INDUSTRIAL TRAINING REPORT

NUR ATIKAH BINTI MOHAMED ABBU BAKAR

BACHELOR OF BIOLOGICAL SCIENCE

DEPARTMENT OF FUNDAMENTAL SCIENCE

UNIVERSITY MALAYSIA TERENGGANU

AUGUST 2017
 DECLARATION

Name: Nur Atikah Binti Mohamed Abbu Bakar

Matric no.: UK34984

I sincerely declare that:

1. I am the sole writer of this report;

2. The details of training and experience contain in this report describe my

involvement as a trainee in the field bioinformatics

3. All the information contains in this report is certain and correct to the
knowledge of the author.

Students signature:

Date:

ii
 ACKNOWLEDGEMENT

First and foremost, I would like to express my gratitude to my supervisor, Dr.

Chong Yee Siew because without her guide, assistance and involvement in every step
throughout the process, this internship would never accomplished its objective. Dr.
Chong Yee Siew is the coolest lecturer in Bioinformatics that make me fell in love
with this subject too. This training further exposing me the life of researchers. I finally
realised researches are not only about experiment planning and designing, laboratory
skills, thinking and analytic skills, but also involving knowledge regarding research
funds, legislation and laboratory management.

Moreover, my greatest thankful to Jia Seng, Yin Yeng and Nur Izzati for their
helping hand whenever I need. At the same time, I take this opportunity to record the
most sincere thanks to all the members of the Bioinformatics Lab of INFORMM
named as Safirah, Nissa and Nabila for their help when facing hardship during
solving mini project. Most importantly is my mother who is the one that give
continuous support and my father that keep me motivated and being passionate all
the time. Finally, I would like to thank those whoever contribute to mini project
whether directly or indirectly made this project become possible to achieve.

iii
 ABSTRACT

This report documented the tasks completed during the first seven weeks of my
industrial training at Biotechnology Research Institute, Universiti Malaysia Sabah.
The industrial training period started on 30 June 2014 and ended on 22 August 2014
under the supervision of Associate Professor Dr Vijay Kumar, the director of the
organisation. On the first week of the training, I was exposed to the laboratory
environment and learnt the organisation structure, rules and regulations of the
laboratories; from second week onward, I worked on my mini project on DNA
barcoding and microsatellite primer testing on the coral samples. Besides, minor tasks
such as finding research grant, understanding the legislation of Sabah as well as to
learn the way in managing an institute was also assigned as part of this industrial
training. Apart from the skills on handling laboratory works, it is a lesson to learn that
a researcher should possesses enough general knowledge on research grant application,
legislation as well as laboratory or institute management. Besides, a researcher should
also equip himself/herself with soft skills such as communication skill, work
organisation, presentation skill and problem solving skills. In short, this working
experience widen my perspective on the jobs of a researcher and I believe it will be
very beneficial on my career.

iv
 TABLE OF CONTENTS

DECLARATION ......................................................................................................... ii
ACKNOWLEDGEMENT .......................................................................................... iii
ABSTRACT ................................................................................................................ iv
LIST OF FIGURES .................................................................................................... vi
LIST OF TABLES ..................................................................................................... vii
LIST OF SYMBOLS AND ABBREVIATIONS ..................................................... viii
LIST OF APPENDICES ............................................................................................. ix
CHAPTER 1 INTRODUCTION ................................................................................. 1
CHAPTER 2 DETAILS OF THE WORKING EXPERIENCE .................................. 3
2.1 Internship Tasks ............................................................................................ 3
2.1.1 Mini project ............................................................................................ 3
2.1.2 Minor tasks ........................................................................................... 10
2.2 Relation of task with academic course ........................................................ 10
2.3 Knowledge and personal learning ............................................................... 10
2.4 Theoretical and Practical Knowledge from the Academic Courses Applied
12
2.5 Problems Encountered during Execution of Tasks ..................................... 13
2.6 Conclusion and Professional Comments ..................................................... 14
CHAPTER 3 CONCLUSION AND SUGGESTIONS .............................................. 15
REFERENCES........................................................................................................... 16
APPENDIX 1: DAILY RECORD ............................................................................. 19
APPENDIX 2: PHOTO OF GEL EXTRACTION AND RECOMBINANT CLONE
.................................................................................................................................... 26

v
 LIST OF FIGURES

Figure 2.1: Flow Chart of the Mini Project .................................................................. 4

Figure 2.2: Genomic DNA Extraction for First Set of Coral Samples. ....................... 6
Figure 2.3: Genomic DNA Extraction for Second Set of Coral Samples. ................... 6
Figure 2.4: PCR Result Using COI Primer.. ................................................................ 7
Figure 2.5: PCR Result Using COI Primer.. ................................................................ 7
Figure 2.6: PCR Result Using Cytb Primer. ................................................................ 8
Figure 2.7: PCR Result Using Cytb Primer. ................................................................ 8
Figure 2.8: PCR Result for Microsatellite Primer Testing on SD46. .......................... 9

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 LIST OF TABLES

Table 1.1: Research Groups in BRI and Their Respective Head. ................................ 1
Table 1.2: Training Schedule Planned by BRI............................................................. 2
Table 2.1: PCR Condition Used for COI and Cytb Amplification. ............................. 5
Table 2.2: Expected PCR Product Size of the Primer (Shinzato, et al., 2014). ........... 9
Table 2.3: Research Grant Offer by MOE and MOSTI (Department of Higher
Education, 2013; MyGRANTS, 2014; MOSTI, 2014). ............................................. 11

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 LIST OF SYMBOLS AND ABBREVIATIONS

BRI Biotechnology Research Institute

DNA Deoxyribonucleic acid
LB Luria-Bertani
MOE Ministry of Education
MOSTI Ministry of Science, Technology and Innovation
PCR Polymerase chain reaction
UM University of Malaya
UMS Universiti Malaysia Sabah

viii
 LIST OF APPENDICES

Appendix 1: Daily Records ............... 19

Appendix 2: Photo of Gel Extraction and Recombinant Clone .. 26

ix
 CHAPTER 1 INTRODUCTION

Biotechnology Research Institute (BRI) is one of the centres of excellent in

Universiti Malaysia Sabah (UMS), alongside with Borneo Marine Research Institute
and Biology Tropical and Conservation Institute. The institute was established in
January 2002, initially it exists as a temporary building with the School of Science and
Technology. In 2011, BRI was assigned a permanent research complex named as
Biotechnology Research Institute Research Complex. This research complex consists
of an administration block and a laboratory block which houses 10 laboratories, which
are the genomic lab, microbiology lab, biochemistry lab, tissue culture lab,
fermentation lab, instrumentation lab, natural products lab, bioinformatics lab,
biosafety level 3 lab and pilot plant. Apart from promoting postgraduate study and
training in the field of biotechnology, BRI is also serving as biotechnology hub for
Sabah as well as to develop corporate partnerships to drive the nations biotechnology
industry. By 2014, BRI has employed 43 staffs and enrolled more than 70 postgraduate
students. BRI focuses on three main research area, namely industrial biotechnology,
agro-biotechnology and healthcare biotechnology, its niche areas include molecular
marker and biomarker, molecular microbiology as well as natural products and drug
discovery. Six research groups have been established and each group being led by a
lecturer as shown in Table 1.1.

Table 1.1: Research Groups in BRI and Their Respective Head.

Research Group
Tissue culture and micropropagation
Natural products and drug discovery
Molecular microbiology
Molecular genetics
Bioprocessing engineering
Biosensor
Head
Mr Wilson Yong Thau Lym
Assoc Prof Dr Mohammad Iqbal
Prof Dr Michael Wong
Assoc Prof Dr Vijay Kumar
Dr Clarence Ongkudon
Dr Shafiqizzaman Siddiquee

I was attached to this organisation and performed my industrial training from

30 June 2014 until 22 August 2014, under the supervision of Associate Professor Dr
Vijay Kumar, director of Biotechnology Research Institute. Apart from the mini
project (which will be elaborated more in section 2.1.1) assigned by my supervisor, I
was also given other tasks like finding research funds, study the budget required in
setting up a laboratory, learning the procedure in applying license to access biological

1
resources in Sabah and to export biological samples from the state. Besides, I have
also given a chance to learn the ways to manage an institute (which is scheduled in
week 8 of the industrial training and will not be included in this report). Table 1.2
shows the training schedule planned by the organisation for this industrial training
programme.

Table 1.2: Training Schedule Planned by BRI.

Week (Date) Training Location Note
30 Jun 2014 Reporting to BRI
Directors office Introduction to the director, staffs
Administration in the administration office.
office Briefing regarding lab safety
1 Jul 2014
Genomic lab
Bioinformatics lab
1st Week Tissue Culture lab Introduction to the labs, lab
(30 Jun 4 Jul 2014) 2 Jul 2014 coordinators, lab assistants.
Biochemistry lab Rules and regulations of the labs
Pilot Plant Lab equipment and its function
3 Jul 2014 Recording system (for
Fermentation lab equipment, chemicals, etc.)
Microbiology lab Daily activities in the labs
4 Jul 2014
Natural product lab
Instrumentation lab
2nd Week 7th Week
(7 Jul 15 Aug Laboratory / Field Project assigned by supervisor
2014)
Directors office Institute management
8th Week
Administration Daily activities in the office
(18 22 Aug 2014)
office Preparation for the presentation
22 Aug 2014 Tutorial room Presentation

2
 CHAPTER 2 DETAILS OF THE WORKING EXPERIENCE

2.1 Internship Tasks

I was attached to BRI for eight weeks during this industrial training programme.
Since the period of eight weeks is relatively short, instead of one huge project which
cannot be accomplished within the given time frame, I was assigned mini project and
some minor tasks for self-study and improvement.

2.1.1 Mini project

The mini project consists two main parts, DNA barcoding and microsatellite
primer testing. For DNA barcoding, I would have to sequence the cytochrome b (Cytb)
gene and cytochrome oxidase I (COI) gene from coral samples and the identity of those
corals are then identified by comparing the sequence with the GenBank. This task can
be divided into five major steps, genomic DNA extraction, polymerase chain reaction
(PCR) to amplify the Cytb and COI gene, gene cloning, sequencing and analysis of
result. Section 2.1.1.1 further elaborates the objectives, methodology and outcomes of
DNA barcoding.
As for microsatellite primer testing, I was entitled a task in testing whether the
14 microsatellite primers published by Shinzato, et al. are suitable for genotyping
purpose for the Acropora sp. in Sabah. The laboratory skill included in this task is
PCR, basically I have to investigate whether the primers will amplify the microsatellite
loci of the coral samples. If the result is positive then it implies that the primers can be
used for genotyping purpose. Figure 2.1 shows the flow chart of this mini project.

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 Genomic DNA extraction

PCR using COI and Cytb PCR using microsatellite

primer primer published by Shinzato,
et al.

Gel extraction COI and Cytb

band

Cloning of COI and Cytb gene

Sequencing of COI and Cytb

gene

Analysis of sequencing result

Figure 2.1: Flow Chart of the Mini Project

2.1.1.1 DNA Barcoding

This task was aimed to identify the coral species in Sabah using DNA
barcoding. The genomic DNA of ten coral samples were extracted with DNeasy
Blood & Tissue Kit (Qiagen) using the kit protocol (QIAGEN, 2014a). PCR was then
conducted using COI and Cytb primer respectively under condition as shown in Table
2.1. The COI and Cytb band were extracted using QIAquick Gel Extraction Kit
(Qiagen) with the default kit protocol (QIAGEN, 2014b) and the genes were cloned
into pJET1.2/blunt Cloning Vector (supplied in CloneJET PCR Cloning Kit (Thermo
Scientific)) using the sticky-end cloning protocol as described in the product handbook
of the kit (Thermo Fisher Scientific Inc, 2012a). The plasmid were transformed into
Escherichia coli for cloning using calcium chloride transformation method described
by the European Molecular Biology Laboratory (European Molecular Biology
Laboratory, 2014). After the selection of transformed E. coli cells, plasmid extraction
were carried out using GeneJET Plasmid Miniprep Kit (Thermo Scientific) in

4
accordance to the kit protocol (Thermo Fisher Scientific Inc, 2012b). At the point of
writing, the extracted plasmid were not analysed yet, analysis of the plasmid (which
are the recombinant clone) using PCR, sequencing and analysis will be done after the
plasmid are verified to possess the COI and Cytb fragment.

Table 2.1: PCR Condition Used for COI and Cytb Amplification.

Stages Temperature (C) Duration

Initial denaturation 96 3 minutes
PCR cycle (35 cycles)
Denaturation 95 30 seconds
Annealing
COI 45 30 seconds
Cytb 56 30 seconds
Extension 72 1 minute
Final extension 72 8 minutes

The genomic DNA extraction was fairly successful, out of the ten samples, the
extraction was only successful for seven samples. As shown in Figures 2.2 and 2.3,
bands were only observed in samples BMBRI07, AN02, BMBRI39, BRI023 and
BRI021. However, after carried out PCR using COI and Cytb primer (as shown in
Figures 2.4, 2.5, 2.6 and 2.7), it was found that DNA was present in samples
BMBRI07, BRI002, IPB053, BRI087, AN02, BMBRI39 and BRI095 as these samples
gave positive result in PCR.. Meanwhile, the bands in negative control (Figure 2.5)
was caused by cross contamination of the negative control during PCR mix
preparation.
As mentioned earlier, at the point of writing this report, the mini project was
only proceeded until cloning step, i.e. clone the COI and Cytb into the pJET1.2/blunt
Cloning Vector and then transform the E. coli with the plasmid. Colonies from seven
recombinant clones (out of ten recombinant clone) were observed, the recombinant
clones are not analysed yet and thus have no confirmation whether the genes have been
cloned successfully. Appendix 2 shows a photo of gel extraction and a plate of
recombinant clone.

5
 M 1 2 3 4 5

Figure 2.2: Genomic DNA Extraction for First Set of Coral Samples. Lane M:
lambda marker; Lane 1: BMBRI07; Lane 2: BRI002; Lane 3: IPB053; Lane 4:
BRI087; Lane 5: AN02.

M 1 2 3 4 5

Figure 2.3: Genomic DNA Extraction for Second Set of Coral Samples. Lane M:
lambda marker; Lane 1: BMBRI39; Lane 2: BRI095; Lane 3: BRI037; Lane 4:
BRI023; Lane 5: BRI021.

6
 M 1 2 3 4 5 6

700bp

Figure 2.4: PCR Result Using COI Primer. Lane M: 100bp marker; Lane 1:
BMBRI07; Lane 2: BRI002; Lane 3: IPB053; Lane 4: BRI087; Lane 5: AN02;
Lane 6: Negative control.

M 1 2 3 4 5 6

700bp

Figure 2.5: PCR Result Using COI Primer. Lane M: 100bp marker; Lane 1:
BMBRI39; Lane 2: BRI095; Lane 3: BRI037; Lane 4: BRI023; Lane 5: BRI021;
Lane 6: Negative control.

7
 M 1 2 3 4 5 6

800bp

Figure 2.6: PCR Result Using Cytb Primer. Lane M: 100bp marker; Lane 1:
BMBRI07; Lane 2: BRI002; Lane 3: IPB053; Lane 4: BRI087; Lane 5: AN02;
Lane 6: Negative control.

M 1 2 3 4 5 6

800bp

Figure 2.7: PCR Result Using Cytb Primer. Lane M: 100bp marker; Lane 1:
BMBRI39; Lane 2: BRI095; Lane 3: BRI037; Lane 4: BRI023; Lane 5: BRI021;
Lane 6: Negative control.

2.1.1.2 Microsatellite Primer Testing

The objective of this primer test was to investigate whether 14 microsatellite
primers published by Shinzato, et al. can be applied on Acropora sp. in Sabah.
Genomic DNA of an Acropora sample (sample ID: SD46) was extracted with
DNeasy Blood & Tissue Kit (Qiagen) using the kit protocol (QIAGEN, 2014a). PCR
was done by including 14 PCR reaction (each with 1 primer pair) with SD46, with the
PCR condition as described in Shinzato, et al. except that the annealing temperature

8
 was set to 45C. After that, the PCR band size Figure 2.8 shows the result of the PCR
reaction.

M 1 2 3 4 5 6 7 8 9 10 11 12 13 14

400bp
300bp
200bp

Figure 2.8: PCR Result for Microsatellite Primer Testing on SD46. Lane M:
100bp marker; Lane 1: 8346m3 primer; Lane 2: 7961m4 primer; Lane 3:
11745m3 primer; Lane 4: 12406m3 primer; Lane 5: 11543m5 primer; Lane 6:
530m4 primer; Lane 7: 11401m4 primer; Lane 8: 441m6 primer; Lane 9:
11292m4 primer; Lane 10: 8499m4 primer; Lane 11: 7203m5 primer; Lane 12:
10366m5 primer; Lane 13: 12130m5 primer; Lane 14: 4546m2 primer.

As shown in Figure 2.8, multiple bands were observed. This event was due to
non-specific binding caused by low annealing temperature (45C instead of 58C
which was recommended by Shinzato, et al.. However, by comparing the band size
with the expected size as described in Shinzato, et al., it was found that the primers
8346m3, 11745m3, 12406m3, 11543m5, 530m4 and 11401m4 were giving the correct
PCR product (based on product size comparison), meanwhile, optimisation is needed
for the other primer in order to obtain the correct PCR product. Table 2.2 shows the
expected PCR product size of the primer in accordance to Shinzato, et al..

Table 2.2: Expected PCR Product Size of the Primer (Shinzato, et al., 2014).

Primer Expected PCR Product Size (bp)

8346m3 162 213
7961m4 174 208
11745m3 171 269
12406m3 163 188
11543m5 125 142
530m4 269 405
11401m4 364 418

9
 441m6 268 312
11292m4 443 502
8499m4 340 361
7203m5 279 319
10366m5 216 232
12130m5 248 295
4546m2 231 282

2.1.2 Minor tasks

Apart from the mini project on the genotyping and DNA barcoding, the minor
tasks assigned by BRI to me including the search for research funds, studying the
procedure in applying access to biological resources in Sabah as well as to learn how
to manage an institute. The aims of the minor tasks were to expose and equip the
students with soft skills in addition to the laboratory skills (which can be obtained from
the mini project). The outcomes of the minor tasks will be explained in section 2.3.

2.2 Relation of task with academic course

The mini project as mention in section 2.1.1 is part of the molecular taxonomy,
in which the species identity and variation based on DNA sequences. DNA barcoding
utilises species specific DNA sequence for species identification, the most popular
gene for DNA barcoding is the mitochondrial cytochrome c oxidase 1 (CO1), as this
gene is short enough to be sequenced quickly and cheaply but long enough to identify
variations among species (International Barcode of Life, 2014). Meanwhile,
microsatellite can be used for detecting variation within species and between species,
and thus studying the genetic structure of subpopulations and populations (Guo, et al.,
2010; Lv, Yang, & Wang, 2014). The dawn of DNA barcoding and discovery of
microsatellite marker suggest the fact that the application of genetics and molecular
biology is getting more diverse.

2.3 Knowledge and personal learning

From my working experience at BRI, I realised that as a researchers job is not
only consists of laboratory works, it also involves a variety of soft skills such as writing
and presentation skills, problem solving, planning and organising. For instance, he
might need to learn how to apply the research fund and how to gain access to protected
area for sampling threaten species.

10
 Laboratory equipment is expensive, it can cost from a few thousand ringgit to
millions of ringgit. Thus, large budget is required in setting up a laboratory, due to this
obstacle, various financial support (research grant) have been established for
researchers so that they can have a better equipped laboratory and able produce high
impact research. Research fund can be from the university itself. For instance, UMS
did offer New Lecturer Grant Scheme in assisting young lecturers in their research
(BRI, UMS, 2012); meanwhile, University of Malaya (UM) offers University of
Malaya Research Grand (UMRG), University of Malaya Research Fund Assistance
(BKP) and Postgraduate Research Fund (PPP) (University of Malaya, 2012).
Research fund can also be obtained through government bodies such as the
Department of Higher Education (formerly known as Ministry of Higher Education
but now is a department under Ministry of Education) and the Ministry of Science,
Technology and Innovation (MOSTI). The research grants offered by Department of
Higher Education and MOSTI are as shown in Table 2.2. Application of Innofund,
Technofund and ScienceFund can be made directly to MOSTI by submitting the
application form and supporting documents to the InnoFund Secretariat, TechnoFund
Secretariat and ScienceFund Secretariat respectively. Meanwhile, the grant offered by
MOE can be applied via online portal MyGRANTS (MyGRANTS, 2014).

Table 2.3: Research Grant Offer by MOE and MOSTI (Department of Higher
Education, 2013; MyGRANTS, 2014; MOSTI, 2014).

Research Grant Department in Charge

Fundamental Research Grant Scheme MOE
(FRGS)
Long Term Research Grant Scheme MOE
(LRGS)
Exploratory Research Grant Scheme MOE
(ERGS)
Prototype Development Grant Scheme MOE
(PRGS)
Niche Research Grand Scheme MOE
Transdisciplinary Research Grant MOE
Scheme
Research Acculturation Grant Scheme MOE
(RAGS)
Research Acculturation Collaboration MOE
Effort
Accolades Grant Research (GSP- MOE
KPM)
Innofund MOSTI
11
 TechnoFund MOSTI
ScienceFund MOSTI

Besides, research grant can also be obtained from non-government sectors. For
instance, Yayasan Sime Darby, American Cancer Society and Mohamed bin Zayed
Species Conservation Fund have been providing financial assistance to research
project (Mohamed bin Zayed Species Conservation Fund, 2013; American Cancer
Society, 2014; Yayasan Sime Darby, 2014).
In addition to research grand, I have also learnt that before we carry out
sampling on any species from a place, we must have some knowledge regarding the
legislation first. For instance, Sabah Biodiversity Enactment 2000 enforces that one
should possesses an access license (which can be applied from the Sabah Biodiversity
Council) in order to gain access to the biological resources of the State (Sabah
Biodiversity Centre, 2014a). Besides, export license (which can be applied from the
Sabah Biodiversity Council) is required for a researcher to export biological resources
out of Sabah (Sabah Biodiversity Centre, 2014b).

2.4 Theoretical and Practical Knowledge from the Academic Courses Applied
The tasks assigned by BRI is totally related to my academic courses especially
SHES1202 Biology of Organism, SHEN2341 Genetic Resources and Conservation,
SHEN3174 Current Issues in Genetics and Molecular Biology as well as my final year
project (SHEN3184).
During my year one, SHES1202 Biology of Organism introduced me different
kingdoms and phylum of living organisms. Corals are sessile Cnidarian (kingdom
Animalia, phylum Cnidaria) that can either live at shallow water or deep under the sea
bed. It mainly feeds on plankton or obtain its energy from zooxanthella which is a type
of photosynthetic unicellular algae that live within the coral's tissue.
The course SHEN2341 Genetic Resources and Conservation and SHEN3174
have introduced me microsatellite marker and DNA barcoding. This knowledge
enabled me to have a clearer idea on my mini project. Together with my mini project,
I realised that species identification via DNA barcoding is done by comparing the
sequence of specific region (such as cytochrome oxidase 1 gene) with the sequence
from the GenBank. Meanwhile, microsatellite can be used for genotyping in order to
study the extent of genetic diversity of the corals. Species identification and genetic

12
diversity of species are major step in conservational biology; without proper species
identification, a vulnerable species might not be concerned, or the conservation work
might focuses on hybrid species which is least concern.
Besides, the course SHEN3174 has also introduced me about Innofund,
ScienceFund and TechnoFund. Further online reading has exposed me to the research
grant offered by MOE as well as those from private sectors.
Last but not least, the laboratory skills I learnt from my final year project
SHEN3184 are very helpful in performing laboratory work during my training in BRI.
From the hand on project, I learnt how to perform DNA purification, how to
manipulate a PCR machine, how to perform gel electrophoresis and so on. This
enabled me to have a better understanding on the instructions written on a kits
protocol as well as the instructions from my supervisor and supervising postgraduate
student.

2.5 Problems Encountered during Execution of Tasks

The main problem faced throughout my industrial training period is the
genomic DNA extraction from corals. Unlike banana (which I have performed RNA
extraction during my SHEN3184 project), corals consist of hard, calcium carbonate
exoskeleton that protect its tissue from exposing to the lytic enzyme. As a result, the
DNA of the coral tissue might not be released as the cells are not lysed completely.
My first genomic DNA extraction was failed, this was indicated by the result of gel
electrophoresis and PCR (not shown here). Possible cause to this failure is that the
coral tissues are not lysed properly and thus the DNA were not released by the cells.
Thus, in my second attempt, I grinded the coral tissue in chilled buffer ATL (supplied
in DNeasy Blood & Tissue Kit), this step was aimed to help the cell lysis and the
release of genomic DNA from the tissue. This method was found to be more successful,
however, the DNA yield is low, as shown in Figure 2.2, no bands were observed in
sample 2 4, however, after carried out PCR on the COI gene, positive results were
observed in all samples (Figure 2.4), indicating that genomic DNA exists but in low
concentration.
As for the minor task, I did not face obstacles as all the information regarding
the research funds, export and access license application are available on the website
of the respective department.

13
2.6 Conclusion and Professional Comments
Corals play crucial role in ecosystem. According to National Oceanic and
Atmospheric Administration, corals reefs support more species per unit area than any
other marine environment, this include about 4000 species of fish ( National Oceanic
and Atmospheric Administration, 2008). However, most corals are in the red list of
threaten species. However, in accordance of IUCN database (IUCN, 2014) most corals
are in the red list of threaten species. Thus, conservation must be done so as to prevent
extinction of this valuable species. Since sequencing of the COI gene was scheduled
in week 7, until now there is no data regarding the species identity of the samples.
Despite this, based on their morphology, these coral samples are expected to be a
member of the genera Acropora, Pectinia and Pavona. Meanwhile, the microsatellite
primers from Shinzato, et al. are able to amplify the microsatellite loci of the coral
samples from Sabah under a PCR condition with low annealing temperature. However,
multiple PCR product was found, thus, optimisation of PCR condition is still needed
in order to obtain a more specific result.

14
 CHAPTER 3 CONCLUSION AND SUGGESTIONS

This industrial training programme further explore me the life of a researcher.

Apart from the skills in handling routine laboratory work, a researcher should also
possesses some general knowledge especially on research grant, legislation as well as
laboratory management. This training is not only a chance to improve the laboratory
skills, but also an opportunity to improve our soft skills such as communication skills
(as we are now working outside UM environment, good communication skill is needed
for us to interact with the supervisor and other colleagues), problem solving,
presentation skill (as there is a presentation scheduled at the last day of my industrial
training) and planning (the way I arrange my work plan).
In term of improvement of the programme, I would suggest earlier coordination
between the UM and the organisation (BRI) should be made. Based on UM industrial
training schedule, a student have to submit his/her report by week 7 of the training,
however, according the training schedule planned by BRI, industrial training report is
written on week 8; thus, by the time of report submission, I am still missing one section
in my report (the way to manage an institute, this training was scheduled on week 8).
Despite this, I still found myself pleased during the industrial training. I found that
BRI is a suitable place for industrial training, it possesses ten laboratories in one
building thus facilitating the transfer of working samples from laboratory to laboratory.
The most gratifying facility in BRI is the biosafety level 3 laboratory which is
internationally certified, besides, it possesses high end laboratory equipment such as
transmission electron microscope, next generation sequencer (Pacbio RS II) and
confocal fluorescence microscope which allows high impact research in the institute.
Apart from laboratory skill, BRI will also provide training in institute management
which will enhance the planning, organisation and leadership of the student.

15
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Red List of Threatened Species: http://www.iucnredlist.org

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Lv, S.-J., Yang, Y., & Wang, X.-B. (2014). Genetic diversity analysis by
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 APPENDIX 1

DAILY RECORDS

WEEK NO. 1 (DATE: 30/06/2014 04/07/2014)

DATE DUTIES PERFORMED / TASK ROLE

SETTING
30.06.2014 1. Reported to the organisation. TRAINEE
2. Introduction to staffs of the
administration office.
3. Briefing regarding laboratory safety.
01.07.2014 1. Visited to Genomic lab, Bioinformatics TRAINEE
lab, Biochemistry lab and Loji Pandu
lab.
2. Learnt the function, organisation
structure, rules and regulation of these
labs.
02.07.2014 1. Meeting with the director. TRAINEE
2. Visited to Tissue Culture lab and learnt
the function, organisation structure, rules
and regulation of the lab.
03.07.2014 1. Visited to Fermentation lab and TRAINEE
Microbiology lab.
2. Learnt the function, organisation
structure, rules and regulation of these
labs.
04.07.2014 1. Visited to Natural Product lab and TRAINEE
Instrumentation lab.
2. Learnt the function, organisation
structure, rules and regulation of these
labs.

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Supervisors signature:

DAILY RECORDS

WEEK NO. 2 (DATE: 07/07/2014 11/07/2014)

DATE DUTIES PERFORMED / TASK SETTING ROLE

07.07.2014 Studied the function of BRI. TRAINEE
08.07.2014 Searched for the various source of research TRAINEE
fund.
09.07.2014 1. Attended seminar regarding the latest TRAINEE
product from Invitrogen.
2. Meeting with supervisor and obtained task
list.
10.07.2014 Carried out genomic DNA extraction from five RESEARCH
coral samples. ASSISTANT
11.07.2014 Carried out genomic DNA extraction from RESEARCH
another five coral samples. ASSISTANT

Supervisors signature:

20
DAILY RECORDS

WEEK NO. 3 (DATE: 14/07/2014 18/07/2014)

DATE DUTIES PERFORMED / TASK SETTING ROLE

14.07.2014 Performed PCR on the ten coral samples. RESEARCH
ASSISTANT
15.07.2014 Performed gel electrophoresis. RESEARCH
ASSISTANT
16.07.2014 1. Performed DNA extraction from five coral RESEARCH
samples. ASSISTANT
2. Ran PCR.
3. Performed gel electrophoresis.
17.07.2014 1. Performed DNA extraction from five coral RESEARCH
samples. ASSISTANT
2. Ran PCR.
3. Performed gel electrophoresis.
18.07.2014 1. Ran PCR. RESEARCH
2. Performed gel electrophoresis. ASSISTANT

Supervisors signature:

21
DAILY RECORDS

WEEK NO. 4 (DATE: 21/07/2014 25/07/2014)

DATE DUTIES PERFORMED / TASK SETTING ROLE

21.07.2014 Ran PCR to test the microsatellite primer on RESEARCH
twenty coral samples. ASSISTANT
22.07.2014 Ran PCR to test the microsatellite primer on RESEARCH
twenty coral samples. ASSISTANT
23.07.2014 Ran PCR to test the microsatellite primer on RESEARCH
twenty coral samples. ASSISTANT
24.07.2014 Ran PCR to test the microsatellite primers RESEARCH
(different primers) on one coral sample. ASSISTANT
25.07.2014 Ran PCR for genotyping on three coral RESEARCH
samples. ASSISTANT

Supervisors signature:

22
DAILY RECORDS

WEEK NO. 5 (DATE: 28/07/2014 01/08/2014)

DATE DUTIES PERFORMED / TASK SETTING ROLE

28.07.2014 PUBLIC HOLIDAY -
29.07.2014 PUBLIC HOLIDAY -
30.07.2014 Gel extraction RESEARCH
ASSISTANT
31.07.2014 Gel extraction RESEARCH
ASSISTANT
01.08.2014 Gel electrophoresis for PCR product. RESEARCH
Attended colleague presentation. ASSISTANT

Supervisors signature:

23
DAILY RECORDS

WEEK NO. 6 (DATE: 04/08/2014 08/08/2014)

DATE DUTIES PERFORMED / TASK SETTING ROLE

04.08.2014 Ran a gradient PCR to determine the optimal RESEARCH
annealing temperature of seven microsatellite ASSISTANT
primers.
05.08.2014 Ran a gradient PCR to determine the optimal RESEARCH
annealing temperature of seven microsatellite ASSISTANT
primers.
06.08.2014 Industrial training report writing INDUSTRIAL
TRAINING
STUDENT
07.08.2014 1. Cloning the COI and Cytb genes into RESEARCH
cloning vector. ASSISTANT
2. Preparing media for Escherichia coli
culture.
08.08.2014 Prepare LB agar plate for transformation RESEARCH
selection. ASSISTANT
09.08.2014 1. Transform E. coli with the cloning vector RESEARCH
(Saturday) prepared on 7 Aug 2014. ASSISTANT
2. Spread the putative E. coli transformant on
amphicilin agar plate for selection purpose.
10.08.2014 Prepare E. coli broth culture for plasmid RESEARCH
(Sunday) extraction on 11 Aug 2014. ASSISTANT

Supervisors signature:

24
DAILY RECORDS

WEEK NO. 7 (DATE: 11/08/2014 15/08/2014)

DATE DUTIES PERFORMED / TASK SETTING ROLE

11.08.2014 1. Plasmid extraction from E. coli. RESEARCH
2. Redo E. coli transformation for samples ASSISTANT
BMBRI39 Cytb, BRI095 Cytb, BRI087
COI and BMBRI07 COI; and spread the
putative transformant on amphicilin agar
plate for selection.
3. Prepare E. coli broth culture for plasmid
extraction on 12.08.2014
12.08.2014 1. Plasmid extraction from E. coli. RESEARCH
2. Measured optical density and gel ASSISTANT
electrophoresis for plasmid extracted on 11
Aug 2014.
3. Redo E. coli transformation for samples
BMBRI39 Cytb, BRI095 Cytb and BRI087
COI; and spread the putative transformant
on amphicilin agar plate for selection.
4. Prepare E. coli broth culture for plasmid
extraction on 13.08.2014
13.08.2014
14.08.2014
15.08.2014

Supervisors signature:

25
 APPENDIX 2

Preparation of gel extraction: Illuminating the gel using ultraviolet illumination

A plate of recombinant clone (analysis on the clone has not proceed yet)

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