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Dept Diagnostic lu vaccine


Dept Diagnostic lu vaccine

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									Department of

T    o take advantage of the near completion of the sequencing of the human and many microbial genomes the Department
of Microbiology is concentrating on the development of DNA based microbial diagnosis and vaccines. The Department of
Microbiology is also involved in a Bioengineering initiative in which bioinformatics and computation biology are utilized to
unravel the interaction between viral (EBV, HCV) peptides and the host major histocompatibility antigens. Such precise
prediction of the interaction may generate vaccines and immunotherapeutic procedures against certain infectious diseases
and cancer. The department intends to blend powerful tools developed in the physical and computational sciences into
biology to develop cutting edge capabilities in the life sciences.

The following are some of our current research interests :
• Rapid diagnosis and molecular biology of microbes including dengue, hepatitis B & C, Epstein Barr Virus, Varicella-zoster,
  papillomavirus, B pseudomallei, Legionella and parasites
• Microbial fermentation - algae, Helicobacter pylori, yeast
• Nasopharyngeal carcinoma and primary liver cancer
• Genetics – Human Leucocyte Antigen, T cell receptors, microsatellite markers
• Epstein Barr Virus serology – development of better diagnostic markers
• Liver cancer – HBX gene enhancers and screening methods for drugs
• Oncogenes and anti-oncogenes
• Restriction enzyme & antibiotic screening
• Molecular biology of Saccharomycopsis fibuligea and Yarrowia lipolytica, Neisseria gonorrhoeae, Pseudomonas
• H. pylori – better diagnostic and vaccine development
• Molecular typing of microbes
• Molecular cloning and expression of useful genes of microbes
• Detection and control of antibiotic-resistant bacteria
• Novel strategies for the treatment of intracellular and multiply-resistant bacteria

The following centres/registries are under the auspices of the department :
• WHO Collaborating Centre for Immunology
• Bone Marrow Registry
• Cord Blood Registry
• National Hepatitis Reference Centre
• National Malaria Reference Centre

Services provided by the department are as follows :
• HLA typing for transplants
• EBV testing for NPC diagnosis and follow-up
• Hepatitis virus and antibody quality assurance
• Parasitology diagnostics
• Tests for H. pylori, legionella, melioidosis, CMV and dengue
                                           Project Description
                                            G r a n t s a w a r d e d t o t h e D e p a r t m e n t i n 2000
                                           Molecular studies on the structure-function                  NUS Engineering Initiative – Biocomputing
                                           relationship of a putative autolusin gene of                 Principal Investigator : Prof Chan Soh Ha
                                           Clostridium difficile                                        Collaborators           : Assoc Prof Ren Ee Chee,
                                           Principal Investigator : Dr. Song Keang Peng                                           Chen YZ,
                                                                                                                                  Leow CK,
                                           The goal of the proposal is to determine the activity(ies)                             P Kolatkar
                                           of TcdE of C. diffiicle in order to understand the
FITC staining of virus envelope proteins
in Vero Cells
                                           mechanism(s) of toxin production and release in the          To predict and verify EBV and HCV peptide binding to
                                           organism. The hypothesis to be tested is that TcdE           oriental HLA molecules.
                                           functions as a type of autolysin , thus self-destruct a
                                           small proportion of the bacteria for the release of toxins   Diversity and molecular characterization of multiple
                                           to the environment so that other C. diffiicle can survive    antibiotic resistance determinants in Vibrio harveyi
                                           and proliferate.                                             Principal Investigator : Assoc Prof Poh Chit Laa

                                           Molecular typing of enterovirus 71 isolates from             Vibrio harveyi has been implicated as the casual
                                           Singapore by PCR and potential development of a              agent for “luminous” disease or vibriosis in shrimps.
                                           DNA vaccine                                                  To treat this disease, the shrimp farmers preferred to
                                           Principal Investigator : Assoc Prof Poh Chit Laa             use b-lactam antibiotics such as ampicillin since
                                           Collaborators          : Assoc Prof Vincent Chow,            these groups of antibiotics did not cause significant
                                                                    AE Ling,                            side-effects. Unfortunately, many type of b-lactam
                                                                    KP Chan (Pathology, SGH)            antibiotics were no longer able to prevent virbiosis.
                                                                                                        In addition, many V. harveyi strains also showed
                                           To develop a specific and sensitive method based on          resistance to multiple antibiotics such as
                                           RT-PCR to detect enterovirus 71 (EV71), the causative        tetracycline, chloramphenicol, streptomycin and
                                           agne for hand, foot and mouth disease. This rapid            spectinomycin. Therefore, it is crucial to understand
                                           identification of EV71 will help to elucidate the            the genetic basis of antibiotic resistance in this
                                           genotypes involved in an outbreak and enable prompt          microorganism that is associated with shrimp larvae
                                           implementation of measures that will minimize further        and shrimps. The results of this study should be able
                                           transmission of the virus. Real time based PCR methods       to provide basic research findings that are
                                           have been developed to enable rapid detection of EV21        publishable and in addition, strategies can be
                                           directly from clinical specimens without the need to         developed to prevent the occurrence of vibriosis.
                                           further culture the virus.

                                            Ongoing Projects
                                           Studies on the immune response to hepatitis C virus:         and 10 mers in length. Using the HCV E2 protein as a
                                           Applications towards vaccine design and                      test system, we were able to select about 60-70
                                           immunotherapy                                                peptides of 8,9 and 10mers. These will be tested in a
                                           Principal Investigator : Assoc Prof Ren Ee Chee              validation assay using recombinant HLA molecules.
                                           Collaborators          : Assoc Prof Leow Chon Kar            The system for generating the recombinant HLA is
                                                                    (Surgery),                          also being worked out.
                                                                    Dr Prasanna Kolatkar (BIC)
                                                                                                        Molecular characterization of periodontal diseases
                                           The aim of this project is on establishing the               Principal Investigator : Dr. Song Keang Peng
                                           common serotypes of HCV in Singapore. This is                Collaborator           : Assoc Prof Grace Ong
                                           important to allow us to determine which variants                                     (Faculty of Dentistry)
                                           and hence their peptides would be most relevant for
                                           vaccine design. The peptide selection protocols are          Aims :
                                           also being worked out and we have designed an                1. To develop molecular markers for the detection of
                                           algorithm to determine candidate peptides of 8, 9,              periodontal diseases.

      48       Faculty of Medicine Research Report 2000
2. To use the markers for the monitoring of the               DNA vaccine approach for dengue fever/dengue
   treatment and prognosis of periodontal diseases.           haemorrhagic fever
3. To provide service for the detection of microbial          Principal Investigator : Assoc Prof Mary Ng
   agents in periodontal diseased patients.                   Collaborator           : Assoc Prof Vincent Chow
4. To develop chair-side rapid detection and
   diagnostic kit for periodontal diseases.                   To use this approach to design an effective vaccine
                                                              against dengue virus infection.
Role of Lentinus edodes (Shiitake mushroom) as an
immunomodulator for antitumour and antiviral                  Degradation of phenolic wastes by Pseudomonas
activities                                                    species via the gentisate pathway : cosmid cloning and
Principal Investigator : Assoc Prof Mary Ng                   genetic organization of the genes in P25X and P35X
                                                              Principal Investigator : Assoc Prof Poh Chit Laa
The objective is to do pre-clinical trials in a mouse
model on the effectiveness of lentinan (a purified            Elucidating the molecular biology of the gentisate
form of b-glucan from shiitake mushrooms) as an               pathway degradation.
anti-tumour and anti-viral agent before going into
Phase 1 clinical trials on human.

 International Publications                                                                                                     Graduate Students

Chen, H, C K Lim, Y K Lee and Y N Chan,                       Hua, J, KL Ling, HS Ng and B Ho                                   THESES PASSED
Comparative analysis of the genes coding for 23S-5S           Isolation of a single strain of Helicobacter pylori from          (PhD)
intergenic spacer regions of rRNA of Lactobacillus            antrum and body. European Journal of Gastroenterology             Feng Yongmei
casei related strains. International Journal of               and Hepatology, 12 (2000): 1129-1134. (United Kingdom).           (Biochemical and molecular
Systematic and Evolutionary Microbiology, 50 (2000):                                                                            characterization of gentisate 1,2-
471-478. (United Kingdom).                                    Hua, J, P Zheng, K G Yeoh and B Ho                                dioxygenases from Pseudomonas
                                                              The status of the CagA gene does not predict Helicobacter         alcaligenes NCIB 9867 and
Chow, V T K, E Loh, WM Yeo, S.Y. Tan and R Chan               pylori - associated peptic ulcer disease in Singapore.            Pseudomonas putida NCIB 9869)
Identification of multiple genital HPV types and              Microbios, 102 (2000): 113-120. (United Kingdom).
sequence variants by consensus and nested type-                                                                                 Zhu Congju
specific PCR coupled with cycle sequencing. Pathology         Jin, R, B H Bay, V T K Chow, P H Tan and V C Lin                  (w-3 polyunsaturated fatty acid
32, no. 3 (August 2000): 204-208. (United Kingdom).           Metallothiionein 1E mRNA is highly expressed in                   production by Isochrysis galbana
                                                              oestrogen receptor-negative human invasive ductal                 TK1)
Chow, V T K, P A Tambyah, W M Yeo, M C Phoon                  breast cancer. British Journal of Cancer, 83(3) (August
and J Howe                                                    2000): 319-323. (United Kingdom).                                 (MSc)
Diagnosis of Nipah virus encephalitis by electron                                                                               Bai Xin Lai
microscopy of cerebrospinal fluid. Journal of Clinical        Kangueane, P, M K Sakharkar, K Lim, H Hao, E C Ren                (Structure and function relationship of
Virology, 19, no.3 (November 2000): 143-147. (Ireland).       and P R Kolatkar                                                  toxins A and B of Clostridium difficile)
                                                              Knowledge based grouping of modeled HLA peptide
Frecer, V, B Ho and J L Ding                                  complexes. Human Immunology, 61 (2000): 460-466.                  Cedric Ng Chuang Young
Interpretations of biological activity data of bacterial                                                                        (Genomic organisation of Factor C
endotoxins by simple molecular models of mechanism            Kwong, SM, C C Yeo, S Antonius and C L Poh                        from Carcinoscorpius Rotundicauda)
of action. European Journal of Biochemistry, 267 (2000):      Characterizaton of the endogenous plasmid from
837-852. (The Netherlands).                                   Pseudomonas alcaligenes NCIB 9867 : DNA sequence                  Ji Zhiliang
                                                              and mechanism of transfer. Journal of Bacteriology, 182,          (Molecular study of ocular infection)
Frecer, V, B Ho and J L Ding                                  no.1 (January 2000): 81-90.
Molecular dynamics study of lipid A from E. coli and its                                                                        Li Geling
monophospho and dephospho analogues. Biochimica               Loke, P, CP Ng and T S Sim                                        (Dynamics of interferon-gamma,
et Biophysica Acta, 1466 (2000): 87-104. (The Netherlands).   PCR cloning, heterologous expression and                          interleukin-12 and interleukin-18 in
                                                              characterisation of isopenicillin N synthase from                 acute graft-versus-host disease :
Gan, Y Y, D Chai, T T M Tan, Y H Gan and S H Chan             Streptomyces lipmanii NRRL 3584. Canadian Journal                 Potential of using interleukin-18
The distribution of Epstein-Barr virus antigenic sites        of Microbiology, 46 (2000): 166-170. (Canada).                    directed immunotoxin to eliminate
on the carboxyl terminal end of ribonucleotide reductase                                                                        activated alloreactive T cells)
against nasopharyngeal carcinoma serum antibodies             Loke, P and T S Sim
using immuno-absorption method. Journal of Medical            Mutational analysis of tyrosine-191 in the catalysis of
Virology, 58 (2000): 385-396. (United States).                Cephalosporium acremonium isopenicillin N synthase.
                                                              Journal of Biochemistry, 127, (2000) no. 4.
Ho, L C, A Armugam, K Jeyaseelan, E H Yap and M Singh
Blastocystis elongation factor-1alpha:Genomic organization,   Liu, BH, DH Zhang and Y K Lee
taxonomy and phylogenetic relationships. Parasitology, 121,   Effect of nutrient levels on cell growth and secondary
2 (1 August 2000): 135-144. (United Kingdom).                 carotenoids formation in the fresh water green algae,

                                                                                                                          Department of Microbiology           49
                                       Chlorococum sp. Journal of Microbial Biotechnology,        Soh, S W-L, C L Poh and R V T P Lin
Graduate Students                      10 (2000): 201-207. (South Korea).                         Serotype distribution and antimicrobial resistance of
                                                                                                  Streptococcus pneumoniae isolates from Pediatric
                                       Monteiro, MA, P Zheng, B Ho, S Yokota, K Amano, Z          Patients in Singapore. Antimicrobial Agents and
THESES PASSED                          Pan, DE Berg, KH Chan, LL MacLean and MB Perry             Chemotherapy, No. 8, (2000): 2193-2196. (United States).
(MSc)                                  Expression of histo-blood group antigens by
Ng Chee Pang                           lipopolysaccharides of Helicobacter pylor strains from     Song, K P, T K Chan, ZL Ji and S W Wong
(Phylogenetic analysis of              Asian hosts : the propensity to express type 1 blood-      Rapid identification of P. aeruginosa from ocular isolates
isopenicillin N-synthase genes in      group antigens. Glycobiology, 10 (2000): 701-713.          by PCR using exotoxin A-specific primers. Molecular and
selected beta-lactam antibiotic        (United Kingdom).                                          Cellular Probes, 14, no. 4 (2000): 199-204.
producing Streptomyces species)
                                       Ngan, WY, B H Nga, D Pridmore, B Mollet and H M Tan        Subramanian, S, B Huang, H Loh, J Kwang, H M Tan, K
Sheree Yiin                            Transformation of Endomyces fibuliger based on its         L Chua and J Frey
(Group II introns from Pseudomonas     gene for orotidine-5'-phosphate decarboxylase. Gene,       Characterization of a predominant Immunogenic outer
alcaligenes NCIB 9867 [P25X] and       254 (2000): 97-103. (The Netherlands).                     membrane protein of Riemerella anatipestifer. Clinical
Pseudomonas putida NICB 9869 [P35X])                                                              and Diagnostic Laboratory Immunology, 7, (2000): 168-
                                       Norman, RA, C L Poh, LH Pearl, BP O’ Hara and RE Drew      174. (United States).
Shirlena Soh Wee Ling                  Steric hindrance regulation of the Pseudomonas
(Molecular epidemiological study of    aeruginosa amidase operon. Journal of Biological           Tan, K S W, M Ibrahim, G C Ng, AMA Nasirdeen, L C Ho,
Streptococcus pneumoniae)              Chemistry, 39, (2000), 275. (United States).               E H Yap and M Singh
                                                                                                  Exposure of Blastocystis species to a cytotoxic
Wang Wee Fuen                          Ren, E C                                                   monoclonal antibody. Parasitology Research (2000) :
(Isolation and identification of       The role of HLA matching in unrelated donor bone           534 - 538
Alcanivorax borkumensis LE4, and       marrow transplant. Transplantation Proceedings, 32, 7
cloning of a putative aldehyde         (2000): 1541-1542.                                         Tan, K S W, G C Ng, E Quek, J L C Howe, N P
dehydrogenase gene)                                                                               Ramachandran, E H Yap and M Singh
                                       Ren, E C, P Kangueane, P R Kolatkar, MT Lin, LH Tseng      Blastocystis hominis : A simplified, high-efficiency
                                       and JA Hansen,                                             method for clonal growth. Experimental Parasitology,
                                       Molecular modeling of the minor histocompatibility         96 (2000): 9-15. (United States).
                                       antigen HA-1 peptides brinding to HLA-A alleles and
                                       its relevance in stem cell transplant matching. Tissue     Tan, N S, M L Ng, Y H Yau, B Ho and J L Ding
                                       Antigens, 55 (2000): 24-30. (United States).               Definition of endotoxin-binding sites in horseshoe crab
                                                                                                  Factor C recombinant sushi proteins and neutralisation
                                       Seow, T K, S.E Ong, RCMY Liang, E C Ren, L Chan, K L       of endotoxin by sushi peptides. FASEB Journal, 14
                                       Ou and M C M Chung                                         (2000): 1801-1813. (United States).
                                       Two-dimensional electrophoresis map of the human
                                       hepatocellular carcinoma cell line, HCC-M, and             Tan, N S, B Ho and J L Ding
                                       identificaiton of the separated proteins by mass           High affinity LPS-binding domain(s) in recombinant Factor
                                       spectrometry. Electrophoresis, 21, (2000), 9 : 1787-       C of a horseshoe crab neutralises LPS-induced
                                       1813. (Germany).                                           lethality. FASEB Journal, 14 (2000): 859-870. (United States).

                                       Se Thoe, SY, AE Ling and M M L Ng                          Tay, A H N, E C Ren, B Murugasu, S K Sim, P H Tan, A H
                                       Alteration of virus entry mode a neutralisation            Cohen and H K Yap
                                       mechanism for dengue-2 virus. Journal of Medical           Membranous nephropathy with anti-tubular basement
                                       Virology, 62, no.3 (2000): 364-376. (Austria).             membrane antibody may be X-linked. Paediatric
                                                                                                  Nephrology, 14, (8-9) (August 2000): 747-753.
                                       Sim, J and T S Sim
                                       Mutational evidence supporting the involvement of          Teo, J.W.P., A Suwanto and C L Poh
                                       tripartite residues His183, Asp185, and His243 in          Novel beta-lactamase genes from two environmental
                                       Streptomyces clavuligerus deacetoxy cephalosporin C        isolates of Vibrio harveyi. Antimicrobial Agents and
                                       synthase for catalysis. Bioscience, Biotechnology,         Chemotherapy, 44, no.5 (May 2000): 1309-1314. (United States).
                                       Biochemistry, 64, no. 4 (2000): 828-832.
                                                                                                  Yap, C, MT Loh, KK Heng, P Tan, SL Yu, S H Chan and E
                                       Singh, S, V T K Chow, K.P. Chan, A.E. Ling and C L Poh     C Ren,
                                       RT-PCR nucleotide, amino acid and phylogenetic             Variability in CD34+ cell counts in umblical cord blood
                                       analyses of enterovirus type 71 strains from Asia.         : Implications for cord blood transplant. Gynecologic &
                                       Journal of Virological Methods, 88, no. 2 (August 2000):   Obstetric Investigation, 50, no.4 (2000): 258-259.
                                       193-204. (Ireland).
                                                                                                  Zhu, Y Z, G N Chimon, Y C Zhu, Q Lu, B Li, H Z Hu, E H
                                                                                                  Yap, H S Lee and P T H Wong
                                                                                                  Expression of angiotensin II AT 2 receptor in the acute phase
                                                                                                  of stroke in rats. Neuroreport, 11 (2000): 1191-1194.

  50     Faculty of Medicine Research Report 2000
Zaman, V, J L C Howe and M M L Ng                             Research, 86 (January 2000): 54-56. (Austria).
Scanning electron microscopy of Chilomastix mesnili
:(Wenyon, 1910) A lexieieff, 1912. Parasitology Research,     Zheng, P, J Hua, K G Yeoh and B Ho
86 (2000): 327-329. (Austria).                                Association of peptic ulcer with increased expression
                                                              of Lewis antigens in Helicobacter pylori in an Asian
Zaman, V, J L C Howe, M M L Ng and T K Goh                    population. Gut, 47 (2000): 18-22.
Ultrastructure of Endolimax nama cyst. Parasitology

 Staff Profile
                                                              Assoc Professorial Fellow: Nga Been Hen
                                                                                                                                   Microtubule Networks (Texas Red Stained)
Professor and Head       : Prof Chan Soh Ha                   Senior Fellow            : Mark Taylor                                                            of Vero cells
Associate Professors     : Yap Eu Hian                        Senior Research Fellow : Hu Huaizhong
                           Mulkit Singh                                                  (no pay leave to exercise
                           Vincent Chow Tak Kwong                                        own patent in US)
                           Mary Ng Mah Lee                    Assistant Professor      : Song Keang Peng
                           Ho Bow                             Senior Tutors            : Seah Geok Teng (Post doc
                           Lee Yuan Kun                                                  at Albert Einstein University)
                           Sim Tiow Suan                                                 Koh Woon Puay
                           Poh Chit Laa                                                  Justin Wong Soon Boon
                           Ren Ee Chee                                                   (PhD in Johns Hopkins
                           Tan Hai Meng                                                  University, Baltimore)
                           (on no pay leave)                  Research Fellows         : Yeo Chew Chieng
Fellows                  : Lim Chor Kiang                                                Wang Yawen
                           Ooi Eng Eong (seconded to          Research Scientist       : Sinnakarrupan Mathavan
                           Ministry of Environment)           Research Assistants : Liew Chong Wee
                           Kevin Tan Shyong Wei                                          Paxton Loke
                           (Post doc in Rockefeller                                      Tan Sioh Yang
                           University)                                                   Adrian Png

 Contact Info
Address                  : Department of Microbiology         Contact Person           : Ms Geetha Baskaran
                           Faculty of Medicine                Tel                      : 874 3276
                           National University of Singapore   Email                    : micgb@nus.edu.sg
                           5 Science Drive 2
                           Singapore 117597                   Contact Person           : Ms Siti Masnor
Contact Person           : Ms Christina So                    Tel                      : 874 7891
Tel                      : 874 3275                           Email                    : micsmm@nus.edu.sg
Email                    : micsoc@nus.edu.sg
                                                              Fax                      : 776 6872
Contact Person           : Mr Ishak Ideriess                  Homepage                 : http://www.med.nus.edu.sg
Tel                      : 874 3275                                                      /mbio
Email                    : micii@nus.edu.sg

                                                                                                                          Department of Microbiology              51

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