SYLLABUS Fall, 2011 GENES TO GENOMES, BIOL 5375, FO 2.208 (TR 11:30am - 12:45pm) Instructor: Bulla (FN3.

112) & Liu (BE 3.204D) lee.bulla@utdallas.edu; lliu@utdallas.edu

The course will be an expansive coverage of molecular genetics with emphasis on genomes rather than genes. The course will begin with a summary of the basic principles of molecular genetics and end with a thorough analysis of genome expression and molecular phylogenetics. The course will offer a new perspective on how genes function together and in concert in living cells, focusing at the genome level. It will incorporate the recent major advances in genome sciences. The course will be structured to involve students directly in the individual topics by class discussions of research papers and reviews, the latest advances in genome science and new and innovative techniques. Three exams will be conducted during the course of the semester. No make-up exam will be given for absence from an exam other than for official university business or the students individual illness (both require either a written university authorization or a physicians statement). All issues regarding the exams or scores MUST be resolved WITHIN SEVEN DAYS of the exam date. No exams will be re-evaluated after this time period. All hand-held electronic devices, including cell phones, must be stored away during exams. The final grade will be based on the following: three exams 25% each; oral presentation of assigned research/review article 25%. LECTURE 1 2 3 4 5 DATE
25 Aug 30 Aug 1 Sept

LECTURE SCHEDULE TOPIC

Organizational Meeting Basic Molecular Biology Gene Cloning Induction of Transformation by a DNA Fraction Isolated from Pneumococcus Type III (Avery et al., J. Exptl. Medicine 1944) - Stacey Abraham Genome Manipulation How Restriction Enzymes Became the Workhorses of Molecular Biology (RJ Roberts, PNAS 2005) - Neeraja Ashok Bhangre Vectors Strategies for manufacturing recombinant adeno-associated virus vectors for gene therapy applications exploiting baculovirus technology (Negrete and Kotin, Briefings in Functional Genomics and Proteomics 2008) - Richa Bhatt PCR The Unusual Origin of the Polymerase Chain Reaction (K. Mullis, Scientific American 1990) - Nazim Chandani Genomic and cDNA Libraries The current status of cDNA cloning (Harbers, Genomics 2008) - Nashid Chowdhury Screening A cDNA library functional screening strategy based on fluorescent protein complementation assays to identify novel components of signaling pathways (Remy and Michnick, Methods 2004) - Anthony Lewis Gene and Genome Sequencing Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA (Riordan et al., Science 1989) - Jing Lu Tools for Analyzing Sequences Identification of the Cyctic Fibrosis Gene: genetic analysis (Keram et al, Science 1989) - Anissa Mahmoudi REVIEW Exam 1

6 Sept

8 Sept

6 7 8

13 Sept

15 Sept 20 Sept

9 10

22 Sept
27 Sept

29 Sept
4 Oct

11

6 Oct

Products from Native and Cloned Genes Genetics of Global Gene Expression (Rockman and Kruglyak, Nature Genetics Reviews, 2006) - Niana K Mahrouq Analysis of Gene Expression Serial Analysis Of Gene Expression (Velculescu et al., Science, 1995) - Belle Marco Global Structure of Chromosomes Controlling the Double Helix (Felsenfeld and Groudine, Nature 2003) - Eric X Medina Genome Mapping A Physical Map of the Human Genome (The International Human Genome Mapping Consortium, Nature 2001) - Aditya Satish Muley Genomic Analysis Initial impact of the sequencing of the human genome (Lander, Nature 2011) - Karen Jasina Padilla Next-generation Sequencing Technology Sequencing technologies - the next generation (Metzker, Nature Reviews Genetics 2010) - Miteshkumar D Patel REVIEW Exam 2 Analysis of Genetic Variation Genetic Variation, Classification and Race (Jorde and Wooding, Nature Genetics, 2004) - Fidel Ajmain Quraishi Post-Genomic Analysis Molecular Machines that Control Genes (Tjian, Scientific American 1995) Nandhini Raman Synthesis and Processing of RNA The evolution of RNAs with multiple functions (Dinger and Mattick, 2011) - Priya Richards Transgenics Overview: Engineering Transgenic Constructs and Mice (Kulkarni, Current Protocols in Cell Biology 2009) - Stefanie Dionne Sneed Eukaryotic Organellar Genomes Structural Dynamics of Eukaryotic Chromosome Evolution (Eichler and Sankoff, Science 2003) - Elham Taherzadeh Genetics of Cancer and Cancer Genome Exploring the Genomes of Cancer Cells: Progress and Promise (Stratton, Science 2011) - Tamara Sue Terrones Patterns of Inheritance From Atoms to Traits (Kingsley, Scientific American 2008) Epigenetics Bookmarking the Genome: Maintenance of Epigenetic Information (Zaidi and Stein, Journal of Biological Chemistry 2011) REVIEW Exam 3

12 13 14 15 16

11 Oct 13 Oct

18 Oct

20 Oct

25 Oct

17 18 19 20 21 22 23 24

27 Oct 1 Nov 3 Nov

8 Nov

10 Nov

15 Nov

17 Nov

22 Nov

29 Nov 1 Dec

6 Dec 8 Dec