Journal Club

Fall 2017 - Circadian Rhythms and Sleep

October 4: Organizational Meeting
Introductions, GTP advising committee, how to critique a paper, selection of Fall topic.

October 11: Overview– Emily Wheeler, Yeo Lab
Review: Takahashi (2016) Transcriptional architecture of the mammalian clock. Nat Rev Gent. 18: 164-179. [NRG]

October 11: Michael Baughn, Cleveland Lab
Classic Paper: Konopka and Benzer (1971) Clock mutants of Drosophila melanogaster. PNAS 68: 2112-2116. [PNAS] [PMC]

October 18: Spencer Goodman, Cherqui Lab
Curtis (2015) Circadian control of innate immunity in macrophages by miR-155 targeting Bmal1. PNAS 112: 7231–7236. [PNAS] [PMC]

October 25: Samuel Lin, Wasserman Lab
He et al. (2009) The Transcriptional Repressor DEC2 Regulates Sleep Length in Mammals. Science 325: 866-870. [Science] [PMC]

November 1: Alannah Miranda, Kelsoe Lab
Zhang et al. (2016) A PERIOD3 variant causes a circadian phenotype and is associated with a seasonal mood trait. PNAS 113: E1536-44. [PNAS] [PMC]

November 8: Shanna Newton, Mellon Lab
Vitaterna et al. (1994) Mutagenesis and mapping of a mouse gene, Clock, essential for circadian behavior. Science 264: 719-725. [Science] [PMC]

November 15: Alison Parisian, Furnari Lab
Etchegaray et al. (2003) Rhythmic histone acetylation underlies transcription in the mammalian circadian clock. Nature 421: 177-182. [Nature]

November 22: Thanksgiving Holiday

November 29: Brian Reilly, Bejar Lab
Terajima et al. (2017) ADARB1 catalyzes circadian A-to-I editing to regulate RNA rhythm. Nature Genetics 49: 146-151. [Nature Genetics]

December 6: Emily Wheeler, Yeo Lab
Perelis et al. (2015) Pancreatic b cell enhancers regulate rhythmic transcription of genes controlling insulin secretion. Science 350: aac4250. [Science] [PMC]

December 13: Responsible Conduct of Research
Timely public access to data from publicly funded research. Selection of Winter Topic.
Faculty panel

Winter 2018 - Preprints

January 10: Andrew Cooper, Schroeder Lab
Ruan et al. (2017) A cassava drought inducible CC-type glutaredoxin, MeGRX232, negatively regulates drought tolerance in Arabidopsis by inhibition of ABA-dependent stomatal closure. bioRxiv April 12, 2017. [preprint]

January 17: Elie Farah, Chi Lab
Friedman et al. (2017) Cardiac directed differentiation using small molecule Wnt modulation at single-cell resolution. bioRxiv December 7, 2017. [preprint]

January 24: Responsible Conduct of Research
Human subjects in international collaborations. Prof. Joseph Gleeson.

January 31: Nina Gao, Nizet Lab
Charlesworth et al. (2018) Identification of pre-existing adaptive immunity to Cas9 proteins in humans. bioRxiv January 5, 2018. [preprint]

February 7: Shereen Georges, Gleeson Lab
Breuss et al. (2017) Quantification of recurrence risk by direct assessment of paternal sperm mosaicism. bioRxiv October 24, 2017. [preprint]

February 14: Natalie Hollingsworth, Oegema Lab
Melesse et al. (2017) Genetic Identification of Novel Separase regulators in Caenorhabditis elegans. bioRxiv September 22, 2017. [preprint]

February 21: Ryan Marina, Yeo Lab
Saito et al. (2018) Neuron-specific cTag-CLIP reveals cell-specific diversity of functional regulation in the brain. bioRxiv January 8, 2018. [preprint]

February 28: Caroline Sferrazza, Goldstein Lab
Barthet et al. (2018) Presenilin-mediated cleavage of APP regulates synaptotagmin-7 and presynaptic plasticity. bioRxiv February 1, 2018. [preprint]

March 7: Mike Vaill, Varki Lab
Roessler et al. (2017) JIP2 haploinsufficiency contributes to neurodevelopmental abnormalities in human pluripotent stem cell-derived neural progenitors and cortical neurons. bioRxiv September 30, 2017. [preprint]

March 14: Mike Valdez, Farley Lab
Cusanovich et al. (2017) The cis-regulatory dynamics of embryonic development at single cell resolution. bioRxiv. July 20, 2017 [preprint]

Select Spring quarter topic.

Spring 2018 - Synthetic Genomes

April 4: Joshua Chiou, Gaulton Lab
Mercy et al. (2017) 3D organization of synthetic and scrambled chromosomes. Science 355: eaaf4597. [Science] [PMC]

April 11: Ryan Geusz, Sander Lab
Zhang et al. (2017) A semisynthetic organism engineered for the stable expansion of the genetic alphabet. PNAS 114: 1317-1322. [PNAS] [PMC]

Letter from Hettinger [PNAS] and reply [PNAS]

April 18: Emily Griffin, Ackerman Lab
Richardson et al. (2017) Design of a synthetic yeast genome. Science 355: 1040-1044. [Science]

April 25: Madeline Luth, Winzeler Lab
Cello et al. (2002) Chemical synthesis of poliovirus cDNA: Generation of infectious virus in the absence of natural template. Science 297: 1016-1018. [Science]

May 2: Krystyna Kolodziej, Mukamel & Ren Labs
Frieda et al. (2017) Synthetic recording and in situ readout of lineage information in single cells. Nature 541: 107-111. [Nature] [author pdf]

May 9: Tunmise Olayinka, Muotri Lab
Gibson et al. (2010) Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science 329: 52-56. [Science]

May 16: Nathan Palmer, Mali Lab
Plesa, et al (2018). Multiplex gene synthesis in emulsions for exploring protein functional landscapes. Science 359: 343-347. [Science] [preprint]

May 23: Saugat Poudel, Nizet Lab
Shipman et al. (2017) CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature 547: 345-349. [Nature] [PMC]

May 30: Cedric Snethlage, Muotri Lab
Annaluru et al. (2014) Total synthesis of a functional designer eukaryotic chromosome. Science 344: 55-58. [Science] [PMC]

June 6: Responsible Conduct of Research Discussion – Synthetic Genomes
Professor John Glass, JCVI