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

Friday Lectures

Friday, November 30, 2018  3:45 p.m

Caspary Auditorium

Molly Przeworski Ph.D.


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

Recommended Readings: Alison North, Ph.D. Monday March 26, 2018

Monday Lectures

Monday, March 26, 2018  4:00 p.m.

Carson Family Auditorium

Alison North, Ph.D.

Research Associate Professor and Senior Director

Bio-Imaging Resource Center

The Rockefeller University

A Resolution to Avoid an Evil: The Truth about Resolution, Aberrations, and Co-Localization

Recommended Readings:

Empirical Articles

Demmerle, Justin; Innocent, Cassandravictoria; North, Alison J.; et al. (2017). Strategic and practical guidelines for successful structured illumination microscopy. NATURE PROTOCOLS. 12 (5): 988-1010

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   

Smith, Barry H.; Gazda, Lawrence S.; Conn, Bryan L.; et al. (2011). Hydrophilic Agarose Macrobead Cultures Select for Outgrowth of Carcinoma Cell Populations That Can Restrict Tumor Growth. CANCER RESEARCH. 71 (3): 725-735

Yu, Wei-Ming; Chen, Zu-Lin; North, Alison J.; et al. (2009). Laminin is required for Schwann cell morphogenesis. JOURNAL OF CELL SCIENCE. 122 (7): 929-936

Review Paper

North, AJ. (2006). Seeing is believing? A beginners’ guide to practical pitfalls in image acquisition. JOURNAL OF CELL BIOLOGY. 172 (1): 9-18

Book Chapter

Galdeen, Shawn A.; North, Alison J. (2011). Live Cell Fluorescence Microscopy Techniques. METHODS IN MOLECULAR BIOLOGY.  769: 205-222

Recommended Readings: Lewis Cantley, Ph.D. Friday March 16, 2018

Friday Lectures

Friday, March 16, 2018  3:45 p.m.

Caspary Auditorium

Lewis Cantley, Ph.D.

Meyer Director of the Sandra and Edward Meyer Cancer Center


Professor of Cancer Biology in Medicine

Weill Cornell Medicine and New York-Presbyterian Hospital

PI 3-Kinase: Linking Obesity, Insulin Resistance, and Cancer

Recommended Readings:

Empirical Articles

Liu H, Murphy CJ, Karreth FA, Emdal KB, White FM, Elemento O, Toker A, Wulf GM, Cantley LC. (2018). Identifying and Targeting Sporadic Oncogenic Genetic Aberrations in Mouse Models of Triple-Negative Breast Cancer. CANCER DISCOVERY. 8 (3):354-369

Waldhart, Althea N.; Dykstra, Holly; Peck, Anderson S.; et al. (2017).  Phosphorylation of TXNIP by AKT Mediates Acute Influx of Glucose in Response to Insulin. CELL REPORTS. 19 (10)2005-2013

Croessmann S, Sheehan JH, Lee KM, Sliwoski G, et al. (2017). PIK3CA C2 Domain Deletions Hyperactivate Phosphoinositide 3-kinase (PI3K), Generate Oncogene Dependence, and Are Exquisitely Sensitive to PI3Kα Inhibitors. CLINICAL CANCER RESEARCH. doi: 10.1158/1078-0432.CCR-17-2141

Fruman, David A.; Chiu, Honyin; Hopkins, Benjamin D.; et al. (2017). The PI3K Pathway in Human Disease. CELL. 170 (4)605-635 

Thorpe, Lauren M.; Spangle, Jennifer M.; Ohlson, Carolynn E.; et al. (2017). PI3K-p110 alpha mediates the oncogenic activity induced by loss of the novel tumor suppressorPI3K-p85 alpha. PNAS.114 (27)7095-7100

Juvekar, Ashish; Hu, Hai; Yadegarynia, Sina; et al. (2016). Phosphoinositide 3-kinase inhibitors induce DNA damage through nucleoside depletion. PNAS. 113 (30): E4338-E4347

Review Papers

Fruman, David A.; Chiu, Honyin; Hopkins, Benjamin D.; et al. (2017). The PI3K Pathway in Human Disease. CELL. 170 (4): 605-635

Heiden, Matthew G. Vander; Cantley, Lewis C.; Thompson, Craig B. (2009). Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation. SCIENCE. 324 (5930): 1029-1033

Yuan, T. L.; Cantley, L. C. (2008). PI3K pathway alterations in cancer: variations on a theme. ONCOGENE. 27 (41): 5497-5510

Book Chapter

Lien, Evan C.; Lyssiotis, Costas A.; Cantley, Lewis C. (2016). Metabolic Reprogramming by the PI3K-Akt-mTOR Pathway in Cancer. METABOLISM IN CANCER. 207: 39-72

Yuan, Tina L.; Cantley, Lewis C. (2010). Phosphoinositide 3-kinase in Health and Disease Volume 1 Introduction. PHOSPHOINOSITIDE 3-KINASE IN HEALTH AND DISEASE, VOL1. Current Topics in Microbiology and Immunology. 346: 1-7


Recommended Readings: Edward H. Egelman, Ph.D. Friday January 19th, 2018

Friday Lectures

Friday, January 19, 2018  3:45 p.m.

Caspary Auditorium

Edward Egelman, Ph.D.

Harrison Distinguished Professor

Biochemistry and Molecular Genetics

University of Virginia Medical School

Cryo-EM of Protein and Nucleoprotein Polymers at Near-Atomic Resolution

Recommended Readings:

Science News

Kenny Walter. Virus Holds Key to Durable Material. (2017, Jul 20). Virus Holds Key to Durable Material. R&D Magazine

Empirical Articles

Egelman, Edward H. (2017). Cryo-EM of bacterial pili and archaeal flagellar filaments. CURRENT OPINION IN STRUCTURAL BIOLOGY. 46: 31-37

Wang, Fengbin; Burrage, Andrew M.; Postel, Sandra; et al. (2017). A structural model of flagellar filament switching across multiple bacterial species. NATURE COMMUNICATIONS. 8: 960

Wang, Fengbin; Coureuil, Mathieu; Osinski, Tomasz; et al. (2017). Cryoelectron Microscopy Reconstructions of the Pseudomonas aeruginosa and Neisseria gonorrhoeae Type IV Pili at Sub-nanometer Resolution. STRUCTURE. 25 (9): 1423-+

Kasson, Peter; DiMaio, Frank; Yu, Xiong; et al. (2017). Model for a novel membrane envelope in a filamentous hyperthermophilic virus. ELIFE. 6  

Kolappan, Subramania; Coureuil, Mathieu; Yu, Xiong; et al. (2016). Structure of the Neisseria meningitidis Type IV pilus. NATURE COMMUNICATIONS. 7: 13015

Braun, Tatjana; Vos, Matthijn R.; Kalisman, Nir; et al. (2016). Archaeal flagellin combines a bacterial type IV pilin domain with an Ig-like domain. PNAS. 113 (37): 10352-10357

Egelman, Edward H. (2016). The Current Revolution in Cryo-EM. BIOPHYSICAL JOURNAL. 110 (5): 1008-1012

Wang, Ray Yu-Ruei; Kudryashev, Mikhail; Li, Xueming; et al. (2015). De novo protein structure determination from near-atomic-resolution cryo-EM maps. NATURE METHODS. 12 (4): 335-U84

DiMaio, Frank; Yu, Xiong; Rensen, Elena; et al. (2015). A virus that infects a hyperthermophile encapsidates A-form DNA. SCIENCE. 348 (6237): 914-917

Review Papers

Egelman, Edward H. (2015). Three-dimensional reconstruction of helical polymers. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS. 581: 54-58

Recommended Readings: Nancy A. Moran, Ph.D., Friday September 22th, 2017

Friday Lectures

Friday, September 22, 2017  3:45 p.m.

Caspary Auditorium

Nancy A. Moran, Ph.D.

Leslie Surginer Endowed Professor

Department of Integrative Biology

University of Texas

The evolution and function of gut communities in social bees

Recommended Readings:

Ashley P. Taylor. March 29, 2017. In Certain Social Bees, Gut Microbiomes Follow Phylogeny. TheScientist

Kwong, Waldan K.; Moran, Nancy A. (2017). Gut microbial communities of social bees. NATURE REVIEWS MICROBIOLOGY. 14 (6): 374-384

Kwong, Waldan K; Medina, Luis A; Koch, Hauke; et al. (2017). Dynamic microbiome evolution in social bees. SCIENCE ADVANCES. 3 (3): e1600513

Powell, Elijah; Ratnayeke, Nalin; Moran, Nancy A. (2016). Strain diversity and host specificity in a specialized gut symbiont of honeybees and bumblebees. MOLECULAR ECOLOGY. 25 (18): 4461-4471

Engel, Philipp; Moran, Nancy A. (2013). The gut microbiota of insects – diversity in structure and function. FEMS MICROBIOLOGY REVIEW. 37 (5): 699-735

Schloissnig, Siegfried; Arumugam, Manimozhiyan; Sunagawa, Shinichi; et al. (2013). Genomic variation landscape of the human gut microbiome. NATURE. 493 (7430): 45-50

Tian, Baoyu; Fadhil, Nibal H.; Powell, J. Elijah; et al. (2012). Long-Term Exposure to Antibiotics Has Caused Accumulation of Resistance Determinants in the Gut Microbiota of Honeybees. MBIO. 3 (6): e00377-12