INDICIUM 2021/22
Congratulations to the participating members of our second annual INDICIUM Research Competition at UBC!
In the 2021-2022 school year, yet another successful Indicium Research Conference took place over zoom.
Despite some COVID-19 restrictions, mentors and students created insightful and interesting projects that we had the honour of showcasing at the event.
On behalf of UBC STEM Fellowship and the Indicium Team, we are eternally grateful for your patience, perseverance, and participation. We hope to see you next year!
We would like to acknowledge our amazing panel of judges for Indicium 2021/22:
Dr. Evelyn Sun, PhD Microbiology and Immunology at the University of British Columbia
Dr. Hila Behar, PhD Biochemistry and Molecular Biology at the University of British Columbia
Dr. Jean-Denys Hamel, PhD Chemistry and Associate Professor of Chemistry and Biochemistry at the University of Lethbridge
Dr. Miranda Meents, PhD Botany and Lecturer at the Simon Fraser University
“It was an honour to have worked alongside an incredible set of mentors, mentees, and executive team members for a second year in a row. Indicium would not be possible without the drive of those who choose to indulge in this platform in pursuit of knowledge, mentorship, and future opportunity”
Muskan Tuli, UBC Indicium Lead and National Indicium Lead
Indicium Research Competition Winner:
Mentor: Karol Buda, PhD candidate in Biochemistry and Molecular Biology at UBC
Team: Sherard Ryan Vethanayagam, Sze Lok Ng, Arnaz Dhalla
“Indicium provided a great opportunity for students looking to get into research and meet professionals in the field. It was a great learning experience and I highly recommend joining”
Mentee from INDICIUM 2020/21
Indicium Research Competition Projects:
Aberrantly expressed transcription factors are associated with oncogenic pathways in Chronic Lymphocytic Leukemia
Mentor: Rashedul Islam, PhD Candidate in Microbiology and Immunology at UBC
Team: Karina To, Roy Hung, Vera Pu, Chelsea Wenyou, Kevin Han
Abstract: Chronic lymphocytic leukemia (CLL) is a malignancy of B-cell and can originate from different subsets of B-cells. Epigenetic aberrations are frequently reported in CLL where the enhancer landscape undergoes hypomethylation that allows the binding of transcription factors (TFs) e.g., NFAT, EGR etc. Recent large-scale RNA sequencing (RNA-seq) studies identified a large number of genes are differentially expressed including TFs in CLL compared to B-cells. However, aberrantly expressed TFs in CLL and their role in oncogenic pathways are not well explored. Thus, we hypothesize that aberrantly expressed transcription factors are associated with the pathogenesis of CLL through activating oncogenic signaling pathways. To test this hypothesis, we have collected publicly available gene expression matrices generated using RNA- seq for 7 CLL and 12 B-cell samples derived from human primary tissues. Using differential gene expression analysis, we identified there are 3,173 genes down-regulated and 1,471 are up- regulated in CLL compared with B-cells. Among the up-regulated genes 7% (104/1,471) of them are TFs. Those TFs are significantly (P-value <= 0.001) enriched in transcriptional dysregulation in cancer, Wnt signaling, and other cancer-related pathways. This is suggesting that higher expression of TFs is associated with downstream transcriptional dysregulation and the oncogenic Wnt signaling is activated through over-expression of associated TFs e.g., TCF7L2, TCF7, LEF1, PPARD in CLL. This study showed that aberrantly expressed TFs could be associated with potential oncogenic pathways driving CLL pathogenesis. Further studies are required to understand the binding patterns of aberrantly expressed TFs and their roles in downstream transcription program alterations in CLL.
Structural and Functional Implications of TMPRSS2 Evolution
Mentor: Karol Buda, PhD candidate in Biochemistry and Molecular Biology at UBC
Team: Sherard Ryan Vethanayagam, Sze Lok Ng, Arnaz Dhalla
Abstract: The type-II transmembrane serine protease (TMPRSS2) is a host enzyme that is used in normal physiological processes, but also plays a key role in host-virus interactions including SARS-CoV-2. Indeed, it has been shown that mouse and human TMPRSS2s show different proteolytic activation of influenza H3N2. The goal of this study was to determine whether the basis of host-virus interactions could be linked to structural elements of TMPRSS2s. This was done by identifying human TMPRSS2 (hTMPRSS2) homologues using BLAST, performing multiple sequence alignment, inferring a phylogenetic tree, and performing ancestral sequence reconstruction. Structures of mouse TMPRSS2 (mTMPRSS2) and key ancestors were predicted using AlphaFold2, then structurally compared to the hTMPRSS2. Our analysis suggests no observable changes in the active sites between hTMPRSS2, mTMPRSS2 and their common ancestors. As a result, we are unable to directly explain the host-virus interactions with structural data of TMPRSS2s. Furthermore, the highly conserved nature of the TMPRSS2 active site across homologues and ancestors suggests the importance of TMPRSS2’s function in the organisms encompassed by our study. The role that TMPRSS2 plays in various virus-host interactions can be further explored using our homologues and ancestors. Future studies can use a mammalian CRISPR-Cas9 gene-edited model to explore the functional consequences of the various non-active site mutations observed in the TMPRSS2 homologues and ancestors.
Common Blueberry Agrochemicals and their Effects on Honey Bee Health
Mentor: Rhonda Thygesen, PhD Candidate in Biochemistry & Molecular Biology at UBC
Team: Ibraheem Babar, Ana Timpano, Conner Fransoo, Amanda Yang
Abstract: Honey bees that pollinate blueberries are exposed to a wide variety of agrochemicals, including pesticides, herbicides, synthetic fertilizers, and soil conditioners used on blueberry crops, and it is known that certain agrochemicals can negatively impact honey bees. However, a detailed database of these agrochemicals and their specific effects on the honey bee proteome does not yet exist. By reviewing, analyzing, and compiling existing literature on blueberry agrochemicals and their effects on honey bee health, we aim to create a database which will help future researchers determine which agrochemicals need further study and will provide insights into the existing body of knowledge on this topic. Our work could be furthered by conducting experiments to determine the changes in the proteome of honey bees that are exposed to different agrochemicals. This knowledge would allow for the development of honey bee-specific, proteomic diagnostic health tests, similar to what currently exists for humans and certain livestock.
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