Recommended Readings: Rachel Green, Ph.D. December 10

Special Seminar Series
Wednesday, December 10, 2014
4:00 p.m., Carson Family Auditorium (CRC)

Rachel Green, Ph.D.
Professor,
Department of Molecular Biology and Genetics,
Johns Hopkins University School of Medicine
Investigator,
Howard Hughes Medical Institute

Intimate Connections Between mRNA Decay and Translation

Recommended Readings

Empirical Articles

Djuranovic, S., Nahvi, A., & Green, R. (2012). miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science, 336(6078), 237–240. doi:10.1126/science.1215691

Koutmou, K. S., McDonald, M. E., Brunelle, J. L., & Green, R. (2014). RF3:GTP promotes rapid dissociation of the class 1 termination factor. RNA, 20(5), 609–620. doi:10.1261/rna.042523.113

Shoemaker, C. J., Eyler, D. E., & Green, R. (2010). Dom34:Hbs1 promotes subunit dissociation and peptidyl-tRNA drop-off to initiate no-go decay. Science, 330(6002), 369–372. doi:10.1126/science.1192430

Shoemaker, C. J., & Green, R. (2011). Kinetic analysis reveals the ordered coupling of translation termination and ribosome recycling in yeast. Proceedings of the National Academy of Sciences, 108(51), E1392–8. doi:10.1073/pnas.1113956108

Review Papers

Dever, T. E., & Green, R. (2012). The elongation, termination, and recycling phases of translation in eukaryotes. Cold Spring Harbor Perspectives in Biology, 4(7), a013706. doi:10.1101/cshperspect.a013706

Shoemaker, C. J., & Green, R. (2012). Translation drives mRNA quality control. Nature Structural & Molecular Biology, 19(6), 594–601. doi:10.1038/nsmb.2301

Recommended Readings: Rudolph Jaenisch, M.D. December 12

Friday Lecture Series
Friday, December 12, 2014
3:45 p.m., Caspary Auditorium

Rudolph Jaenisch, M.D.
Professor of Biology,
Massachusetts Institute of Technology
Member,
Whitehead Institute for Biomedical Research

iPS Cell Technology, Gene Editing and Disease Research

Recommended Readings

Empirical Articles

Chung, C. Y., Khurana, V., Auluck, P. K., Tardiff, D. F., Mazzulli, J. R., Soldner, F., … Lindquist, S. (2013). Identification and rescue of α-synuclein toxicity in Parkinson patient-derived neurons. Science, 342(6161), 983–987. doi:10.1126/science.1245296

Li, Y., Wang, H., Muffat, J., Cheng, A. W., Orlando, D. a, Lovén, J., … Jaenisch, R. (2013). Global transcriptional and translational repression in human-embryonic-stem-cell-derived Rett syndrome neurons. Cell Stem Cell, 13(4), 446–458. doi:10.1016/j.stem.2013.09.001

Soldner, F., Laganière, J., Cheng, A. W., Hockemeyer, D., Gao, Q., Alagappan, R., … Jaenisch, R. (2011). Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations. Cell, 146(2), 318–331. doi:10.1016/j.cell.2011.06.019

Wang, H., Yang, H., Shivalila, C. S., Dawlaty, M. M., Cheng, A. W., Zhang, F., & Jaenisch, R. (2013). One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell, 153(4), 910–918. doi:10.1016/j.cell.2013.04.025

Review Papers

Buganim, Y., Faddah, D. A., & Jaenisch, R. (2013). Mechanisms and models of somatic cell reprogramming. Nature Reviews Genetics, 14(6), 427–439. doi:10.1038/nrg3473

Theunissen, T. W., & Jaenisch, R. (2014). Molecular Control of Induced Pluripotency. Cell Stem Cell, 14(6), 720–734. doi:10.1016/j.stem.2014.05.002

Recommended Readings: Thomas Südhof, M.D. December 5

Friday Lecture Series
Friday, December 5, 2014
3:45 p.m., Caspary Auditorium

Thomas Südhof, M.D.
Avram Goldstein Professor,
Department of Molecular and Cellular Physiology,
Stanford School of Medicine
Investigator,
Howard Hughes Medical Institute

Cracking the Neurexin Code – Towards a Molecular Logic of Neural Circuits

Recommended Readings

Empirical Articles

Gokce, O., & Südhof, T. C. (2013). Membrane-tethered monomeric neurexin LNS-domain triggers synapse formation. The Journal of Neuroscience, 33(36), 14617–14628. doi:10.1523/JNEUROSCI.1232-13.2013

Rothwell, P. E., Fuccillo, M. V, Maxeiner, S., Hayton, S. J., Gokce, O., Lim, B. K., … Südhof, T. C. (2014). Autism-associated neuroligin-3 mutations commonly impair striatal circuits to boost repetitive behaviors. Cell, 158(1), 198–212. doi:10.1016/j.cell.2014.04.045

Treutlein, B., Gokce, O., Quake, S. R., & Südhof, T. C. (2014). Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing. Proceedings of the National Academy of Sciences, 111(13), E1291–E1299. doi:10.1073/pnas.1403244111

Tsetsenis, T., Boucard, a. a., Arac, D., Brunger, a. T., & Sudhof, T. C. (2014). Direct visualization of trans-synaptic neurexin-neuroligin interactions during synapse formation. Journal of Neuroscience, 34(45), 15083–15096. doi:10.1523/JNEUROSCI.0348-14.2014

Review Articles

Südhof, T. C. (2008). Neuroligins and neurexins link synaptic function to cognitive disease. Nature, 455(7215), 903–911. doi:10.1038/nature07456

Südhof, T. C. (2014). The molecular machinery of neurotransmitter release (Nobel Lecture). Angewandte Chemie, 53(47), 12696–12717. doi:10.1002/anie.201406359

Recommended Readings: Charles D. Gilbert, M.D., Ph.D. December 15

Monday Lecture Series
Monday, December 15, 2014
4:00 p.m., Carson Family Auditorium

Charles D. Gilbert, M.D., Ph.D.
Arthur and Janet Ross Professor and Head,
Laboratory of Neurobiology,
The Rockefeller University

The Dynamic Brain

Recommended Readings

Empirical Articles

Piëch, V., & Li, W., & Gilbert, C. D. (2013). Network model of top-down influences on local gain and contextual interactions in visual cortex. Proceedings of the National Academy of Sciences. 110(43), E4108-E4117. doi:10.1073/pnas.1317019110

Ramalingam, N., McManus, J. N. J., Li, W., & Gilbert, C. D. (2013). Top-down modulation of lateral interactions in visual cortex. The Journal of Neuroscience, 33(5), 1773–1789. doi:10.1523/JNEUROSCI.3825-12.2013

Yamahachi, H., Marik, S., McManus, J., Denk, W., & Gilbert, C. D. (2009). Rapid axonal sprouting and pruning accompany functional reorganization in primary visual cortex. Neuron, 64(5), 719-729. doi:10.1016/j.neuron.2009.11.026

Review Papers

Gilbert, C. D., & Li, W. (2013). Top-down influences on visual processing. Nature Reviews Neuroscience, 14(5), 350–363. doi:10.1038/nrn3476

Gilbert, C., & Li, W. (2012). Adult visual cortical plasticity. Neuron, 75(2), 250–264. doi:10.1016/j.neuron.2012.06.030

Recommended Readings: Ali H. Brivanlou, Ph.D. November 24

Monday Lecture Series
Monday, November 24, 2014
4:00 p.m., Carson Family Auditorium

Ali H. Brivanlou, Ph.D.
Robert and Harriet Heilbrunn Professor and Head,
Laboratory of Stem Cell Biology and Molecular Embryology,
The Rockefeller University

Dynamic Patterns: Self-Organization of Human Embryonic Cells

Recommended Readings

Empirical Articles

Arduini, B., & Brivanlou, A. (2012). Modulation of FOXD3 activity in human embryonic stem cells directs pluripotency and paraxial mesoderm fates. Stem Cells, 30(10), 2188–2198. doi:10.1002/stem.2012

Ozair, M., Noggle, S., & Warmflash, A. (2013). SMAD7 directly converts human embryonic stem cells to telencephalic fate by a default mechanism. Stem Cells, 31(1), 35–47. doi:10.1002/stem.1246.SMAD7

Rosa, A., Papaioannou, M. D., Krzyspiak, J. E., & Brivanlou, A. H. (2014). miR-373 is regulated by TGFβ signaling and promotes mesendoderm differentiation in human embryonic stem cells. Developmental Biology, 391(1), 81–88. doi:10.1016/j.ydbio.2014.03.020

Warmflash, A., Sorre, B., Etoc, F., Siggia, E. D., & Brivanlou, A. H. (2014). A method to recapitulate early embryonic spatial patterning in human embryonic stem cells. Nature Methods, 11(8). doi:10.1038/nmeth.3016

Review Article

Muñoz-Sanjuán, I., & Brivanlou, A. H. (2002). Neural induction, the default model, and embryonic stem cells. Nature Reviews Neuroscience, 3(4), 271–280. doi:10.1038/nrn786

Recommended Readings: Charles Zuker, Ph.D. November 20

Harvey Society Lecture Series
Thursday, November 20, 2014
8:00 p.m., Caspary Auditorium

Charles Zuker, Ph.D.
Professor of Biochemistry and Molecular Biophysics and Neuroscience
Columbia University Medical Center
Janelia Senior Fellow and Investigator
Howard Hughes Medical Institute

Receptors, Neurons and Circuits: The Biology of Mammalian Taste

Recommended Readings

Empirical Articles

Chandrashekar, J., Kuhn, C., Oka, Y., Yarmolinsky, D. A., Hummler, E., Ryba, N. J. P., & Zuker, C. S. (2010). The cells and peripheral representation of sodium taste in mice. Nature, 464(7286), 297–301. doi:10.1038/nature08783

Chen, X., Gabitto, M., Peng, Y., Ryba, N. J. P., & Zuker, C. S. (2011). A gustotopic map of taste qualities in the mammalian brain. Science, 333(6047), 1262–1266. doi:10.1126/science.1204076

Huang, A. L., Chen, X., Hoon, M. A, Chandrashekar, J., Guo, W., Tränkner, D., … Zuker, C. S. (2006). The cells and logic for mammalian sour taste detection. Nature, 442(7105), 934–938. doi:10.1038/nature05084

Mueller, K., Hoon, M., & Erlenbach, I. (2005). The receptors and coding logic for bitter taste. Nature, 434(7030), 225–230. doi:10.1038/nature03366.1.

Zhao, G., Zhang, Y., & Hoon, M. (2003). The receptors for mammalian sweet and umami taste. Cell, 115(3), 255–266. doi:10.1016/S0092-8674(03)00844-4

Review Paper

Chandrashekar, J., Hoon, M. A., Ryba, N. J. P., & Zuker, C. S. (2006). The receptors and cells for mammalian taste. Nature, 444(7117), 288–294. doi:10.1038/nature05401

Recommended Readings: Stephen C. Harrison, Ph.D. November 21

Friday Lecture Series
Friday, November 21, 2014,
3:45 p.m., Caspary Auditorium

Stephen C. Harrison, Ph.D.
Giovanni Armenise-Harvard Professor of Basic Medical Sciences,
Professor of Biological Chemistry and Molecular Pharmacology,
Professor of Pediatrics,
Director of the Center for Molecular and Cellular Dynamics,
Harvard Medical School
Head of the Laboratory of Molecular Medicine,
Children’s Hospital, Boston
Investigator,
Howard Hughes Medical Institute

Molecular Mechanisms of Membrane Penetration When Viruses Enter Cells

Recommended Readings

Empirical Articles

Abdelhakim, A. H., Salgado, E. N., Fu, X., Pasham, M., Nicastro, D., Kirchhausen, T., & Harrison, S. C. (2014). Structural correlates of rotavirus cell entry. PLoS Pathogens, 10(9), e1004355. doi:10.1371/journal.ppat.1004355

Ivanovic, T., Choi, J. L., Whelan, S. P., van Oijen, A. M., & Harrison, S. C. (2013). Influenza-virus membrane fusion by cooperative fold-back of stochastically induced hemagglutinin intermediates. eLife, 2(1), e00333. doi:10.7554/eLife.00333

Schmidt, A. G., Xu, H., Khan, A. R., O’Donnell, T., Khurana, S., King, L. R., … Harrison, S. C. (2013). Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody. Proceedings of the National Academy of Sciences, 110(1), 264–269. doi:10.1073/pnas.1218256109

Review Article

Harrison, S. C. (2008). Viral membrane fusion. Nature Structural & Molecular Biology, 15(7), 690–698. doi:10.1038/nsmb.1456

Recommended Readings: Timothy Ryan, Ph.D. December 8

Monday Lecture Series
Monday, December 8, 2014,
4:00 p.m., Carson Family Auditorium (CRC)

Timothy Ryan, Ph.D.
Tri-Institutional Professor,
Department of Biochemistry,
Weill Cornell Medical College

How Synapses Regulate Their Diet: the Balance of Fuel Production and Expenditure and Single Synapses

Recommended Readings

Empirical Articles

Cottrell, J. R., Levenson, J. M., Kim, S. H., Gibson, H. E., Richardson, K. a, Sivula, M., … Gerber, D. J. (2013). Working memory impairment in calcineurin knock-out mice is associated with alterations in synaptic vesicle cycling and disruption of high-frequency synaptic and network activity in prefrontal cortex. The Journal of Neuroscience, 33(27), 10938–10949. doi:10.1523/JNEUROSCI.5362-12.2013

Fernandez-Alfonso, T., & Ryan, T. A. (2008). A heterogeneous “resting” pool of synaptic vesicles that is dynamically interchanged across boutons in mammalian CNS synapses. Brain Cell Biology, 36(1-4), 87–100. doi:10.1007/s11068-008-9030-y

Kim, S. H., & Ryan, T. A. (2010). CDK5 serves as a major control point in neurotransmitter release. Neuron, 67(5), 797–809. doi:10.1016/j.neuron.2010.08.003

Rangaraju, V., Calloway, N., & Ryan, T. A. (2014). Activity-driven local ATP synthesis is required for synaptic function. Cell, 156(4), 825–835. doi:10.1016/j.cell.2013.12.042

Review Paper

Dittman, J., & Ryan, T. a. (2009). Molecular circuitry of endocytosis at nerve terminals. Annual Review of Cell and Developmental Biology, 25, 133–160. doi:10.1146/annurev.cellbio.042308.113302

Recommended Readings: Howard Hang, Ph.D. November 17

Monday Lecture Series
Monday, November 17, 2014,
4:00 p.m., Carson Family Auditorium (CRC)

Howard Hang, Ph.D.
Professor and Head,
Laboratory of Chemical Biology and Microbial Pathogenesis,
The Rockefeller University

A C. elegans Model for Commensal Bacteria Function Reveals a Secreted Peptidoglycan Hydrolase Activator of Host Immunity

Recommended Readings

Empirical Articles

Charron, G., Zhang, M. M., Yount, J. S., Wilson, J., Raghavan, A. S., Shamir, E., & Hang, H. C. (2009). Robust fluorescent detection of protein fatty-acylation with chemical reporters. Journal of the American Chemical Society, 131(13), 4967–4975. doi:10.1021/ja810122f

Hang, H. C., Geutjes, E.-J., Grotenbreg, G., Pollington, A. M., Bijlmakers, M. J., & Ploegh, H. L. (2007). Chemical probes for the rapid detection of Fatty-acylated proteins in Mammalian cells. Journal of the American Chemical Society, 129(10), 2744–2745. doi:10.1021/ja0685001

Yount, J. S., Moltedo, B., Yang, Y.-Y., Charron, G., Moran, T. M., López, C. B., & Hang, H. C. (2010). Palmitoylome profiling reveals S-palmitoylation-dependent antiviral activity of IFITM3. Nature Chemical Biology, 6(8), 610–614. doi:10.1038/nchembio.405

Review Paper

Grammel, M., & Hang, H. C. (2013). Chemical reporters for biological discovery. Nature Chemical Biology, 9(8), 475–484. doi:10.1038/nchembio.1296

Recommended Readings: Jean-Laurent Casanova, Ph.D. December 1

Monday Lecture Series
Monday, December 1, 2014,
4:00 p.m., Carson Family Auditorium (CRC)

Jean-Laurent Casanova, Ph.D.,
Professor and Head,
St. Giles Laboratory of Human Genetics of Infectious Diseases,
The Rockefeller University
Investigator,
Howard Hughes Medical Institute

Toward a Genetic Theory of Childhood Infectious Diseases

Recommended Readings

Empirical Articles

Puel, A., Cypowyj, S., Bustamante, J., Wright, J. F., Liu, L., Lim, H. K., … Casanova, J.-L. (2011). Chronic mucocutaneous candidiasis in humans with inborn errors of interleukin-17 immunity. Science, 332(6025), 65–68. doi:10.1126/science.1200439

Sabri, A., Grant, A. V, Cosker, K., El Azbaoui, S., Abid, A., Abderrahmani Rhorfi, I., … El Baghdadi, J. (2014). Association study of genes controlling IL-12-dependent IFN-γ immunity: STAT4 alleles increase risk of pulmonary tuberculosis in Morocco. The Journal of Infectious Diseases, 210(4), 611–618. doi:10.1093/infdis/jiu140

Review Papers

Alcaïs, A., Quintana-Murci, L., Thaler, D. S., Schurr, E., Abel, L., & Casanova, J.-L. (2010). Life-threatening infectious diseases of childhood: single-gene inborn errors of immunity? Annals of the New York Academy of Sciences, 1214, 18–33. doi:10.1111/j.1749-6632.2010.05834.x

Casanova, J.-L., & Abel, L. (2005). Inborn errors of immunity to infection: the rule rather than the exception. The Journal of Experimental Medicine, 202(2), 197–201. doi:10.1084/jem.20050854