Proceedings 2021-22 Undergraduate Research Opportunities Program
* Abstracts from each School are listed rst by alphabetical order of the Department code, and then by Advisor’s surname. Message from the President i Sharing by Students ii-iii UROP Overview 2021-22 iv Mr. Armin &Mrs. Lillian Kitchell UG Research Awardees 2022 v-vi UROP Sponsorship Recipients 2021-22 vii Abstracts of UROP Projects – 2021-22* School of Science (CHEM, LIFS, MATH, OCES, PHYS) 2-68 School of Engineering (CBE, CIVL, CSE, ECE, IEDA, ISD, MAE) 70-163 School of Business and Management (ACCT, ECON, FINA, ISOM, MARK, MGMT) 166-197 School of Humanities and Social Science (HUMA, SOSC) 200-214 Interdisciplinary Programs Office (EMIA, ENVR, PPOL) 216-228 Institutes and Centers (IEMS) 230 Table of Contents
UROP 1000 Undergraduate Research Opportunities Program (0 credit with stipend option, o ered in summer sessions only) UROP 1100 Undergraduate Research Opportunities Program Series 1 (1 credit, o ered throughout the year) UROP 2100 Undergraduate Research Opportunities Program Series 2 (1 credit, o ered throughout the year; prerequisite is pass in UROP 1100, with approval by project advisors) UROP 3100 Undergraduate Research Opportunities Program Series 3 1 credit, o ered throughout the year; prerequisite is pass in UROP 2100, with approval by project advisors) UROP 4100 Undergraduate Research Opportunities Program Series 4 (1 credit, o ered throughout the year; prerequisite is pass in UROP 3100, with approval by project advisors) Summary of UROP Courses
Message from the President Since its launch in 2005, the Undergraduate Research Opportunities Program (UROP) has garnered a strong reputation within the community of the Hong Kong University of Science and Technology (HKUST). As one of HKUST’s signature programs, UROP has been successfully engaging our undergraduate students in research, providing early hands-on research experience alongside world-class researchers. This volume of proceedings showcases the program’s accomplishments this past academic year and covers a wide range of UROP projects conducted by our undergraduate students under the guidance of their faculty supervisors. Read through these proceedings, and you will better understand UROP and learn about the numerous research ideas developed by our young students. During the 2021/22 academic year, 143 faculty members served as project supervisors for more than 570 projects for the 602 students who participated in UROP. I would like to express my sincere gratitude to those faculty supervisors for generously taking on responsibilities beyond their regular teaching activities. By doing so, they are helping to build a vibrant research culture at HKUST in which our undergraduates can explore their research interests and thrive. I am proud that one-third of our UROP students have continued their research journey by pursuing graduate studies. Building upon the foundation of excellence we have created in the 30 years since HKUST was established, the University will continue providing diverse and stimulating learning experiences to foster young, future researchers for the betterment of society and the world. As such, I am pleased that UROP will be further developed by being included in the University’s Common Core Framework in 2024. I also hope for your continued support and participation in the pilot of the new UROP course to be launched in the coming semesters. Please look out for the of ce’s announcement. Sincerely, Professor Nancy IP President HKUST i
Sharing by Students CHANG Cheuk Yan Atta BEng in Bioengineering CHEN Zehan BSc in Physics UROP was the most valuable course throughout my HKUST journey. It allowed me to explore different fields and reinforce my career goal. Being an absolute UROP fan, I have taken three different UROP projects, each of which gave me the precious opportunity to learn and grow as a mature researcher. HKUST has a huge network of excellent supervisors and researchers. On top of learning laboratory techniques, they taught me the right attitude to fight challenges we encountered. Research is never about random trials and errors. I have learnt how to make hypotheses and systematically justify them. I was beyond grateful that UROP gave me the chance to explore what I am truly passionate about, as well as inspired me to become a researcher that can contribute to the betterment of society in the future. To me, the 3-year UROP experience was priceless in showing me what exactly scientific research is. Although doing research seems out of reach for an undergraduate, do not be afraid. There is no need to know everything. You just need to learn a certain topic, be familiar with previous research work, and make your own improvement. In my UROP career, I encountered numerous difficulties, and felt anxious and tired from time to time. However, when I finally solved a problem, it was worth the effort. These are the valuable treasure and the fun of innovation and research that UROP brings to everyone who joins it. ii
CHENG Chun Hong BEng in Computer Science YAP Shan Qi BSc in Chemistry UROP is one of the best opportunities provided by HKUST for students who wish to gain hand-on research experience and dive deeper into the academia. I fully enjoyed participating in this program. It allowed me to learn more about cutting-edge technology and how to write an academic paper to illustrate the exciting ideas started from 0 to 100. Not only research techniques, I also learnt how to collaborate with different colleagues within a research group to discuss and brainstorm ideas. I believe this program has equipped me well for my postgraduate study. For students who want to know more about academic research, please do not hesitate to participate in this program. Having no prior experience in research, I figured that participating in UROP would be a great way for me to start exploring my interests in research. Indeed, being able to really work on research projects has been a fruitful experience, as it has not only allowed me to gain insights into what research is about, but has also taught me skills and knowledge that I would not have learnt in the classroom. Besides, it has provided me a wonderful opportunity to work together with people who are passionate about research. Overall, I have benefitted tremendously from this research experience, and I am so glad to have chosen UROP to kickstart my journey in research. iii
In the 2021-22 academic year, the Undergraduate Research Opportunities Program (UROP) has seen a substantial growth in participation compared to the previous year. Over 210 faculty supervisors from four Schools and from the Interdisciplinary Programs Of ce offered around 580 projects for our undergraduates. We also received more than 950 applications throughout the academic year, with 602 students were successfully enrolled to the program. To enhance the continuous development of existing UROP projects, the UROP Support Grant Scheme continued providing nancial support for faculty supervisors and their students. Through the Scheme, students also experienced the process of applying for research grants by submitting a joint application with their supervisors. In 2021-22, 38 out of 47 received applications were awarded with an aggregate funding amount of over HK$670,000, after the review by the UROP Of ce and by the UROP Advisory Board. In the year 2022, 34 students with outstanding research performance were nominated by their UROP supervisors for the Mr. Armin and Mrs. Lillian Kitchell Undergraduate Research Awards. Among the nominees, 12 candidates were shortlisted and invited to give an oral presentation on their research ndings to the UROP Advisory Board. The Board recommended 1 Champion, 2 First Runner-Ups and 3 Second Runner-Ups. The faculty supervisors of those 6 student awardees were also recognized by the UROP Faculty Research Award. The award presentation ceremony was held via Zoom on 29 April 2022. UROP Overview 2021-22 The 2022 Mr. Armin and Mrs. Lillian Kitchell Undergraduate Research Award and the UROP Faculty Research Award iv
Mr. Armin and Mrs. Lillian Kitchell Undergraduate Research Award 2022 LIST OF AWARDEES CHEN Zehan Major / Year: PHYS / 4 Supervised by: SHAO Qiming / ECE Project Title: Rational Design of Magnetic Devices Using Micromagnetic Simulations Champion & Best Poster Award YAN Qiaolin Major / Year: CHEM / 4 Supervised by: SUN Jianwei / CHEM Project Title: Development of New Catalytic Organic Processes First Runner-up YAP Shan Qi Major / Year: CHEM / 4 Supervised by: SU Haibin / CHEM Project Title: Dynamic Expedition of Leading Mutations in SARS-CoV-2 Spike Glycoproteins First Runner-up v
CHANG Cheuk Yan Atta Major / Year: BIEN / 4 Supervised by: CHAU Ying / CBE Project Title: Nucleic Acid Delivery by Self-Assembled Nanocarrier Second Runner-up CHENG Chun Hong Major / Year: COMP / 4 Supervised by: SO Hau Yue Richard / IEDA Project Title: Remote Vital Signs Monitoring Second Runner-up ZHOU Yangbo Major / Year: BCB / 3 Supervised by: PARK Hyo Keun / LIFS & PHYS Project Title: Real-time Imaging of Single Motor Proteins Second Runner-up vi
UROP Sponsorship Recipient 2021-22 UROP PUBLICATION SPONSORSHIP CHENG Chun Hong Major: COMP Supervised by: SO Hau Yue Richard / IEDA Publication: MDPI Sensors Issue: Sep 2021, Vol. 21(18) Paper: Deep Learning Methods for Remote Heart Rate Measurement: A Review and Future Research Agenda The UROP sponsorship scheme is intended to provide UROP students with financial support to publish their papers in international journals, to present their posters or papers at academic conferences, or to participate in research-related summer schools or workshops during their undergraduate studies. One student who has been awarded the UROP sponsorship in the 2021-22 academic year is listed as follows: vii
Abstracts of UROP Projects 2021-22 School of Science
School of Science Department of Chemistry 2 Department of Chemistry Lead-free Perovskite Nanocrystals for Photo-induced Water Splitting Supervisor: HALPERT Jonathan Eugene / CHEM Student: OUYANG Boyu / CHEM-IRE Course: UROP1100, Spring UROP2100, Summer Colloidal photocatalytic hydrogen generation is a field that is gaining popularity in recent years. It allows conversion of solar energy into hydrogen gas to be stored as a fuel very easily. As a strong candidate in achieving large scale solar to hydrogen production, different photocatalysts have been synthesized. However, none of them achieved high enough efficiency or life spam long enough for commercial use. In this UROP project my work is to synthesize and study Cobalt(II) oxide (CoO) nanocrystal, a famous material for photo induced water splitting, and try my best to improve the system. Construction and Application of Surface Enhanced Raman Spectrometer in Biomolecules Characterization Supervisor: HUANG Jinqing / CHEM Student: CHAU Cheuk Yui Sherman / BICH Course: UROP1100, Fall With its highly distinct, non-destructive characterization of chemical samples, Raman spectroscopy is utilized in a plethora of fields, including pharmaceuticals, cosmetics, and geology. Its rapid identification of samples could therefore prove useful in differentiating between cancerous and non-cancerous breast tissue from the same patient. This report presents the application and viability of surface enhanced Raman spectroscopy in the characterization of biomolecules. The results provide evidence that the biochemical composition of tumor, papilloma, and fibroadenoma are notably different but contain a similar spectra pattern. To analyse the spatial configuration of the tissue sample, Raman mapping is also utilized to visually identify the discrepancy between cancerous and noncancerous breast tissue and its influence on Raman scattering. Construction and Application of Surface Enhanced Raman Spectrometer in Biomolecules Characterization Supervisor: HUANG Jinqing / CHEM Student: ZHOU Daoyu / SSCI Course: UROP1100, Summer In this research, we utilized Raman imaging combined with unsupervised machine learning (UMAP-DBSCAN) as an assistance to achieve the goal of determining the margin of the breast ductal carcinoma sample. So far, we have finished the Raman peak assignment and performed analysis based on the clusters obtained from DBSCAN, Raman imaging, and mean spectra of each cluster thereby some preliminary conclusions have been drawn. The clusters generated from machine learning show a well transitional pattern from collagens to malignant cells in many cases. We found malignant cells have higher lipids and protein contents and altered configurations in specific bands of Raman spectra compared with cells adjacent to ECM in the same region. Several possible reasons for these have been interpreted.
School of Science Department of Chemistry 3 Prediction of Inorganic Solar Cell Materials with Double Perovskite Structure Using Machine Learning Approach Supervisor: SU Haibin / CHEM Student: CHEUNG Ka Key / CHEM Course: UROP1100, Fall Solving the covalency and ionicity partition in solid states has many useful applications. For example, ionicity affects grain boundary which Jahn-Teller distortion can happen and directly determines the strength of the solid. In this work, we investigate CsPbI3, solid state material with cubic perovskite structure. Vienna Ab initio Simulation Package (VASP) is used for the simulation which gives useful parameters such as potential and electron density in different locations of the lattice. We can break down the energy into ionic and polarization energy partition to understand the ionicity. Deep Learning in Synthesis Planning Supervisor: SU Haibin / CHEM Student: CHUI Sin Yu / CHEM Course: UROP3100, Fall UROP4100, Spring Nickel-catalyzed reactions raised more attention in the development of organic synthesis. The benefits of using nickel compound as the homogeneous transition metal catalyst for cross-coupling reactions have been recognized by different researchers. Cross-coupling reactions involving C-O bond activation, C-N bond activation and C-H bond activation have also been developed to form organic compounds. This report will be focused on using computational methods to collect research papers on homo-nickel-catalyzed crosscoupling reactions. Further analysis of photochemistry will also be mentioned. Deep Learning in Synthesis Planning Supervisor: SU Haibin / CHEM Student: DOO Kwan Lam / CHEM Course: UROP1000, Summer Synthesis planning is essential for many reactions. Using this technique, it is possible to discover many new reactions to make different molecules in a faster and cheaper way. It would have many applications in drug discovery, medicinal chemistry, etc. This summer I learned about the synthesis planning of homogeneous nickel catalysis. This report is an overview of my data extraction progress in 2022 June, July, and August. The task includes data extraction of homogeneous nickel catalysis and some copper catalysis reactions. I will analyze the data I collected from the three aspects of leaving group, reactant group, and ligands with figures.
School of Science Department of Chemistry 4 Deep Learning in Synthesis Planning Supervisor: SU Haibin / CHEM Student: WANG Yizhou / CHEM Course: UROP2100, Fall Most of organic reactions require catalysts in order to occur and end efficiently, in which metal catalysts attract a lot of interest of researchers to study. Unlike heavy metals, which are rare and toxic, some light metals, such as nickel, can also perform wonderfully in catalyzing various kinds of organic reactions, like reductive coupling, C-O activation, etc. Besides, nickel is also capable of catalyzing the conversion of carbon dioxide into acetic acid in order to absorb the greenhouse gas. This report is an overview of reactions and conditions using nickel catalysts with bidentate nitrogen ligands, and will analyze the conditions including ligand types, base and so on. Virtual Reality in Chemistry Supervisor: SU Haibin / CHEM Student: KONG Yui Hin / CHEM Course: UROP1100, Fall Molecular dynamics (MD) refers to using computer simulations to study and predict physical movement of atoms and molecules over time. MD spans across multiple fields of science as a easy and efficient tool to predict or verify experiments. MD as a field of computational chemistry is becoming more popular as computing power becomes more cheaper and easily available. Here, a brief review of history and principles of molecular dynamics is given. Then, multiple MD scenarios are simulated on a consumer level computer to compare efficiency. Futures and limitations of MD are discussed. The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU Haibin / CHEM Student: ANGELA Donna / SENG Course: UROP1000, Summer The COVID-19 pandemic has been a global challenge people are facing. One of the main issues is the development of new variants, making it more dangerous for us. Despite many efforts given by various parties, the team and I involve in finding a novel way to track mutations of the spike protein, mainly RBD and NTD discussed here. One of the methods in fulfilling our goals is through variant decomposition, which gives access to specific mutation information of the unique sequences we have and discovers the significant mutation trend related to relevant amino acid types for variants of concern or interest targeted.
School of Science Department of Chemistry 5 The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU Haibin / CHEM Student: CHANG Ka Pui / CHEM Course: UROP1100, Summer The COVID-19-causing virus SARS-CoV-2 have mutated frequently since its debut in December 2019, mainly in its spike glycoprotein. By having the combination of different types of amino acid mutations in the spike, for example, amino acids substitution on a site (SAP) which may have altering chemical properties, deletion and glycosylation, commonly N-linked glycosylation, the emerged variants have quite distinct viral properties such as a change in virulence or transmissibility. Here, sequence tracking is used to detect a pattern of mutations using representative sequences found before the emergence of VoC/VoI, to account for their viral properties, effects to the pandemic and to have a more accurate prediction for the next VoC/VoI. The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU Haibin / CHEM Student: JUSMIN Frederick Gabriel / CHEM Course: UROP1000, Summer The rapid mutation of SARS-CoV-2 leads to the emergence of new variants and numerous key mutations which are conserved in the viral genome. The positive selection of these mutations produce evolutionary adaptations allowing the virus to be more infectious and more virulent. As a way to track new mutations appearing in future sequences, a moving reference chosen from past sequences with highest genetic similarity is used instead of the original strain. Through observation of monthly plots, leading counts in mutated sites reveal some insights to key mutations which later appear in SARS-CoV-2 variants while counts of reference sequences shows the previous key mutations. Additionally, further analysis of these mutated sites will definitely be a contributing factor to determine the evolutionary trajectory of SARS-CoV-2. The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU Haibin / CHEM Student: LAM Chak Fai / CHEM Course: UROP1100, Spring UROP2100, Summer COVID-19 pandemic has been affecting the world for almost 3 years, continuous records of mutations of the acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were made. Spikes proteins in the new variants are mutated with improvements in both transmissibility and immune escape, leaving the lives of billions in danger. Investigations and predictions of the spike glycoproteins of SARS-CoV-2 mutation, which is the key to the entrance into target cells, are done worldwide. Using the data from January 2022 to June 2022 in the GISAID hCoV-19 database, this report aims to compare different approaches that assist the tracking of emerging variants. Data of dynamic expedition of leading mutations (deLemus) and escape fraction are the two methods used to compare with the results of this report for further analysis.
School of Science Department of Chemistry 6 The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU Haibin / CHEM Student: LEUNG Cheuk Fung Alvin / SSCI Course: UROP1100, Summer The spike (S) glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for cell entry by binding to human angiotensin-converting enzyme 2 (hACE2). Despite being distal from the S-hACE2 interface, the two subunit 1 (S1) subdomains (SD1 and SD2) and subunit 2 (S2) play important roles in viral functions via allosteric modulation of hACE2-binding and mediation of membrane fusion respectively. Hence, mutations in these regions confer significant impacts to SARS-CoV-2 functions. Here, the time-resolved dynamic expedition of leading mutations (deLemus) method is applied to screen for sites of interest (SOIs) in aforementioned domains based on their weighted L-index scores derived from single amino acid polymorphism (SAP) analyses. These findings would allow the potential projection of S evolution trajectory. The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU Haibin / CHEM Student: TSANG Kwok Kiu / CHEM Course: UROP1100, Spring Amidst the CoVID-19 pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone rapid, ongoing genomic evolution, forming numerous variants that have developed increased transmissibility and antibody evasion. The spike glycoprotein of the virus is crucial for antibody development and is also integral in the receptor recognition and cell membrane fusion process, hence monitoring and prediction of mutations for this protein is of importance. Here, we propose a method of identifying new active sites of mutation for the spike glycoprotein by employing a direct counting method, used in conjunction with statistic coupling analysis (SCA), for continuous monitoring of its mutation patterns. The identified new active sites of interest (SOIs) show promise in predicting the emergence of future variants of concern. Text Mining of Synthesis Methods of Metal Organic Framework Supervisor: SU Haibin / CHEM Student: SIU Chun Hey / SSCI Course: UROP1000, Summer Metal Organic Frameworks (MOFs) has gained rising interests in recent studies for their huge internal surface area and astonishingly high porosity which, coupled with the extremely flexible nature of its organic and inorganic constituents, revealed countless possibilities for a plethora of novel applications. However, there is still a lack of understanding on the specifications of the synthesis of MOFs. This UROP project works on overcoming this limitation by extracting and evaluating synthesis methods and conditions from thousands of studies. Via an automation software that allows customization of document digitization workflow, Text Mining and Graph Mining are performed extensively on selected studies to gather a wide range of data for MOFs.
School of Science Department of Chemistry 7 Data Analytics of Homogeneous Transition Metal Catalyzed Reactions Supervisor: SU Haibin / CHEM Student: WANG Yizhou / CHEM Course: UROP3100, Summer Coupling reaction is a significant type of reactions in organic synthesis. In the past decades, researchers have found many transition metals that are able to catalyze various kinds of coupling reactions. As a cheap transition metal, nickel is thought to be an excellent metal to effectively catalyze coupling reactions, and many groups have made a lot of experiments and data about nickel catalyzed C-O activation reactions. This report will try to review different C-O activation reactions catalyzed by nickel and give some characteristics or rules about this reaction field. Development of New Catalytic Organic Processes Supervisor: SUN Jianwei / CHEM Student: HO Hang Chi / CHEM Course: UROP1100, Spring Synthetic organic chemistry is commonly used to synthesize important molecules in our daily lives such as drug molecules and pharmaceuticals. However, many of these molecules contain a chiral carbon atom and have two non-superimposable mirror images, or enantiomers, which can have vastly different biological activity. Therefore, reactions that can preferentially form one enantiomer over the other has seen rapid development in the past century precisely because of its applications in the pharmaceutical industry. Such asymmetric reactions can be catalyzed by either enzymes, transition metal complexes, or organocatalysts. Development of New Catalytic Organic Processes Supervisor: SUN Jianwei / CHEM Student: LI Yuxuan / CHEM Course: UROP1100, Fall Based on preceding results, further optimization of catalytic enantioselective 1,6-addition of 5-methide-5Hindoles, which are generated in situ from dehydration of corresponding indolyl alcohols, has been attempted. Starting from modification on structures of the substrates, different chiral phosphoric acids were used to catalyze the reaction. With the result of catalysts screening in hand, evaluation of common solvents, concentration of reactants, and temperature has been performed. As a continuation of the previous project, this work successfully enhanced the enantioselectivity of the reaction (ee value up to 78%). Although the enantioselectivity of such reaction mode requires further enhancement, the increase in ee value could still prove that optimization on the reaction is effective.
School of Science Department of Chemistry 8 Development of New Catalytic Organic Processes Supervisor: SUN Jianwei / CHEM Student: LO Wai Yam / CHEM-IRE Course: UROP1000, Summer Catalysis plays a crucial role in the synthesis of biologically active molecules. Many drug molecules are synthesized via organic synthesis with the aid of catalysts where natural occurrences are much lower, and resources are scarce. While metal catalyzed reactions provide a powerful tool in drug synthesis, the recent development of organocatalysts provides new advantages over metal catalysts, including increased robustness, recyclability, decreased risk of metal contamination, and eliminated the need for consuming precious noble metals, while maintaining good selectivity and yield. Making Valuable Organic Molecules with Green Chemistry Supervisor: TONG Rongbiao / CHEM Student: HE Chenxi / CHEM Course: UROP1100, Fall Alcohol oxidation is an important reaction in organic chemistry and many chemists have spent great efforts to develop various conditions for multiple complicated substrates. However, most popular methods used at current have drawbacks in environment-friendliness, safety and operation difficulty. Therefore, we aim at developing a new method with Fenton Chemistry to achieve low-cost reagents, non-hazard waste, broad scope and high reaction yield. In this report, background information of both the present alcohol oxidation methods and the Fenton reaction will be provided first, including some important references. Then the motivation and whole research plan of timeline will be briefly discussed. After that, the research progress till 25th November will be discussed in detail for three stages, including the mechanism prediction and examination, the reaction condition modification, and the substrate scope extension. Last but not least, the reflection and limitation, following by the future direction of this project will be presented at the end. The references for this reported will be listed in the last page. Design of Controllable Enzymes for Therapeutic Applications Supervisor: VONG Kenward King Ho / CHEM Student: LAU Chi Hin / CHEM Course: UROP1100, Summer Conventional inflammation-suppressing drugs mainly target the synthesis of PGH2 from arachidonic acid, which is catalyzed by cyclooxygenase-2 (COX-2). This project aims to explore the possibility of utilizing the rigid binding between MUC1-N and MUC1-C to regulate the activity of 15-hydroxyprostaglandin dehydrogenase (15-PGDH), the key enzyme controlling PGH2 catabolism. With such modification, the enzyme could be injected into sites of inflammation, leading to the controlled breakdown of PGH2. For this project, expression and purification of the modified 15-PGDH was performed.
School of Science Department of Chemistry 9 Design of Controllable Enzymes for Therapeutic Applications Supervisor: VONG Kenward King Ho / CHEM Student: WAN Kai Yui / IRE Course: UROP1000, Summer Stroke is a serious and fatal disease, but antithrombotic agents can be applied to interrupt plaque formation to significantly reduce mortality rates. The protease known as nattokinase is also a viable antithrombotic agent, but may cause brain bleeding from excessive protease activity. In this UROP project, a modified nattokinase will be produced using recombinant DNA technology. Following expression in Escherichia coli, protein purification was performed using techniques like Fast Protein Liquid Chromatograph (FPLC), centrifugal filtration, and High-Performance Liquid Chromatography (HPLC). The goal of this project was to optimize purification conditions for these therapeutic proteins.
School of Science Division of Life Science 10 Division of Life Science Mechanisms of Golgi Membrane Protein Retention Supervisor: BANFIELD David Karl / LIFS Student: LI Caifan / SSCI Course: UROP1100, Summer Vps74p provides a protein retention mechanism in Golgi to maintain the steady-state distribution of glycosyltransferases (GTs) and has always been an important topic in cell biology study. There have been many studies using fusion expression of fluorescent proteins assay showed that Vps74p bound both the binding motifs on the cytoplasmic tail of GTs and the COPI coat then achieved the protein retention in the Golgi. However, this method has limitations in the quantitative analysis of retained protein content. Thereby, in this report, we imitated a mammalian cell quantitative Golgi retention assay to demonstrate its applicability in yeast. However, our result showed when VPS74 was deleted, a reconstructed reporter protein with a Vps74p binding tail, which localized on the plasma membrane in wide-type cells (WT), could not go back to the plasma membrane as we expected but further accumulated in vacuoles. To improve the experiment, we excluded the interference of a mutation on the SI TMD, but the result was still not good. Finally, we offered several possible causes for this problem and a way to improve it. Studying Novel Cell Cycle Signalling Pathways in Yeast Cells Supervisor: BANFIELD David Karl / LIFS Student: SINCE Alec Victor / BIBU Course: UROP2100, Spring This literature review aims to investigate the role of TORC1 in regard to the various checkpoints in the cell cycle. This paper suggests that TORC1 is crucial for cell cycle progression due to its effect on the subcellular localization of a polo-kinase called Cdc5. Our lab used dcr2-6 ted1Δ yeast cells and made contradictory findings where we determined that TORC1 is required for spindle assembly checkpoint (SAC) activation at non-permissive temperatures in those strains. We came to this conclusion as the inhibition of TORC1 led to the inactivation of SAC. Further studies are required to determine whether Cdc5 also has an effect on dcr26 ted1Δ yeast cells. Studying Novel Cell Cycle Signalling Pathways in Yeast Cells Supervisor: BANFIELD David Karl / LIFS Student: YUK Tin Cheung / BTGBM Course: UROP1100, Fall GPI-Anchors contain mannose molecules, of which Man2 is attached to EtNP (Glycosylphosphatidylinositol) normally by the action of enzyme Gpi7p. After the attachment of EtNP to the GPI-Anchor protein, the Ted1p/Dcr2p enzymes would do the opposite to detach the EtNP from these GPI-Anchor proteins. Previously, it was found out that on the mutant strain of yeast(PGAL1GPI7ted1Δdcr2Δ), which lost the ability to produce Ted1p/Dcr2p enzyme, a lethal effect was demonstrated. This somehow revealed the toxicity of EtNP on the survival of cells.
School of Science Division of Life Science 11 Molecular Regulation of Muscle Stem Cell Quiescence by Non-coding RNAs Supervisor: CHEUNG Tom / LIFS Student: CHEUNG Lok To Curtis / BCB Course: UROP1100, Summer Muscle stem cells are often found in quiescence, a cellular state which exists in a dormant, reversible G0 cell cycle state outside of the cell cycle. Quiescent muscle stem cells could be activated and enter the cell cycle for proliferation or activation, fulfilling the tissue homeostasis and repair role of stem cells. It is important to understand the various governing mechanism by which quiescent stem cells rely on to switch between quiescent and activated states in order to further the research on the application of adult stem cell rejuvenation. In this report, we will discuss how autophagy, one of the proposed mechanisms could be correlated to the muscle stem cells' cell fate and their autophagy flux, using FACS isolated mice adult skeletal stem cells. Molecular Regulation of Muscle Stem Cell Quiescence by Non-coding RNAs Supervisor: CHEUNG Tom / LIFS Student: CHIU Yui Hei / BIOT Course: UROP1100, Fall M2 is a potential anti-cancer drug candidate studied in Dr Liang Chun’s laboratory. The drug candidate shows its exceptional potential and specificity in inhibiting the growth of cancer cells, particularly Hela cells. However, the long-term use of the drug exhibits a critical issue– Drug resistance. Previously, 2-8, 4-5 and 56 clones from the R10 population (Highest drug resistance HeLa population available in our laboratory) were studied in depth through various assays, confirming their morphology. This project devoted itself into studying another two clones; 2-9, 4-4 in comparison with the HeLa population by conducting various assays. We found that 2-9 and 4-4 exhibited similar trends as the previous R10 clones with slower growth, higher survivability after drug treatment and smaller in size. Unlike the previous clones, 2-9 and 4-4 exhibited different behaviours implying different degree of resistance to the M2 drug. Molecular Regulation of Skeletal Muscle Stem Cell Quiescence and Activation Supervisor: CHEUNG Tom / LIFS Student: TSE Chun Mong / IRE Course: UROP1100, Summer Pax7 is a marker of satellite cells (SC)1, so in order to aid the study of SC, transgenic Tg:Pax7-nGFP mice was developed. Expression of nuclear localised EGFP (nGFP) transgene corresponds with that of the endogenous Pax7 gene2, thus marks SC with green fluorescent protein (GFP). However, GFP signals may not fully represent Pax7 expression6. Here, we would like to see to what extent does GFP marks Pax7, taking this to wrap up things done in this summer.
School of Science Division of Life Science 12 Molecular Regulation of Skeletal Muscle Stem Cell Quiescence and Activation Supervisor: CHEUNG Tom / LIFS Student: WONG Tsz Yan / BIBU Course: UROP1100, Summer Quiescence and activation of stem cells have been previously proven to be correlated to autophagy, which is the process of self-degradation of proteins. Utilizing muscle stem cells, or satellite cells isolated from adult skeletal muscle fromhindlimb of mice with fluorescence-activated cell sorter (FACS), the cell fate is examined from inhibition and promotion of autophagy. The autophagy granules, namely autophagosomes and autolysosomes are also evaluated with confocal microscope. As autophagy is closely related to ageing, the study of autophagy of satellite cell can provide insights for therapeutic development. Construction of a Signal Transduction Pathway Reporter Indicator for Monitoring Signaling Strength Supervisor: CHOW King Lau / LIFS Student: YUEN Yan Yi Macy / BIOT Course: UROP3100, Fall This project will manipulate the genetic model system, Caenorhabditis elegans, to recruit two of the gene components regulated by the transforming growth factor-β related ligand, DBL-1, as the indirect indicators of the dbl-1 signaling strength. sma-6, one of the target genes for the project, encodes the type I receptor for DBL-1 ligands and is positively regulated by the dbl-1 signaling. The second gene, gcy-28, is a receptortype guanylate cyclase and acts as a repression target in the BMP pathway. Thus, the gene expression of sma-6 and gcy-28 can reflect the intensity of the BMP transduction signal. This project will develop the sma6 and gcy-28 transcription reporters responding to the dbl-1 signaling and amplify the readout of signal strength through the manipulation of these two reporters in a variety of dbl-1 mutant strains. Monitoring the Norm of Human Morphology Supervisor: CHOW King Lau / LIFS Student: LUI Yuen Yee / SSCI Course: UROP1000, Summer The purpose of this paper is to test whether the body shape of modern human beings can also be described with parameter defined by the “Vitruvian man”. Quantitative and qualitative data were collected through the measurement of online photos. The data collected indicate that most of the statements described on the Vitruvian man are not correlated to the experimental observations. Distinct differences were found when comparing the results of two races and two sex groups. These distinct differences further act as several defining parameters to distinguishing two different races and two sex groups. This paper and experimental results can be used in investigating the biological correlation of distinct body proportion difference.
School of Science Division of Life Science 13 Monitoring the Norm of Human Morphology Supervisor: CHOW King Lau / LIFS Student: RUPANI Rakshita / SSCI Course: UROP1000, Summer This paper re-evaluates the facial proportions of the Vitruvian Man - a drawing constructed by Leonardo da Vinci in about 1490 that defines human body proportions - and determines how accurate it is to African, Caucasian, and Hispanic ethnicities today. The paper also deduces the numerical ratios that define certain facial features that allow differentiation between ethnicities. Measurements of facial features - in samples collected from the Internet - were done to calculate ratios. The ratios obtained from samples of different ethnicities (same gender) were compared using t-tests. Only some ratios allowed differentiation between ethnicities. Data from females gave more consistent measurements than men. Africans were less related to Caucasians and Hispanics, while Caucasians and Hispanics has a stronger correlation. Genetic Identification of Negative Regulator of Bone Morphogenetic Protein Signaling Pathway Negative Regulator Supervisor: CHOW King Lau / LIFS Student: CHOI You Jin / BIOT Course: UROP1100, Summer Body size is one of the most important phenotypic features in animal species. Although we understand that signaling pathways control body size, the molecular mechanism and how the downstream effectors are regulated are poorly understood. In Caenorhabditis elegans, a conserved Bone Morphogenetic Protein (BMP) signaling pathway, the Sma/Mab pathway, is the predominant regulator of body size. LON-1, a member of the cysteine-rich secretory protein (CRISP) family, acts as the negative regulator to suppress the small body size phenotype when mutations in lon-1 gene occur. To understand why lon-1 worms are long, we aim to understand whether the Lon phenotype of lon-1 mutant can be modulated by different collagen gene functions to control the body size of C. elegans. Analysis of Surface Delivery of Epidermal Growth Factor Receptors Supervisor: GUO Yusong / LIFS Student: CHENG Guo / SSCI Course: UROP1000, Summer In intracellular trafficking, Trans-Golgi Network (TGN) is the transportation hub that sorts proteins to various downstream destinations including endosomes, plasma membrane, etc. The surface delivery of Vangl2, a conserved signaling receptor regulating Planar Cell Polarity (PCP), has been one important research direction in understanding the elaborate sorting mechanisms. It was previously demonstrated that both AP1 and Arfrp1 are involved in the transportation of Vangl2 from TGN to the plasma membrane. (Guo, Zanetti & Schekman, 2013) Here we purified AP1 core to study the interaction between AP1 core and Vangl2, as well as the function of Arfrp1 in regulating the TGN export of Vangl2.
School of Science Division of Life Science 14 Analysis of Surface Delivery of Epidermal Growth Factor Receptors Supervisor: GUO Yusong / LIFS Student: HUNG Shing Hei / IRE Course: UROP1000, Summer The analysis of EGFR is highly related to understanding the development of cancer cells. The L858R mutation on EGFR is one of the most common mutations identified in lung cancer. T790M mutation on EGFR causes drug resistance of EGFR(L858R). This project is trying to introduce the further mutation T790M on EGFR(L858R) for further biological analysis. Analysis of Surface Delivery of Epidermal Growth Factor Receptors Supervisor: GUO Yusong / LIFS Student: LI Chun Wa / BCB Course: UROP1100, Fall UROP2100, Spring Mitochondria has been extensively studied since its discovery of the organelle in 1857 by physiologist Albert von Kolliker, unravelling many features of this bacterial descendent, from its fission and fusion machinery, to its interactions with other organelles via signaling or membrane contact sites. Mitochondrial-derived vesicles (MDVs) is an emerging field that is comparatively less studied yet exciting in terms of understanding mitochondrial regulations and their physiological relevance. MDVs are responsible for diverse cellular processes, in which its role in mitochondria quality control (MQC), peroxisome biogenesis and mitochondria antigen presentation (MitAP). The molecular machineries controlling cargo selection, budding and trafficking of these processes will be discussed in this review. Analysis of Surface Delivery of Epidermal Growth Factor Receptors Supervisor: GUO Yusong / LIFS Student: PARK Jihye / BIOT Course: UROP1100, Spring Sonic Hedgehog (Shh), one of the three Hedgehog (Hh) family members, is an important signalling molecule involved in many key developmental processes, such as embryonic patterning, cell differentiation, and organ development. The Shh protein undergoes two major changes in the endoplasmic reticulum (ER). It is first auto-cleaved into two parts, a C-terminal fragment (ShhC) and an N-terminal fragment (ShhN). ShhC is degraded, while ShhN is exported from the ER after lipid modification and delivered to the cell membrane to initiate signal transduction. Although the signal transduction pathway is well-understood, the complete mechanism behind Shh protein secretion is still undiscovered. Therefore, this paper examines the transport of the N-terminal fragment of Shh without the lipid modification (ShhN) in vitro to unravel the molecular mechanisms that direct the trafficking and secretion of Shh.
School of Science Division of Life Science 15 Molecular Mechanisms Regulating Biogenesis of Peroxisomes Supervisor: GUO Yusong / LIFS Student: LI Chun Wa / BCB Course: UROP3100, Summer Peroxisomes are vital organelles for most eukaryotes, while they undergo growth and division under homeostatic conditions, they can be generated de novo when depleted. Although the biogenesis of organelle occurs in the ER of yeasts and plants, peroxisomes in mammalian cells have an interesting dual origin from the ER and the mitochondria, in which peroxins Pex3 and Pex16 are the key players in the formation process. To unravel the underlying mechanisms regulating this event, we aim to utilize retention using selective hooks (RUSH) assay to study the trafficking machineries of these peroxins from these 2 donor organelles by synchronizing the vesicle release of these proteins. In UROP 3100, immunofluorescence was performed to determine the localization of Str-Ii_Pex16-SBPEGFP and Str-HA-MAO_VSVG-SBP-EGFP, the ER and mitochondria hook for Pex16 and Pex3, respectively. Our study shows that while VSVG-SBP-EGFP successfully retained in the mitochondria, Str-Ii failed to lock Pex16-SBP-EGFP in ER but instead allowed it to be transported to the ER. Molecular Mechanisms Regulating Biogenesis of Peroxisomes Supervisor: GUO Yusong / LIFS Student: YAU Yin Lam / SSCI Course: UROP1100, Summer In the eukaryotic secretory system, endoplasmic reticulum (ER) and Golgi apparatus play important roles. During the secretion process, coat protein complex II (COPII) captures cargo proteins at ER and form vesicles in a bid to transfer the proteins to Golgi apparatus. Previous studies have shown that PRRC1, a cytosolic factor, may be involved in COPII disassembly, and knockdown of PRRC1 can affect the efficiency of ER transport as well as membrane associations of COPII coats. The C-terminus(263-445) of PRRC1 contains a nucleotide phosphatase (NTPase) domain. To investigate whether the NTPase domain of PRRC1 is critical for its function, His-PRRC1(263-445)-HA has to be generated for carrying on further experiments. CRISPR Cas9 Based Therapeutic Strategy for Alzheimer's Disease Supervisor: IP Nancy Y / LIFS Co-supervisor: FU Kit Yu / LIFS Student: WONG Lok Yin / IRE Course: UROP1100, Summer Familial Alzheimer’s disease(FAD), which accounts for about 5% of all Alzheimer’s disease cases, is caused by one of more than 330 gain-of-function mutations in amyloid precursor protein (APP), presenilin 1 (PSEN1), and presenilin 2 (PSEN2) genes. Previous studies have shown that allele-specific disruption of mutated APP or PSEN1 by targeting mutations directly with CRISPR-Cas9 can effectively alleviate amyloid-related pathologies. Although this gives a promising cure to FAD, more than 330 CRISPR–Cas9 constructs are required for all identified FAD-related mutations, which is not feasible. This project aims to develop a generalized treatment for all FAD patients by targeting non-disease-causing single-nucleotide polymorphism(SNP). Here, this report systematically validated performance of sgRNAs for targeting candidate SNPs.
School of Science Division of Life Science 16 Deciphering Epigenetic Changes in Cancer -**UROP-EPIC program** Supervisor: LEUNG Danny Chi Yeu / LIFS Student: KANG Juwon / BIOT Course: UROP1100, Spring The purpose of the UROP 1100 was to equip myself with techniques widely used in the field of molecular biology to proceed with coming up a feasible research question that could be explored for the FYP. The following content of the report introduces a detailed timeline and the learnings that I had over the UROP period. Receptor Based Drug Development from Chinese Herbal Medicine Supervisor: LI Ning / LIFS Co-supervisor: XUE Hong / LIFS Student: HO Wing Chi / BIBU Course: UROP1100, Spring Interactions of drugs with specific molecular targets allow them to alter the activities of these targets. Receptors have always been a major category of target and enabled the discovery of many drugs. Meanwhile, there is a revival of drug development from plants, due to issues such as severe side effects. Practised for thousands of years, Chinese herbal medicine presents a huge source of effective medicinal herbs and therefore plays an important role in this recent trend of drug development. This review will briefly present some recent progress in receptor-based drug development from Chinese herbal medicine in the novel COVID-19 and diabetes. Although there are hurdles to be overcome, Chinese herbal medicine still possesses enormous potential in receptor-based drug development. Receptor Based Drug Development from Chinese Herbal Medicine Supervisor: LI Ning / LIFS Co-supervisor: XUE Hong / LIFS Student: KOT Yung Kei / BIBU Course: UROP1100, Summer Anxiety is one of the most common mental issues around the world. It is much related to the benzodiazepine (BZD) binding site of the gamma-aminobutyric acid type A (GABAA) receptor. Therefore, it is indispensable to understand the principle behind and find possible method to minimize the impacts from it. In this review paper, the types of ligand-gated ions channels (LGICs), structure, functions and detailed inhibitory process of GABAA receptor and the introduction of BZD are to be discussed. Wogonin and baicalin are the flavones isolated from Scutellaria baicalensis Georgi (S. baicalensis) which show significant anxiolytic effect. They have valuable potential to be applied in the therapy in the upcoming future.
School of Science Division of Life Science 17 Receptor Based Drug Development from Chinese Herbal Medicine Supervisor: LI Ning / LIFS Co-supervisor: XUE Hong / LIFS Student: LAU Ming Ho / BIBU Course: UROP1100, Summer Insomnia has always been a serious public health problem, affecting millions of people. Compared to common insomnia drugs like benzodiazepines, certain Chinese herbal medicine can manage insomnia with fewer side effects. The mechanism of action is mainly associated with the activation of GABAA receptors, which create sedative and hypnotic effects when the binding sites interact with agonists like GABA neurotransmitters. In this review paper, two kinds of GABA receptors will be introduced. Several sedative herbal medicines and their mechanism will be listed and explained. Some modern extraction procedures of herbal drugs like fractionation, chromatographic identification, and diverse identification will also be included. Chinese Herbal Medicine for General Health Supervisor: LIANG Chun / LIFS Student: CHAN Yi Kai / BCB Course: UROP1100, Fall UROP2100, Spring Inulin and stevioside are both acclaimed sugar substitutes in food industry since they manifest a healthier lifestyle to customers. Besides their competent sweetness, they have been reported to possess certain antidiabetic effects subject to the practical formulas of administration. And the single-ingredient antidiabetic effect of both inulin and stevioside were well-verified by my experiments conducted during UROP 1100. Besides the intriguing antidiabetic effects of these two natural sweeteners, their anti hyperlipidemic effects are also studied by several papers. (Huang, 2016) (Ahmad, 2018) Therefore, in these semester, non-alcoholic fatty liver HepG cells were exploited as a hyperlipidemic model undergoing regular treatments with different concentrations of inulin and stevioside to further investigate and characterise the anti-hyperlipidemic effects of inulin. Protein assay, TG measurement, western blotting, and fluorescence microscopy were utilized to provide the proof of concepts for a satisfactory performance of both inulin and stevioside in acting against hyperlipidaemia.
School of Science Division of Life Science 18 Chinese Herbal Medicine for General Health Supervisor: LIANG Chun / LIFS Student: KWON Daye / BIOT PARK Joo Hyoung / BIOT Course: UROP2100, Fall UROP1100, Fall Traditional Chinese Medicine has been studied to have various applications in diseases and disorders, including that of the metabolic syndrome. In the present experiment, the efficiencies in the treatment of insulin resistance of three popular TCMs—Astragalus membranaceus, Poria cocos, Taraxacum were compared to that of a commonly known diabetes drug, Metformin. Insulin-resistant HepG2 cells were treated with each drug solution and were screened with addition of a glucose assay kit. Absorbance at 490 nm of the treated HepG2 was measured and a western blotting analysis was performed for quantification of Akt protein. Although Taraxacum showed the highest uptake of glucose, the results also suggested high efficiencies of glucose uptake stimulation and potentials of Astragalus membranaceus and Poria cocos. Chinese Herbal Medicine for General Health Supervisor: LIANG Chun / LIFS Student: NG Cheuk Yan Gloria / SSCI Course: UROP1000, Summer Diabetes is a major global medical issue that jeopardizes general public health. There is an increasing interest on the approach of Traditional Chinese Medicines (TCM) to complement diabetes treatment in Western medicines. The study aims to evaluate the effect of some TCM, Momordica Charantia (MC), Glycyrrhiza Uralensis (GU), and Ginseng (GS), on insulin resistance (IR) of HepG2 cells. The glucose uptake of drug-treated cells is measured to test the anti-insulin-resistant effect of drugs. The experiment results show that MC, GU, and GS exhibit an anti-insulin-resistant impact, where its effectiveness increases with increasing concentration and during drug treatment. In conclusion, using TCM as an anti-diabetic treatment can be a possible approach in Western therapies for diabetes. Chinese Herbal Medicine for General Health Supervisor: LIANG Chun / LIFS Student: TSANG Chun Kit / SSCI Course: UROP1000, Summer Certain herbal medicines have been used in Traditional Chinese medical practices to treat diabetic symptoms. Astragalus membranacues and Codonopsis pilosula are considered to possess hypoglycemic effects in a dose dependent manner 48 hours after adding to insulin resistance HepG2 cells. This effect does not manifest a dose dependent manner in the 24 hours trial which might be related to experimental flaws. The usage of TCMs demonstrates much smaller toxicity to HepG2 cells compared to typical anti-diabetic medicine metformin.ebookshelf.ust.hk