Recommended Readings: David Reich, Ph.D. Friday April 27, 2018

Friday Lectures

Friday, April 27, 2018  3:45 p.m.

Caspary Auditorium

David Reich Ph.D.

Professor

Department of Genetics

Harvard Medical School

Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past

Recommended Readings:

Science News

Jared Diamond. A Brand-New Version of Our Origin Story. (April 20, 2018). The New York Times

Robin McKie. Neanderthals were perhaps capable of many modern human behaviours. (April 7, 2018). The Guardian

Turi King. Sex, power and ancient DNA. (March 13, 2018). Nature

Empirical Articles

Loreille, Odile ; Ratnayake, Shashikala ; Bazinet, Adam L.; et al. (2018). Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens. GENES. 9 (3): 135

Olalde, Inigo; Brace, Selina; Allentoft, Morten E.; et al. (2018). The Beaker phenomenon and the genomic transformation of northwest Europe. NATURE. 555 (7695): 190-196

Mathieson, Iain; Alpaslan-Roodenberg, Songul; Posth, Cosimo; et al. (2018). The genomic history of southeastern Europe. NATURE. 555 (7695): 197-203

Hajdinjak, Mateja; Fu, Qiaomei; Huebner, Alexander; et al. (2018). Reconstructing the genetic history of late Neanderthals. NATURE. 555 (7698): 652-656

Lipson, Mark; Skoglund, Pontus; Spriggs, Matthew; et al. (2018). Population Turnover in Remote Oceania Shortly after Initial Settlement. CURRENT BIOLOGY. 28 (7): 1157-+

Palkopoulou, Eleftheria; Lipson, Mark; Mallick, Swapan; et al. (2018). A comprehensive genomic history of extinct and living elephants. PNAS. 115 (11): E2566-E2574

Tassi, Francesca; Vai, Stefania; Ghirotto, Silvia; et al. (2017). Genome diversity in the Neolithic Globular Amphorae culture and the spread of Indo-European languages. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. 284 (1867

Haak, Wolfgang; Lazaridis, Iosif; Patterson, Nick; et al. (2015). Massive migration from the steppe was a source for Indo-European languages in Europe. NATURE. 522 (7555): 207-+

Altshuler, David M.; Durbin, Richard M.; Abecasis, Goncalo R.; et al. (2012). An integrated map of genetic variation from 1,092 human genomes. NATURE. 491 (7422): 56-65

Review Paper

Pickrell, Joseph K.; Reich, David. (2014). Toward a new history and geography of human genes informed by ancient DNA. TRENDS IN GENETICS.  30 (9): 377-389

Book

David Reich, Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past (Pantheon Books, New York, and Oxford University Press, Oxford, 2018)

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: Clare Waterman, Ph.D. Friday April 6, 2018

Friday Lectures

Friday, April 6, 2018  3:45 p.m.

Caspary Auditorium

Clare Waterman Ph.D.

NIH Distinguished Investigator

Laboratory of Cell and Tissue Morphodynamics

National Institutes of Health

Integrating Actin Dynamics and Adhesion in Cell Migration and Immune Function

Recommended Readings:

Science News

Live-Cell Microscopy Reveals How Cell Movement is Driven. Dec 11, 2017. GEN News

Empirical Articles

Nordenfelt, Pontus; Moore, Travis I.; Mehta, Shalin B.; et al. (2017). Direction of actin flow dictates integrin LFA-1 orientation during leukocyte migration. NATURE COMMUNCATIONS. 8

Swaminathan, Vinay; Kalappurakkal, Joseph Mathew; Mehta, Shalin B.; et al. (2017). Actin retrograde flow actively aligns and orients ligand-engaged integrins in focal adhesions. PNAS. 114 (40): 10648-10653

Wu, Yicong; Chandris, Panagiotis; Winter, Peter W.; et al. (2016). Simultaneous multiview capture and fusion improves spatial resolution in wide-field and light-sheet microscopy. OPTICA. 3 (8): 897-910

Plotnikov, Sergey V.; Pasapera, Ana M.; Sabass, Benedikt; et al. (2012). Force Fluctuations within Focal Adhesions Mediate ECM-Rigidity Sensing to Guide Directed Cell Migration. CELL. 151 (7): 1513-1527

Kanchanawong, Pakorn; Shtengel, Gleb; Pasapera, Ana M.; et al. (2010). Nanoscale architecture of integrin-based cell adhesions. NATURE. 468 (7323): 580-U262

Review Paper

Case, Lindsay B.; Waterman, Clare M. (2015). Integration of actin dynamics and cell adhesion by a three-dimensional, mechanosensitive molecular clutch. NATURE CELL BIOLOGY. 17 (8): 955-963

Fischer, Robert S.; Wu, Yicong; Kanchanawong, Pakorn; et al. (2011). Microscopy in 3D: a biologist’s toolbox. TRENDS IN CELL BIOLOGY. 21 (12): 682-691

Book Chapter

Skau, Colleen T.; Waterman, Clare M. (2015). Specification of Architecture and Function of Actin Structures by Actin Nucleation Factors. ANNUAL REVIEW OF BIOPHYSICS. 44: 285-310

Gardel, Margaret L.; Schneider, Ian C.; Aratyn-Schaus, Yvonne; et al. (2010). Mechanical Integration of Actin and Adhesion Dynamics in Cell Migration. ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY. 26: 315-333

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: Christopher D. Lima, Ph.D. Friday March 30th, 2018

Friday Lectures

Friday, March 30th, 2018  3:45 p.m.

Caspary Auditorium

Christopher D. Lima, Ph.D.

Professor

Structural Biology Program

Memorial Sloan Kettering Cancer Center

Targeting RNA for Degradation by the Eukaryotic RNA Exosome

Recommended Readings:

Empirical Articles

Wasmuth, Elizabeth V.; Lima, Christopher D. (2017). The Rrp6 C-terminal domain binds RNA and activates the nuclear RNA exosome. NUCLEIC ACIDS RESEARCH. 45 (2): 846-860

Januszyk, Kurt; Lima, Christopher D. (2014). The eukaryotic RNA exosome. CURRENT OPINION IN STRUCTURAL BIOLOGY. 24: 132-140

Zinder, John C.; Wasmuth, Elizabeth V.; Lima, Christopher D. (2016). Nuclear RNA Exosome at 3.1 angstrom Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3. MOLECULAR CELL. 64 (4): 734-745

Wasmuth, Elizabeth V.; Januszyk, Kurt; Lima, Christopher D. (2014). Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA. NATURE. 511 (7510): 435-+

Wasmuth, Elizabeth V.; Lima, Christopher D. (2012). Exo- and Endoribonucleolytic Activities of Yeast Cytoplasmic and Nuclear RNA Exosomes Are Dependent on the Noncatalytic Core and Central Channel. MOLECULAR CELL. 48 (1): 133-144

Liu, Quansheng; Greimann, Jaclyn C.; Lima, Christopher D. (2006). Reconstitution, activities, and structure of the eukaryotic RNA exosome. CELL. 127 (6): 1223-1237

Review Paper

Zinder, John C.; Lima, Christopher D. (2017). Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors. GENES & DEVELOPMENT. 31 (2): 88-100

Book Chapter

Greimann, Jaclyn C.; Lima, Christopher D. (2008). RECONSTITUTION of RNA Exsomes From Human And Saccharomyces Cerevisiae: Clonning, Expression, Purification, And  Activity Assays. METHODS IN ENZYMOLOGY. 448: 185-210

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: Winrich Freiwald, Ph.D. Friday March 23, 2018

Friday Lectures

Friday, March 23rd, 2018  3:45 p.m.

Caspary Auditorium

Winrich Freiwald, Ph.D.

Associate Professor and Head

Laboratory of Neural Systems

The Rockefeller University

On the Neural Circuits of Social Cognition

Recommended Readings:

Science News

Cory Rosenberg. July 8, 2017. How do we know what other people are thinking? This monkey study may offer clues. Mother Nature Network.

Empirical Articles

Sliwa, J.; Freiwald, W. A. (2017). A dedicated network for social interaction processing in the primate brain. SCIENCE. 356 (6339): 745-+

Landi, Sofia M.; Freiwald, Winrich A. (2017). Two areas for familiar face recognition in the primate brain. SCIENCE. 357 (6351): 591-595   

Schwiedrzik, Caspar M.; Freiwald, Winrich A. (2017). High-Level Prediction Signals in a Low-Level Area of the Macaque Face-Processing Hierarchy. NEURON. 96 (1): 89-+

Fisher, Clark; Freiwald, Winrich A. (2015). Whole-agent selectivity within the macaque face-processing system. PNAS. 112 (47): 14717-14722

Schwiedrzik, Caspar M.; Zarco, Wilbert; Everling, Stefan; et al. (2015). Face Patch Resting State Networks Link Face Processing to Social Cognition. PLOS BIOLOGY. 13 (9) 

Meyers, Ethan M.; Borzello, Mia; Freiwald, Winrich A.; et al. (2017). Intelligent Information Loss: The Coding of Facial Identity, Head Pose, and Non-Face Information in the Macaque Face Patch System. JOURNAL OF NEUROSCIENCE. 35 (18): 7069-7081

Freiwald, Winrich A.; Tsao, Doris Y. (2010). Functional Compartmentalization and Viewpoint Generalization Within the Macaque Face-Processing System. SCIENCE. 330 (6005): 845-851

Review Papers

Brecht, Michael; Freiwald, Winrich A. (2012). The many facets of facial interactions in mammals. CURRENT OPINION IN NEUROBIOLOGY. 22 (2): 259-266

Miller, Cory T.; Freiwald, Winrich A.; Leopold, David A.; et al. (2016). Marmosets: A Neuroscientific Model of Human Social Behavior. NEURON. 90 (2): 219-233

Book Chapter

Freiwald, Winrich; Duchaine, Bradley; Yovel, Galit. (2016). Face Processing Systems: From Neurons to Real-World Social Perception.  ANNUAL REVIEW OF NEUROSCIENCE. 39: 325-346

 

Markus Library – Author Book Talk Dr. Siddhartha Mukherjee Thursday March 15, 2018 3:15 p.m.

Dr. Siddhartha Mukherjee
Cancer Physician, Researcher, and Pulitzer Prize winning Author
of The Emperor of All Maladies – New York, NY

Markus Library,  Welch Hall, Level Two Main Reading Room

Thursday, March 15, 2018

Reception at 3:15 and following the presentation.   Author presentation at 3:30

Dr. Mukherjee will share his thoughts and experiences on becoming a best selling author skilled at presenting science effectively to the non science community.

Copies of his 2016 book  The Gene: an Intimate History  will be available for sale at the book talk.