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Table of Contents

Foreword from Dean of the Centre for Postgraduate Studies (CPS) 2

Foreword from Director of Biotechnology Research Institute (BRI) 3

Foreword from Chairperson of the 24th BRI Postgraduate Seminar 4

Seminar Programme 5

Student’s Profiles and Abstract 12

24th BRI PGS Organizing Committee 72

Sponsorships 74

2

Foreword from Dean of Centre for Postgraduate Studies (CPS)

First and foremost, I would like to congratulate Biotechnology Research Institute (BRI) for their

success in previous Postgraduate Seminar (PGS) and for their endless effort and

commitment in conveying the 24th BRI Postgraduate Seminar (PGS).

The Postgraduate Seminar (PGS) has always served as a platform to keep track of the students’

research progress. This two-way communication between lecturers and students also

helps the students improve their research and presentation skills. From this event, students

will be able to see their research from a different perspective as many experts from the same field

and other fields will be there to share their knowledge and opinions.

I believe this seminar will help the students to excel in their research and spark new ideas. The

Centre for Postgraduate Studies (CPS) fully supports this academic discourse and hope that this

seminar will be continuously organized. I wish all the students an engaging and enriching session in

the 24th PGS.

Prof. Dr. Hjh. Arsiah Bahron Dean of Centre for Postgraduate Studies (CPS), Universiti Malaysia Sabah

3

Foreword from Director of Biotechnology Research Institute (BRI)

First and foremost, it gives me immense of pleasure and incredible honor to welcome all of you to the

24th BRI PGS. Ever since its inception in January 2002, our biannual Postgraduate Seminar (PGS) has

been playing an imperative role in monitoring students’ research progress and moulding their

interpersonal skills through presentations as well as erudite discussions with the academic staffs.

This three-day seminar involves the participation of each and every postgraduate student registered

under BRI comprising of Masters (Research and Coursework) and Ph.D. candidates. Students share

the details of their research progress and showcase their current research findings upon which they

are evaluated and given feedback so as to improve their research quality. Students in the past have

also utilized this platform to overcome predicaments faced in their research projects as it channels

the constructive ideas of our academic experts as well as invited research scholars. Hence, over the

years, the postgraduate seminars have been continuously held in the spirit to ensure student

progress well and graduate on time, producing well-rounded researchers with great deliberation and

soft skills.

The execution of this seminar proudly encompasses organizing, planning and efforts by BRI students

themselves. Their active participation in organizing the seminar is laudable and I would like to thank

the PGS24 advisor, Dr. Suryani Saallah, the chairperson of PGS24, Ms. Rafida Razali, and the entire

crew for their hardwork in making it a success. I also would like to seize this opportunity to express

our profound appreciation to the Centre of Postgraduate Studies (CPS) for their ardent support.

Dr. Zarina Binti Amin

Director of the Biotechnology Research Institute (BRI), Universiti Malaysia Sabah

4

Foreword from Chairperson of 24th Postgraduate Seminar

First and foremost, we would like to warmly welcome all our respected lecturers, beloved staffs,

fellow students and honourable guests to the 24th Biotechnology Research Institute Postgraduate

Seminar. This Postgraduate Seminar (PGS) is an event conducted twice a year in each semester,

which serve as a platform for all Biotechnology Research Institute (BRI) students to present their

current proposal or progress report of their studies. The open-discussions between examiners from

different expertise and students will offer new perspectives and suggestions on the projects, which

will enable the students to move forward toward success with a better insight of their studies. Apart

from that, in the spirit of this event, this seminar will encourage our fellow friends to embrace this

opportunity not only to train ourselves to become better presenters but also to explore the knowledge

readily offered by the academicians. We are optimistic that the intellectual exchange in this event will

be beneficial for our growth as researchers and members of the community. It is my hope that

ultimately, the constructive criticism from all the academicians can motivate the students in our

journey towards becoming respectable scientists. Not to forget, I wish to convey my utmost

appreciation towards our advisor, Dr. Suryani Saallah and the entire organising committee, for their

tireless and strong commitment that everyone has poured into this event. I would also like to express

my gratitude towards the BRI management team for their unwavering guidance and to the Centre for

Postgraduate Studies (CPS) for their tremendous support. To the guests, we are honoured to have

you with us. Lastly, I hope that everyone will find this seminar beneficial and enjoyable. All the best!

"It is the long history of humankind (and animal kind, too) that those who learned to

collaborate and improvise most effectively have prevailed." Charles Darwin

RAFIDA BINTI RAZALI Rafida Binti Razali

Chairperson 24th Postgraduate Seminar

5

DAY 1

23rd JULY 2019 (TUESDAY)

OPENING CEREMONY

08:30 Arrival of students, supervisors and invited guests

Registration

08:50 Arrival of Dr. Zarina Binti Amin, Director of Biotechnology Research Institute

09:00 Recital of Doa

Welcoming speech by Ms. Rafida Razali, Chairperson of 24th BRI Postgraduate Seminar

09:10 Opening speech by Dr. Zarina Amin, Director of Biotechnology

Research Institute

09:25 Photo Session and Tea Break

SESSION 1 Page

09:50 PROPOSAL

01

PP01 Rajeena Sugumaran (M.Sc. Candidate) Investigating horizontal gene transfer from Pseudomonas aeruginosa to Escherichia coli via natural and chemical transformation in-vitro.

12

10:05 PROPOSAL

02

PP02 Pamela David (M.Sc. Candidate) Identification of regulatory genes responsible for microRNA biogenesis pathway in carnivorous plant Nephentes gracilis.

13

10:20 PROPOSAL

03

PP03 Rojilin Binti Donol (M.Sc. Candidate) Identification of genomic regions exhibiting signals of natural selection on Bajau Laut.

14

10:35 PROPOSAL

04

PP04 Siti Kasmah Md Yusuf (M.Sc. Candidate) Characterization of putative antimicrobial peptides from Pedobacter sp. strain BG5.

15

10:50 PROPOSAL

05

PP05 Diana Binti Lorons (M.Sc. Candidate) Molecular dynamics of harmful algal blooms: a case study based on Cochlodinium Polykrikoides.

16

11:05 PROPOSAL

06

PP06 Jerlyn Joan Jenius (M.Sc. Candidate) Species identification and genetic stability of endemic bamboo germplasm in vitro.

17

11:20 PROPOSAL

07

PP07 Nurul Sakinah Binti Saapilin (M.Sc. Candidate) Effect of artificial lighting on photosynthethic efficiency of Brassica sp.

18

11:35 PROPOSAL

08

PP08 Nur Shafrina Aida Binti Yahya (M.Sc. Candidate) Screening, isolation and characterization of thermostable cellulases from Sabah, Malaysia.

19

6

11:50 PROPOSAL

09

PP09 Nur Nasyiroh Izayati BT Mastor (Ph.D. Candidate) Molecular characterization of Vancomycin Resistance Enterococcus (VRE) genes isolated from clinical, environmental and animal samples from Kota Kinabalu Sabah.

20

12:05 LUNCH BREAK

SESSION 2 Page

13:35

PROPOSAL

10

PP10 Khairul Nizam Bin Sehat (M.Sc. Candidate) Role and mechanisms of miRNA regulation in phase transition and growth enhancement of MD2 pineapple.

21

13:50

PROPOSAL

11

PP11 Evra Raunie Bt Ibrahim (Ph.D. Candidate) Development of molecular marker for sago palm (Metroxylon sagu Rottb.) and its application for screening somaclonal variation.

22

14:05

PROPOSAL

12

PP12 Kasra Binti Mukti (M.Sc. Candidate) Biofilm inhibition of pathogenic bacteria by mangrove plants extraction.

23

14:20

PROGRESS

13

PG13 Syva Hednella (Ph.D. Candidate) Comparison of microRNA expression profiling of Human Amnion and Wharton’s Jelly Mesenchymal stem cells during adipogenic differentiation

24

14:35

PROGRESS

14

PG14 Dexter Lee Jiunn Herng (Ph.D. Candidate) Removal of impurities, noise and low-confidence peaks from data acquired from mass spectrometer: a proposed general workflow.

25

14:50

PROGRESS

15

PG15 Azriah Asis (Ph.D. Candidate) Isolation of fungi from agricultural soils in Sabah for its phosphate-solubilizing potential in composting of food wastes.

27

15:05

PROGRESS

16

PG16 Sylbryanie Salister (M.Sc. Candidate) Characterization of the phage lysin and PH.D. genes from Antarctic bacteria.

28

15:20

PROGRESS

17

PG17 Makdi Masnoddin (Ph.D. Candidate) Elucidation of structure and function of conserved hypothetical proteins related to thermal stress response in Glaciozyma antarctica and Pedobacter cryoconitis.

29

15:35

PROGRESS

18

PG18 Abigail Lorna Eric (M.Sc. Candidate) Screening and identification of locally isolated lignin-degrading fungi.

30

7

15:50

PROGRESS

19

PG19 Gilbert Anak Ringgit (M.Sc. Candidate) Development of electrochemical sensor for determination of zinc, manganese and aluminium ions in drinking water.

31

16:05

PROGRESS

20

PG20 MD Shafiqul Islam (Ph.D. Candidate) Study of entomopathogenic fungi and its pathogenicity for controlling sugarcane stem borer, Chilo tumidicostalis hampson.

32

16:20 TEA BREAK AND END OF DAY 1

DAY 2

25th JULY 2019 (THURSDAY)

SESSION 1 Page


08:45

PROGRESS

21

PG21 MD Safiul Alam Bhuiyan (Ph.D. Candidate) Isolation and molecular characterization of infectious bronchitis virus from local isolated of Sabah, Malaysia.

33

09:00

PROGRESS

22

PG22 Mohd Zulhilmi Bin Abdul Rahman (Ph.D. Candidate) Construction, cloning and expression of synthetic genes encoding artificial transcription factors of Theobroma cacao LEC2.

34

09:15

PROGRESS

23

PG23 Sylvia Yahumin (M.Sc. Candidate) Characterization of the Saxitoxin Biosynthetic Starting Gene, sxtA in the toxic dinoflagellate Pyrodinium bahamense var. compressum.

35

09:30

PROGRESS

24

PG24 Herman Umbau Lindang (Ph.D. Candidate) Genome analysis of Paenibacillus sp. and its alkaline phosphatase characterizations.

36

09:45 TEA BREAK

10:05

PROGRESS

25

PG25 Tamar Kansil (Ph.D. Candidate) Evaluation of total phenolic content and DPPH radical scavenging activity of ethanolic extracts of selected mangroves in Sulaman Lake Mangrove Forest Tuaran.

37

10:20

PROGRESS

26

PG26 Ranjita Subramaniam (Ph.D. Candidate) Targeting Induced Local Lesions In Genomes (TILLING) analysis of Ethyl Methane Sulphonate (EMS)-induced M2 mutant populations of eggplant (Solanum melongena).

38

8

10:35

PROGRESS

27

PG27 Rima Fatira Binti Dahari (M.Sc. Candidate) Immobilization of b-galatosidase on polymethacrylate monolith for galactooligosaccharides production.

39

10:50

PROGRESS

28

PG28 Iffa Ridha Binti Luqman Ridha (M.Sc. Candidate) Qualitative and quantitative based analysis of porcine DNA in pharmaceutical capsules.

40

11:05

PROGRESS

29

PG29 Nur Faezah Ibadat (M.Sc. Candidate) Synthesis and characterization of microspheres-based polymeric microemulsion as template for monolith.

41

11:20

PROGRESS

30

PG30 Adznila Eberahim (Ph.D. Candidate) Screening, characterization and optimization of lignin-degrading fungi from Sabah for optimum ligninolytic potential.

42

11:35

PROGRESS

31

PG31 Senty Vun Sang (Ph.D. Candidate) Hepatoprotective effect of Ficus lepicarpa against carbon-tetrachloride induces oxidative stress in rats: histopathological assessment of liver tissue.

43

11:50

PROGRESS

32

PG32 Nur Fatihah Zamri (M.Sc. Candidate) Characterization of nano-sized calcium carbonate powder from chicken eggshell as dietary supplement.

44

12:00 LUNCH BREAK

SESSION 2 Page

13:30

PROGRESS

33

PG33 Alex Walzico Robert (M.Sc. Candidate) The effect of betulin on morphology (SEM) and protein expression.

45

13:45

PROGRESS

34

PG34 Riana Binti Awang Saman (M.Sc. Candidate) Phytochemical constituents, antioxidative and hepatoprotective effects of Lygodium circinnatum against carbon tetrachloride (CCl4)-induced hepatic damage and toxicity in rats.

46

14:00

PROGRESS

35

PG35 Chua Chuen Yang (Ph.D. Candidate) Effects of simulated warming on potentially pathogenic bacteria in soils collected from Kota Kinabalu.

47

14:15

PROGRESS

36

PG36 Nur Syahadatain Binti Abd Razak (Ph.D. Candidate) FTIR investigation of LPS-pDNA in the presence of cation.

48

9

14:30

PROGRESS

37

PG37 Hiew Vun Vun (Ph.D. Candidate) The involvement of ERK1/2 in osteogenic differentiation of Wharton’s Jelly-derived mesenchymal stem cells cultured with graphene oxide and collagen scaffolds.

49

14:45

PROGRESS

38

PG38 Noor Aini Binti Bohari (Ph.D. Candidate) Development of nanocomposite nanofiber based on Indium Tin Oxide (ITO) for mercury detection in cosmetic products.

50

15:00

PROGRESS

39

PG39 Chin Lai Mun (Ph.D. Candidate) Changes of soil pathogenic bacteria in an in vitro simulated temperature rise environment.

51

15:15

PROGRESS

40

PG40 Wan Nur Shuhada Binti Wan Mahadi (M.Sc. Candidate) Construction, over-expression, purification, enzymatic activity of active-site mutant of an α-mannanase from Arthrobacter sp.

52

15:30

PROGRESS

41

PG41 Helena Biun (Ph.D.Candidate) Microsattellite DNA diversity of tor douronensis from Sabah.

53

15:45

PROGRESS

42

PG42 Azniza Mahyudin (Ph.D. Candidate) Development of genetic markers and screening for viruses in insectivorous bats from Madai cave, Lahad Datu, Sabah.

54

16:00

PROGRESS

43

PG43 Mayridzatul Farhain Binti Misrah (M.Sc. Candidate) Antioxidant activity and total phenolic content in aqueous extracts of selected mangrove plant in Sabah.

55

16:15

PROGRESS

44

PG44 Jennifer Charles Labo (M.Sc. Candidate) Cloning, expression and purification of Hsp70 from Psychrophilic yeast, Glaciozyma antarctica.

56


10

DAY3

31st JULY 2019 (WEDNESDAY)

SESSION 1 Page


08:45

PROGRESS

45

PG45 Low Yi Yik (Ph.D. Candidate) Preliminary bacterial diversity study of abandoned mining site and surrounding areas of former Mamut Copper Mine, Sabah.

57

09:00

PROGRESS

46

PG46 Ching Xin Jie (Ph.D. Candidate) Analyses of thermal adaptation among bacteria using comparative genomics and transcriptomic approaches.

59

09:15

PROGRESS

47

PG47 Devina David (Ph.D. Candidate) Metabolomics study of wild and in vitro cultivated Sabah jewel orchid Macodes limii JJ Wood & AL Lamb.

60

09:30 TEA BREAK

09:45

PROGRESS

48

PG48 Chee Fong Tyng (Ph.D. Candidate) Molecular screening, characterization and evaluation of Sabahans traditional rice germplasm for the presence of aromatic trait.

61

10:00

PROGRESS

49

PG49 Mohammad Munir Hossain (Ph.D. Candidate) Formulation of bacterial consortia for kenaf (Hibiscus cannabinus) bast fibre retting.

63

10:15

PROGRESS

50

PG50 Farhan Nazaie (M.Sc. Candidate) Characterisation of structure and function relationship of heat shock protein 20-like chaperones in the Psychrophilic Yeast, Glaciozyma antartica.

64

10:30

PROGRESS

51

PG51 Nur Asfariena Binti Tupah (M.Sc. Candidate) Inferring the genetic relatedness of Sabah indigenous ethnic groups based on complete Mitochondrial DNA Hypervariable Region.

65

10:45

NOTICE

52

NS52 Rennielyn Rupert (M.Sc. Candidate) Isolation and characterization of biofilm forming bacteria from soil samples at Kelantan River Basin (KRB).

66

11:00

NOTICE

53

NS53 Calvin Jiksing (M.Sc. Candidate) Identification of unique DNA sequences from Salmonella serogroup C genome.

67

11

11:15

NOTICE

54

NS54 Teoh Chui Peng (Ph.D. Candidate) Molecular basis of thermal adaptation strategies among bacterial from tropical and Antarctica regions.

68

11:30

NOTICE

55

NS55 Rafida Razali (M.Sc. Candidate) Heterologous expression, purification and characterization of bromelain from MD2 pineapple.

69

11:45

NOTICE

56

NS56 Norzulaiha Binti Abd Karim (M.Sc. Candidate) Characterisation of mature region of 2S albumin, a mabinlin-like protein from Theobroma cacao.

70

12:00

NOTICE

57

NS57 Haselamirrah Binti MD Akhir (M.Sc. Candidate) Modulation of biomaterials on the proliferation and gene expression of amnion-derived mesenchymal stem cell.

71

12:15 LUNCH BREAK

14:30 Special Talk by Guest Speaker

15:30 Closing Remarks


PP: Proposal presentation; PG: Progress presentation; NS: Have submitted ‘Notice for Thesis Submission’

12

Horizontal gene transfer (HGT) is the movement of genetic material laterally from one organism to

another. Examples of HGT are the transfer of antibiotic resistance, virulence and adaptation abilities

between bacteria. Three mechanisms are involved; conjugation, transduction and transformation, this

investigation will focus on the latter. Numerous HGT reports have concentrated on antibiotic

resistance of pathogenic P. aeruginosa strains but limited studies have been done involving

environmental strains. We posit that P. aeruginosa and E. coli can participate in HGT in vitro as

evinced by the transformed E. coli colonies containing P. aeruginosa’s DNA exhibiting the altered

phenotype. The objectives are to evaluate the process of HGT in co-cultures of bacteria via

transformation, to assess the stability of transformed cultures and to observe any phenotypic and

morphological changes that occur. P. aeruginosa strain MCMY15 was obtained from the Mamut

Copper Mine, Sabah. Natural transformation was carried out using co-cultures of both bacteria,

morphological characteristics were studied to identify altered phenotypes. E. coli TOP10 strain is

chemically transformed with P. aeruginosa using plasmid pUC19. Selective media was used to identify

successful transformation and plasmid stability is tested by growing successful transformants for

several generations. Preliminary results indicate no significant morphological changes of co-cultures

tested for natural transformation. Expected results using chemical transformation is that E. coli will

exhibit altered adaptation abilities similar to P. aeruginosa. This research provides a basis to continue

in-depth HGT studies in a locally isolated environmental P. aeruginosa strain and its impact on the

environmental gene pool.

This M.Sc. candidate is under the supervision of Assoc. Prof. Dr. Kenneth Francis

Rodrigues

Latest Publication & Awards: -

Investigating horizontal gene transfer from Pseudomonas

aeruginosa to Escherichia coli (Top 10) via natural and

chemical transformation in-vitro

(M.Sc. Candidate)

Rajeena Sugumaran

PP01

13

Carnivorous plants are unique compared to other plants as it capable of trapping and digesting

insects (and small animals), to be used as a source of nutrients. To date, the mechanism of gene

regulatory by miRNA in carnivorous plants has never been reported. Therefore, this study aims to

identify the miRNA biogenesis pathway possessed by carnivorous plants, whether it is of a plant,

animal, or a combination of both pathways. Given that the miRNA biogenesis pathway in animals and

plants are regulated by different genes, therefore, the conservation of any of these genes will be

used as a measuring criterion to identify pathway possessed by carnivorous plants in this study.

Throughout this research, pitcher plant (Nephentes gracilis) will be used to represent carnivorous

plant, while human and tomato will be used as a positive control, representing animal and plant

samples. DNA will be extracted from all samples and subsequently used for genes amplification. A

total of ten genes will be amplified, of which five are coding for proteins involved in animal miRNA

biogenesis pathway (Drosha, DGCR8, EXP5, DCL1 and TRBP2A proteins), while another five in plant

(DDL, SE, HST, HYL1, DCL1, HEN, and AGO1 proteins). The presence and/or absence of these genes

in N. gracilis will give an overview on the pathway possessed by carnivorous plants. Identification of

miRNA biogenesis pathway possessed by this organism is important as it will help in determining the

right criteria/parameters to be used in the identification and characterization of miRNA in the future.

This M.Sc. candidate is under the supervision of Dr. Noor Hydayaty Md. Yusuf


Identification of regulatory genes responsible for

microRNA biogenesis pathway in carnivorous plant

Nephentes gracilis

(M.Sc. Candidate)

Pamela David

PP02

14

Natural selection is the evolutionary process that allows survival of the fittest against environmental

challenges such as high altitude, limited food source and climate change. This has resulted to genetic

adaptation that favours alleles that provide protection against the environmental challenges. Bajau

Laut or known as Sea Gypsies, a population residing off the east coast of Sabah, subsists on marine

resource with their extraordinary diving capability. They live around small islands and have been

exposed to strong UV light in the open sea. It is hypothesized that their subsistence and exposure to

strong UV light act as the force of natural selection that lead to genetic adapation. This proposed

work will firstly, to identify mitochondrial DNA haplogropus among the Bajau Laut based on the

sequence variations on the hypervariable region (HVR); secondly, to determine genetic structure

among Bajau Laut and other ethnic groups in Sabah and surrounding regions; thirdly, to identify

genomic regions that exhibit signal of natural selection due to their subsistence and living

environment. Briefly, the complete HVR (1.15 kbp) will be amplified and sequenced for identification

of mtDNA haplogroups. Individual with non-identical haplogroups will be selected for genotyping with

~660,000 genome-wide single nucleotide polymorphism (SNP) markers, using Asian Screening Array

panel (Illumina). The genotyping data will then be used for inferring genetic structure and

identification of natural selection signals. It is expected that the outcome of this work will help in

better understandings on genetic diversity of the multi-ethnic population in Sabah, as well as the

effect of natural selection on genetic adaptation of the Bajau Laut to their current subsistence and

environment. As a preliminary result, a total of 90 samples were collected from three islands offshore

of Semporna. The complete HVR will be amplified and sequenced.

This M.Sc. candidate is under the supervision of Dr. Yew Chee Wei


Identification of genomic regions exhibiting signals of

natural selection on Bajau Laut

(M.Sc. Candidate)

Rojilin Donol

PP03

15

Nowadays multidrug resistance organisms (MRO) is the main problem in the medical field and already

widespread in Malaysia. Existing antibiotics also contribute to environment pollution and cause some

side effects to the recipients. In this case, new antimicrobial drugs are needed to replace the existing

antibiotics with consistent production, cause less problem and safe for consumption. New drugs

discovery involve a lot of studies from many aspects such as understanding of the fundamental,

clinical trial and biosafety. The production of antibiotics can be obtained from microorganisms, plants,

animals and chemically synthesized. One of the increasingly studied is the antimicrobial peptides from

microorganisms that has potential as a new mechanism to destroy pathogens. Antimicrobial peptides

such as Toxin-antitoxin system (TA system), bacteriocin and phage lysine. In this study, the

fundamental of TA System is studied by using Paedobacter cryoconitis strain BG5 as the source of the

protein. P. cryoconitis was selected because it produces antimicrobial activity from the study of Wong

et al, 2011. It also carries plasmid pMWHK1 which has the ability to withstand extreme conditions

such as elevated temperature. The aims of this study are to determine whether orf5, orf6 orf1, orf7

and orf8 in plasmid pMWHK1 encode antimicrobial peptides and to characterize the orf in plasmid

pMWHK1 that has antimicrobial activity.

This M.Sc. candidate is under the supervision of Prof. Dr. Michael Wong Vui Ling


Characterization of putative antimicrobial peptides from

Pedobacter sp. strain BG5

(M.Sc. Candidate)

Siti Kasmah Binti Md Yusof

PP04

16

Aquaculture has been an important economic resource of many countries, however the increase in

frequency and intensity of algal bloom cases in coastal waters is worrying the fisheries industry.

Occurrence of Cochlodinium polykrikoides bloom are seasonal specifically in Sabah, Malaysia; where it

occasionally occurred during monsoon season due to heavy rainfall which bring high nutrients to

water surface. Upon various studies that have been focusing in bloom outbreak, there are limited

information on the potential molecular targets for bloom characterization to better understanding the

bloom formation in Sabah. Thus, this study aims in using comparative metatranscriptomics to

investigate the molecular mechanism associated with C. polykrikoides bloom; where gene expression

will be shown in depth including the coding and non-coding RNA that might expressed differently on

both occasion. Besides that, the role of environmental factors associated with HABs will be

investigated by analyzing transcripts associated with specific environmental cues. The research areas

include Gaya Island or Sepanggar Bay where two occasions of blooms at three different stations will

be collected. Furthermore, total RNA extraction of three replicates of bloom and non-bloom

environmental samples will be sequence to see the differential expression of dinoflagellates-

associated gene. Data collected will reveal the interactions of C. Polykrikoides with neighboring

dinoflagellate and bacteria in response to surrounding environment changes. Thus, findings of this

study will provide deeper understanding of bloom formation in the molecular level so that bloom

management efforts could be done more efficiently.

This M.Sc. candidate is under the supervision of Mdm. Grace Joy Chin Wei Lie, Assoc.

Prof. Dr. Kenneth Francis Rodrigues and Dr. Madihah Jafar Sidik


Molecular dynamics of harmful algal blooms: a case

study based on Cochlodinium polykrikoides

(M.Sc. Candidate)

Diana binti Lorons

PP05

17

Bamboos are a group of woody perennial grass belonging to the family of Poaceae, subfamily

Bambusoideae and grow in most tropical and subtropical zone. The characteristics of lignified culms,

fast growth, intricate rhizome system and sustainability make bamboo valuable in both industrial and

non-industrial sectors. Sabah has at least nine genera of bamboo with approximately 35 species

where the local people use bamboo to maintain their livelihood and the environment. There is a wide

genetic diversity of bamboo in Sabah and this pool of genetic variation may serve as a basis for

selection and plant improvement. However, a decline in the range and diversity of endemic bamboos

arise due to overexploitation of bamboo resources and destruction of their natural habitat. Despite

little has been documented regarding their genetic diversity, conservation of the genetic resources of

Sabah endemic bamboos is urgently needed. This study aims to confirm the genetic identity of

endemic bamboo from Sabah using DNA Barcoding and to access the genetic stability of in vitro

cultured bamboo using a mutation detection assay. A fast-growing species with diverse utilization

potential will be selected for tissue culture and their growth in vitro will be optimised by using

different culture media and combinations of plant growth regulators. The bamboo germplasm is

expected to exhibit genetic stability in vitro and achieve germplasm conservation purpose. This study

will contribute to fill a knowledge gap in genetic identification of Sabah endemic bamboos and

establish a tissue culture system for mass propagation of bamboo varieties.

This M.Sc. candidate is under the supervision of Dr. Wilson Yong Thau Lym,

Assoc. Prof. Dr. Kenneth Francis Rodrigues and Mr. Julius Kulip


Species identification and genetic stability of endemic

bamboo germplasm in vitro

(M.Sc. Candidate)

Jerlyn Joan Jenius

PP06

18

The use of artificial lights in indoor farming has been growing due to its cost effectiveness and

efficiency for plant growth. Appropriate combination of lighting types and photoperiod can be

optimized for high yield production. Artificial farming is recommended as it could achieve maximum

productivity with minimum resources in controlled-environment cultivation. Despite consistency in

production under artificial lights, however, there is little knowledge on effect of light intensities and

photoperiod on Brassica sp. This study aims to assess the growth, chlorophyll content and

biochemical composition of Brassica sp. under different light intensities and photoperiods. Artificial

and natural lightings with photoperiods of 12:12 and 6:6 (light:dark) will be tested. The growth and

chlorophyll content of Brassica sp. under each treatment will be measured and recorded. The

biochemical composition of treated plants will be profiled using gas chromatography for volatile

compounds and liquid chromatography coupled with QTOF for non-volatile compounds. Artificial

farming is expected to produce higher yield and chlorophyll content in Brassica sp. under optimized

conditions than natural farming. The photosynthetic efficiency of plants is predicted to be reflected on

their biochemical profile and the chromatograms between different light treatments will be analyzed

for significant compositions. This study is important to provide information on specific light intensity

and photoperiod for optimized plant growth and the effects of artificial lighting on the biochemical

composition of Brassica sp.

This M.Sc. candidate is under the supervision of Dr. Wilson Yong Thau Lym and Assoc.

Prof. Dr. Kenneth Francis Rodrigues


PP07

Photosynthetic efficiency of artificial lighting on

Brassica sp.

(M.Sc. Candidate)

Nurul Sakinah

19

Cellulose is the most abundant bio-polymer on Earth, of enormous commercial value in fibre

industries. The use of cellulose as a raw material in bio-industry requires cellulose-degrading enzymes

(cellulases E.C. 3.2.1.4). Sabah houses hot springs and mud volcanoes that have not been explored

optimally as sources of indigenous thermostable cellulases. The use of thermostable enzymes has

been gaining wide interest due to their versatile industrial and biotechnological applications

performed under harsh condition (high temperature). This study aims to screen, isolate and

characterize thermostable cellulases from extreme environment in Sabah. Two locations in Sabah for

hot spring (Poring and Tawau) and three locations for mud volcano (Kalabakan, Tabin Wildlife

Reserve, and Pulau Tiga) will be chosen which in nature posses higher temperature condition that

might harbour thermostable cellulases. The bacteria producing thermostable cellullases will be

screened under carboxymethyl celullose (CMC)-based agar plate system. The colonies displaying

widest halo zone will be selected and subject to whole genome sequence for the identification of the

gene encoding its cellulases. The gene will be then cloned into expression system for production of

the enzyme under recombinant system. The expressed and purified enzyme will be then catalytically

characterized to decipher its catalytic adaptation mechanism at high temperature. This study should

contribute to the availability of indigenous thermostable cellulases and provide new insight into their

catalytic adaptation mechanisms.

This M.Sc. candidate is under the supervision of Dr. Cahyo Budiman/ Prof. Dr. Clemente

Michael Wong Vui Ling/ Dr. Zarina Amin


PP08

Screening, isolation and characterization of

thermostable celullases from Sabah, Malaysia

(M.Sc. Candidate)

Nurshafrina Aida binti Yahya

20

Vancomycjn Resistance Enterococci (VRE) is a worldwide problem and is increasingly becoming a

prevafent nosocomiat pathogen. Reports indicate that it causes endocarditis, sepsis and infection of

the skin, urinary or the respiratory tract. This opportunistic gram-positive bacterium is part of the

normal human flora in the intestine. The most dominance human VRE strain is Entencoccus faecalis

and Enterococcus faecium and broad-spectrum antimicrobial use seem to accelerate the process of

acquiring colonization and increases susceptibility to diseases. The resistance of E. faecalis and E.

faecium to vancomycin is caused by the acquisition of vanA and vanB genes, the two most common

VRE genes which are important in clinical settings. Recent research has showed that clinical setting is

not the only sources for VRE strains but also from environmental settings and food animal and retail

meats transmitted to non-hospitalized people. It is hypothesised that the rampant use of broad range

antibiotics in animal husbandry particularly in cattle, poulty and pig farms in Sabah has a chain-effect

that leads to the widespread acquisition of VRE genes in non-nosocomial settings. This research aims

to identify and characterise the VRE genes and to determine possible epidemiological association

among the three different reservoirs i.e. clinical, environmental and animal isolates. There are several

sets of expected results from this study. Firstly, the colonization distribution of E. faecalis and E.

faecium bacteria obtained from clinical settings. Secondly, the identification of VRE genes isolated

from different sources i.e. HA-VRE and CA-VRE and its interaction (transmission). Finally, the data will

reveal the genomic diversity of circulating VRE in Kota Kinabalu Sabah, which may provide leads to

potential environmental and animal reservoirs. Hence, this study will provides insight on the emerging

VRE gene patterns to assist health authorities on mitigation steps needed to slow down the antibiotic

resistant infection.

This Ph.D. candidate is under the supervision of Assoc. Prof. Dr. Mohammad Zahirul

Hoque and Assoc. Prof. Dr. Vijay Kumar


PP09

Molecular characterisation of Vancomycin Resistance

Enterococcus (VRE) genes isolated from clinical,

environmental and animal samples from Kota Kinabalu,

Sabah

(Ph.D. Candidate)

Nur Nashyiroh Izayati binti Mastor

21

MD2 Pineapple is a commercial tropical fruit and its demand in the global market is inclining steadily.

However, its slow growth rate hinders maximum profit as it takes approximately 18 to 30 months

before the fruit can be harvested. The key element in controlling fast growth of pineapple is yet to be

discovered. MicroRNA (miRNA) is a small RNA (sRNA) that controls gene expression (up- or down-

regulated) and is known as a regulator of phase transition. Thus, this research aims to identify key

miRNAs that regulate phase transition, as it is hypothesized to control (accelerate or slow) the growth

of pineapple. In order to identify these specific miRNAs in pineapple, six sRNA libraries will be

constructed representing six different developmental stages (shoot development, inflorescence,

flowering, fruit maturation (index 1), the onset of fruit ripening (index 4), and fruit senescence (index

7) through high-throughput sequencing technology. Bioinformatics analyses will be performed to

identify miRNAs from sRNA libraries together with genes and their target protein. Differential

expression of the newly identified miRNAs will be verified by using stem-loop RT-qPCR analysis. This

study will help to identify the key miRNAs controlling phase transition in MD2 pineapple. As the

growth of the pineapple involves the transition of multiple growth stages, in the near future,

manipulating these key miRNAs controlling the transition between one or more of these phases may

lead to significant enhancements in the growth of pineapples.

This Ph.D. candidate is under the supervision Dr. Noor Hydayaty Md. Yusuf


PP10

Role and mechanisms of miRNA regulation in phase

transition and growth enhancement of MD2 pineapple

(M.Sc. Candidate)

Khairul Nizam Bin Sehat

22

Sago has been cultivated in Sarawak for over a century as a cottage industry but it has now become

one of the major export commodities for the state. Institutions such as CRAUN Research have led the

way by successfully developing an in vitro propagation system for sago. However, the last batch of

sago clone planted in 2015 exhibited an increase in abnormalities i.e. from 1% (standard) to 5%. This

is a big concern since the abnormal clones were not trunking and subsequently not producing

succession suckers leading to a loss of income for farmers. It is hypothesised that the somaclonal

variation in sago tissue culture are suspected to occur after three years of exposure to high hormones

concentration (18th subculture). There is a need to develop highly polymorphic sago specific markers.

In this study, genomic DNA for sago will be sequenced using RSII Pac Bio sequencer to produce

shotgun sequence data which will be used to developed microsatellite markers. These markers will be

used to screen for polymorphisms in sago tissue culture samples through PCR amplification which will

confirm the hypothesis. In addition, a low coverage high throughput sequencing utilising Illumina’s

SkimSeq approach will be performed on abnormals clonal sago palms from Craun’s research plot, in

order to obtain Single Nucleotide Variant (SNV) information of regions with high genetic hot spots in

sago palm. The results of this study is expected to be used to control and maintain high quality sago

clonal planting material for the sustainable sago industry.

This Ph.D. candidate is under the supervision of Assoc. Prof Dr. Vijay Kumar

Latest Publication & Awards:

1. Genetic Transformation of Metroxylon sagu (Rottb.) Cultures via Agrobacterium-Mediated and Particle Bombardment. BioMed Research International, Volume 2014 (2014), Article ID 348140, 9 pages. Evra

Raunie Ibrahim, Md. Anowar Hossain and Hairul Azman Roslan. 2. Minimal Inhibitory Concentration of BastaTM for Sago Palm (Metroxylon Sagu Rottb.) Transformant

Selection.Proceedings of the 12th International Sago Symposium, September 15-16, 2015. Tokyo, Japan. Evra Raunie Ibrahim1*, Hairul Azman Roslan 2 , Noraini Busri1 and Yusup Sobeng1

PP11

Development of molecular marker for sago palm

(Metroxylon Sagu Rottb.) and its application for

screening somaclonal variation

(Ph.D. Candidate)

Evra Raunie Ibrahim

23

Biofilm is a population of microorganisms where microbial cells are attached to one another on living

or non-living surfaces within the matrix of extracellular polymeric substance produced by the

bacteria themselves. Meanwhile, early studies have revealed that extraction of mangrove plants

shows antibacterial activity against pathogenic bacterial due to their rich source of secondary

metabolites and bioactive compounds. The aim of this study is to investigate the anti-biofilm activity

of selected mangrove plants extract from Sulaman Wet Land, Sabah against Pseudomonas

aeruginosa and Escherichia coli. Three species of mangrove (Avicennia marina, Bruguiera

gymnorrhiza and Xylocarpus granatum) were selected in this study and the leaves of these plants

were extracted using ethanol. The result shows that the X. granatum ethanolic extract has the

highest percentage yield with 11.60%, followed by B. gymnorrhiza (9.08%), and A. marina (2.95%).

The extracts will be subjected to a Folin-Ciocalteu method for its phenolic content and DPPH radical

scavenging assay for antioxidant activity. The anti-biofilm activity of extracts will be tested on

selected pathogenic bacteria using quantitative biofilm production assay. The differential expressions

of specific biofilm related genes in P. aeruginosa and E. coli will be examined by using Real Time

PCR machine. As a conclusion, mangroves have been widely used to treat various kinds of infection

as they possess biological activities including antifungal, antibacterial and pesticidal properties. Thus,

these plants are crucial to global bioprospecting programs dedicated to searching new (chemical)

alternatives to prevent diseases of high-impact on humanity and may increase their possible

application.

This M.Sc. candidate is under the supervision of Dr. Ruzaidi Azli Bin Mohd Mokhtar and



Biofilm inhibition of pathogenic bacteria by mangrove

plants extraction

(M.Sc. Candidate)

Kasra Mukti

PP12

24

Abstract not submitted

PG13

Comparison of microRNA expression profiling of Human

Amnion and Wharton’s Jelly Mesenchymal stem cells

during adipogenic differentiation

(Ph.D. Candidate)

Syva Hednella Sabanting

25

Non-polar metabolites were extracted from previously morphologically identified marine sponges

using a modified Folch’s extraction method to increase the amount of non-polar metabolites

extracted. The extracted non-polar metabolites were analysed using untargeted UHPLC-HRMS/MS

with a reverse-phase, multistep gradient, targeting small molecules (50 Da to 1500 Da). The high

sensitivity of the mass spectrometer tend to introduce detectable noise peaks during analysis, the

number of which can vary depending on the pre-set intensity threshold set during the data

acquisition. UHPLC-HRMS/MS analyses on the HPLC grade methanol blanks and the non-polar layer of

the extraction buffer suggests that there are impurities present, and that these impurities are likely to

be present in the samples as well. Neither the identities, nor the exact sources of these impurities

were determined at this point in time. The alignment of the detected peaks among technical

replicates of the same samples, as well as subsequent gap-filling of the said alignments suggests that

there are low-confidence peaks (aligned peaks with minority support) present across all the samples.

Although the number of peaks removed by removing low-confidence peaks and peaks contributed by

impurities from the aligned, gap-filled peaks are similar across all marine sponge samples, the

number of remaining aligned, gap-filled peaks greatly vary from one sponge sample to another. This

suggests that the marine sponges (and their associated symbionts) produce different types of small,

non-polar metabolites at varying degrees. Peaks contributed by impurities, noise peaks and low-

confidence peaks should be removed as it will affect subsequent downstream analyses.

This Ph.D. candidate is under the supervision of Professor Dr. Jualang Azlan Gansau, Dr.

Lum Mok Sam, and Dr. Christopher Voo Lok Yung.


1. Ling, Y. S., Lim, L. R., Yong, Y. S., Lee, D. J. H., Puah, P. Y., and Tamin, O. 2018. Programmed cell death driven by down-regulation of phospholipids in cancer cells: A potential anticancer compound from Bornean Jaspis sp.. PEREKA: Gold medal.

2. Lum, M. S., Benedick, S., Rahman, H., Ling, Y. S., Gobilik, J., Lee, D. J. H., Lim, R. A. H., Ariffin, J., Ador, K., and Kasim, H. A. 2018. Honey characterization produced by contract beekeepers in various areas in Sabah. PEREKA: Silver medal.

PG14

Removal of impurities, noise and low-confidence peaks

from data acquired from mass spectrometer: a

proposed general workflow

(Ph.D. Candidate)

Dexter Lee Jiunn Herng

26

3. Benedick, S., Gobilik, J., Ling, Y. S., Lum, M. S., Lim, R. A. H., Lee, D. J. H., and Ador, K. 2018. Evaluation of phenolic compounds properties in honey of three species of stingless bees: A comparison

with Apis cerana honey and sugar. PEREKA: Bronze medal.

27

Phosphorus is one of the major growth-limiting macronutrients required for proper plant growth,

particularly in tropical areas, due to its low availability in the soil. Approximately, 95-99% of

phosphorus present in organic forms that insoluble and poorly available for plant intake. Meanwhile,

various organisms particularly fungi found to be effectively transform insoluble phosphate into soluble

forms that can easily absorb by plants. Exploitation of fungi as inoculants for bio-fertilizer is

considered to some extent an alternative to chemical fertilizer in agricultural sector due to their

extensive potentiality in enhancing crop production and food safety. Thus, the aim of this study was

to isolate and identify the potential phosphate-solubilizing fungi (PSF) from different agricultural soil

for organic composting of food wastes. A total of 13 soil samples were collected respectively from

banana, groundnut and corn in Kundasang and Ranau. A total of 73 fungal isolates cultured from

these areas. The isolates were successfully characterized on the basis of its morphological characters

including macroscopic and microscopic observations. Further, the species level identification of the

isolates will be analysed based on its internal transcribed spacer (ITS) of the rDNA and translation

elongation factor-1α (TEF-1α) gene. The potential PSF will be screened using both quantitative and

qualitative methods. Thus, this study will provide the PSF diversity and its distribution across

Kundasang and Ranau, Sabah.

This Ph.D. candidate is under the supervision of Assoc. Prof. Dr. Md. Shafiquzzaman

Siddiquee and Assoc. Prof. Dr. Vijay Kumar.


PG15

Isolation of fungi from agricultural soils in Sabah for its

phosphate-solubilizing potential in composting of food

wastes

(Ph.D. Candidate)

Azriah Binti Asis

28

The development of multiple-antibiotic-resistant strains of bacteria is a major concern as there are

fewer classes of antibiotic that are effective to kill them. This drives research on new antimicrobial

compounds against those bacteria. Among the new potential antimicrobial compounds are the PemK

gene in the toxin-antitoxin system and the bacteriophage lysin (phage lysin) gene. Therefore, this

work aims to determine whether PemK and phage lysin genes from Antarctic bacteria have

antimicrobial activity towards the indicator pathogens. The objectives of this study are (1) to clone

the PemK and phage lysin gene from Cryobacterium sp. SO1 and Pedobacter cryoconitis BG5

respectively and (2) to determine the effect the gene products toward pathogenic bacteria. The PemK

and phage lysin genes were cloned into the pBAD and used to transform Escherichia coli , TOP10.

After cloning, Plasmids containing genes PemK and phage lysin were sent for sequencing. The crude

pemK and phage lysin protein extract were tested on Salmonella typhimurium, Salmonella

braenderup, Enterobacter cloacae, Klebsiella pneumonia, Vibrio haemolyticus, Bacillus cereus, Listeria

monocytogenes, Yersenia enterocolita, Salmonella biafra, Staphylococcus aereus and Pseudomonas

aeruginosa. None of this protein shows inhibition of pathogens. It is assumed that the protein might

active in different condition such as temperature. Thus, next step is to test the protein on pathogens

in different temperature.

This M.Sc. candidate is under supervision of Prof. Dr. Clemente Michael Wong Vui Ling


PG16

Characterization of the phage lysin and PemK

genes from Antarctic bacteria

(M.Sc. Candidate)

Sylvbryanie Salister

29

The limited information of hypothetical proteins (HPs) in Glaciozyma antarctica (yeast) and

Pedobacter cryoconitis (bacterium) proved to be an immense challenge in our effort to understand

their cellular defence mechanisms. This study aims to solve the relationship between structure and

function of the conserved HPs related to thermal stress response. The in-silico analysis of HPs will be

conducted using bioinformatics analysis, followed by in vitro approach where all selected HPs will be

cloned, expressed in Escherichia coli, purified and subjected to crystal screening for structural

determination. The bioinformatics screening revealed a total of twelve P. cryoconitis and three G.

antartica conserved HPs with significant thermal stress responses and fulfilled the criteria for

crystallization. All the target genes for P. cryoconitis have been successfully amplified with different

annealing temperatures (45–55°C) and cloned. Currently, three P. cryoconitis proteins (Pc_CHP1,

Pc_CHP2, Pc_CHP7) have been successfully overexpressed in the presence of 0.5 Isopropyl β-D-1-

thiogalactopyranoside (IPTG) at 16°C. Recombinant Pc_CHPc2 was produced in soluble form,

successfully purified via His-Tag (HisTrap™ HP 5 ml) and size exclusion (HiLoad® 16/600 Superdex®

200 pg) column. Future work will focus on the crystal screening of Pc_CHPc2 proteins for structural

determination and functional analysis.

This Ph.D. candidate is under the supervision of Dr. Nur Athirah Yusof and Prof. Dr.

Clemente Michael Wong


1. Gold Medallist (Innovation), Research and Innovation Competition (PEREKA) (24-25 October 2018)

2. Grantee, Asean Workshop on Protein Crystallography (AWPX2018)

PG17

Elucidation of structure and function of conserved

hypothetical proteins related to thermal stress response in

psychrophilic microorganism; Glaciozyma antarctica and

Pedobacter cryoconitis.

(Ph.D. Candidate)

Makdi Masnoddin

30

Approximately 17 million tons of oil palm empty fruit bunch (OPEFB) was produced yearly in Malaysia,

and instead of treating it as a plant-based waste, OPEFB actually has the potential to be utilized as

raw material for biopolymer, namely lignin. Numerous studies had reported the capability of both

chemical and mechanical pretreatment in degrading lignin from OPEFB, however, studies on the

biodegradation of lignin in OPEFB still remains limited. It was hypothesized that locally isolated fungi

are capable in degrading lignin from OPEFB. Hence, this hypothesis was proved using degradation

assays that was conducted on the locally isolated fungi. A total of 50 potential lignin-degrading fungi

were identified using RBBR and followed by Sundman and Nase assays with Phanerochaete

chrysosporium as a positive control. The secretion of ligninolytic enzymes by fungi causes the

decolourisation of RBBR. Positive fungi were than evaluated using Sundman and Nase assay, a simple

method that exhibit colour changes when lignin degradation occurred. The results suggested that

most of the fungus that had shown positive results in RBBR, appeared to be positive in Sundman and

Nase assay as well. For future work, lignin characterisation using NMR will be conducted, followed by

DNA extraction and gene sequencing to identify the potential lignin-degrading fungi.

This M.Sc. candidate is under the supervision of Dr. Clarence M. Ongkudon


PG18

Screening and identification of lignin-degrading fungi

isolated from local biodiversity

(M.Sc. Candidate)

Abigail Lorna Eric

31

Electrochemical sensor has drawn growing attention among researchers and industries due to its

cost-effectiveness, time-efficient, easy operation and portability for heavy metal ions detection. In the

present study, an electrochemical method for detection of zinc, manganese and aluminium ions was

performed by means of differential pulse voltammetry (DPV) with different concentrations of zinc (1

to 10 ppm), manganese (0.05 to 1.0 ppm) and aluminium (0.1 to 0.7 ppm) ions. The fixed potential

peak current was at 0.662689 V for the three heavy metal ions. The limits of detection were found at

0.0028 ppm for zinc, 0.075 ppm for manganese and 7.527 ppm for aluminium ions. In addition, the

sensitivity of zinc, manganese and aluminium ions were 0.019 mA, 0.256 µA and 6.259 µA,

respectively. The findings of this study indicate that the electrochemical method was able to detect

the present of heavy metal ions in drinking water at concentration far below the safety limit. Thus,

the proposed sensor method is a promising tool for detection heavy metal ion in drinking water.

This M.Sc. candidate is under supervision of Assoc. Prof. Dr. Shafiquzzaman Siddiquee,

Dr. Suryani Saallah and Dr. Mohammad Tamrin Mohamad Lal


1. Gilbert, R., Siddiquee, S., Mohammad Tamrin M.L. 2018. Electrochemical Methods for the Analysis of Zinc Ion. In: Kenneth F.R., Methods in Biotechnology Volume II, pp.77-81. Biotechnology Research Institute.

2. Gilbert, R., Siddiquee, S., Mohamad Lal, M.T., Suryani S., Nor Hydayaty M.Y., Amin, Z. 2018. Electrochemical methods for detection of zinc ion in drinking water. International Journal of Pharma and Bio Sciences 9(SP – 01/12): 161-166

3. Gilbert, R., Siddiquee, S., Saallah, S. and Tamrin M. Lal. 2019. Optimisation of parameters for detection of manganese ion using electrochemical method. IOP Conference Series (Submitted to UMS FKJ).

PG19

Electrochemical sensor based determination of zinc,

manganese and aluminium ions

(M.Sc. Candidate)

Gilbert Anak Ringgit

32

Sugarcane stem borer, Chilo tumidicostalis Hampson (pyralidae: lepidoptera), is one of the most

abundant and destructive insect pests in sugarcane. The usage of chemical pesticides have caused in

serious environmental problems and food pollution as well as having many diseases in human health.

The potential candidate of entomopathogenic strains will be selected based on enzymatic activities

(lipases, proteases and chitinases) against sugarcane stem borer. The aim of this research was to

isolate and characterize of entomopathogenic soil-borne fungi in sugarcane, corn and cassava,

located in Tuaran, Sabah, Malaysia. Insect mealworm,Tenebrio molitor L. larvae were collected from

Penampung Harvest Fish & Agriculture Sdn. Bhd., Sabah, Malaysia. Sugarcane was planted in the

plant transenic facility site of BRI, UMS for observing the incidence of sugarcane stem borer. Fungi

were isolated based on insect bait method. Soil samples were baited with the mealworm larvae and

incubated in the dark at 270C for 5 days. A total of 20 isolates were screened from 60 isolates on the

basis of colony forming units (CFU) color and physiological characters. Identification of the potential

strains will be applied on sugarcane stem borer for determination of their effectiveness.

This Ph.D. candidate is under the supervision of Associate Prof. Dr. Md. Shafiquzzaman

Siddiquee and Associate Prof. Dr. Vijay Kumar A/L Subbiah


PG20

Study of entomopathogenic fungi and its

pathogenicity for controlling sugarcane stem borer,

Chilo tumidicostalis hampson

(Ph.D. Candidate)

Md. Shafiqul Islam

33

Infectious bronchitis virus (IBV) is categorized as a contagious acute respiratory, reproductive, and

renal system in commercial poultry farm. The molecular characterizations of IBV are very important

for accurately diagnosis due to continuous emergence of IBV strain or serotypes with high mutation

and replication. The main aim of current study was to identify of IBV in poultry farm, Sabah,

Malaysia. IBV samples were isolated from local broiler farms based on clinical sign. The quality tests

were conducted by Real-Time qRT-PCR using universal designed primers and reference primers with

highly conserved nucleocapsid (N) gene and spike (S1) gene. The universal designed primers were

conducted as conformation study with other related respiratory chicken virus such as Avian Influenza

(AI), Infectious Coryza (IC), Escherichia coli, and Avian Pneumovirus (APV), Infectious

Laryngotracheitis virus (ILT) and Newcastle virus (ND). The amplified PCR products were found

approximately 1720 bp for S1 gene and 406 bp for N gene, respectively. The blast analysis revealed

with the similarity values of 96.8%-100%. These findings suggest to monitoring the prevalence of

IBV variants in chicken farm as well as genetic divergence with suitable vaccination strategy.

This Ph.D. candidate is under the supervision of Assoc. Prof. Dr. Md Shafiquzzaman

Siddiquee, Dr. Zarina Amin and Prof. Dr. Sharifudin Md. Shaarani


Isolation and molecular characterization of infectious

bronchitis virus from local isolated of Sabah, Malaysia

(Ph.D. Candidate)

Md. Safiul Alam Bhuiyan

PG21

34

LEAFY COTYLEDON 2 (LEC2) exerts significant impacts on determining embryogenic potential and

various metabolic processes through a complicated genetic regulatory network and is sufficient to

induce somatic embryo development in vegetative cells. Previously, five new designs of TcLEC2

artificial transcription factors (ATFs) were successfully designed and constructed that comprised a

modular structure. The synthetic genes encoding recombinant TcLEC2 ATFs (L1, L2, L6, L7 and L8)

have been constructed and cloned into the expression vector pET100/D-TOPO. Constructions of the

recombinants L1, L2, L6, L7 and L8 were confirmed by PCR amplification and sanger sequencing.

Soluble fusion proteins of the TcLEC2 ATFs were induced by 0.1mM IPTG and were expressed in

Escherichia coli KRX under optimal conditions. The results showed that the proteins induced from

recombinants pET100/D-TOPO-L1 and pET100/D-TOPO-L2 were 20 and 16 kDa repectively. For

pET100/D-TOPO-L6, pET100/D-TOPO-L7 and pET100/D-TOPO-L8 the results showed that they

shared a similar protein size as 7 kDa. The recombinant proteins were separately purified by HisTrap

HP, a nickel-charged IMAC columns for high resolution his-tagged protein purification with high

binding capacity for maximized recovery using ÄKTA pure protein purification system.

This Ph.D. candidate is under the supervision of Assoc. Prof. Dr. Kenneth Francis

Rodrigues and Assoc. Prof. Dr. Zaleha Abdul Aziz


PG22

Construction, cloning and expression of synthetic genes

encoding artificial transcription factors of Theobroma

cacao LEC2

(Ph.D. Candidate)

Mohd Zulhilmi Abdul Rahman

35

Harmful algal bloom (HAB) has become a frequent phenomenon in coastal waters of West Sabah

where one of the causative organisms is the toxic dinoflagellate, Pyrodinium bahamense var.

compressum. Previous studies have well elucidated the genes responsible for the toxin production in

several dinoflagellates such as Alexandrium sp. and cyanobacteria, however little is known for the

major tropical PST-producing dinoflagellate; Pyrodinium bahamense var. compressum. In this study,

we focused on the unique starting gene of saxitoxin biosynthesis sxtA, which includes two domains;

SAM-dependent methyltransferase, sxtA1 and the class II aminotransferase coding gene, sxtA4.

Through BLAST analyses, it was found that the gene sxtA1 and sxtA4 in Pyrodinium bahamense var.

compressum shared high sequence similarity and identity with sxtA domains of other STX-producing

dinoflagellate. Besides that, phylogenetic analyses also revealed close relationships of both the sxtA1

and sxtA4 genes with the other genes from other STX-producing dinoflagellates. Hence, our work

helps broaden the knowledge underlying toxin production in Pyrodinium bahamense var. compressum

for future works.

This M.Sc. candidate is under the supervision of Mdm. Grace Joy Chin Wei Lie and Assoc.



PG23

Characterization of the saxitoxin biosynthetic starting

gene, sxtA in the toxic dinoflagellate Pyrodinium

bahamense var. compressum.

(M.Sc. Candidate)

Sylvia Yahumin

36

Tropical rainforest soil bacteria is known to secrete alkaline phosphatases (ALP), a group of

phosphate solubilizing enzymes, that plays an important role in the rainforest unique phosphorous

partitioning properties. It is interesting that the differences on the phosphorus properties between

forest and non-forest soil are possibly due to the unique features of the bacteria. Hence, this study

aims to screen, isolate and characterize the phosphate solubilizing bacteria from Danum Valley

rainforest. The screening yielded 5 isolates of bacteria displaying remarkable tricalcium phosphate

solubilizing activity. 16s rDNA sequence revealed that these 5 bacteria are Staphylococcus spp.,

Bacillus spp., Pseudomonas spp. and Paenibacillus spp. (Paeni-DV01). As there is no study on

phosphatase activity of Paenibacillae family, Paeni-DV01 was selected for further characterization.

The genomic DNA of this mesophilic Gram negative rod shaped bacterium was subsequently

sequenced using a Pacific Biosciences’ single molecule real time long-read DNA sequencing platform.

The draft genome size was determined as 7,323,160 bp with a G+C content of 53.2%. The analysis

of the genome using RAST revealed 43 annotated genes for phosphoric monoester hydrolases (EC

3.1.3) of which 2 genes encoded ALP (EC 3.1.3.1) were specifically categorised under two

subsystems. The specific phosphatase activity of extracellular fraction of this bacteria was 7378.12 U

mg-1 which is the highest activity compared to previous studies. Although these findings are

promising, in depth understanding and further experimental work are required to unravel the full

potential application of Paeni-DV01 alkaline phosphatase for industrial uses.

This Ph.D. candidate is under the supervision of Dr. Cahyo Budiman, Assoc. Prof. Dr. Vijay

Kumar and Assoc. Prof. Dr. Kenneth F. Rodrigues


1. Lindang, H.U., Budiman, C., Kumar, S.V., and Rodrigues, K.F. 2019. Isolation and Characterization of Phosphate Degrading Bacteria from the Tropical Rainforest Soil of Danum Valley, Sabah. Presented in 6th International Biotechnology Symposium, 10-11 July 2019. The Pacific Sutera Hotel, Kota Kinabalu, Sabah.

PG24

Genomic analysis of Paenibacillus spp. and

characterization of its alkaline phosphatase enzyme

(Ph.D. Candidate)

Herman Umbau anak Lindang

37

Mangrove plants are potential natural source of micronutrients in neutralizing free radical because

their ability to grow in extreme environmental conditions such as high salinity and anaerobic soil. This

study aims to evaluate the total phenolic content (TPC) and antioxidant activity (AA) of ethanolic

extract from different parts (leaves, root and stem) of selected mangrove plants; Rhizophora

mucronata, Xylocarpus granatum, Avicennia Marina, Ceriops tagal, Rhizophora apiculata and

Bruguiera gymnorhiza. TPC was determined by Folin-Ciocalteu’s method while AA was evaluated

using 1,1-diphenyl-2-picrylhydrazyl (DPPH) assays. The ethanol extract of Xylocarpus granatum leaf

exhibited the highest percentage yield of 11.61% followed by Bruguiera gymnorhiza (9.08%).

Appreciable quantities of TPC, ranging from 64.57 to 528.58 mg GAE/g while the highest value was

found in leaves of Ceriops tagal (528.58 mg/g), followed by stem (297.86 mg/g) and leaf (280.99) of

Rhizophora mucronata. Interestingly, a profound similar trend was found between TPC and AA of

respective extracts. The highest antioxidant activity was obtained in leaves of Ceriops tagal with EC50

value of 11.39 μg/ml, followed by leaves of Rhizophora mucronata (21.45 μg/ml). As a conclusion,

study shows that mangrove species are promising antioxidants that would pave the way for further

studies on new medicinal uses.

This Ph.D. candidate is under the supervision of Dr. Ruzaidi bin Azli Mokhtar, Dr. Zarina

Amin and Dr. Cahyo Budiman


PG25

Total phenolic content and antioxidant activity of

ethanolic extracts of selected mangroves from Sulaman

Lake Mangrove Forest, Tuaran

(Ph.D. Candidate)

Tamar Kansil

38

Eggplant (Solanum melongena) is a crop of nutritional and economic importance. The lack of new

eggplant varieties is hampering the development of the crop. The aim of this study

is to develop Ethyl Methane Sulphonate (EMS)-generated novel alleles in eggplants by using the

‘Targeting Induced Local Lesions in Genomes’ (TILLING) platform. Pure inbred eggplant lines were

obtained from the World Vegetable Center, Taiwan. EMS treatment of the seeds gave rise to M1

mutant populations from which seeds for subsequent M2 generation were derived. After several

rounds of planting, the final cultivation of M2 generation was performed for the following varieties,

i.e. Surya, Pant Samrat, Arka Nidhi and EP-47 Annamalai. In order to ensure the homogeneity of the

induced mutation, M2 fruits were harvested to obtain genetically stable M3 generation seeds from the

mutant eggplants. The phenotypic variations across the mutant family members encompassing plant

height, flowering time, number of flowers and the area of the largest leaf were measured and further

analysed to narrow down the number of candidate mutants for subsequent molecular analysis. The

screening of mutations in these EMS-treated offspring will be carried out at the Flowering Locus T

(FT)/ Terminal Flower 1 (TFL1) genic regions through amplicon sequencing via the Pacbio RSII

platform. Thus far, total DNA has been extracted from all the mutant lines using the CTAB protocol.

PCR amplification of eight FT/TFL1 target genes are currently being amplified (with internal primers

using universally- tagged target-specific sequence) and purified complying to the SMRT amplicon

sequencing protocols. The amplified products will be further amplified using Pacbio Barcoded

Universal Primers (BUP) and subsequently constructed to SMRTbell libraries before sequencing on the

Pacbio system. The sequences will be analysed for mutations in the FT/TFL1 gene regions. The new

variants produced through this project will constitute a newly developed biological resource database

to broaden the genetic pool of eggplant.

This Ph.D. candidate is under the supervision of Assoc. Prof Dr. Vijay Kumar


PG26

Targeting Induced Local Lesions in Genomes (TILLING)

analysis of Ethyl Methane Sulphonate (EMS)-induced M2

mutant populations of eggplant (Solanum melongena)

(Ph.D. Candidate)

Ranjita Subramaniam

39

β-galactosidase or lactase is an enzyme that liable to catalyses the hydrolysis from disaccharide

lactose to its two mono carbohydrates glucose and galactose by breaking down B-1,4 de-galactose in

lactose. This particular attribute gives rise of its used in application for health, food biotechnology,

and environment. This study was conducted to analyse the interaction effects among process

variables during β-galactosidase immobilization and optimized the enzyme activity. β-galactosidase

was immobilized via covalent binding on polymethacrylate monolith activated by glutaraldehyde.

Three parameter including enzyme concentration, reaction time, and substrate concentration were

studied for the optimization of β-galactosidase enzyme activity using response surface methodology

(RSM) as statistical analysis. The range that has been used was (0.7-2.2) mg/ml for enzyme

concentration, reaction time (3-10) minutes and substrate concentration (8-30) mM respectively.

Ortho-nitrophenyl- β-galactoside (ONPG) was used as a substrate for enzymatic analysis. From the

result, the enzyme activity was observed. Overall, the model generated in this study by response

surface methodology (RSM) satisfied all the necessary arguments for its use in the optimization.

This M.Sc. candidate is under the supervision of Dr. Mailin Misson and Dr. Clarence M.

Ongkudon


PG27

Optimal immobilization of β-galactosidase on

polymethacrylate monolith via covalent binding using

response surface methodology

(M.Sc. Candidate)

Rima Fatira Binti Dahari

40

Gelatine is a type of polypeptide mixture obtained from the hydrolysis of collagen. The raw sources of

this material are largely produced from pig and cow, with over 47% of gelatine source in the industry

came from pig skin. In the pharmaceutical industry, gelatine is mostly used in the production of

pharmaceutical capsules, which are used to encapsulate medicines. These porcine-based gelatine

capsules contradict with a few religious beliefs that forbids the consumption of pork. This project aims

to optimise an efficient DNA extraction method by modifying the current available methods. Three

DNA extraction methods were conducted; commercial kit, the conventional phenol-chloroform (PC),

and CTAB method. The extractions were conducted on vegetable and bovine pharmaceutical capsules

from Halalgen Sdn. Bhd. For commercial kit and phenol-chloroform methods, both methods are not

able to give acceptable pure DNA as the OD reading did not reach the range of 1.80 to 2.00 for both

bovine and vegetable capsules. The modified CTAB method resulted in both bovine and vegetable

capsules having excellent pure DNA quality in the range of 1.80 – 2.00. PCR is conducted on DNA

extracted from the capsules; however, it is still on optimization process. In the future, the

development of extraction methods involving multiple brands of pharmaceutical capsules will be

conducted along with PCR (qualitative analysis) and qPCR (quantitative analysis).

This M.Sc. candidate is under the supervision of Assoc. Prof. Dr. Shafiquzzaman

Siddiquee, Assoc. Prof. Dr. Sazmal Effendi Arshad and Dr. Mailin Misson

Latest Publication & Awards:-

PG28

Qualitative and quantitative based analysis of porcine

DNA in pharmaceutical capsules

(M.Sc. Candidate)

Iffa Ridha Luqman

41

Microspheres have been of biotechnological interest owing to their low density and high permeability

which made them highly potential in the field of separation, drug delivery system and

chromatography. However, poor heat dissipation and uneven pore size distribution across monolith

remain as a key challenge in monolith fabrication. This study aims to synthesize and characterize

microsphere based polymeric micro-emulsion as new template for monolith. Oil/water emulsification

technique was employed by dissolving polymer into solvent by continuous stirring to form micro-

emulsion prior to evaporating the organic phase. The operating conditions for the synthesis of the

microsphere-based polymeric micro-emulsion were designed by Response Surface Methodology

(RSM) comprising polymer concentration (14-35 wt%), surfactant concentration (1-9 wt%),

temperature (30-70 oC) and stirring rate (500-1000 rpm). Characterizations of the resulting particles

were performed using Scanning Electron Microscope (SEM), Inverted Microscope and Fourier

Transform Infrared (FTIR) spectrometer. Out of 30 samples using polystyrene polymer, some

resultant microspheres demonstrated homogeneous particle indicating good quality particle size while

some formed aggregations. Further experiments were continued using different type of polymer

(polystyrene, polyethylene, polyvinylalcohol, polycaprolactone, polypropylene) at different

concentrations (35 wt%, 30 wt%, 20 wt%, 10 wt%). The findings indicated that the average particle

size reduced as the polymer concentration decreased at all tested polymers. The findings of this study

provide useful insights on the feasibility of microsphere based polymeric micro-emulsion as a directing

template for monolith fabrication with structured pores.

This M.Sc. candidate is under the supervision of Dr. Mailin Misson, Dr. Suryani Saallah

and Dr. Clarence M Ongkudon.


1. Nurfaezah I, Clarence M.O, Suryani S, Mailin .M*. Production of Polystyrene as a Template for Monolith Production. In Proc. of 4th International Conference on Science and Natural Resources (ICSNR4), 7th-8th April 2019.Grand Borneo Hotel, Kota Kinabalu.

PG29

Synthesis and characterization of microspheres based

polymeric microemulsion as template for monolith

(M.Sc. Candidate)

Nur Faezah Ibadat

42

Empty fruit brunch (EFB) is one of the main biomass wastes produced from oil palm industry. EFB is

usually disposed by incineration or used as biofertilizer. However, the increase of EFB wastes

production caused environmental pollution. This study is done to utilize locally isolated fungi to

degrade EBF wastes into more value-added product. From previous results showed that all the fungal

isolates able to decolourize the remozol brilliant blue R thus these fungal isolates were further

screened for their lignin degrading capability by using real lignin substrate which are Kraft Lignin and

EFB in Sundman and Nӓse assay. Fungal isolates that able to degrade Kraft Lignin though subtle but

also able to degrade EFB. In addition to that, there are two fungi isolate selected for preliminary test

of NMR-based metabolite profiling of the lignin degradation products. Unfortunately, due to the short

incubation time thus no lignin degradation products have been detected. Hence, longer incubation

time will be done on the next experiment.

This Ph.D. candidate is under the supervision of Dr Clarence M. Ongkudon and Assoc.



1. Adznila, E., Abigail, L.E., Intan, N.M., Clarence, M.O., & Mailin, M. (2018). Screening, characterization and optimisation of lignin degrading microorganisms from Sabah mega biodiversity for optimum bioconversion of oil palm waste. UMS Research and Innovation Competition (PEREKA 2018). 24th - 25th October 2018. Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia. (Bronze award)

PG30

Screening, characterization and optimization of lignin-

degrading microorganisms from Sabah biodiversity for

optimum ligninolytic potential

(Ph.D. Candidate)

Adznila Binti Eberahim

43

Ficus lepicarpa belongs to family Moraceae and commonly known as ‘Saraca fig’. It has been used by

local people as a vegetable dish, jaundice treatment, as a tonic and to treat aliments such as fever

and ringworm. However, there is no scientific basis or reports in the modern literature regarding its

usefulness as a hepatoprotective agent. The present study was carried out to evaluate the

hepatoprotective activity of methanolic leaves extract of Ficus lepicarpa in CCl4 induced hepatotoxicity

in Sprague Dawley rats through histopathological studies of liver tissue. A portion of the liver from

each rat was removed and preserved in 10% phosphate buffered formalin and subjected further to

tissue processing, embedding, trimming and sectioning, fishing and Haematoxylin and Eosin (H&E)

staining. Assessment of histopathological alteration of liver tissue sections showed control group has

normal cellular architecture with distant hepatic cells compared with the CCl4 – intoxicated group,

which showed severe hepatocellular damage such as fatty changes, lymphocytes vacuolization, mild

degree of cellular infiltration and hepatocellular necrosis. Pre-treatment group by Ficus lepicarpa

extracts showed less degree of hepatic lesion such as fatty changes and necrosis, indicate the

recovery in dose dependent manner. Further studies are still in progress to evaluate the antioxidant

enzymes and immunohistochemical observations of the liver samples obtained from all groups.

This Ph.D. candidate is under the supervision of Assoc. Prof. Dr Mohammad Iqbal, Assoc.

Prof. Dr Kenneth Francis Rodrigues and Assoc. Prof. Dr Teoh Peik Lin.


1. Vun-Sang, S., Peik-Lin, T., Rodrigues, K.F. and Iqbal, M. 2017. Phytochemical analysis and antioxidant activity of Ficus lepicarpa leaves from Sabah, Malaysia. Transactions on Science and

Technology. 4 (3-3): 360 - 365.

PG31

Hepatoprotective effect of Ficus lepicarpa against

carbon-tetrachloride induced oxidative stress in rats:

histopathological assessment of liver tissue

(Ph.D. Candidate)

Senty Vun Sang

44

Chicken eggs are a versatile cuisine and contain essential nutrients such as protein, vitamins, and

mineral for a balance diet. It is a simple to prepare and affordable for the low-income household. Day

by day, the consumption of egg has increased from 16.6 kg/capita/year in 2013 to 22.2

kg/capita/year in 2018. The increase in consumption of chicken eggs lead to high production of

eggshell waste. Intriguingly, the wastes eggshell contained about 94% of calcium carbonate (CaCO3)

compound in which has similar structure to human bone and teeth. The aim of this study was to

produce nano-sized calcium carbonate from chicken eggshell using blending & grinding (BG) and ball-

milling & sonication (BMS) methods. Both methods were successfully produced nano-sized CaCO3.

Scanning Electron Microscopy (SEM) result showed that BMS method produced hollow and porous

particles whereas BG method produced nonporous particles. Energy Dispersive X-ray Analyzer (EDX)

results found high purity with Carbon, Oxygen and Calcium. In chronic assay, six groups of rats

containing positive control (commercial calcium supplement), negative control (vessel), highest

dosage (2000 mg/kg bw) and lowest dosage (500 mg/kg bw) were carried out for the dosages

optimization in rats. Total number of 12 rats with two rats in each group were used. The analysis of

blood serums, kidney and liver tissues were conducted. In future, histopathology study will be

conducted for further validation of nano-sized CaCO3 as dietary supplement.

This M.Sc. candidate is under the supervision of Assoc. Prof. Dr. Shafiquzzaman

Siddiquee, Prof. Ts. Dr. Sharifudin Md. Shaarani and Assoc. Prof. Dr. Mohammad Iqbal.


PG32

Characterization of nano-sized calcium carbonate (caco3)

powder from chicken eggshell as dietary supplement

(M.Sc. Candidate)

Nurfatihah Binti Zamri

45

Despite the advancements of chemo therapy, there are some vital side effects that should be

considered in every breast cancer treatment. Previous studies have shown that breast cancer cells

undergo surface alterations and detailed characterization of these cell lines seems necessary for

further use in future research. The detailed fine surface features of the cells can only be

stereoscopically visualized by scanning electron microscopy (SEM). This present study attempted to

understand the effect of selected terpenoids (betulin) treatment on MCF-7 and MDA-MB-231 cancer

cells. Three concentrations of betulin were applied on MCF-7 and MDA-MB-231 in dose-increasing

manner, and subjected to visualization using Scanning Electron Microscopy (SEM). The results

indicated the shedding of cell surface microvilli and alteration the shaping of cells treated with betulin,

compared to untreated cells. The overall cellular morphology shows these cells lose the characteristics

of tumour cells upon treatment with betulin.

This M.Sc. candidate is under the supervision of Assoc. Prof. Dr Teoh Peik Lin.


PG33

Morphology evaluation by scanning electron microscopy

(SEM) of breast cancer cells treated with betulin

(M.Sc. Candidate)

Alex Walzico Robert

46

The chosen subject of this research is a species of climbing fern, known as Lygodium circinnatum.

This plant is reportedly being used as a wound poultice. The study aims to prove the antioxidative

and hepatoprotective effects of the selected plant against induced lipid peroxidation. In this study,

the dosage optimization test has been performed. 5 groups of rats in which 2 groups consisted of the

minimum and maximum dosage (100, 400 mg/body weight) has been prepared. CCl4 has been orally

fed for 2 days at the end of the treatment to induce lipid peroxidation in the liver of the rats. After

dissection, kidney and liver tissues were kept and further biochemical assays were done.

Histopathological examination was done and the photomicrographs of the liver tissues were taken.

The results were presented. The study of liver immunostaining is currently ongoing and the obtained

results should present basic understanding of the localization of potential biomarkers for liver

damage. Further studies should be conducted in order to fully identify the plant’s full medicinal

potential.

This M.Sc. Candidate is under the supervision of Assoc. Prof. Dr. Mohammad Iqbal and Dr.

Ruzaidi Ali Mohd. Mokhtar.


PG34

Phytochemical constituents, antioxidative and

hepatoprotective effects of Lygodium circinnatum

against carbon tetrachloride (ccl4)-induced hepatic

damage and toxicity in rats

(M.Sc. Candidate)

Riana binti Awang Saman

47

Global warming is affecting the climate and biodiversity of various biomes and this will affect soil

bacterial communities and their ecological function. The increase in environmental temperature also

raises the concern of pathogenic outbreak from soil. It is therefore crucial to determine how

temperature rise will affect soil bacterial diversity and whether an outbreak of pathogenic bacteria will

occur. Previous results showed that the relative abundance of potentially pathogenic bacteria such as

Bacillus spp., Chlamydia spp. and Mycobacterium spp. increased after simulated warming. Further

confirmation is therefore carried out using qPCR to determine the presence of pathogenic bacteria

such as Bacillus cereus, Chlamydia pneumoniae and Mycobacterium tuberculosis in this study.

Extraction of bacterial RNA was done using a previously described method with several modifications.

RNA extraction was carried out for 0th, 3rd, 6th, 9th and 12th month sampling of soil from a site in Kota

Kinabalu subjected to simulated warming. The quality and quantity of RNA obtained was measured

using NanoDrop spectrophotometer. The quantity of RNA obtained was between 6.08 and 12.03 µg

per gram of soil used. In terms of purity, the A260/A280 ratio ranged from 2.02 to 2.25, while A260/A230

ratio was between 1.32 and 1.91. The primers used for this research will be targeting 16SrRNA, bceT

and HblA genes for Bacillus cereus; 16S rRNA and ompA genes for Chlamydia pneumoniae, and 16S

rRNA, mpb70 and atpE genes for Mycobacterium tuberculosis.

This Ph.D. candidate is under the supervision of Prof. Dr. Clemente Michael Wong Vui

Ling


1. Chua C.Y., S.T., Yong, M. A. González, Lavin, P., Cheah, Y.K., Tan, G.Y.A. and Wong, C.M.V.L. (2018).

Analysis of Bacterial Communities of King George And Deception Islands, Antarctica using High-

throughput Sequencing. Current Science 115(9):1701-1705.

PG35

Effects of simulated warming on potentially pathogenic

bacteria in soils collected from Kota Kinabalu

(Ph.D. Candidate)

Chua Chuen Yang

48

The properties of lipopolysaccharides (LPS) or known as endotoxin have been extensively investigated

due to its pathogenicity that may lead to pathophysiological effects including death. Their unique

amphipathic nature consisting of hydrophilic core polysaccharide chain and hydrophobic lipid A is

responsible for the toxicity effect. The potential of several divalent cations (Zn2+, Ca2+, Mg2+) as

aggregation agents for LPS removal from plasmid DNA (pDNA) was studied using Fourier-transform

infrared (FTIR). Previously, Forster Resonance Energy Transfer (FRET) spectroscopy showed the

highest aggregation potential of Zn2+ towards LPS in the LPS-pDNA mixture compared to Ca2+ and

Mg2+. Thus, FTIR analysis was conducted to investigate the chemical bonds and to observe the

presence or absence of functionalized bonds. Post-investigation reports showed that some chemical

bonds were preserved and some were absence confirming each divalent cation behaved

physiologically different.

This Ph.D. candidate is under the supervision of Dr. Clarence M. Ongkudon


PG36

FTIR investigation of lps-pdna in the presence of

divalent cation

(Ph.D. Candidate)

Nur Syahadatain Abdul Razak

49

Utilization of WJ-M.SC.s (Wharton’s jelly-derived mesenchymal stem cells) with the aid of biomaterials

have grown towards clinical studies for a wide spectrum of medical treatments including bone

regeneration. However, little is known about the intracellular mechanisms involved in the osteogenic

differentiation of M.SC.s. This study aimed to investigate how GO (graphene oxide) and COL

(collagen) regulate gene expression of differentiated WJ-M.SC.s. WJ-M.SC.s were cultured in the

presence of GO/COL in normal- and induced condition media. MAPKs (Mitogen activated protein

kinases) including P38 and ERK1/2 were analyzed in WJ-M.SC.s by Western blotting. The result

demonstrated that there was no involvement of P38 and ERK1/2 in both WJ-M.SC.s-GO and WJ-

M.SC.s-COL in normal condition media. Interestingly, when WJ-M.SC.s-GO and WJ-M.SC.s-COL were

induced with osteogenic media, ERK1/2 expression was upregulated. Additionally, phosphorylated

P38 was also upregulated in WJ-M.SC.s-COL when induced with osteogenic media. These findings

suggested that p38 and ERK1/2 phosphorylation play an important role in inducing osteogenic

differentiation in WJ-M.SC.s.

This Ph.D. candidate is under the supervision of Assoc. Prof. Dr. Teoh Peik Lin.


PG37

The involvement of ERK1/2 in osteogenic

differentiation of Wharton’s Jelly-derived mesenchymal

stem cells cultured with graphene oxide and collagen

scaffolds

(Ph.D. Candidate)

Hiew Vun Vun

50

The multi-walled carbon nanotubes–polyaniline (MWCNTs/PANI) composites were deposited

onto indium tin oxide (ITO) for the analysis of mercury in cosmetic products. The aim of this study

was to conduct the reproducibility, selectivity (interference study), concentration window and storage

stability using the optimum condition with modified ITO electrode (MWCNTs, PANI, and gold

nanoparticles (AuNPs)). The morphology of nanomaterial and nanocomposites were characterized

using transmission electron microscopy (TEM). Under optimal condition, differential pulse

voltammetry (DPV) method was detected with different concentrations of mercury on the ranged of

4-10 ppm, with detection limit of 3 ppm. Nanomaterials and nanocomposites based developed

electrochemical method is giving new inputs to detect mercury in cosmetic products.

This Ph.D. candidate is under the supervision of Assoc. Prof. Dr. Shafiquzzaman

Siddiquee, Assoc. Prof. Dr. Sazmal Effendi Arshad and Dr. Mailin Misson


PG38

Development of electrochemical sensor for

determination of mercury based on the modified

indium tin oxide (ITO)

(Ph.D. Candidate)

Noor Aini Bohari

51

Population growth, industrial development and burning of fossil fuels have contributed significantly

towards global warming. The gradual rise in global average temperatures as a result of global

warming raises the concern of bacterial pathogens proliferating in new habitats as most bacterial

pathogens that are relevant to human health thrive in warmer environments. Thus, it is noteworthy

to study how the pathogenic bacteria in tropical soils react to elevated temperature and will these

changes benefit or harm human being. In order to fulfill the research objectives, an in vitro simulated

temperature rise experiment was carried out on soils from three sampling sites, S2, S3, and S4

around Sabah. Five replicates of each sample were incubated at 25ºC (control) and 27ºC (simulated

warming) in a growth chamber. Other parameters such as humidity, day length, water and

photosynthetic active radiation (PAR) were constants for both conditions. Total RNA was extracted

separately from each of the five replicates taken per sampling site. The RNAs were treated with

DNase and purified twice to remove any contaminants and humic acids before quantified using

NanoVue nano spectrophotometer. Purified RNAs were converted to cDNA via SuperScript III Reverse

Transcriptase before subjected to real time polymerase chain reaction (qPCR). Primers were designed

to target several pathogenic bacteria and key genes in nutrient cycles in order to investigate the

changes after 16 months of simulated warming based on published primer sequences. The results

provide information and better overview on how well bacteria adapt and thrive in higher temperature,

assisting in soil bacterial management and related future studies.

This Ph.D. candidate is under the supervision of Prof. Dr. Clemente Michael Wong Vui

Ling


1. Chin, L.M and Wong, C.M.V.L. 2017. Changes in soil bacterial diversity and composition due to simulated temperature rise. PEREKA UMS 2017. 24th-25th October 2018. UMS, Sabah.

2. Chin, L.M and Wong, C.M.V.L. 2017. Changes in soil bacterial diversity and composition in an in vitro simulated temperature rise environment. In Proc. of International Congress of the Malaysian Society for Microbiology (ICMSM), 4th-7th December 2017. Hotel Bangi Putrajaya, Malaysia, pp.35.

PG39

Changes of soil pathogenic bacteria in an in vitro

simulated temperature rise environment

(Ph.D. Candidate)

Chin Lai Mun

52


PG40

Construction, over-expression, purification,

enzymatic activity of active-site mutant of an α-

mannanase from Arthrobacter sp.

(M.Sc. Candidate)

Wan Nur Shuhaida Binti Wan Mahadi

53

Tor douronensis, also locally known as Pelian, is a species of ray-finned fish of the family Cyprinidae

in the genus Tor. It has an aquaculture potential and of conservational value. T. douronensis can be

found in headwaters and tributaries of most Sabah river systems. Although T. douronensis is currently

assessed as “data deficient” on the IUCN Red List, it is suspected that the overall population of this

species is decreasing due to anthropogenic modification of river morphology, logging, deforestation,

agriculture and overfishing. The DNA of 176 samples collected from 18 populations in Sabah was

extracted and amplified using 12 microsatellite markers to estimate its genetic diversity and

population structure. Of the 12 loci examined, MICROCHECKER detected presence of null alleles at

five loci, D01, H08, C10, E11 and B02, as suggested by the general excess of homozygotes for most

allele size classes. These five loci were excluded from subsequent analyses. A total of 50 alleles were

detected across seven loci, ranging from 5 to 13 alleles at F04 and B01 respectively. Across the

localities, B01 had the highest mean Ho (0.5657), whereas the least variable locus was F02, with a

mean Ho of 0.0114. Exact tests for all loci revealed significant deviation from Hardy–Weinberg

equilibrium in four localities, which had observed heterozygosities higher than expected. Three

localities, SPO, WCGO and IME, showed the highest number of private alleles (2). All pairwise

comparisons of allele frequencies between localities were significant after Bonferroni correction.

Calculation of ΔK from the STRUCTURE output produced a modal value of the statistic at K = 2. The

highest order clustering evident in the data set (K = 2) clearly grouped samples from the West Coast

to East Coast populations separated by Crocker Range. All localities except WCTO and SPO showed

very low degrees of admixture in that each had greater than 0.85 proportional ancestry from just one

cluster. Further data analysis will be performed to understand the microsatellite DNA diversity and

population structure of T. douronensis in Sabah.

This Ph.D. candidate is under the supervision of

Assoc. Prof. Dr. Kenneth Rodrigues and Dr. Christopher Voo Lok Yung.


PG41

Microsatellite DNA diversity of Tor douronensis

(CYPRINIDAE) from Sabah, Malaysia

(Ph.D. Candidate)

Helena Biun

54


PG42

Development of genetic markers and screening for

viruses in insectivorous bats from Madai Cave, Lahad

Datu, Sabah

(Ph.D. Candidate)

Azniza binti Mahyudin

55

In recent years, research on medicinal plants has attracted much attention due to their wide

range of pharmacological significance. A mangrove is a unique group of vascular plants that are able

to survive in extreme conditions of the coastal area and may have been assisted by a type of defence

metabolites. Six species of mangrove (Avicennia marina, Bruguiera gymnorrhiza, Ceriops tagal,

Rhizohora apiculata, Rhizophora mucronata and Xylocarpus granatum) from different parts were

extracted successively using aqueous, ethanol, ethyl acetate and hexane extraction. Based on the

results, the highest extraction yield was obtained from aqueous extraction. The yield of aqueous

extract of Xylocarpus granatum leaves (14.25 %) is the highest among the 13 samples whereas

Bruguiera gymnorrhiza root (0.04% %) from hexane extraction is the lowest compared to the other

samples. This study aims to measure quantitatively the total phenolic content and assess the radical

scavenging activity of the selected mangrove extracts. All the extracts were subjected to Follin-

Ciocalteu method for its phenolic content and DPPH radical scavenging assay for antioxidant activity.

The highest total phenolic content was observed in Ceriops tagal leaves extract (236.24 mgGAE/g),

followed by Bruguiera gymnorrhiza stem extract (199.55 mgGAE/g) then Rhizophora mucronata root

extract (89.15 mgGAE/g). However, the EC50 value of all extract could not be determined because of

the inhibition percentage was below 50%. As a conclusion, Ceriops tagal leaves extract has high

phenolic content with promising bioactive compounds in producing new drugs against anti-bacterial,

anti-fungal and anti-diabetic.

The M.Sc. candidate is under supervision of Dr. Ruzaidi Azli Bin Mohd. Mokhtar, Dr. Zarina

Binti Amin and Dr. Nur Athirah Binti Yusof


PG43

Antioxidant activity and total phenolic in aqueous

extracts of selected mangrove plant in Sabah

(M.Sc. Candidate)

Mayrlidzatul Farhain Binti Misrah

56

The 70 kilodalton heat shock proteins (HSP70) family are ubiquitous and highly conserved ATP-

dependent molecular chaperone that is involved in protecting cells from various stresses. HSP70

chaperone protein are the central components of cellular network in protein folding mechanisms.

They involve in folding of newly synthesize proteins, protection of hydrophobic regions of denatured

proteins, regulation of apoptosis, the immune response and several other cellular processes. Many

have studied the correlation between structure and function of the HSP70 from other organisms but

the knowledge specifically in psychrophilic yeast under low energy environment still remain indefinite.

In this project, we have successfully cloned Ga_Hsp70-1 into a pET32-Ek/LIC vector (Novagen),

expressed in BL21(DE3) cells and purified using IMAC. The Ga_Hsp70-1 was overexpressed at 20℃

indicating optimal protein expression in cold. From the thermotolerance assay, Ga_Hsp70-1 was able

to withstand temperatures up to 45℃. Intriguingly, homology modelling showed a missing beta-sheet

at N-terminal ATPase binding domain that might be hampering its ability towards lethal heat. The

comparative of structural and functional analysis of Ga_Hsp70-1 may explain some possible

mechanism which allow Ga_Hsp70-1 to function in low energy environment.

This M.Sc. candidate is under the supervision of Dr. Nur Athirah Yusof


PG44

Cloning, expression and purification of HSP70 from

Psychrophilic yeast, Glaciozyma Antarctica

(M.Sc. Candidate)

Jennifer Charles Labo

57

The former Mamut Copper Mine was the only copper mine in Malaysia, since the operations had

been ceased in 1999, Acid mine Drainage was recorded at the mining site. Mining processes can

alter the physical and chemical attributes of the soil environment, subsequently the bacterial

communities in soil may change drastically from time to time. Despite that the mining site had

been abandoned for a long time, the bacterial diversity in the mining site and surrounding areas

have never been investigated. Seven soil samples were collected from the abandoned mining site and

the surrounding areas, including the bank of the mine pit, the water drainage channeling to the mine

pit, the former mining factory, sludge pond, tailing areas, the meeting point between the outflow and

Mamut River. The highest average colony forming unit (CFU) counted was recorded at 34146.34

CFU/g at the meeting point between the mine water outflow and Mamut River, followed by 26022.73

CFU/g at the sampling site adjacent to the mine pit and the lowest

CFU was recorded from the soil of the water drainage channeling into the mine pit, no colony

was grown from this sample. A total of 35 distinct MTUs were identified from 48 pure isolates,

25species were successfully identified after DNA extraction, 16s rRNA PCR amplification and

sequencing. The genera of bacteria identified are Bacillus, Pseudomonas, Chryseobacterium,

Sinomonas, Streptomyces, Kitasatospora, Mucilaginibacter and Arthrobacter. The knowing of the

bacterial diversity in this abandoned mining site can contribute to the understanding of the natural

bioremediation process and provide useful insight in order to manage this important landmark.

This Ph.D. candidate is under the supervision of Assoc. Prof. Dr. Kenneth Francis

Rodrigues and Mdm. Grace Joy Wei Lie Chin


1. Low, Y.Y., Chin, G.J.W.L., Budiman, C., Joseph, C.G., Musta, B., Rodrigues, K.F. 2018. Adaptive strategies of bacterial communities at Mamut Copper Mine, Sabah. At Pertandingan Penyelidikan & Rekacipta (PEREKA) 2018, 24th-25th October 2018. Kompleks Dewan Kuliah Pusat Ke-2, Universiti Malaysia Sabah, Malaysia.

2. Low, Y.Y., Chin, G.J.W.L., Joseph, C.G., Rodrigues, K.F. 2018. Comparative genomic analysis of Bacillus thuringiensis reveals molecular adaptations to copper tolerance. bioRxiv. 2nd July 2018. http://dx.doi.org/10.1101/360354.

PG45

Preliminary bacterial diversity study of abandoned mining

site and surrounding areas of former Mamut Copper Mine,

Sabah

(Ph.D. Candidate)

Low Yi Yik

58

3. Low, Y.Y., Chin, G.J.W.L., Budiman, C., Joseph, C.G., Musta, B., Rodrigues, K.F. 2018. Adaptive strategic of Bacillus thuringiensis isolated from acid mine drainage site in Sabah, Malaysia. Indian Journal of Microbiology. 4th January 2018. http://dx.doi.org/10.1007/s12088-017-0701-1.

4. Low, Y.Y., Chin, G.J.W.L., Budiman, C., Joseph, C.G., Musta, B., Rodrigues, K.F. 2017. Adaptive mechanisms of bacillus cereus isolated from Mamut Copper Mine soil sample. In Proc. of the International Meeting & 42nd Annual Conference of MSBMB, 16th-17th August 2017. Pullman Hotel, Kuala Lumpur Bangsar, Malaysia.

59

Bacteria from genus Parageobacillus are thermophilic bacteria which can survive and grow at high

temperature. In order to study the strategies adopted by these bacteria in respond to thermal shift,

transcriptomic analysis was carried out on P. caldoxylosiluticus ER4B, a tropical thermophilic

bacterium which grows best at 64°C. In previous studies, cold shock was induced to the bacterium.

RNA-Seq and the subsequent transcriptomic analyses suggested that there are total of 37 and 50

genes which are considered as significantly differentially expressed when cold shock was induced at

54°C and 10°C respectively. Real-time PCR was then carried out to further validate the transcriptomic

results. In order to generate decent standard curves, several methods were devised to improve the

existing protocol. First, the RNA samples were further purified using conventional ethanol

precipitation method, followed by DNase Max Kit and PowerClean clean-up kit. All the samples were

then diluted to the same concentration for primer efficiency test. R2 value of 0.98 and 0.99 was

obtained for rpoB and pyruvate kinase gene respectively, showing that the primers were good

enough for amplification. The resulting standard curve was then analysed and template concentration

of 1-5ng was determined to be the best to prevent amplification of non-specific products. Preliminary

real-time PCR on several related genes shows that pyruvate is being synthesized upon cold-shock,

suggesting pyruvate might be useful in thermal adaptation.

This Ph.D. Candidate is under the supervision of Prof. Dr. Clemente Michael Wong Vui

Ling


PG46

Optimization of real-time PCR protocol for

transcriptomics analyses of thermophilic bacterium,

Parageobacillus caldoxylosilyticus ER4B

(Ph.D. Candidate)

Ching Xin Jie

60

Jewel orchid belongs to Orchidaceae family and has been well known for their attractive foliar

venation. Macodes limii is one of Sabah’s understudied endemic jewel orchid and this species has a

great potential to be commercialized as an ornamental plant due to their extraordinarily beautiful

foliage. This study optimized an efficient protocol for mass propagation of Macodes limii. Six-month

old of in vitro raised seedling of M.limii was cut in four nodal positions, cultured on half strength

Murashige and Skoog (MS) supplemented with various types and concentrations of auxins and

cytokinins either singly or in combinations. Control medium is basal medium devoid of any plant

growth regulators. All cultures were incubated at 25ºC ± 2ºC with 12h photoperiod. Each treatment

consists of five replicates and subculture was performed every 30 days of culture. Growth and

development of explants were observed for six months and parameters including initiation day,

number of axillary shoots and roots formation were recorded. The results revealed that effects of

nodal positions and supplementation of plant growth regulators either singly or in combinations were

significant to influence the axillary shoot formation and multiplication of M. limii. The present protocol

is beneficial for large scale commercial propagation as well as the conservation of this endemic

species.

This Ph.D. candidate is under supervision of Prof. Dr. Jualang Azlan Gansau and Dr.

Ruzaidi Azli Mohd Mokhtar


1. Devina D., Chuwan L.E. and Jualang A.G. 2018. Optimizing sucrose and BAP concentrations for in vitro microrhizome induction of Zingiber officinale Rosc. ‘Tambunan’. Malaysian Applied Biology Journal 47(6): 47-52

2. Hartinie M., Ozayanna C., Devina D. and Jualang A.G. 2018. In vitro shoot regeneration from stem

explant of commercially important medicinal herb Labisia pumila var. Pumila. ASM Journal Science 11, Special Issue 2 for SANREM: 171-180

3. Fung V.A.C, Gobilik, J. and David, D. 2018. Effects of Fertilizer Application and Successive Harvesting on Clipping Yield, Phytochemical Contents and Antioxidant Activity of Cynodon dactylon (L.) Pers. Notulae Scientia Biologicae 10 (1): 130-136

PG47

Micropropagation of Sabah jewel orchid Macodes limii J.J

Wood & A.L Lamb

(Ph.D. Candidate)

Devina David

61

Mutation in the badh2 gene is responsible for the production of 2AP, a volatile compound that causes

fragrance in rice. Previously, a total of 24 Sabah’s traditional rice samples were found positive for

mutations in exons 7 and 10 of the gene via long-amplicon targeted sequencing. In this report, the

24 rice samples were further examined to identify possible association between the genetic variants

and phenotypic traits, particularly, seed-morphology, cooking characteristics and physico-chemical

properties. Non-aromatic samples (i.e. no mutations in the badh2 gene) were also included in the

study as controls for comparison purposes. Qualitative data such as awning, bran colour, grain size

and shape, apparent amylose content (AAC) and soft to hard gel consistency (GC) were analysed

using chi-square (2). While quantitative data such as 100-grain weight, elongation, volume

expansion were analysed using one-way ANOVA. The statistical tests revealed there was no

significant association between the badh2 genetic variants and seed-morphology and physico-

chemical properties. There was also no significant difference between the cooking properties of

aromatic and non-aromatic rice. Meanwhile, hierarchical clustering divided the samples into 12 sub-

groups. The characters of the major groups were Group I: purple bran; group II: very low AAC;

group III: red bran, group IV: mutation at Exon 10; group V: mutation at exon 7; Group VI: no-

mutation, intermediate ACC, medium chalkiness; group VII: no-mutation, mild aroma, hard GC; group

VIII: no-mutation, long grain, medium grain weight, high ACC, high gelatinization temperature. The

result indicates that Sabah’s aromatic rice has high potential to be marketed as premium rice as it has

the same rice quality as demanded by local consumer but with the addition of inherent desired

fragrance.

This Ph.D. candidate is under supervision of Assoc. Prof. Dr Dr Vijay Kumar and Prof.

Datin Dr. Mariam Abd Latip


1. Chee, F.T., Mariam, A.L. and Kumar, S.V. 2017. Cooking Properties of Sabah Traditional Rice Germplasm. Short communications in Biotechnology 4: 43-49

2. Chee, F.T., Mariam, A.L. and Kumar, S.V. 2017. Efficient use of PacBio’s long reads to detect sequence variations and allelic differences in a 6 kb long amplicon of the BADH2 gene in Rice. 5th International Biotechnology Symposium 2017. 15-16 November, 2017, Ming Garden Hotel, Sabah, Malaysia.

PG48

Association between genetic variants of the badh2 gene

and seed-morphology, cooking characteristics and

physico-chemical properties of Sabah rice germplasm

(Ph.D. Candidate)

Chee Fong Tyng

62

3. Noor Hydayaty, M.Y., Chee, F.T., Azniza, M. and Kumar, S.V. 2017. Common plant DNA extraction and purification kit. PEREKA UMS 2017. 24 – 25 October 2017. UMS

4. Chee, F.T., Mariam, A.L. and Kumar, S.V. 2016. Aromatic Compounds in Traditional Rice Germplasm of Sabah. 3rd International Plant Breeding Conference 2016. 15 - 16 November 2016, Hotel Bangi-Putrajaya, Malaysia.

5. Chee, F.T., Mariam, A.L. and Kumar, S.V. 2015. Detection of fragrance in Sabah traditionally cultivated rice germplasm. PEREKA UMS 2015. 9th - 10th December 2015. UMS, Sabah

63

Kenaf is an important natural bast fibre producing plants grown for its multipurpose uses. These

fibers are extracted by combine actions of maceration and microbes mainly alkalophilic bacteria.

However, existing conventional microbial retting takes long period of time and yields low quality fibre.

In this research main aim to isolate the potential candidate of alkalophilic-pectinolytic bacteria from

wet paddy soil (WPS) and kenaf retting niche (KRN). Therefore, WPS samples were collected from

Tuaran area of Sabah. For, KRN plants were grown at transgenic facilities sites, BRI and harvested at

100 days after sowing. KRN were prepared by using different types of water, namely sea water, tap

water and fresh water. The optimum numbers of cultivable bacteria strains were found on basal

alkalophilic H1 media using 10-5 dilution factor. Isolates were screened on pectin agar plates and

measured pectinolytic activity by holozone production surrounding their colony on the agar medium

where pectin was used as sole carbon source. Isolates produced colony and holozone diameter ratio

were selected greater 3 and above. A total 9 strains from KRN and 6 strains from WPS were screened

from 25 isolates. Microscopic characteristics were found rod shaped and gram positive Bacilli. Most of

the microbes were grown very-well in alkaline media, while poor growth was observed in neutral

media. In KRN initial average pH was 4.5 and finally increased up to 10.5. In future, alkaline

pectinase activity will be determined by dinitrosalicylic acid method and alkaline enzyme assays both

pectin lyase and polygalacturnase. Accurately identification of strains will perform based on DNA gene

sequencing.

This Ph.D. candidate is under the supervision of Associate Prof. Dr. Md. Shafiquzzaman

Siddiquee and Associate Prof. Dr. Vijay Kumar A/L Subbiah.


PG49

Isolation, characterization and identification of

alkalophilic pectinolytic bacteria from wet land paddy

soil and kenaf (Hibiscus cannabinus) retting niche

(Ph.D. Candidate)

Mohammad Munir Hossain

64

Studies have shown that molecular chaperones acquire the ability to prevent proteins from thermal

degradation and refold denatured proteins to their functional stage in low temperatures. Extensive

studies on small heat shock proteins (sHSP) ranging from mammals, yeasts, plants and bacteria have

elucidated their vital role in promoting thermotolerance and preventing protein aggregation in cells.

The sHSPs help to maintain protein homeostasis by interacting with partly unfolded, aggregate-prone

proteins to prevent cell damage. However, discovery on psychrophilic organisms are still in the

infancy level. The exclusive ability of psychrophilic sHSP to function efficiently at low temperatures

offer a great opportunity for scientists to study the relationship between the protein function and

structure in terms of stability, flexibility and dynamic conformation. Hence, this study aims to

determine the function of HSP20 chaperones from Glaciozyma antartica and investigate the

relationship between the molecular structures of HSP20 and the thermal adaption. In this study, all 4

target HSP20 genes from G. antartica were successfully amplified from total RNA. Currently, 2 genes

were verified by sequencing and cloned into pET32 Ek/LIC plasmid. The expressions of the

recombinant proteins were conducted under heterologous E. coli expression system. Protein

expression was done in 37°C where the 2 target genes managed to be expressed in soluble proteins

and purified using nickel affinity chromatography. Thermo tolerance assay (qualitative assay) has

been performed in 50oC. Future work will focus on functional characterisation of all G. antarctica

HSP20 target of interest and gene expression analysis related to thermal response. The findings of

this study are expected to provide more insight into the thermal protection mechanism of HSP20.

This M.Sc. candidate is under the supervision of Dr. Nur Athirah Yusof


PG50

Characterisation of structure and function relationship

of heat shock protein 20-like chaperones in the

Psychrophilic yeast, Glaciozyma antartica

(M.Sc. Candidate)

Farhan Nazaie Bin Nasib

65

Sabah is strategically located at the centre of Southeast Asia surrounded with the Philippines,

Indonesia and Peninsular Malaysia. Despite a number of hypothesis on the human migration history

in Southeast Asia, the genetic relatedness of the Sabah indigenous ethnic groups has been vaguely

inferred based on locality labeled as ‘Kota Kinabalu’ in the previous studies. To overcome this

limitation, the selection of samples in this study is based on defined ethnicity. The study aims to

identify the mtDNA haplogroups among the indigenous ethnic groups in Sabah based on sequence

variations on the complete hypervariable region (HVR). It is 1.15 Kbp in length comprising of three

hypervariable regions known as HVI, HVII and HVIII. The findings will be used to postulate the

genetic relatedness among the Sabah indigenous ethnic groups to neighboring populations from

Southeast Asia. A total of 242 unrelated individuals representing Dusun, Orang Sungai, Bajau Laut,

Tidung and Murut were recruited. The DNA sequences of HVR were then compared with the revised

Cambridge reference to identify haplogroups. Subsequently, phylogenetic analyses will be conducted.

Sequence comparison of 34 samples led to the identification of 11 mtDNA haplogroups from 55

polymorphic variable sites, in which 33 were unique and the other 22 sites were shared by more than

two individuals. Both Dusun and Orang Sungai shared 3 mtDNA haplogroups (R9c1a, M7c1a4a &

E1a1a1) while another haplogroups are unique to Sabahan populations. In comparison, the Orang

Sungai ethnic group has a distinguished profile of mtDNA haplogroups as they have high number of

E1a2 & M7b1a, which are not found on the Dusun ethnic group. Meanwhile, R9c and M7c1 are

commonly found in Southeast Asia. The haplogroups D4, U2, N8 and C are found due to probable

genetic admixture with population from Pakistan and India.

This M.Sc. Candidate is under the supervision of Dr. Yew Chee Wei and co-supervision of

Assoc. Prof. Dr. Vijay Kumar


PG51

Inferring the genetic relatedness of Sabah indigenous

ethnic groups based on complete Mitochondrial DNA

Hypervariable Region

(M.Sc. Candidate)

Nur Asfariena Binti Tupah

66

Bacteria can be exhibited into two different forms, the planktonic and biofilm forms. They are

ubiquitous in the environment, particularly in soil system. In contrast to their planktonic forms,

bacteria within biofilm improve their survival rate under growth-limiting conditions via the mechanism

of aggregation involves the production of Extracellular Polymeric Substances (EPS) and biofilm. The

self-produced polymeric matrix provides a shield for the maintenance and colonization of bacterial

cells in the soil. The matrixes, in turn, contribute stability to soils and reduce soil disruption during

flooding. We investigated the biofilm formation ability in 49 isolates from the Kelantan River Basin

(KRB). DNA ribotyping was performed to ascertain the identity of environmental isolates.

Subsequently, the bacterial isolates were cultured in a static polystyrene tube to identify biofilm

formation using crystal violet assay. To further characterize the biofilm structure, a scanning

microscopy examination was carried out. Our findings revealed 7 types of isolates from KRB which

demonstrated the ability to form biofilm in vitro by forming a halo and biomass at the surface and air-

liquid interface of polystyrene tube along with the increased in optical density (OD) reading. The OD

values were measured spectrophotometrically at 420 nm which represented the quantity of biofilm

formation. The current data may facilitate better insight into the understanding of bacterial survival

and growth which influence the extent of bacterial survival under adverse environment and contribute

to soil stability.


Rodrigues and Mdm. Grace Joy Chin Wei Lie.


NS52

Characterization of biofilm-forming soil bacteria

isolated from the River Basin, Kelantan

(M.Sc. Candidate)

Rennielyn Rupert

67

Salmonella bacteria can cause a wide range of diseases such as gastroenteritis, typhoid fever and

septicaemia and is receiving a significant public health concern worldwide. Most of the Salmonella

infection in humans and animals is originated from Salmonella serogroups A to E. The identification of

Salmonella serogroup and serotype using immunological based method have few drawbacks such as

a false-positive reaction due to weak and non-specific agglutination between antiserum used and the

antigen present on Salmonella cell surface. To compensate this drawback, identification of Salmonella

serogroup and serotype using molecular method can be done by targeting specific DNA sequences

present in specific serogroup or serotype. The objective of this study is to detect specific DNA

sequences present in Salmonella serogroup C genome. In this study, two genome from Salmonella

serogroup C were extracted and sequenced using Illumina platform (150 Paired End reads). The raw

sequenced reads obtained from Illumina sequencer (HiSeq 4000) were trimmed using Trimmomatic

software to remove the adapter added during library preparation step. Prior to genome annotation

part, the trimmed raw sequenced reads were assemble using SPAdes software. Genome annotation

was then conducted using the RAST (Rapid Annotation using Subsystem Technology) server. The

resulted contigs from both sequenced genomes were compared with four other genomes from

different serogroups (serogroup B, C, D and E) using the CCT (CGView Comparison Tool) software.

The comparative genomic analysis reveal the presence of unique DNA sequences in the sequenced

genomes. PCR was conducted and the result obtained support this finding.


Rodrigues and Dr. Christopher Voo Lok Yung


NS53

Identification of unique DNA sequences from

Salmonella serogroup c genome

(M.Sc. Candidate)

Calvin Jiksing

68


NS54

Cold adaptation strategies of Cryobacterium sp. SO1

(Ph.D. Candidate)

Teoh Chui Peng

69

MD2 pineapple contains 14 genes encoding bromelain with the sizes ranging from 19 kDa to more

than 500 kDa. Accordingly, MD2 bromelain is classified into three groups of small-, medium- and

large-sized of bromelain. Bromelain is a member of cysteine protease mainly found in stem and fruit

of pineapple. This protein is a papain homolog with versatile applications in food and pharmaceutical

industries. In previous presentation, heterologous production and catalytic properties of small- and

medium-sized of MD2 bromelain (designated as MD2-SBro and MD2-MBro, respectively), were

compared, indicating that the MD2-MBro exhibited higher kcat/KM by more than 200-folds. Besides,

MD2-MBro had showed remarkable activity to tenderize meat. In this presentation, ability of MD2-

MBro to tenderize the meat was re-confirmed through its ability to degrade the meat myofibril protein

fraction of the meat. Specific activity of MD2-MBro towards the myofibril protein was found to be

higher than other proteases. These might be due discrepancies on the substrate specificities of those

proteases. Further, changes on the meat structures due to the protein degradation was also

confirmed under scanning electron microscope. Altogether, these results confirmed that the

mechanism of meat tenderizing by MD2-MBro lies on proteolytic activity of MD2-MBro towards meat

myofibril proteins. These proteins, along with connective tissue, are known to be the major

contributor to the meat structure. Therefore, the results from the whole study will lead towards better

understanding on the application of recombinant MD2 bromelain for industrial usage.

This M.Sc. Candidate is under the supervision of Dr. Cahyo Budiman and Assoc. Prof. Dr.

Vijay Kumar


NS55

The effects of MD2 Bromelain on meat structure and

myofibril proteins

(M.Sc. Candidate)

Rafida Razali

70


NS56

Molecular study on 2S albumin, a mabinlin-like protein

from Theobroma cacao under heterologous expression

system.

(M.Sc. Candidate)

Norzulaiha Binti Abdul Karim

71


NS57

Phosphorylation of extracellular signal-regulated

kinase in determining differentiation of amnion-

derived mesenchymal stem cell

(M.Sc. Candidate)

Haselamirrah Binti Mohd Akhir

72

Organizing Committee of 24th Biotechnology Research Institute Postgraduate Seminar

Patron


Advisor

Dr. Suryani Saallah

Chairperson Rafida Binti Razali

Vice Chairperson Riana Binti Awang Saman

Head of Secretariat Tamar Kansil

Head of Finances Herman Umbau Lindang

Head of Programmes Nurfaezah Ibadat

Head of Scientific Committee Rennielyn Rupert

Head of Design and Publicity Abigail Lorna Eric

Head of Technical Affairs Dexter Lee Jiunn Herng

Head of Refreshment and Hospitality Senty Vun Sang

Head of Protocol and Registration Azriah Asis

Head of Emcee Jennifer Charles Labo

73

SECRETARIAT:

1. Mayrlidzatul Farhain Binti

Misrah

2. Nur Syahadatain Abdul Razak

3. Syva Hednella Sabanting

4. Mohd Zulhilmi Bin Abdul

Rahman

FINANCES:

1. Iffa Ridha Binti Luqman Ridha

2. Md. Shafiul Alam Bhuiyan

3. Teoh Chui Peng

PROGRAMMES:

1. Khairul Nizam Bin Sehat

2. Nur Shafrina Aida Yahya

3. Rojilin Donal

4. Jerelyn Joan Jenius

5. Adznilla Binti Eberahim

6. Calvin Jiksing

SCIENTITFIC COMMITTEE:

1. Sylvbryanie Salister

2. Diana Lorons

3. Sylvia Yahumin

4. Wan Nur Syuhaida

5. Ranjita Subramanian

6. Chee Fong Tyng

7. Rajeena

TECHNICAL AFFAIRS:

1. Gilbert Anak Ringgit

2. Chua Chuen Yang

3. Farhan Nazaie

4. Ching Xin Jie

5. Mohammad Munir Hossain

6. Shafiqul

REFRESHMENT AND

HOSPITALITY:

1. Rima Fatira Dahari

2. Nurul Sakinah Binti Saapilin

3. Devina David

4. Haselamirrah Mohd Akhir

5. Nur Nashyiroh Izayati Binti

Mastor

PROTOCOL AND

REGISTRATION:

1. Nur Fatihah Zamri

2. Noor Aini Binti Bohari

3. Hiew Vun Vun

4. Nur Asfariena Binti Tupah

5. Adznila Binti Eberahim

6. Norzulaiha Abd Karim

EMCEE:

1. Azniza Mahyuddin

2. Makdi Masnoddin

3. Low Yi Yik

4. Helena Biun

5. Pamela DESIGN AND PUBLICITY:

1. Alex Walzico Robert

2. Chin Lai Mun

74

SPECIAL THANKS

MEDISCH SDN BHD

Block J-2-2, Sinsuran Complex,

Jalan Dua Puluh,

88000 Kota Kinabalu, Sabah.

Contact Number / WhatsApp: +60138807955

E-mail: [email protected]

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- Scientific & Laboratory Chemicals / Disposables / Test Kits / Glasswares /

Plasticwares / Equipment

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- Chemical Wastes Disposal Service

- Geological Exploration

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NEOSCIENCE SDN BHD

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URL: www.neoscience.com

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