Recommended Readings: Edward H. Egelman, Ph.D. Friday January 19th, 2018

Friday Lectures

Friday, January 19, 2018  3:45 p.m.

Caspary Auditorium

Edward Egelman, Ph.D.

Harrison Distinguished Professor

Biochemistry and Molecular Genetics

University of Virginia Medical School

Cryo-EM of Protein and Nucleoprotein Polymers at Near-Atomic Resolution

Recommended Readings:

Science News

Kenny Walter. Virus Holds Key to Durable Material. (2017, Jul 20). Virus Holds Key to Durable Material. R&D Magazine

Empirical Articles

Egelman, Edward H. (2017). Cryo-EM of bacterial pili and archaeal flagellar filaments. CURRENT OPINION IN STRUCTURAL BIOLOGY. 46: 31-37

Wang, Fengbin; Burrage, Andrew M.; Postel, Sandra; et al. (2017). A structural model of flagellar filament switching across multiple bacterial species. NATURE COMMUNICATIONS. 8: 960

Wang, Fengbin; Coureuil, Mathieu; Osinski, Tomasz; et al. (2017). Cryoelectron Microscopy Reconstructions of the Pseudomonas aeruginosa and Neisseria gonorrhoeae Type IV Pili at Sub-nanometer Resolution. STRUCTURE. 25 (9): 1423-+

Kasson, Peter; DiMaio, Frank; Yu, Xiong; et al. (2017). Model for a novel membrane envelope in a filamentous hyperthermophilic virus. ELIFE. 6  

Kolappan, Subramania; Coureuil, Mathieu; Yu, Xiong; et al. (2016). Structure of the Neisseria meningitidis Type IV pilus. NATURE COMMUNICATIONS. 7: 13015

Braun, Tatjana; Vos, Matthijn R.; Kalisman, Nir; et al. (2016). Archaeal flagellin combines a bacterial type IV pilin domain with an Ig-like domain. PNAS. 113 (37): 10352-10357

Egelman, Edward H. (2016). The Current Revolution in Cryo-EM. BIOPHYSICAL JOURNAL. 110 (5): 1008-1012

Wang, Ray Yu-Ruei; Kudryashev, Mikhail; Li, Xueming; et al. (2015). De novo protein structure determination from near-atomic-resolution cryo-EM maps. NATURE METHODS. 12 (4): 335-U84

DiMaio, Frank; Yu, Xiong; Rensen, Elena; et al. (2015). A virus that infects a hyperthermophile encapsidates A-form DNA. SCIENCE. 348 (6237): 914-917

Review Papers

Egelman, Edward H. (2015). Three-dimensional reconstruction of helical polymers. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS. 581: 54-58

Recommended Readings: Ruslan Medzhitov, Ph.D. Friday January 12th, 2018

Friday Lectures

Friday, January 12, 2018  3:45 p.m.

Caspary Auditorium

Ruslan Medzhitov, Ph.D.

Sterling Professor

Department of Immunobiology

Yale University

Evolutionary Perspectives on Health and Disease

 

Recommended Readings:

Science News

Ziba Kashef. May 8, 2017. Study pinpoints key pathway in inflammation and aging. YaleNews

Empirical Articles

Ip, W. K. Eddie; Hoshi, Namiko; Shouval, Dror S.; et al. (2017). Anti-inflammatory effect of IL-10 mediated by metabolic reprogramming of macrophages. SCIENCE. 356 (6337): 513-519

Kotas, Maya E.; Medzhitov, Ruslan (2015). Homeostasis, Inflammation, and Disease Susceptibility. CELL. (5): 816-827

Iwasaki, Akiko; Medzhitov, Ruslan (2015). Control of adaptive immunity by the innate immune system. NATURE IMMUNOLOGY. 16 (4): 343-353

Palm, Noah W.; Rosenstein, Rachel K.; Medzhitov, Ruslan (2012). Allergic host defences. NATURE. 484 (7395): 465-472

Review Papers

Medzhitov, Ruslan; Schneider, David S.; Soares, Miguel P. (2012). Disease Tolerance as a Defense Strategy. SCIENCE. 335 (6071): 936-941

Okin, Daniel; Medzhitov, Ruslan (2012). Evolution of Inflammatory Diseases. CURRENT BIOLOGY. 22 (17): R733-R740

Iwasaki, Akiko; Medzhitov, Ruslan (2010). Regulation of Adaptive Immunity by the Innate Immune System. SCIENCE. 327 (5963): 291-295

Recommended Readings: Joan A. Steitz, Ph.D. Friday January 5th, 2018

Friday Lectures

Friday, January 5, 2018  3:45 p.m.

Caspary Auditorium

Joan A. Steitz, Ph.D.

Sterling Professor

Molecular Biophysics and Biochemistry

Yale University

RNA Triple Helices in Cellular and Viral Biology

 

Recommended Readings:

Science News

Michael White. Oct 17, 2017. The Women Who Should Win the Nobel Prize—but Haven’t. PacificStandard

Empirical Articles

Brown, Jessica A.; Kinzig, Charles G.; DeGregorio, Suzanne J.; et al. (2016). Methyltransferase-like protein 16 binds the 3 ‘-terminal triple helix of MALAT1 long noncoding RNA. PNAS. 113 (49): 14013-14018

Brown, Jessica A.; Kinzig, Charles G.; Degregorio, Suzanne J.; et al. (2016). Hoogsteen-position pyrimidines promote the stability and function of the MALAT1 RNA triple helix. RNA. 22 (5): 743-749

Brown, Jessica A.; Bulkley, David; Wang, Jimin; et al. (2014). Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 21 (7): 633-640

Guo, Yang Eric; Riley, Kasandra J.; Iwasaki, Akiko; et al. (2014). Alternative Capture of Noncoding RNAs or Protein-Coding Genes by Herpesviruses to Alter Host T Cell Function. MOLECULAR CELL. 54 (1): 67-79

Brown, Jessica A.; Valenstein, Max L.; Yario, Therese A.; et al. (2012). Formation of triple-helical structures by the 3 ‘-end sequences of MALAT1 and MEN beta noncoding RNAs. PNAS. 109 (47): 19202-19207

Borah, Sumit; Darricarrere, Nicole; Darnell, Alicia; et al. (2011). A Viral Nuclear Noncoding RNA Binds Re-localized Poly(A) Binding Protein and Is Required for Late KSHV Gene Expression. PLOS PATHOGENS. 7 (10)

Mitton-Fry, Rachel M.; DeGregorio, Suzanne J.; Wang, Jimin; et al. (2010). Poly(A) Tail Recognition by a Viral RNA Element Through Assembly of a Triple Helix. SCIENCE. 330 (6008): 1244-1247

Review Papers

Tycowski, Kazimierz T.; Guo, Yang Eric; Lee, Nara; et al. (2015). Viral noncoding RNAs: more surprises. GENES & DEVELOPMENT. 29 (6): 567-584

Cech, Thomas R.; Steitz, Joan A. (2014). The Noncoding RNA Revolution-Trashing Old Rules to Forge New Ones. CELL. 157 (1): 77-94

Recommended Readings: Rachel Wilson, Ph.D. Friday December 15th, 2017

Friday Lectures

Friday, December 15, 2017  3:45 p.m.

Caspary Auditorium

Rachel Wilson, Ph.D.

Martin Family Professor

Department of Neurobiology

Harvard Medical School

Neural Correlates of Orienting Behaviors and Latent Action Biases

 

Recommended Readings:

Empirical Articles

Azevedo, Anthony W.; Wilson, Rachel I. (2017). Active Mechanisms of Vibration Encoding and Frequency Filtering in Central Mechanosensory Neurons. NEURON. 96 (2): 446-+

Tobin, William F.; Wilson, Rachel I.; Lee, Wei-Chung Allen (2017). Wiring variations that enable and constrain neural computation in a sensory microcircuit. ELIFE. 6: e24838

Tuthill, John C.; Wilson, Rachel I. (2016). Parallel Transformation of Tactile Signals in Central Circuits of Drosophila. CELL. 164 (5): 1046-1059

Chang, Allison E. B.; Vaughan, Alex G.; Wilson, Rachel I. (2016). A Mechanosensory Circuit that Mixes Opponent Channels to Produce Selectivity for Complex Stimulus Features. NEURON. 92 (4): 888-901  

Jeanne, James M.; Wilson, Rachel I. (2015). Convergence, Divergence, and Reconvergence in a Feedforward Network Improves Neural Speed and Accuracy. NEURON. 88 (5)

Olsen, Shawn R.; Wilson, Rachel I. (2008). Lateral presynaptic inhibition mediates gain control in an olfactory circuit. NATURE. 452 (7190): 956-U3

Review Papers

Tuthill, John C.; Wilson, Rachel I. (2016). Mechanosensation and Adaptive Motor Control in Insects. CURRENT BIOLOGY. 26 (20): R1022-R1038

Olsen, Shawn R.; Wilson, Rachel I. (2008). Cracking neural circuits in a tiny brain: new approaches for understanding the neural circuitry of Drosophila. TRENDS IN NEUROSCIENCES. 31(10): 512-520

Book Chapter

Wilson, Rachel I. (2013). Early Olfactory Processing in Drosophila: Mechanisms and Principles. ANNUAL REVIEW OF NEUROSCIENCE. Book Series: Annual Review of Neuroscience. 36: 217-241

 

 

 

 

Recommended Readings: Philip Cole, M.D., Ph.D. Friday December 8th, 2017

Friday Lectures

Friday, December 8, 2017  3:45 p.m.

Caspary Auditorium

Philip Cole, M.D., Ph.D.

Professor

Department of Medicine, Biological Chemistry and Molecular Pharmacology

Harvard Medical School

Targeting Reversible Lysine Acetylation with Designed Small Molecules

 

Recommended Readings:

Empirical Articles

Boija, Ann; Mahat, Dig Bijay; Zare, Aman; et al. (2017). CBP Regulates Recruitment and Release of PromoterProximal RNA Polymerase II.  MOLECULAR CELL. 68 (3): 491-+

Lasko, Loren M.; Jakob, Clarissa G.; Edalji, Rohinton P.; et al. (2017). Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours. NATURE. 550 (7674): 128-+

Maksimoska, Jasna; Segura-Pena, Dario; Cole, Philip A.; et al. (2014). Structure of the p300 Histone Acetyltransferase Bound to Acetyl-Coenzyme A and Its Analogues. BIOCHEMISTRY. 53 (21): 3415-3422

Bowers, Erin M.; Yan, Gai; Mukherjee, Chandrani; et al. (2010). Virtual Ligand Screening of the p300/CBP Histone Acetyltransferase: Identification of a Selective Small Molecule Inhibitor.  CHEMISTRY & BIOLOGY. 17 (5): 471-482

Dancy, Beverley M.; Crump, Nicholas T.; Peterson, Daniel J.; et al. (2012). Live-Cell Studies of p300/CBP Histone Acetyltransferase Activity and Inhibition. CHEMBIOCHEM. 13 (14): 2113-2121

Liu, Xin; Wang, Ling; Zhao, Kehao; et al. (2008). The structural basis of protein acetylation by the p300/CBP transcriptional coactivator. NATURE. 451 (7180): 846-850

Review Papers

Dancy, Beverley M.; Cole, Philip A. (2013). Protein Lysine Acetylation by p300/CBP. CHEMICAL REVIEWS. 115 (6): 2419-2452

Cole, Philip A. (2008). Chemical probes for histone-modifying enzymes.  NATURE CHEMICAL BIOLOGY. 4 (10): 590-597

Recommended Readings: Vamsi Mootha, M.D. Friday November 17th, 2017

Friday Lectures

Friday, November 17, 2017  3:45 p.m.

Caspary Auditorium

Vamsi Mootha, M.D.

Professor

Systems Biology and Medicine

Harvard Medical School and Massachusetts General Hospital

Genome-scale Approaches to Mitochondrial Disease

Recommended Readings:

Science News

Howard Hughes Medical Institute. (2017, May 8). Low oxygen reverses mitochondrial disease in mice. ScienceDaily

Empirical Articles

Ferrari, Michele; Jain, Isha H.; Goldberger, Olga; et al. (2017). Hypoxia treatment reverses neurodegenerative disease in a mouse model of Leigh syndrome. PNAS. 114 (21): E4241-E4250

Jain, Isha H.; Zazzeron, Luca; Goli, Rahul; et al. (2016). Hypoxia as a therapy for mitochondrial disease. SCIENCE. 352 (6281): 54-61  

Titov, Denis V.; Cracan, Valentin; Goodman, Russell P.; et al. (2016). Complementation of mitochondrial electron transport chain by manipulation of the NAD(+)/NADH ratio. SCIENCE. 352 (6282): 231-235

Calvo, Sarah E.; Clauser, Karl R.; Mootha, Vamsi K. (2016). MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins.  NUCLEIC ACIDS RESEARCH. 44 (D1): D1251-D1257

Lake, Nicole J.; Bird, Matthew J.; Isohanni, Pirjo; et al. (2015). Leigh Syndrome: Neuropathology and Pathogenesis. JOURNAL OF NEUROPATHOLOGY AND EXPERIMENTAL NEUROLOGY. 74 (6): 482-492  

Lieber, Daniel S.; Calvo, Sarah E.; Shanahan, Kristy; et al. (2013). Targeted exome sequencing of suspected mitochondrial disorders. NEUROLOGY. 80 (19): 1762-1770

Calvo, Sarah E.; Compton, Alison G.; Hershman, Steven G.; et al. (2012). Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing. SCIENCE TRANSLATIONAL MEDICINE. 4 (118)

Calvo, S; Jain, M; Xie, XH; et al. (2006). Systematic identification of human mitochondrial disease genes through integrative genomics. NATURE GENETICS. 38 (5): 576-582

Review Papers

Kamer, Kimberli J.; Mootha, Vamsi K. (2015). The molecular era of the mitochondrial calcium uniporter.  NATURE REVIEWS MOLECULAR CELL BIOLOGY. 16 (9): 545-553

Vafai, Scott B.; Mootha, Vamsi K. (2012). Mitochondrial disorders as windows into an ancient organelle. NATURE. 491 (7424): 374-383

Book Chapter

Calvo, Sarah E.; Mootha, Vamsi K. (2010). The Mitochondrial Proteome and Human Disease. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. Book Series: Annual Review of Genomics and Human Genetics. 11: 25-44

 

Recommended Readings: Sten Linnarsson, Ph.D. Friday November 10th, 2017

Friday Lectures

Friday, November 10, 2017  3:45 p.m.

Caspary Auditorium

Sten Linnarsson, Ph.D.

Professor

Department of Medical Biochemistry and Biophysics

Karolinska Institute

Unraveling Brain Development using Single-cell Technologies

Recommended Readings:

News

Ed Yong. Oct 14, 2016. A Google Maps for the Human Body. The Atlantic

Empirical Articles

Cervo, Pia Rivetti di Val; Romanov, Roman A.; Spigolon, Giada; et al. (2017). Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson’s disease model. NATURE. 35 (5): 444-+

La Manno, Gioele; Gyllborg, Daniel; Codeluppi, Simone; et al. (2016). Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells. CELL. 167 (2): 566-+  

Marques, Sueli; Zeisel, Amit; Codeluppi, Simone; et al. (2016). Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. SCIENCE. 352 (6291): 1326-1329

Zeisel, Amit; Munoz-Manchado, Ana B.; Codeluppi, Simone; et al. (2015). Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. SCIENCE. 347 (6226): 1138-1142

Islam, Saiful; Zeisel, Amit; Joost, Simon; et al. (2014). Quantitative single-cell RNA-seq with unique molecular identifiers.  NATURE METHODS. 11 (2): 163-+

Review Paper

Shapiro, Ehud; Biezuner, Tamir; Linnarsson, Sten (2013). Single-cell sequencing-based technologies will revolutionize whole-organism science.  NATURE REVIEWS GENETICS. 14 (9): 618-630

 

 

 

Recommended Readings: Sohail Tavazoie, M.D., Ph.D. Friday November 3rd, 2017

Friday Lectures

Friday, November 3, 2017  3:45 p.m.

Caspary Auditorium

Sohail Tavazoie, M.D., Ph.D.,

Leon Hess Associate Professor and Head

Elizabeth and Vincent Meyer Laboratory of Systems Cancer Biology

The Rockefeller University

Small RNA Regulation of Cancer Metastasis: Molecular Mechanisms and Therapeutic Application

Recommended Readings:

Kingham, T. Peter; Nguyen, Hoang C. B.; Zheng, Jian; et al. (2017). MicroRNA-203 predicts human survival after resection of colorectal liver metastasis.  ONCOTARGET. 8 (12): 18821-18831

Sengelaub, Caitlin A.; Navrazhina, Kristina; Ross, Jason B.; et al. (2016). PTPRN2 and PLCb1 promote metastatic breast cancer cell migration through PI(4,5)P-2-dependent actin remodeling. EMBO JOURNAL. 35 (1): 62-76  

Goodarzi, Hani; Nguyen, Hoang C. B.; Zhang, Steven; et al. (2016). Modulated Expression of Specific tRNAs Drives Gene Expression and Cancer Progression. CELL. 165 (6): 1416-1427

Lee, Hyeseung; Goodarzi, Hani; Tavazoie, Sohail F.; et al. (2016). TMEM2 Is a SOX4-Regulated Gene That Mediates Metastatic Migration and Invasion in Breast Cancer. CANCER RESEARCH. 76 (17): 4994-5005

Alarcon, Claudio R.; Lee, Hyeseung; Goodarzi, Hani; et al. (2015). N-6-methyladenosine marks primary microRNAs for processing. NATURE. 519 (7544): 482-+

Loo, Jia Min; Scherl, Alexis; Alexander Nguyen; et al. (2015). Extracellular Metabolic Energetics Can Promote Cancer Progression. CELL. 160 (3): 393-406

Pencheva, Nora; Tavazoie, Sohail F. (2013). Control of metastatic progression by microRNA regulatory networks. NATURE CELL BIOLOGY. 15 (6) : 546-554

 

Recommended Readings: Thomas Tuschl, Ph.D., Monday October 30th, 2017

Monday Lectures

Monday, October 30, 2017  3:45 p.m.

Carson Family Auditorium

Thomas Tuschl, Ph.D.

Professor and Head

Laboratory of RNA Molecular Biology

The Rockefeller University

Molecular and Textual RNA Quality Control

Recommended Readings:

Garzia, Aitor; Jafarnejad, Seyed Mehdi; Meyer, Cindy; et al. (2017). The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs.  NATURE COMMUNICATIONS. Article Number:16056

Juszkiewicz, Szymon; Hegde, Ramanujan S. (2017). Initiation of Quality Control during Poly(A) Translation Requires Site-Specific Ribosome Ubiquitination. MOLECULAR CELL.  65 (4): 743-+

Garzia, Aitor; Meyer, Cindy; Morozov, Pavel; et al. (2017). Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNAbinding proteins. METHODS. 118: 24-40

Sundaramoorthy, Elayanambi; Leonard, Marilyn; Mak, Raymond; et al. (2017). ZNF598 and RACK1 Regulate Mammalian Ribosome-Associated Quality Control Function by Mediating Regulatory 40S Ribosomal Ubiquitylation. MOLECULAR CELL. 65 (4 ): 751-+

Gerstberger, Stefanie; Hafner, Markus; Tuschl, Thomas (2014). A census of human RNA-binding proteins. NATURE REVIEWS GENETICS. 15 (12): 829-845

Zhao, Shanrong; Prenger, Kurt; Smith, Lance; et al. (2013). Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing. BMC GENOMICS. 14

Hafner, Markus; Landthaler, Markus; Burger, Lukas; et al. (2010). Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP. CELL. 41 (1): 129-141

Recommended Readings: Sean F. Brady, Ph.D., Friday October 27th, 2017

Friday Lectures

Friday, October 27, 2017  3:45 p.m.

Caspary Auditorium

Sean F. Brady, Ph.D.

Evnin Associate Professor and Head

Laboratory of Genetically Encoded Small Molecules

The Rockefeller University

Watch your step, there is new chemistry everywhere

Recommended Readings:

Cohen LJ, Han S, Huang YH, Brady SF. (2017). Identification of the Colicin V Bacteriocin Gene Cluster by Functional Screening of a Human Microbiome Metagenomic Library.  ACS Infect Dis.  In Press doi: 10.1021/acsinfecdis.7b00081

Fierer, Noah (2017). Embracing the unknown: disentangling the complexities of the soil microbiome. NATURE REVIEWS MICROBIOLOGY. 15 (10): 579-590

Chu, John; Vila-Farres, Xavier; Inoyama, Daigo; et al. (2016). Discovery of MRSA active antibiotics using primary sequence from the human microbiome.  NATURE CHEMICAL BIOLOGY. 12 (12): 1004-+

O’Brien, Sarah L.; Gibbons, Sean M.; Owens, Sarah M.; et al. (2016). Spatial scale drives patterns in soil bacterial diversity.  ENVIRONMENTAL MICROBIOLOGY. 18 (6): 2039-2051

Medema, Marnix H.; Kottmann, Renzo; Yilmaz, Pelin; et al. (2015). Minimum Information about a Biosynthetic Gene cluster. NATURE CHEMICAL BIOLOGY. (11) 9: 625-631

Owen, Jeremy G.; Reddy, Boojala Vijay B.; Ternei, Melinda A.; et al. (2013). Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products. PNAS. 110 (29): 11797-11802