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Journal Club

Journal Club: Wednesdays at 1:00pm in Genentech Hall Auditorium

October 16, 2019

***Will meet in GH N114***

Fred Chang

“Building the cell wall: Mechanosensitive regulation of cell wall thickness"

Davi V., Minc N. et al..  Mechanosensation Dynamically Coordinates Polar Growth and Cell Wall Assembly to Promote Cell Survival. Dev Cell. 2018 Apr 23;45(2):170-182.e7. doi: 10.1016/j.devcel.2018.03.022.

Stephen Floor

“Noise in gene expression: cut it out”

Bryan Sands, Soo Yun, Alexander R. Mendenhall. Introns Control Intrinsic Noise. BioRxiv doi: https://doi.org/10.1101/746263. This article is a preprint and has not been certified by peer review.

October 23, 2019

***Will meet in GH N114***


Elphege Nora

"Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells"



Zhang Y, Ren B, et al.  Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells.  Nat Genet. 2019 Sep;51(9):1380-1388. doi: 10.1038/s41588-019-0479-7. Epub 2019 Aug 19.

Sophie Dumont

“How mammalian oocytes build a spindle without centrosomes”


So C, Schuh M, et al. A liquid-like spindle domain promotes acentrosomal spindle assembly in mammalian oocytes. Science. 2019 Jun 28;364(6447). pii: eaat9557. doi: 10.1126/science.aat9557.

October 30, 2019

***Will meet in GH N114***

Matt Nalley
Madhani Lab

“How did we get here? scATAC-seq reveals developmental trajectories of cellular differentiation.”

Satpathy AT et al. Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion. Nat Biotechnol. 2019 Aug;37(8):925-936. doi: 10.1038/s41587-019-0206-z. Epub 2019 Aug 2.

Martin Kampmann

“Care packages nurture a long-distance relationship”

Cioni JM et al. Late Endosomes Act as mRNA Translation Platforms and Sustain Mitochondria in Axons. Cell. 2019 Jan 10;176(1-2):56-72.e15. doi: 10.1016/j.cell.2018.11.030. Epub 2019 Jan 3.

November 6, 2019

***Will meet in GH N114***

Megan Chong
Dumont Lab

“Read the room! Migrating amoeboid cells sample their local environment to move along the path of least resistance”

Renkawitz J et al. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 2019 Apr;568(7753):546-550. doi: 10.1038/s41586-019-1087-5. Epub 2019 Apr 3.

Sarah Heater
Sil Lab

“Anyrin Bacteria to Sea Sponges”

Jahn MT et al. A Phage Protein Aids Bacterial Symbionts in Eukaryote Immune Evasion. Cell Host Microbe. 2019 Oct 9;26(4):542-550.e5. doi: 10.1016/j.chom.2019.08.019. Epub 2019 Sep 24.

November 13, 2019

***Will meet in GH N114***

Lorenzo Del Castillo
Reiter Lab

“Use It or Lose It! ER Hormesis in aging”

Matai L et al. Dietary restriction improves proteostasis and increases life span through endoplasmic reticulum hormesis. Proc Natl Acad Sci U S A. 2019 Aug 27;116(35):17383-17392. doi: 10.1073/pnas.1900055116. Epub 2019 Aug 14.

Jocelyne Lopez
McCormick Lab

“How getting RIDD of Blos1 protects cells from ER stress”

Bae D, Moore KA, Mella JM, Hayashi SY, Hollien J. Degradation of Blos1 mRNA by IRE1 repositions lysosomes and protects cells from stress. J Cell Biol. 2019 Apr 1;218(4):1118-1127. doi: 10.1083/jcb.201809027. Epub 2019 Feb 20.

November 20, 2019

***Will meet in GH N114***

Connie Yan
Marshall Lab

“Finishing a tail: Caudal fin injury responses in larval zebrafish”

Miskolci V et al.  Distinct inflammatory and wound healing responses to complex caudal fin injuries of larval zebrafish. Elife. 2019 Jul 1;8. pii: e45976. doi: 10.7554/eLife.45976.

Dave Toczyski

“Selfish centromere shenanigans skews segregation”

Akera T, Trimm E, Lampson MA. Molecular Strategies of Meiotic Cheating by Selfish Centromeres. Cell. 2019 Aug 22;178(5):1132-1144.e10. doi: 10.1016/j.cell.2019.07.001. Epub 2019 Aug 8.

December 4, 2019

***Will meet in GH N114***

Lili Kim
Rosenberg Lab

“Playing by the rules of piRNA targeting”

Zhang D, Tu S, Stubna M, Wu WS, Huang WC, Weng Z, Lee HC.  The piRNA targeting rules and the resistance to piRNA silencing in endogenous genes.  Science. 2018 Feb 2;359(6375):587-592. doi: 10.1126/science.aao2840. Epub 2018 Feb 1.

Max Nachury

“Tiger flatworms see the light ... with 421 cilia ... inside a phaosome”

Rawlinson KA et al. Extraocular, rod-like photoreceptors in a flatworm express xenopsin photopigment. Elife. 2019 Oct 22;8. pii: e45465. doi: 10.7554/eLife.45465.

January 15, 2020

***Will meet in GH N114***

Greg Mohl
Kampmann Lab

“Deuterosomes and Parent Centrioles: Who needs them?”

Mercey O. et al.  Massive centriole production can occur in the absence of deuterosomes in multiciliated cells. Nat Cell Biol. 2019 Dec;21(12):1544-1552. doi: 10.1038/s41556-019-0427-x. Epub 2019 Dec 2.

David Raleigh

“Pediatric Rhabdoid Tumors: Genomically boring, immunologically interesting, and (thankfully) really rare”

Leruste A. et al.  Clonally Expanded T Cells Reveal Immunogenicity of Rhabdoid Tumors. Cancer Cell. 2019 Dec 9;36(6):597-612.e8. doi: 10.1016/j.ccell.2019.10.008. Epub 2019 Nov 7.

January 22, 2020

***Will meet in GH N114***

Evelyn Hernandez
Irannejad Lab

“Gaining a new mitochondrial zip code via alternative translation initiation”

Monteuuis G et al. Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins. Nucleic Acids Res. 2019 Jun 20;47(11):5777-5791. doi: 10.1093/nar/gkz301.

Pat O'Farrell

“Assessing the impact of genetic conflict”

Luo S. et al. Biparental Inheritance of Mitochondrial DNA in Humans. Proc Natl Acad Sci U S A. 2018 Dec 18;115(51):13039-13044. doi: 10.1073/pnas.1810946115. Epub 2018 Nov 26.

January 29, 2020

***Will meet in GH N114***

Harold Marin
Buchwalter Lab

“When monocytes meet Toxo: Oh, the places you’ll go!”

Drewry LL, Jones NG, Wang Q, Onken MD, Miller MJ, Sibley LD. The secreted kinase ROP17 promotes Toxoplasma gondii dissemination by hijacking monocyte tissue migration. Nat Microbiol. 2019 Nov;4(11):1951-1963. doi: 10.1038/s41564-019-0504-8. Epub 2019 Jul 22.

Jesslyn Park
El-Samad Lab

“From parasite to programmer: how Toxoplasma reroutes inflammatory response”

He H. et al. Characterization of a Toxoplasma effector uncovers an alternative GSK3/β-catenin-regulatory pathway of inflammation. Elife. 2018 Oct 15;7. pii: e39887. doi: 10.7554/eLife.39887.

February 5, 2020

***Will meet in GH N114***

Katie Augspurger
Buchwalter/Panning Labs

“The Sixth Sense: ZNFX1 senses viral RNA in the innate immune response”

Wang Y, Yuan S, Jia X, Ge Y, Ling T, Nie M, Lan X, Chen S, Xu A. Mitochondria-localised ZNFX1 functions as a dsRNA sensor to initiate antiviral responses through MAVS. Nat Cell Biol. 2019 Nov;21(11):1346-1356. doi: 10.1038/s41556-019-0416-0. Epub 2019 Nov 4.

Todd Nystul

“Hidden signals and other cautionary tales in pseudotime analysis”

Weinreb C, Rodriguez-Fraticelli A, Camargo FD, Klein AM. Lineage tracing on transcriptional landscapes links state to fate during differentiation. Science. 2020 Jan 23. pii: eaaw3381. doi: 10.1126/science.aaw3381. [Epub ahead of print]

February 12, 2020

***Will meet in GH N114***

Hayden Saunders
Narlikar Lab

“Autophagy beyond homeostasis: evidence for a novel role in meiotic exit”

Wang F, Zhang R, Feng W, Tsuchiya D, Ballew O, Li J, Denic V, Lacefield S. Autophagy of an Amyloid-like Translational Repressor Regulates Meiotic Exit. Dev Cell. 2020 Jan 27;52(2):141-151.e5. doi: 10.1016/j.devcel.2019.12.017.

Seesha Takagishi
El-Samad Lab

““Better every loop: tubulin autoregulation by a feedback mechanism”

Lin Z, Gasic I, Chandrasekaran V, Peters N, Shao S, Mitchison TJ, Hegde RS. TTC5 mediates autoregulation of tubulin via mRNA degradation. Science. 2020 Jan 3;367(6473):100-104. doi: 10.1126/science.aaz4352. Epub 2019 Nov 14.

February 19, 2020

***Will meet in GH N114***

Wei Gordon
Ahituv Lab

“Non-muscle Myosin II, How will I develop without you?”

Kasza KE, Supriyatno S, Zallen JA. Cellular defects resulting from disease-related myosin II mutations in Drosophila. Proc Natl Acad Sci U S A. 2019 Oct 29;116(44):22205-22211. doi: 10.1073/pnas.1909227116. Epub 2019 Oct 15.

Caroline Vissers

“Coordination of the epitranscriptome and transcriptional regulation in embryonic stem cells”

Liu J et al. N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription. Science. 2020 Jan 31;367(6477):580-586. doi: 10.1126/science.aay6018. Epub 2020 Jan 16.

February 26, 2020

***Will meet in GH N114***

Tom Moss
Mukherjee Lab

“Let’s stall, K?: the basics of ribosome stalling on poly(A) tails”

Chandrasekaran V et al. Mechanism of ribosome stalling during translation of a poly(A) tail. Nat Struct Mol Biol. 2019 Dec;26(12):1132-1140. doi: 10.1038/s41594-019-0331-x. Epub 2019 Nov 25.

Haley Gause
Johnson Lab

“The Enemy of my Enemy is my Friend: Bacterial Plant Pathogen Co-Opts Host to Fight Niche Competitor”

Wu D. et al.  A Plant Pathogen Type III Effector Protein Subverts Translational Regulation to Boost Host Polyamine Levels. Cell Host Microbe. 2019 Nov 13;26(5):638-649.e5. doi: 10.1016/j.chom.2019.09.014. Epub 2019 Oct 15.

March 4, 2020

***Will meet in GH N114***

Jose Liboy
Floor Lab

“Guardians of the fragile world of translation: G3BPs rescue 40S ribosomal subunits from oblivion”

Meyer C, Garzia A, Morozov P, Molina H, Tuschl T. The G3BP1-Family-USP10 Deubiquitinase Complex Rescues Ubiquitinated 40S Subunits of Ribosomes Stalled in Translation from Lysosomal Degradation. Mol Cell. 2020 Jan 20. pii: S1097-2765(19)30954-2. doi: 10.1016/j.molcel.2019.12.024. [Epub ahead of print]

Sushil Sobti
Weinberger Lab

“A stalled engine: inhibitory codon pairs and poly(A) tracts throw a wrench in the ribosome’s gears”

Tesina P et al. Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts. EMBO J. 2020 Feb 3;39(3):e103365. doi: 10.15252/embj.2019103365. Epub 2019 Dec 20.

March 11, 2020

***Will meet in GH N114***

Fatema Saifuddin
L'Etoile Lab

“The Evolution of Sex Chromosomes”

Ellison CE, Bachtrog D. Dosage compensation via transposable element mediated rewiring of a regulatory network. Science. 2013 Nov 15;342(6160):846-50. doi: 10.1126/science.1239552.

Matthew Kim
El-Samad Lab

“Flying through time: Convergent evolution of dosage compensation”

Ellison C, Bachtrog D. Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila. PLoS Biol. 2019 Feb 11;17(2):e3000094. doi: 10.1371/journal.pbio.3000094. eCollection 2019 Feb.

March 18, 2020

***Will meet in GH N114***  ***POSTPONED***

This is the last journal club for the quarter.  Presentations for the remaining speakers have been postponed.  We strongly encourage viewing Natasha's presentation via the live feed link provided below, however, registered students (up to 25 people) and coaches can attend in person.

Natasha Puri
Irannejad Lab

“The Ultimate sacrifice: Innate Immune Cell Death”

Chen KW et al. Noncanonical inflammasome signaling elicits gasdermin D-dependent neutrophil extracellular traps. Sci Immunol. 2018 Aug 24;3(26). pii: eaar6676. doi: 10.1126/sciimmunol.aar6676.

https://bit.ly/2QaPDdQ