2024-25 Journal Clubs

2024-25 Schedule

 

Friday, October 25, 2024 - 12:00-1:30 - Room: S-214

Dan Wagner, PhD
"Evolution of novel developmental trains: fish with legs!" 
Allard, Corey A. H., Amy L. Herbert, Stephanie P. Krueger, Qiaoyi Liang, Brittany L. Walsh, Andrew L. Rhyne, Allex N. Gourlay, et al. 2024. “Evolution of Novel Sensory Organs in Fish with Legs.” Current Biology: CB 34 (19): 4349-4356.e7.

Companion Paper: Herbert, Amy L., Corey A. H. Allard, Matthew J. McCoy, Julia I. Wucherpfennig, Stephanie P. Krueger, Heidi I. Chen, Allex N. Gourlay, et al. 2024. “Ancient Developmental Genes Underlie Evolutionary Novelties in Walking Fish.” Current Biology: CB 34 (19): 4339-4348.e6.

Andrew Cesiulis (student)
"What makes a big brain?"
Barão, S. et al. (2024) ‘Conserved transcriptional regulation by BRN1 and BRN2 in neocortical progenitors drives mammalian neural specification and neocortical expansion’, Nature Communications, 15(1). doi:10.1038/s41467-024-52443-x.
Journal Club Coaches: Mercedes Paredes and Trent Watkins

 

Wednesday, October 30, 2024 - 5:00-7:00 - Room: MH-1407

Bivas Nag (student)
Developmental emergence of first- and higher-order thalamic neuron molecular identities
Quentin Lo Giudice, Robin J. Wagener, Philipp Abe, Laura Frangeul, Denis Jabaudon; Developmental emergence of first- and higher-order thalamic neuron molecular identities. Development 15 September 2024; 151 (18): dev202764. doi: https://doi.org/10.1242/dev.202764

Miriam Minsk
TBD
Shahriar, S., Biswas, S., Zhao, K. et al. VEGF-A-mediated venous endothelial cell proliferation results in neoangiogenesis during neuroinflammation. Nat Neurosci 27, 1904–1917 (2024). https://doi.org/10.1038/s41593-024-01746-9

 

Wednesday, November 6, 2024 - 5:00-7:00 - Room: MH-1407

Gabriel Avillion
"A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells"
Li L, Bowling S, McGeary SE, et al. A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells. Cell. 2023;186(23):5183-5199.e22. doi:10.1016/j.cell.2023.09.019
 

Brindha Rathinasabapathi
"Advancement of Stem Cell Therapy for Type I Diabetes"
Wang, S., Du, Y., Zhang, B. et al. Transplantation of chemically induced pluripotent stem-cell-derived islets under abdominal anterior rectus sheath in a type 1 diabetes patient. Cell (2024). https://doi.org/10.1016/j.cell.2024.09.004

 

Friday, November 15, 2024 - 12:00-1:30 - Room: S-214

David Booth, PhD (faculty)

"The evolution of toxic cell types"

Kitchen, Sheila A. et al. Cell, Volume 187, Issue 14, 3563 - 3584.e26

 

Francesco Dalla Ricca (student)

TBD

Iyer DP, et al. mTOR activity paces human blastocyst stage developmental progression. Cell. 2024 Sep 18:S0092-8674(24)00977-2. doi: 10.1016/j.cell.2024.08.048. Epub ahead of print. PMID: 39332412.

Journal Club Coaches: Daniel Lim, MD, PhD and Keith Mostov, MD, PhD

 

Wednesday, November 20, 2024 - 5:00-7:00 - Room: MH-1407

Feeling Chen (student)
"A NPAS4–NuA4 complex couples synaptic activity to DNA repair"
Pollina, E.A., Gilliam, D.T., Landau, A.T. et al. A NPAS4–NuA4 complex couples synaptic activity to DNA repair. Nature 614, 732–741 (2023). https://doi.org/10.1038/s41586-023-05711-7

Edward Valenzuela (student)
TBD
Marichal N, Péron S, Beltrán Arranz A, et al. Reprogramming astroglia into neurons with hallmarks of fast-spiking parvalbumin-positive interneurons by phospho-site-deficient Ascl1. Sci Adv. 2024 Oct 25;10(43):eadl5935. doi: 10.1126/sciadv.adl5935. Epub 2024 Oct 25. PMID: 39454007; PMCID: PMC11506222.

 

Friday, January 17, 2025 - 12:00-1:30 - Room: S-214

Nicole Suren (student)

"Lipid metabolism is a critical regulator of embryo longevity during diapause"

Van der Weijden, V. A., Stötzel, M., Iyer, D. P., Fauler, B., Gralinska, E., Shahraz, M., Meierhofer, D., Vingron, M., Rulands, S., Alexandrov, T., Mielke, T., & Bulut-Karslioglu, A. (2024). FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy. Nature Cell Biology 2024 26:2, 26(2), 181–193. https://doi.org/10.1038/s41556-023-01325-3

Coaches: John Vaughen, PhD and Serine Avagyan, MD, PhD

Gabriel Avillion (student)

"An injury-induced mesenchymal-epithelial cell niche coordinates regenerative responses in the lung"

Dakota L. Jones et al., An injury-induced mesenchymal-epithelial cell niche coordinates regenerative responses in the lung. Science 386, eado5561 (2024). DOI: 10.1126/science.ado5561

Coaches: Saul Villeda, PhD and Alex Pollen, PhD

Moderators: Nitya Kopparapu and Brindha Rathinasabapathi

Location: Parnassus Campus, Room S-214

 

Wednesday, January 22, 2025 - 5:00-7:00 - Room: MH-1407

Carine Joubran (student)

"EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling"

Chiara M. Schröder, Lea Zissel, Sophie-Luise Mersiowsky, Mehmet Tekman, Simone Probst, Katrin M. Schüle, Sebastian Preissl, Oliver Schilling, H. Th. Marc Timmers, Sebastian J. Arnold, EOMES establishes mesoderm and endoderm differentiation potential through SWI/SNF-mediated global enhancer remodeling, Developmental Cell, 2024,,https://doi.org/10.1016/j.devcel.2024.11.014

Mika Matera-Vatnick (student)

"From Gut to Brain: Unraveling the Microbiome and GLP-1 Agonists in Inflammation Regulation"

Wong, C. K., McLean, B. A., Baggio, L. L., Koehler, J. A., Hammoud, R., Rittig, N., Yabut, J. M., Seeley, R. J., Brown, T. J., & Drucker, D. J. (2024). Central glucagon-like peptide 1 receptor activation inhibits Toll-like receptor agonist-induced inflammation. Cell metabolism, 36(1), 130–143.e5. https://doi.org/10.1016/j.cmet.2023.11.009

 

Wednesday, February 12, 2025 - 5:00-7:00 - Room: MH-1407

Naomi Cinque

"Adipose tissue retains an epigenetic memory of obesity after weight loss"

Hinte, L.C., Castellano-Castillo, D., Ghosh, A. et al. Adipose tissue retains an epigenetic memory of obesity after weight loss. Nature 636, 457–465 (2024). https://doi.org/10.1038/s41586-024-08165-7

 

Friday, February 28, 2025 - 12:00-1:30 - Room: S-214

Nitya Kopparapu (student)

"Mechanisms of Lumen Expansion in Human Epiblast Models: The Role of Apical Actin and Osmotic Pressure"

Indana, D., Zakharov, A., Lim, Y., Dunn, A. R., Bhutani, N., Shenoy, V. B., & Chaudhuri, O. (2024). Lumen expansion is initially driven by apical actin polymerization followed by osmotic pressure in a human epiblast model. Cell Stem Cell, 31(5), 640–656.e8. https://doi.org/10.1016/j.stem.2024.03.016

Coaches: Diana Laird, PhD and Mark Pownall, PhD

Feeling Chen (student)

"CRISPR-Cas9 Screens reveal regulators of ageing in neural stem cells"

Ruetz, T.J., Pogson, A.N., Kashiwagi, C.M. et al. CRISPR–Cas9 screens reveal regulators of ageing in neural stem cells. Nature 634, 1150–1159 (2024). https://doi.org/10.1038/s41586-024-07972-2

Coaches: Alex Marson,MD, PhD and Betsy Crouch, MD, PhD

Moderators: Tayma Handal & Gabriel Avillion

 

Wednesday, March 12, 2025 - - Room: MH-1407

RIPs

 

Wednesday, March 12, 2025 - - Room: MH-1407

RIPs

 

Friday, March 14, 2025 - 12:00-1:30 - Room: S-214

Brindha Rathinasabapathi (student)

"Exploring the Role of the Immune Response in Heart Regeneration"

Goumenaki, P., Günther, S., Kikhi, K. et al. The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration. Nat Cardiovasc Res 3, 1158–1176 (2024). https://doi.org/10.1038/s44161-024-00538-5

Coaches: Michael Alexanian, PhD and Dan Wagner, PhD

Carine Joubran (student)

"Multi-chamber cardioids unravel human heart development and cardiac defects"

Clara Schmidt, et al. Multi-chamber cardioids unravel human heart development and cardiac defects, Cell, Volume 186, Issue 25, 2023, Pages 5587-5605.e27, ISSN 0092-8674, https://doi.org/10.1016/j.cell.2023.10.030.

Coaches: Julie Sneddon, PhD and Faranak Fattahi, PhD

Moderators: Andrew Cesiulis & Feeling Chen

 

Friday, April 11, 2025 - 12:00-1:30 - Room: S-214

Bivas Nag (student)

"Evolutionary convergence of sensory circuits in the pallium of amniotes"

Eneritz Rueda-Alaña et al. ,Evolutionary convergence of sensory circuits in the pallium of amniotes.Science387,eadp3411(2025).DOI:10.1126/science.adp3411

Coaches: Mercedes Paredes, MD, PhD and Alex Pollen, PhD

Tayma Handal (student)

TBD

O'Keeffe M, Booker SA, Walsh D, Li M, et al. Typical development of synaptic and neuronal properties can proceed without microglia in the cortex and thalamus. Nat Neurosci. 2025 Feb;28(2):268-279. doi: 10.1038/s41593-024-01833-x. Epub 2025 Jan 6. PMID: 39762658; PMCID: PMC11802452.

Coaches: Elizabeth Crouch, MD, PhD and Michael Oldham, PhD

Moderators: Naomi Cinque & Mika Matera-Vatnick

 

Wednesday, April 23, 2025 - - Room: MH-1407

RIPs

David Wen (student)

"Deep Transfer Learning to Identify Mechanisms of Context Specificity"

Reed McMullen (student)

TBD

 

 

Wednesday, May 7, 2025 - - Room: MH-1407

RIPs

Sneha Rao (student) and Elysse Phillips (student) 

"Choose your own adventure: Embryo edition"

 

Friday, May 9, 2025 - 12:00-1:30 - Room: S-214

Edward Valenzuela (student)

TDB

Chadarevian, J.P., Davtyan, H., Chadarevian, A.L., Nguyen, J., Capocchi, J.K., Le, L., Escobar, A., Chadarevian, T., Mansour, K., Deynega, E., et al. (2025). Harnessing human iPSC-microglia for CNS-wide delivery of disease-modifying proteins. Cell Stem Cell. 10.1016/j.stem.2025.03.009

Coaches: Cathryn Cadwell, MD, PhD and Kyle Cromer, PhD

Naomi Cinque (student)

"Glycocalyx dysregulation impairs blood–brain barrier in ageing and disease"

Shi, S.M., Suh, R.J., Shon, D.J. et al. Glycocalyx dysregulation impairs blood–brain barrier in ageing and disease. Nature 639, 985–994 (2025). https://doi.org/10.1038/s41586-025-08589-9

Coaches: Andrew Yang, PhD and Saul Villeda, PhD

Moderators: Carine Joubran & Miriam Minsk

 

Friday, May 30, 2025 - 12:00-1:30 - Room: S-214

Mika Matera-Vatnick (student)

“Gut Feeling: How Microbes Help Keep Colorectal Cancer in Check”

Zhang, S., Peng, L., Goswami, S., Li, Y., Dang, H., Xing, S., Feng, P., Nigro, G., Liu, Y., Ma, Y., Liu, T., Yang, J., Jiang, T., Yang, Y., Barker, N., Sansonetti, P., & Kundu, P. (2025). Intestinal crypt microbiota modulates intestinal stem cell turnover and tumorigenesis via indole acetic acid. Nature microbiology, 10(3), 765–783. https://doi.org/10.1038/s41564-025-01937-5

Coaches: Peter Turnbaugh, PhD and Jeroen Roose, PhD

Miriam Minsk (student)

"Brain pericytes and perivascular fibroblasts are stromal progenitors with dual functions in cerebrovascular regeneration after stroke"

Bernier, L.P., Hefendehl, J.K., Scott, R.W. et al. Brain pericytes and perivascular fibroblasts are stromal progenitors with dual functions in cerebrovascular regeneration after stroke. Nat Neurosci 28, 517–535 (2025). https://doi.org/10.1038/s41593-025-01872-y

Coaches: Elizabeth Crouch, MD, PhD and Fernando Gonzalez, MD

Moderators: Edward Valenzuela & Bivas Nag