Recommended Readings: Jue Chen, Ph.D., February 27

Friday Lecture Series / Ph.D. Recruitment Lecture
Friday, February 25, 2015
3:45 p.m., Caspary Auditorium

Jue Chen, Ph.D.,
Head of Laboratory of Membrane Biology and Biophysics,
The Rockefeller University
Investigator, Howard Hughes Medical Institute

Structural Biology of Molecular Pumps

Recommended Readings

Empirical Articles

Chen, S., Oldham, M. L., Davidson, A. L., & Chen, J. (2013). Carbon catabolite repression of the maltose transporter revealed by X-ray crystallography. Nature, 499(7458), 364-368. doi:10.1038/nature12232

Jin, M. S., Oldham, M. L., Zhang, Q., & Chen, J. (2012). Crystal structure of the multidrug transporter P-glycoprotein from Caenorhabditis elegans. Nature. 490(7421), 566-569. doi:10.1038/nature11448

Oldham, M. L., Chen, S., & Chen, J. (2013). Structural basis for substrate specificity in the Escherichia coli maltose transport system. Proceedings of the National Academy of Sciences, 110(45), 18132-18137. doi:10.1073/pnas.1311407110

Review Papers

Chen, J. (2013). Molecular mechanism of the Escherichia coli maltose transporterCurrent Opinion in Structural Biology, 23(4), 492-498. doi: 10.1016/j.sbi.2013.03.011

Recommended Readings: Lingyin Li, Ph.D., February 25

Special Lecture
Wednesday, February 25, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Lingyin Li, Ph.D.,
Merck Fellow of the Jane Coffins Child Memorial Fund,
Department of Systems Biology,
Harvard Medical School

Chemical Biology of Anti-Cancer Innate Immunity

Recommended Readings

Kim, S., Li, L., Maliga, Z., Yin, Q., Wu, H., & Mitchison, T. J. (2013). Anticancer flavonoids are mouse-selective STING agonists. ACS Chemical Biology, 8(7), 1396–1401. doi:10.1021/cb400264n

Li, L., Yin, Q., Kuss, P., Maliga, Z., Wu, H., & Mitchison, T. J. (2014). Hydrolysis of 2′3′-cGAMP by ENPP1 and design of nonhydrolyzable analogs. Nature Chemical Biology, 10(12), 1043–1048. doi:10.1038/nchembio.1661

Recommended Readings: Eva Nogales, Ph.D., February 20

Friday Lecture Series
Friday, February 20, 2015
3:45 p.m., Caspary Auditorium

Eva Nogales, Ph.D.
Professor of Biochemistry, Biophysics, and Structural Biology,
University of California, Berkeley
Senior Faculty Scientist,
Deputy Director of the Bioenergy/GTL & Structural Biology Department
Life Sciences Division,
Lawrence Berkeley National Laboratory,
Investigator, Howard Hughes Medical Institute

Cryo-EM Studies of the Human Transcription Initiation Machinery

Recommended Readings

Cianfrocco, M. a, & Nogales, E. (2013). Regulatory interplay between TFIID’s conformational transitions and its modular interaction with core promoter DNA. Transcription, 4(3), 1–7. doi:10.4161/trns.25291

Cianfrocco, M. A., Kassavetis, G. A., Grob, P., Fang, J., Juven-Gershon, T., Kadonaga, J. T., & Nogales, E. (2013). Human TFIID binds to core promoter DNA in a reorganized structural state. Cell, 152(1-2), 120–131. doi:10.1016/j.cell.2012.12.005

He, Y., Fang, J., Taatjes, D. J., & Nogales, E. (2013). Structural visualization of key steps in human transcription initiation. Nature, 495(7442), 481–486. doi:10.1038/nature11991

Recommended Readings: Robert McGinty, M.D., Ph.D., March 2

Special Lecture,
Monday, March 2, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Robert McGinty, M.D., Ph.D.
Damon Runyun Postdoctoral Fellow,
Dale F. Frey Breakthrough Scientist,
Department of Biochemistry & Molecular Biology,
The Pennsylvania State University

Chemistry, Crystallography and Nucleosome Ubiquitylation

Recommended Readings

Empirical Articles

Kim, J., Kim, J., McGinty, R. K., Nguyen, U. T., Muir, T. W., Allis, C. D., & Roeder, R. G. (2013). The n-SET domain of Set1 regulates H2B ubiquitylation-dependent H3K4 methylation. Molecular Cell, 49(6), 1121-1133. doi:10.1016/j.molcel.2013.01.034

McGinty, R. K., Henrici, R. C., & Tan, S. (2014). Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome. Nature, 514(7524), 591-596. doi:10.1038/nature13890

Tang, Z., Chen, W. Y., Shimada, M., Nguyen, U. T., Kim, J., Sun, X. J., … & Roeder, R. G. (2013). SET1 and p300 act synergistically, through coupled histone modifications, in transcriptional activation by p53. Cell, 154(2), 297-310. doi:10.1016/j.cell.2013.06.027

Review Papers

McGinty, R. K., & Tan, S. (In Press). Nucleosome structure and function. Chemical Reviews. doi:10.1021/cr500373h

Recommended Readings: Pietro De Camilli, M.D., February 13

Friday Lecture Series
Friday, February 13, 2015
3:45 p.m., Caspary Auditorium

Pietro De Camilli, M.D.
John Klingenstein Professor of Neuroscience,
Professor of Cell Biology,
Director, Program in Cellular Neuroscience, Neurodegeneration, and Repair,
Yale University School of Medicine
Investigator, Howard Hughes Medical Institute

Lipid Signaling in the Control of Membrane Dynamics and Interactions

Recommended Readings

Empirical Articles

Giordano, F., Saheki, Y., Idevall-Hagren, O., Colombo, S. F., Pirruccello, M., Milosevic, I., … De Camilli, P. (2013). PI(4,5)P(2)-dependent and Ca(2+)-regulated ER-PM interactions mediated by the extended synaptotagmins. Cell, 153(7), 1494–1509. doi:10.1016/j.cell.2013.05.026

Schauder, C. M., Wu, X., Saheki, Y., Narayanaswamy, P., Torta, F., Wenk, M. R., … Reinisch, K. M. (2014). Structure of a lipid-bound extended synaptotagmin indicates a role in lipid transfer. Nature, 510(7506), 552–555. doi:10.1038/nature13269

Wu, X., Chi, R., Baskin, J., Lucast, L., Burd, C., DeCamilli, P., & Reinisch, K. (2014). Structural insights into assembly and regulation of the plasma membrane phosphatidylinositol 4-kinase complex. Developmental Cell, 28(1), 19–29. doi:10.1016/j.devcel.2013.11.012

Review Paper

Idevell-Hagren, O., & De Camilli, P. (In Press). Detection and manipulation of phosphoinositides. Biochimica et Biophysica Acta Journal. doi:10.1016/j.bbalip.2014.12.008

Recommended Readings: Jorge E. Galán, Ph.D., DVM, February 6

Friday Lecture Series
Friday, February 6, 2015
3:45 p.m., Caspary Auditorium

Jorge E. Galán, Ph.D., DVM
Lucille P. Markey Professor of Microbial Pathogenesis,
Professor of Cell Biology,
Chair, Department of Microbial Pathogenesis,
Yale University School of Medicine

Typhoid fever: new insight into the pathogenesis of an old disease

Recommended Readings

Empirical Articles

Lefebre, M. D., & Galán, J. E. (2014). The inner rod protein controls substrate switching and needle length in a Salmonella type III secretion system. Proceedings of the National Academy of Sciences, 111(2), 817–822. doi:10.1073/pnas.1319698111

Song, J., Gao, X., & Galán, J. E. (2013). Structure and function of the Salmonella Typhi chimaeric A(2)B(5) typhoid toxin. Nature, 499(7458), 350–354. doi:10.1038/nature12377

Spanò, S., & Galán, J. E. (2012). A Rab32-dependent pathway contributes to Salmonella typhi host restriction. Science, 338(6109), 960–963. doi:10.1126/science.1229224

Review Papers

Hicks, S. W., & Galán, J. E. (2013). Exploitation of eukaryotic subcellular targeting mechanisms by bacterial effectors. Nature Reviews Microbiology, 11(5), 316–326. doi:10.1038/nrmicro3009

Recommended Readings: Eve Marder, Ph.D., January 23

Friday Lecture Series
Friday, January 23, 2015
3:45 p.m., Caspary Auditorium

Eve Marder, Ph.D.
Victor and Gwendolyn Beinfield Professor of Neuroscience,
Volen National Center for Complex Systems,
Brandeis University

Robustness, Variability, and Neuromodulation in Neurons and Networks

Recommended Readings

Empirical Articles

Caplan, J. S., Williams, A. H., & Marder, E. (2014). Many parameter sets in a multicompartment model oscillator are robust to temperature perturbations. The Journal of Neuroscience, 34(14), 4963–4975. doi:10.1523/JNEUROSCI.0280-14.2014

O’Leary, T., Williams, A. H., Franci, A., & Marder, E. (2014). Cell types, network homeostasis, and pathological compensation from a biologically plausible ion channel expression model. Neuron, 82(4), 809–821. doi:10.1016/j.neuron.2014.04.002

Soofi, W., Goeritz, M. L., Kispersky, T. J., Prinz, A. A., Marder, E., & Stein, W. (2014). Phase maintenance in a rhythmic motor pattern during temperature changes in vivo. Journal of Neurophysiology, 111(12), 2603–2613. doi:10.1152/jn.00906.2013

Review Papers

Marder, E., O’Leary, T., & Shruti, S. (2014). Neuromodulation of circuits with variable parameters: single neurons and small circuits reveal principles of state-dependent and robust neuromodulation. Annual Review of Neuroscience, 37, 329–346. doi:10.1146/annurev-neuro-071013-013958

Recommended Readings: Jonathan Wiessman, Ph.D., January 21

Special Lecture Series
Wednesday, January 21, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Jonathan S. Weissman, Ph.D.
Professor of Cellular and Molecular Pharmacology and of Biochemistry and Biophysics,
University of California, San Francisco School of Medicine
Investigator,
Howard Hughes Medical Institute

Monitoring Translation in Space and Time with Ribosome Profiling

Recommended Readings

Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S., & Weissman, J. S. (2009). Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 324(5924), 218–223. doi:10.1126/science.1168978

Jan, C. H., Williams, C. C., & Weissman, J. S. (2014). Principles of ER cotranslational translocation revealed by proximity-specific ribosome profiling. Science, 346(6210), 1257521. doi:10.1126/science.1257521

Williams, C. C., Jan, C. H., & Weissman, J. S. (2014). Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling. Science, 346(6210), 748–751. doi:10.1126/science.1257522

Recommended Readings: Eiman Azim, Ph.D., February 9

Special Lecture Series
Monday, February 9, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Eiman Azim, Ph.D.
Postdoctoral Fellow,
Department of Biochemistry and Molecular Biophysics,
Columbia University Medical Center

Neural Circuits for Skilled Movement

Recommended Readings

Empirical Articles

Azim, E., Jiang, J., Alstermark, B., & Jessell, T. M. (2014). Skilled reaching relies on a V2a propriospinal internal copy circuit. Nature, 508(7496), 357–363. doi:10.1038/nature13021

Fink, A. J. P., Croce, K. R., Huang, Z. J., Abbott, L. F., Jessell, T. M., & Azim, E. (2014). Presynaptic inhibition of spinal sensory feedback ensures smooth movement. Nature, 509(7498), 43–48. doi:10.1038/nature13276

Review Papers

Miri, A., Azim, E., & Jessell, T. M. (2013). Edging toward entelechy in motor control. Neuron, 80(3), 827–834. doi:10.1016/j.neuron.2013.10.049

Recommended Readings: Celine Riera, Ph.D., February 2

Special Lecture Series
Monday, February 2, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Celine Riera, Ph.D.
Postdoctoral Fellow,
Li Ka Shing Center,
Department of Molecular and Cell Biology,
University of California, Berkeley

Identification of Sensory Circuits Controlling Metabolism and Longevity

Recommended Readings

Riera, C. E., Huising, M. O., Follett, P., Leblanc, M., Halloran, J., Van Andel, R., … Dillin, A. (2014). TRPV1 pain receptors regulate longevity and metabolism by neuropeptide signaling. Cell, 157(5), 1023–1036. doi:10.1016/j.cell.2014.03.051

Riera, C. E., Menozzi-Smarrito, C., Affolter, M., Michlig, S., Munari, C., Robert, F., … le Coutre, J. (2009). Compounds from Sichuan and Melegueta peppers activate, covalently and non-covalently, TRPA1 and TRPV1 channels. British Journal of Pharmacology, 157(8), 1398–1409. doi:10.1111/j.1476-5381.2009.00307.x

Riera, C. E., Vogel, H., Simon, S. a, Damak, S., & le Coutre, J. (2009). Sensory attributes of complex tasting divalent salts are mediated by TRPM5 and TRPV1 channels. The Journal of Neuroscience, 29(8), 2654–2662. doi:10.1523/JNEUROSCI.4694-08.2009