Scientia

Scientia is The Triple Helix’s primary student research publication. Scientia is a space for UChicago’s undergraduate scholars to contribute to the dynamic and ever-expanding field of science. Each issue of our journal is an affirmation of our commitment to fostering scholarly inquiry and intellectual growth among undergraduates.

Here you can find Scientia’s most recent issue.

THE POTENTIAL USE OF THE HYDRA VULGARIS TOXIN HYDRAMACIN-1 AS AN ANTIBIOTIC AGENT AGAINST THE CORAL BACTERIUM VIBRIO CORALLILYTICUS by Jessie Palmer

1. De’ath, G., Fabricius, K. E., Sweatman, H., & Puotinen, M. The 27–year decline of coral cover on the Great Barrier Reef and its causes, Proc. Natl. Acad. Sci. U.S.A. 109 (44) 17995-17999, https://doi.org/10.1073/pnas.1208909109 (2012).

2. Efrony, R., Loya, Y., Bacharach, E., & Rosenberg, E. (2006). Phage therapy of coral disease. Coral Reefs, 26(1), 7–13. https://doi.org/10.1007/s00338-006-0170-1.

3. Sussman, M., Willis, B. L., Victor, S., & Bourne, D. G. (2008). Coral pathogens identified for white syndrome (WS) epizootics in the Indo-Pacific. PLoS ONE, 3(6). https://doi.org/10.1371/journal.pone.0002393.

4. Ushijima, B., Meyer, J. L., Thompson, S., Pitts, K., Marusich, M. F., Tittl, J., Weatherup, E., Reu, J., Wetzell, R., Aeby, G. S., Häse, C. C., & Paul, V. J. (2020). Disease diagnostics and potential coinfections by Vibrio coralliilyticus during an ongoing coral disease outbreak in Florida. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.569354.

5. Gibbin, E., Gavish, A., Krueger, T., Kramarsky-Winter, E., Shapiro, O., Guiet, R., Jensen, L., Vardi, A., & Meibom, A. (2018). Vibrio coralliilyticus infection triggers a behavioural response and perturbs nutritional exchange and tissue integrity in a symbiotic coral. The ISME Journal, 13(4), 989–1003. https://doi.org/10.1038/s41396-018-0327-2.

6. Tout, J., Siboni, N., Messer, L. F., Garren, M., Stocker, R., Webster, N. S., Ralph, P. J., & Seymour, J. R. (2015). Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the Coral Pocillopora damicornis. Frontiers in Microbiology, 6. https://doi.org/10.3389/fmicb.2015.00432.

7. Cohen, Y., Joseph Pollock, F., Rosenberg, E., & Bourne, D. G. (2012). Phage therapy treatment of the coral pathogen Vibrio coralliilyticus. MicrobiologyOpen, 2(1), 64–74. https://doi.org/10.1002/mbo3.52.

8. Shilling, E. N., Combs, I. R., & Voss, J. D. (2021). Assessing the effectiveness of two intervention methods for stony coral tissue loss disease on Montastraea cavernosa. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-86926-4.

9. Messyasz, A., Rosales, S. M., Mueller, R. S., Sawyer, T., Correa, A. M., Thurber, A. R., & Vega Thurber, R. (2020). Coral bleaching phenotypes associated with differential abundances of nucleocytoplasmic large DNA viruses. Frontiers in Marine Science, 7. https://doi.org/10.3389/fmars.2020.555474.

10. Mariottini, G., & Grice, I. (2016). Antimicrobials from cnidarians. A new perspective for Anti-Infective Therapy? Marine Drugs, 14(3), 48. https://doi.org/10.3390/md14030048.

11. Jung, S., Sönnichsen, F. D., Hung, C.-W., Tholey, A., Boidin-Wichlacz, C., Haeusgen, W., Gelhaus, C., Desel, C., Podschun, R., Waetzig, V., Tasiemski, A., Leippe, M., & Grötzinger, J. (2012). Macin family of antimicrobial proteins combines antimicrobial and nerve repair activities. Journal of Biological Chemistry, 287(17), 14246–14258. https://doi.org/10.1074/jbc.m111.336495.

12. Jung, S., Dingley, A. J., Augustin, R., Anton-Erxleben, F., Stanisak, M., Gelhaus, C., Gutsmann, T., Hammer, M. U., Podschun, R., Bonvin, A. M. J. J., Leippe, M., Bosch, T. C. G., & Grötzinger, J. (2009). Hydramacin-1, structure and antibacterial activity of a protein from the basal metazoan hydra. Journal of Biological Chemistry, 284(3), 1896–1905. https://doi.org/10.1074/jbc.m804713200.

13. Michalek, M., Vincent, B., Podschun, R., Grötzinger, J., Bechinger, B., & Jung, S. (2013). Hydramacin-1 in action: Scrutinizing the Barnacle Model. Antimicrobial Agents and Chemotherapy, 57(7), 2955–2966. https://doi.org/10.1128/aac.02498-12.

14. Xue, R., Han, Y., Li, F., Chen, L., Yang, D., & Zhao, J. (2021). Identification, antibacterial activities and action mode of two macins from Manila Clam Venerupis Philippinarum. Fish & Shellfish Immunology, 118, 411–420. https://doi.org/10.1016/j.fsi.2021.09.031.

15. Altincicek, B., & Vilcinskas, A. (2008). Comparative analysis of septic injury-inducible genes in phylogenetically distant model organisms of regeneration and stem cell research, the Planarian Schmidtea Mediterranea and the cnidarian Hydra vulgaris. Frontiers in Zoology, 5(1), 6. https://doi.org/10.1186/1742-9994-5-6.

16. Aichelman, H. E., Zimmerman, R. C., & Barshis, D. J. (2019). Adaptive signatures in thermal performance of the temperate coral Astrangia poculata. Journal of Experimental Biology, 222(5). https://doi.org/10.1242/jeb.189225.

17. American Type Culture Collection. (n.d.). Vibrio coralliilyticus Ben-Haim et al. – baa-450 | ATCC. ATCC. https://www.atcc.org/products/baa-450.

18. Awkerman, N. (2021). Vibrio coralliilyticus RE22 Type VI Secretion Systems Contribute to Temperate Coral Lysis and Endosymbiont Death (thesis). https://doi.org/10.23860/thesis-awkerman-nathaniel-2021.

19. Ben-Haim, Y., Thompson, F. L., Thompson, C. C., Cnockaert, M. C., Hoste, B., Swings, J., & Rosenberg, E. (2003). Vibrio coralliilyticus sp. nov., a temperature-dependent pathogen of the Coral Pocillopora damicornis. International Journal of Systematic and Evolutionary Microbiology, 53(1), 309–315. https://doi.org/10.1099/ijs.0.02402-0.

20. Christensen, D. G., & Visick, K. L. (2020). Vibrio fischeri: Laboratory cultivation, storage, and common phenotypic assays. Current Protocols in Microbiology, 57(1). https://doi.org/10.1002/cpmc.103.

21. Cleves, P. A., Strader, M. E., Bay, L. K., Pringle, J. R., & Matz, M. V. (2018). CRISPR/Cas9-mediated genome editing in a reef-building coral. Proceedings of the National Academy of Sciences, 115(20), 5235–5240. https://doi.org/10.1073/pnas.1722151115.

22. Dimond, J. L., Kerwin, A. H., Rotjan, R., Sharp, K., Stewart, F. J., & Thornhill, D. J. (2012). A simple temperature-based model predicts the upper latitudinal limit of the temperate coral Astrangia poculata. Coral Reefs, 32(2), 401–409. https://doi.org/10.1007/s00338-012-0983-z.

23. Dimond, J., & Carrington, E. (2007). Temporal variation in the symbiosis and growth of the temperate scleractinian coral Astrangia Poculata. Marine Ecology Progress Series, 348, 161–172. https://doi.org/10.3354/meps07050.

24. Leslie, J., & Rodgers, K. (2024, April 15). NOAA confirms 4th Global Coral Bleaching Event. National Oceanic and Atmospheric Administration. https://www.noaa.gov/news-release/noaa-confirms-4th-global-coral-bleaching-event#:~:text=The%20world%20is%20currently%20experiencing%20a%20global,Watch%20(CRW)%2C%20has%20been%20%E2%80%94%20and%20continues.

25. Levin, R. A., Voolstra, C. R., Agrawal, S., Steinberg, P. D., Suggett, D. J., & van Oppen, M. J. (2017). Engineering strategies to decode and enhance the genomes of coral symbionts. Frontiers in Microbiology, 8. https://doi.org/10.3389/fmicb.2017.01220.

26. Li, R., Dang, H., Huang, Y., Quan, Z., Jiang, H., Zhang, W., & Ding, J. (2020). Vibrio coralliilyticus as an agent of red spotting disease in the sea urchin Strongylocentrotus intermedius. Aquaculture Reports, 16, 100244. https://doi.org/10.1016/j.aqrep.2019.100244.

27. Peters, E., Caims, S. D., Pilson, M., Wells, J. W., Jaap, W. C., & Lang, J. (1988). Nomenclature and biology of Astrangia poculata (= A. danae, = A. astreiformis) (Cnidaria: Anthozoa). Proceedings of the Biological Society of Washington, 101. http://hdl.handle.net/10088/7383.

28. Schröder, K., & Bosch, T. C. (2016). The origin of mucosal immunity: Lessons from the holobiont Hydra. mBio, 7(6). https://doi.org/10.1128/mbio.01184-16.

29. Sharp, K. H., Pratte, Z. A., Kerwin, A. H., Rotjan, R. D., & Stewart, F. J. (2017). Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata. Microbiome, 5(1). https://doi.org/10.1186/s40168-017-0329-8.

30. Sheffey, H. L. (2023). Do Microplastics, Vibrio Bacteria, and Warming Water Temperatures Cause Disease in the Northern Star Coral, Astrangia poculata? (thesis). https://doi.org/10.1016/j.marpolbul.2025.118066.

31. Ushijima, B., Videau, P., Burger, A. H., Shore-Maggio, A., Runyon, C. M., Sudek, M., Aeby, G. S., & Callahan, S. M. (2014). Vibrio coralliilyticus strain OCN008 is an etiological agent of Acute Montipora White syndrome. Applied and Environmental Microbiology, 80(7), 2102–2109. https://doi.org/10.1128/aem.03463-13.

32. Vidal-Dupiol, J., Dheilly, N. M., Rondon, R., Grunau, C., Cosseau, C., Smith, K. M., Freitag, M., Adjeroud, M., & Mitta, G. (2014). Thermal stress triggers broad Pocillopora damicornis transcriptomic remodeling, while Vibrio coralliilyticus infection induces a more targeted immuno-suppression response. PLoS ONE, 9(9). https://doi.org/10.1371/journal.pone.0107672.

33. Weinnig, A. M., Gómez, C. E., Hallaj, A., & Cordes, E. E. (2020). Cold-water coral (Lophelia pertusa) response to multiple stressors: High temperature affects recovery from short-term pollution exposure. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-58556-9.

MACRO ADVANCEMENTS ON THE MICRO SCALE: HOW QUANTUM SENSING IS RESHAPING BIOMEDICAL RESEARCH by Naomi Geffer

1. U.S. Department of Energy. DOE Explains… Quantum Mechanics. U.S. Department of Energy. https://www.energy.gov/science/doe-explainsquantum-mechanics.

2. Yu, C.-J., et al. A Molecular Approach to Quantum Sensing. ACS Central Science, 7(5), 712-723. https://pmc.ncbi.nlm.nih.gov/articles/PMC8161477/ (2021)

3. IonQ Staff. Quantum Computing 101: Introduction, Evaluation, and Applications. IonQ. https://ionq.com/resources/quantum-computing-101-introduction-evaluation-applications (2025, January 8)

4. Aliro. What is quantum entanglement? Aliro. https://www.aliroquantum.com/blog/what-is-quantum-entanglement.

5. MacCormick, H. A. Quantum measurements induce new phases of entanglement. Stanford School of Humanities and Sciences. https://humsci.stanford.edu/feature/quantum-measurements-induce-new-phases-entanglement#:~:text=Moreover%2C%20this%20collapse%20affects%20not,in%20superposition%2C%20which%20is%20a (2023, October 20).

6. Kraft, A., et al. Superconducting Quantum Interference Device (SQUID). https://phas.ubc.ca/~berciu/TEACHING/PHYS502/PROJECTS/17SQUID.pdf (2017).

7. Aslam, N., et al. Quantum sensors for biomedical applications. Nature Review Physics, 5, 157-169. https://www.nature.com/articles/s42254-023-00558-3 (2023)

8. Valich, L. New method to control electron spin paves the way for efficient quantum computers. The University of Rochester News Center. https://www.rochester.edu/newscenter/electron-spin-valley-coupling-quantum-computers-548282/ (2023, January 27)

9. Awschalom Group. The Nitrogen-Vacancy Center in Diamond. The University of Chicago Pritzker School of Molecular Engineering. https://pme.uchicago.edu/awschalom-group/nitrogen-vacancy-center-diamond.

10. Fred, A. L., et al. A Brief Introduction to Magnetoencephalography (MEG) and Its Clinical Applications. Brain Sciences, 12(6). https://doi.org/10.3390/brainsci12060788 (2022).

11. Tierney, T. M., et al. Optically pumped magnetometers: From quantum origins to multi-channel magnetoencephalography. NeuroImage, Optically pumped magnetometers: From quantum origins to multi-channel magnetoencephalography, 598-608. https://doi.org/10.1016/j.neuroimage.2019.05.063 (2019)

ALZHEIMER'S AND TYPE 3 DIABETES: IS COGNITIVE DECLINE A METABOLIC DISORDER IN DISGUISE? by Urja Vohra

[1] National Institute on Aging. What Happens to the Brain in Alzheimer’s Disease? National Institute on Aging.
https://www.nia.nih.gov/health/alzheimers-causes-and-risk-factors/what-happens-brain-alzheimers-disease.

[2] De Widt, L. Researchers link Alzheimer’s gene to Type 3 diabetes. https://newsnetwork.mayoclinic.org/discussion/researchers-link-alzheimers-gene-to-type-iii-diabetes/.

[3] Mullin, Melissa. “Diabetes of the Brain: Are You at Risk?” Mind Body Harmony Medicine, October 18, 2023.
https://thehealthymelissa.com/diabetes-of-the-brain-are-you-at-risk/?v=34f435c6b599.

[4] Alzheimer’s Disease International. Dementia Statistics. Alzheimer’s Disease International. https://www.alz
int.org/about/dementia-facts-figures/dementia-statistics/.

[5] Shaheen E Lakhan, MD. “Alzheimer Disease Workup.” Approach Considerations, Blood Studies, Brain MRI
or CT Scanning, August 2, 2024. https://emedicine.medscape.com/article/1134817-workup?form=.

[6] Mattson, M. Pathways towards and away from Alzheimer’s disease. Nature 430, 631–639 (2004). https://doi.org/10.1038/nature02621.

[7] De Widt, Lynda. 2017. “Researchers Link Alzheimer’s Gene to Type 3 Diabetes.” Https://Newsnetwork.
mayoclinic.org. October 25, 2017. https://newsnetwork.mayoclinic.org/discussion/researchers-link-alzhei
mers-gene-to-type-iii-diabetes/.

[8] Zhao, N.; Liu, C.-C.; Van Ingelgom, A. J.; Martens, Y. A.; Linares, C.; Knight, J. A.; Painter, M. M.; Sullivan,
P. M.; Bu, G. Apolipoprotein E4 Impairs Neuronal Insulin Signaling by Trapping Insulin Receptor in the Endo
somes. Neuron 2017, 96 (1), 115-129.e5. https://doi.org/10.1016/j.neuron.2017.09.003.

[9] “OpeniNgWeb.” U.S. National Library of Medicine. Accessed November 13, 2024. https://openi.nlm.nih.gov/
detailedresult?img=PMC4586536_nutrients-07-05341-g001&req=4.

[10] Farris W;Mansourian S;Chang Y;Lindsley L;Eckman EA;Frosch MP;Eckman CB;Tanzi RE;Selkoe DJ;Guen
ette S; “Insulin-Degrading Enzyme Regulates the Levels of Insulin, Amyloid Beta-Protein, and the Beta-Amyloid
Precursor Protein Intracellular Domain in Vivo.” Proceedings of the National Academy of Sciences of the United
States of America. Accessed November 14, 2024. https://pubmed.ncbi.nlm.nih.gov/12634421/.

[11] Zhang, Ge, Taiyuan Liu, Wei Wei, Rui Zhang, Huilin Wang, and Meiyun Wang. “Evaluation of Altered Brain
Activity in Type 2 Diabetes Using Various Indices of Brain Function: A Resting-State Functional Magnetic Res
onance Imaging Study.” Frontiers, December 5, 2022. https://www.frontiersin.org/journals/human-neuroscience/articles/10.3389/fnhum.2022.1032264/full.

[12] Barbagallo, Mario, and Ligia J Dominguez. “Type 2 Diabetes Mellitus and Alzheimer’s Disease.” World
journal of diabetes, December 15, 2014. https://pmc.ncbi.nlm.nih.gov/articles/PMC4265876/.

[13] TP, Crowe, Kellar D, Vandal M, Freiherr J, Lourenco MV, Schilling TM, Novak P, et al. “Nasal Insulin.”
ALZFORUM. Accessed November 14, 2024. https://www.alzforum.org/therapeutics/nasal-insulin.

[14] Kullmann, Stephanie, Julia Hummel, Robert Wagner, Corinna Dannecker, Andreas Vosseler, Louise Fritsche,
Ralf Veit, et al. “Empagliflozin Improves Insulin Sensitivity of the Hypothalamus in Humans with Prediabetes: A
Randomized, Double-Blind, Placebo-Controlled, Phase 2 Trial.” Diabetes care, February 1, 2022. https://doi.org/10.2337/dc21-1136.