Journal Club

Wed
16

Journal Club

November
1:00 pm

Philipp Huettemann
Kortemme Lab

"Arts and crafts for scientists: synthetic multicellular patterning"

Kim, H., Skinner, D.J., Glass, D.S. et al. 4-bit adhesion logic enables universal multicellular interface patterning. Nature 608, 324–329 (2022). https://doi.org/10.1038/s41586-022-04944-2

Caroline Wilson
Gilbert Lab

"To Me or not to Me: Charting DNA methyltransferase activity through base editor scanning. "

Lue, N.Z., Garcia, E.M., Ngan, K.C. et al. Base editor scanning charts the DNMT3A activity landscape. Nat Chem Biol (2022). https://doi.org/10.1038/s41589-022-01167-4

Wed
09

Journal Club

November
1:00 pm

Tracy Knight
Buchwalter Lab

“The Mitosis Roundup: Microtubule disassembly triggers cell rounding in early mitosis”

Leguay, Kévin et al. “Interphase microtubule disassembly is a signaling cue that drives cell rounding at mitotic entry.” The Journal of cell biology vol. 221,6 (2022): e202109065. doi:10.1083/jcb.202109065

Gabriel Viramontes
Booth Lab

"If the food is right, we belong together: regulated life cycles cue us into the evolution of multicellularity"

Alternating selection for dispersal and multicellularity favors regulated life cycles
Julien Barrere, Piyush Nanda, Andrew W. Murray
bioRxiv 2022.10.14.512267; doi: https://doi.org/10.1101/2022.10.14.512267

Class Capture: https://lecture.ucsf.edu/ets/Channel/9cb5d8c3d8ec44b19c54915aeec32dfb5f/

Wed
02

Journal Club

November
1:00 pm

Kenya Bonitto
Ruggero Lab

“Trick or translate: Spooky Splicing in
Myc-driven oncogenesis”

Cieśla, Maciej, et al. “Oncogenic Translation Directs Spliceosome Dynamics Revealing an Integral Role for SF3A3 in Breast Cancer.” Molecular Cell, vol. 81, no. 7, Elsevier BV, Apr. 2021, pp. 1453-1468.e12. Crossref, doi:10.1016/j.molcel.2021.01.034.


Angela Phillips

“Epistatic Drift Causes Gradual Decay of Predictability in Protein Evolution”

Park, Yeonwoo, et al. “Epistatic Drift Causes Gradual Decay of Predictability in Protein Evolution.” Science, vol. 376, no. 6595, American Association for the Advancement of Science (AAAS), 20 May 2022, pp. 823–830. Crossref, doi:10.1126/science.abn6895.

Class Capture: https://lecture.ucsf.edu/ets/Channel/9cb5d8c3d8ec44b19c54915aeec32dfb5f/

 

 

Wed
26

Journal Club

October
1:00 am

Camille Derderian

Reiter Lab

 

These boots were made for destroying: Kinesins tear up microtubules as they walk

 

Budaitis, Breane G et al. “A kinesin-1 variant reveals motor-induced microtubule damage in cells.” Current biology : CB vol. 32,11 (2022): 2416-2429.e6. doi:10.1016/j.cub.2022.04.020

 
 
Wed
16

Journal Club

March
1:00 pm

CJ San Felipe
Fraser Lab

“The Real SLiM Shady? Sequence- and chemical specificity define the functional landscape of intrinsically disordered regions”


Iris Langstein-Skora, Andrea Schmid, Ryan J. Emenecker, Mary O.G. Richardson, Maximilian J. Götz, Sarah K. Payer, Philipp Korber, Alex S. Holehouse. Sequence- and chemical specificity define the functional landscape of intrinsically disordered regions. bioRxiv 2022.02.10.480018
 
Margaux Pinney
 
"Breaking the Code: tryptophan depletion results in tryptophan-to-phenylalanine substitutants"
 
Pataskar, A., Champagne, J., Nagel, R. et al. Tryptophan depletion results in tryptophan-to-phenylalanine substitutants. Nature (2022).

Wed
09

Journal Club

March
1:00 pm

Candace Chan
Ahituv Lab

“Knowing when to fold: Exploring association of G4s in promoters and transcriptional activity ”


Shen J, Varshney D, Simeone A, Zhang X, Adhikari S, Tannahill D, Balasubramanian S. Promoter G-quadruplex folding precedes transcription and is controlled by chromatin. Genome Biol. 2021 May 7;22(1):143. PMID: 33962653; PMCID: PMC8103603.
 
Andrew Yang
 
"Building a better home for the brain"
 
Martin M et al. Engineered Wnt ligands enable blood-brain barrier repair in neurological disorders. Science. 2022 Feb 18;375(6582):eabm4459. Epub 2022 Feb 18. PMID: 35175798.

Wed
02

Journal Club

March
1:00 pm

Addie Dwyer Cady
Raleigh Lab

“Employing proteomics to improve targeted brain cancer therapies”


Petralia F et al; Children’s Brain Tumor Network; Clinical Proteomic Tumor Analysis Consortium. Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer. Cell. 2020 Dec 23;183(7):1962-1985.e31. Epub 2020 Nov 25. PMID: 33242424; PMCID: PMC8143193.
 
Abby Buchwalter
 
"When stiffness is a signal: mechanical signaling from the extracellular matrix to the nuclear lamina controls Wnt signaling and cell fate"
 
Tang Y, Zhu L, Cho JS, Li XY, Weiss SJ. Matrix remodeling controls a nuclear lamin A/C-emerin network that directs Wnt-regulated stem cell fate. Dev Cell. 2022 Feb 4:S1534-5807(22)00040-5. Epub ahead of print. PMID: 35150612.

Wed
23

Journal Club

February
1:00 pm

Trase Aguigam
J. Gross/Narlikar Lab

“What’s the FUS? Paramagnetic spectroscopy reveals compaction of the RNA-binding protein FUS upon phase separation.”


Emmanouilidis L, Esteban-Hofer L, Damberger FF, de Vries T, Nguyen CKX, Ibáñez LF, Mergenthal S, Klotzsch E, Yulikov M, Jeschke G, Allain FH. NMR and EPR reveal a compaction of the RNA-binding protein FUS upon droplet formation. Nat Chem Biol. 2021 May;17(5):608-614. Epub 2021 Mar 8. PMID: 33686294.
 
Todd Nystul
 
"O, wind, if winter comes, can spring be far behind?"
 
Easwaran S, Van Ligten M, Kui M, Montell DJ. Enhanced germline stem cell longevity in Drosophila diapause. Nat Commun. 2022 Feb 7;13(1):711. PMID: 35132083.

Wed
16

Journal Club

February
1:00 pm

Alexis Villani
Bondy-Denomy Lab

“My PriON will go ON: A prion's epigenetic role in an active chromatin state”


Harvey ZH, Chakravarty AK, Futia RA, Jarosz DF. A Prion Epigenetic Switch Establishes an Active Chromatin State. Cell. 2020 Mar 5;180(5):928-940.e14. Epub 2020 Feb 27. PMID: 32109413; PMCID: PMC7195540.
 
Armando Martinez
McCormick Lab
 
"Good Cop, Bad Cop. Cop1 modulates macrophage infiltration"
 
Xiaoqing Wang et al. In Vivo CRISPR Screens Identify E3 Ligase Cop1 as a Modulator of Macrophage Infiltration and Cancer Immunotherapy Target. bioRxiv 2020.12.09.418012.

Wed
09

Journal Club

February
1:00 pm

GH N114 (indoor masking required) and Class Capture

CJ Sarabia
Irannejad Lab

“Matter Over Mind: How the cellular mechano-environment influences nuclear organization and cellular differentiation”


Seelbinder B, Ghosh S, Schneider SE, Scott AK, Berman AG, Goergen CJ, Margulies KB, Bedi KC Jr, Casas E, Swearingen AR, Brumbaugh J, Calve S, Neu CP. Nuclear deformation guides chromatin reorganization in cardiac development and disease. Nat Biomed Eng. 2021 Dec;5(12):1500-1516. Epub 2021 Dec 2. PMID: 34857921.
 

Babak Javid

“Moonlighting as the day job? Non-translation functions of the multi-synthase complex”


Cui H, Kapur M, Diedrich JK, Yates JR, Ackerman SL, Schimmel P. Regulation of ex-translational activities is the primary function of the multi-tRNA synthetase complex. Nucleic Acids Res. 2021 Apr 19;49(7):3603-3616. PMID: 33341895; PMCID: PMC8053116.

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