Recommended Readings: Peter Reddien, Ph.D. Friday September 28, 2018

Friday Lectures

Friday, September 28, 2018  3:45 p.m.

Caspary Auditorium

Peter Reddien Ph.D.

Professor and Associate Department Head

Department of Biology

Massachusetts Institute of Technology

How Stem Cells and Positional Information Lead to Planarian Regeneration

Recommended Readings:

Science News

Lisa Girard. A blueprint for regeneration. March 15, 2018. MIT News

Empirical Articles

Fincher, Christopher T.; Wurtzel, Omri; de Hoog, Thom; et al. (2018). Cell type transcriptome atlas for the planarian Schmidtea mediterranea. SCIENCE.  360 (6391): 874-+

Atabay KD, LoCascio SA, de Hoog T, Reddien PW. (2018). Self-organization and progenitor targeting generate stable patterns in planarian regeneration. SCIENCE. 360 (6387):404-409

Scimone, M. Lucila; Cote, Lauren E.; Reddien, Peter W. (2017). Orthogonal muscle fibres have different instructive roles in planarian regeneration. NATURE. 551 (7682): 623-+  

Raz, Amelie A.; Srivastava, Mansi; Salvamoser, Ranja; et al. (2017). Acoel regeneration mechanisms indicate an ancient role for muscle in regenerative patterning. NATURE COMMUNCATIONS. 8

Wurtzel, Omri; Oderberg, Isaac M.; Reddien, Peter W. (2017). Planarian Epidermal Stem Cells Respond to Positional Cues to Promote Cell-Type Diversity. DEVELOPMENTAL CELL. 40 (5): 491-504  

Scimone, M. Lucila; Kravarik, Kellie M.; Lapan, Sylvain W.; et al. (2014). Neoblast Specialization in Regeneration of the Planarian Schmidtea mediterranea. STEM CELLS REPORTS. 3 (2): 339-352

van Wolfswinkel, Josien C.; Wagner, Daniel E.; Reddien, Peter W. (2014). Single-Cell Analysis Reveals Functionally Distinct Classes within the Planarian Stem Cell Compartment. CELL STEM CELL. 15 (3): 326-339

Wagner, Daniel E.; Wang, Irving E.; Reddien, Peter W. (2011). Clonogenic Neoblasts Are Pluripotent Adult Stem Cells That Underlie Planarian Regeneration. SCIENCE. 332 (6031): 811-816  

Review Paper

Tanaka, Elly M.; Reddien, Peter W. (2011). The Cellular Basis for Animal Regeneration. DEVELOPMENTAL CELL. 21 (1): 172-185

Reddien, Peter W. (2011). Constitutive gene expression and the specification of tissue identity in adult planarian biology.  TRENDS IN GENETICS. 27 (7): 277-285  

Book Chapter

Wang IE, Wagner DE, Reddien PW. (2018). Clonal Analysis of Planarian Stem Cells by Subtotal Irradiation and Single-Cell Transplantation. Planarian Regeneration. 1774:479-495

Recommended Readings: David Pellman, M.D. Friday June 1, 2018

Friday Lectures

Friday, June 1, 2018  3:45 p.m.

Caspary Auditorium

David Pellman M.D.

Margaret M. Dyson Professor

Department of Cell Biology

Harvard Medical School

Mechanisms of Rapid Genome Evolution

Recommended Readings:

Science News

Dana-Farber Cancer Institute. Researchers identify origin of chromosomal oddity in some cancer cells. May 27, 2015. EurekAlert

Empirical Articles

Marteil, Gaelle; Guerrero, Adan; Vieira, Andre F.; et al. (2018). Over-elongation of centrioles in cancer promotes centriole amplification and chromosome missegregation. NATURE COMMUNICATIONS. 9    

Zhang, Cheng-Zhong; Spektor, Alexander; Cornils, Hauke; et al. (2015). Chromothripsis from DNA damage in micronuclei. NATURE. 522 (7555): 179-+

Selmecki, Anna M.; Maruvka, Yosef E.; Richmond, Phillip A.; et al. (2015). Polyploidy can drive rapid adaptation in yeast. NATURE. 519 (7543): 349-+

Crasta, Karen; Ganem, Neil J.; Dagher, Regina; et al. (2012). DNA breaks and chromosome pulverization from errors in mitosis. NATURE. 482 (7383): 53-U70

Carter, Scott L.; Cibulskis, Kristian; Helman, Elena; et al. (2012). Absolute quantification of somatic DNA alterations in human cancer. NATURE BIOTECHNOLOGY. 30 (5): 413-+

Ganem, Neil J.; Godinho, Susana A.; Pellman, David. (2009). A mechanism linking extra centrosomes to chromosomal instability. NATURE. 460 (7252): 278-U146

Review Paper

Zhang, Cheng-Zhong; Leibowitz, Mitchell L.; Pellman, David. (2013). Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements. GENES AND DEVELOPMENT. 27 (23): 2513-2530   

Gordon, David J.; Resio, Benjamin; Pellman, David. (2012). Causes and consequences of aneuploidy in cancer. NATURE REVIEWS GENETICS. 13 (3): 189-203

Book Chapter

Leibowitz, Mitchell L.; Zhang, Cheng-Zhong; Pellman, David. (2015). Chromothripsis: A New Mechanism for Rapid Karyotype Evolution. ANNUAL REVIEW OF GENETICS. 49: 183-211

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: 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: 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: Elaine Fuchs, Ph.D. Friday February 23rd, 2018

Friday Lectures

Friday, February 23rd, 2018  3:45 p.m.

Caspary Auditorium

Elaine Fuchs, Ph.D.

Rebecca C. Lancefield Professor and Head

Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development

The Rockefeller University

Stem Cells in Silence, Action, and Cancer

Recommended Readings:

Science News

David Nield. Our Skin Can ‘Remember’ Inflammation, And It Could Help Us Understand Psoriasis. (2017, Oct 21). ScienceAlert

Empirical Articles

Naik, Shruti; Larsen, Samantha B.; Gomez, Nicholas C.; et al. (2017). Inflammatory memory sensitizes skin epithelial stem cells to tissue damage. NATURE. 550 (7677): 475-+

Ge, Yejing; Gomez, Nicholas C.; Adam, Rene C.; et al. (2017). Stem Cell Lineage Infidelity Drives Wound Repair and Cancer. CELL. 169 (4): 636-650

Yang, Hanseul; Adam, Rene C.; Ge, Yejing; et al. (2017). Epithelial-Mesenchymal Micro-niches Govern Stem Cell Lineage Choices. CELL. 69 (3): 483-+  

Asare, Amma; Levorse, John; Fuchs, Elaine. (2017). Coupling organelle inheritance with mitosis to balance growth and differentiation. SCIENCE. 355 (6324): 493-+

Sendoel, Ataman; Dunn, Joshua G.; Rodriguez, Edwin H.; et al. (2017). Translation from unconventional 5 ‘ start sites drives tumour initiation. NATURE. 541 (7638)

Lay, Kenneth; Kume, Tsutomu; Fuchs, Elaine (2016). FOXC1 maintains the hair follicle stem cell niche and governs stem cell quiescence to preserve long-term tissue-regenerating potential. PNAS. 113 (11): E1506-E1515

Ouspenskaia, Tamara; Matos, Irina; Mertz, Aaron F.; et al. (2016). WNT-SHH Antagonism Specifies and Expands Stem Cells prior to Niche Formation. CELL. 164 (1-2): 156-169

Yang, Hanseul; Schramek, Daniel; Adam, Rene C.; et al. (2015). ETS family transcriptional regulators drive chromatin dynamics and malignancy in squamous cell carcinomas. ELIFE. 4. # e10870

Review Papers

Gonzales, Kevin Andrew Uy; Fuchs, Elaine (2017). Skin and Its Regenerative Powers: An Alliance between Stem Cells and Their Niche.  DEVELOPMENTAL CELL. 43 (4): 387-401

Blanpain, Cedric; Fuchs, Elaine (2014). STEM CELL PLASTICITY Plasticity of epithelial stem cells in tissue regeneration. SCIENCE. 344 (6189): 1243-+

Hsu, Ya-Chieh; Li, Lishi; Fuchs, Elaine (2014). Emerging interactions between skin stem cells and their niches. NATURE MEDICINE. 20 (8): 847-856

Book Chapter

Fuchs, Elaine (2016). Epithelial Skin Biology: Three Decades of Developmental Biology, a Hundred Questions Answered and a Thousand New Ones to Address. ESSAYS ON DEVELOPMENTAL BIOLOGY, PT A  Book Series: Current Topics in Developmental Biology. 116: 357-+  

 

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