Recommended Readings: Titia de Lange, Ph.D., Monday October 15, 2018

Monday Lectures

Monday, October 15, 2018  4:00 p.m.

Carson Family Auditorium

Titia de Lange, Ph.D.

Leon Hess Professor and Head

Laboratory of Cell Biology and Genetics

The Rockefeller University

 

Understanding DSB Repair: How Telomeres Gave Us a Break(through)

 

Recommended Readings:

Science News

Scientists discover a mechanism of drug resistance in breast and ovarian cancer. July 18, 2018. ScienceDaily 

Empirical Articles

Mirman Z, Lottersberger F, Takai H, Kibe T. et al. (2018). 53BP1-RIF1-shieldin counteracts DSB resection through CST- and Polα-dependent fill-in. NATURE. 560 (7716): 112-116

Gong, Yi; Handa, Naofumi; Kowalczykowski, Stephen C.; et al. (2017). PHF11 promotes DSB resection, ATR signaling, and HR. GENES AND DEVELOPMENT. 31 (1): 46-58

Doksani, Ylli; de Lange, Titia. (2016). Telomere-Internal Double-Strand Breaks Are Repaired by Homologous Recombination and PARP1/Lig3-Dependent End-Joining. CELL REPORTS. 17 (6)1646-1656

Lottersberger, Francisca; Karssemeijer, Roos Anna; Dimitrova, Nadya; et al. (2015). 53BP1 and the LINC Complex Promote Microtubule-Dependent DSB Mobility and DNA Repair. CELL. 163 (4):  880-893 

Doksani Y, de Lange T. (2014). The role of double-strand break repair pathways at functional and dysfunctional telomeres. COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY. 6 (12)

Zimmermann, Michal; Lottersberger, Francisca; Buonomo, Sara B.; et al. (2013). 53BP1 Regulates DSB Repair Using Rif1 to Control 5 ‘ End Resection. SCIENCE. 339 (6120): 700-704

Lottersberger, Francisca; Bothmer, Anne; Robbiani, Davide F.; et al. (2013). Role of 53BP1 oligomerization in regulating double-strand break repair. PNAS. 110 (6): 2146-2151

Review Papers

Maciejowski, John; de lange, Titia. (2017). Telomeres in cancer: tumour suppression and genome instability. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 18 (3): 175-186

Zimmerman, Michal; de Lange, Titia. (2014). 53BP1: pro choice in DNA repair. TRENDS IN CELL BIOLOGY. 24 (2)108-117 

Recommended Readings: Michael W. Young, Ph.D., Monday October 8, 2018

Monday Lectures

Monday, October 8, 2018  4:00 p.m.

Carson Family Auditorium

Michael W. Young, Ph.D.

Richard and Jeanne Fisher Professor and Head

Laboratory of Genetics

The Rockefeller University

Genes Controlling Sleep and Circadian Rhythms

Recommended Readings:

Science News

Rosemary Braun. A Simple Blood Test Could Tell You the Time Inside Your Body. September 12, 2018. Discover Magazine

Empirical Articles

Young, Michael W. (2018). Time Travels: A 40-Year Journey from Drosophila’s Clock Mutants to Human Circadian Disorders (Nobel Lecture).  ANGEWANDTE CHEMIE-INTERNATIONAL EDITION. 57 (36): 11532-11539

Top, Deniz; Young, Michael W. (2018). Coordination between Differentially Regulated Circadian Clocks Generates Rhythmic Behavior. COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY. 10 (7)

Lin, Changfan; Top, Deniz; Manahan, Craig C.; et al. (2018). Circadian clock activity of cryptochrome relies on tryptophan-mediated photoreduction. PNAS. 115 (15): 3822-3827

Top, Deniz; O’Neil, Jenna L.; Merz, Gregory E.; et al. (2018). CK1/Doubletime activity delays transcription activation in the circadian clock. ELIFE. 7

Patke, Alina; Murphy, Patricia J.; Onat, Onur Emre; et al. (2017). Mutation of the Human Circadian Clock Gene CRY1 in Familial Delayed Sleep Phase Disorder. CELL.  169 (2): 203-215

Rogulja, Dragana; Young, Michael W. (2012). Control of Sleep by Cyclin A and Its Regulator. SCIENCE. 335 (6076): 1617-1621  

Zoltowski, Brian D.; Vaidya, Anand T.; Top, Deniz; et al. (2011). Structure of full-length Drosophila cryptochrome. NATURE. 480 (7377): 396-U156

Review Papers

Wijnen, Herman; Naef, Felix; Boothroyd, Catharine; et al. (2006). Control of daily transcript oscillations in Drosophila by light and the circadian clock. PLOS GENETICS. 2 (3): 326-343

Book Chapter

Axelrod, Sofia; Saez, Lino; Young, Michael W. (2015). Studying Circadian Rhythm and Sleep Using Genetic Screens in Drosophila. METHODS IN ENZIMOLOGY. 551: 3-27  

Crane, Brian R.; Young, Michael W. (2014). Interactive Features of Proteins Composing Eukaryotic Circadian Clocks. ANNUAL REVIEW OF BIOCHEMISTRY. 83: 191-219

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: Shai Shaham, Ph.D., Monday April 16, 2018

Monday Lectures

Monday, April 16, 2018  4:00 p.m.

Carson Family Auditorium

Shai Shaham, Ph.D.

Richard E. Salomon Family Professor and Head

Laboratory of Developmental Genetics

The Rockefeller University

Uncovering Cell Death Treasure Hiding in Plain Sight

Recommended Readings:

Science News

Brandon Specktor. See How a Single Cell Dies in Gory, Intricate Detail. (March 28, 2018). Live Science

Empirical Articles

Ghose P, Rashid A, Insley P, Trivedi M, Shah P, Singhal A, Lu Y, Bao Z, Shaham S. (2018). EFF-1 fusogen promotes phagosome sealing during cell process clearance in Caenorhabditis elegans. NATURE CELL BIOLOGY. 20 (4):393-399

Malin, Jennifer A.; Kinet, Maxime J.; Abraham, Mary C.; et al. (2016). Transcriptional control of non-apoptotic developmental cell death in C-elegans. CELL DEATH AND DIFFERENTIATION. 23 (12): 1985-1994

Schwendeman, Andrew R.; Shaham, Shai. (2016). A High-Throughput Small Molecule Screen for C-elegans Linker Cell Death Inhibitors. PLOS ONE. 11 (10) 

Kinet, Maxime J.; Malin, Jennifer A.; Abraham, Mary C.; et al. (2016). HSF-1 activates the ubiquitin proteasome system to promote non-apoptotic developmental cell death in C. elegans. ELIFE. 5

Blum, Elyse S.; Abraham, Mary C.; Yoshimura, Satoshi; et al. (2012). Control of Nonapoptotic Developmental Cell Death in Caenorhabditis elegans by a Polyglutamine-Repeat Protein. SCIENCE. 335 (6071): 970-973

Review Papers

Kutscher, Lena M.; Shaham, Shai (2017). Non-apoptotic cell death in animal development. CELL DEATH AND DIFFERENTIATION. 24 (8): 1326-1336

Blum, Elyse S.; Schwendeman, Andrew R.; Shaham, Shai. (2013). PolyQ disease: misfiring of a developmental cell death program? TRENDS IN CELL BIOLOGY. 23 (4): 168-174  

Book Chapters

Malin, Jennifer Zuckerman; Shaham, Shai. (2015). Cell Death in C. elegans Development. CURRENT TOPICS IN DEVELOPMENTAL BIOLOGY. 114: 1-42

Kinet, Maxime J.; Shaham, Shai. (2014). Noncanonical Cell Death in the Nematode Caenorhabditis elegans. METHODS IN ENZYMOLOGY. 545: 157-180

 

Recommended Readings: Daniel Kronauer, Ph.D. Monday April 9, 2018

Monday Lectures

Monday, April 9, 2018  4:00 p.m.

Caspary Auditorium

Daniel Kronauer, Ph.D.

Stanley S. and Sydney R. Shuman Associate Professor and Head

Laboratory of Social Evolution and Behavior

The Rockefeller University

The Evolution of Eusociality in Ants

Recommended Readings:

Science News

Substance that guides ant trail is produced by symbiotic bacteria. April 9, 2018. ScienceDaily

Empirical Articles

von Beeren, Christoph; Brueckner, Adrian; Maruyama, Munetoshi; et al. (2018). Chemical and behavioral integration of army ant-associated rove beetles – a comparison between specialists and generalists. FRONTIERS IN ZOOLOGY. 15

Ulrich, Yuko; Burns, Dominic; Libbrecht, Romain; et al. (2016). Ant larvae regulate worker foraging behavior and ovarian activity in a dose-dependent manner. BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY. 70 (7): 1011-1018

Libbrecht, Romain; Oxley, Peter Robert; Keller, Laurent; et al. (2016). Robust DNA Methylation in the Clonal Raider Ant Brain. CURRENT BIOLOGY. 26 (3): 391-395

Oxley, Peter R.; Ji, Lu; Fetter-Pruneda, Ingrid; et al. (2014). The Genome of the Clonal Raider Ant Cerapachys biroi. CURRENT BIOLOGY. 24 (4): 451-458

Abbot, Patrick; Abe, Jun; Alcock, John; et al. (2011). Inclusive fitness theory and eusociality. NATURE. 471 (7339): E1-E4  

Review Papers

Trible, Waring; Kronauer, Daniel J. C. (2017). Caste development and evolution in ants: it’s all about size. JOURNAL OF EXPERIMENTAL BIOLOGY. 220 (1): 53-62

Libbrecht, Romain; Oxley, Peter R.; Kronauer, Daniel J. C.; et al. (2013). Ant genomics sheds light on the molecular regulation of social organization. GENOME BIOLOGY. 14 (7)

Book Chapter

Ivens, Aniek B. F.; von Beeren, Christoph; Bluethgen, Nico; et al. (2016). Studying the Complex Communities of Ants and Their Symbionts Using Ecological Network Analysis. ANNUAL REVIEW OF ENTOMOLOGY. 6: 353-+

 

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: Alison North, Ph.D. Monday March 26, 2018

Monday Lectures

Monday, March 26, 2018  4:00 p.m.

Carson Family Auditorium

Alison North, Ph.D.

Research Associate Professor and Senior Director

Bio-Imaging Resource Center

The Rockefeller University

A Resolution to Avoid an Evil: The Truth about Resolution, Aberrations, and Co-Localization

Recommended Readings:

Empirical Articles

Demmerle, Justin; Innocent, Cassandravictoria; North, Alison J.; et al. (2017). Strategic and practical guidelines for successful structured illumination microscopy. NATURE PROTOCOLS. 12 (5): 988-1010

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   

Smith, Barry H.; Gazda, Lawrence S.; Conn, Bryan L.; et al. (2011). Hydrophilic Agarose Macrobead Cultures Select for Outgrowth of Carcinoma Cell Populations That Can Restrict Tumor Growth. CANCER RESEARCH. 71 (3): 725-735

Yu, Wei-Ming; Chen, Zu-Lin; North, Alison J.; et al. (2009). Laminin is required for Schwann cell morphogenesis. JOURNAL OF CELL SCIENCE. 122 (7): 929-936

Review Paper

North, AJ. (2006). Seeing is believing? A beginners’ guide to practical pitfalls in image acquisition. JOURNAL OF CELL BIOLOGY. 172 (1): 9-18

Book Chapter

Galdeen, Shawn A.; North, Alison J. (2011). Live Cell Fluorescence Microscopy Techniques. METHODS IN MOLECULAR BIOLOGY.  769: 205-222

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: Thomas Walz, Ph.D. Monday December 11th, 2017

Monday Lectures

Monday, December 11, 2017  3:45 p.m.

Carson Family Auditorium

Thomas Walz, Ph.D.

Professor and Head

Laboratory of Molecular Electron Microscopy

The Rockefeller University

An Experimental Look at Hydrophobic Mismatch

Recommended Readings:

Empirical Articles

Mi, Wei; Li, Yanyan; Yoon, Sung Hwan; et al. (2017). Structural basis of MsbA-mediated lipopolysaccharide transport. NATURE. Volume: 549 (7671): 233-+

Saboe, Patrick O.; Rapisarda, Chiara; Kaptan, Shreyas; et al. (2017). Role of Pore-Lining Residues in Defining the Rate of Water Conduction by Aquaporin-0. BIOPHYSICAL JOURNAL. 112 (5): 953-965

Hite, Richard K.; Yuan, Peng; Li, Zongli; et al. (2015). Cryo-electron microscopy structure of the Slo2.2 Na+-activated K+ channel.  NATURE. 527 (7577): 198-+

Shen, Yue-xiao; Si, Wen; Erbakan, Mustafa; et al. (2015). Highly permeable artificial water channels that can self-assemble into two-dimensional arrays. PNAS. 112 (32):9810-9815

Gonen, T; Cheng, YF; Sliz, P; et al. (2005). Lipid-protein interactions in double-layered two-dimensional AQPO crystals. NATURE. 438 (7068): 633-638

Gonen, T; Sliz, P; Kistler, J; et al. (2004).  Aquaporin-0 membrane junctions reveal the structure of a closed water pore. NATURE. 429 (6988): 193-197

 

Review Paper

Hite, Richard K.; Raunser, Stefan; Walz, Thomas (2007). Revival of electron crystallography. CURRENT OPINION IN STRUCTURAL BIOLOGY. 17 (4): 389-395

Gonen, Tamir; Walz, Thomas (2006). The structure of acquaporins. QUARTERLY REVIEWS OF BIOPHYSICS. 39 (4): 361-396

Book Chapter

Schenk, Andreas D.; Hite, Richard K.; Engel, Andreas; et al. (2010). ELECTRON CRYSTALLOGRAPHY AND AQUAPORINS. METHODS IN ENZYMOLOGY. Book Series: Methods in Enzymology. 483: 91-119

Raunser, Stefan; Walz, Thomas (2009). Electron Crystallography as a Technique to Study the Structure on Membrane Proteins in a Lipidic Environment. ANNUAL REVIEW OF BIOPHYSICS. Book Series: Annual Review of Biophysics. 38: 89-105

 

 

Recommended Readings: Ali H. Brivanlou, Ph.D. Monday November 20th, 2017

Monday Lectures

Monday, November 20, 2017  3:45 p.m.

Carson Family Auditorium

Ali H. Brivanlou, Ph.D.

Robert and Harriet Heilbrunnand Professor and Head

Laboratory of Stem Cell Biology and Molecular Embryology

The Rockefeller University

 

Self-organization of Spatial Patterns in Artificial Human Embryos and Organoids

Recommended Readings:

News

Patrick Monahan.

Empirical Articles

Deglincerti, Alessia; Croft, Gist F.; Pietila, Lauren N.; et al. (2016). Self-organization of the in vitro attached human embryo. NATURE.  533 (7602): 251-+

Etoc, Fred; Metzger, Jakob; Ruzo, Albert; et al. (2016). A Balance between Secreted Inhibitors and Edge Sensing Controls Gastruloid Self-Organization. DEVELOPMENTAL CELL. 39 (3): 302-315  

Haremaki, Tomomi; Deglincerti, Alessia; Brivanlou, Ali H. (2015). Huntingtin is required for ciliogenesis and neurogenesis during early Xenopus development. DEVELOPMENTAL BIOLOGY. 408 (2): 305-315

Warmflash, Aryeh; Sorre, Benoit; Etoc, Fred; et al. (2014). A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. NATURE METHODS. 11 (8): 847-854

Bedzhov, Ivan; Leung, Chuen Yan; Bialecka, Monika; et al. (2014). In vitro culture of mouse blastocysts beyond the implantation stages. NATURE PROTOCOLS.  9 (12): 2732-2739

Review Paper

Simunovic, Mijo; Brivanlou, Ali H. (2017). Embryoids, organoids and gastruloids: new approaches to understanding embryogenesis.  DEVELOPMENT. 144 (6): 976-985

Clevers, Hans (2016). Modeling Development and Disease with Organoids. CELL. 165 (7): 1586-1597