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Journal Club

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

September 26, 2018

***Will meet in GH N114***

Joy Li
von Zastrow Lab

“Goldilocks and the introns: H2A.Z helps optimize kinetic coordination of cotranscriptional splicing”

Neves LT, Douglass S, Spreafico R, Venkataramanan S, Kress TL, Johnson TL. The histone variant H2A.Z promotes efficient cotranscriptional splicing in S. cerevisiae. Genes Dev. 2017 Apr 1;31(7):702-717. doi: 10.1101/gad.295188.116.

Max Nachury

“Microtubule dynamics: no longer just at the ends”

Vemu A, Szczesna E, Zehr EA, Spector JO, Grigorieff N, Deaconescu AM, Roll-Mecak A. Severing enzymes amplify microtubule arrays through lattice GTP-tubulin incorporation. Science. 2018 Aug 24;361(6404). pii: eaau1504. doi: 10.1126/science.aau1504.

October 3, 2018

***Will meet in GH N114***



Clara Herrera
Engel Lab



"Poxviruses deregulate mTOR activity to evade host cytoplasmic sensors"

Meade N, Furey C, Li H,

Verma R, Chai Q, Rollins MG, DiGiuseppe S, Naghavi MH, Walsh D. Poxviruses Evade Cytosolic Sensing through Disruption of an mTORC1-mTORC2 Regulatory Circuit. Cell. 2018 Aug 23;174(5):1143-1157.e17. doi: 10.1016/j.cell.2018.06.053. Epub 2018 Aug 2.


Amanda Chung
Gilbert/Panning Labs


“HEY! LOOK! LISTEN! An environment-to-epigenome Link between diabetes and cancer via AMPK and TET2”


Wu D. et al. Glucose-regulated phosphorylation of TET2 by AMPK reveals a pathway linking diabetes to cancer. Nature. 2018 Jul;559(7715):637-641. doi: 10.1038/s41586-018-0350-5. Epub 2018 Jul 18.


October 10, 2018

***Will meet in GH N114***

Varun Bhadkamkar
Mukherjee Lab

"Mechanistic Insights into SARM1 activity during Wallerian Degeneration"

Gerdts J, Brace EJ, Sasaki Y, DiAntonio A, Milbrandt J. SARM1 activation triggers axon degeneration locally via NAD destruction. Science. 2015 Apr 24;348(6233):453-7. doi: 10.1126/science.1258366. Epub 2015 Apr 23.

Leor Weinberger

“A Luria-Delbruck encore”

Sydney M Shaffer, Benjamin L Emert, Ann E. Sizemore, Rohit Gupte, Eduardo Torre, Danielle S Bassett, Arjun Raj. Memory sequencing reveals heritable single cell gene expression programs associated with distinct cellular behaviors. BioRxiv doi: https://doi.org/10.1101/379016 [This article is a preprint and has not been peer-reviewed]

October 17, 2018

***Will meet in GH N114***



Lana Harshman
Ahituv Lab



"Determining the mechanism of Hsp70-substrate binding"

Sekhar A, Velyvis A, Zoltsman G, Rosenzweig R, Bouvignies G, Kay LE. Conserved conformational selection mechanism of Hsp70 chaperone-substrate interactions. Elife. 2018 Feb 20;7. pii: e32764. doi: 10.7554/eLife.32764.

Chris Carlson
Morgan Lab

“A single NaK channel conformation is not enough for non-selective ion conduction”


Shi C, He Y, Hendriks K, de Groot BL, Cai X, Tian C, Lange A, Sun H. A single NaK channel conformation is not enough for non-selective ion conduction. Nat Commun. 2018 Feb 19;9(1):717. doi: 10.1038/s41467-018-03179-y.

October 24, 2018

***Will meet in GH N114***


Robbie Diaz
Fraser Lab



“small RNAs, great responsibilities — small RNAs in mouse sperm are essential for embryonic development”

Conine CC, Sun F, Song L, Rivera-Pérez JA, Rando OJ. Small RNAs Gained during Epididymal Transit of Sperm Are Essential for Embryonic Development in Mice. Dev Cell. 2018 Aug 20;46(4):470-480.e3. doi: 10.1016/j.devcel.2018.06.024. Epub 2018 Jul 26.

David Raleigh

“Patch(ing) together the structure and function of the Hedgehog pathway”

Gong X, Qian H, Cao P, Zhao X, Zhou Q, Lei J, Yan N. Structural basis for the recognition of Sonic Hedgehog by human Patched1. Science. 2018 Aug 10;361(6402). pii: eaas8935. doi: 10.1126/science.aas8935. Epub 2018 Jun 28.

October 31, 2018

***Will meet in GH N114***


Natalie Whitis
Rosenberg Lab



“Using super-resolution microscopy to determine the architecture of the mammalian centriole distal appendages”

Yang TT et al. Super-resolution architecture of mammalian centriole distal appendages reveals distinct blade and matrix functional components. Nat Commun. 2018 May 22;9(1):2023. doi: 10.1038/s41467-018-04469-1.

Sophie Dumont

“Chromosome segregation fidelity: The tissue context matters”

Knouse KA, Lopez KE, Bachofner M, Amon A. Chromosome Segregation Fidelity in Epithelia Requires Tissue Architecture. Cell. 2018 Sep 20;175(1):200-211.e13. doi: 10.1016/j.cell.2018.07.042. Epub 2018 Aug 23.

November 7, 2018

***Will meet in GH N114***


Francesca Del Frate
Johnson Lab



“Putting a selfish spindle on the spindle: Asymmetry in the meiotic spindle and how it is exploited by selfish gene elements”

Akera T, Chmátal L, Trimm E, Yang K, Aonbangkhen C, Chenoweth DM, Janke C, Schultz RM, Lampson MA. Spindle asymmetry drives non-Mendelian chromosome segregation. Science. 2017 Nov 3;358(6363):668-672. doi: 10.1126/science.aan0092.

Ben Herken
Gilbert Lab

“Cohesin squeeze in of ssDNA is the reason for the freeze in releasin’”

Murayama Y, Samora CP, Kurokawa Y, Iwasaki H, Uhlmann F. Establishment of DNA-DNA Interactions by the Cohesin Ring. Cell. 2018 Jan 25;172(3):465-477.e15. doi: 10.1016/j.cell.2017.12.021. Epub 2018 Jan 18.

November 14, 2018

***Will meet in GH N114***


Reuben Saunders
Weismann Lab



“The first rule of Tetrad is: You do not talk about Epigenetics. The second rule of Tetrad is: You do not talk about Epigenetics.”

Yu R, Wang X, Moazed D. Epigenetic inheritance mediated by coupling of RNAi and histone H3K9 methylation. Nature. 2018 Jun;558(7711):615-619. doi: 10.1038/s41586-018-0239-3. Epub 2018 Jun 20.

Joe Bondy-Denomy

“It takes a village to raise a child”

Watarai A, Arai N, Miyawaki S, Okano H, Miura K, Mogi K, Kikusui T. Responses to pup vocalizations in subordinate naked mole-rats are induced by estradiol ingested through coprophagy of queen's feces. Proc Natl Acad Sci U S A. 2018 Sep 11;115(37):9264-9269. doi: 10.1073/pnas.1720530115. Epub 2018 Aug 27.

November 28, 2018

***Will meet in GH N114***


Gabi Canales
Reiter Lab



“Choo Choo! How intraflagellar transport trains avoid a tug of war in the cilium”

Jordan MA, Diener DR, Stepanek L, Pigino G. The cryo-EM structure of intraflagellar transport trains reveals how dynein is inactivated to ensure unidirectional anterograde movement in cilia. Nat Cell Biol. 2018 Nov;20(11):1250-1255. doi: 10.1038/s41556-018-0213-1. Epub 2018 Oct 15.

Henry Ng
Al-Sady Lab

“Cell division is more twisted than it seems”

Novak M, Polak B, Simunić J, Boban Z, Kuzmić B, Thomae AW, Tolić IM, Pavin N. The mitotic spindle is chiral due to torques within microtubule bundles. Nat Commun. 2018 Sep 3;9(1):3571. doi: 10.1038/s41467-018-06005-7.

December 5, 2018

***Will meet in GH N114***


Janine Sengstack
Hao Li Lab



“Amyloid Beta, Good vs Evil: Protect Against Herpes Infections, But Seed Alzheimer's Plaques”

Eimer WA et al. Alzheimer's Disease-Associated β-Amyloid Is Rapidly Seeded by Herpesviridae to Protect against Brain Infection. Neuron. 2018 Jul 11;99(1):56-63.e3. doi: 10.1016/j.neuron.2018.06.030.

Todd Nystul

“How your centromeres try to win at all cost”

Takashi Akera, Emily Trimm, Michael Lampson. Molecular and evolutionary strategies of meiotic cheating by selfish centromeres. bioRxiv 405068; doi: https://doi.org/10.1101/405068 [This article is a preprint and has not been peer-reviewed]

January 16, 2019

***Will meet in GH N114***

Eric Simental
Al-Sady/Panning Labs

“Wild Hydra Actin or Hydra Actin Wild? You Decide”

Livshits A, Shani-Zerbib L, Maroudas-Sacks Y, Braun E, Keren K. Structural Inheritance of the Actin Cytoskeletal Organization Determines the Body Axis in Regenerating Hydra. Cell Rep. 2017 Feb 7;18(6):1410-1421. doi: 10.1016/j.celrep.2017.01.036.

Isha Jain

“Contracting Spleens and Evolutionary Adaptations to Deep Diving”

Ilardo MA et al.  Physiological and Genetic Adaptations to Diving in Sea Nomads. Cell. 2018 Apr 19;173(3):569-580.e15. doi: 10.1016/j.cell.2018.03.054.

January 23, 2019

***Will meet in GH N114***

Michael Schoof
Walter Lab

“Leeman's Lovely Lysosomes: The Role of Lysosomes in Aggregate Clearance and Neural Stem Cell Activation”

Leeman DS et al. Lysosome activation clears aggregates and enhances quiescent neural stem cell activation during aging. Science. 2018 Mar 16;359(6381):1277-1283. doi: 10.1126/science.aag3048. Epub 2018 Mar 15.

Jeremy Willsey

“Perturb-ATAC: Multiplexed CRISPRi and Single Cell ATAC-Seq”

Rubin AJ et al. Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks. Cell. 2019 Jan 10;176(1-2):361-376.e17. doi: 10.1016/j.cell.2018.11.022. Epub 2018 Dec 20.

January 30, 2019

***Will meet in GH N114***

Ady Steinbach
Mukherjee Lab

“AAAAAG, There's a G in My Tail! Poly(A) Tail Guanylation Stalls mRNA Deadenylation”

Lim J et al. Mixed tailing by TENT4A and TENT4B shields mRNA from rapid deadenylation. Science. 2018 Aug 17;361(6403):701-704. doi: 10.1126/science.aam5794. Epub 2018 Jul 19.

Bassem Al-Sady

“No strand left behind? Adventures in the (a)symmetry of inheritance"

Petryk N, Dalby M, Wenger A, Stromme CB, Strandsby A, Andersson R, Groth A. MCM2 promotes symmetric inheritance of modified histones during DNA replication. Science. 2018 Sep 28;361(6409):1389-1392. doi: 10.1126/science.aau0294. Epub 2018 Aug 16.

February 6, 2019

***Will meet in GH N114***

Victor Lam
John Gross Lab

“ac4Counting for mRNA modifications: Cytidine acetylation promotes RNA stability and protein expression”

Arango D et al.  Acetylation of Cytidine in mRNA Promotes Translation Efficiency. Cell. 2018 Dec 13;175(7):1872-1886.e24. doi: 10.1016/j.cell.2018.10.030. Epub 2018 Nov 15.

Fred Chang

“To branch or not to branch: a new way to make Y-shaped microtubules"

Basnet N et al.  Direct induction of microtubule branching by microtubule nucleation factor SSNA1. Nat Cell Biol. 2018 Oct;20(10):1172-1180. doi: 10.1038/s41556-018-0199-8. Epub 2018 Sep 24.

February 12, 2019

Uises Diaz
Marshall Lab

“TBA”

TBA

Danny Conrad
Gartner Lab

“TBA”

TBA

February 13, 2019

***Will meet in GH N114***

Claire Lorenzo
McCormick Lab

“A kinesin-5, Cin8 on the Kinetochore…what’s it doing there?”

Suzuki A, Gupta A, Long SK, Evans R, Badger BL, Salmon ED, Biggins S, Bloom K. A Kinesin-5, Cin8, Recruits Protein Phosphatase 1 to Kinetochores and Regulates Chromosome Segregation. Curr Biol. 2018 Sep 10;28(17):2697-2704.e3. doi: 10.1016/j.cub.2018.08.038. Epub 2018 Aug 30.

Abby Buchwalter

“Picking a Favourite: determinants of non-random chromatid segregation in stem cells"

Watase G, Yamashita Y. Ribosomal DNA and the rDNA-binding protein Indra mediate non-random sister chromatid segregation in Drosophila male germline stem cells. BioRxiv doi: http://dx.doi.org/10/1101/498352. [This article is a preprint and has not been peer-reviewed]

February 20, 2019

***Will meet in GH N114***

Gabby Estevam
Fred Chang Lab

“Stressed out: defining ribosome translation elongation states and regulation under stress with high-resolution ribosome profiling”

Wu CC, Zinshteyn B, Wehner KA, Green R. High-Resolution Ribosome Profiling Defines Discrete Ribosome Elongation States and Translational Regulation during Cellular Stress. Mol Cell. 2019 Jan 11. pii: S1097-2765(18)31063-3. doi: 10.1016/j.molcel.2018.12.009. [Epub ahead of print]

Elise Munoz
Narlikar Lab

“Caught in Translation: Ribosome collision as a means to convey translation status to quality control pathways”

Juszkiewicz S, Chandrasekaran V, Lin Z, Kraatz S, Ramakrishnan V, Hegde RS. ZNF598 Is a Quality Control Sensor of Collided Ribosomes. Mol Cell. 2018 Nov 1;72(3):469-481.e7. doi: 10.1016/j.molcel.2018.08.037. Epub 2018 Oct 4.

February 27, 2019

***Will meet in GH N114***

Chari Noddings
Agard Lab

“To Thine Own Cell Be True: How MDA5 Distinguishes 'Self' from 'Non-Self' dsRNA”

Ahmad S, Mu X, Yang F, Greenwald E, Park JW, Jacob E, Zhang CZ, Hur S. Breaching Self-Tolerance to Alu Duplex RNA Underlies MDA5-Mediated Inflammation. Cell. 2018 Feb 8;172(4):797-810.e13. doi: 10.1016/j.cell.2017.12.016. Epub 2018 Jan 25.

Seth Shipman

“A virus, a bacterium, and an archaeon walk into a bar...”"

Mehta AP et al. Engineering yeast endosymbionts as a step toward the evolution of mitochondria. Proc Natl Acad Sci U S A. 2018 Nov 13;115(46):11796-11801. doi: 10.1073/pnas.1813143115. Epub 2018 Oct 29.

March 6, 2019

***Will meet in GH N114***

Ulises Diaz
Marshall Lab

“Waking up in the morning sucks for zebrafish too: Period2, Cryptochrome1a, and Cryptochrome2a establish light dependent behavioral rhythms”

Hirayama J et al.  The clock components Period2, Cryptochrome1a, and Cryptochrome2a function in establishing light-dependent behavioral rhythms and/or total activity levels in zebrafish. Sci Rep. 2019 Jan 17;9(1):196. doi: 10.1038/s41598-018-37879-8.

Danny Conrad
Gartner Lab

“Nemuri: NyQuil for fruit flies”

Toda H, Williams JA, Gulledge M, Sehgal . A sleep-inducing gene, nemuri, links sleep and immune function in Drosophila. Science. 2019 Feb 1;363(6426):509-515. doi: 10.1126/science.aat1650.

March 13, 2019

Dana Kennedy
Al-Sady Lab


“A few (Q)tips from Phage: How a phage utilizes its host signaling molecules to fine tune its fate”

Silpe JE, Bassler BL. A Host-Produced Quorum-Sensing Autoinducer Controls a Phage Lysis-Lysogeny Decision. Cell. 2019 Jan 10;176(1-2):268-280.e13. doi: 10.1016/j.cell.2018.10.059. Epub 2018 Dec 13.

Martin Kampmann

“Friend or foe? A neurodegeneration-associated amyloid in regenerating muscle”

Vogler TO et al.  TDP-43 and RNA form amyloid-like myo-granules in regenerating muscle. Nature. 2018 Nov;563(7732):508-513. doi: 10.1038/s41586-018-0665-2. Epub 2018 Oct 31.

March 20, 2019

Manuela Richter
Dumont Lab


“Deciding your fate before birth: How metabolic markers can predict a yeast cell's decision before it's born”

Argüello-Miranda O, Liu Y, Wood NE, Kositangool P, Doncic A. Integration of Multiple Metabolic Signals Determines Cell Fate Prior to Commitment. Mol Cell. 2018 Sep 6;71(5):733-744.e11. doi: 10.1016/j.molcel.2018.07.041. Epub 2018 Aug 30.

Dan Southworth

“How Mitochondrial AAA+ Machines Enable Protein Quality Control"

Puchades C. et al. Unique structural features of the mitochondrial AAA+ protease AFG3L2 reveal the molecular basis for activity in health and disease. BioRxiv [This article is a preprint and has not been peer-reviewed]

March 27, 2019

Pervin Choksi
Ingraham Lab


“Rindr: where fungi meet fun bacteria”

Zhang Y, Kastman EK, Guasto JS, Wolfe BE. Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes. Nat Commun. 2018 Jan 23;9(1):336. doi: 10.1038/s41467-017-02522-z.

Tomasz Nowakowski

“Lost in (local) Translation: A Tale of an Aged Endosome and a Lonely Mitochondrion”

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.