Recommended Readings: Kivanç Birsoy, Ph.D. Monday May 20, 2019

Monday Lectures

Monday, May 20, 2019  4:00 p.m.

Carson Family Auditorium

Kivanç Birsoy, Ph.D.

Chapman Perelman Assistant Professor and Head

Laboratory of Metabolic Regulation and Genetics

The Rockefeller University

Metabolic Limitations of Cancer Cell Proliferation

  

Recommended Readings:

Science News

Oxygen-Starved Cancer Cells Languish without Aspartate. Jun 25, 2018. Genetic Engineering & Biotechnology News

Empirical Articles

Garcia-Bermudez, Javier; Baudrier, Lou; Bayraktar, Erol Can; et al. (2019). Squalene accumulation in cholesterol auxotrophic lymphomas prevents oxidative cell death. NATURE. 567 (7746): 118-+

Phillips, Richard E.; Yang, Yanhong; Smith, Ryan C.; et al. (2019). Target identification reveals lanosterol synthase as a vulnerability in glioma. PNAS. 116 (16): 7957-7962

Bayraktar, Erol C.; Baudrier, Lou; Ozerdem, Ceren; et al. (2019). MITO-Tag Mice enable rapid isolation and multimodal profiling of mitochondria from specific cell types in vivo. PNAS. 116  (1) : 303-312

Garcia-Bermudez, Javier; Baudrier, Lou; La, Konnor; et al. (2018). Aspartate is a limiting metabolite for cancer cell proliferation under hypoxia and in tumours. NATURE CELL BIOLOGY. 20 (7): 775-+

Peng, Xinxin; Chen, Zhongyuan; Farshidfar, Farshad; et al. (2018). Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. CELL REPORTS. 23 (1): 255-+

Reczek, Colleen R.; Birsoy, Kivanc; Kong, Hyewon; et al. (2017). A CRISPR screen identifies a pathway required for paraquat-induced cell death. NATURE CHEMICAL BIOLOGY. 13 (12): 1274-+

Chen, Walter W.; Freinkman, Elizaveta; Wang, Tim; et al. (2016). Absolute Quantification of Matrix Metabolites Reveals the Dynamics of Mitochondrial Metabolism. CELL. 166 (5): 1324-+

Recommended Readings: George R. Stark, Ph.D. Friday May 10, 2019

Friday Lectures

Friday, May 10, 2019  3:45 p.m

Caspary Auditorium

George R. Stark Ph.D.

Distinguished Scientist

Department of Cancer Biology

Lerner Research Institute, Cleveland Clinic

 

Complex Regulation of Interferon-dependent Signaling in Cancer and Infectious Disease

 

Recommended Readings:

Science News

Promising New Combination Drug Therapy Treats Several Models of Lethal Lung Cancer. March 1, 2018. Cleveland Clinic

Empirical Articles

Banerjee, Shuvojit; Gusho, Elona; Gaughan, Christina; et al. (2019). OAS-RNase L innate immune pathway mediates the cytotoxicity of a DNA-demethylating drug. PNAS. 116 (11): 5071-5076

Nan, Jing; Wang, Yuxin; Yang, Jinbo; et al. (2018). IRF9 and unphosphorylated STAT2 cooperate with NF-kappa B to drive IL6 expression. PNAS. 115 (15): 3906-3911

Stark, George R.; Cheon, HyeonJoo; Wang, Yuxin. (2018). Responses to Cytokines and Interferons that Depend upon JAKs and STATs. COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY. 10 (1)

Wang, Yuxin; Nan, Jing; Willard, Belinda; et al. (2017). Negative regulation of type I IFN signaling by phosphorylation of STAT2 on T387. EMBO JOURNAL. 36 (2): 202-212

Cheon, HyeonJoo; Holvey-Bates, Elise G.; Schoggins, John W.; et al. (2013). IFN beta-dependent increases in STAT1, STAT2, and IRF9 mediate resistance to viruses and DNA damage. EMBO JOURNAL. 32 (20): 2751-2763

Review Papers

Cheon, HyeonJoo; Borden, Ernest C.; Stark, George R. (2014). Interferons and Their Stimulated Genes in the Tumor Microenvironment. SEMINARS IN ONCOLOGY. 41 (2): 156-173

Stark, George R.; Darnell, James E., Jr. (2012). The JAK-STAT Pathway at Twenty. IMMUNITY. 36 (4): 503-514

Cheon, HyeonJoo; Yang, Jinbo; Stark, George R. (2011). The Functions of Signal Transducers and Activators of Transcriptions 1 and 3 as Cytokine-Inducible Proteins. JOURNAL OF INTERFERON AND CYTOKINE RESEARCH. 31 (1): 33-40

Book Chapter

Lu, Tao; Stark, George R. (2015). Using Sequential Immunoprecipitation and Mass Spectrometry to Identify Methylation of NF-kappa B. NF-KAPPA B: METHODS AND PROTOCOLS. 1280: 383-393

 

Recommended Readings: Beth Shapiro, D.Phil, Friday May 3, 2019

Friday Lectures

Friday, May 3, 2019  3:45 p.m

Caspary Auditorium

Beth Shapiro D.Phil

Professor

Department of Ecology and Evolutionary Biology

University of California

 

Can Ancient DNA Reveal What Makes Us Human?

Recommended Readings:

Science News

How to Clone a Mammoth: The Science of De-extinction. April 23, 2019. Technology Networks

Empirical Articles

Fregel, Rosa; Ordonez, Alejandra C.; Santana-Cabrera, Jonathan; et al. (2019). Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands. PLOS ONE. 14 (3)

Fregel, Rosa; Mendez, Fernando L.; Bokbot, Youssef; et al. (2018). Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe. PNAS. 115 (26): 6774-6779

Barlow, Axel; Cahill, James A.; Hartmann, Stefanie; et al. (2018). Partial genomic survival of cave bears in living brown bears. NATURE ECOLOGY & EVOLUTION. 2 (10): 1563-1570. PLEASE REQUEST FROM MARKUS LIBRARY.

Schaefer, Nathan K.; Shapiro, Beth; Green, Richard E. (2016). Detecting hybridization using ancient DNA. MOLECULAR ECOLOGY. 25 (11): 2398-2412

Seguin-Orlando, Andaine; Gamba, Cristina; Sarkissian, Clio Der; et al. (2015). Pros and cons of methylation-based enrichment methods for ancient DNA. SCIENTIFIC REPORTS. 5

Schubert, Mikkel; Jonsson, Hakon; Chang, Dan; et al. (2014). Prehistoric genomes reveal the genetic foundation and cost of horse domestication. PNAS. 111 (52): E5661-E5669

Dalen, Love; Orlando, Ludovic; Shapiro, Beth; et al. (2012). Partial Genetic Turnover in Neandertals: Continuity in the East and Population Replacement in the West. MOLECULAR BIOLOGY AND EVOLUTION. 29 (8): 1893-1897

Review Paper

Supple, Megan A.; Shapiro, Beth (2018). Conservation of biodiversity in the genomics era. GENOME BIOLOGY. 19

Book Chapters

Shapiro, Beth; Hofreiter, Michael (2012). Ancient DNA Methods and Protocols Preface. ANCIENT DNA: METHODS AND PROTOCOLS. 840: V-VII

Nichols RV, Curd E, Heintzman PD, Shapiro B. (2019). Targeted Amplification and Sequencing of Ancient Environmental and Sedimentary DNA. ANCIENT DNA: METHODS AND PROTOCOLS. 1963: 149-161

 

Recommended Readings: Coleen Murphy, Ph.D. Friday April 26, 2019

                                               Friday Lectures

Friday, April 26, 2019  3:45 p.m

Caspary Auditorium

Coleen Murphy Ph.D.

Professor and Director

Glenn Center for Quantitative Aging Research

Princeton University

Transgenerational Inheritance of Pathogen Avoidance (or, How Getting Food Sickness Might Save Your Species)

 

Recommended Readings:

Science News

In a tiny worm, a close-up view of where genes are working. September 18, 2018. Science Daily

Empirical Articles

Moore RS, Kaletsky R, Murphy Coleen Tara. (2018). C. elegans pathogenic learning confers multigenerational pathogen avoidance. BioRxiv

Tabuchi, Tomoko M.; Rechtsteiner, Andreas; Jeffers, Tess E.; et al. (2018). Caenorhabditis elegans sperm carry a histone-based epigenetic memory of both spermatogenesis and oogenesis. NATURE COMMUNICATIONS. 9

Kaletsky, Rachel; Yao, Victoria; Williams, April; et al. (2018). Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression. PLOS GENETICS. 14 (8)

Review Paper

Templeman, Nicole M.; Murphy, Coleen T. (2018). Regulation of reproduction and longevity by nutrient-sensing pathways. JOURNAL OF CELL BIOLOGY. 217 (1): 93-106

Book Chapter

Shi, Cheng; Murphy, Coleen T. (2017). Reproductive Ageing. AGEING: LESSONS FROM C. ELEGANS. 5: 137-162

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