tissue sections for the first time. Tissue-specific expression: Gene function which is restricted to a particular tissue or cell type. For example, the glycoprotein hormone alpha subunit is produced only in certain cell types of the anterior pituitary and placenta, not in lungs or skin; thus expression of the glycoprotein hormone alpha-chain gene is said to be tissue-specific. Tissue specific expression is usually the result of an enhancer which is activated only in the proper cell type. T-Lymphocytes: Lymphocytes responsible for cell- mediated immunity. Two types have been identified - cytotoxic (TLYMPHOCYTES, CYTOTOXIC) and helper T-lymphocytes (T-LYMPHOCYTES, HELPER- INDUCER). They are formed when lymphocytes circulate through the thymus gland and differentiate to thymocytes. When exposed to an antigen, they divide rapidly and produce large numbers of new T cells sensitized to that antigen. Tm - The midpoint of the temperature range over which DNA is melted or denatured by heat; the temperature at which a duplex nucleic acid molecule is 50% melted into single strands, it is dependent upon the number and proportion of G-C base pairs as well as the ionic conditions. Often referred to as a measure of the thermal stability of a nucleic acid probe:target sequence hybrid. Topoisomerase A homodimeric chromosomal unwinding enzyme that introduces a double-stranded nick in DNA, which allows the unwinding necessary to permit DNA replication, followed by religation. Inhibition of topoisomerases leads to blockade of cell division, the target of several chemotherapeutic agents (e.g., etoposide). # A class of enzymes that convert DNA from one topological form to another. During DNA replication, they facilitate the untwisting of supertwisted DNA (see also gyrase and helicase). # an enzyme that can unwind the supercoiling of a dna helix. Totipotent <embryology> Capable of giving rise to all types of differentiated cell found in that organism. A single totipotent cell could, by division, reproduce the whole organism. [OMD]. Tracheae -- internal tubes through which air is taken for respiration. Vertebrates with lungs have a single trachea carrying air to the lungs, while insects and some other land-

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living arthropods have a complex network of tracheae carrying air from the spiracles to all parts of the body. Tracheophyte -- any member of the clade of plants possessing vascular tissue; a vascular plant. Trait. See Phenotype. Trans - As used in molecular biology, an interaction that involves two sites which are located on separate molecules. Trans capsidation. The partial of full coating of the nucleic acid of one virus with a coat protein of a differing virus. See Coat protein. Trans configuration: the situation in which the mutant allele of one gene and the wildtype allele of another gene are located on the same homologue; the two mutant alleles of the two different genes are located on different chromosomes of a homologous pair. Trans-acting factors Proteins that are involved in the transcriptional regulation of a gene of interest. Trans-acting gene: A gene acting on or co-operating with another gene on a different chromosome (see also cis-acting gene). Transcript - A newly made RNA molecule which has been copied from DNA. Transcription - the process by which messenger RNA is synthesized from a DNA template. # The copying of a DNA template into a single-stranded RNA molecule. The processes whereby the transcriptional activity of eukaryotic genes are regulated are complex, involve a variety of accessory transcriptional factors which interact with promoters and polymerases, and constitute one of the most important areas of biological research today. # Transcription is the act of generating a primary RNA molecule from the double-stranded DNA gene. Regulation of gene expression is predominantly at the level of regulating the initiation and elongation of transcription. The enzyme RNA polymerase is the key feature of the system, which acts to generate the RNA copy of the gene in combination with a number of important proteins.There is usually a fixed start to transcription and a fixed ending. Transcription factor: A protein which is involved in the transcription of genes. These usually bind to DNA as part of their function (but not necessarily). A transcription factor may be general (i.e. acting on many or all genes in all tissues), or tissue-specific (i.e. present only in a particular cell type, and activating the genes restricted to that cell type). Its activity may be constitutive, or may depend on the presence of some stimulus; for example, the glucocorticoid receptor is a transcription factor which is active only when glucocorticoids are present. # Specific proteins that bind to control elements of genes. Several families of transcription factors have been identified and include helix-loop-helix proteins, helix-turnhelix proteins, and leucine zipper proteins. Each protein includes several distinct domains such as activation and DNAbinding regions. # Proteins that are directly involved in regulation of transcription initiation by binding to the control elements and allowing RNA polymerase to act. There are ubiquitous transcription factors as well as cell and tissuespecific ones. Several families have been identified including helix-loop-helix proteins, helix-turn-helix proteins, leucine zipper proteins and zinc finger proteins. Transcription start site: The position in a gene where the mRNA synthesis starts. The first nucleotide transcribed is denoted +1.

Transcription terminator A short base sequence found at the 3' end of a gene which causes the RNA polymerase to stop transcription. Transcription unit: The region of DNA that extends between the promoter and the termination codon. Transcription/Translation Reaction - An in vitro series of reactions, involving the synthesis (transcription) of an mRNA from a plasmid (usually with T7 or SP6 R A polymerase), followed by use of the mRNA to program translation in a cellfree system such as a rabbit reticulocyte lysate. The polypeptide product of translation in usually labelled with [35S]-methionine, and examined in an SDS-PAGE gel with or without prior immunoprecipitation. This series of reactions permits the synthesis of a polypeptide from DNA in vitro. Transcriptional regulation Gene regulation is determined by the rate of transcriptional initiation. This usually results from alteration in the level of activity of trans-acting proteins, which, in turn, are regulated either by the amount of the transcriptionally active protein or by their state of activation. Transcriptional Start Site - The nucleotide of a gene or cistron at which transcription (RNA synthesis) starts; the most common triplet at which transcription begins in E. coli is CAT. Primer extension identifies the transcriptional start site. Transducing phage. See Transduction. Transduction -- viral transfer of dna to new host. # The transfer of DNA sequences from one bacterium to another via lysogenic infection by a bacteriophage (transducing phage). # the transfer of bacterial genetic material from one bacterium to another using a phage as a vector. #: Transfer of genes from one bacterium to another by means of a bacteriophage. Transfection - The process of introducing foreign DNA (or RNA) into a host organism, usually a eukaryotic cell. # A general term to describe the introduction of recombinant or vector DNA into host cells. # Once the expression vector has been assembled, it must be inserted into the host of interest. Several methods are available for such transfections and include calcium/phosphate/DNA complexes, DEAE Dextran, electroporation, liposome, and retrovirus-mediated gene transfer. # The uptake and expression of a foreign DNA sequence by cultured eukaryotic cells. # A method by which experimental DNA may be put into a cultured mammalian cell. Such experiments are usually performed using cloned DNA containing coding sequences and control regions (promoters, etc) in order to test whether the DNA will be expressed. Since the cloned DNA may have been extensively modified (for example, protein binding sites on the promoter may have been altered or removed), this procedure is often used to test whether a particular modification affects the function of a gene. # Addition of foreign DNA into a eukaryotic cell by exposing them to naked DNA (i.e., not in a bacteriophage as in transduction). In bacterial genetics, it is also called transformation. Transfer D A. See T-DNA. Transfer R A (tR A). See tRNA. Transformant. In prokaryotes, a cell that has been genetically altered through the uptake of foreign DNA. In higher eukaryotes, a cultured cell that has acquired a malignant phenotype.(See Transformation.) Transformation - Multiple meanings. With respect to cloning of DNA, refers to the transformation of bacteria (usually to specific antibiotic resistance) due to the uptake of foreign DNA. With respect to eukaryotic cells, usually means conversion to

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less-restrained or unrestrained growth. # In prokaryotes, the natural or induced uptake and expression of a foreign DNA sequence--typically a recombinant plasmid in experimental systems. In higher eukaryotes, the conversion of cultured cells to a malignant phenotype--typically through infection by a tumor virus or transfection with an oncogene. (See Transformant, Transformation efficiency.) # In bacterial transformation, it means the transfer of genes from one bacterium to another in the forms of soluble fragments of DNA; in malignant transformation, it means conversion of normal animal cell state to unregulated growth. # the phenomenon by which genes are transmitted from one bacterial strain to another in the form of soluble fragments of dna that may originate from live or dead cells; once inside, a fragment usually replaces, by recombination, a short section of the dna of the receptor cell that contains a zone of homology. # Usually refers to passive uptake of DNA by cells, although in nature some bacterial species have a specific active uptake system. Transformation is normally used to introduce plasmids into bacterial cells, but the process is increasingly inefficient with increasing size of plasmid. E. coli cells must be made competent before transformation can be carried out. Transformation (with respect to bacteria): The process by which a bacteria acquires a plasmid and becomes antibiotic resistant. This term most commonly refers to a bench procedure performed by the investigator which introduces experimental plasmids into bacteria. Transformation (with respect to cultured cells): A change in cell morphology and behavior which is generally related to carcinogenesis. Transformed cells tend to exhibit characteristics known collectively as the "transformed phenotype" (rounded cell bodies, reduced attachment dependence, increased growth rate, loss of contact inhibition, etc). There are different "degrees" of transformation, and cells may exhibit only a subset of these characteristics. Not well understood, the process of transformation is the subject of intense research. Transformation efficiency. The number of bacterial cells that uptake and express plasmid DNA divided by the mass of plasmid used (in transformants/microgram). (See Transformation.) Transforming oncogene. A gene that upon transfection converts a previously immortalized cell to the malignant phenotype. (See Oncogene.) Transgene See Transgenic. A foreign gene which has been introduced into the germ line of an animal species. Transgenic - An animal (usually a mouse) or plant into which a foreign gene has been introduced in the germ line. An example: transgenic mice expressing the human receptor for poliovirus are susceptible to human polioviruses. Transgenic animal. Genetically enginnered animal or offspring of genetically engineered animals. The transgenic animal usually contains material from at lease one unrelated organism, such as from a virus, plant, or other animal. See Transgenic. # By introducing an intact or manipulated gene into the germline of mice, the effects of promoter expression in specific cell lineages can be investigated. In contrast to highly artificial in vitro studies using reporter gene analysis, such transgenic animals provide an important in vivo model of gene function. The methods for production of transgenic mice have been extensively reviewed and are based on the microinjection of linear DNA into the pronucleus of a

fertilized egg. Several types of experiments can be performed. First, the effect of aberrant expression of a gene can be investigated, as was recently performed by expressing GM-CSF in a wide variety of tissues. Second, the necessary elements for tissue- and developmental level-specific expression of a gene can be studied, as has been performed for the -globin locus. Third, the tissue distribution of a specific gene can be determined by engineering a marker gene adjacent to a specific promoter. A specific example of this strategy employs a suicide gene, the herpes virus thymidine kinase (TK). When animals carrying such genes are exposed to gancyclovir, cells expressing the promoter of interest will express TK, be killed, and be readily detected. Transgenic mouse: A mouse which carries experimentally introduced DNA. The procedure by which one makes a transgenic mouse involves the injection of DNA into a fertilized embryo at the pro-nuclear stage. The DNA is generally cloned, and may be experimentally altered. It will become incorporated into the genome of the embryo. That embryo is implanted into a foster mother, who gives birth to an animal carrying the new gene. Various experiments are then carried out to test the functionality of the inserted DNA. Transgenic plant. Genetically engineered plant or offspring of genetically engineered plants. The transgenic plant usually contains material from at least one unrelated organisms, such as from a virus, animal, or other plant. See Transgenic. Transgenic Refers to an organism which carries a stable copy of a gene originating from another species introduced by DNA technology. # An organism in which a foreign DNA gene (a transgene) is incorporated into its genome early in development. The transgene is present in both somatic and germ cells, is expressed in one or more tissues, and is inherited by offspring in a Mendelian fashion. See Transgenic animal, Transgenic plant. Transient transfection: When DNA is transfected into cultured cells, it is able to stay in those cells for about 2-3 days, but then will be lost (unless steps are taken to ensure that it is retained see Stable transfection). During those 2-3 days, the DNA is functional, and any functional genes it contains will be expressed. Investigators take advantage of this transient expression period to test gene function. Transition - A nucleotide substitution in which one pyrimidine is replaced by the other pyrimidine, or one purine replaced by the other purine (e.g., A is changed to G, or C is changed to T) (contrast with TRANSVERSION) .# A nucleotide substitution between two purine nucleotides (A and G) or between pyrimidines (C and T/U) in DNA or RNA. Transition-type substitution is more common than transversion. # state intermediate. In a chemical reaction, an unstable and highenergy configuration assumed by reactants on the way to making products. Enzymes are thought to bind and stabilize the transition state, thus lowering the energy of activation needed to drive the reaction to completion. Translation - the process in which the information present in messenger RNA is used in the synthesis of a polypeptide (using transfer RNA) # The process whereby mR A directs the synthesis of a protein molecule; carried out by the ribosome in association with a host of translation initiation, elongation and termination factors. Eukaryotic genes may be regulated at the level of translation, as well as the level of transcription. # The process of converting the genetic information of an mRNA on ribosomes into a polypeptide. Transfer RNA molecules carry the

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appropriate amino acids to the ribosome, where they are joined by peptide bonds. # the formation of a protein directed by a specific messenger RNA molecule. # The process of converting the RNA sequence into the linear sequence of amino acids in a protein product. Translation start site contains a codon (AUG) for methionine but not all proteins start with a methionine as most of the time it is cleaved off posttranslationally. # The process of decoding a strand of mRNA, thereby producing a protein based on the code. This process requires ribosomes (which are composed of rRNA along with various proteins) to perform the synthesis, and tRNA to bring in the amino acids. Sometimes, however, people speak of "translating" the DNA or RNA when they are merely reading the nucleotide sequence and predicting from it the sequence of the encoded protein. This might be more accurately termed "conceptual translation". Translocation - a chromosomal mutation involving the detachment of a chromosome segment and its reattachment on a different chromosome. # The process by which a newly synthesized protein is directed toward a specific cellular compartment (i.e, the nucleus, the endoplasmic reticulum). # The movement or reciprocal exchange of large-chromosomal segments, typically between two different chromosomes. # a chromosome aberration which results in a change in position of a chromosomal segment within the genome, but does not change the total number of genes present. # Transfer of chromosomal material between chromosomes (usually reciprocal). Transposable element Section of DNA which can copy itself and insert the copy into another position in the chromosome or another chromosome. Free transposons are not found; they spread via transposition into mobile DNA molecules such as plasmids. Bacterial transposonsmay carry, in addition to genes encoding enzymes needed for transposition, genes for antibiotic resistance or other functions. Transposable genetic element. See Transposon. Transposase: An enzyme that catalyzes the insertion of a transposon. Transposition - The movement of DNA from one location to another location on the same molecule, or a different molecule within a cell. Transposition. The movement of a DNA segment within the genome of an organism. Transposon - A transposable genetic element; certain sequence elements which are capable of moving from one site to another in a DNA molecule without any requirement for sequence relatedness at the donor and acceptor sites. Many transposons carry antibiotic resistance determinants and have insertion sequences at both ends, and thus have two sets of inverted repeats. # (transposable, or movable genetic element). A relatively small DNA segment that has the ability to move from one chromosomal position to another. #: A long mobile DNA element that moves in the genome by a mechanism involving DNA synthesis and transposition. Transspecies evolution: The favored type of evolution of the MHC allelic diversity. The age of an allele or an allelic lineage is greater than the species. Therefore, common allelic lineages have been inherited from a common ancestor and species-specific mutational diversification occurred within these lineages. For example, no single MHC class I allele is shared between humans and chimpanzees, but numerous similarities in lineage, polymorphic motifs and individual

substitutions can be observed. One consequence is that certain alleles will be more similar to their correspondent alleles in another species than to the other alleles of the same locus in the same species. The long-term persistence of families of MHC alleles whose origins predate speciation events is called transspecies evolution. Transversion - A nucleotide substitution in which a purine replaces a pyrimidine, or vice versa (e.g., A is changed to T, or T is changed to G) (see TRANSITION) # A mutation caused by the substitution of a purine (A and G) for a pyrimidine (C and T/U) or vice versa in DNA or RNA (see also transition). Tree any tall plant, including many conifers and flowering plants, as well as extinct lycophytes and sphenophytes. # tall plant with a central trunk. The term does not imply anything about relationships, but is a growth pattern that has evolved several times in plants. Trichocyst -- organelle in ciliates and dinoflagellates which releases long filamentous proteins when the cell is disturbed. Used as a defense against would-be predators. Triplet - A three-nucleotide sequence; a codon. Triplet repeat: In this situation, a triplet of nucleotides increases in number within a gene. A mutation especially occurring in central nervous system disorders is the increased number of triplets repeats. Examples include myotonic dystrophy, Huntingtons disease, Friedreichs ataxia and fragile X syndrome. Also in polycystic ovary syndrome, androgen receptor gene has increased number of CAG repeats (Hickey et al, 2002). Expansion may be greater depending on the transmitting parent (eg, the mother in myotonic dystrophy, the father in Huntingtons disease); thus, a parent-of-origin effect and genetic anticipation can be observed. Increased number of repeats of a triplet may trigger methylation of the gene that causes the disease (see Mitas M, 1997 for a review). Trisomic - having three copies of one chromosome instead of two. # a diploid organism that possesses one extra copy of a homologous pair of chromosomes. tR A (transfer R A). - Small, tightly folded RNA molecules which act to bring specific amino acids into translationally active ribosomes in a fashion which is dependent upon the mR A sequence. One end of the tRNA molecule recognizes the nucleotide triplet which is the codon of the mRNA, while the other end (when activated) is covalently linked to the relevant amino acid. #The class of small RNA molecules that transfer amino acids to the ribosome during protein synthesis. See Transfer RNA. # "transfer RNA"; one of a class of rather small RNAs used by the cell to carry amino acids to the enzyme complex (the ribosome) which builds proteins, using an mRNA as a guide. Fairly abundant. # transfer rna; an rna molecule that transfers an amino acid to a growing polypeptide chain during translation. Tropical -- region in which the climate undergoes little seasonal change in either temperature or rainfall. Tropical regions of the earth lie primarily between 30 degrees north and south of the equator. Trypsin. A proteolytic enzyme that hydrolyzes peptide bonds on the carboxyl side of the amino acids arginine and lysine. Tube feet -- extensions of the water-vascular system of echinoderms, protruding from the body and often ending in suckers. May be used for locomotion and/or for maintaining a tight grip on prey or on the bottom. Tuber -- an underground stem which has been modified for storage of nutrients, such as a potato.

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Tubercle -- any small rounded protrusion. In pycnogonids and some cheliceramorph arthropods, the central eyes are carried on a tubercle. Tumor D A. See T-DNA. Tumor suppressor: A gene that inhibits progression towards neoplastic transformation. The best-known examples of tumor suppressors are the proteins p53 and Rb. Tumor virus. A virus capable of transforming a cell to a malignant phenotype. (See Virus.) Tumor-inducing plasmid. See Ti plasmid Turgor pressure -- force exerted outward on a cell wall by the water contained in the cell. This force gives the plant rigidity, and may help to keep it erect. More info?

strands and thus oriented in opposite directions. Upstream or downstream is only used on conjunction with a given gene. Upwelling -- the raising of benthic nutrients to the surface waters. This occurs in regions where the flow of water brings currents of differing temperatures together, and increases productivity of the ecosystem. Ustilago: A genus in Basidiomycetes Phylum of the Fungal Kingdom. It represents the smut fungi that are well known for their highly polymorphic mating types.

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Vaccine. A preparation of dead or weakened pathogen, or of derived antigenic determinants, that is used to induce formation of antibodies or immunity against the pathogen. (See Polyvalent vaccine, Subunit vaccine.) Vaccinia. The cowpox virus used to vaccinate against smallpox and, experimentally, as a carrier of genes for antigenic determinants cloned from other disease organisms. Vacuole -- membrane-bound fluid-filled space within a cell. In most plant cells, there is a single large vacuole filling most of the cell's volume. Some bacterial cells contain gas vacuoles. Van Baers Rule: The general features of a large group of animals appear earlier in the embryo than the special features. Variable expression: A variation in phenotype between affected members of the same family (i.e. individuals carrying identical mutations). It occurs in many dominant conditions and may be associated with reduced penetrance [see also penetrance]. Variable surface glycoprotein (VSG). One of a battery of antigenic determinants expressed by a microorganism to elude immune detection. Variant: Although commonly used to mean allele, mutant or to denote any genetic polymorphism, its precise use should be reserved for genetic markers that occur in less than 1% frequency in the population (hence cannot be called polymorphism). Variation. Differences in the frequency of genes and traits among individual organisms within a population. Vascular -- refers to a network of tubes which distribute nutrients and remove wates from the tissues of the body. Large multicellular animals must rely on a vascular system to keep their cells nourished and alive. # refers to the xylem and phloem tissues, which conduct water and nutrients through the plant body. Vector - A plasmid, cosmid, bacteriophage, or virus which carried foreign nucleic acid into a host organism. # Generally a carrier nucleic acid molecule which allows transfer of inserted (recombinant) DNA into a host cell. Normally refers to molecules such as plasmids and bacteriophages which replicate so that they are maintained in the host cell population. Vector replication which is independent of the host cell DNA replication may allow amplification of the vector to produce large numbers of copies (as in cloning). # An autonomously replicating DNA molecule into which foreign DNA fragments are inserted and then propagated in a host cell. Also living carriers of genetic material (such as pollen) from plant to plant, such as insects. # A plasmid, phage, or cosmid into which foreign DNA may be inserted for cloning. # The DNA "vehicle" used to carry experimental DNA and to clone it. The vector provides all sequences essential for replicating the test DNA. Typical vectors include plasmids, cosmids, phages and YACs.

U
Ubiquitin: A small protein that becomes covalently linked to a protein targeted for degradation. Unconformity -- any interruption of the continuity of a depositional sequence. Underdominance: Also called heterozygous disadvantage. This unusual selection process occurs when heterozygotes are less fit than either homozygote. This situation is likely to arise when two adjacent populations are isolated and become homozygous for different alleles, and then come into secondary contact at the borders of their ranges. This is the opposite of overdominance. Undulipodium -- another term for a eukaryotic flagellum. Uniparental disomy: Inheritance of both homologues of a chromosome from one parent, with loss of the corresponding homologue from the other parent. Uniramious -- among arthropods, uniramous refers to appendages that have only one branch. Insects, centipedes and millipedes, and their relatives are uniramous arthropods; landliving chelicerates such as scorpions, spiders,and mites are also uniramous but probably descended from ancestors with biramous appendages. Contrast with biramous. Untranslated R A - See NONTRANSLATED RNA. Upstream - The region extending in a 5' direction from a gene # Identifies sequences located in a direction opposite to that of expression; for example, the bacterial promoter is upstream of the initiation codon. In an mRNA molecule, upstream means toward the 5' end of the molecule. Occasionally used to refer to a region of a polypeptide chain which is located toward the amino terminus of the molecule. # Sequences located to the opposite direction to transcription (which runs from 5 to 3 on the sense strand of the DNA). A nucleotide 25 bp upstream to the first transcribed nucleotide is at position -25. Upstream activator sequence: A binding site for transcription factors, generally part of a promoter region. A UAS may be found upstream of the TATA sequence (if there is one), and its function is (like an enhancer) to increase transcription. Unlike an enhancer, it can not be positioned just anywhere or in any orientation. Upstream/Downstream: In an RNA, anything towards the 5' end of a reference point is "upstream" of that point. This orientation reflects the direction of both the synthesis of mRNA, and its translation - from the 5' end to the 3' end. In DNA, the situation is a bit more complicated. In the vicinity of a gene (or in a cDNA), the DNA has two strands, but one strand is virtually a duplicate of the RNA, so it's 5' and 3' ends determine upstream and downstream, respectively. NOTE that in genomic DNA, two adjacent genes may be on different

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Vegetative growth -- growth of a plant by division of cells, without sexual reproduction. Venation -- the arrangement and pattern of veins in a leaf. Vertebra -- a component of the vertebral column, or backbone, found in vertebrates. Vertebrates: A subphylum in the Phylum Chordata of the Kingdom Animalia. All members have a notochord and a cranium (skull). Includes the Classes: Fishes, Amphibians, Reptiles, Birds, and Mammals (monotremes, marsupials, placentals). Link to the vertebrates page in the tree of life. Vicariance -- speciation which occurs as a result of the separation and subsequent isolation of portions of an orginal population. Viral oncogene. A viral gene that contributes to malignancies in vertebrate hosts.(See Oncogene.) Viral transduction vectors Retroviral vectors are based on murine retroviruses. They can carry 6 to 7 kb of foreign DNA (promoter + cDNA) but suffer from the drawbacks of requiring the development of high titer packaging lines, requiring that target cells be dividing, and are subject to host cell down-modulation. Adenoviral vectors can be produced at high levels and do not require a dividing target cell, but they do not normally integrate, resulting in only transient expression. Adeno-associated viral vectors are defective parvoviruses that integrate into a non-dividing host cell at a specific location (19q). Disadvantages are genetic instability, small range of insert size (24.5 kb), and thus far, only transient expression. Viral-derived kinases These enzymes are utilized in recombinant DNA technology to transfer phosphate groups (either unlabeled or 32P-labeled) to oligonucleotides or DNA fragments. The most commonly used kinase is T4 polynucleotide kinase. Viroid. A plant pathogen that consists of a naked RNA molecule of approximately 250-350 nucleotides, whose extensive base pairing results in a nearly correct double helix. (See Satellite RNA.) # A disease-causing agent consisting of only a single-stranded, short (270 to 380 nucleotides) RNA molecule. Virulence. The degree of ability of an organism to cause disease. Virulent: possessing the ability to produce disease. Virus. An infectious particle composed of a protein capsule and a nucleic acid core, which is dependent on a host organism for replication. A double-stranded DNA copy of an RNA virus genome that is integrated into the host chromosome during lysogenic infection. (See Coat protein, DNA, Genome, Host, Nucleic acid, RNA, Tumor virus.) # An entity that is capable of reproducing only by infecting a bacterial or eukaryotic cell. Viruses are incapable of autonomous replication and have to use a host cells translational system. They consist of a nucleic acid molecule and protein coat. The genetic material of a virus may be DNA or RNA. If it is RNA, it will have to be converted to DNA first by the reverse transcriptase enzyme encoded by the viral nucleic acid. These viruses are called retrovirus. V TR Variable number tandem repeat. A type of DNA sequence found in eukaryotic genomes, in which a short sequence is repeated. The number of repeats varies between individuals and is used as a basis for genetic identification. Volcanic -- applies to igneous rocks that cool on the surface of the earth, including beneath water; typically with small

crystals due to the rapidity of cooling. Synonym of extrusive. Antonym of plutonic. VSG. See Variable surface glycoprotein.

W
W, Z chromosomes: Sex chromosomes in species (like snakes, birds, moths) where the female is the heterogametic sex (WZ). Wahlund effect: The finding of excess homozygosity in a large sample of population consisted of several subpopulations. It is due to differences in gene frequencies in the subpopulations and purely a mathematical complication. Link to lectures on Wahlund effect (1), (2) and a simulation. Waring blender: an electric kitchen appliance used to homogenize mixtures, but used in the laboratory to generate the shearing forces required to detach conjugating bacteria, to strip bacteriophages from host cells, to homogenize tissue samples, etc. Weed. An undesirable plant. Weediness. Unwanted effects of a plant. Weismanns hypothesis: Evolutionary function of sex is to provide variation for natural selection to act on (link to an abstract of a review by Burt discussing Weismanns hypothesis). Western Blot - Proteins are separated by SDS-PAGE, then electrophoretically transferred to a solid-phase matrix such as nitrocellulose, then probed with a labelled antibody (or a series of antibodies) # Protein blot taken from an electrophoresis gel. Normally probed with a specific antibody. # A technique for analyzing mixtures of proteins to show the presence, size and abundance of one particular type of protein. Similar to Southern or Northern blotting (see "Blotting"), except that (1) a protein mixture is electrophoresed in an acrylamide gel, and (2) the "probe" is an antibody which recognizes the protein of interest, followed by a radioactive secondary probe (such as 125I-protein A). Western blotting This technique is designed to detect specific protein present in a heterogenous sample. Proteins are denatured and size-fractionated by polyacrylamide gel electrophoresis, transferred to nitrocellulose or other synthetic membranes, and then probed with an antibody to the protein of interest. The immune complexes present on the blot are then detected using a labeled second antibody (for example, a 125I-labeled or biotinylated goat anti-rabbit IgG). As the original gel electrophoresis was done under denaturing and reducing conditions, the precise size of the target protein can be determined. Whorl -- an arrangement of appendages, such as branches or leaves, such that all are equally spaced around the stem at the same point, much like the spokes of a wheel or the ribs of an umbrella. Wild type. An organism as found in nature; the organism before it is genetically engineered. # The customary phenotype or standard for comparison. Deviants from this type are said to be mutant. # The most common allele (or sometimes phenotype) in a population. # The native or predominant genetic constitution before mutations, usually referring to the genetic consitution normally existing in nature. Wobble hypothesis: Hypothesis to explain how one tRNA can recognize two codons. The third base in the anticodon can pair with more than one bases. This is due to the degeneracy of the genetic code which results in more than one triplet codes for some amino acids.

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Wobble Position - The third base position within a codon, which can often (but not always) be altered to another nucleotide without changing the encoded amino acid (see DEGENERACY). Wobble theory: a hypothesis developed to explain how one trna may recognize two codons; the third base in the anticodon may pair with a variety of bases occupying the third position of a codon. Wood -- a secondary tissue found in seed plants which consists largely of xylem tissue.

X
Xenopus: An amphibian (frog) who shared a common ancestor with mammals about 350 million years ago. The oldest species in which all three regions of the MHC are linked. Its eggs are very large and have front-to-back orientation even before they are fertilized. See Xenopus website. X-linked disease: A genetic disease caused by a mutation on the X chromosome. In X-linked recessive conditions, a normal female "carrier" passes on the mutated X chromosome to an affected son. X-linked methylation patterns Several loci present on the X chromosome become highly methylated when inactive but remain unmethylated on the active X chromosome (Lyon hypothesis). Should a polymorphic site for a methylationsensitive restriction endonuclease exist at such an X-linked locus, one can distinguish between the active and inactive X chromosome by the pattern of restriction endonuclease digestion of that gene. However, in order to be widely useful for determining clonality of hematopoietic cells, the allelic frequency must be close to equality. Several Xlinked genes meet these criteria and include phosphoglycerate kinase (PGK), hypoxanthine phosphoribosyltransferase (HPRT), the human androgen receptor gene (HUMARA), and the hyper-variable DXS255 locus. Both Southern blotting and PCR methods can be applied to this type of analysis. X-ray crystallography. The diffraction pattern of X-rays passing through a pure crystal of a substance. Xylem -- water-conducting tissue of vascular plants.

Yeast Artificial Chromosomes YACS: Chromosomes in which fragments of exogenous DNA ranging in length up to several hundred kilobase pairs have been cloned into yeast through ligation to vector sequences. These artificial chromosomes are used extensively in molecular biology for the construction of comprehensive genomic libraries of higher organisms. [MeSH, 2002] Yeast: The genus Saccharomycetes of the unicellular fungi. See Yeast website. Y-junction: the point at which a dna molecule is being replicated; the two template strands separate, forming the arms, and the unreplicated double-stranded dna forms the base of the y.

Z
Z-D A. A region of DNA that is "flipped" into a lefthanded helix, characterized by alternating purines and pyrimidines, and which may be the target of a DNA-binding protein. Zebrafish: A model organism (Danio rerio) to study vertebrate biology, physiology and human disease. Its high fecundity and short generation time make it useful for genetic studies as well. Another useful feature is that their fry are transparent. Hundreds of mutants resembling human diseases have been identified. Link to Zebrafish website. See also Fugu. Zinc finger domain proteins The presence of conserved histidine and cysteine residues allows chelation of a zinc atom and results in the formation of a loop structure called the zinc finger domain. This feature is present in a large family of transcriptionally active proteins such as the steroid hormone receptors. Zinc finger protein: A DNA-binding domain of a protein that has a characteristic pattern of cysteine and histidine residues that complex with zinc ions. This motif occurs in several types of eukaryotic transcription factors. Zinc finger: A protein structural motif common in DNA binding proteins. Four Cys residues are found for each "finger" and one finger can bind a molecule of zinc. A typical configuration is: CysXxxXxxCys--(intervening 12 or so aa's) CysXxxXxxCys. Zooplankton: tiny, free-floating organisms in aquatic systems. Unlike phytoplankton, zooplankton cannot produce their own food, and so are consumers. Zooxanthellae: symbiotic dinoflagellates in the genus symbiodinium that live in the tissues of a number of marine invertebrates and protists, notably in many foraminiferans, cnidarians, and some mollusks. Zygote: the product of gamete fusion. In organisms with a haploid life cycle, the zygote immediately undergoes meiosis, but in organisms with a multicellular diploid stage, the zygote is merely the first stage in the diploid portion of the life cycle. # A cell formed by the fusion of sperm and egg. It develops to become an embryo. Zygotic selection: the forces acting to cause differential mortality of an organism at any stage (other than gametes) in its life cycle.

Y
YAC (yeast artificial chromosome) A yeast artificial chromosome (YAC) utilizes centromeric and telomeric elements from yeast chromosomes to construct genetic elements that can be propagated in yeast and transferred into mammalian cells. Such vehicles allow the introduction of up to 200 kb or more of genetic material into the host cells. YACs are now being used to study the physiologic regulation of large genetic loci such as the -globin region of chromosome 11. #Yeast artificial chromosome. This is a method for cloning very large fragments of DNA. Genomic DNA in fragments of 200-500 kb are linked to sequences which allow them to propagate in yeast as a mini-chromosome (including telomeres, a centromere and an ARS - an autonomous replication sequence). This technique is used to clone large genes and intergenic regions, and for chromosome walking. # An artificial chromosome created from DNA, centromere and telomere of yeast chromosomes. Heavily used in cloning of very large genomic fragments.

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