Recommended Readings: Stephen Goff, Ph.D. Friday May 11, 2018

Friday Lectures

Friday, May 11, 2018  3:45 p.m.

Caspary Auditorium

Stephen Goff Ph.D.

Higgins Professor

Department of Biochemistry and Molecular Biophysics

Columbia University College of Physicians and Surgeons

Quiet, Please: Silencing Retroviral DNAs

Recommended Readings:

Empirical Articles

Lee, Andreia; CingOz, Oya; Sabo, Yosef; et al. (2018). Characterization of interaction between Trim28 and YY1 in silencing proviral DNA of Moloney murine leukemia virus. VIROLOGY. 516: 165-175

Geis, Franziska K.; Galla, Melanie; Hoffmann, Dirk; et al. (2017). Potent and reversible lentiviral vector restriction in murine induced pluripotent stem cells. RETROVIROLOGY. 14

Wang, Gary Z.; Goff, Stephen P. (2017). Transcriptional Silencing of Moloney Murine Leukemia Virus in Human Embryonic Carcinoma Cells. JOURNAL OF VIROLOGY. 91 (1)

Wang, Cheng; Goff, Stephen P. (2017). Differential control of retrovirus silencing in embryonic cells by proteasomal regulation of the ZFP809 retroviral repressor. PNAS. 114 (6): E922-E930

Wang, Gary Z.; Wang, Ying; Goff, Stephen P. (2016). Histones Are Rapidly Loaded onto Unintegrated Retroviral DNAs Soon after Nuclear Entry. CELL HOST MICROBE.  20 (6): 798-809

Griffin, Daniel O.; Goff, Stephen P. (2015). HIV-1 Is Restricted prior to Integration of Viral DNA in Primary Cord-Derived Human CD34(+) Cells. JOURNAL OF VIROLOGY. 89 (15): 8096-8100

Yang, Bin Xia; El Farran, Chadi A.; Guo, Hong Chao; et al. (2015). Systematic Identification of Factors for Provirus Silencing in Embryonic Stem Cells. CELL. 163 (1): 230-245

Review Paper

Schlesinger, Sharon; Goff, Stephen P. (2015). Retroviral Transcriptional Regulation and Embryonic Stem Cells: War and Peace. MOLECULAR AND CELLULAR BIOLOGY. 35 (5): 770-777

Studamire, Barbara; Goff, Stephen P. (2010). Interactions of Host Proteins with the Murine Leukemia Virus Integrase. VIRUSES. 2 (5): 1110-1145

Recommended Readings: Gabriel D. Victora, Ph.D., Monday April 23, 2018

Monday Lectures

Monday, April 23, 2018  4:00 p.m.

Carson Family Auditorium

Gabriel D. Victora, Ph.D.

Laurie and Peter Grauer Assistant Professor and Head

Laboratory of Lymphocyte Dynamics

The Rockefeller University

Clonal and Cellular Dynamics of Antibody Evolution

Recommended Readings:

Science News

New tool for tracking ‘kiss-and-run’ communication between cells. January 30, 2018. ScienceDaily

Empirical Articles

Pasqual G, Chudnovskiy A, Tas JMJ, Agudelo M, Schweitzer LD, Cui A, Hacohen N, Victora GD. (2018). Monitoring T cell-dendritic cell interactions in vivo by intercellular enzymatic labelling. NATURE. 553 (7689): 496-500

Degn, Soren E.; van der Poel, Cees E.; Firl, Daniel J.; et al. (2017). Clonal Evolution of Autoreactive Germinal Centers. CELL. 170 (5): 913-+

Ersching, Jonatan; Efeyan, Alejo; Mesin, Luka; et al. (2017). Germinal Center Selection and Affinity Maturation Require Dynamic Regulation of mTORC1 Kinase. IMMUNITY. 46 (6): 1045-+

Amitai, Assaf; Mesin, Luka; Victora, Gabriel D.; et al. (2017). A Population Dynamics Model for Clonal Diversity in a Germinal Center. FRONTIERS IN MICROBIOLOGY. 8  

Tas, Jeroen M. J.; Mesin, Luka; Pasqual, Giulia; et al. (2016). Visualizing antibody affinity maturation in germinal centers. SCIENCE. 351 (6277): 1048-1054

Shulman, Ziv; Gitlin, Alexander D.; Targ, Sasha; et al. (2013). T Follicular Helper Cell Dynamics in Germinal Centers. SCIENCE. 341 (6146): 673-677

Victora, Gabriel D.; Dominguez-Sola, David; Holmes, Antony B.; et al. (2012). Identification of human germinal center light and dark zone cells and their relationship to human B-cell lymphomas. BLOOD. 120 (11): 2240-2248

Victora, Gabriel D.; Schwickert, Tanja A.; Fooksman, David R.; et al. (2010). Germinal Center Dynamics Revealed by Multiphoton Microscopy with a Photoactivatable Fluorescent Reporter. CELL. 143 (4): 592-605

Review Papers

Mesin, Luka; Ersching, Jonatan; Victora, Gabriel D. (2016). Germinal Center B Cell Dynamics. IMMUNITY. 45 (3): 471-482

Victora, Gabriel D.; Wilson, Patrick C. (2015). Germinal Center Selection and the Antibody Response to Influenza. CELL. 163 (3): 545-548

Victora, Gabriel D.; Mesin, Luka. (2014). Clonal and cellular dynamics in germinal centers. CURRENT OPINION IN IMMUNOLOGY. 28: 90-96 

Book Chapter

Victora, Gabriel D.; Nussenzweig, Michel C. (2012). Germinal Centers. ANNUAL REVIEW OF IMMUNOLOGY. 30: 429-457    

Recommended Readings: Michael P. Rout, Ph.D. Monday April 2, 2018

Monday Lectures

Monday, April 2, 2018  4:00 p.m.

Carson Family Auditorium

Michael P. Rout, Ph.D.


Laboratory of Cellular and Structural Biology

The Rockefeller University

A Hole New View: Structure-Function Mapping of the Nuclear Pore Complex

Recommended Readings:

Science News

March 15, 2018. Scientists map the portal to the cell’s nucleus. Science Daily.

Empirical Articles

Upla, Paula; Kim, Seung Joong; Sampathkumar, Parthasarathy; et al. (2017). Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex. STRUCTURE. 25 (3): 434-445

Hayama, Ryo; Rout, Michael P.; Fernandez-Martinez, Javier. (2017). The nuclear pore complex core scaffold and permeability barrier: variations of a common theme. CURRENT OPINION IN CELL BIOLOGY. 46: 110-118

Fernandez-Martinez, Javier; Kim, Seung Joong; Shi, Yi; et al. (2016). Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. CELL. 167 (5): 1215-+

Raveh, Barak; Karp, Jerome M.; Sparks, Samuel; et al. (2016). Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. PNAS. 113 (18): E2489-E2497

Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy; et al. (2014). Integrative Structure-Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex. MOLECULAR & CELLULAR PROTEOMICS. 13 (11): 2911-2926

Wente, Susan R.; Rout, Michael P. (2010). The Nuclear Pore Complex and Nuclear Transport. COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY. 2 (10)

Review Papers

Field, Mark C.; Koreny, Ludek; Rout, Michael P. (2014). Enriching the Pore: Splendid Complexity from Humble Origins. TRAFFIC. 15 (2): 141-156

Strambio-De-Castillia, Caterina; Niepel, Mario; Rout, Michael P. (2010). The nuclear pore complex: bridging nuclear transport and gene regulation. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 11 (7): 490-501

Book Chapter

Jovanovic-Talisman, Tijana; Chait, Brian T.; Rout, Michael P. (2014). NPC Mimics: Probing the Mechanism of Nucleocytoplasmic Transport. METHODS IN CELL BIOLOGY. 122: 379-393  

Recommended Readings: Sanford M. Simon, Ph.D. Monday March 19, 2018

Monday Lectures

Monday, March 19, 2018  4:00 p.m.

Carson Family Auditorium

Sanford M. Simon, Ph.D.

Professor and Head

Laboratory of Cellular Biophysics

The Rockefeller University

ESCRTing Viruses out of the Cell: Lessons from HIV-1

Recommended Readings:

Empirical Articles

Itano, Michelle S.; Arnion, Helene; Wolin, Sandra L.; et al. (2018). Recruitment of 7SL RNA to assembling HIV-1 virus-like particles. TRAFFIC. 19 (1): 36-43

Itano, Michelle S.; Bleck, Marina; Johnson, Daniel S.; et al. (2016). Readily Accessible Multiplane Microscopy: 3D Tracking the HIV-1 Genome in Living Cells. TRAFFIC. 17 (2): 179-186

Bleck, Marina; Itano, Michelle S.; Johnson, Daniel S.; et al. (2014). Temporal and spatial organization of ESCRT protein recruitment during HIV-1 budding. PNAS. 111 (33): 12211-12216

Jouvenet, Nolwenn; Zhadina, Maria; Bieniasz, Paul D.; et al. (2011). Dynamics of ESCRT protein recruitment during retroviral assembly. NATURE CELL BIOLOGY. 13 (4): 394-U124

Jouvenet, Nolwenn; Simon, Sanford M.; Bieniasz, Paul D. (2009). Imaging the interaction of HIV-1 genomes and Gag during assembly of individual viral particles. PNAS. 106 (45): 19114-19119

Jouvenet, Nolwenn; Bieniasz, Paul D.; Simon, Sanford M. (2008). Imaging the biogenesis of individual HIV-1 virions in live cells. NATURE. 454 (7201): 236-240

Review Papers

Jouvenet, Nolwenn; Simon, Sanford M.; Bieniasz, Paul D. (2011). Visualizing HIV-1 Assembly.  JOURNAL OF MOLECULAR BIOLOGY. 410 (4): 501-511

Book Chapter

Woolf, Steven H.; Purnell, Jason Q.; Simon, Sarah M.; et al. (2015). Translating Evidence into Population Health Improvement: Strategies and Barriers. ANNUAL REVIEW OF PUBLIC HEALTH. 36: 463-482


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  


Recommended Readings: Luciano Marraffini, Ph.D., Friday October 20th, 2017

Friday Lectures

Friday, October 20, 2017  3:45 p.m.

Caspary Auditorium

Luciano Marraffini, Ph.D.

Associate Professor and Head

Laboratory of Bacteriology

The Rockefeller University

CRISPR-Cas, Acquired Immunity in Prokaryotes


Recommended Readings:

Niewoehner, Ole; Garcia-Doval, Carmela; Rostol, Jakob T.; et al. (2017). Type III CRISPR-Cas systems produce cyclic oligoadenylate second messengers.  NATURE. 548 (7669): 543-+

Modell, Joshua W.; Jiang, Wenyan; Marraffini, Luciano A. (2017). CRISPR-Cas systems exploit viral DNA injection to establish and maintain adaptive immunity. NATURE. 544 (7648): 101-+  

Marraffini, Luciano A. (2017). Sensing danger. PNAS. 114 (1): 15-16

Heler, Robert; Wright, Addison V.; Vucelja, Marija; et al. (2017). Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response. MOLECULAR CELL. 65 (1): 168-175

Marraffini, Luciano A. (2015). CRISPR-Cas immunity in prokaryotes. NATURE. 526 (7571): 55-61

McGinn, Jon; Marraffini, Luciano A. (2016). CRISPR-Cas Systems Optimize Their Immune Response by Specifying the Site of Spacer Integration. MOLECULAR CELL. 64 (3): 616-623

Barrangou, Rodolphe; Marraffini, Luciano A. (2014). CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity. MOLECULAR CELL. 54 (2): 234-244

Cong, Le; Ran, F. Ann; Cox, David; et al. (2013). Multiplex Genome Engineering Using CRISPR/Cas Systems.  SCIENCE. 339 (6121): 819-823