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School of Biosciences & Biotechnology,
Faculty of Science & Technology,
Universiti Kebangsaan Malaysia,
43600 UKM Bangi

Tel: +6 03 89215961
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Faculty of Science & Technology
Centre for Postgraduate Studies
Universiti Kebangsaan Malaysia




Research summary:
Our research is primarily directed at understanding molecular function regulation by exploring the mechanistic interactions that effect molecular level switching and the associated regulatory pathways. To accomplish this, my research group study: (i) the structure and function of non-coding RNA molecules and how their interactions with other macromolecules effect regulatory changes in the cell and (ii) the structure, function and evolution of proteins with currently uncharacterized functions (hypothetical proteins). The approaches employed in exploring these key areas of interest include bioinformatics, computational biology, genomics, X-ray crystallography, synthetic biology and systems biology. The insights revealed from these investigations can provide clues as to how molecular level regulation and responses in living systems are carried out that eventually lead to an organism’s capacity to adapt to extreme (ie. extremophiles) or diverse environments (ie. pathogenic soil bacteria) as well as the discovery of novel factors associated with bacterial pathogenesis. More recent work in my group include the genome and transcriptome sequencing of several species of wide interest; examples include the Rafflesia holoparasitic flower, extremophilic organisms and a Malaysian firefly species that is noted for synchronous flashing.   

Current research areas:

  1. Molecular function regulation by epigenomic elements – sRNA/RNome.
  2. Structural analysis and function mechanisms of molecular switches and triggers.
  3. Structure and function of complex RNAs and hypothetical proteins.
  4. Molecular mechanisms of microbial environmental adaptation and pathogenesis.

Non-technical Research Summary
My research group works to discover new mechanisms in biological processes and from there, attempt to understand how a living system is able to control life’s many chemical processes at the molecular level. For our investigations, we use various tools that range from high performance computing to cutting edge analytical instruments. By understanding how biological processes are regulated at the molecular level, we can understand how diseases occur and in turn take steps towards the discovery and design of new therapeutic agents. These efforts include the use of programmable nano-materials that can be applied for diagnostic and therapy.

The Molecular Function Regulation Lab is primarily involved in exploring two major research themes: (1) the discovery and studies of interactions for non-coding RNA and (2) studies on the molecular mechanisms of microbial pathogenicity. Diverse approaches and technologies such as computational biology, bioinformatics, genomics, X-ray crystallography, systems biology and synthetic biology are deployed to achieve these objectives.

The knowledge and technology generated from our primary research is applicable to numerous other downstream research areas. As a result, the technology and knowledge acquired are further deployed to projects with collaborating labs in diverse areas which range from cancer epigenomics to bioremediation and bioenergy.

RNA Biology
Ribonucleic acids (RNA) have long been known as intermediary molecules between the information coded in DNA and the proteins encoded by those genes. Research has however shown that RNA molecules can also fold into complex structures which are crucial factors in determining their function just as in proteins. These RNA molecules are also involved in numerous cellular processes from regulatory roles to their long recognized roles in protein synthesis. RNA molecules such as ribozymes, riboswitches, ribosomal RNA and other families of non-coding RNA fall into this category. Studies of the occurrences and corresponding structural interactions which make up these molecules are therefore of great scientific interest. In our lab, two areas which we currently investigate are: (i) the use of computational approaches to study RNA structural interactions and 3D motifs and (ii) the discovery and annotation of non-coding RNA (novel and known) in genomic data. 

Molecular Mechanisms of Pathogenesis
The research group has also endeavoured to further understand molecular mechanisms of bacterial pathogenicity. This work involves the use of the bacterium Burkholderia pseudomallei as a model. This bacterial species is the causative agent of melioidosis and has been known to have a latent period prior to active infection which can last for decades in the host. Such an organism therefore provides an interesting avenue to further study mechanisms of host-pathogen interactions, bacterial survival and the systems which regulate the transition from latent survival to active pathogenicity. As a result, knowledge on the roles of non-coding RNAs as regulatory elements, protein-glycan interactions and the potential of products encoded by essential genes as drug targets in such a pathogen are of great value.We have also used B. pseudomallei as a platform for the study of bacterial methylomes and how methylation events regulate gene expression and various functions at the molecular level.

Structural Biology / Structural Bioinformatics
The research group is primarily interested in the the annotation and comparisons of bio-macromolecular 3D structures. We have thus developed the search tools to analyse large volumes of structural data. These annotations are used to identify novel structural arrangements/motifs, annotate function and explore applications such as drug repurposing. Using the tools developed, we have also been able to compile derive datasets into databases for use by the respective research communities.

Key specialization areas:
Computational structural biology, RNA bioinformatics, bacterial genomics

Other Research
The reearch listed here are mainly carried out in collaboration with other research groups.
-Rafflesia genomics
-G. antarctica genomics
-Phylogenomics of Galapagos iguanas
-Nucleic acid nanotechnology

Collaborators (External to faculty)
Prof. Peter Artymiuk (up to 2014)
Prof. David Rice
Prof. Peter Willett (up to 2014)
Prof. Per Bullough
Krebs Institute for Biomolecular Research
University of Sheffield

The Malaysia Genome Institute

Dr. Shandar Ahmad
Jawarharlal Nehru University
New Delhi, India

Dr. Gabriele Gentile
University of Rome Tor Vergata
Rome, Italy

Last updated: September 2012