Recommended Readings: Li Zhao, Ph.D. Monday April 15, 2019

Monday Lectures

Monday, April 15, 2019  4:00 p.m.

Carson Family Auditorium

Li Zhao, Ph.D.

Assistant Professor and Head

Laboratory of Evolutionary Genetics and Genomics

The Rockefeller University

The Origin and Evolution of De Novo Genes

 

Recommended Readings:

Empirical Articles

Matthews, Benjamin J.; Dudchenko, Olga; Kingan, Sarah B.; et al. (2018). Improved reference genome of Aedes aegypti informs arbovirus vector control. NATURE. 563 (7732): 501-+

Zhao, Li; Begun, David J. (2017). Genomics of parallel adaptation at two timescales in Drosophila. PLOS GENETICS. 13 (10)

Svetec, Nicolas; Cridland, Julie M.; Zhao, Li; et al. (2016). The adaptive significance of natural genetic variation in the DNA damage response of Drosophila melanogaster. PLOS GENETICS. 12 (3)

Li, Xueyan; Fan, Dingding; Zhang, Wei; et al. (2015). Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies. NATURE COMMUNICATIONS. 6

Zhao, Li; Wit, Janneke; Svetec, Nicolas; et al. (2015). Parallel gene expression differences between low and high latitude populations of Drosophila melanogaster and D. simulans. PLOS GENETICS. 11 (5)

Zhao, Li; Saelao, Perot; Jones, Corbin D.; et al. (2014). Origin and spread of de novo genes in Drosophila melanogaster populations. SCIENCE. 343 (6172): 769–772

Ding, Yun; Zhao, Li; Yang, Shuang; et al. (2010). A Young Drosophila Duplicate Gene Plays Essential Roles in Spermatogenesis by Regulating Several Y- Linked Male Fertility Genes. PLOS GENETICS. 6 (12)

Recommended Readings: Mandë Holford, Ph.D., Thursday April 25th, 2019

Special Seminar Series

Thursday, April 25, 2019  4:00 p.m.

Carson Family Auditorium

Mandë Holford, Ph.D.

Associate Professor

Department of Chemistry and Biology

The City University of New York – Hunter College & Graduate Center

 

 

The Transformative Power of Venom in Evolution and Biomedical Applications

Recommended Readings:

Science News

Emily Driscoll and Luke Groskin. (2017, Nov 2). Breakthrough: The Killer Snail Chemist. Science Friday

Empirical Articles

Eriksson, Anders; Anand, Prachi; Gorson, Juliette; et al. (2018). Using Drosophila behavioral assays to characterize terebrid venom-peptide bioactivity. SCIENTIFIC REPORTS. 8

Leffler, Abba E.; Kuryatov, Alexander; Zebroski, Henry A.; et al. (2017). Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models. PNAS. 114 (38): E8100-E8109

Kelly, Patrick; Anand, Prachi; Uvaydov, Alexander; et al. (2015). Developing a Dissociative Nanocontainer for Peptide Drug Delivery. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH. 12 (10): 12543-12555

Gorson, Juliette; Ramrattan, Girish; Verdes, Aida; et al. (2015). Molecular Diversity and Gene Evolution of the Venom Arsenal of Terebridae Predatory Marine Snails. GENOME BIOLOGY AND EVOLUTION. 7 (6): 1761-1778

Anand, Prachi; Grigoryan, Alexandre; Bhuiyan, Mohammed H.; et al. (2014). Sample Limited Characterization of a Novel Disulfide-Rich Venom Peptide Toxin from Terebrid Marine Snail Terebra variegate. PLOS ONE. 9 (4)

Review Papers

Napolitano, Tanya; Holford, Mande. (2018). Breakthroughs in Venom Peptide Screening Methods to Advance Future Drug Discovery. PROTEIN AND PEPTIDE LETTERS. 25 (12): 1137-1148. PLEASE REQUEST FROM MARKUS LIBRARY.

Verdes, Aida; Anand, Prachi; Gorson, Juliette; et al. (2016). From Mollusks to Medicine: A Venomics Approach for the Discovery and Characterization of Therapeutics from Terebridae Peptide Toxins. TOXINS. 8 (4)

Book Chapters

Verdes, Aida; Holford, Mande. (2018). Beach to Bench to Bedside: Marine Invertebrate Biochemical Adaptations and Their Applications in Biotechnology and Biomedicine. Marine Organisms as Model Systems in Biology and Medicine. RESULTS AND PROBLEMS IN CELL DIFFERENTIATION Book Series. 65. PLEASE REQUEST FROM MARKUS LIBRARY.

Fry, Bryan G.; Koludarov, Ivan; Jackson, Timothy N. W.; et al. (2015). Seeing the Woods for the Trees: Understanding Venom Evolution as a Guide for Biodiscovery. VENOMS TO DRUGS: VENOM AS A SOURCE FOR THE DEVELOPMENT OF HUMAN THERAPEUTICS. 42: 1-36. PLEASE REQUEST FROM MARKUS LIBRARY.

Recommended Readings: Sebastian Klinge, Ph.D. Friday April 12, 2019

Friday Lectures

Friday, April 12, 2019  3:45 p.m

Caspary Auditorium

Sebastian Klinge Ph.D.

Assistant Professor and Head

Laboratory of Protein and Nucleic Acid Chemistry

The Rockefeller University

Nucleolar Assembly of the Small Ribosomal Subunit

 

Recommended Readings:

Empirical Articles

Chaker-Margot, Malik; Klinge, Sebastian. (2019). Assembly and early maturation of large subunit precursors. RNA. 25 (4): 465-471

Chaker-Margot, Malik; Barandun, Jonas; Hunziker, Mirjam; et al. (2017). Architecture of the yeast small subunit processome. SCIENCE. 355 (6321)

Barandun, Jonas; Chaker-Margot, Malik; Hunziker, Mirjam; et al. (2017). The complete structure of the small-subunit processome. NATURE STRUCTURAL AND MOLECULAR BIOLOGY. 24 (11): 944-+

Hunziker, Mirjam; Barandun, Jonas; Petfalski, Elisabeth; et al. (2016). UtpA and UtpB chaperone nascent pre-ribosomal RNA and U3 snoRNA to initiate eukaryotic ribosome assembly. NATURE COMMUNICATIONS. 7

Chaker-Margot, Malik; Hunziker, Mirjam; Barandun, Jonas; et al. (2015). Stage-specific assembly events of the 6-MDa small-subunit processome initiate eukaryotic ribosome biogenesis. NATURE STRUCTURAL AND MOLECULAR BIOLOGY. 22 (11): 920-923

Review Papers

Klinge, Sebastian; Woolford, John L., Jr. (2019). Ribosome assembly coming into focus. NATURE REVIEWS MOLECULAR CELL BIOLOGY. 20 (2): 116-131

Barandun, Jonas; Hunziker, Mirjam; Klinge, Sebastian. (2018). Assembly and structure of the SSU processome-a nucleolar precursor of the small ribosomal subunit. CURRENT OPINION IN STRUCTURAL BIOLOGY. 49: 85-93

Recommended Readings: Paul Bieniasz, Ph.D. Monday April 1, 2019

Monday Lectures

Monday, April 1, 2019  4:00 p.m.

Carson Family Auditorium

Paul Bieniasz, Ph.D.

Professor and Head

Laboratory of Retrovirology

The Rockefeller University

Virus and host discrimination of self and non-self RNA in HIV-1 infection

Recommended Readings:

Empirical Articles

Takata MA, Soll SJ, Emery A, Blanco-Melo D, Swanstrom R, Bieniasz PD. (2018). Global synonymous mutagenesis identifies cis-acting RNA elements that regulate HIV-1 splicing and replication. PLOS  PATHOGENS.14 (1)

Takata MA, Gonçalves-Carneiro D, Zang TM, Soll SJ, et al. (2017). CG dinucleotide suppression enables antiviral defence targeting non-self RNA. NATURE. 550 (7674): 124-127

Kessl, Jacques J.; Kutluay, Sebla B.; Townsend, Dana; et al. (2016). HIV-1 Integrase Binds the Viral RNA Genome and Is Essential during Virion Morphogenesis. CELL. 166 (5): 1257

Review Paper

Bieniasz, Paul D.; Kutluay, Sebla B. (2018). CLIP-related methodologies and their application to retrovirology. RETROVIROLOGY. 15 (1)

Bieniasz, Paul D. (2012). An overview of intracellular interactions between immunodeficiency viruses and their hosts. AIDS. 26 (10): 1243-1254

Blanco-Melo, Daniel; Venkatesh, Siddarth; Bieniasz, Paul D. (2012). Intrinsic Cellular Defenses against Human Immunodeficiency Viruses. IMMUNITY. 37 (3): 399-411

Book Chapter

Bieniasz, Paul; Telesnitsky, Alice. (2018). Multiple, Switchable Protein: RNA Interactions Regulate Human Immunodeficiency Virus Type 1 Assembly. ANNUAL REVIEW OF VIROLOGY. 5: 165-183

Kutluay, Sebla B.; Bieniasz, Paul D. (2016). Analysis of HIV-1 Gag-RNA Interactions in Cells and Virions by CLIP-seq. HIV PROTOCOLS. 1354: 119-131

 

Recommended Readings: Christopher Chang, Ph.D. Wednesday March 6, 2019

Special Seminar Series

Wednesday, March 6, 2019  4:00 p.m.

Carson Family Auditorium

Christopher Chang, Ph.D.

Chair Professor

Department of Chemistry and Molecular and Cell Biology

University of California, Berkeley

Deciphering Transition Metal Signaling with Activity-Based Sensing

 

Recommended Readings:

Empirical Articles

Su TA, Shihadih DS, Cao W, Detomasi TC, Heffern MC, Jia S, Stahl A, Chang CJ. (2018). A Modular Ionophore Platform for Liver-Directed Copper Supplementation in Cells and Animals. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 140 (42): 13764–13774

Xiao, T.; Ackerman, C. M.; Carroll, E. C.; Jia, S.; et al. (2018). Copper regulates rest-activity cycles through the locus coeruleus-norepinephrine system. NATURE CHEMICAL BIOLOGY. 14: 655-663

Smith, P. T.; Benke, B. P.; Cao, Z.; Kim, et al. (2018). Iron Porphyrins Embedded into a Supramolecular Porous Organic Cage for Electrochemical CO2 Reduction in Water. ANGEWANDTE CHEMIE INTERNATIONAL EDITION. 57: 9684-9688

Aron, Allegra T.; Loehr, Morten O.; Bogena, Jana; et al. (2016). An Endoperoxide Reactivity-Based FRET Probe for Ratiometric Fluorescence Imaging of Labile Iron Pools in Living Cells. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 138 (43): 14338-14346

Dodani, Sheel C.; Firl, Alana; Chan, Jefferson; et al. (2014). Copper is an endogenous modulator of neural circuit spontaneous activity. PNAS. 11 (46): 16280-16285

Dodani, Sheel C.; Domaille, Dylan W.; Nam, Christine I.; et al. (2011). Calcium-dependent copper redistributions in neuronal cells revealed by a fluorescent copper sensor and X-ray fluorescence microscopy. PNAS. 108 (15): 5980-5985

Review Papers

Chang CJ. (2017). Bioinorganic Life and Neural Activity: Toward a Chemistry of Consciousness? ACCOUNTS OF CHEMICAL RESEARCH. 50 (3): 535-538

Ackerman, Cheri M.; Lee, Sumin; Chang, Christopher J. (2017). Analytical Methods for Imaging Metals in Biology: From Transition Metal Metabolism to Transition Metal Signaling. ANALYTICAL CHEMISTRY. 89 (1): 22-41

Cotruvo, Joseph A., Jr.; Aron, Allegra T.; Ramos-Torres, Karla M. et al. (2015). Synthetic fluorescent probes for studying copper in biological systems. CHEMICAL SOCIETY REVIEWS. 44 (13): 4400-4414

 

Recommended Readings: Howard C. Hang, Ph.D. Monday February 25, 2019

Monday Lectures

Monday, February 25, 2019  4:00 p.m.

Carson Family Auditorium

Howard C. Hang Ph.D.

Richard E. Salomon Family Associate Professor and Head

Laboratory of Chemical Biology and Microbial Pathogenesis

The Rockefeller University

Microbiota Modulation of Host Immunity, the SagA continues

Recommended Readings:

Empirical Articles

Liu W, Zhou Y, Peng T, Zhou P, Ding X, Li Z, Zhong H, Xu Y, Chen S, Hang HC, Shao F. (2018). Nε-fatty acylation of multiple membrane-associated proteins by Shigella IcsB effector to modulate host function. NATURE MICROBIOLOGY. 3 (9): 996-1009

Thinon, Emmanuelle; Fernandez, Joseph P.; Molina, Henrik; et al. (2018). Selective Enrichment and Direct Analysis of Protein S-Palmitoylation Sites. JOURNAL OF PROTEOME RESEARCH. 17 (5): 1907-1922

Rangan, Kavita J.; Pedicord, Virginia A.; Wang, Yen-Chih; et al. (2016). A secreted bacterial peptidoglycan hydrolase enhances tolerance to enteric pathogens. SCIENCE. 353 (6306): 1434-1437

Pedicord, Virginia A.; Lockhart, Ainsley A. K.; Rangan, Kavita J.; et al. (2016). Exploiting a host-commensal interaction to promote intestinal barrier function and enteric pathogen tolerance. SCIENCE IMMUNOLOGY. 1 (3)    

Review Paper

Rangan, Kavita J.; Hang, Howard C. (2017). Biochemical Mechanisms of Pathogen Restriction by Intestinal Bacteria. TRENDS IN BIOCHEMICAL SCIENCES. 42 (11): 887-898

Westcott, Nathan P.; Hang, Howard C. (2014). Chemical reporters for exploring ADP-ribosylation and AMPylation at the host-pathogen interface.  CURRENT OPINION IN CHEMICAL BIOLOGY. 23: 56-62

Grammel, Markus; Hang, Howard C. (2013). Chemical reporters for biological discovery. NATURE CHEMICAL BIOLOGY. 9 (8): 475-484

Recommended Readings: Jodi Nunnari, Ph.D. Friday February 15, 2019

Friday Lectures

Friday, February 15, 2019  3:45 p.m

Caspary Auditorium

Jodi Nunnari Ph.D.

Professor and Chair

Department of Molecular and Cellular Biology

University of California

Natural Products as Probes of the Pain Pathway: From Physiology to Atomic Structure

Recommended Readings:

Empirical Articles

Mallat, A.; Uchiyama, L. F.; Lewis, S. C.; et al. (2018). Discovery and characterization of selective small molecule inhibitors of the mammalian mitochondrial division dynamin, DRP1. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS. 499  (3): 556-562

Lewis, Samantha C.; Uchiyama, Lauren F.; Nunnari, Jodi. (2016). ER-mitochondria contacts couple mtDNA synthesis with mitochondrial division in human cells. SCIENCE. 353 (6296)

Labbe, Katherine; Murley, Andrew; Nunnari, Jodi. (2014). Determinants and Functions of Mitochondrial Behavior. ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY. 30: 357-391

Review Papers

Murley, Andrew; Nunnari, Jodi. (2016). The Emerging Network of Mitochondria-Organelle Contacts. MOLECULAR CELL. 61 (5): 648-653

Friedman, Jonathan R.; Nunnari, Jodi. (2014). Mitochondrial form and function. NATURE. 505 (7483): 335-343

Nunnari, Jodi; Suomalainen, Anu. (2012). Mitochondria: In Sickness and in Health. CELL. 148 (6): 1145-1159

Book Chapter

Labbe, Katherine; Murley, Andrew; Nunnari, Jodi. (2014). Determinants and Functions of Mitochondrial Behavior. ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY. 30: 357-391

Recommended Readings: Jue Chen, Ph.D., Monday December 10, 2018

Monday Lectures

Monday, December 10, 2018  4:00 p.m.

Carson Family Auditorium

Jue Chen, Ph.D.

William E. Ford Professor and Head

Laboratory of Membrane Biology and Biophysics

The Rockefeller University

CFTR, the Odd ABC Transporter Responsible for Cystic Fibrosis

 

Recommended Readings:

Empirical Articles

Kim, Youngjin; Chen, Jue. (2018). Molecular structure of human P-glycoprotein in the ATP-bound, outward-facing conformation. SCIENCE. 359 (6378): 915-919

Zhang, Zhe; Liu, Fangyu; Chen, Jue. (2017). Conformational Changes of CFTR upon Phosphorylation and ATP Binding. CELL. 170 (3): 483-+

Liu, Fangyu; Zhang, Zhe; Csanady, Laszlo; et al. (2017). Molecular Structure of the Human CFTR Ion Channel. CELL. 169 (1): 85-+

Zhang, Zhe; Chen, Jue. (2016). Atomic Structure of the Cystic Fibrosis Transmembrane Conductance Regulator. CELL. 167 (6): 1586-+

Oldham, Michael L.; Davidson, Amy L.; Chen, Jue. (2008). Structural insights into ABC transporter mechanism. CURRENT OPINION IN STRUCTURAL BIOLOGY. 18 (6): 726-733

Review Paper

Davidson, Amy L.; Dassa, Elie; Orelle, Cedric; et al. (2008). Structure, function, and evolution of bacterial ATP-binding cassette systems. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS. 72 (2): 317-364

 

Recommended Readings: Alexander Rudensky, Ph.D. Friday December 7, 2018

Friday Lectures

Friday, December 7, 2018  3:45 p.m

Caspary Auditorium

Alexander Rudensky Ph.D.

Tri-institutional Professor and Chair

Immunology Program

Memorial Sloan Kettering Cancer Center

Faces and Functions of Regulatory T Cells

 

Recommended Readings:

Empirical Articles

Fan, Xiying; Moltedo, Bruno; Mendoza, Alejandra; et al. (2018). CD49b defines functionally mature Treg cells that survey skin and vascular tissues. JOURNAL OF EXPERIMENTAL MEDICINE. 215 (11): 2796-2814  

Levine, Andrew G.; Medoza, Alejandra; Hemmers, Saskia; et al. (2017). Stability and function of regulatory T cells expressing the transcription factor T-bet. NATURE. 546 (7658): 421-+

Plitas, George; Konopacki, Catherine; Wu, Kenmin; et al. (2016). Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer. IMMUNITY. 45 (5): 1122-1134

Chinen, Takatoshi; Kannan, Arun K.; Levine, Andrew G.; et al. (2016). An essential role for the IL-2 receptor in T-reg cell function. NATURE IMMUNOLOGY. 17 (11): 1322-1333

By: Feng, Yongqiang; Arvey, Aaron; Chinen, Takatoshi; et al. (2014). Control of the Inheritance of Regulatory T Cell Identity by a cis Element in the Foxp3 Locus. CELL. 158 (4): 749-763

Zheng, Ye; Josefowicz, Steven; Chaudhry, Ashutosh; et al. (2010). Role of conserved non-coding DNA elements in the Foxp3 gene in regulatory T-cell fate. NATURE. 463 (7282): 808-U120  

Review Paper

Li, Ming O.; Rudensky, Alexander Y. (2016). T cell receptor signalling in the control of regulatory T cell differentiation and function. NATURE REVIEWS IMMUNOLOGY. 16 (4): 220-233

Fan, Xiying; Rudensky, Alexander Y. (2016). Hallmarks of Tissue-Resident Lymphocytes. CELL. 164 (6): 1198-1211

Rudensky, Alexander Y. (2011). Regulatory T cells and Foxp3. IMMUNOLOGICAL REVIEWS. 241: 260-268

Book Chapter

Josefowicz, Steven Z.; Lu, Li-Fan; Rudensky, Alexander Y. (2012). Regulatory T Cells: Mechanisms of Differentiation and Function. ANNUAL REVIEW OF IMMUNOLOGY. 30: 531-564

 

Recommended Readings: Molly Przeworski, Ph.D. Friday November 30, 2018

Friday Lectures

Friday, November 30, 2018  3:45 p.m

Caspary Auditorium

Molly Przeworski Ph.D.

Professor

Department of Biological Sciences and Systems Biology

Columbia University

An Evolutionary Perspective on Meiotic Recombination in Vertebrates

 

Recommended Readings:

Science News

Hakhamanesh Mostafavi, Joe Pickrell and Molly Przeworski. Evolutionary geneticists spot natural selection happening now in people. September 11, 2017. The Conversation

Empirical Articles

Schumer, Molly; Xu, Chenling; Powell, Daniel L.; et al. (2018). Natural selection interacts with recombination to shape the evolution of hybrid genomes. SCIENCE. 360 (6389): 656-659  

Baker, Zachary; Schumer, Molly; Haba, Yuki; et al. (2017). Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates. ELIFE. 6

Singhal, Sonal; Leffler, Ellen M.; Sannareddy, Keerthi; et al. (2015). Stable recombination hotspots in birds. SCIENCE. 350 (6263): 928-932

Auton, Adam; Fledel-Alon, Adi; Pfeifer, Susanne; et al. (2012). A Fine-Scale Chimpanzee Genetic Map from Population Sequencing. SCIENCE. 336 (6078): 193-198

Segurel, Laure; Leffler, Ellen Miranda; Przeworski, Molly. (2011). The Case of the Fickle Fingers: How the PRDM9 Zinc Finger Protein Specifies Meiotic Recombination Hotspots in Humans. PLOS BIOLOGY. 9 (12)

Fledel-Alon, Adi; Leffler, Ellen Miranda; Guan, Yongtao; et al. (2011). Variation in Human Recombination Rates and Its Genetic Determinants. PLOS ONE.

Review Paper

Sella, Guy; Petrov, Dmitri A.; Przeworski, Molly; et al. (2009). Pervasive Natural Selection in the Drosophila Genome?. PLOS GENETICS. 5 (6)

Coop, Graham; Przeworski, Molly. (2007). An evolutionary view of human recombination. NATURE REVIEWS GENETICS. 8 (1): 23-34  

Book Chapter

Segurel, Laure; Wyman, Minyoung J.; Przeworski, Molly. (2014). Determinants of Mutation Rate Variation in the Human Germline. ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS. 15: 47-70