Papers for MD9A8 – 2023 edition

By reading

It’s a New Year and so it is time to post the papers I have selected for a module that I teach on (MD9A8, the module formerly known as MD997). Previous selections are grouped here or here.

The list serves as a snapshot of interesting papers published in the previous 12 months or so. I hope it is useful to others who are looking for lists of papers to read, for student selections or for anything else.

For this module, each student picks a paper from the list and then uses it to write a “grant application” for a research project. They also present the paper to the class and finally we do a grant panel where projects are scored!

The selection is biased towards papers that suit the students’ interdisciplinary backgrounds and their likely PhD topics. They are papers that caught my eye or were recommended to me. Thanks to the people who responded to my post about this:

I got some great recommendations. I have to check that they are suitable for the students on the course, but most of the ones people suggested made the final cut. This year I am using the same list for a second module that does a similar exercise with a different cohort of students.

Here is the almighty list of papers:

  1. Brusini, L., N. Dos Santos Pacheco, E.C. Tromer, D. Soldati-Favre, and M. Brochet. 2022.Composition and organization of kinetochores show plasticity in apicomplexan chromosome segregation. Journal of Cell Biology. 221:e202111084. doi:10.1083/jcb.202111084.
  2. Caragliano, E., S. Bonazza, G. Frascaroli, J. Tang, T.K. Soh, K. Grünewald, J.B. Bosse, and W. Brune. 2022. Human cytomegalovirus forms phase-separated compartments at viral genomes to facilitate viral replication. Cell Reports. 38:110469. doi:10.1016/j.celrep.2022.110469.
  3. Chen, P., X. Liu, C. Gu, P. Zhong, N. Song, M. Li, Z. Dai, X. Fang, Z. Liu, J. Zhang, R. Tang, S. Fan, and X. Lin. 2022. A plant-derived natural photosynthetic system for improving cell anabolism. Nature. 612:546–554. doi:10.1038/s41586-022-05499-y.
  4. Czerniak, T., and J.P. Saenz. 2022. Lipid membranes modulate the activity of RNA through sequence-dependent interactions. Proc. Natl. Acad. Sci. U.S.A. 119:e2119235119. doi:10.1073/pnas.2119235119.
  5. Fard, G.G., D. Zhang, F.L. Jiménez, and O. Peleg. 2022. Crystallography of honeycomb formation under geometric frustration. Proc. Natl. Acad. Sci. U.S.A. 119:e2205043119. doi:10.1073/pnas.2205043119.
  6. Fung, H.K., Y. Hayashi, V.T. Salo, A. Babenko, I. Zagoriy, A. Brunner, J. Ellenberg, C.W. Müller, S. Cuylen-Haering, and J. Mahamid. 2022. Genetically encoded multimeric tags for intracellular protein localisation in cryo-EM. bioRxiv. doi:10.1101/2022.12.10.519870.
  7. Gallusser, B., G. Maltese, G. Di Caprio, T.J. Vadakkan, A. Sanyal, E. Somerville, M. Sahasrabudhe, J. O’Connor, M. Weigert, and T. Kirchhausen. 2023. Deep neural network automated segmentation of cellular structures in volume electron microscopy. Journal of Cell Biology. 222:e202208005. doi:10.1083/jcb.202208005.
  8. Grigoryan, A., D. Zacharaki, A. Balhuizen, C.R. Côme, A.G. Garcia, D. Hidalgo Gil, A.-K. Frank, K. Aaltonen, A. Mañas, J. Esfandyari, P. Kjellman, E. Englund, C. Rodriguez, W. Sime, R. Massoumi, N. Kalantari, S. Prithiviraj, Y. Li, S.J. Dupard, H. Isaksson, C.D. Madsen, B.T. Porse, D. Bexell, and P.E. Bourgine. 2022. Engineering human mini-bones for the standardized modeling of healthy hematopoiesis, leukemia, and solid tumor metastasis. Sci. Transl. Med. 14:eabm6391. doi:10.1126/scitranslmed.abm6391.
  9. Klunk, J., T.P. Vilgalys, C.E. Demeure, X. Cheng, M. Shiratori, J. Madej, R. Beau, D. Elli, M.I. Patino, R. Redfern, S.N. DeWitte, J.A. Gamble, J.L. Boldsen, A. Carmichael, N. Varlik, K. Eaton, J.-C. Grenier, G.B. Golding, A. Devault, J.-M. Rouillard, V. Yotova, R. Sindeaux, C.J. Ye, M. Bikaran, A. Dumaine, J.F. Brinkworth, D. Missiakas, G.A. Rouleau, M. Steinrücken, J. Pizarro-Cerdá, H.N. Poinar, and L.B. Barreiro. 2022. Evolution of immune genes is associated with the Black Death. Nature. 611:312–319. doi:10.1038/s41586-022-05349-x.
  10. Lanna, A., B. Vaz, C. D’Ambra, S. Valvo, C. Vuotto, V. Chiurchiù, O. Devine, M. Sanchez, G. Borsellino, A.N. Akbar, M. De Bardi, D.W. Gilroy, M.L. Dustin, B. Blumer, and M. Karin. 2022. An intercellular transfer of telomeres rescues T cells from senescence and promotes long-term immunological memory. Nat Cell Biol. 24:1461–1474. doi:10.1038/s41556-022-00991-z.
  11. Louvel, V., R. Haase, O. Mercey, Marine.H. Laporte, D. Soldati-Favre, V. Hamel, and P. Guichard. 2022. Nanoscopy of organelles and tissues with iterative ultrastructure expansion microscopy (iU-ExM). bioRxiv. doi:10.1101/2022.11.14.516383.
  12. Mathieu, J., P. Michel-Hissier, V. Boucherit, and J.-R. Huynh. 2022. The deubiquitinase USP8 targets ESCRT-III to promote incomplete cell division. Science. 376:818–823. doi:10.1126/science.abg2653.
  13. Michaud, A., M. Leda, Z.T. Swider, S. Kim, J. He, J. Landino, J.R. Valley, J. Huisken, A.B. Goryachev, G. von Dassow, and W.M. Bement. 2022. A versatile cortical pattern-forming circuit based on Rho, F-actin, Ect2, and RGA-3/4. Journal of Cell Biology. 221:e202203017. doi:10.1083/jcb.202203017.
  14. Park, Y., B.P.H. Metzger, and J.W. Thornton. 2022. Epistatic drift causes gradual decay of predictability in protein evolution. Science. 376:823–830. doi:10.1126/science.abn6895.
  15. Rajasekaran, R., C.-C. Chang, E.W.Z. Weix, T.M. Galateo, and S.M. Coyle. 2022. A programmable reaction-diffusion system for spatiotemporal cell signaling circuit design. bioRxiv. doi:10.1101/2022.11.15.516470.
  16. Rodrigues-Oliveira, T., F. Wollweber, R.I. Ponce-Toledo, J. Xu, S.K.-M.R. Rittmann, A. Klingl, M. Pilhofer, and C. Schleper. 2022. Actin cytoskeleton and complex cell architecture in an Asgard archaeon. Nature. doi:10.1038/s41586-022-05550-y.
  17. Schiapparelli, L.M., P. Sharma, H.-Y. He, J. Li, S.H. Shah, D.B. McClatchy, Y. Ma, H.-H. Liu, J.L. Goldberg, J.R. Yates, and H.T. Cline. 2022. Proteomic screen reveals diverse protein transport between connected neurons in the visual system. Cell Reports. 38:110287. doi:10.1016/j.celrep.2021.110287.
  18. Sheu, S.-H., S. Upadhyayula, V. Dupuy, S. Pang, F. Deng, J. Wan, D. Walpita, H.A. Pasolli, J. Houser, S. Sanchez-Martinez, S.E. Brauchi, S. Banala, M. Freeman, C.S. Xu, T. Kirchhausen, H.F. Hess, L. Lavis, Y. Li, S. Chaumont-Dubel, and D.E. Clapham. 2022. A serotonergic axon-cilium synapse drives nuclear signaling to alter chromatin accessibility. Cell. 185:3390-3407.e18. doi:10.1016/j.cell.2022.07.026.
  19. Vázquez Torres, S., P.J.Y. Leung, I.D. Lutz, P. Venkatesh, J.L. Watson, F. Hink, H.-H. Huynh, A.H.-W. Yeh, D. Juergens, N.R. Bennett, A.N. Hoofnagle, E. Huang, M.J. MacCoss, M. Expòsit, G.R. Lee, P.M. Levine, X. Li, M. Lamb, E.N. Korkmaz, J. Nivala, L. Stewart, J.M. Rogers, and D. Baker. 2022. De novo design of high-affinity protein binders to bioactive helical peptides. bioRxiv. doi:10.1101/2022.12.10.519862.
  20. Venkataram, S., H.-Y. Kuo, E.F.Y. Hom, and S. Kryazhimskiy. 2021. Mutualism-enhancing mutations dominate early adaptation in a microbial community. bioRxiv. doi:10.1101/2021.07.07.451547.
  21. Volland, J.-M., S. Gonzalez-Rizzo, O. Gros, T. Tyml, N. Ivanova, F. Schulz, D. Goudeau, N.H. Elisabeth, N. Nath, D. Udwary, R.R. Malmstrom, C. Guidi-Rontani, S. Bolte-Kluge, K.M. Davies, M.R. Jean, J.-L. Mansot, N.J. Mouncey, E.R. Angert, T. Woyke, and S.V. Date. 2022. A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles. Science. 376:1453–1458. doi:10.1126/science.abb3634.
  22. Walpole, G.F.W., J. Pacheco, N. Chauhan, J. Clark, K.E. Anderson, Y.M. Abbas, D. Brabant-Kirwan, F. Montaño-Rendón, Z. Liu, H. Zhu, J.H. Brumell, A. Deiters, L.R. Stephens, P.T. Hawkins, G.R.V. Hammond, S. Grinstein, and G.D. Fairn. 2022. Kinase-independent synthesis of 3-phosphorylated phosphoinositides by a phosphotransferase. Nat Cell Biol. 24:708–722. doi:10.1038/s41556-022-00895-y.
  23. Winding, M., B.D. Pedigo, C.L. Barnes, H.G. Patsolic, Y. Park, T. Kazimiers, A. Fushiki, I.V. Andrade, A. Khandelwal, J. Valdes-Aleman, F. Li, N. Randel, E. Barsotti, A. Correia, R.D. Fetter, V. Hartenstein, C.E. Priebe, J.T. Vogelstein, A. Cardona, and M. Zlatic. 2022. The connectome of an insect brain. bioRxiv. doi:10.1101/2022.11.28.516756.
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