STUDENT TRAINING SCHEME

FACULTY OF RESOURCE SCIENCE AND TECHNOLOGY

LOG BOOK
STUDENT NAME

PROGRAMME

TRAINING LOCATION

JONATHAN CHAN CHIA JUI

Resource Biotechnology

Sarawak Biodiversity Centre (SBC)

KM20, Jalan Puncak Borneo,
93250 Kuching, Sarawak.

WEEK : 1

DATE / TIME
06/07/2015

ACTIVITY
Morning: Familiarizing with buildings, facilities, admin office and Research &
Development Centre in Sarawak Biodiversity Centre (SBC). LI students meeting with
research coordinator, Mdm. Bernadine Jinam, who assigned the rules and regulations
and documents to fill.
Afternoon: Entering Molecular Biology lab, meeting with supervisor, Mdm. Belinda Ng,
and observing while learning protein purification and SDS-PAGE.

07/07/2015

Morning: Cleaning up MB laboratory and equipments. Filling pipette tips and assisting in
gel preparation.
Afternoon: Meeting with Head of Communications, Miss Asha who introduces SBC, its
vision, mission, long-term projects and current developments.

08/07/2015

Morning: Visiting Resource Centre of SBC. PCR product purification and PCR samples
preparation. Running Thermal Cycler.
Afternoon: Visiting SBC nurseries and gardens. SBC staff meeting with CEO, Dr. Yeo at
Lecture theater.

09/07/2015

Morning: A 50 mins meeting with Safety & Health Committee which provides talk on
Laboratory Safety Procedures. Gel preparation AGE, and gel viewing.
Afternoon: PCR samples preparation and running overnight thermal cycler.

10/07/2015

Morning: Running AGE of PCR products, gel imaging and analysis. PCR sample
preparation, running thermal cycler.
Afternoon: Gel preparation, AGE and gel analysis.

11/07/2015
12/07/2015

Name and Signature of Supervisor

Date

WEEK : 2

DATE / TIME
13/07/2015

ACTIVITY
Morning: PCR product purification of full-length target transcript and gel viewing.
Afternoon: Dilution and preparation of template DNA and primer for sequencing. Filling
pipette tips.

14/07/2015

Morning: Colony PCR of 16 samples and re-streaking of the selected transformants.

Viewing gel.
Afternoon: Helping out purification of colleague's PCR samples.

15/07/2015

Morning: Routine cleaning of lab benches, desks, and floors. Guiding colleague to purify
5 PCR samples.
Afternoon: Preparing CMC plates for streaking actinomycetes samples cultured in CMC
broth. Set up overnight cultures for selected transformants in 5ml LB broth with
kanamycin.

16/07/2015

Morning: Familiarizing with protocol for TOPO TA Cloning kit. Extracting protein from
actinomycetes samples.
Afternoon: Sorting stuff to be autoclaved and learning how to operate autoclave
machine. Refilling new cotton plugs in glass pipettes to be autoclaved.

17/07/2015

Holiday: Hari Raya Aidilfitri, National.

18/07/2015
19/07/2015

Name and Signature of Supervisor

Date

WEEK : 3

DATE / TIME
20/07/2015

21/07/2015

22/07/2015

ACTIVITY
Morning & afternoon: Peeling and cutting lemon skins for potpouri bags for the coming
Bario festival. Drying strips of cut lemon skins in oven for 2 days.

Morning: Cleaning and doing lab maintenance. Afternoon: Subculturing clones carrying
plasmids from agar plates to LB broth supplemented with kanamycin.

Morning: Cutting lemongrass for potpouri bags for the coming Bario festival. Extracting
DNA from actinomycetes strains.
Afternoon: Incubating cut lemongasses in oven for 2 days.

23/07/2015

Morning: Glassware cleaning in MB lab. Plate streaking of seed culture for competent E.
coli onto LB agar plates with and without kanamycin or streptomycin.
Afternoon: Cleaning of HPLC vials. Incubating streaked cultures overnight.

24/07/2015

Morning: LB agar plate preparation supplemented with kanamycin. Lab cleaning and
floor mopping.
Afternoon: Molecular cloning of target DNA. Transforming and spreading culture onto LB
agar plate for overnight incubation.

25/07/2015

26/07/2015

Name and Signature of Supervisor

Date

WEEK : 4

DATE / TIME
27/07/2015

ACTIVITY
Morning: Cleaning lab. Performing PCR of target gene and subsequent gel purification.
Afternoon: Purifying PCR product for cloning.

28/07/2015

Morning: Cloning target PCR DNA using TOPO TA cloning kit (Invitrogen) and transform
into electrocompetent E. coli.
Afternoon: Spreading culture onto LB agar plates. Preparing ampicillin stock solution
(20ml) and stored at -20.

29/07/2015

Morning: Performing PCR colony screening.

Afternoon: Viewing gel. Preparing 2M D-(+)-glucose and 2M MgCl2 and syringe filtered.

30/07/2015

Morning: Cleaning lab. Assisting colleagues with PCR and plate streaking.
Afternoon: Culturing selected transformants in bijou bottles with LB broth for tomorrow's
plasmid isolation.

31/07/2015

Morning: Plasmid extraction using alkaline lysis method. Running gel to check plasmid
conditions.
Afternoon: Performing purity and concentration checks of isolated plasmids. Washing
lab glasswares.

01/08/2015
02/08/2015

Name and Signature of Supervisor

Date

WEEK : 5

DATE / TIME
03/08/2015

ACTIVITY
Morning: Glassware cleaning. Cloning of target DNA from selected actinomycetes
strains. S.O.C. medium preparation.
Afternoon: Performing E.coli transformation. Filling glass pipettes with cotton wools.

04/08/2015

05/08/2015

Morning: PCR colony screening for positive transformants.

Morning: SBC's 5S Day. SBCs staffs birthday celebration.

Afternoon: Analysis of DNA sequences to check for sequence similarity.

06/08/2015

Morning: Contig assembly of target gene sequences and aligning to reference

sequence.
Afternoon: Troubleshooting and sketching out plan to redo experiment.

07/08/2015

Morning: Plasmid isolation using alkaline lysis method.

Afternoon: Planning for upcoming experiments.

08/08/2015
09/08/2015

Name and Signature of Supervisor

Date

WEEK : 6

DATE / TIME
10/08/2015

ACTIVITY
Morning: Preparing mortar and pestle and isolating total RNA from plant sample using
RiboSpin Plant RNA Isolation kit.
Afternoon: Gel viewing and spectrophotometric analysis of RNA.

11/08/2015

Morning: Isolating total RNA from plant sample using mirVana miRNA Isolation kit.
Spectrophotometric analysis.
Afternoon: Performing reverse transcription/RT-PCR.

12/08/2015

Morning: Gel viewing from overnight PCR run. Repeating PCR with different primer
pairs.
Afternoon: Gel viewing of PCR products.

13/08/2015

Morning: Repeating experiment, converting cDNA from total RNA.

Afternoon: Performing PCR with different primer pairs..

14/08/2015

Morning: Repeating PCR with different cDNA concentration and different PCR cycle
conditions. 2 L LB agar preparation.
Afternoon: Gel viewing. Refilling pipette tips and glassware cleaning. Preparation of LB
agar plates supplemented with ampicillin.

15/08/2015
16/08/2015

Name and Signature of Supervisor

Date

WEEK : 7

DATE / TIME
17/08/2015

ACTIVITY
Morning: Total RNA extraction from Aglaia stellatopilosa. Running RNA on gel and
checking RNA purity and concentration with nanovue.
Afternoon: cDNA synthesis using M-MLV reverse transcription kit.

18/08/2015

Morning: Cleaning glasswares. Performing PCR using cDNA as template .

Afternoon: Running agarose gel electrophoresis.

19/08/2015

Morning: Repeating PCR with different primer pairs.

Afternoon: Running agarose gel electrophoresis.

20/08/2015

Morning: Repeating PCR using Pfu and Taq DNA polymerase.

Afternoon: Running gel electrophoresis. PCR of actinomycetes strains.

21/08/2015

Morning: Lab cleaning. Purifying actino PCR products.

Afternoon: Performing agarose gel electrophoresis and troubleshooting failed PCR.

22/08/2015
23/08/2015

Name and Signature of Supervisor

Date

WEEK : 8

DATE / TIME
24/08/2015

ACTIVITY
Morning: Repeating PCR using cDNA obtained from colleague with different primer
pairs.
Afternoon: Running gel electrophoresis.

25/08/2015

Morning: Preparing agarose gels for running colleague's PCR products. Assisting in
preparing SDS-PAGE gels.
Afternoon: Cleaning glasswares.

26/08/2015

Morning: PCR of full-length target transcript.

Afternoon: Preparing gel and running gel electrophoresis.

27/08/2015

Morning: Performing gel purification for PCR products amplified from both MyTaq and
Pfu DNA polymerases.
Afternoon: Cloning purified PCR products, transformation, spreading culture onto agar
plates and incubating the plates overnight.

28/08/2015

Morning: Preparing gels for gel purification.

Afternoon: Purification of PCR product.

29/08/2015
30/08/2015

Name and Signature of Supervisor

Date

WEEK : 9

DATE / TIME
31/08/2015

01/09/2015

ACTIVITY
National holiday: National Day

Morning: TOPO cloning of full-length target transcript.

Afternoon: Filling pipette tips and cleaning lab.

02/09/2015

Morning: PCR colony screening for positive transformants.

Afternoon: Preparation of electrocompetent cells. Viewing and analysing gel photo of
PCR products.

03/09/2015

Morning: Re-amplification of full-length PCR product and gel purification.

Afternoon: Viewing gel. Preparing overnight culture of selected colonies.

04/09/2015

Morning: Plasmid isolation for overnight-grown cultures.

Afternoon: Double digestion of plasmids with restriction enzymes.

05/09/2015
06/09/2015

Name and Signature of Supervisor

Date

WEEK : 10

DATE / TIME
07/09/2015

ACTIVITY
Morning: Preparing plasmids to be sent for sequencing. Assisting research officer to gel
purify PCR products.
Afternoon: Cloning of 3 genes from actino strains. Preparing overnight culture of E. coli
harboring expression plasmid.

08/09/2015

Morning: Isolating expression plasmid by using alkaline lysis method. Preparing 4L LB

broth.
Afternoon: Purification of PCR products.

09/09/2015

Morning: Preparing SDS-PAGE staining solution. Cleaning lab.

Afternoon: Preparing overnight cultures of competent strains of E. coli and some
selected colonies.

10/09/2015

Morning: Plasmid isolation. Preparing competent E. coli. Performing restriction digestion.

Afternoon: Performing gel purification of cut plasmids.

11/09/2015

Morning: Performing agarose gel electrophoresis. Gel viewing.

Afternoon: PCR colony screening. Lab cleaning.

12/09/2015
13/09/2015

Name and Signature of Supervisor

Date

WEEK : 11

DATE / TIME
14/09/2015

15/09/2015

16/09/2015

17/09/2015

ACTIVITY
Morning: Vector and insert DNA ligation. Afternoon: Report-writing. Preparation of
overnight culture for selected clones.

Afternoon: Preparation of glycerol stock from overnight cultures. Transformation of

ligated vectors into competent E. coli.

National holiday: Malaysia Day.

Morning: PCR colony screening of transformants.

Afternoon: Glassware cleaning.

18/09/2015

Morning: Plasmid minipreparations from overnight cultures.

Afternoon: Preparation of LB agar plates supplemented with kanamycin.

19/09/2015
20/09/2015

Name and Signature of Supervisor

Date

WEEK : 12

DATE / TIME
21/09/2015

ACTIVITY
Morning: Report-writing and preparation of presentation slides.
Afternoon: Trimming DNA sequences, aligning them, and annotating their amino acid
sequences.

22/09/2015

Morning: Industrial training presentation.

Afternoon: Performing bioinformatics analysis: phylogenic tree construction.

2309/2015

Morning: Report corrections.

Afternoon: Transformation of competent E. coli. Laboratory cleaning.

24/09/2015

25/09/2015

National holiday: Hari Raya Haji.

Morning: PCR colony screening. Gel viewing.
Afternoon: Submitting industrial training report and obtaining signature for logbook.

26/09/2015
27/09/2015

Name and Signature of Supervisor

Date