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: Laura Landweber, Ph.D. Friday February 2nd, 2018

Friday Lectures

Friday, February 2nd, 2018  3:45 p.m.

Caspary Auditorium

Laura Landweber, Ph.D.

 Professor

Biochemistry and Molecular Biophysics and Biological Sciences

Columbia University

RNA-programmed genome rearrangement and editing in the ciliate Oxytricha

Recommended Readings:

Science News

Greg Miller. This Bizarre Organism Builds Itself a New Genome Every Time It Has Sex. (2014, Sep 17). Wired

Empirical Articles

Khurana, Jaspreet S.; Clay, Derek M.; Moreira, Sandrine; et al.(2018). Small RNA-mediated regulation of DNA dosage in the ciliate Oxytricha. RNA. 24 (1): 18-29

Lindblad, Kelsi A.; Bracht, John R.; Williams, April E.; et al. (2017). Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development. RNA. 23 (8): 1200-1208

Chen, Xiao; Bracht, John R.; Goldman, Aaron David; et al. (2014). The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development. CELL. 158 (5): 1187-1198

Swart, Estienne C.; Bracht, John R.; Magrini, Vincent; et al. (2013). The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes. PLOS BIOLOGY. 11 (1).

Goldman, Aaron David; Landweber, Laura F. (2012). Oxytricha as a modern analog of ancient genome evolution. TRENDS IN GENETICS. 28 (8): 382-388

Fang, Wenwen; Wang, Xing; Bracht, John R.; et al. (2012). Piwi-Interacting RNAs Protect DNA against Loss during Oxytricha Genome Rearrangement. CELL. 151 (6): 1243-1255

Nowacki, Mariusz; Haye, Joanna E.; Fang, Wenwen; et al. (2010). RNA-mediated epigenetic regulation of DNA copy number. PNAS. 107 (51): 22140-22144

Nowacki, Mariusz; Vijayan, Vikram; Zhou, Yi; et al. (2008). RNA-mediated epigenetic programming of a genome-rearrangement pathway. NATURE. 451 (7175): 153-U4

Review Papers

Bracht, John R.; Fang, Wenwen; Goldman, Aaron David; et al. (2013). Genomes on the Edge: Programmed Genome Instability in Ciliates. CELL. 152 (3): 406-416

Goldman, Aaron David; Landweber, Laura F. (2012). Oxytricha as a modern analog of ancient genome evolution. TRENDS IN GENETICS. 28 (8): 382-388

Book Chapter

Nowacki, Mariusz; Shetty, Keerthi; Landweber, Laura F. (2011). RNA-Mediated Epigenetic Programming of Genome Rearrangements. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. Book Series: Annual Review of Genomics and Human Genetics. 12: 367-389

Edited Books

Landweber, L. F. and Winfree, E., eds. (2003) Evolution as Computation. Springer Verlag.

Landweber, L. F. and Dobson, A. P., eds. (1999) Genetics and the Extinction of Species: DNA and the Conservation of Biodiversity. Princeton University Press. PLEASE REQUEST FROM MARKUS LIBRARY.

Landweber, L. and Baum, E., eds. (1998) DNA Based Computers II. American Mathematical Society. PLEASE REQUEST FROM MARKUS LIBRARY.

 

Recommended Readings: Thomas Tuschl, Ph.D., Monday October 30th, 2017

Monday Lectures

Monday, October 30, 2017  3:45 p.m.

Carson Family Auditorium

Thomas Tuschl, Ph.D.

Professor and Head

Laboratory of RNA Molecular Biology

The Rockefeller University

Molecular and Textual RNA Quality Control

Recommended Readings:

Garzia, Aitor; Jafarnejad, Seyed Mehdi; Meyer, Cindy; et al. (2017). The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs.  NATURE COMMUNICATIONS. Article Number:16056

Juszkiewicz, Szymon; Hegde, Ramanujan S. (2017). Initiation of Quality Control during Poly(A) Translation Requires Site-Specific Ribosome Ubiquitination. MOLECULAR CELL.  65 (4): 743-+

Garzia, Aitor; Meyer, Cindy; Morozov, Pavel; et al. (2017). Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNAbinding proteins. METHODS. 118: 24-40

Sundaramoorthy, Elayanambi; Leonard, Marilyn; Mak, Raymond; et al. (2017). ZNF598 and RACK1 Regulate Mammalian Ribosome-Associated Quality Control Function by Mediating Regulatory 40S Ribosomal Ubiquitylation. MOLECULAR CELL. 65 (4 ): 751-+

Gerstberger, Stefanie; Hafner, Markus; Tuschl, Thomas (2014). A census of human RNA-binding proteins. NATURE REVIEWS GENETICS. 15 (12): 829-845

Zhao, Shanrong; Prenger, Kurt; Smith, Lance; et al. (2013). Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing. BMC GENOMICS. 14

Hafner, Markus; Landthaler, Markus; Burger, Lukas; et al. (2010). Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP. CELL. 41 (1): 129-141

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: Daniel Kronauer, Ph.D., Friday September 15th, 2017

Friday Lectures

Friday, September 15, 2017  3:45 p.m.

Caspary Auditorium

Daniel Kronauer, Ph.D.

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

Laboratory of Social Evolution and Behavior

The Rockefeller University

Communication and Social Behavior in Ants

Recommended Readings:

News provided by NYU Langone Health (2017). Mutant Ants provide insights into social interaction.

Trible, Waring; Olivos-Cisneros, Leonora; McKenzie, Sean K.; et al. (2017). orco Mutagenesis Causes Loss of Antennal Lobe Glomeruli and Impaired Social Behavior in Ants. CELL. 170 (4): 727-+  

McKenzie, Sean K.; Fetter-Pruneda, Ingrid; Ruta, Vanessa; et al. (2016). Transcriptomics and neuroanatomy of the clonal raider ant implicate an expanded clade of odorant receptors in chemical communication. PNAS. 113 (49): 14091-14096

Leonhardt, Sara Diana; Menzel, Florian; Nehring, Volker; et al. (2016). Ecology and Evolution of Communication in Social Insects. CELL. 164 (6): 1277-1287

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  

Sumner, Seirian (2014). The importance of genomic novelty in social evolution. MOLECULAR ECOLOGY. 23 (1): 26-28

 

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: 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