September 5, 2013-June 12, 2014
Journal Club Chairs: Mike German, MD and Brad Stohr, MD, PhD
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: Spring 2014, Winter 2014, Fall 2013 (UCSF MyAccess login required)
September 05, 2013
Christina Hueschen (student)
"How to get a-head in life: Rescuing head regrowth in regeneration-limited planarians"
Liu SY, et al. Reactivating head regrowth in a regeneration-deficient planarian species. Nature. 2013 Aug 1;500(7460):81-4.
Coaches: Jeremy Reiter and Arnold Kriegstein
Chris Allen (faculty)
"Dangerous cleavage: allergen activation of innate immunity"
Millien VO, et al. Cleavage of fibrinogen by proteinases elicits allergic responses through Toll-like receptor 4. Science. 2013 Aug 16;341(6147):792-6.
September 12, 2013
Aude Bouagnon (student)
"Live long and prosper: Mitonuclear protein imbalance as a conserved longevity mechanism"
Houtkooper RH, et al. Mitonuclear protein imbalance as a conserved longevity mechanism. Nature. 2013 May 23;497(7450):451-7.
Coaches: Kaveh Ashrafi and Aimee Kao
Bob Farese (faculty)
"A chance to cut is a chance to cure: How does the surgery on the gut cure diabetes?"
Saeidi N, et al. Reprogramming of intestinal glucose metabolism and glycemic control in rats after gastric bypass. Science. 2013 Jul 26;341(6144):406-10.
September 19, 2013
Brittany Gianetti (student)
Eskandarian HA, et al. A role for SIRT2-dependent histone H3K18 deacetylation in bacterial infection. Science. 2013 Aug 2;341(6145):1238858.
Coaches: Suzanne Noble, Joanne Engel, and Anna Bakardjiev
Terren Niethamer (student)
"Finding the "Rett" Answer: A suppressor screen to identify pathways of disease pathogenesis in Rett syndrome"
Buchovecky CM, et al. A suppressor screen in Mecp2 mutant mice implicates cholesterol metabolism in Rett syndrome. Nat Genet. 2013 Aug 28;45(9):1013-20.
Coaches: Elliott Sherr and Doug Gould
September 26, 2013
Carlos Rojo (student)
"Adding in-salt to injury: tissue damage detection by osmotic surveillance"
Enyedi B, et al. Tissue damage detection by osmotic surveillance. Nat Cell Biol. 2013 Sep;15(9):1123-30.
Coaches: Daniel Hart and De'Broski Herbert
De'Broski Herbert (faculty)
"The painful necessity of inflammation"
Chiu, Isaac M., et al. Bacteria activate sensory neurons that modulate pain and inflammation. Nature 2013/08/21
October 03, 2013
Emily Tang (student)
"Clostridia cocktail to suppress inflammation"
Atarashi K, et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature. 2013 Aug 8;500(7461):232-6.
Coaches: Susan Lynch and Averil Ma
Scott Seeley (faculty)
"Stuck in traffic: Endocytic defects and the development of myeloid leukemia"
Nagamachi A, et al. Haploinsufficiency of SAMD9L, an Endosome Fusion Facilitator, Causes Myeloid Malignancies in Mice Mimicking Human Diseases with Monosomy 7. Cancer Cell. 2013 Sep 9;24(3):305-17.
October 10, 2013
Juliet Goldsmith (student)
Curry NL, et al. Pten-Null Tumors Cohabiting the Same Lung Display Differential AKT Activation and Sensitivity to Dietary Restriction. Cancer Discov. 2013 Aug;3(8):908-921.
Coaches: Trever Bivona, Eric Collisson and Jay Debnath
Melissa McCreery (student)
"Genetic Signatures of Cancer and Implications for Personalized Medicine"
Ciriello G, et al. Emerging landscape of oncogenic signatures across human cancers. Nat Genet. 2013 Sep 26;45(10):1127-1133.
Coaches: Allan Balmain and TBD
October 17, 2013
David Pardo (student)
"Blurred lines in epidermal wounding but not homeostasis"
Page ME, et al. The Epidermis Comprises Autonomous Compartments Maintained by Distinct Stem Cell Populations. Cell Stem Cell. 2013 Oct 3;13(4):471-482.
Coaches: Todd Nystul and Jason Rock
Marta Margeta (faculty)
"A double-edged sword: How interplay of host defense systems can lead to disease"
Ichimura Y, et al. Phosphorylation of p62 Activates the Keap1-Nrf2 Pathway during Selective Autophagy. Mol Cell. 2013 Sep 12;51(5):618-31.
October 24, 2013
Kurt Weiberth (student)
"I'll Take That: PolyQ Proteins Sequester Sis1p and Impair Nuclear Degradation of Cytosolic Proteins"
Sae-Hun Park, et al. PolyQ Proteins Interfere with Nuclear Degradation of Cytosolic Proteins by Sequestering the Sis1p Chaperone. Cell, Volume 154, Issue 1, 3 July 2013, Pages 134–145.
Coaches: Doug Gould and Jason Gestwicki
Eric Dang (student)
"Lin(c)ing RNA to Innate Immune Activation"
Carpenter S et al. A Long Noncoding RNA mediates both Activation and Repression of Immune Response Genes. Science. 2013 Aug 16;341(6147):789-92. doi: 10.1126/science.1240925. Epub 2013
Coaches: Mark Ansel and Mark Anderson
October 31, 2013
Kamena Kostova (student)
"Mutant mice from MIT: One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering"
Yang H, et al. One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering. Cell. 2013 Sep 12;154(6):1370-9. doi: 10.1016/j.cell.2013.08.022. Epub 2013 Aug 29. PubMed PMID: 23992847
Coaches: Martin McMahon and Davide Ruggero
Manish Aghi (faculty)
"Trick or Treat: Dual Functions of CDK6 link the cell cycle to angiogenesis"
Kollmann K, et al.A kinase-independent function of CDK6 links the cell cycle to tumor angiogenesis. Cancer Cell. 2013 Aug 12;24(2):167-81.
November 07, 2013
TJ Hu (student)
Christianson HC, et al. Cancer cell exosomes depend on cell-surface heparan sulfate proteoglycans for their internalization and functional activity. Proc Natl Acad Sci U S A. 2013 Oct 7.
Coaches: Jay Debnath and Steve Rosen
Michael Rosenblum (faculty)
"Not in my house! - Tregs provide a safe haven for stem cells…"
Fujisaki J, et al. In vivo imaging of Treg cells providing immune privilege to the haematopoietic stem-cell niche. Nature. 2011 Jun 8;474(7350):216-9.
November 14, 2013
Alex Samocha (student)
"Mind the GAP! The RasGAP gene, RASAL2, is a tumor and metastasis suppressor"
McLaughlin SK, et al. The RasGAP gene, RASAL2, is a tumor and metastasis suppressor. Cancer Cell. 2013 Sep 9;24(3):365-78.
Coaches: Jeroen Roose and Scott Oakes
Susan Fisher (faculty)
"Mucus as a Mediator"
Shan M, et al. Mucus enhances gut homeostasis and oral tolerance by delivering immunoregulatory signals. Science. 2013 Oct 25;342(6157):447-53.
November 21, 2013
Dana Neel (student)
"The MLLephant in the room: MLL fusion proteins require NF-kB for leukemogenesis"
Kuo HP, et al. Epigenetic Roles of MLL Oncoproteins Are Dependent on NF-κB. Cancer Cell. 2013 Oct 14;24(4):423-37.
Coaches: Neil Shah and Ben Braun
Roger Chang (student)
"The Itchy and Scratchy Show: TSLP and Itch Neurons"
Wilson SR, et al. The Epithelial Cell-Derived Atopic Dermatitis Cytokine TSLP Activates Neurons to Induce Itch. Cell. 2013 Oct 10;155(2):285-95.
Coaches: Anatol Kreitzer and Roger Nicoll
December 05, 2013
Arman Jahangiri (student)
"The Few, The Proud, The Cancer Cells That Survive Metastasis"
Shibue T, et al. An integrin-linked machinery of cytoskeletal regulation that enables experimental tumor initiation and metastatic colonization. Cancer Cell. 2013 Oct 14;24(4):481-98.
Jinwoo Lee (student)
"PI3King on PIDs: Using Exome Sequencing to Identify Novel Disease-Causing Mutations"
Angulo I, et al. Phosphoinositide 3-kinase δ gene mutation predisposes to respiratory infection and airway damage. Science. 2013 Nov 15;342(6160):866-71.
Coaches: Art Weiss and Jennifer Puck
December 12, 2013
Daniel Holohan (student)
"The mystery of Themis in thymus: controlling selection of low-affinity TCRs during T cell development"
Fu G, et al. Themis sets the signal threshold for positive and negative selection in T-cell development. Nature. 2013 Nov 13.
Coaches: Jeroen Roose and Art Weiss
Thomas Hennings (student)
"Insulin's long lost cousin leptin: leptin maintains life through the hypothalamus in the absence of insulin"
Fujikawa T, et al. Leptin engages a hypothalamic neurocircuitry to permit survival in the absence of insulin. Cell Metab. 2013 Sep 3;18(3):431-44.
Coaches: Allison Xu and Shingo Kajimura
January 09, 2014
Tony Gao (student)
"Show and TEL: Telomere length regulator RTEL1 interacts with the replisome to mediate DNA replication"
Vannier JB, et al. RTEL1 is a replisome-associated helicase that promotes telomere and genome-wide replication. Science. 2013 Oct 11;342(6155):239-42.
Coaches: Brad Stohr and John Murnane
Briana Fitch (student)
"Infiltrating the stromal network: Irradiated macrophages direct tumor immune rejection"
Klug F, et al. Low-dose irradiation programs macrophage differentiation to an iNOS⁺/M1 phenotype that orchestrates effective T cell immunotherapy. Cancer Cell. 2013 Nov 11;24(5):589-602.
Coaches: Scott Kogan and Neil Shah
January 16, 2014
Jillian Jespersen (student)
"High-density lipoprotein mediates anti-inflammatory reprogramming of macrophages via the transcriptional regulator ATF3"
De Nardo D, et al. High-density lipoprotein mediates anti-inflammatory reprogramming of macrophages via the transcriptional regulator ATF3. Nat Immunol. 2013 Dec 8.
Coaches: Suneil Koliwad and JJ Miranda
Andrew Lechner (student)
"Game of Clones: an immune-restricted progenitor challenges the HSC"
Böiers C, et al. Lymphomyeloid contribution of an immune-restricted progenitor emerging prior to definitive hematopoietic stem cells. Cell Stem Cell. 2013 Nov 7;13(5):535-48.
Coaches: Tippi MacKenzie and Jason Rock
January 23, 2014
*Special Time - 5:00 p.m.*
Evan Markegard (student)
"A Lesson from Melanocytes: When you’re feeling sad, reactivate your ancestral program"
Johannessen CM, et al. A melanocyte lineage program confers resistance to MAP kinase pathway inhibition. Nature. 2013 Dec 5;504(7478):138-42.
Coaches: Martin McMahon and Jeroen Roose
Frank McCormick (faculty)
"A CRISPR way of knocking down genes"
Shalem O, et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2014 Jan 3;343(6166):84-7.
January 30, 2014
John Liu (student)
"LncRNAs in Polycomb Recruitment"
Kaneko S, et al. Interactions between JARID2 and Noncoding RNAs Regulate PRC2 Recruitment to Chromatin. Mol Cell. 2014 Jan 23;53(2):290-300.
Coaches: Dan Lim and Bassem Al-Sady
Misty Montoya (student)
"A look into the gut microbiome-brain interaction"
Hsiao EY, et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell. 2013 Dec 19;155(7):1451-63.
Coaches: Susan Lynch and Lauren Weiss
February 06, 2014
*Special Time - 5:00 p.m.*
Samira Khakpour (student)
"cGAMP too shall pass: Cell intrinsic immunity spreads via intercellular transfer of cGAMP"
Ablasser A, et al. Cell intrinsic immunity spreads to bystander cells via the intercellular transfer of cGAMP. Nature. 2013 Nov 28;503(7477):530-4.
Coaches: Jeff Cox and Anna Bakardjiev
Max Krummel (faculty)
"Injured Lung? Don't call the AM-bulance, Its already there!"
Westphalen K,et al. Sessile alveolar macrophages communicate with alveolar epithelium to modulate immunity. Nature. 2014 Jan 19;doi:10.1038/nature12902
February 13, 2014
Dylan Lowe (student)
"BAIBA don't you break my heart"
Roberts LD, et al. β-Aminoisobutyric Acid Induces Browning of White Fat and Hepatic β-Oxidation and Is Inversely Correlated with Cardiometabolic Risk Factors. Cell Metab. 2014 Jan 7;19(1):96-108.
Coaches: Shingo Kajimura and Gregory Ku
Linda Noble (faculty)
"Promoting recovery after brain injury- Never say NO!(se)"
Scafidi J, et al. Intranasal epidermal growth factor treatment rescues neonatal brain injury. Nature. 2013 Dec 25.
February 20, 2014
Jerome Kahiapo (student)
"A tabula rasa for human pluripotency"
Gafni O, et al. Derivation of novel human ground state naive pluripotent stem cells. Nature. 2013 Dec 12;504(7479):282-6.
Coaches: Robert Blelloch and Barbara Panning
Sarah Knox (faculty)
"It takes two: Kit and FGFR2b join forces during organogenesis"
Lombaert IM, et al. Combined KIT and FGFR2b Signaling Regulates Epithelial Progenitor Expansion during Organogenesis. Stem Cell Reports. 2013 Dec 12;1(6):604-19.
February 27, 2014
Kelly Remedios (student)
"For a happy gut, listen to your circadian clock: a role for the circadian clock in Th17 differentiation"
Yu X, et al. TH17 cell differentiation is regulated by the circadian clock. Science. 2013 Nov 8;342(6159):727-30.
Coaches: Mike Rosenblum and Rich Locksley
Melissa Sandoval (student)
"A New Approach to Pluripotency: just incubate somatic cells with low pH?"
Obokata H, et al. Stimulus-triggered fate conversion of somatic cells into pluripotency. Nature. 2014 Jan 30;505(7485):641-7.
Coaches: Diane Barber and Todd Nystul
March 06, 2014
Mark Noviski (student)
"Becoming who you want to B: The role of Ikaros in early B cell development"
Schwickert TA, et al. Stage-specific control of early B cell development by the transcription factor Ikaros. Nat Immunol. 2014 Feb 9.
Coaches: Markus Müschen and Julie Zikherman
March 13, 2014
Stephanie Moquin (student)
McFarland AP, et al. The favorable IFNL3 genotype escapes mRNA decay mediated by AU-rich elements and hepatitis C virus-induced microRNAs. Nat Immunol. 2014 Jan;15(1):72-9.
Coaches: JJ Miranda and Mark Ansel
Phil Nova (student)
"When we get together, bad things happen": Neural activity promotes colocalization of key players in the ABeta synthesis pathway
Das U, Scott DA, Ganguly A, Koo EH, Tang Y, Roy S. Activity-induced convergence of APP and BACE-1 in acidic microdomains via an endocytosis-dependent pathway. Neuron. 2013 Aug 7;79(3):447-60.
Coaches: Yadong Huang and Li Gan
March 20, 2014
Joe Udeochu (student)
"Gliaful Synapses: Microglia BDNF promotes synapse formation in the adult brain"
Parkhurst CN, et al. Microglia promote learning-dependent synapse formation through brain-derived neurotrophic factor. Cell. 2013 Dec 19
Coaches: Saul Villeda and David Rowitch
April 03, 2014
Roman Camarda (student)
Israelsen WJ, et al. PKM2 isoform-specific deletion revelas a differential requirement for pyruvate kinase in tumor cells. Cell 2013 Oct 10;155(2):397-409
Coaches: Diane Barber and Shingo Kajimura
Yvanka De Soysa (student)
"Hungry Hungry Hippos: Hippo Signaling Regulates microRNA Biogenesis in a Cell-Density-Dependent Manner"
Mori M, et al. Hippo Signaling Regulates Microprocessor and Links Cell-Density-Dependent miRNA Biogenesis to Cancer. Cell. 2014 Feb 27;156(5):893-906.
Coaches: Scott Oakes and Michael McManus
April 10, 2014
Lindsey Jones (student)
"Obesity-associated variants in FTO interact with a novel body mass determinant, IRX3"
Smemo S, et al. Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature. 2014 Mar 20;507(7492):371-5.
Coaches: Joe Costello and Christian Vaisse
Annalise Petriello (student)
"Man the gates with mucus: NLRP6 inflammasome promotes intestinal mucus secretion and defense against an enteric pathogen"
Wlodarska M, et al. NLRP6 Inflammasome Orchestrates the Colonic Host-Microbial Interface by Regulating Goblet Cell Mucus Secretion. Cell. 2014 Feb 27;156(5):1045-59.
Coaches: Mike McCune and Susan Lynch
April 17, 2014
James Jung (student)
"How do you like me now? Group 2 Innate Lymphoid Cells are Critical Mediators of Allergic Lung Inflammation"
Halim TY, et al. Group 2 Innate Lymphoid Cells Are Critical for the Initiation of Adaptive T Helper 2 Cell-Mediated Allergic Lung Inflammation. Immunity. 2014 Mar 4.
Coaches: Chris Allen and Mark Ansel
Meera Shenoy (student)
Mazzini E, et al. Oral Tolerance Can Be Established via Gap Junction Transfer of Fed Antigens from CX3CR1(+) Macrophages to CD103(+) Dendritic Cells. Immunity. 2014 Feb 20;40(2):248-61.
Coaches: Mike Rosenblum and Shomi Sanjabi
April 24, 2014
Vassily Kutyavin (student)
"Clec12a helps keep inflammation in check"
Neumann K, et al. Clec12a Is an Inhibitory Receptor for Uric Acid Crystals that Regulates Inflammation in Response to Cell Death. Immunity. 2014 Mar 20;40(3):389-99.
Coaches: Anthony DeFranco and Clifford Lowell
Dimitre Simeonov (student)
Gröschel S, et al. A Single Oncogenic Enhancer Rearrangement Causes Concomitant EVI1 and GATA2 Deregulation in Leukemia. Cell. 2014 Apr 10;157(2):369-81.
Coaches: Nadav Ahituv and Alexander Marson
May 01, 2014
Christina Adams (student)
"The unfolded protein response and hypoxia drive triple-negative breast cancer"
Chen X, et al. XBP1 promotes triple-negative breast cancer by controlling the HIF1α pathway. Nature. 2014 Apr 3;508(7494):103-7.
Coaches: Denise Chan and Scott Oakes
Melissa Spear (student)
"Breaking the habit: Mitosis inhibits DNA repair to protect against telomere fusions"
Orthwein A, et al. Mitosis inhibits DNA double-strand break repair to guard against telomere fusions. Science. 2014 Apr 11;344(6180):189-93.
Coaches: John Murnane and Brad Stohr
May 08, 2014
Ibraheem Ali (student)
"A Tale of Two miRNAs: miR-146a and miR-155 Delineate a MicroRNA Fingerprint Associated with Toxoplasma persistence in the Host Brain"
Cannella D, et al. miR-146a and miR-155 Delineate a MicroRNA Fingerprint Associated with Toxoplasma Persistence in the Host Brain. Cell Rep. 2014 Mar 13;6(5):928-37.
Coaches: Hiten Madhani and Jeff Cox
Adrienne Stormo (student)
"The Quiet Game: Trinucleotide repeats in FMR1 mRNA drive epigenetic silencing in Fragile X Syndrome"
Colak D, et al. Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in fragile X syndrome. Science. 2014 Feb 28;343(6174):1002-5.
Coaches: Michael McManus and Elliott Sherr
May 15, 2014
Tim Marsh (student)
"Long Distance Relationships: Cancer’s Significant Other – the Metastatic Organ"
Zhou W, et al. Cancer-Secreted miR-105 Destroys Vascular Endothelial Barriers to Promote Metastasis. Cancer Cell. 2014 Apr 14;25(4):501-15.
Coaches: Jayanta Debnath and Michael McManus
Alice Taubes (student)
"Finding the evil gene-iuses: Integrative genomics identifies APOE ε4 effectors in Alzheimer's disease"
Rhinn H et al. Integrative genomics identifies APOE ε4 effectors in Alzheimer's disease. Nature. 2013 Aug 1;500(7460):45-50
Coaches: Yadong Huang and Lauren Weiss
May 22, 2014
Aaron Mattingly (student)
"With a little help from my friends: Cancer-associated fibroblasts maintain lung cancer stemness through paracrine signaling"
Chen WJ et al., Cancer-associated fibroblasts regulate the plasticity of lung cancer stemness via paracrine signalling. Nat Commun. 2014 Mar 25;5:3472
Coaches: Anders Persson, Edward Hsiao
Yixuan Wu (student)
"Great Vax-pectations: Pre-vaccination immune subsets predict the influenza vaccine response in humans"
Tsang JS et al., Global analyses of human immune variation reveal baseline predictors of postvaccination responses. Cell. 2014 Apr 10; 157(2) : 499-513
Coaches: Anthony DeFranco and Noah Zaitlen
May 29, 2014
Melissa Ng (student)
"A new way to suppress: Protein kinase C-η controls CTLA-4-mediated regulatory T cell function"
Kong et al., Protein kinase C-η controls CTLA-4 mediated regulatory T cell function, Nat Immunology, 2014 Apr 06, 15, 466-472
Coaches: Tang Qizhi and Jeoung-Sook Shin
Yang Zhang (student)
"Metabolites: A Bridge Between Monocytes and Macrophages"
Haldar M et al., Heme-Mediated SPI-C Induction Promotes Monocyte Differentiation into Iron-Recycling Macrophages. Cell. 2014 Mar 13;156(6):1223-34
Coaches: Jason Cyster and Mark Ansel
June 05, 2014
KT Nguyen (student)
"Grow Lights for Oligodendrocytes: Optogenetic activation of neurons promotes oligodendrogenesis"
Gibson E, et al. Neuronal Activity Promotes Oligodendrogenesis and Adaptive Myelination in the Mammalian Brain. Science. 2014 May 2;344(6183)
Coaches: Stephen Fancy and Jonah Chan
Mario Zubia (student)
"Out with the old and in with the new: How learning can lead to forgetting"
Hippocampal Neurogenesis Regulates Forgetting During Adulthood and Infancy. Akers KG, et al. Science. 2014 May 9; 344 (6184), 598-602.
Coaches: Saul Villeda and Arturo Alvarez-Buyulla
June 12, 2014
Rachel O'Keefe (student)
"Who Wants to Be a MLLionaire?: Accumulation of MLL Fusion Proteins Triggers Cell Cycle Arrest and Apoptosis in Pro-B MLL Leukemia Cells"
Liu H et al, Proteasome inhibitors evoke latent tumor suppression programs in pro-B MLL leukemias through MLL-AF4. Cancer Cell. 2014 Apr 14;25(4):530-42
Coaches: Scott Oakes and Neil Shah
Pallavi Penumetcha (student)
"Diet and Immunity: How Fiber Intake Can Reduce Peripheral Inflammation"
Trompette A et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med. 2014 Feb;20(2):159-66. doi: 10.1038/nm.3444. Epub 2014 Jan 5.
Coaches: Susan Lynch and Jeoung-Sook Shin