BIOL Comps Questions 2023-24

1) Effects of latitude on ecological patterns and processes (Hernández or McKone)

There is evidence that latitude influences the patterns of diversity and the controls on ecological processes at regional and global scales. Latitudinal patterns are due to its correlation with climate, geologic and evolutionary history, the strength of ecological interactions, or all of these factors combined. For this question, consider the ways in which ecological systems or processes are affected by latitude and the mechanisms underlying these patterns. Possible approaches include a comparison of how and why ecological processes differ in ecosystems at different latitudes (e.g., the differences between temperate and tropical ecosystems), or the ways in which latitude itself helps to explain patterns of diversity or ecological functioning.

Recommended courses: Ecosystem ecology, Landscape Ecology, Population Ecology, or Evolution

Suggested reading:

Ashton, G.V., A.L. Freestone, J.E. Duffy, et al. 2022. Predator control of marine communities increases with temperature across 115 degrees of latitude. Science 376: 1215-1219.

Brodie, J.F. and P.D. Mannion. 2023. The hierarchy of factors predicting the latitudinal diversity gradient. Trends in Ecology and Evolution 38: 15-23.

Du, E., C. Terrer, A.F.A. Pellegrini, A. Ahlström, C.J. van Lissa, X. Zhao, N. Xia, X. Wu, R.B. Jackson. 2020. Global patterns of terrestrial nitrogen and phosphorus limitation. Nature Geoscience 13: 221–226.

Zvereva, E.L. and M.V. Kozlov. 2021. Latitudinal gradient in the intensity of biotic interactions in terrestrial ecosystems: Sources of variation and differences from the diversity gradient revealed by meta-analysis. Ecology Letters 24:2506-2520.

2) Intrinsically disordered proteins (Sung, Fall/Winter only)

A fundamental tenet of understanding protein function is the importance of protein shape—how does the tertiary and quaternary structure of a protein facilitate its functional role in the cell? Key to this idea is that a protein must have a specific shape in order to function—bind to substrate, interact with the correct signaling molecules etc. However, intrinsically disordered proteins subvert this dogma by being proteins that, as their name suggests, do not necessarily have a fixed shape. Even more mind boggling is the fact that this lack of a fixed shape is critical for the function of these proteins! For this question, explore how the lack of shape is important for facilitating the function of intrinsically disordered proteins and consider the molecular mechanism(s) (at the cellular and organismal level) that can result from this novel functionality.

Recommended courses: Biochemistry or Cell biology

Suggested readings:

Wright, P and Dyson J. 2015. Intrinsically disordered proteins in cellular signaling and regulation. Nature Reviews: Molecular Cell Biology, 16: 19-29.

Uversky, V. 2019. Intrinsically disordered proteins and their “mysterious” (meta)physics. Frontiers in Physics, 7 (10): 1-18.

Trivedi, R and Nagarajaram, H. 2022 Intrinsically disordered proteins: a review. International Journal of Molecular Sciences, 23 (14050): 1-30.

Berlow, R, et al. 2022. Multivalency enables unidirectional switch-like competition between intrinsically disordered proteins. PNAS, 119 (3): 1-10.

3) Human evolution (McKone)

Humans have always been fascinated by our own origins.  Recent evidence from genomics (including sequencing ancient DNA) and some spectacular new fossil finds have greatly improved our understanding of human evolution since our last common ancestor with  chimpanzees.  Review some aspect of human evolution in light of these recent advances. 

Recommended courses: Evolution, Genetics, or Genomics & Bioinformatics

Suggested Reading:

Liu, Y., X. Mao, J. Krause, and Q. Fu. 2021. Insights into human history from the first decade of ancient human genomics. Science 373:1479–1484.  DOI:10.1126/science.abi8202

Mangan, R. J., F. C. Alsina, F. Mosti, J. E. Sotelo-Fonseca, D. A. Snellings, E. H. Au, J. Carvalho, et al. 2022. Adaptive sequence divergence forged new neurodevelopmental enhancers in humans. Cell 185:4587-4603.  DOI:0.1016/j.cell.2022.10.016

Stoneking, M., L. Arias, D. Liu, S. Oliveira, I. Pugach, and J. J. R. B. Rodriguez. 2023. Genomic perspectives on human dispersals during the Holocene. Proceedings of the National Academy of Sciences of the United States of America 120:e2209475119.  DOI:10.1073/pnas.2209475119

Xue, J. R., A. Mackay-smith, K. Mouri, M. F. Garcia, M. X. Dong, J. F. Akers, M. Noble, et al. 2023. The functional and evolutionary impacts of human-specific deletions in conserved elements. Science 380:eabn2253.  DOI:10.1126/science.abn2253

4) Gram-negative bacterial pathogens (Mitra)

Gram-negative bacterial pathogens affect a number of different organisms.  Human pathogens, such as Escherichia coli, Yersinia pestis and Shigella flexneri cause disease. Plant pathogens such as Xanthomonas campestris, Ralstonia solanacearum and Xylella fastidiosa result in major crop losses. Bordetella bronchiseptica causes kennel cough in dogs. Serratia marcescens kills honey bees. The list goes on.

A better understanding of the molecular mechanisms these types of pathogens employ may help in fighting off these diseases. Choose a gram-negative pathogen to study and investigate a key pathogenic strategy employed by this pathogen.  Focus on the cellular, molecular and biochemical level, and highlight open questions in this area.

Recommended courses: Cell Biology or Microbiology

Suggested Reading:

Bengoechea, J.A., and Sa Pessoa, J. (2019). Klebsiella pneumoniae infection biology: living to counteract host defences. FEMS Microbiology Reviews 43, 123–144.

Chen, K.W., and Brodsky, I.E. (2023). Yersinia interactions with regulated cell death pathways. Current Opinion in Microbiology 71, 102256.

Galán, J.E. (2021). Salmonella Typhimurium and inflammation: a pathogen-centric affair. Nat Rev Microbiol 19, 716–725.

Mondino, S., Schmidt, S., Rolando, M., Escoll, P., Gomez-Valero, L., and Buchrieser, C. (2020). Legionnaires’ Disease: State of the Art Knowledge of Pathogenesis Mechanisms of Legionella. Annual Review of Pathology: Mechanisms of Disease 15, 439–466.

Rossi, E., La Rosa, R., Bartell, J.A., Marvig, R.L., Haagensen, J.A.J., Sommer, L.M., Molin, S., and Johansen, H.K. (2021). Pseudomonas aeruginosa adaptation and evolution in patients with cystic fibrosis. Nat Rev Microbiol 19, 331–342.

Stelzner, K., Vollmuth, N., and Rudel, T. (2023). Intracellular lifestyle of Chlamydia trachomatis and host–pathogen interactions. Nat Rev Microbiol 1–15.

Timilsina, S., Potnis, N., Newberry, E.A., Liyanapathiranage, P., Iruegas-Bocardo, F., White, F.F., Goss, E.M., and Jones, J.B. (2020). Xanthomonas diversity, virulence and plant–pathogen interactions. Nat Rev Microbiol 18, 415–427.

5) Immunology or physiology of intestinal homeostasis (Rand Fall/Winter only and Walser-Kuntz Winter/Spring only) 

Intestinal homeostasis relies on the activities of the gut microbiota, intestinal epithelial cells, neuronal and endocrine signaling, and immune cells. When the gut is functioning correctly, the epithelial cells not only provide a barrier, but they communicate with the gut microbes, cells of the immune system, and the brain. In turn, T regulatory cells help prevent food allergies and both Crohns and Celiac disease. Further, disruption of the communication between these gut-associated cells may lead to weight gain, dysregulation of glucose homeostasis, or changes in feeding behavior. Depending on your course background, explore these interactions from either an immunological or a physiological perspective. 

Recommended courses: Immunology and/or Physiology

Suggested Reading:

Asadi A, Shadab Mehr N, Mohamadi MH, Shokri F, Heidary M, Sadeghifard N, Khoshnood S. (2022) Obesity and gut-microbiota-brain axis: A narrative review. J Clin Lab Anal. doi: 10.1002/jcla.24420. Epub 2022 Apr 14. PMID: 35421277; PMCID: PMC9102524.

Jacobsi, J. et. al. (2021) Intestinal Regulatory T Cells as Specialized Tissue-Restricted Immune Cells in Intestinal Immune Homeostasis and Disease. Frontiers in Immunology 12: 1-23.

Rath, E. and D. Haller. (2022) Intestinal epithelial cell metabolism at the interface of microbial dysbiosis and tissue injury. Mucosal Immunology 15: 595-604.

Rezende, R. and H. Weiner (2022) Oral tolerance: an updated review. Immunology Letters 245: 29-37.

Teratani T, et al. (2020) The liver-brain-gut neural arc maintains the Treg cell niche in the gut. Nature. 585(7826):591-596. doi: 10.1038/s41586-020-2425-3. Epub 2020 Jun 11. PMID: 32526765.

6) Biological impacts of heatwaves (Nishizaki) 

Heatwaves are extended periods of unusually high temperatures in the atmosphere or the ocean. Characterized by significantly elevated temperatures compared to the regional and seasonal averages, these events typically persist for several days to weeks. Over the past century, heatwaves have intensified and become more frequent, raising concerns about their role as pervasive stressors. Students are encouraged to investigate the mechanistic effects of extreme events on biological systems, in conjunction with longer-term environmental trends. Potential areas of study may include the comparison of marine heatwave impacts on surface versus bottom waters, the examination of daytime and nighttime warming influences on physiological processes in terrestrial environments, and the exploration of heatwave effects on predator-prey relationships.

Recommended courses: Ecological Physiology, Ecological Biomechanics, and/or Animal Physiology

Suggested Reading:

Amaya, D. J., Jacox, M. G., Alexander, M. A., Scott, J. D., Deser, C., Capotondi, A., & Phillips, A. S. (2023). Bottom marine heatwaves along the continental shelves of North America. Nature Communications, 14(1), 1038.

Harvey, B. P., Marshall, K. E., Harley, C. D., & Russell, B. D. (2022). Predicting responses to marine heatwaves using functional traits. Trends in Ecology & Evolution, 37(1), 20-29.

Perkins-Kirkpatrick, S. E., & Lewis, S. C. (2020). Increasing trends in regional heatwaves. Nature Communications, 11(1), 3357. 

Smith, K. E., Burrows, M. T., Hobday, A. J., King, N. G., Moore, P. J., Sen Gupta, A., … & Smale, D. A. (2023). Biological impacts of marine heatwaves. Annual Review of Marine Science, 15, 119-145.

7) Independent question

On the Google form, provide a one paragraph description of your proposed research topic and include references for two recent articles that would provide background on your research topic. We suggest that you contact your potential comps advisor to ask if they’d be willing to advise you for that question.