September 6, 2012-June 13, 2013
Journal Club Chairs: Doug Gould, PhD and Mike German, MD
Day/Time: Thursdays, 12:00-1:00 p.m. except as noted
Location: N-225, Parnassus & videoconferenced to Room GH-S271, Mission Bay
Live stream & archive will be available: Fall 2012, Winter 2013, and Spring 2013 (UCSF MyAccess login required)
September 6, 2012
Hanna Kuznetsov (student)
"Leaky Pipes: R-Ras Regulates the Integrity of Tumor Vasculature"
Sawada J, et al. Small GTPase R-Ras Regulates Integrity and Functionality of Tumor Blood Vessels. Cancer Cell. 2012 Aug 14;22(2):235-49.
Coaches: Jay Debnath and Scott Seeley
Mark Moasser (faculty)
"Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization"
Shan Y, et al. Oncogenic mutations counteract intrinsic disorder in the EGFR kinase and promote receptor dimerization. Cell. 2012 May 11;149(4):860-70.
September 13, 2012
Amy Chen (student)
"Parp1 and Tet2 set the stage for somatic cell reprogramming"
Doege CA, et al. Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2. Nature. 2012 Aug 19.
Coaches: Miguel Ramalho-Santos and Michael McManus
Ann Zovein (faculty)
"ApoB - the link between circulating fats and bad vessels"
Avraham-Davidi I, et al. ApoB-containing lipoproteins regulate angiogenesis by modulating expression of VEGF receptor 1. Nat Med. 2012 Jun;18(6):967-73.
September 20, 2012
Mark Jeng (student)
"Coaxing out the Enemy: Using HDAC inhibitors to purge HIV-1 from Latent Viral Reservoirs"
Archin NM, et al. Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy. Nature. 2012 Jul 25;487(7408):482-5.
Coaches: Eric Verdin and Shomyseh Sanjabi
Brad Stohr (faculty)
"Multiple roads to cancer immortality"
Hu J, et al. Antitelomerase therapy provokes ALT and mitochondrial adaptive mechanisms in cancer. Cell. 2012 Feb 17;148(4):651-63.
September 27, 2012
Katherine Farrar (student)
""Are We Exclusive?" A host-specific microbiota appears to be critical for mammalian immune maturation."
Chung H, et al. Gut immune maturation depends on colonization with a host-specific microbiota. Cell. 2012 Jun 22;149(7):1578-93.
Coaches: Anita Sil and Tony DeFranco
Sophie Dumont (faculty)
"Getting the right number of chromosomes: Chromosomes holding on to microtubules for dear life"
Gonen S, et al. The structure of purified kinetochores reveals multiple microtubule-attachment sites. Nat Struct Mol Biol. 2012 Sep;19(9):925-9.
October 4, 2012
Emily Bradford (student)
"Spare the bacillus, spoil the child: The microbiome limits iNKT cell numbers and protects against IBD and asthma"
Olszak T, et al. Microbial exposure during early life has persistent effects on natural killer T cell function. Science. 2012 Apr 27;336(6080):489-93.
Coaches: Anna Bakardjiev and Lewis Lanier
Ophir Klein (faculty)
"No slow-cycling stem cells? That’s hard to swallow"
Doupé DP, et al. A single progenitor population switches behavior to maintain and repair esophageal epithelium. Science. 2012 Aug 31;337(6098):1091-3.
October 11, 2012
Nicolas Strauli (student)
"Time-Lapse Evolution: Watching The Emergence of a Complex Trait"
Blount ZD, et al. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature. 2012 Sep 19.
JJ Miranda (faculty)
"HIV Infection in Motion"
Murooka TT, et al. HIV-infected T cells are migratory vehicles for viral dissemination. Nature. 2012 Aug 1.
October 18, 2012
Ysbrand Nusse (student)
"A Game of Niches"
van Es, et al. Dll1C secretory progenitor cells revert to stem cells upon crypt damage. Nature Cell Biology. 2012 Sep 23.
Coaches: Todd Nystul and Jason Rock
Jeff Bush (faculty)
"A sense of closure in the neural-tube or just a polarized view?"
Nishimura T, Honda H, Takeichi M. Planar cell polarity links axes of spatial dynamics in neural-tube closure. Cell. 2012 May 25;149(5):1084-97.
October 25, 2012
Gianne Souza (student)
"Maybe the Dingo Ate Your Baby: Extrathymic Tregs in Placental Mammals Mitigates Maternal-Fetal Conflict"
Samstein RM, et al. Extrathymic generation of regulatory T cells in placental mammals mitigates maternal-fetal conflict. Cell. 2012 Jul 6;150(1):29-38.
Coaches: Jeff Cox and Anna Bakardjiev
Yuriy Kirichok (faculty)
"A fifty-years-old mitochondrial mystery is solved?"
De Stefani D, et al. A forty-kilodalton protein of the inner membrane is the mitochondrial calcium uniporter. Nature. 2011 Jun 19;476(7360):336-40.
November 01, 2012
Amanda Paulson (student)
"Cells of a Feather Stick Together"
Maître JL, et al. Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells. Science. 2012 Oct 12;338(6104):253-6.
Coach: Zev Gartner
Ajay Chawla (faculty)
"Colors of Fat: White, Brown and Beige"
Wu J, et al. Beige adipocytes are a distinct type of thermogenic fat cell in mouse and human. Cell. 2012 Jul 20;150(2):366-76.
November 08, 2012
Bianca Lee (student)
"Resistance is Only "Skin" Deep: Dissecting the interactions between tumor cells and their micro-environment in melanoma"
Straussman R, et al. Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion. Nature. 2012 Jul 26;487(7408):500-4.
Coaches: Neil Shah and Andrei Goga
Long-Cheng Li (faculty)
"The mighty Argonautes take a tailor’s job"
Ameyar-Zazoua M, et al. Argonaute proteins couple chromatin silencing to alternative splicing. Nat Struct Mol Biol. 2012 Sep 9;19(10):998-1004.
November 15, 2012
Lauren Shields (student)
"A Splitting Headache: Disrupted Mitochondrial Fission Mediates Tau Toxicity"
DuBoff B, et al. Tau promotes neurodegeneration via DRP1 mislocalization in vivo. Neuron. 2012 Aug 23;75(4):618-32.
Coaches: Ken Nakamura and Yadong Huang
Jenny Qi (student)
"Fanning the flames: inflammasome-regulated IL-22BP controls colon tumorigenesis"
Huber S et al. IL-22BP is regulated by the inflammasome and modulates tumorigenesis in the intestine, Nature, 2012 Oct 17.
Coaches: Brad Stohr and Susan Lynch
November 22, 2012
No Journal Club
November 29, 2012
Sky Feuer (student)
"Three cells and a baby: towards germline gene therapy of inherited mitochondrial diseases"
Tachibana M, et al. Towards germline gene therapy of inherited mitochondrial diseases. Nature. 2012 Oct 24.
Coach: Paolo Rinaudo
Valerie Weaver (faculty)
Nakasone ES, et al. Imaging tumor-stroma interactions during chemotherapy reveals contributions of the microenvironment to resistance. Cancer Cell. 2012 Apr 17;21(4):488-503.
December 06, 2012
Meghan McKeon (student)
"Making Sense of Antisense Transcriptional Regulation"
Tan-Wong SM, et al. Gene loops enhance transcriptional directionality. Science. 2012 Nov 2;338(6107):671-5.
Robert Nussbaum (faculty)
"Is alpha-synuclein a prion wannabe?"
Luk KC, et al. Pathological α-synuclein transmission initiates Parkinson-like neurodegeneration in nontransgenic mice. Science. 2012 Nov 16;338(6109):949-53.
January 03, 2013
Avantika Chitre (student)
"Serendipity 3: The Role of TLR3 in Nuclear Reprogramming"
Lee J, et al. Activation of innate immunity is required for efficient nuclear reprogramming. Cell. 2012 Oct 26;151(3):547-58.
Coaches: Jeff Cox and Mike McCune
Markus Müschen (faculty)
"Self-recognizing antibodies and molecular mimicry in B cell leukemia"
Dühren-von Minden M, et al. Chronic lymphocytic leukaemia is driven by antigen-independent cell-autonomous signalling. Nature. 2012 Sep 13;489(7415):309-12
January 10, 2013
Sarah Gerhart (student)
"Secrets of the gonad: what you don't know can kill you!"
Shen Y, et al. A steroid receptor-microRNA switch regulates life span in response to signals from the gonad. Science. 2012 Dec 14;338(6113):1472-6.
Coaches: Aimee Kao and Todd Nystul
Rosemary Akhurst (faculty)
"Cancer Drug Resistance Mediated By Loss Of A Mediator"
Huang S, et al. MED12 Controls the Response to Multiple Cancer Drugs through Regulation of TGF-β Receptor Signaling. Cell. 2012 Nov 21;151(5):937-50.
January 17, 2013
Aarati Asundi (student)
"Neurons Gone Wild: Lowered synaptic inhibition in autism spectrum disorders"
Banerjee A, et al. Impairment of cortical GABAergic synaptic transmission in an environmental rat model of autism. Int J Neuropsychopharmacol. 2012 Dec 11:1-10.
Coaches: Lauren Weiss and Jeff Bush
Rob Judson (postdoc)
Journal Lab tutorial/demo
January 24, 2013
*Special Time - 5:00 p.m.*
Christine Moore Sheridan (student)
"A Silver Lining?: Using Tumor Microparticles to Target Cancer"
Tang K, et al. Delivery of chemotherapeutic drugs in tumour cell-derived microparticles. Nat Commun. 2012 Dec 18;3:1282.
Coaches: Scott Oakes and Davide Ruggero
Emmanuelle Passegue (faculty)
"Hematopoietic stem cells don't do aerobics"
Takubo K, et al. Regulation of glycolysis by pdk functions as a metabolic checkpoint for cell cycle quiescence in hematopoietic stem cells. Cell Stem Cell. 2013 Jan 3;12(1):49-61.
January 31, 2013
Alex Samocha (student)
"Tyk Talk: Better Understanding Brown Adipose Tissue Differentiation"
Derecka M, et al. Tyk2 and stat3 regulate brown adipose tissue differentiation and obesity. Cell Metab. 2012 Dec 5;16(6):814-24.
Coaches: Allison Xu and Suneil Koliwad
Aude Bouagnon (student)
"Now that's crisp: Mammalian genome engineering using CRISPR/Cas systems"
Cong L, et al. Multiplex Genome Engineering Using CRISPR/Cas Systems. Science. 2013 Jan 3.
Coaches: De'Broski Herbert and Anita Sil
February 07, 2013
*Special Time - 5:00 p.m.*
Erin Oswald (student)
"Complements to the chef!: Hungry microglia enjoy synaptic gastronomy"
Schafer DP, et al. Microglia sculpt postnatal neural circuits in an activity and complement-dependent manner. Neuron. 2012 May 24;74(4):691-705.
Coaches: Rich Locksley and Max Krummel
Mark Anderson (faculty)
"The regulators of T-regulators"
Sekiya T, et al. Nr4a receptors are essential for thymic regulatory T cell development and immune homeostasis. Nat Immunol. 2013 Jan 20.
February 14, 2013
Darienne Myers (student)
"Will You "B" My Valentine?: Regulatory B cells Control T Cell Autoimmunity"
Yoshizaki A, et al. Regulatory B cells control T-cell autoimmunity through IL-21-dependent cognate interactions. Nature. 2012 Nov 8;491(7423):264-8.
Coaches: Michelle Hermiston and Jeroen Roose
Anders Persson (faculty)
"Neurons are not excited to turn cancerous"
Friedmann-Morvinski D, et al. Dedifferentiation of neurons and astrocytes by oncogenes can induce gliomas in mice. Science. 2012 Nov 23;338(6110):1080-4.
February 21, 2013
Raul Torres (student)
"The Population Bomb: Explosive population growth and the excess of rare, deleterious variation within the human genome"
Fu W, et al. Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature. 2013 Jan 10;493(7431):216-20.
Coaches: Mark Seielstad and Ryan Hernandez
Shomi Sanjabi (faculty)
"What! T cell memory against commensals??"
Hand TW, et al. Acute gastrointestinal infection induces long-lived microbiota-specific T cell responses. Science. 2012 Sep 21;337(6101):1553-6.
February 28, 2013
Robin Kageyama (student)
"There and Back Again: Mouse models of MeCP2 overexpression reveal a Th1 defect in patients with MeCP2 duplication syndrome"
Yang T, et al. Overexpression of methyl-CpG binding protein 2 impairs T(H)1 responses. Sci Transl Med. 2012 Dec 5;4(163):163ra158.
Coaches: Mark Ansel and Brad Stohr
Mark Seielstad (faculty)
"Of Mice and NOT Men: what a waste it all has been"
Seok J, et al. Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc Natl Acad Sci USA. 2013 Feb 11.
March 07, 2013
Adriana Mujal (student)
"Putting cancer to rest: TH1 cytokines induce tumor cell senescence"
Braumüller H, et al. T-helper-1-cell cytokines drive cancer into senescence. Nature. 2013 Feb 3.
Coaches: Max Krummel and Brad Stohr
March 14, 2013
Lauren Rodda (student)
"Not in my house!"
Aachoui Y, et al. Caspase-11 protects against bacteria that escape the vacuole. Science. 2013 Feb 22;339(6122):975-8.
Coaches: Averil Ma and Tony DeFranco
Brittany Gianetti (student)
"How can you mend a broken heart?: microRNAs induce cardiomyocyte proliferation."
Eulalio A, et al. Functional screening identifies miRNAs inducing cardiac regeneration. Nature. 2012 Dec 20;492(7429):376-81.
Coaches: Mark Ansel and Takashi Mikawa
March 21, 2013
Stephanie Parker (student)
"A twist in the plot: Is dynamic supercoiling important for gene regulation?"
Kouzine F, et al. Transcription-dependent dynamic supercoiling is a short-range genomic force. Nat Struct Mol Biol. 2013 Mar;20(3):396-403.
Coaches: Maximiliano D'Angelo
Gorjan Hrustanovic (student)
"Finding an Achilles Heel in KRAS-mutant NSCLC"
Shackelford DB, et al. LKB1 Inactivation Dictates Therapeutic Response of Non-Small Cell Lung Cancer to the Metabolism Drug Phenformin. Cancer Cell. 2013 Feb 11;23(2):143-58.
Coaches: Trever Bivona and James Fraser
April 04, 2013
Christina Hueschen (student)
"A Kiss Goodbye: A Spindle-Membrane Link is Required for Cytokinesis"
Lekomtsev S, et al. Centralspindlin links the mitotic spindle to the plasma membrane during cytokinesis. Nature. 2012 Dec 13;492(7428):276-9.
Coaches: Sophie Dumont and Brad Stohr
Carlos Rojo (student)
"Search and transcribe: How does RNA polymerase find its targets in a sea of non-specific DNA?"
Wang F, et al. The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion. Nat Struct Mol Biol. 2013 Feb;20(2):174-81.
Coaches: Daniel Hart and Alan Frankel
April 11, 2013
Emily Tang (student)
"New Kids on the Block: Role of Innate Lymphoid Cells in Atopic Dermatitis"
Kim BS, et al. TSLP elicits IL-33-independent innate lymphoid cell responses to promote skin inflammation. Sci Transl Med. 2013 Jan 30;5(170):170ra16.
Coaches: Mark Ansel and Chris Allen
Juliet Goldsmith (student)
"Different strokes for different neurons: protection against ischemic stroke by autophagy"
Papadakis M, et al. Tsc1 (hamartin) confers neuroprotection against ischemia by inducing autophagy. Nat Med. 2013 Feb 24;19(3):351-7.
Coaches: Jay Debnath and Jialing Liu
April 18, 2013
David Pardo (student)
"Keep your cool and live longer: Thermosensitive TRP Channel Promotes C. Elegans Longevity"
Xiao R, et al. A genetic program promotes C. elegans longevity at cold temperatures via a thermosensitive TRP channel. Cell. 2013 Feb 14;152(4):806-17.
Coaches: Brad Stohr and Noelle L'Etoile
Julia Ye (student)
"RNA biology comes a full circle: Novel regulatory roles for circular RNAs"
Memczak S, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013 Mar 21;495(7441):333-8.
Hansen TB, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013 Mar 21;495(7441):384-8.
Coaches: Christine Guthrie and Raul Andino
April 25, 2013
Kurt Weiberth (student)
"The New Gene on the Block: Hexanucleotide expansion within C9ORF72 mRNA is sufficient for neurodegeneration"
Xu Z, et al. Expanded GGGGCC repeat RNA associated with amyotrophic lateral sclerosis and frontotemporal dementia causes neurodegeneration. Proc Natl Acad Sci U S A. 2013 Apr 3.
Coaches: Steven Finkbeiner and Aimee Kao
Kamena Kostova (student)
"If you're happy and you know it, CLP your t: CLP1 links tRNA metabolism to progressive motor-neuron loss"
Hanada T, et al. CLP1 links tRNA metabolism to progressive motor-neuron loss. Nature. 2013 Mar 28;495(7442):474-80.
Coaches: Davide Ruggero and Aimee Kao
May 02, 2013
Kelly Remedios (student)
"One fate NOT to rule them all: Individual CD8 T cell undergo heterogeneous differentiation"
Gerlach C, et al. Heterogeneous Differentiation Patterns of Individual CD8+ T Cells. Science. 2013 Mar 14.
Coaches: Shomyseh Sanjabi and Mehrdad Matloubian
Evan Markegard (student)
"Pancreatic Cancer "Bulks Up" With Glutamine: A Therapeutic Window!?"
Son J, et al. Glutamine supports pancreatic cancer growth through a KRAS-regulated metabolic pathway. Nature. 2013 Apr 4;496(7443):101-5.
Coaches: Trever Bivona and Scott Oakes
May 09, 2013
Jerome Kahiapo (student)
"Expand your mind with Trnp1"
Ronny Stahl, et al. Trnp1 Regulates Expansion and Folding of the Mammalian Cerebral Cortex by Control of Radial Glial Fate. Cell - 25 April 2013 (Vol. 153, Issue 3, pp. 535-549)
Coaches: Stavros Lomvardas and Eric Huang
Dylan Lowe (student)
"Beige Cells Bring the heat! Compensatory thermogenic role of beige cells after brown fat ablation."
Schulz TJ, et al. Brown-fat paucity due to impaired BMP signalling induces compensatory browning of white fat. Nature. 2013 Mar 21;495(7441):379-83.
Coaches: Shingo Kajimura and Suneil Koliwad
May 16, 2013
Joe Udeochu (student)
"∫(new dentate granule cells) = f(Zif268)"
Veyrac A, et al. Zif268/egr1 gene controls the selection, maturation and functional integration of adult hippocampal newborn neurons by learning. Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):7062-7.
Coaches: Saul Villeda and Scott Oakes
Melissa Sandoval (student)
"Screening for Liver Regeneration Therapies in the JNK Yard"
Wuestefeld T, et al. A Direct In Vivo RNAi Screen Identifies MKK4 as a Key Regulator of Liver Regeneration. Cell. 2013 Apr 11;153(2):389-401.
Coaches: Holger Willenbring and Jackie Maher
May 23, 2013
Mark Noviski (student)
"A guest that just won't leave: Why cancer vaccines have limited efficacy"
Hailemichael Y, et al. Persistent antigen at vaccination sites induces tumor-specific CD8+ T cell sequestration, dysfunction and deletion. Nat Med. 2013 Apr;19(4):465-72.
Coaches: Michael Rosenblum and Michelle Hermiston
Samira Khakpour (student)
"Interferon Interference: Type I interferon suppresses type II interferon-triggered anti-mycobacterial responses"
Teles RM, et al. Type I interferon suppresses type II interferon-triggered human anti-mycobacterial responses. Science. 2013 Mar 22;339(6126):1448-53.
Coaches: Anita Sil and Mehrdad Matloubian
May 30, 2013
Lisandro Maya-Ramos (student)
Jamieson AM, et al. Role of Tissue Protection in Lethal Respiratory Viral-Bacterial Coinfection. Science. 2013 Apr 25.
Stephanie Moquin (student)
"Achoo! A new therapy for severe cases of the flu?"
Morita M, et al. The lipid mediator protectin D1 inhibits influenza virus replication and improves severe influenza. Cell. 2013 Mar 28
Coaches: Melanie Ott and Jeff Cox
June 06, 2013
TJ Hu (student)
"A non-optimal solution to a FRQuent problem: Non-optimal codon usage affects expression, structure and function of clock protein FRQ."
Zhou M, et al. Non-optimal codon usage affects expression, structure and function of clock protein FRQ. Nature. 2013 Mar 7;495(7439):111-5.
Coaches: Davide Ruggero and Louis Ptacek
Terren Niethamer (student)
"You Are What (Your Gut Microbes) Eat: Intestinal microbiota metabolism of L-carnitine contributes to atherosclerosis."
Koeth RA, et al. Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med. 2013 May;19(5):576-85.
Coaches: Susan Lynch and Ethan Weiss
June 13, 2013
Philip Nova (student)
"I can see clearly now, the lipids are gone: imaging intact tissues with CLARITY"
Chung K, et al. Structural and molecular interrogation of intact biological systems. Nature. 2013 Apr 10.
Coaches: Yadong Huang and Eric Huang