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

Recommended Readings: Anna Wedell, M.D., Ph.D., Friday November 2, 2018

Friday Lectures

Friday, November 2, 2018  3:45 p.m.

Caspary Auditorium

Anna Wedell, M.D., Ph.D.

Professor

Department of Molecular Medicine and Surgery

Karolinska Institute

 

Clinical Whole Genome Sequencing Sheds Light on Novel Metabolic Pathways in the Brain

 

Recommended Readings:

Empirical Articles

Baric, Ivo; Staufner, Christian; Augoustides-Savvopoulou, Persephone; et al. (2017). Consensus recommendations for the diagnosis, treatment and follow-up of inherited methylation disorders. JOURNAL OF INHERITED METABOLIC DISEASE. 40 (1): 5-20

Siibak, Triinu; Clemente, Paula; Bratic, Ana; et al. (2017). A multi-systemic mitochondrial disorder due to a dominant p.Y955H disease variant in DNA polymerase gamma.  26 (13): 2515-2525

Dahlin, Maria; Martin, Daniel A.; Hedlund, Zandra; et al. (2015). The ketogenic diet compensates for AGC1 deficiency and improves myelination. EPILEPSIA. 56 (11): e176-e181

Brownstein, Catherine A.; Beggs, Alan H.; Homer, Nils; et al. (2014). An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. GENOME BIOLOGY. (15) 3

Stranneheim, Henrik; Engvall, Martin; Naess, Karin; et al. (2014). Rapid pulsed whole genome sequencing for comprehensive acute diagnostics of inborn errors of metabolism. BMC GENOMICS. 15

Gidlof, Sebastian; Falhammar, Henrik; Thilen, Astrid; et al. (2013). One hundred years of congenital adrenal hyperplasia in Sweden: a retrospective, population-based cohort study. LANCET DIABETES & ENDOCRINOLOGY. 1 (1): 35-42

Bjursell, Magnus K.; Blom, Henk J.; Cayuela, Jordi Asin; et al. (2011). Adenosine Kinase Deficiency Disrupts the Methionine Cycle and Causes Hypermethioninemia, Encephalopathy, and Abnormal Liver Function. AMERICAN JOURNAL OF HUMAN GENETICS. 89 (4): 507-515

Wibom, Rolf; Lasorsa, Francesco M.; Tohonen, Virpi; et al. (2009). AGC1 Deficiency Associated with Global Cerebral Hypomyelination.  NEW ENGLAND JOURNAL OF MEDICINE. 361 (5): 489-495

Recommended Readings: Mary E. Hatten, Ph.D., Monday November 12, 2018

Monday Lectures

Monday, November 12, 2018  4:00 p.m.

Carson Family Auditorium

Mary E. Hatten, Ph.D.

Frederick P. Rose Professor and Head

Laboratory of Developmental Neurobiology

The Rockefeller University

Neuronal Migration and the Formation of the Cerebellar Circuitry

Recommended Readings:

Science News

Florian Rosado. Insights Into Autism From The Protein Modulator ASTN2. . RELIAWIRE

Empirical Articles

Behesti, Hourinaz; Fore, Taylor R.; Wu, Peter; et al. (2018). ASTN2 modulates synaptic strength by trafficking and degradation of surface proteins. PNAS. 115 (41): E9717-E9726

Govek, Eve-Ellen; Hatten, Mary E.; Van Aelst, Linda. (2011). The Role of Rho GTPase Proteins in CNS Neuronal Migration. DEVELOPMENTAL NEUROBIOLOGY. 71 (6): 528-553

Wilson, Perrin M.; Fryer, Robert H.; Fang, Yin; et al. (2010). Astn2, A Novel Member of the Astrotactin Gene Family, Regulates the Trafficking of ASTN1 during Glial-Guided Neuronal Migration. JOURNAL OF NEUROSCIENCE. 30 (25): 8529-8540

Solecki, David J.; Trivedi, Niraj; Govek, Eve-Ellen; et al. (2009). Myosin II Motors and F-Actin Dynamics Drive the Coordinated Movement of the Centrosome and Soma during CNS Glial-Guided Neuronal Migration. NEURON. 63 (1): 63-80

Review Paper

Hatten, Mary E.; Roussel, Martine F. (2011). Development and cancer of the cerebellum. TRENDS IN NEUROSCIENCES. 34 (3): 134-142

Book Chapter

Roussel, Martine F.; Hatten, Mary E. (2011). CEREBELLUM: Development and Medulloblastoma. CANCER AND DEVELOPMENT. 94: 235-282

Recommended Readings: Christopher D. Lima, Ph.D. Friday March 30th, 2018

Friday Lectures

Friday, March 30th, 2018  3:45 p.m.

Caspary Auditorium

Christopher D. Lima, Ph.D.

Professor

Structural Biology Program

Memorial Sloan Kettering Cancer Center

Targeting RNA for Degradation by the Eukaryotic RNA Exosome

Recommended Readings:

Empirical Articles

Wasmuth, Elizabeth V.; Lima, Christopher D. (2017). The Rrp6 C-terminal domain binds RNA and activates the nuclear RNA exosome. NUCLEIC ACIDS RESEARCH. 45 (2): 846-860

Januszyk, Kurt; Lima, Christopher D. (2014). The eukaryotic RNA exosome. CURRENT OPINION IN STRUCTURAL BIOLOGY. 24: 132-140

Zinder, John C.; Wasmuth, Elizabeth V.; Lima, Christopher D. (2016). Nuclear RNA Exosome at 3.1 angstrom Reveals Substrate Specificities, RNA Paths, and Allosteric Inhibition of Rrp44/Dis3. MOLECULAR CELL. 64 (4): 734-745

Wasmuth, Elizabeth V.; Januszyk, Kurt; Lima, Christopher D. (2014). Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA. NATURE. 511 (7510): 435-+

Wasmuth, Elizabeth V.; Lima, Christopher D. (2012). Exo- and Endoribonucleolytic Activities of Yeast Cytoplasmic and Nuclear RNA Exosomes Are Dependent on the Noncatalytic Core and Central Channel. MOLECULAR CELL. 48 (1): 133-144

Liu, Quansheng; Greimann, Jaclyn C.; Lima, Christopher D. (2006). Reconstitution, activities, and structure of the eukaryotic RNA exosome. CELL. 127 (6): 1223-1237

Review Paper

Zinder, John C.; Lima, Christopher D. (2017). Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors. GENES & DEVELOPMENT. 31 (2): 88-100

Book Chapter

Greimann, Jaclyn C.; Lima, Christopher D. (2008). RECONSTITUTION of RNA Exsomes From Human And Saccharomyces Cerevisiae: Clonning, Expression, Purification, And  Activity Assays. METHODS IN ENZYMOLOGY. 448: 185-210

Recommended Readings: Sanford M. Simon, Ph.D. Monday March 19, 2018

Monday Lectures

Monday, March 19, 2018  4:00 p.m.

Carson Family Auditorium

Sanford M. Simon, Ph.D.

Professor and Head

Laboratory of Cellular Biophysics

The Rockefeller University

ESCRTing Viruses out of the Cell: Lessons from HIV-1

Recommended Readings:

Empirical Articles

Itano, Michelle S.; Arnion, Helene; Wolin, Sandra L.; et al. (2018). Recruitment of 7SL RNA to assembling HIV-1 virus-like particles. TRAFFIC. 19 (1): 36-43

Itano, Michelle S.; Bleck, Marina; Johnson, Daniel S.; et al. (2016). Readily Accessible Multiplane Microscopy: 3D Tracking the HIV-1 Genome in Living Cells. TRAFFIC. 17 (2): 179-186

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

Jouvenet, Nolwenn; Zhadina, Maria; Bieniasz, Paul D.; et al. (2011). Dynamics of ESCRT protein recruitment during retroviral assembly. NATURE CELL BIOLOGY. 13 (4): 394-U124

Jouvenet, Nolwenn; Simon, Sanford M.; Bieniasz, Paul D. (2009). Imaging the interaction of HIV-1 genomes and Gag during assembly of individual viral particles. PNAS. 106 (45): 19114-19119

Jouvenet, Nolwenn; Bieniasz, Paul D.; Simon, Sanford M. (2008). Imaging the biogenesis of individual HIV-1 virions in live cells. NATURE. 454 (7201): 236-240

Review Papers

Jouvenet, Nolwenn; Simon, Sanford M.; Bieniasz, Paul D. (2011). Visualizing HIV-1 Assembly.  JOURNAL OF MOLECULAR BIOLOGY. 410 (4): 501-511

Book Chapter

Woolf, Steven H.; Purnell, Jason Q.; Simon, Sarah M.; et al. (2015). Translating Evidence into Population Health Improvement: Strategies and Barriers. ANNUAL REVIEW OF PUBLIC HEALTH. 36: 463-482

 

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

and

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: Michael Greenberg, Ph.D. Friday March 9th, 2018

Friday Lectures

Friday, March 9th, 2018  3:45 p.m.

Caspary Auditorium

Michael Greenberg, Ph.D.

Department Chair and Nathan Marsh Pusey Professor

Department of Neurobiology

Harvard Medical School

How Nature and Nurture Conspire to Control Brain Development and Function

Recommended Readings:

Empirical Articles

Kalish, Brian T.; Cheadle, Lucas; Hrvatin, Sinisa; et al. (2018). Single-cell transcriptomics of the developing lateral geniculate nucleus reveals insights into circuit assembly and refinement. PNAS. 115 (5): E1051-E1060

Hrvatin, Sinisa; Hochbaum, Daniel R.; Nagy, M. Aurel; et al. (2018). Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex. NATURE NEUROSCIENCE. 21 (1): 120-+

Gabel, Harrison W.; Kinde, Benyam; Stroud, Hume; et al. (2015). Disruption of DNA-methylation-dependent long gene repression in Rett syndrome. NATURE. 522 (7554): 89-U221

Malik, Athar N.; Vierbuchen, Thomas; Hemberg, Martin; et al. (2014). Genome-wide identification and characterization of functional neuronal activity-dependent enhancers. NATURE NEUROSCIENCE. 17 (10): 1330-1339

West, Anne E.; Greenberg, Michael E. (2011). Neuronal Activity-Regulated Gene Transcription in Synapse Development and Cognitive Function. COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY. 3 (6)

Greer, Paul L.; Hanayama, Rikinari; Bloodgood, Brenda L.; et al. (2010). The Angelman Syndrome Protein Ube3A Regulates Synapse Development by Ubiquitinating Arc. CELL. 140 (5): 704-716

Review Papers

Hardingham, Giles E.; Pruunsild, Priit; Greenberg, Michael E.; et al. (2018). Lineage divergence of activity-driven transcription and evolution of cognitive ability. NATURE REVIEWS NEUROSCIENCE. 19 (1): 9-15

Ebert, Daniel H.; Greenberg, Michael E. (2013). Activity-dependent neuronal signalling and autism spectrum disorder. NATURE. 493 (7432): 327-337

Book Chapter

Flavell, Steven W.; Greenberg, Michael E. (2008). Signaling mechanisms linking neuronal activity to gene expression and plasticity of the nervous system. ANNUAL REVIEW OF NEUROSCIENCE. 31: 563-590

 

Recommended Readings: Philip Cole, M.D., Ph.D. Friday December 8th, 2017

Friday Lectures

Friday, December 8, 2017  3:45 p.m.

Caspary Auditorium

Philip Cole, M.D., Ph.D.

Professor

Department of Medicine, Biological Chemistry and Molecular Pharmacology

Harvard Medical School

Targeting Reversible Lysine Acetylation with Designed Small Molecules

 

Recommended Readings:

Empirical Articles

Boija, Ann; Mahat, Dig Bijay; Zare, Aman; et al. (2017). CBP Regulates Recruitment and Release of PromoterProximal RNA Polymerase II.  MOLECULAR CELL. 68 (3): 491-+

Lasko, Loren M.; Jakob, Clarissa G.; Edalji, Rohinton P.; et al. (2017). Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours. NATURE. 550 (7674): 128-+

Maksimoska, Jasna; Segura-Pena, Dario; Cole, Philip A.; et al. (2014). Structure of the p300 Histone Acetyltransferase Bound to Acetyl-Coenzyme A and Its Analogues. BIOCHEMISTRY. 53 (21): 3415-3422

Bowers, Erin M.; Yan, Gai; Mukherjee, Chandrani; et al. (2010). Virtual Ligand Screening of the p300/CBP Histone Acetyltransferase: Identification of a Selective Small Molecule Inhibitor.  CHEMISTRY & BIOLOGY. 17 (5): 471-482

Dancy, Beverley M.; Crump, Nicholas T.; Peterson, Daniel J.; et al. (2012). Live-Cell Studies of p300/CBP Histone Acetyltransferase Activity and Inhibition. CHEMBIOCHEM. 13 (14): 2113-2121

Liu, Xin; Wang, Ling; Zhao, Kehao; et al. (2008). The structural basis of protein acetylation by the p300/CBP transcriptional coactivator. NATURE. 451 (7180): 846-850

Review Papers

Dancy, Beverley M.; Cole, Philip A. (2013). Protein Lysine Acetylation by p300/CBP. CHEMICAL REVIEWS. 115 (6): 2419-2452

Cole, Philip A. (2008). Chemical probes for histone-modifying enzymes.  NATURE CHEMICAL BIOLOGY. 4 (10): 590-597