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

 

Recommended Readings: Anja Groth, Ph.D., Friday October 13th, 2017

Friday Lectures

Friday, October 13, 2017  3:45 p.m.

Caspary Auditorium

Anja Groth, Ph.D.

Professor and Group Leader

Biotech Research and Innovation Centre (BRIC)

 University of Copenhagen

Chromatin Replication and Epigenome Maintenance

 

Recommended Readings:

Hammond, Colin M.; Stromme, Caroline B.; Huang, Hongda; et al. (2017). Histone chaperone networks shaping chromatin function. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 18 (3): 141-158

Saredi, Giulia; Huang, Hongda; Hammond, Colin M.; et al. (2016). H4K20me0 marks post-replicative chromatin and recruits the TONSL-MMS22L DNA repair complex. NATURE. 534 (7609): 714-+   

Alabert, Constance; Barth, Teresa K.; Reveron-Gomez, Nazaret; et al. (2015). Two distinct modes for propagation of histone PTMs across the cell cycle. GENES & DEVELOPMENT 29 (6): 585-590

Huang, Hongda; Stromme, Caroline B.; Saredi, Giulia; et al. (2015). A unique binding mode enables MCM2 to chaperone histones H3-H4 at replication forks. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 22 (8): 618-626

Alabert, Constance; Bukowski-Wills, Jimi-Carlo; Lee, Sung-Bau; et al. (2014). Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components.  NATURE CELL BIOLOGY. 16 (3): 281-+

Alabert, Constance; Groth, Anja (2012). Chromatin replication and epigenome maintenance. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 13 (3): 153-167

 

 

Recommended Readings: Kenneth Zaret, Ph.D., Friday May 26th, 2017

Friday Lectures

Friday, May 26, 2017  3:45 p.m.

Caspary Auditorium

Kenneth Zaret, Ph.D.

Joseph Leidy Professor, Department of Cell and Developmental Biology

Director, Institute for Regenerative Medicine

Perelman School of Medicine, University of Pennsylvania

Overcoming Chromatin Barriers to Control Cell Fate

Recommended Readings:

Zaret, Kenneth S.; Lerner, Jonathan; Iwafuchi-Doi, Makiko (2016). Chromatin Scanning by Dynamic Binding of Pioneer Factors. MOLECULAR CELL. 62 (5): 665-667

Zaret, Kenneth S.; Mango, Susan E. (2016). Pioneer transcription factors, chromatin dynamics, and cell fate control. CURRENT OPINION IN GENETICS & DEVELOPMENT. 37: 76-81

Iwafuchi-Doi, Makiko; Donahue, Greg; Kakumanu, Akshay; et al. (2016). The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation. MOLECULAR CELL. 62(1): 79-91

Soufi, Abdenour; Garcia, Meilin Fernandez; Jaroszewicz, Artur; et al. (2015). Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming. CELL. 161(3): 555-568

Zaret, Kenneth S.; Carroll, Jason S. (2011). Pioneer transcription factors: establishing competence for gene expression. GENES & DEVELOPMENT. 25 (21): 2227-2241

 
 

Recommended Readings: Michael P. Rout, Ph.D., Monday May 15th, 2017

Monday Lectures

Monday, May 15, 2017  3:45 p.m.

Carson Family Auditorium

Michael P. Rout, Ph.D.

 Professor and Head,

Laboratory of Cellular and Structural Biology

The Rockefeller University

Getting the Hole Picture: Structure-Function Mapping of the Nuclear Pore Complex

Recommended Readings:

http://www.the-scientist.com/?articles.view/articleNo/47529/title/Nuclear-Pores-Come-into-Sharper-Focus/

Timney, Benjamin L.; Raveh, Barak; Mironska, Roxana; et al. (2016). Simple rules for passive diffusion through the nuclear pore complex. JOURNAL OF CELL BIOLOGY. 215(1): 57-76

Raveh, Barak; Karp, Jerome M.; Sparks, Samuel; et al. (2016). Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA . 113(18): E2489-E2497

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-+

Tu, Li-Chun; Fu, Guo; Zilman, Anton; et al. (2013). Large cargo transport by nuclear pores: implications for the spatial organization of FG-nucleoporins.EMBO JOURNAL. 32(24): 3220-3230

Fernandez-Martinez, Javier; Phillips, Jeremy; Sekedat, Matthew D.; et al. (2012). Structure-function mapping of a heptameric module in the nuclear pore complex. JOURNAL OF CELL BIOLOGY. 196(4): 419-434

Grossman, Einat; Medalia, Ohad; Zwerger, Monika (2012). Functional Architecture of the Nuclear Pore Complex. ANNUAL REVIEW OF BIOPHYSICS. 41: 557-584

Recommended Readings: Sue Biggins, Ph.D., Friday May 5th, 2017

Friday Lectures

Friday, May 5th, 2017   3:45 p.m.

Caspary Auditorium

Sue Biggins, Ph.D.

Member and Associate Director

Division of Basic Sciences

Fred Hutchinson Cancer Research Center

Sensing Tension at Kinetochores

Recommended Readings:

https://www.ibiology.org/ibioseminars/chromosome-segregation.html 

Miller, Matthew P.; Asbury, Charles L.; Biggins, Sue (2016). A TOG Protein Confers Tension Sensitivity to Kinetochore-Microtubule Attachments. CELL. 165(6): 1428-1439

Musacchio, Andrea (2015). The Molecular Biology of Spindle Assembly Checkpoint Signaling Dynamics. CURRENT BIOLOGY.  25(20): R1002-R1018

Biggins, Sue (2015). Under tension: Kinetochores and Basic Research. GENETICS. 200(3): 681-682

London, Nitobe; Biggins, Sue (2014). Signalling dynamics in the spindle checkpoint response. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 15 (11): 735-747

Sarangapani, Krishna K.; Duro, Eris; Deng, Yi; et al. (2014). Sister kinetochores are mechanically fused during meiosis I in yeast. SCIENCE. 346(6206): 248-251

Biggins, Sue (2013). The Composition, Functions, and Regulation of the Budding Yeast Kinetochore. GENETICS. 194(4): 817-846

Gonen, Shane; Akiyoshi, Bungo; Iadanza, Matthew G.; et al. (2012). The structure of purified kinetochores reveals multiple microtubule-attachment sites. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 19( 9): 925-929

 

 

 

 
 
 

 

 

Recommended Readings: Alipasha Vaziri, Ph.D., Monday May 1, 2017

Monday Lectures

Monday, May 1, 2017  3:45 p.m.

Carson Family Auditorium

Alipasha Vaziri, Ph.D.

Associate Professor and Head,

Laboratory of Neurotechnology and Biophysics

The Rockefeller University

Optical Tools for Unraveling Whole-brain Neuronal Circuit Dynamics Underlying Behavior

Recommended Readings:

http://www.news-medical.net/news/20170302/Advances-in-optogenetics.aspx

http://news.mit.edu/2017/multifunctional-tiny-fibers-brain-0221

Prevedel, Robert; Verhoef, Aart J.; Pernia-Andrade, Alejandro J.; et al. (2016).  Fast volumetric calcium imaging across multiple cortical layers using sculpted light. NATURE METHODS. 13(12): 1021-U215

Rupprecht, Peter; Prevedel, Robert; Groessl, Florian; et al. (2015). Optimizing and extending light-sculpting microscopy for fast functional imaging in neuroscience. BIOMEDICAL OPTICS EXPRESS. 6(2): 353-368

Prevedel, Robert; Yoon, Young-Gyu; Hoffmann, Maximilian; et al. (2014). Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy. NATURE METHODS. 11(7): 727-U161

Schrodel, Tina; Prevedel, Robert; Aumayr, Karin; et al. (2013). Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light. NATURE METHODS. 10(10)1013-+

Fenno, Lief; Yizhar, Ofer; Deisseroth, Karl. (2011). The Development and Application of Optogenetics.  ANNUAL REVIEW OF NEUROSCIENCE. 34: 389-412

Andrasfalvy, Bertalan K.; Zemelman, Boris V.; Tang, Jianyong; et al. (2010).Two-photon single-cell optogenetic control of neuronal activity by sculpted light. PNAS. 107(26): 11981-11986

 

 

 

 

 


 

Recommended Readings: Jack W. Szostak, Ph.D., Friday April 24, 2017

Friday Lectures

Friday, April 28, 2017   3:45 p.m.

Caspary Auditorium

Jack W. Szostak, Ph.D.

Professor of Genetics, Chemistry and Chemical Biology

Harvard University

Distinguished Investigator

Department of Molecular Biology and Center for Computational and Integrative Biology

Massachusetts General Hospital

The Surprising Chemistry of Nonenzymatic RNA Replication

Recommended Readings:

https://pandasthumb.org/archives/2013/12/new-szostak-pro.html

Li, Li; Prywes, Noam; Tam, Chun Pong; et al. (2017). Enhanced Nonenzymatic RNA Copying with 2-Aminoimidazole Activated Nucleotides. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 139(5): 1810-1813

Prywes, Noam; Blain, J. Craig; Del Frate, Francesca; et al. (2016). Nonenzymatic copying of RNA templates containing all four letters is catalyzed by activated oligonucleotides. ELIFE.  Article Number: e17756

Szostak, Jack W. (2016). ON THE ORIGIN OF LIFE. MEDICINA-BUENOS AIRES. 76(4): 199-203. PLEASE REQUEST FROM MARKUS LIBRARY

Adamala, Katarzyna; Szostak, Jack W. (2013). Nonenzymatic Template-Directed RNA Synthesis Inside Model Protocells. SCIENCE. 342(6162): 1098-1100

Jack W Szostak. (2012). The eightfold path to non-enzymatic RNA replication. Journal of systems chemistry. 3(2) DOI: 10.1186/1759-2208-3-2

Wochner, Aniela; Attwater, James; Coulson, Alan; et al. (2011). Ribozyme-Catalyzed Transcription of an Active Ribozyme. SCIENCE. 332(6026): 209-212

 

Recommended Readings: Edith Heard, Ph.D., Friday, April 21, 2017

Friday Lectures

Friday, April 21, 2017   3:45 p.m.

Caspary Auditorium

Edith Heard, Ph.D.

Professor and Chair, Epigenetics and Cellular Memory, Collège de France

Director, Department of Genetics and Developmental Biology

Institut Curie

The Epigenetic Dynamics of X-chromosome Inactivation: Fine-tuning Gene Dosage during Development

Recommended Readings:

https://www.sciencedaily.com/releases/2017/04/170417114752.htm

da Rocha, Simao T.; Heard, Edith (2017). Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 24(3): 197-204

Borensztein, Maud; Syx, Laurene; Ancelin, Katia; et al. (2017). Xist-dependent imprinted X inactivation and the early developmental consequences of its failure. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 24(3): 226-+

Giorgetti, Luca; Lajoie, Bryan R.; Carter, Ava C.; et al. (2016). Structural organization of the inactive X chromosome in the mouse. NATURE. 535(7613): 575-+

Wu, Hao; Luo, Junjie; Yu, Huimin; et al. (2014). Cellular Resolution Maps of X Chromosome Inactivation: Implications for Neural Development, Function, and Disease. NEURON. 81(1): 103-119

Gendrel, Anne-Valerie; Heard, Edith (2014). Noncoding RNAs and Epigenetic Mechanisms During X-Chromosome Inactivation.  ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY. 30: 561-580

Nora, Elphege P.; Lajoie, Bryan R.; Schulz, Edda G.; et al. (2012). Spatial partitioning of the regulatory landscape of the X-inactivation centre. NATURE. 485(7398): 381-385
 

Recommended Readings: Peter Campbell, Ph.D. March 31, 2017

Friday Lectures

Friday, March 31, 2017   3:45 p.m.

Caspary Auditorium

Peter Campbell, Ph.D.

Head of Cancer Genetics and Genomics,

The Wellcome Trust Sanger Institute

Interrogating the Architecture of Cancer Genomes

Recommended Readings:

The Past, Present and Future of Genome Sequencing

Forbes, Simon A.; Beare, David; Gunasekaran, Prasad; et al. (2015). COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. NUCLEIC ACIDS RESEARCH. 43(D1): D805-D811

Martincorena, Inigo; Campbell, Peter J. (2015). Somatic mutation in cancer and normal cellsSCIENCE.  349(6255): 1483-1489

Alioto, Tyler S.; Buchhalter, Ivo; Derdak, Sophia; et al. (2015). A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencingNATURE COMMUNICATIONS. 6(10001)

Alexandrov, Ludmil B.; Nik-Zainal, Serena; Wedge, David C.; et al. (2013). Signatures of mutational processes in human cancer. NATURE. 500(7463): 415-+

Yates, Lucy R.; Campbell, Peter J. (2012). Evolution of the cancer genome. NATURE REVIEWS GENETICS. 13(11): 795-806  

 

 

Recommended Readings: Jon Clardy, Ph.D. March 24, 2017

Friday Lectures

Friday, March 24, 2017   3:45 p.m.

Caspary Auditorium

Jon Clardy, Ph.D.

Hsien Wu and Daisy Yen Wu Professor,

Department of Biological Chemistry and Molecular Pharmacology

The Rockefeller University

Small Molecule Modulators of Multilateral Symbioses

Recommended Readings:

https://www.sciencedaily.com/releases/2017/02/170215084450.htm

Pupo, Monica T.; Currie, Cameron R.; Clardy, Jon (2017). Microbial Symbionts of Insects are the Focus of the First International Cooperative Biodiversity Group (ICBG) in Brazil. JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY. 28 (3): 393-401

Ruzzini, Antonio C.; Clardy, Jon (2016). Gene Flow and Molecular Innovation in Bacteria. CURRENT BIOLOGY. 26(18)R859-R864

Cantley, Alexandra M.; Clardy, Jon (2015). Animals in a bacterial world: opportunities for chemical ecology.  NATURAL PRODUCT REPORTS. 32(7): 888-892

Sit, Clarissa S.; Ruzzini, Antonio C.; Van Arnam, Ethan B.; et al. (2015). Variable genetic architectures produce virtually identical molecules in bacterial symbionts of fungus-growing ants. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 112(43)13150-13154

Ramadhar, Timothy R.; Beemelmanns, Christine; Currie, Cameron R.; et al. (2014). Bacterial symbionts in agricultural systems provide a strategic source for antibiotic discover. JOURNAL OF ANTIBIOTICS. 67(1): 53-58

Crawford, Jason M.; Clardy, Jon (2011). Bacterial symbionts and natural products. CHEMICAL COMMUNICATIONS. 47(27): 7559-7566

Oh, Dong-Chan; Poulsen, Michael; Currie, Cameron R.; et al. (2009). Dentigerumycin: a bacterial mediator of an ant-fungus symbiosis.  NATURE CHEMICAL BIOLOGY. 5(6) 391-393