RESEARCH & PUBLICATIONS
Link to Richard's Google Scholar Profile
My primary research interest is in the field of bioinformatics, systems biology, and medical physics. I have also done work in the field of regenerative medicine during my undergraduate studies at the Hong Kong Polytechnic University with Dr. Xin Zhao. Please see below for a list of my research work.
DETERMINING NOVEL NATURAL RESERVOIRS AND STRAINS OF YERSINIA PESTIS THROUGH SRA DATABASE MINING
This paper is submitted as a part of my undergraduate thesis project at the University of Waterloo.
Yersinia pestis is a deadly bacterium that is responsible for multiple pandemics throughout history and still causes hundreds of deaths yearly in the less developed part of the world. To better monitor the evolution of this bacterium, a database search from the NCBI Sequence Read Archive (SRA) was conducted as an attempt to discover novel reservoirs and strains of Y. pestis. By using various bioinformatic tools to reconstruct the genome and phylogenetically classify the samples, it was found that Pseudogymnoascus destructans, commonly known as white-nose fungus from bats and is a previously undocumented reservoir for Y. pestis, carried four distinct strains of the bacterium, with one of them being a highly divergent and potentially novel strain from existing Y. pestis references. The results of this study illustrated the importance of genetic surveillance, and further investigations into the pathogenicity of those strains should be conducted in order to avoid future pandemics caused by Y. pestis.
Keywords: Genomic Surveillance; Sequence Read Archive; Yersinia pestis; Pseudogymnoascus destructans
APPLICATION OF HYDROGELS AS A DRUG DELIVERY SYSTEM FOR BONE REGENERATION
This paper is submitted as the course final research project for PHYS 380: Cellular and Molecular Biophysics at the University of Waterloo.
Treating bone diseases such as bone fracture and bone tumour has become a major topic in biomedicine due to increasing demand. However, it is often accompanied with high prices because of the complexity associated with the process. To tackle this issue, one of the biopolymer materials called hydrogels has attracted significant attention in the field of bone repair and regeneration. The physical properties of hydrogel, which include high adhesion, high biocompatibility, high functionality, and high volume of water content, enable hydrogels to promote the interaction of cells by mimicking the extracellular environment of human tissues and use itself as a vector for bone regeneration drugs. To help future researchers better utilize the potential of hydrogels, this review aims to provide a comprehensive guide for developing hydrogels to be used as a bone regeneration drug delivery system through the discussion of hydrogel materials, techniques for modifying hydrogels, and drugs that can be loaded onto hydrogels. It is hoped that with the help of an effective hydrogel, the above-mentioned problems with bone regeneration can be addressed in order to promote the development of biomedicine and benefit patients worldwide.
Keywords: Hydrogels, Bone Regeneration, Tissue Engineering, Drug Delivery
MATHEMATICAL MODELLING OF SARS-COV-2 IN-HOST VIRAL DYNAMICS AND ITS POTENTIAL ANTIVIRAL TREATMENTS
This paper is submitted as a part of the course final project for AMATH/BIOL 382: Computational Modelling in Cellular Systems at the University of Waterloo.
The COVID-19 pandemic caused by the SARS-CoV-2 virus presents an unprecedented challenge for the global health care system. As an effort to end this pandemic through the discovery of SARS-CoV-2 antiviral drug targets, the in-host dynamic of SARS-CoV-2 is simulated and analyzed using system biology and differential equation models. Once the validity of the models is confirmed, several potential target sites for the antiviral drugs are investigated and simulated by incorporating their interactions into the models. It is found that a hypothetical antiviral drug can effectively combat SARS-CoV-2 by activating the interferon production in the innate immune response, suggesting a potential path for COVID-19 drug development.
Keywords: mathematical modelling; SARS-CoV-2; systems biology; viral dynamics; antiviral drug
EVAPORATION-BASED, CO-AXIAL LOCK-AND-KEY FIBROUS RESERVOIR FOR LONG-TERM PREVENTION OF HYPERTROPHIC SCARS
Many diseases and conditions such as hypertrophic scarring require long-term maintenance over the healing cycle to achieve full recovery. However, there is a lack of wound dressings that can sustain over 90 days of therapeutic release. Inspired by the enhancement of wound healing by the nanofibrous morphology and diverse structures of electrospinning, we report an evaporation-based co-axial electrospun fibrous scaffold incorporating polymer brush gatekept nanocarriers for sustained delivery of therapeutics. The release rates of the system were demonstrated to be tunable through polymer graft length, while the system experienced minimal burst release when submerged under aqueous conditions. As a proof-of-concept, we target hypertrophic scarring by loading the system with doxorubicin, which led to inhibition of fibroblast activity without interfering with cell adhesion. Application of our scaffolds on rabbit ear hypertrophic scar models displayed that our scaffolds effectively reduced collagen density and scar-related gene expression in healing tissues, with improved tissue elevation outcomes. We envision that our long-term release scaffolds will be useful in combating long unresolved clinical dilemma such as tendon adhesion and tumor regression.
AN INVESTIGATION INTO THE PATHOGENICITY OF YERSINIA PESTIS
This paper is submitted as a part of the course project of BIOL 469: Genomics at the University of Waterloo.
With improved sanitation and the development of antibiotics to treat infections (Riedel, 2017), the plague has been viewed by many in developed nations as a problem of the past. Despite this, the modern plague remains a major public health issue in many less-developed parts of the world. The number of countries reporting incidences of this disease is increasing and the plague has been attributed to thousands of deaths within the previous decade (Stenseth et al., 2008; Keeling and Gilligan, 2000). Furthermore, there is also the possibility of a multi-drug resistant strain emerging and the consequential utilization of plague as a bioweapon for terrorism attacks (Tan et al., 2015). In response to these issues, the objective of this report is to determine the source of pathogenicity for the most recent modern plague-causing strain of Y. pestis CO92 (Orientalis) at the genetic level. This will be accomplished through the comparison of the genome for Y. pestis CO92 and other human pathogens (Y. pseudotuberculosis and Y. enterocolitica), as well as human non-pathogens (Yersinia kristensenii and Yersinia ruckeri) from the Yersinia genus. The results of this analysis can be used to understand the underlying mechanisms of Y. pestis pathogenicity so that more effective treatment methods and vaccines can be developed.
APPLICATION OF TPMS STRUCTURE IN BONE REGENERATION
Bone defect repair, due to its complex process in nature, has become a costly issue in modern day medicine. This causes a growing demand for a bone substitute that is effective and easy to construct. Recently, triply periodic minimal surface (TPMS) scaffolds, which embody trabecular bone-mimicking hyperboloidal topography, have become a promising candidate for this exact role due to their unique structure to promote many cellular processes. In response to the growing popularity of TPMS scaffolds amongst researchers, this review discusses the effect of different parameters (including pore size, porosity, and pore shape, as well as their influences on mechanical property, permeability, and curvature), along with the controlling and designing of such parameters, on bone regeneration to serve as a guide for future researchers in designing and utilizing TPMS scaffolds for bone regeneration purposes.
SITUATION REPORT REGARDING THE 2019 NOVEL CORONAVIRUS OUTBREAK
This report, initially written as a work term report in Winter 2020 for the employer, is selected as the exemplar report to be published in the course material for PD 11: Processes for Technical Report Writing at the University of Waterloo.
The purpose of this report is to provide the individuals at U-Link Business Solution with some key information regarding the current outbreak of the 2019 Novel Coronavirus Disease (COVID-19) in China. These pieces of information include but are not limited to the methods of spreading, the characteristics of the high-risk population, and the proactive measures that can be taken in order to prevent the spread of the virus within the company. The information included in this report is very important for employees to understand, because as the outbreak is happening in China, fear has grown within the company, which has greatly affected the employees’ productivity and mental health. Therefore, only through understanding the situation of the outbreak and the nature of the virus, people can regain confidence, restore their mental health, and be productive again.