Recommended Readings: Richard A. Young, Ph.D.

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Friday Lecture Series

Cancer Biology Lecture

Transcriptional Control of Cell Identity

Richard A. Young, Ph.D., professor of biology and member,

Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology

May 17, 2013

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Guenther, M. G., & Young, R. A. (2010). Repressive transcription. Science, 329(5988), 150-151

Jaenisch, R., & Young, R. (2008). Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell, 132(4), 567-582

Mazzoni, E. O., Mahony, S., Iacovino, M., Morrison, C. A., Mountoufaris, G., Closser, M., . . . Wichterle, H. (2011). Embryonic stem cell-based mapping of developmental transcriptional programs. Nature Methods, 8(12), 1056-1060

Newman, J. J., & Young, R. A. (2010). Connecting transcriptional control to chromosome structure and human disease. Cold Spring Harbor Symposia on Quantitative Biology 75 , pp. 227-235

Novershtern, N., Subramanian, A., Lawton, L. N., Mak, R. H., Haining, W. N., McConkey, M. E., . . . Ebert, B. L. (2011). Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell, 144(2), 296-309

Young, R. A. (2011). Control of the embryonic stem cell state. Cell, 144(6), 940-954

 

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Recommended Readings:Detlev Arendt, Ph.D.

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Friday Lecture Series

The Evolutionary Origin of the Vertebrate Brain

Detlev Arendt, Ph.D., honorary professor, University of Heidelberg, Germany;

group leader and senior scientist, European Molecular Biology Laboratory

May 3, 2013

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Arendt, D., Tessmar-Raible, K., Snyman, H., Dorresteijn, A. W., & Wittbrodf, J. (2004). Ciliary photoreceptors with a vertebrate-type opsin in an invertebrate brain. Science, 306(5697), 869-871

Christodoulou, F., Raible, F., Tomer, R., Simakov, O., Trachana, K., Klaus, S., . . . Arendt, D. (2010). Ancient animal microRNAs and the evolution of tissue identity. Nature, 463(7284), 1084-1088

Raible, F., Tessmar-Raible, K., Osoegawa, K., Wincker, P., Jubin, C., Balavoine, G., . . . Arendt, D. (2005). Evolution: Vertebrate-type intron-rich genes in the marine annelid platynereis dumerilii. Science, 310(5752), 1325-1326

Tessmar-Raible, K., & Arendt, D. (2003). Emerging systems: Between vertebrates and arthropods, the lophotrochozoa. Current Opinion in Genetics and Development, 13(4), 331-340

Tomer, R., Denes, A. S., Tessmar-Raible, K., & Arendt, D. (2010). Profiling by image registration reveals common origin of annelid mushroom bodies and vertebrate pallium. Cell, 142(5), 800-809

 

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Recommended Readings: Alexander Varshavsky, Ph.D.

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Friday Lecture Series

William H. Stein Memorial Lecture

Recent Discoveries about the Ubiquitin System and the N-end Rule Pathway

Alexander Varshavsky, Ph.D.,

Howard and Gwen Laurie Smits Professor of Cell Biology,

California Institute of Technology

April 26, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Graciet, E., Walter, F., Maoiléidigh, D. Ó., Pollmann, S., Meyerowitz, E. M., Varshavsky, A., & Wellmer, F. (2009). The N-end rule pathway controls multiple functions during arabidopsis shoot and leaf development. Proceedings of the National Academy of Sciences of the United States of America, 106(32), 13618-13623

Hwang, C. -., Shemorry, A., Auerbach, D., & Varshavsky, A. (2010). The N-end rule pathway is mediated by a complex of the RING-type Ubr1 and HECT-type Ufd4 ubiquitin ligases. Nature Cell Biology, 12(12), 1177-1185

Hwang, C. -., Shemorry, A., & Varshavsky, A. (2010). N-terminal acetylation of cellular proteins creates specific degradation signals. Science, 327(5968), 973-977

Hwang, C. -., Shemorry, A., & Varshavsky, A. (2009). Two proteolytic pathways regulate DNA repair by cotargeting the Mgt1 alkylguanine transferase. Proceedings of the National Academy of Sciences of the United States of America, 106(7), 2142-2147

Varshavsky, A. (2006). The early history of the ubiquitin field. Protein Science, 15(3), 647-654

Varshavsky, A. (2011). The N-end rule pathway and regulation by proteolysis. Protein Science, 20(8), 1298-1345

Xia, Z., Webster, A., Du, F., Piatkov, K., Ghislain, M., & Varshavsky, A. (2008). Substrate-binding sites of UBR1, the ubiquitin ligase of the N-end rule pathway. Journal of Biological Chemistry, 283(35), 24011-24028

 

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Recommended Readings: Robert H. Singer, Ph.D.

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Friday Lecture Series

Following Single mRNAs from Birth to Death

Robert H. Singer, Ph.D., professor and co-chair,

Department of Anatomy and Structural Biology, Albert Einstein College of Medicine

April 12, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Ben-Ari, Y., Brody, Y., Kinor, N., Mor, A., Tsukamoto, T., Spector, D. L., . . . Shav-Tal, Y. (2010). The life of an mRNA in space and time. Journal of Cell Science, 123(10), 1761-1774

Darzacq, X., Yao, J., Larson, D. R., Causse, S. Z., Bosanac, L., De Turris, V., . . . Singer, R. H. (2009). Imaging transcription in living cells . Annual Review of Biophysics 38 (1) , pp. 173-196

Grünwald, D., & Singer, R. H. (2010). In vivo imaging of labelled endogenous Β-actin mRNA during nucleocytoplasmic transport. Nature, 467(7315), 604-607

Katz, Z. B., Wells, A. L., Park, H. Y., Wu, B., Shenoy, S. M., & Singer, R. H. (2012). β-Actin mRNA compartmentalization enhances focal adhesion stability and directs cell migration. Genes and Development, 26(17), 1885-1890

Lionnet, T., Czaplinski, K., Darzacq, X., Shav-Tal, Y., Wells, A. L., Chao, J. A., . . . Singer, R. H. (2011). A transgenic mouse for in vivo detection of endogenous labeled mRNA. Nature Methods, 8(2), 165-170

Park, H. Y., Buxbaum, A. R., & Singer, R. H. (2010). Single mRNA tracking in live cells. Methods in Enzymology, 472, 387-406

Trcek, T., Larson, D. R., Moldón, A., Query, C. C., & Singer, R. H. (2011). Single-molecule mRNA decay measurements reveal promoter-regulated mRNA stability in yeast. Cell, 147(7), 1484-1497

 

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Recommended Readings: Erin Schuman, Ph.D.

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Friday Lecture Series

Transcriptomes and Proteomes at Synapses

Erin Schuman, Ph.D., director, department of synaptic plasticity, and professor,

Max Planck Institute for Brain Research

 March 22, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Bingol, B., & Schuman, E. M. (2005). Synaptic protein degradation by the ubiquitin proteasome system. Current Opinion in Neurobiology, 15(5), 536-541

Sutton, M. A., & Schuman, E. M. (2006). Dendritic protein synthesis, synaptic plasticity, and memory. Cell, 127(1), 49-58

Sutton, M. A., & Schuman, E. M. (2005). Local translational control in dendrites and its role in long-term synaptic plasticity. Journal of Neurobiology, 64(1), 116-131

Sutton, M. A., & Schuman, E. M. (2009). Partitioning the synaptic landscape: Distinct microdomains for spontaneous and spike-triggered neurotransmission. Science Signaling, 2(65)

Tai, H. -., & Schuman, E. M. (2008). Ubiquitin, the proteasome and protein degradation in neuronal function and dysfunction. Nature Reviews Neuroscience, 9(11), 826-838

 

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Recommended Readings: Edward A. Fisher, M.D., Ph.D., M.P.H.

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Friday Lecture Series

The Regression of Atherosclerosis and its Molecular Regulation: Insights from Novel Mouse Models

Genetics of Lipid Disorders and Atherosclerosis: A Symposium in Honor of Jan Breslow’s 70th Birthday

Edward A. Fisher, M.D., Ph.D., M.P.H.,

Leon Charney Professor of CardiovascularMedicine, director, Center for the Prevention of Cardiovascular Disease and director,

Marc and Ruti Bell Program in Vascular Biology,

New York University School of Medicine

 March 15, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Amirbekian, V., Aguinaldo, J. G. S., Amirbekian, S., Hyafil, F., Vucic, E., Sirol, M., . . . Fayad, Z. A. (2009). Atherosclerosis and matrix metalloproteinases: Experimental molecular MR imaging in vivo. Radiology, 251(2), 429-438

Cormode, D. P., Chandrasekar, R., Delshad, A., Briley-Saebo, K. C., Calcagno, C., Barazza, A., . . . Fayad, Z. A. (2009). Comparison of synthetic high density lipoprotein (HDL) contrast agents for MR imaging of atherosclerosis. Bioconjugate Chemistry, 20(5), 937-943

Fayad, Z. A. (2010). Atherosclerotic plaque composition: Analysis with multicolor CT and targeted gold nanoparticles. Radiology, 256(3), 774-782

Feig, J. E., Rong, J. X., Shamir, R., Sanson, M., Vengrenyuk, Y., Liu, J., . . . Fisher, E. A. (2011). HDL promotes rapid atherosclerosis regression in mice and alters inflammatory properties of plaque monocyte-derived cells. Proceedings of the National Academy of Sciences of the United States of America, 108(17), 7166-7171

Parathath, S., Grauer, L., Huang, L. -., Sanson, M., Distel, E., Goldberg, I. J., & Fisher, E. A. (2011). Diabetes adversely affects macrophages during atherosclerotic plaque regression in mice. Diabetes, 60(6), 1759-1769

Van Gils, J. M., Derby, M. C., Fernandes, L. R., Ramkhelawon, B., Ray, T. D., Rayner, K. J., . . . Moore, K. J. (2012). The neuroimmune guidance cue netrin-1 promotes atherosclerosis by inhibiting the emigration of macrophages from plaques. Nature Immunology, 13(2), 136-143

 

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Recommended Readings: Maria M. Mota PhD March 13, 2013

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Special Seminar Series

Malaria Infection, Superinfection and Co-infections: From Simple Models to Complex Interactions

Maria M. Mota,   PH.D.

Unit Leader, Malaria Unit

Instituto de Medicina Molecular

Monday      March 18,  2013

Recommended Readings:

Pinkevych, Mykola; Petravic, Janka; Chelimo, Kiprotich; et al.  2012.  The Dynamics of Naturally Acquired Immunity to Plasmodium falciparum Infection.   PLOS COMPUTATIONAL BIOLOGY.   8(10): e1002729   DOI: 10.1371/journal.pcbi.1002729  

 Klein, Eili Y.; Smith, David L.; Laxminarayan, Ramanan; et al.  2012. Superinfection and the evolution of resistance to antimalarial drugs. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES.   279( 1743):3834-3842   DOI: 10.1098/rspb.2012.1064  

 Portugal, Silvia; Drakesmith, Hal; Mota, Maria M. 2011. Superinfection in malaria: Plasmodium shows its iron will.  EMBO REPORTS.  12(12):1233-1242    DOI: 10.1038/embor.2011.213  

van Santen, Susanne; de Mast, Quirijn; Swinkels, Dorine W.; et al. 2011.  Hepcidin in malaria superinfection: can findings be translated to humans? NATURE MEDICINE.  17(11):1341-1341   DOI: 10.1038/nm.2488  

 Portugal, Silvia; Carret, Celine; Recker, Mario; et al. 2011.  Host-mediated regulation of superinfection in malaria.   NATURE MEDICINE.  17(6):732-U126    DOI: 10.1038/nm.2368  

 Templeton, TJ; Keister, DB; Muratova, O; et al.  1998. Adherence of erythrocytes during exflagellation of Plasmodium falciparum microgametes is dependent on erythrocyte surface sialic acid and glycophorins.   JOURNAL OF EXPERIMENTAL MEDICINE.  187(10 ):1599-1609   DOI: 10.1084/jem.187.10.1599

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Recommended Readings: Michel C. Nussenzweig, M.D., Ph.D.

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Friday Lecture Series

Ph.D. Recruitment Lecture

The HIV Vaccine Problem

Michel C. Nussenzweig, M.D., Ph.D., Sherman Fairchild Professor,

senior physician, The Rockefeller University;

investigator, Howard Hughes Medical Institute

 March 8, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

 

Recommended Readings

Mouquet, H., Warncke, M., Scheid, J. F., Seaman, M. S., & Nussenzweig, M. C. (2012). Enhanced HIV-1 neutralization by antibody heteroligation. Proceedings of the National Academy of Sciences of the United States of America, 109(3), 875-880

Nchinda, G., Kuroiwa, J., Oks, M., Trumpfheller, C., Chae, G. P., Huang, Y., . . . Steinman, R. M. (2008). The efficacy of DNA vaccination is enhanced in mice by targeting the encoded protein to dendritic cells. Journal of Clinical Investigation, 118(4), 1427-1436

Scheid, J. F., Mouquet, H., Ueberheide, B., Diskin, R., Klein, F., Oliveira, T. Y. K., . . . Nussenzweig, M. C. (2011). Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding. Science, 333(6049), 1633-1637

Trumpfheller, C., Finke, J. S., López, C. B., Moran, T. M., Moltedo, B., Soares, H., . . . Steinman, R. M. (2006). Intensified and protective CD4 + T cell immunity in mice with anti-dendritic cell HIV gag fusion antibody vaccine. Journal of Experimental Medicine, 203(3), 607-617

Zhou, T., Georgiev, I., Wu, X., Yang, Z. -., Dai, K., Finzi, A., . . . Kwong, P. D. (2010). Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01. Science, 329(5993), 811-817

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Recommended Readings: Roderick MacKinnon, M.D.

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Friday Lecture Series

Inaugural Bruce Merrifield Distinguished Lecture; Ph.D. Recruitment Lecture

The Incredible Diversity of K+ Channels

Roderick MacKinnon, M.D., John D. Rockefeller Jr. Professor, and head,

Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University;

investigator, Howard Hughes Medical Institute

 March 1, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Hansen, S. B., Tao, X., & MacKinnon, R. (2011). Structural basis of PIP 2 activation of the classical inward rectifier K + channel Kir2.2. Nature, 477(7365), 495-498

Lee, S. -., Banerjee, A., & MacKinnon, R. (2009). Two separate interfaces between the voltage sensor and pore are required for the function of voltage-dependent K + channels. PLoS Biology, 7(3)

Lee, S. -., Lee, A., Chen, J., & MacKinnon, R. (2005). Structure of the KvAP voltage-dependent K + channel and its on the lipid membrane. Proceedings of the National Academy of Sciences of the United States of America, 102(43), 15441-15446

Long, S. B., Tao, X., Campbell, E. B., & MacKinnon, R. (2007). Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment. Nature, 450(7168), 376-382

Schmidt, D., & MacKinnon, R. (2008). Voltage-dependent K + channel gating and voltage sensor toxin sensitivity depend on the mechanical state of the lipid membrane. Proceedings of the National Academy of Sciences of the United States of America, 105(49), 19276-19281

Tao, X., Avalos, J. L., Chen, J., & MacKinnon, R. (2009). Crystal structure of the eukaryotic strong inward-rectifier K + channel Kir2.2 at 3.1 Å resolution. Science, 326(5960), 1668-1674

 

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Recommended Readings: Kang Shen, Ph.D.

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Friday Lecture Series

Extracellular and Intracellular Mechanisms of Synapse Patterning in C. elegans

Kang Shen, Ph.D., M.P.H., associate professor,

department of biological sciences, Stanford University

 February 22, 2012

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Allen, P. B., Sgro, A. E., Chao, D. L., Doepker, B. E., Edgar, J. S., Shen, K., & Chiu, D. T. (2008). Single-synapse ablation and long-term imaging in live C. elegans. Journal of Neuroscience Methods, 173(1), 20-26

Crane, M. M., Stirman, J. N., Ou, C. -., Kurshan, P. T., Rehg, J. M., Shen, K., & Lu, H. (2012). Autonomous screening of C. elegans identifies genes implicated in synaptogenesis. Nature Methods, 9(10), 977-980

Klassen, M. P., Wu, Y. E., Maeder, C. I., Nakae, I., Cueva, J. G., Lehrman, E. K., . . . Shen, K. (2010). An arf-like small G protein, ARL-8, promotes the axonal transport of presynaptic cargoes by suppressing vesicle aggregation. Neuron, 66(5), 710-723

Maeder, C. I., & Shen, K. (2011). Genetic dissection of synaptic specificity. Current Opinion in Neurobiology, 21(1), 93-99

Margeta, M. A., Wang, G. J., & Shen, K. (2009). Clathrin adaptor AP-1 complex excludes multiple postsynaptic receptors from axons in C. elegans. Proceedings of the National Academy of Sciences of the United States of America, 106(5), 1632-1637

 

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