UNDERGRADUATE RESEARCH OPPORTUNITIES PROGRAM 2022–23 PROCEEDINGS
Message from the President i Sharing by Students ii-iii UROP Overview 2022–23 iv Undergraduate Research Opportunities Program Awardees 2023 v-vi UROP Sponsorship Recipients 2022–23 vii-x Abstracts of UROP Projects - 2022–23* School of Science (CHEM, LIFS, MATH, OCES, PHYS) 2-71 School of Engineering (CBE, CIVL, CSE, ECE, IEDA, MAE) 74-157 School of Business and Management (ACCT, ECON, FINA, ISOM, 160-189 MGMT) School of Humanities and Social Science (HUMA, SOSC) 192-198 Academy of Interdisciplinary Studies (EMIA, ENVR, ISD, PPOL) 200-213 Table of Contents * Abstracts from each School are listed rst by alphabetical order of the Department code, and then by Advisor’s surname.
UROP 1000 Undergraduate Research Opportunities Program (0 credit with stipend option, offered in summer sessions only) UROP 1100 Undergraduate Research Opportunities Program Series 1 (1 credit, offered throughout the year) UROP 2100 Undergraduate Research Opportunities Program Series 2 (1 credit, offered throughout the year; prerequisite is pass in UROP 1100, with approval by project advisors) UROP 3100 Undergraduate Research Opportunities Program Series 3 (1 credit, offered throughout the year; prerequisite is pass in UROP 2100 OR UROP 3200, with approval by project advisors) UROP 3200 *NEW* Undergraduate Research Opportunities with Mini-conference Experience (1 credit, offered throughout the year; prerequisite is pass in two UROP1100 OR pass in UROP 1100 and UROP 2100, with approval by project advisors) UROP 4100 Undergraduate Research Opportunities Program Series 4 (1 credit, offered throughout the year; prerequisite is pass in UROP 3100 OR UROP 3200, with approval by project advisors) Summary of UROP Courses
I am pleased to share with you the exciting research completed by our students in the Undergraduate Research Opportunities Program (UROP) during the 2022–2023 academic year. This volume of proceedings showcases the depth and breadth of research covering emerging technologies from arti cial intelligence and machine learning to sustainability and smart cities. Congratulations to our UROP students on their achievements and contributions! UROP plays a pivotal role in fostering the research culture and faculty–student collaborations within the HKUST community. Through this program, our students can engage in cutting-edge research with our faculty members, gaining valuable hands-on experience and skills that will serve them well in their future academic and professional pursuits. Students are empowered to develop and apply knowledge acquired in the classroom to create positive and impactful changes that contribute to our local and global communities. One of the highlights was the successful launch of a new course—UROP 3200—which provides a unique and interactive mini-conference experience during the summer semester. I would like to take this opportunity to thank the faculty supervisors who have dedicated their time and expertise to guide our students throughout their research projects. Without their unwavering support, the success of UROP would not be possible. I hope this publication inspires and encourages more of our students to embark on their research journey early in their undergraduate studies. I look forward to the continued success of our students and faculty members in their research endeavors. Happy reading! Prof. Nancy IP President HKUST Message from the President i
CHEN, Siyu BSc in Integrative Systems and Design It is incredible to think that just two years ago, I had no prior knowledge of research and had no idea how to start a project. Thanks to UROP, I was given the chance to work with my supervisor and Ph.D students. I learned everything from literature review to problem identi cation, proposing new ideas, conducting experiments, data analysis, and drawing conclusions. This entire process was vastly different from my undergraduate studies, and I learned valuable skills that will stay with me for a lifetime. Participating in UROP has given me a precious taste of research. When I am graduating, I decided to continue my research journey as a Ph.D student without any hesitation. The skills and knowledge I gained from UROP can surely be applied to my Ph.D studies. I am immensely grateful for this experience, and I highly recommend UROP to anyone who is interested in pursuing research. HO, Tsz Fung BEng in Computer Engineering During this UROP project, I have had the invaluable opportunity to work in the state-of-the-art research facilities, which are usually not accessed by undergraduate students. The program is a gateway for us to connect with emerging technologies under the guidance of renowned faculty members, where I can transfer theories I learnt from courses into real applications. I have developed a fruitful lot of analytical and problem-solving skills. It was a joyful experience collaborating with faculty researchers to create novel innovations. UROP helped me identify my career goals and equipped me for my future professional developments. Sharing by Students ii
YAP, Octavius Jessica BEng in Chemical Engineering I have been participating in three different UROP projects, and I really enjoyed every bit of it. UROP gave me an opportunity to experience hands-on academic research and I learned a lot during my time in UROP. I met so many mentors that taught me a lot of research skills and helped shape me into a better researcher, from teaching how to use pipettes correctly to operating some sophisticated equipment like peptide synthesizer and high-performance liquid chromatography. The professors also gave me a lot of input that was really useful for me to improve myself from time to time. There were times when the research project was stuck and the results were not what we expected, but during that time I learned perseverance and resilience in facing the struggles as part of research journey. I really like research, the satisfaction of achieving something in the research project is something that I could not get inside the classroom. In the future, I would like to continue doing research and pursue further studies. I also aspire to become a Principal Investigator in the long term so that I can still conduct research while training the next generation of scientists. ZHANG, Weiwen BSc in Data Science and Technology Throughout my UROP experience, my supervisor and Ph.D students in the research group guided and encouraged me through every stage of the research process. I have learned how to conduct thorough literature reviews, propose effective methodologies, design experiments, write research papers, submit them for conferences, and even prepare rebuttals. Thanks to this valuable and fruitful UROP experience, I have learned how to conduct the research from the perspectives of both a researcher and a paper reader or a reviewer. UROP certainly serves as the source of my motivation and inspiration to pursue my research interests in the future. I feel empowered to continue exploring exciting research topics in my postgraduate works. iii
In the 2022–23 academic year, the Undergraduate Research Opportunities Program (UROP) continues to be supported and recognised by the HKUST community. More than 240 faculty supervisors from four Schools and from the Academy of Interdisciplinary Studies offered around 570 projects for our undergraduates. We also received over 1,000 applications throughout the academic year, with 593 students were successfully enrolled to the program. To enhance the continuous development of existing UROP projects, the UROP Support Grant Scheme continues providing nancial support for faculty supervisors and their students. Through the Scheme, students also experience the process of applying for research grants by submitting a joint application with their supervisors. In 2022–23, 32 out of 36 received applications were awarded with an aggregate funding amount of over HK$530,000, after the review by the UROP Of ce and by the UROP Advisory Board. In the year 2023, 28 students with outstanding research performance were nominated by their UROP supervisors for the Undergraduate Research Opportunities Program Awards. Among the nominees, 13 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 organized on 28 April 2023. UROP Overview 2022–23 The 2023 Undergraduate Research Opportunities Program Awards iv
v List of Awardees Champion MOK, Wan Hin Major / Year: MATH / 3 Supervised by: FUNG, Jimmy Chi Hung / MATH Project Title: A Machine Learning Approach to Study the Relationship between Urban Morphology and Urban Heat Island First Runner-up CHEN, Siyu Major / Year: ISD / 4 Supervised by: CHEN, Hao / CSE Project Title: Deep Learning for Ophthalmology Image Analysis First Runner-up HO, Tsz Fung Major / Year: CPEG / 4 Supervised by: YANG, Yansong / ECE Project Title: Nano/microfabrication Technologies for Microelectronic and Photonics Undergraduate Research Opportunities Program Award 2023
vi Second Runner-up WANG, Ruida Major / Year: DSCT & COSC / 3 Supervised by: WONG, Raymond Chi Wing / CSE Project Title: Neural Decision Forest Enhancement for Session-based Recommendation Second Runner-up YAP, Octavius Jessica Major / Year: CENG / 4 Supervised by: CHAU, Ying / CBE Project Title: Combinatorial Peptide Bound Hydrogel Particle for Immunomodulation Second Runner-up ZHANG, Weiwen Major / Year: DSCT / Graduated Supervised by: CHEN, Hao / CSE Project Title: Deep Learning for Ophthalmology Image Analysis Best Poster Award LEE, Tung Yeung Major / Year: BCB / 3 Supervised by: WONG, Yung Hou / LIFS Project Title: Decoding Key Residues in Gαi1 for the Functional Interaction with Adenylate Cyclase
UROP Sponsorship Recipients 2022–23 The UROP sponsorship scheme is intended to provide UROP students with nancial 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. Students who have been awarded the UROP sponsorships in the 2022–23 academic year are listed as follows: Student: SHIN, June Yeol Major: BIOT UROP Supervisor: CHAU, Ying / CBE Conference: 17th RSC Biomaterials Chemistry Group Annual Meeting (Shef eld) Venue: Shef eld, UK Duration: Jan 9 – 11, 2023 Summary of Research Activities: In early 2023, I was given an opportunity to present the work conducted with Prof. Ying Chau during my UROP project at the RSC Biomaterials Chemistry Group Annual Meeting. The process spanning from submitting our work, to preparing a poster to summarize our ndings and to explain it to fellow scholars and students was an invaluable learning experience. Preparing to explain our work in a concise yet informative way and to elaborate on any questions from the audience helped me to understand the importance of our work even more. The experience of attending an academic conference for the rst time was also interesting. The social atmosphere to freely discuss science was particularly inspiring. Spending three days with experts in scienti c research and listening to their ideas sparked my curiosity to further pursue research. UROP Research Travel Sponsorship (by alphabetical order of student’s surname) vii
viii Student: YAP, Octavius Jessica Major: CENG UROP Supervisor: CHAU, Ying / CBE Conference: Controlled Release Society 2023 Annual Meeting Venue: Las Vegas, USA Duration: July 24 – 28, 2023 Summary of Research Activities: Thanks to UROP, on July 24–28, I attended Controlled Release Society (CRS) 2023 in Las Vegas, USA. It was my very rst conference and I got a chance to share my research in macrophage modulation using peptide bound hydrogel particles in the poster presentation. I had the privilege to meet some fellow researchers and Principal Investigators that are working on drug delivery and biomaterials. The most exciting part was meeting Daniel Anderson in person and getting a chance to talk with him. He is one of the pioneers in this research eld, and I am grateful that I can attend his talk. Other than Dan, I am glad that I can expand my connection with other fellow researchers.
ix Student: LIAO, Yi-tsen Major: ECOF UROP Supervisor: HAGMANN, David / MGMT Activity: Center of Behavioural Experiments Summer School on Behavioural Sciences 2023 Venue: University of New York in Prague, Czech Republic Duration: July 24 – Aug 4, 2023 Summary of Research Activities: The summer school was divided into 3 blocks, each focusing on different angles and techniques that were required in experimental economics research. The rst block covered fundamental R programming skills that were often used in data analysis. It started from how to organize your data set to data visualization using ggplot2. Finally, we conducted our analyses on a data set of interest, practising all the techniques that we learned in this session. The second block surrounded the topic of using behavioural economics in public policy. It rst introduced a brief history of our understanding of human decision-making from an evolutionary biological perspective. Then the lecturer walked us through a few well-studied topics in behavioural economics research, including decision-making under risk and uncertainty, mental accounting and social preference. The last block walked us through the process of conducting experiments. It rst gave us a broad framework of some methods that were frequently used in experimental economics. Then, the lecturer introduced some tools that researchers often used, including zTree, oTree and Qualtrics, and what are the pros and cons of each tool under different circumstances. We were also told about the popularization of preregistration in academia, which guards academic integrity and strengthens the credibility of research. Yi-tsen (middle) UROP Summer School Sponsorship (by alphabetical order of student’s surname)
x Student: MOK, Wan Hin Major: MATH-IRE UROP Supervisor: FUNG, Jimmy Chi Hung / MATH Activity: Non-graduating Programme (Research) Venue: National University of Singapore, Singapore Duration: June 12 – August 22, 2023 Summary of Research Activities: I mainly analyzed two sets of climatological datasets to study the urban heat island effect. The rst one was long term measurements (10 years) from the 22 meteorological stations of the National Environment Agencies scattered across Singapore, and I used them to analyze the urban heat island in the city scale. The second one was short-term measurements (1 year) from the weather stations placed by the research team (Urban Climate Design Lab) in strategic locations in the downtown area, and I used them for studying the effect of greenery, building densities, shading and the building designs on the temperatures and the ventilation within the same neighborhood. For the urban-scale analysis, the major differences in temperatures of the stations of different types were identi ed and analyzed in great detail to account for the diurnal variations and the seasonal variations of the urban heat island effects. Relevant suggestions were also made for Singapore to mitigate the heat islands, whose negative effects on humans were explored thoroughly in the extensive literature review of the project. For the neighborhood-scale analysis, the in uence of building designs on the thermal comfort of the pedestrians (which was based on temperature and the wind speed) was analyzed. In addition, a machine learning model that predicted the urban-rural temperature difference based on the different weather conditions and the station environment (in terms of NDVI, sky view factor and the percentage of ocean nearby) was also trained, with the performance being veri ed outside of the training period. The performance at different weather stations and under different weather conditions were analyzed.
Abstracts of UROP Projects 2022–23 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: LEE, Yan Yee / SSCI Course: UROP1100, Summer Water splitting has attracted considerable scientific attention in recent years due to its ability to produce hydrogen as fuel with minimal pollution. Photoelectrocatalytic processes, among all other ways, have become the most popular topic because they utilize renewable solar power, leading to a more environmentally friendly approach. Consequently, increasing the efficiency of the device has been of utmost importance to the commercialization of this technology. However, finding a catalyst for this reaction has been a challenging task. Hereby, perovskite was tested as one of the photocatalysts. CsPbBr3 and Cs3Sb2Br9, two of the most common perovskites, as well as other possible candidates were synthesized and evaluated. Lead-free Perovskite Nanocrystals for Photo-induced Water Splitting Supervisor: HALPERT, Jonathan Eugene / CHEM Student: OUYANG, Boyu / CHEM-IRE Course: UROP3100, Fall 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 efficiently. 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: CHENG, Yiyang / SSCI Course: UROP1000, Summer In this experiment, optical tweezer and Raman spectroscopy are utilized for singe cancer cell analysis. Optical tweezer is applied to trap, move, and manipulate single cancer cell. And Raman spectroscopy is applied for molecular characterization to reveal the component of the cancer cell. This experiment analyzes one cancer cell, with 7 positions around the center and two Raman spectrum for each position, centered at 1200 cm-1 and 2500 cm-1. Each spectrum is 1s exposure time and 60 accumulations, in total 60s. After that, we get sets of spectrums range from 233 cm-1 to 3219 cm-1. Then, 9 positions distributed along the cell diameter are tested to verify the strongest signal of Raman spectroscopy is located at the center of the cell. After analyzing the repeatability and characteristically of the Raman spectroscopy at the center of the cell, we conclude that the Raman spectroscopy at the cell can be used to represent the characteristic of the cell. Furthermore, different peaks in Raman spectroscopy indicate tentative assignments of the corresponding peaks. This allowed for a more detailed analysis for further study.
School of Science Department of Chemistry 3 Construction and Application of Surface Enhanced Raman Spectrometer in Biomolecules Characterization Supervisor: HUANG, Jinqing / CHEM Student: LI, Hiu Fung / SSCI Course: UROP1000, Summer Cancer cells were being optically trapped by Optical Tweezer and scanned by Raman spectroscopy. The Raman signal of the cancer cells were found to be the strongest at the centre of it by measuring its Raman signal along a horizontal axis. Raman signals were collected from the centre of the cancer cells which several spectrum peaks corresponded to the macromolecules of the cancer cells were located. The data collected can be further used to observe the spectra change of the cancer cells when they are being treated with anticancer drugs. The mechanism and effectiveness of the anti-cancer drugs can then be revealed, improving the development of anti-cancer drugs. Construction and Application of Surface Enhanced Raman Spectrometer in Biomolecules Characterization Supervisor: HUANG, Jinqing / CHEM Student: PARK, Sejeong / CHEM-IRE Course: UROP1100, Fall This research studied the biomolecular composition of breast ductal carcinoma tissue using Raman imaging, with the hope of contributing to the development of a breast cancer diagnostic tool based on Raman spectroscopy. Raman images were generated using unsupervised machine learning, which assisted in the clustering of spectra. Peak ratio analysis of the mean spectra of each cluster obtained in the high wavenumber region showed transitional trends in proteins and lipid components, allowing several interpretations of our ductal carcinoma tissue. The lipid ratio gradient from our study suggests the possibility of enhanced accumulation of certain fatty acids in cancer-associated fibroblasts (CAFs) surrounding breast cancer cells. This study has recently proceeded to use Raman imaging to monitor the binding interactions between cancer cells and T-cells. Medicinal Chemistry on Novel Type I1/2 ALK Inhibitors for Combating Drug-resistant Mutants Supervisor: HUANG, Yong / CHEM Student: YUNG, Zhe Jamie / CHEM-IRE Course: UROP1100, Summer Bifunctional N-heterocyclic carbenes (NHC) are an emerging class of NHC catalysts, where the underlying HOMO-raising activation of the nucleophile from the carbene works in conjunction with the LUMO-lowering activation of the electrophile from the hydrogen-bonding donor. This system has shown greater efficiency than the established tertiary amine-thiourea scaffold system, due to the higher basicity of the carbene. This type of bifunctional catalyst has proven effective in catalyzing asymmetric hetero-Michael addition reactions, such as aza-Michael addition. Novel designs of such catalysts may be able to catalyze asymmetric intermolecular oxa-Michael addition of alcohols, as well as asymmetric 1,6-conjugate addition through the extended conjugated system.
School of Science Department of Chemistry 4 Synthesis, Reactivity and Catalytic Properties of Transition Metal Carbyne Complexes Supervisor: JIA, Guocheng / CHEM Student: SU, Zijie / SSCI Course: UROP1100, Summer This report discusses the synthesis and catalytic properties of RuHI(CO)(PPh3)3 in the hydrogen/deuterium exchange reaction between olefins and D2O. Firstly, there will be a introduction highlighting the importance of developing efficient methods for the production of deuterated compounds, which are widely used in various fields including pharmaceuticals, agrochemicals, and materials science. After that, a detailed procedure and reaction mechanism of the synthesis of RuHI(CO)(PPh3)3 will be displayed. Moreover, the catalytic activity of RuHI(CO)(PPh3)3 in the hydrogen/deuterium exchange reaction between olefins is navigated, and the results demonstrate its high efficiency in promoting the exchange reaction in acid environment. Finally, there will be a short conclusion summarizes the findings of the study and the potential benefits of utilizing RuHI(CO)(PPh3)3 as a promising catalyst for the production of deuterated compounds. Synthesis, Reactivity and Catalytic Properties of Transition Metal Carbyne Complexes Supervisor: JIA, Guocheng / CHEM Student: YIU, Wing Shan / CHEM Course: UROP1100, Spring The study on reactivity of rhenacyclobutadiene complexes with electron-rich alkynescan help to reveal effect of substituents on outcome of the reaction. For this purpose, a series of internal alkynes and of rhenacyclobutadiene complexes were synthesized in this project. Two furan substituted alkynes of the type RC≡CCO2Me (R = C4H3O) were successfully synthesized by Corey-Fuchs reactions. Two internal alkynes of the type R(C6H4)C≡CMe (R = CN, NO2) were successfully synthesized by Sonogashira coupling reaction. Four rhenacyclobutadiene complexes of the type Re{-C(R1)=C(R2)C(OR3)=}(CO4) (R1 = C4H3O, Me, R2 = COOEt, (C6H4)CN, (C6H4)NO2, R3 = tBu, Et) were synthesized by Schemes 4 and two were successful while the other two were unsuccessful.
School of Science Department of Chemistry 5 Reactivity and Bonding Studies of Transition-metal Complexes Supervisor: LIN, Zhenyang / CHEM Student: LAU, Pak Fung / CHEM-IRE Course: UROP1100, Summer Last semester, we put emphasis on the reactions of the two Fe-Al complexes (Figure 1), one undergoes intramolecular C-H activation (Figure 1a) while the other activates the C-H bond in the ortho-position of pyridine (Figure 1b). In this report, we expanded our research by exploring the reactivity and selectivity of the Fe-Al complex used in Figure 1b towards various substituted pyridine as shown in Figure 2. We are also working to explore the reaction pathways involving the complex shown in Figure 3. Figure 1a. The intramolecular C-H activation. Figure 1b. The intermolecular activation of C-H bond of pyridine. Figure 2. Reactivity towards 2-methyl pyridine and 2-ethyl pyridine. Figure 3. The reaction between Al complex and 4-methyl pyridine. It leads to the activation of the sp3-C-H bond in the para-position.
School of Science Department of Chemistry 6 Synthesis and Spectroscopy of Hybrid Donor-acceptor Metal-halide Perovskites Supervisor: LU, Haipeng / CHEM Student: JUSMIN, Frederick Gabriel / CHEM-IRE Course: UROP1100, Summer Hybrid organic-inorganic perovskites are an emerging class of materials which have high tunability in the number of inorganic layers and relaxed tolerance factor. Recently, perovskite structures incorporating functional organic cations have shown unique properties and is a promising approach in designing new materials for optoelectronics. Here in, we incorporate a modified naphthalene diimide core, which is a common electron acceptor used in optoelectronics, into quasi-2D perovskite structures. Compared to typical alkyl spacer cations, bulky conjugated cations contribute to the frontier electronic structure producing a type II bandgap, where holes and electrons are confined in different layers. UV-vis absorption and PL spectra have proven that bulky cations can form quasi-2D perovskite structures. New Methodologies for Organoborane Synthesis Supervisor: QUAN, Yangjian / CHEM Student: CHAN, Fung / CHEM LY, Kit San / CHEM Course: UROP1000, Summer UROP1000, Summer Hydroboration is a useful reaction to introduce boron to unsaturated compounds by reacting with all kinds of borane (Li et al., 2021). The organoborane compounds could be further functionalized by other reactions such as oxidation to get alcohol (Elsherbini et al., 2020) or Suzuki coupling to extent carbon number. New methodologies for hydroboration are highly demanded, therefore alkene synthesis is crucial to test the tolerance of different functional groups in alkene. The following report will focus on the synthesis of a series of unsaturated olefins as starting materials for hydroboration. New Methodologies for Organoborane Synthesis Supervisor: QUAN, Yangjian / CHEM Student: FU, Yiyi / CHEM XU, Yinghe / CHEM Course: UROP1000, Summer UROP1000, Summer A radical process of β-addition of N-heterocyclic carbene borane (NHC-BH3) to phenol- and ester-substituted alkyne by visible light irritation with 4-CzIPN is reported. Theoretically, E (trans) or Z (cis) conformation can be controlled via variation of wavelength of a household light bulb. At 427nm, E (trans) adduct prevails while Z (cis) is suspected to dominate below 427nm. The thermodynamics of E (trans)/Z (cis) isomers and their interconversions are still under investigations. Further experiments are planned in order to check if temperature, reaction time, energy transfer catalysts, and lower wavelengths (below 427nm) can contribute to E (trans)/Z (cis) conversion.
School of Science Department of Chemistry 7 The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU, Haibin / CHEM Student: CHANG, Ka Pui / CHEM Course: UROP2100, Fall UROP3100, Spring The recent emergence of the XBB.1.16 variant, also known as Arcturus, demonstrates the COVID-19-causing virus SARS-CoV-2 is still frequently mutating, particularly in its spike glycoprotein. The virus is constantly finetuning its virulence and transmissibility by different modes of mutations such as SAP, deletion, insertion, and N-linked glycosylation. Here, the refined dynamic expedition of leading mutations (deLemus) method, leading mutations by composite metric, a promising method for identifying mutations of interests in the spike and predicting viral evolution, and the online deLemus platform, which is developed to illustrate the mutation landscape and the evolving structure of the spike, both crucial information for monitoring the viral evolutionary dynamics, are introduced. The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU, Haibin / CHEM Student: LEUNG, Cheuk Fung Alvin / BCB Course: UROP2100, Fall UROP3100, Spring UROP4100, Summer The co-translational transfers of carbohydrate moieties onto proteins contribute to their unique physical and biochemical properties. These regiments of sugars regulate various physiological processes, including the lifecycles of viruses. For one, the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) bears a glycan shield which modulates its infectivity and immune escape capability. Even though slight perturbations of the native glycosylation pattern may pose significant impacts on viral fitness, the evolutionary trajectory of potential N-glycosylation sites (PNGSs) remains poorly understood. In this report, PNGS evolution on the SARS-CoV-2 spike would be unravelled. Interestingly, attempts to quantify the spatial geometry of PNGSs on the N-terminal domain suggest that glycan evolution directs their redistributions differentially in the open and closed conformations. The Impact of Spike Mutations on SARS-CoV-2 Neutralization Supervisor: SU, Haibin / CHEM Student: LIN, Sijia / CHEM Course: UROP1000, Summer The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made a great impact on humans in the past few years. Studying the evolution of the SARS-CoV-2 spike (S) protein may help us understand the virus in depth, which could benefit global public health. Different variants of SARS-CoV-2 were analysed in order of priority. Clade assignment, consensus sequence selection, mutation rate calculation and other analyses were performed on the Alpha variant. At the protein level, the pattern of mutation rates obtained using consensus sequences with different thresholds did not match the trend of the number of all Alpha sequences against time. Further analysis will be continued to find out the insight of viral evolution.
School of Science Department of Chemistry 8 Text Mining of Synthesis Methods of Metal Organic Framework Supervisor: SU, Haibin / CHEM Student: SIU, Chun Hey / CHEM-IRE Course: UROP1100, Fall Metal Organic Frameworks (MOFs), which are formed by mixing metal ions with organic linkers (ligands), have piqued the interest of researchers in recent years due to their numerous practical potentials. The Cambridge Structural Database records more than 80 useable metals, thousands of ligands, and about 5 methods of synthesis for MOFs specifically (Moghadam et al., 2017). There are still significant gaps to fill in order to better the understanding of MOF synthesis. This project extracts and evaluates synthesis methods and reaction conditions from thousands of MOFS experiments. Text Mining and Graph Mining are used extensively on chosen studies to collect a wide range of data for MOFs using personalized automation software. Data Analytics of Homogeneous Transition Metal Catalyzed Reactions Supervisor: SU, Haibin / CHEM Student: LI, Changwen / CHEM Course: UROP1000, Summer This UROP project aims to build a citation network for the team’s research paper on homogeneous nickel catalyzed (HoNiCa) reactions. The project involves analyzing keywords and their trends in the papers, determining the most influential papers, and capturing latent knowledge. Python code was developed to visualize keyword trends, generate word clouds, and provide graphical analysis of the citation network. Cytoscape is the primary tool used for building and visualizing the citation network. ChemBioDraw was employed for data extraction, including drawing chemical structures, and converting them into SMILES notation for training the transformer model. By implementing these methods, we observed an overview of our team’s reference papers, and have a deeper understanding of the research focus and popular topics. Data Analytics of Homogeneous Transition Metal Catalyzed Reactions Supervisor: SU, Haibin / CHEM Student: SHEK, Ching Yee / SSCI Course: UROP1100, Summer The study focus on the evolution pattern of alpha strain of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2, 2019-nCoV), a inflections virus which has caused significant disruption to the world, by analyzing its mutation rate and machine learning. The report presents a workflow that involves the determination of a consensus sequence for each month, followed by graph plotting to analyze the mutation rate over time and population of the virus. Finding that the peak of mutation rate over time lags behind that of the population over time, possible reasons for it is discussed but has not been found. Future directions are also discussed.
School of Science Department of Chemistry 9 Data Analytics of Homogeneous Transition Metal Catalyzed Reactions Supervisor: SU, Haibin / CHEM Student: WANG, Yizhou / CHEM Course: UROP4100, Fall Nowadays, transitional metal catalysis has been more and more popular in organic synthesis. The special properties nickel possesses enable nickel catalysts to stabilize paramagnetic intermediates, access radical pathways and slower the β-elimination. C-O activation reactions has appealed chemists’ attention for a few decades because of the extensive distribution of oxygen-containing functional groups in organic compounds. C-O bonds can sometimes be chemically active under certain conditions, while in some compounds like alcohols or ethers, C-O bonds can be inert and hard to be broken. Data Analytics of Homogeneous Transition Metal Catalyzed Reactions Supervisor: SU, Haibin / CHEM Student: WONG, Jemson Jun Peng / COMP Course: UROP1000, Summer UROP1100, Spring Homogeneous transition metal-catalysed reactions are important chemical reactions for synthesising organic molecules. Our project would be to analyse the trend of the reaction from the past, including the use of the ligand and the reaction condition. In scope, we would use trained machine learning to provide a suitable chemical condition for any new unknown reaction. In the process of analysis, we would also be able to learn the key to the reaction’s success and failure. As a beginner in the research field, I would be working on data extraction and analysis with Mr Imanuel Rava as an entry procedure for the project. In the following, I will illustrate the methodology for data extraction and introduce the fundamental knowledge before the extraction. In the end, report the result from the data analytics. I am grateful for the assistance provided by our project team.
School of Science Department of Chemistry 10 Deep Learning in Synthesis Planning Supervisor: SU, Haibin / CHEM Student: PANG, Chun Pan Terry / SSCI Course: UROP1000, Summer The integration of artificial intelligence and computational software has opened up new possibilities for organic chemists in pursuit of innovative synthetic strategies. This report discusses the development of a software capable of transforming chemical structure images from academic journals into SMILES format, a computer-recognizable language representing chemical structures. SMILES not only provides unique identifiers for chemical compounds but also offer compact representation, which promotes storage and computational efficiency. Our software consists of file handling, segmentation, translation, and output components, enabling efficient and automated chemical information retrieval and standardization. Using OChemR, an open-access algorithm as backbone, molecular recognition and SMILES translation can be achieved. This software addresses the inadequacy of current molecular recognition programs and accelerates the development of meta-heuristic models, such as molecular transformers, by feeding a massive, accurately translated database of organic reactions. While still in the development stage, this software shows potential to advance organic synthesis planning, as well as overall chemical information storage. Development of New Catalytic Organic Processes Supervisor: SUN, Jianwei / CHEM Student: HO, Hang Chi / CHEM-IRE Course: UROP2100, Spring Kinetic resolution represents a powerful strategy for the construction of multiple chiral molecules in one pot. While the asymmetric reactions of ortho- and para- hydroxyl benzylic alcohols and their corresponding quinone methides have been extensively explored, the properties of a meta-hydroxyl group as a directing group in asymmetric organocatalysis is relatively underdeveloped. Herein, we disclose a meta-hydroxyl directed kinetic resolution of biaryl alcohols using sulfur nucleophiles. Green Chemistry in Organic Synthesis Supervisor: TONG, Rongbiao / CHEM Student: MA, Muyang / SSCI Course: UROP1100, Summer Green chemistry is an area which aims to reduce the use of hazardous compounds and maximize the utilization of atoms in the chemical process, and it has been emphasized in recent years. Aryl halides are important intermediates and have been widely used in organic synthesis. Herein, we are going to report a green protocol by using arylboronic acid, oxone and halide salt, which would form C-X bond in situ and just produce a nontoxic byproduct (potassium sulfate), to replace the traditional methods like Sandmeyer reaction and NXS in the halogenation reaction. We also investigate and compare the effect of different substrates and different halogens to screen out the condition for the halogenation reactions.
School of Science Department of Chemistry 11 Design of Controllable Enzymes for Therapeutic Applications Supervisor: VONG, Kenward King Ho / CHEM Student: WAN, Kai Yui / SSCI Course: UROP1100, Fall The project focus on the synthesis and purification of the Mucin 1 N-terminus (MUC1-N) and Mucin 1 Cterminus (MUC1-C). It is believed that the two terminals can strongly interact with each other to form a complex, so they can provide us with a possible way to manipulate the conformation of other proteins containing one of the terminals and control their activity in vitro, serving therapeutic purposes. Further to the experiments carried out in the summer semester, new methods including tricine SDS-PAGE, FPLC in denatured condition, size exclusion, and dialysis are investigated to identify a better direction in producing the pure terminus effectively. Developing metal-catalyzed Reactions for Biological Applications Supervisor: VONG, Kenward King Ho / CHEM Student: CHENG, Ka Ki Ernest / CHEM Course: UROP1000, Summer This report presents the progress of the synthesis of unnatural amino acid (UAA) which is a planned model compound to investigate the feasibility of the proposed metal-catalyzed alkyne hydrothiolation peptide cleavage. Using homocysteine as the starting material, several modifications have been made to the synthetic scheme of UAA including change of protecting group, the addition of catalyst and reaction temperature and it will be described in the report. Until this point, the UAA is in the progress of synthesis, and that the deprotection and incorporation of inactivated alkyne to the UAA is required for further transformation of the UAA into peptide for subsequently exploration of the anticipated alkyne hydrothiolation of the peptide cleavage reaction to shed light on the localized release of cytotoxic onconase at the target tissues such as tumor tissues. The proposed mechanisms will also be described in order to provide the rationale behind this project. Developing metal-catalyzed Reactions for Biological Applications Supervisor: VONG, Kenward King Ho / CHEM Student: CHOY, Tsz Shan / CHEM Course: UROP1000, Summer In this study, gold-activated cell penetrating peptides are introduced for a different application. Using this strategy, relevant bioactive peptides are controlled by their charge to determine their level of penetration into the body. We present the development of activatable cell penetrating peptides (CPPs) by functionalizing them with an alkynylated biaryl-2-amine (ABA) group. In the presence of a gold catalyst, hydroamination and aromatization can produce positively charged phenanthridine for cellular uptake. In this study, 5 types of peptides, 2 types of substrates and 4 types of gold catalysts are used to test biological activity interchangeably in order to find the better match.
School of Science Division of Life Science 12 Division of Life Science Mechanisms of Golgi Membrane Protein Retention Supervisor: BANFIELD, David Karl / LIFS Student: LI, Caifan / BCB Course: UROP2100, Fall Vps74p-based Golgi membrane protein retention mechanism has been an important topic in cell biology studies. Vps74p binds both to the cytoplasmic tail of proteins and the COPI, transporting the mislocalized residents back to Golgi. In former experiments has been completed over the summer, we mimicked the Golgi quantitative retention assay in mammalian cells, which established a chimeric protein reporter with a GOLPH3-recognized tail that was transported to the cell membrane in the absence of GOLPH3 and GOLPH3L genes (which are orthologs of Vps74). But our experiments found that in vps74∆ cells, the chimeric protein reporters with Vps74p-recognized tail are not transported back to the plasma membrane, but instead accumulate in the vacuole. In a subsequent series of experiments, we continued to focus on exploring the reasons for the tendency of chimeric proteins to go to the vacuole and tried to prevent this. This tendency may be related to the preferred TMD length of different organelles or the multiple intracellular pathways to the vacuole. However, our further experiments show that neither elongating TMD length to a more appropriate length of the plasma membrane nor reducing vacuole transporting by blocking the vacuole ALP pathway can localize our chimeric protein reporter to its expected destination, the plasma membrane. Mechanisms of Protein Retention in the Yeast Golgi Supervisor: BANFIELD, David Karl / LIFS Student: LI, Caifan / BCB Course: UROP3100, Spring Vps74p is one of the important proteins in yeast, it binds to the cytoplasmic tail of glycosyltransferases (GTs) and binding groups on the COPI coat to achieve protein retention in the Golgi apparatus and maintain the homeostatic distribution of GTs. GOLPH3 and GOLPH3L are orthologs of Vps74 in humans, the mutations of these genes are closely associated with severe diseases such as cancer, so research into them is of great interest. In this report, we have selected and identified nanobodies (Nb) against GOLPH3 and GOLPH3L using model organisms yeast, with the aim of obtaining information about the binding sites of GOLPH3 and GOLPH3L proteins to other components from these selective nanobodies. Many in vitro and in vivo experiments have been carried out to find these specific nanobodies.
School of Science Division of Life Science 13 Molecular Regulation of Skeletal Muscle Stem Cell Quiescence and Activation Supervisor: CHEUNG, Tom / LIFS Student: KARAMCHANDANI, Gia / BIBU Course: UROP1100, Spring Genotyping works by analyzing DNA to determine genetic makeup, allowing for the investigation of the molecular mechanisms that regulate biological processes. Genotyping of the Pax7creERT2 and ROSA26MetRSGFP mouse lines was conducted to confirm the presence of particular DNA sequences. PCR amplification and gel electrophoresis were utilized to detect specific DNA sequences corresponding to each gene's wildtype or mutant alleles. The results provide a base for further extension into the function and role of these genes in muscle stem cells. Additionally, laboratory techniques and technologies, such as cell culture, fluorescence microscopy analysis, and cryopreservation, can be used to study the different aspects of muscle stem cell behavior and function, enhancing the understanding of muscle stem cell biology. Molecular Regulation of Skeletal Muscle Stem Cell Quiescence and Activation Supervisor: CHEUNG, Tom / LIFS Student: NGAI, Man Yee / BCB Course: UROP1100, Spring This study aimed to optimize the protocol for investigating the role of miR-653 in regulating the quiescent state of stem cells through fluorescence-activated cell sorting (FACS). Adult muscle stem cells were used as the model system, and the protocol was optimized based on previous research. This report presents the progress achieved in optimizing the protocol, although biological replicates were not included in the experiments. We compared the concentrations of antibodies targeting Pax7, Ki67, GFP, and MyoD after 36 and 48 hours. AntiPax7 and anti-Ki67 antibodies did not yield observable results. Anti-GFP exhibited optimal performance at a concentration of 1:100, while anti-MyoD did not show any significant differences among the tested concentrations. Furthermore, no significant reduction in stem cell activation was observed when different concentrations of EdU and Azide were tested. Additionally, horse serum prepared at lower temperatures tended to result in reduced stem cell activation. Molecular Regulation of Skeletal Muscle Stem Cell Quiescence and Activation Supervisor: CHEUNG, Tom / LIFS Student: PARK, Changmo / BIOT Course: UROP1100, Fall Observation of whether stem cells are affected by a specific gene or a microRNA pathway can be done with the help of the RNA interference technique. After the knockdown, phenotypical changes such as the number of stem cells and other expressions of proteins can be easily detected and analyzed with the help of immunofluorescence. Satellite cells are one of the stem cells which play an essential role in maintaining muscle fibers and repairing skeletal muscles by proliferation, self-renewal, and differentiation. In this paper, molecular and genetical methods of the siRNA/miRNA transfection to the satellite cells and the experimented and utilized genes such as the YFP, CKS1B, and MyoD are discussed.
School of Science Division of Life Science 14 Molecular Regulation of Skeletal Muscle Stem Cell Quiescence and Activation Supervisor: CHEUNG, Tom / LIFS Student: SINCE, Alec Victor / BIBU Course: UROP1100, Spring This study aimed to investigate the role of CPEB4 in regard to senescence in skeletal muscle stem cells. As previous research suggested, the decrease in CPEB4 level is correlated with the aging of cells due to its effect on mitochondrial-related translation. We used FACS to sort and isolate satellite cells from the hindlimb muscles of mutant CPEB4-P2A-RFP and Pax7-GFP mice to carry out various assays to confirm the correlation between CPEB4 level decrease and senescence. Further studies are required to confirm why there seems to be a low efficiency of CPEB4-P2A-RFP expression in the transgenic mouse model that we used to carry out this study. Molecular Regulation of Skeletal Muscle Stem Cell Quiescence and Activation Supervisor: CHEUNG, Tom / LIFS Student: SHIN, June Yeol / BIOT Course: UROP1100, Fall Muscle Satellite cells (MuSC) which function to regenerate into myofibers upon muscle damage can also be isolated and cultured for different purposes. An example of such purpose that is recently gaining increased attention is to culture MuSC into differentiated myofibers in vitro for human consumption as cultured meat. For this purpose, several traits such as fast growth rates, ability to form longer and thicker myotubes upon differentiation may be advantageous traits. Therefore, to determine whether specific genes may be responsible for particular phenotypical differences, MuSC from Diversity Outbred (DO) mice strains were isolated then cultured toward differentiation. Any difference in phenotype may be compared against the genome of the DO mice to uncover genes that may play an important role for differentiation. Construction of a Signal Transduction Pathway Reporter Indicator for Monitoring Signaling Strength Supervisor: CHOW, King Lau / LIFS Student: PARK, Jihye / BIOT Course: UROP1100, Fall UROP2100, Spring The bone morphogenetic proteins, a class of TGF- β family, have conserved roles in the bone development and body patterning of many vertebrates and invertebrates. Although much of the basis of the signalling mechanism is understood, there is still a lack of information on the target genes of this signalling pathway. This research focuses on C08E3.13 gene found in Caenorhabditis elegans, previously reported by the paper “Identification of transforming growth factor-beta-regulated genes in Caenorhabditis elegans by differential hybridisation of arrayed cDNAs” (Mochii et al., 1999) to be differentially regulated by the growth factor-β (TGF-β) family. According to the paper, C08E3.13 expression has shown to decrease in mutant C. elegans with mutations in the dbl-1 and sma-2 genes that encode the component of TGF-β signalling pathway and TGF-beta ligand required for activating the TGF-beta signalling pathway and an increase in lon-2 mutant with a defective negative regulator of TGF- β signalling, showing that C08E3.13 may be regulated by the TGF-β pathway. The final goal of this project is to re-create this experiment results by constructing and injecting a fused plasmid of a reporter gene and the promoter of C08E3.13.
School of Science Division of Life Science 15 Cryo-EM Study of Membrane Proteins Supervisor: DANG, Shangyu / LIFS Student: TEMIRBEKOV, Yerassyl / SSCI Course: UROP1100, Summer TMEM168 is an evolutionary conserved eukaryotic membrane protein with an unknown structure and unclear function, appearing in a diverse set of research contexts, that has been shown to have many loosely related interactions. This protein has no apparent homologs outside the TMEM168 family; the sequence analysis shows no defined known domains, which may indicate novel functional mechanisms. We aim to overexpress and purify the target protein and later use it to resolve structure using single-particle cryo-EM and unravel functional role using biochemical methods. Understanding the structure and function of TMEM168 can lead to the discovery of new signal pathways, regulatory mechanisms, and other previously unknown molecular interactions. Analysis of Export of a Planar Cell Polarity Protein, Vangl2, out of the Trans Golgi Network Supervisor: GUO, Yusong / LIFS Student: CHENG, Guo / BCB-IRE Course: UROP1100, Fall UROP2100, Spring 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 et al., 2013) Here we purified AP1 core, Arfrp1 and HAVangl2 to study the interaction between AP1 core and Vangl2, as well as the function of Arfrp1 in regulating the TGN export of Vangl2. Analysis of Surface Delivery of Epidermal Growth Factor Receptors Supervisor: GUO, Yusong / LIFS Student: CHU, Man Kit Christopher / BCB Course: UROP1000, Summer Epidermal Growth Factor Receptor (EGFR) is a well-known biomarker for cancer studies. Newly synthesized EGFR follows conventional protein trafficking route, it first transports from the endoplasmic reticulum (ER) to the Golgi and then delivered to the plasma membrane, allowing ligand binding to activate the EGFR signaling. This project aims to identify a nanobody that can block the export of EGFR and causes its retention at the ER membrane, thereby reducing the abundancy of EGFR on the cell surface to mitigate the activation of EGFR signaling. To commence, we first generated two different “Twin-Strep-EGFR” constructs through molecular cloning. These constructs are used for protein purification and later used for screening nanobody that targets EGFR.
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