Faculty Research Day

Abstract

Biotechnology Cluster Development at HKSTP – Mr. Stephen Lam (HKSTP)

As a statutory body established by the Government of the Hong Kong Special Administrative Region, the Hong Kong Science and Technology Parks Corporation (HKSTP) has the mission to foster the growth and sustainability of several high-tech industries including biotechnology. Hong Kong Science Park plays a key role in bridging the gap between basic research and product commercialisation, with the goal to lower the barrier of entry for tenant companies and speed their products to market.

Envisioned to be built in three phases and to eventually include 22 hectares on the waterfront, Phase I of the Park (approximately 1 million sq. ft.) was completed in October 2004 and is now fully occupied. Construction of Phase II is well under way, with 2 buildings (approximately 200,000 sq. ft.) dedicated to life sciences. A full-service Incubation Programme provides assistance to biotechnology start-ups, offering ready-to-use office space, business support, and a financial aid package.

The Park aims not only to provide physical facilities, equipment, and technical support, but to build communities of entrepreneurs and enterprises within an ecosystem where creativity and ideas can feed on each other. For life sciences, the initial focus is to build on existing areas of strength in Hong Kong, including medical diagnostics and devices, clinical trial support, informatics, and traditional Chinese medicine and nutraceuticals. To help its communities reach collaborators and markets in other parts of the world, the Park has established alliances with other biotech clusters and science regions world-wide, and is continuing to expand its network.

Barcode of Life: Principle, Practice and Challenges – Prof. Ka Hou Chu (Department of Biology)

Species identification forms an important foundation for all fields of biological sciences. Yet the lack of taxonomic expertise in many groups of organisms has hampered research and development in many areas of biological investigations, particularly those involving ecology, biodiversity and conservation. It has been proposed that DNA barcode, i.e., short DNA sequence from a standardized region of the genome, can be used for species identification. Specially, the construction of a database of the mitochondrial cytochrome c oxidase I (COI) gene has been initiated towards the goal of rapid and cost-effective identification of all animal species. In this talk, I will first introduce the rationale, methodology, data interpretation, and applications of DNA barcode. Then I will discuss some of challenges for the development of an effective DNA barcode system, including the following areas: (1) analysis, interpretation, management, and display of barcode data, (2) how the system can be improved (i.e., faster, cheaper more reliable and accessible), and integrated with other biodiversity information, and (3) the feasibility of a portable electronic device for species identification in the field. A multidisciplinary approach involving statistics, computer science, information technology, and engineering will be needed to meet these analytical and technical challenges.

Hardware Acceleration For Bioinformatics – Prof. Philip Leong (Department of Computer Science and Engineering)

In this talk, examples are given of how customized hardware can be used to accelerate computationally expensive problems in bioinformatics. We first compare three technologies for implementing algorithms: microprocessors, integrated circuits and FPGAs, an FPGA being an integrated circuit containing an array of logic gates in which the connections can be configured by downloading a bitstream to its memory. Two case studies are then given, one in DNA sequence alignment and the other in molecular dynamics. It is shown that for these applications, hardware acceleration can offer several orders of magnitude speed improvement over conventional microprocessor-based systems due to their increased levels of parallelism. It is concluded that there is a lot of potential for using hardware acceleration to solve otherwise intractable problems in bioinformatics.

Generation and Dissociation of Protein Radical Ions – A New Dimension for Sequencing of Proteins

By Mass Spectrometry – Prof Dominic Chan (Department of Chemistry)

A proteome is defined as the sum of all proteins present in a cell (or cell compartment), a tissue or complete organism in a defined state. Through the analysis of the proteome of cells, tissues or organisms, it is believed that new drugs and reliable biomarkers for the diagnosis and therapy of diseases can be obtained. In addition to the large number of proteins in human (~ 400,000), the dynamic responses of the proteome to the cell cycle and developmental stage of an organism as well as physiological and pathological conditions make the proteomic research a very challenging task.

In past decades, mass spectrometry has proved to be an indispensable tool for protein identifications and characterization. In this presentation, the principle and usage of mass spectrometry method for protein analysis will be discussed with an emphasis on the processes that are related to the generation of sequence specific information. Recent advances in gas-phase protein radical ion chemistry have led to a new dimension for generation of sequence specific information which is complementary to the more traditional type of even-electron dissociation of proteins. Through the use of a combination of experimental and theoretical studies using model systems, we have acquired important insights of the mechanistic aspects of the decomposition of protein radical ions.

Structural Biology Research at the Centre for Protein Science and Crystallography – Structural Basis of

Protein Thermostability – Prof. Kam Bo Wong (Department of Biochemistry)

Centre for Protein Science and Crystallography (CPX) was established in 2005 with support from the Department of Biochemistry and the Research Committee of the Chinese University of Hong Kong. We employ multi-disciplinary techniques including protein engineering, biophysical characterization, and X-ray crystallography to study the structure-function relationship of proteins. Our aim is to provide a platform to promote collaboration on protein research within the local community and in South China. Research activities of Wong’s research group will be first introduced, followed by a brief description of other activities at the CPX.

Wong’s group uses a ribosomal protein L30e from Thermococcus celer as a model to investigate the structural adaptation of this thermophilic protein to resist thermal unfolding. Structure of T. celer L30e determined by both NMR spectroscopy and X-ray crystallography reveals that the thermophilic protein has more charge-charge interactions. Site-directed mutagenesis studies demonstrated that charge-charge interactions contribute to the thermostability of T. celer L30e. Comparison of thermodynamics parameters of the thermophilic L30e with those of a mesophilic homologue suggests that T. celer L30e achieves thermostability by having a much smaller value of heat capacity change of unfolding (DCp), which differences cannot be explained by established theory that DCp is correlated with change of solvent-accessible surface area. Our work has established for the first time that the reduction in the DCp values commonly found in thermophilic proteins is a result of increased favorable charge-charge interactions.

Biological Pattern Formation and Mathematical Biology – Prof. Jun-Cheng Wei (Department of Mathematics)

In 1952, the British mathematician, Alan Turing, wrote his seminar paper entitled "The chemical Basis of Morphogenesis''. In it, he hypothesized that to understand the mechanism of development in plants and animals, it was essential to investigate how basic process interacted. He showed the remarkable phenommenon that stable process could combine to produce an instability. The particular example he took was of diffusion-driven instability. This phenomenon has now been found in chemistry and it is still controversial in biology. However, the model does produce patterns that are intriguingly similar to those observed in animals and has stimulated a number of laboratories to carry out experiments to test the model. In this talk, I shall describe the recent advances in understanding Turing's diffusion-driven instability, from mathematical point of view, and illustrate how deep mathematics can be used to tackle problems in biology.

Tailoring Surface Plasmon-derived Properties of Gold Nanostructures

– Prof. Jiang Fang Wang (Department of Physics)

Gold nanostructures have great potentials in optical, electronic, and biotechnological applications because gold is chemically inert and biologically compatible and gold nanostructures exhibit rich surface plasmon-derived properties. We have developed synthetic methods to finely tune the surface plasmon-derived properties of gold nanostructures, including surface plasmon wavelengths, extinction cross sections, and local electric field enhancements. The availability of gold nanostructures with their surface plasmon-derived properties covering a wide parameter space will help to realize their full potentials in a variety of areas.

Mining in the Treasure House – Biological Activities from Chinese Herbal Medicines

– Prof. Zhixiu Lin (School of Chinese Medicine)

Traditional Chinese herbal medicines have been used for millennia in the treatment of various medical conditions, and much empirical clinical experience and know-how technical expertise have been accumulated in this area. During the last several decades, there has been a movement in scientific community to find biological activities and identify active ingredients from this traditional treasure house. In recent years, the School of Chinese Medicine has embarked on a number of research programmes to evaluate the mechanisms of action underlying Chinese herbal medicines for disease treatments. In this presentation, focuses are placed on some of the ongoing research projects associated with studying herbal medicines targeting disease entities such as psoriasis and pancreatic cancer.

In Biology and Medicine, information collected from a group of individuals over time is used in studying the dynamics of a system or the time varying effect of a treatment. For example, in Pharmacokinetics\Pharmacodynamics, the drug concentration in the blood is measured from a group of patients after the treatment. Since the same patient is being measured several times, the corresponding

data are obviously correlated. Also, some data series may be sparse because the patients may be very sick and cannot afford to give many measurements. All these post challenges to statistical modelling, analysis and prediction. In this talk, we will review the technique developed by Lai, Shih and Wong (2006) and how it is applied to handle the longitudinal data in Pharmacokinetics\Pharmacodynamics, Ecology and Pediatrics.

Longitudinal Data Analysis in Pharmacokinetics\Pharmacodynamics, Ecology and Pediatrics

– Prof. Samuel Po-Shing Wong (Department of Statistics)