Recommended Readings: Alexander Rudensky, Ph.D. Friday December 7, 2018

Friday Lectures

Friday, December 7, 2018  3:45 p.m

Caspary Auditorium

Alexander Rudensky Ph.D.

Tri-institutional Professor and Chair

Immunology Program

Memorial Sloan Kettering Cancer Center

Faces and Functions of Regulatory T Cells

 

Recommended Readings:

Empirical Articles

Fan, Xiying; Moltedo, Bruno; Mendoza, Alejandra; et al. (2018). CD49b defines functionally mature Treg cells that survey skin and vascular tissues. JOURNAL OF EXPERIMENTAL MEDICINE. 215 (11): 2796-2814  

Levine, Andrew G.; Medoza, Alejandra; Hemmers, Saskia; et al. (2017). Stability and function of regulatory T cells expressing the transcription factor T-bet. NATURE. 546 (7658): 421-+

Plitas, George; Konopacki, Catherine; Wu, Kenmin; et al. (2016). Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer. IMMUNITY. 45 (5): 1122-1134

Chinen, Takatoshi; Kannan, Arun K.; Levine, Andrew G.; et al. (2016). An essential role for the IL-2 receptor in T-reg cell function. NATURE IMMUNOLOGY. 17 (11): 1322-1333

By: Feng, Yongqiang; Arvey, Aaron; Chinen, Takatoshi; et al. (2014). Control of the Inheritance of Regulatory T Cell Identity by a cis Element in the Foxp3 Locus. CELL. 158 (4): 749-763

Zheng, Ye; Josefowicz, Steven; Chaudhry, Ashutosh; et al. (2010). Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate. NATURE. 463 (7282): 808-U120  

Review Paper

Li, Ming O.; Rudensky, Alexander Y. (2016). T cell receptor signalling in the control of regulatory T cell differentiation and function. NATURE REVIEWS IMMUNOLOGY. 16 (4): 220-233

Fan, Xiying; Rudensky, Alexander Y. (2016). Hallmarks of Tissue-Resident Lymphocytes. CELL. 164 (6): 1198-1211

Rudensky, Alexander Y. (2011). Regulatory T cells and Foxp3. IMMUNOLOGICAL REVIEWS. 241: 260-268

Book Chapter

Josefowicz, Steven Z.; Lu, Li-Fan; Rudensky, Alexander Y. (2012). Regulatory T Cells: Mechanisms of Differentiation and Function. ANNUAL REVIEW OF IMMUNOLOGY. 30: 531-564

 

Recommended Readings: Howard C. Hang, Ph.D. Friday October 19, 2018

Friday Lectures

Friday, October 19, 2018  3:45 p.m.

Caspary Auditorium

Howard C. Hang Ph.D.

Richard E. Salomon Family Associate Professor and Head

Laboratory of Chemical Biology and Microbial Pathogenesis

The Rockefeller University

Chemical Dissection of Host-Microbe Interactions

Recommended Readings:

Empirical Articles

Liu W, Zhou Y, Peng T, Zhou P, Ding X, Li Z, Zhong H, Xu Y, Chen S, Hang HC, Shao F. (2018). Nε-fatty acylation of multiple membrane-associated proteins by Shigella IcsB effector to modulate host function. NATURE MICROBIOLOGY. 3 (9): 996-1009

Thinon, Emmanuelle; Fernandez, Joseph P.; Molina, Henrik; et al. (2018). Selective Enrichment and Direct Analysis of Protein S-Palmitoylation Sites. JOURNAL OF PROTEOME RESEARCH. 17 (5): 1907-1922

Westcott N, Fernandez JP, Molina H, Hang HC. (2017). Chemical proteomics reveals ADP-ribosylation of small GTPases during oxidative stress. NATURE CHEMICAL BIOLOGY. 13 (3): 302-308

Peng T, Hang HC. (2016). Site-Specific Bioorthogonal Labeling for Fluorescence Imaging of Intracellular Proteins in Living Cells. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 138 (43): 14423-14433

Rangan, Kavita J.; Pedicord, Virginia A.; Wang, Yen-Chih; et al. (2016). A secreted bacterial peptidoglycan hydrolase enhances tolerance to enteric pathogens. SCIENCE. 353 (6306): 1434-1437

Percher, Avital; Ramakrishnan, Srinivasan; Thinon, Emmanuelle; et al. (2016). Mass-tag labeling reveals site-specific and endogenous levels of protein S-fatty acylation. PNAS. 113 (16): 4302-7

Review Paper

Peng, Tao; Thinon, Emmanuelle; Hang, Howard C. (2016). Proteomic analysis of fatty-acylated proteins. CURRENT OPINION IN CHEMICAL BIOLOGY. 30: 77-86

Westcott, Nathan P.; Hang, Howard C. (2014). Chemical reporters for exploring ADP-ribosylation and AMPylation at the host-pathogen interface.  CURRENT OPINION IN CHEMICAL BIOLOGY. 23: 56-62

Grammel, Markus; Hang, Howard C. (2013). Chemical reporters for biological discovery. NATURE CHEMICAL BIOLOGY. 9 (8): 475-484

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.

Professor

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: 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

 

 

Recommended Readings: James P. Allison, Ph.D., Friday May 12th, 2017

Friday Lectures

Friday, May 2, 2017  3:45 p.m.

Caspary Auditorium

James P. Allison, Ph.D.

Professor and Vivian L. Smith Distinguished Chair of Immunology,

Executive Director of the Immunotherapy Platform

The University of Texas MD Anderson Cancer Center

Immune Checkpoint Blockade in Cancer Therapy: New Insights, Opportunities, and Prospects for a Cure

Recommended Readings:

http://thetartan.org/2017/5/1/scitech/immunotherapy

Hazarika M; Chuk MK; Theoret MR; et al. (2017). U.S. FDA Approval Summary: Nivolumab for Treatment of Unresectable or Metastatic Melanoma Following Progression on Ipilimumab.CLINICAL CANCER RESEARCH. doi: 10.1158/1078-0432

Medina, Patrick J.; Adams, Val R. (2016). PD-1 Pathway Inhibitors: Immuno-Oncology Agents for Restoring Antitumor Immune Responses. PHARMACOTHERAPY. 36(3): 317-334

Sharma, Padmanee; Allison, James P. (2015). Immune Checkpoint Targeting in Cancer Therapy: Toward Combination Strategies with Curative Potential. CELL. 161(2): 205-214

Robert, Caroline; Schachter, Jacob; Long, Georgina V.; et al. (2015). Pembrolizumab versus Ipilimumab in Advanced Melanoma. NEW ENGLAND JOURNAL OF MEDICINE    372(26): 2521-2532

Sharma, Padmanee; Allison, James P. (2015). The future of immune checkpoint therapy. SCIENCE. 348(6230): 56-61

Gubin, Matthew M.; Zhang, Xiuli; Schuster, Heiko; et al. (2014). Checkpoint blockage cancer immunotherapy targets tumour-specific mutant antigens. NATURE. 515(7528): 577-+

Lipson, Evan J.; Drake, Charles G. (2011). Ipilimumab: An Anti-CTLA-4 Antibody for Metastatic Melanoma. CLINICAL CANCER RESEARCH. 17(22): 6958-6962

 

Recommended Readings: Vincent A. Fischetti, Ph.D. April 24, 2017

Monday Lectures

Monday, April 17, 2017  3:45 p.m.

Carson Family Auditorium

Vincent A. Fischetti, Ph.D.

Professor and Head,

Laboratory of Bacterial Pathogenesis and Immunology

The Rockefeller University

Exploiting phage evolution for the development of novel therapeutics

Recommended Readings:

David Bautz. March 20th 2017. CFRX: Phase 2 Trial of CF-301 to Initiate in mid-2017.

Czaplewski, Lloyd; Bax, Richard; Clokie, Martha; et al. (2016). Alternatives to antibiotics-a pipeline portfolio review. LANCET INFECTIOUS DISEASES. 16(2): 239-251

Diez-Martinez, Roberto; De Paz, Hector D.; Garcia-Fernandez, Esther; et al. (2015). A novel chimeric phage lysin with high in vitro and in vivo bactericidal activity against Streptococcus pneumoniae. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY. 70(6): 1763-1773

Bikard, David; Euler, Chad W.; Jiang, Wenyan; et al. (2014). Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. NATURE BIOTECHNOLOGY. 32(11): 1146-1150

Schuch, Raymond; Lee, Han M.; Schneider, Brent C.; et al. (2014). Combination Therapy With Lysin CF-301 and Antibiotic Is Superior to Antibiotic Alone for Treating Methicillin-Resistant Staphylococcus aureus-Induced Murine Bacteremia. JOURNAL OF INFECTIOUS DISEASES. 209(9): 1469-1478

Pastagia, Mina; Schuch, Raymond; Fischetti, Vincent A.; et al. (2013). Lysins: the arrival of pathogen-directed anti-infectives. JOURNAL OF MEDICAL MICROBIOLOGY. 62:1506-1516

Gilmer, Daniel B.; Schmitz, Jonathan E.; Euler, Chad W.; et al. (2013). Novel Bacteriophage Lysin with Broad Lytic Activity Protects against Mixed Infection by Streptococcus pyogenes and Methicillin-Resistant Staphylococcus aureus. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY. 57(6): 2743-2750

 
 

Recommended Readings: Ian A. Wilson D. Phil., D. Sci., Friday February 10, 2017

Friday Lectures

Friday, February 10, 2017   3:45 p.m.

Caspary Auditorium

Ian A. Wilson  D. Phil., D.Sci.

Hansen Professor of Structural Biology, and

Chair, Dept. of Integrative Structural and Computational Biology

The Scripps Research Institute

Broad Neutralization of Influenza Viruses and

Implications for a Universal Vaccine and Therapy

Recommended Readings:

Dreyfus, Cyrille; Laursen, Nick S.; Kwaks, Ted; et al.  (2012). Highly Conserved Protective Epitopes on Influenza B Viruses.  SCIENCE, 337(6100): 1343-1348 

Walker, Laura M.; Huber, Michael; Doores, Katie J.; et al. (2011).  Broad neutralization coverage of HIV by multiple highly potent antibodiesNATURE , 477(7365): 466-U117

Ekiert, Damian C.; Friesen, Robert H. E.; Bhabha, Gira; et al. (2011).  A Highly Conserved Neutralizing Epitope on Group 2 Influenza A VirusesSCIENCE,  333(6044): 843-850 

Gottlieb, Tanya; Ben-Yedidia, Tamar.  (2014)  Epitope-based approaches to a universal influenza vaccine.  JOURNAL OF AUTOIMMUNITY.  54 (Special Issue: SI ):15-20 

He, Fang; Prabakaran, Mookkan; Kumar, Subaschandrabose Rajesh; et al. (2011), Monovalent H5 vaccine based on epitope-chimeric HA provides broad cross-clade protection against variant H5N1 viruses in miceANTIVIRAL RESEARCH,  105: 143-151 

Li, Zhuo; Gabbard, Jon D.; Mooney, Alaina; et al. (2013). Single-Dose Vaccination of a Recombinant Parainfluenza Virus 5 Expressing NP from H5N1 Virus Provides Broad Immunity against Influenza A Viruses.  JOURNAL OF VIROLOGY,  87(10): 5985-5993

Huber, Victor C.; Thomas, Paul G.; McCullers, Jonathan A. (2009).  A multi-valent vaccine approach that elicits broad immunity within an influenza subtypeVACCINE,  27(8): 1192-1200