Recommended Readings: Seth Darst, Ph.D., November 2nd

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

Seth Darst, Ph.D.
Jack Fishman Professor and Head,
Laboratory of Molecular Biophysics,
The Rockefeller University

Structural Studies of Bacterial Transcription

Recommended Readings

Empirical Articles

Bae, B., Chen, J., Davis, E., Leon, K., Darst, S. A., & Campbell, E. A. (2015). CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex. eLife, e08505. doi:10.7554/eLife.08505

Davis, E., Chen, J., Leon, K., Darst, S. A., & Campbell, E. A. (2014). Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD. Nucleic Acids Research, gku1231. doi: 10.1093/nar/gku1231

Srivastava, D. B., Leon, K., Osmundson, J., Garner, A. L., Weiss, L. A., Westblade, L. F., … & Campbell, E. A. (2013). Structure and function of CarD, an essential mycobacterial transcription factor. Proceedings of the National Academy of Sciences, 110(31), 12619-12624. doi:10.1073/pnas.1308270110

Review Papers

Feklístov, A., Sharon, B. D., Darst, S. A., & Gross, C. A. (2014). Bacterial sigma factors: a historical, structural, and genomic perspective. Annual Review of Microbiology, 68, 357-376. doi:0.1146/annurev-micro-092412-155737

Recommended Readings: Winrich Freiwald, Ph.D., October 30th

Friday Lecture Series
Friday, October 30, 2015
3:45 p.m., Carson Family Auditorium (CRC)

Winrich Freiwald, Ph.D.
Assistant Professor,
Laboratory of Neural Systems,
The Rockefeller University

Face to Face: New Vistas on the Neural Mechanisms of Social Cognition

Recommended Readings

Empirical Articles

Fisher, C., & Freiwald, W. A. (2015). Contrasting specializations for facial motion within the macaque face-processing system. Current Biology, 25(2), 261-266. doi:10.1016/j.cub.2014.11.038.

Meyers, E. M., Borzello, M., Freiwald, W. A., & Tsao, D. (2015). Intelligent information loss: The coding of facial identity, head pose, and non-face information in the Macaque face patch system. The Journal of Neuroscience, 35(18), 7069-7081. doi:10.1523/JNEUROSCI.3086-14.2015.

Polosecki, P., Moeller, S., Schweers, N., Romanski, L. M., Tsao, D. Y., & Freiwald, W. A. (2013). Faces in motion: selectivity of macaque and human face processing areas for dynamic stimuli. The Journal of Neuroscience, 33(29), 11768-11773. doi: 10.1523/JNEUROSCI.5402-11.2013.

Schwiedrzik, C. M., Zarco, W., Everling, S., & Freiwald, W. A. (2015). Face patch resting state networks link face processing to social cognition. PLoS Biology, 13(9), e1002245. doi:10.1371/journal.pbio.1002245

Review Papers

Brecht, M., & Freiwald, W. A. (2012). The many facets of facial interactions in mammals. Current Opinion in Neurobiology, 22(2), 259-266. doi:10.1371/journal.pbio.1002245.

Recommended Readings: Stephen Quake, Ph.D., October 19th

Monday Lecture Series
Monday, October 19, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Stephen Quake, Ph.D.
Lee Otterson Professor of Bioengineering and Applied Physics,
Stanford University
Investigator, Howard Hughes Medical Institute

Single Cell Genomics

Recommended Readings

Empirical Articles

Braslavsky, I., Hebert, B., Kartalov, E., & Quake, S. R. (2003). Sequence information can be obtained from single DNA molecules. Proceedings of the National Academy of Sciences, 100(7), 3960-3964. doi:10.1073/pnas.0230489100.

Dalerba, P., Kalisky, T., Sahoo, D., Rajendran, P. S., Rothenberg, M. E., Leyrat, A. A., … & Quake, S. R. (2011). Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nature Biotechnology, 29(12), 1120-1127. doi:10.1126/science.1150427.

Fan, H. C., Wang, J., Potanina, A., & Quake, S. R. (2011). Whole-genome molecular haplotyping of single cells. Nature Biotechnology, 29(1), 51-57. doi:10.1038/nbt.1739.

Harris, T. D., Buzby, P. R., Babcock, H., Beer, E., Bowers, J., Braslavsky, I., … & Xie, Z. (2008). Single-molecule DNA sequencing of a viral genome. Science, 320(5872), 106-109. doi:10.1038/nbt.2038.

Review Papers

Kalisky, T., Blainey, P., & Quake, S. R. (2011). Genomic analysis at the single-cell level. Annual Review of Genetics, 45, 431-445. doi:10.1146/annurev-genet-102209-163607.

Recommended Readings: Michael Lenardo, M.D., October 23rd

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

Michael Lenardo, M.D.
Chief, Molecular Development Section,
Laboratory of Immunology,
Director, NIAID Clinical Genomics Program,
National Institute of Allergy and Infectious Diseases,
National Institutes of Health

Genomic Approaches to Solving Primary Immune Disorders

Recommended Readings

Empirical Articles

Kuehn, H. S., Ouyang, W., Lo, B., Deenick, E. K., Niemela, J. E., Avery, D. T., … & Uzel, G. (2014). Immune dysregulation in human subjects with heterozygous germline mutations in CTLA4. Science, 345(6204), 1623-1627. doi:10.1126/science.1255904.

Lo, B., Zhang, K., Lu, W., Zheng, L., Zhang, Q., Kanellopoulou, C., … & Jordan, M. B. (2015). Patients with LRBA deficiency show CTLA4 loss and immune dysregulation responsive to abatacept therapy. Science, 349(6246), 436-440. doi:10.1126/science.aaa1663.

Lucas, C. L., Zhang, Y., Venida, A., Wang, Y., Hughes, J., McElwee, J., … & Lenardo, M. J. (2014). Heterozygous splice mutation in PIK3R1 causes human immunodeficiency with lymphoproliferation due to dominant activation of PI3K. The Journal of Experimental Medicine, 211(13), 2537-2547. doi:10.1084/jem.20141759.

Review Papers

Grönholm, J., & Lenardo, M. J. (2015). Novel diagnostic and therapeutic approaches for autoimmune diabetes- A prime time to treat insulitis as a disease. Clinical Immunology, 156(2), 109-118. doi:10.1016/j.clim.2014.11.007.

Zhang, Y., Su, H. C., & Lenardo, M. J. (2015). Genomics is rapidly advancing precision medicine for immunological disorders. Nature Immunology, 16(10), 1001-1004. doi:10.1038/ni.3275

Recommended Readings: Graeme Davis, Ph.D., October 2nd

Friday Lecture Series
Friday, October 2nd, 2015
3:45 p.m., Caspary Auditorium

Graeme Davis, Ph.D.
Distinguished Professor of Medicine,
Department of Biochemistry and Biophysics,
University of California San Francisco

The Stable Brain: Homeostatic Control of Neural Function

Recommended Readings

Empirical Articles

Ford, K. J., & Davis, G. W. (2014). Archaerhodopsin voltage imaging: synaptic calcium and BK channels stabilize action potential repolarization at the Drosophila neuromuscular junction. The Journal of Neuroscience, 34(44), 14517-14525. doi:10.1523/JNEUROSCI.2203-14.2014.

Gaviño, M. A., Ford, K. J., Archila, S., & Davis, G. W. (2015). Homeostatic synaptic depression is achieved through a regulated decrease in presynaptic calcium channel abundance. eLife, 4, e05473. doi:10.7554/eLife.05473.

Müller, M., Genç, Ö., & Davis, G. W. (2015). RIM-Binding protein Links synaptic homeostasis to the stabilization and replenishment of high release probability vesicles. Neuron, 85(5), 1056-1069. doi:10.1016/j.neuron.2015.01.024.

Review Papers

Davis, G. W. (2013). Homeostatic signaling and the stabilization of neural function. Neuron, 80(3), 718-728. doi:10.1016/j.neuron.2013.09.044.

Davis, G. W., & Müller, M. (2015). Homeostatic control of presynaptic neurotransmitter release. Annual Review of Physiology, 77, 251-270. doi:10.1146/annurev-physiol-021014-071740.

Recommended Readings: Luciano Marraffini, Ph.D., October 9th

Friday Lecture Series
Friday, October 9th, 2015
3:45 p.m., Caspary Auditorium

Luciano Marraffini, Ph.D.
Assistant Professor and Head,
Laboratory of Bacteriology,
The Rockefeller University

CRISPR-Cas: The Adaptive Immune System of Prokaryotes

Recommended Readings

Empirical Articles

Goldberg, G. W., Jiang, W., Bikard, D., & Marraffini, L. A. (2014). Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting. Nature, 514(7524), 633-637. doi:10.1038/nature13637.

Heler, R., Samai, P., Modell, J. W., Weiner, C., Goldberg, G. W., Bikard, D., & Marraffini, L. A. (2015). Cas9 specifies functional viral targets during CRISPR-Cas adaptation. Nature, 19(7542), 199-202. doi:10.1038/nature14245.

Jiang, W., Maniv, I., Arain, F., Wang, Y., Levin, B. R., & Marraffini, L. A. (2012). Dealing with the evolutionary downside of CRISPR immunity: bacteria and beneficial plasmids. PLoS Genetics, 9(9), e1003844-e1003844. doi:10.1371/journal.pgen.1003844.

Review Papers

Barrangou, R., & Marraffini, L. A. (2014). CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Molecular Cell, 54(2), 234-244. doi:10.1016/j.molcel.2014.03.011.

Hatoum-Aslan, A., & Marraffini, L. A. (2014). Impact of CRISPR immunity on the emergence and virulence of bacterial pathogens. Current Opinion in Microbiology, 17, 82-90. doi:10.1016/j.mib.2013.12.001

Recommended Readings: Denes Hnisz, Ph.D., October 12th

Special Lecture
Monday, October 12th, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Denes Hnisz, Ph.D.
Postdoctoral Fellow,
Whitehead Institute for Biomedical Research

Transcriptional Regulatory Mechanisms Defining Cell Identity

Recommended Readings

Dowen, J. M., Fan, Z. P., Hnisz, D., Ren, G., Abraham, B. J., Zhang, L. N., … & Young, R. A. (2014). Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell, 159(2), 374-387. doi:10.1016/j.cell.2014.09.030.

Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., … & Young, R. A. (2013). Super-enhancers in the control of cell identity and disease. Cell, 155(4), 934-947. doi:10.1016/j.cell.2013.09.053.

Hnisz, D., Schuijers, J., Lin, C. Y., Weintraub, A. S., Abraham, B. J., Lee, T. I., … & Young, R. A. (2015). Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers. Molecular Cell, 58(2), 362-370. doi:10.1016/j.molcel.2015.02.014.

Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., … & Young, R. A. (2013). Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell, 153(2), 307-319. doi:10.1016/j.cell.2013.03.035.

Recommended Readings: Erich Jarvis, Ph.D., September 28th

Special Lecture
Monday, September 28th, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Erich Jarvis, Ph.D.
Associate Professor,
Department of Neurobiology,
Duke University Medical Center
Investigator, Howard Hughes Medical Institute

Dissecting the Molecular Mechanisms of Vocal Learning and Spoken Language

Recommended Readings

Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., … & Samaniego, J. A. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320-1331. doi:10.1126/science.1253451.

Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., … & Avian Phylogenomics Consortium. (2015). Phylogenomic analyses data of the avian phylogenomics project. GigaScience, 4(1), 1-9. doi:10.1186/s13742-014-0038-1.

Pfenning, A. R., Hara, E., Whitney, O., Rivas, M. V., Wang, R., Roulhac, P. L., … & Jarvis, E. D. (2014). Convergent transcriptional specializations in the brains of humans and song-learning birds. Science, 346(6215), 1256846. doi:10.1126/science.1256846.

Whitney, O., Pfenning, A. R., Howard, J. T., Blatti, C. A., Liu, F., Ward, J. M., … & Jarvis, E. D. (2014). Core and region-enriched networks of behaviorally regulated genes and the singing genome. Science, 346(6215), 1256780. doi: 10.1126/science.1256780.

Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., … & Ganapathy, G. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311-1320. doi:10.1126/science.1251385.

Recommended Readings: Beth Levine, M.D., September 25th

Friday Lecture Series
Friday, September, 25th 2015
3:45 p.m., Caspary Auditorium

Beth Levine, M.D.
Charles Cameron Sprague Distinguished Chair in Biomedical Science,
Director, Center for Autophagy Research,
Professor, Department of Internal Medicine and Microbiology,
University of Texas Southwestern Medical Center
Investigator, Howard Hughes Medical Institute

Molecular Regulation and Functions of Beclin 1 and the Autophagy Pathway

Recommended Readings

Empirical Articles

Liu, Y., Shoji-Kawata, S., Sumpter, R. M., Wei, Y., Ginet, V., Zhang, L., … & Levine, B. (2013). Autosis is a Na+, K+-ATPase–regulated form of cell death triggered by autophagy-inducing peptides, starvation, and hypoxia–ischemia. Proceedings of the National Academy of Sciences, 110(51), 20364-20371. doi:10.1073/pnas.1319661110

Nassif, M., Valenzuela, V., Rojas-Rivera, D., Vidal, R., Matus, S., Castillo, K., … & Hetz, C. (2014). Pathogenic role of BECN1/Beclin 1 in the development of amyotrophic lateral sclerosis. Autophagy, 10(7), 1256-1271. doi:10.4161/auto.28784

Pedro, J. M. B. S., Wei, Y., Sica, V., Maiuri, M. C., Zou, Z., Kroemer, G., & Levine, B. (2015). BAX and BAK1 are dispensable for ABT-737-induced dissociation of the BCL2-BECN1 complex and autophagy. Autophagy, 11(3), 452-459. doi:10.1080/15548627.2015.1017191

Review Papers

Galluzzi, L., Pietrocola, F., Levine, B., & Kroemer, G. (2014). Metabolic control of autophagy. Cell, 159(6), 1263-1276. doi: 10.1016/j.cell.2014.11.006.

Levine, B., Liu, R., Dong, X., & Zhong, Q. (2015). Beclin orthologs: integrative hubs of cell signaling, membrane trafficking, and physiology. Trends in Cell Biology, 25(9), 533-544. doi:10.1016/j.tcb.2015.05.004

Recommended Readings: Susan Kaech, Ph.D., September 14th

Monday Lecture Series
Monday, September 14th, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Susan Kaech, Ph.D.
Associate Professor of Immunobiology,
Yale School of Medicine
Early Career Scientist,
Howard Hughes Medical Institute

PEPing Up T Cell-mediated Immunity to Viruses and Cancer

Recommended Readings

Empirical Articles

Cui, G., Staron, M. M., Gray, S. M., Ho, P. C., Amezquita, R. A., Wu, J., & Kaech, S. M. (2015). IL-7-induced glycerol transport and TAG synthesis promotes memory CD8+ T cell longevity. Cell, 161(4), 750-761. doi:10.1016/j.cell.2015.03.021.

Laidlaw, B. J., Cui, W., Amezquita, R. A., Gray, S. M., Guan, T., Lu, Y., … & Kaech, S. M. (2015). Production of IL-10 by CD4+ regulatory T cells during the resolution of infection promotes the maturation of memory CD8+ T cells. Nature Immunology, 16(8), 871-879. doi:10.1038/ni.3224

Laidlaw, B. J., Zhang, N., Marshall, H. D., Staron, M. M., Guan, T., Hu, Y., … & Kaech, S. M. (2014). CD4+ T cell help guides formation of CD103+ lung-resident memory CD8+ T cells during influenza viral infection. Immunity, 41(4), 633-645. doi:10.1016/j.immuni.2014.09.007.

Slütter, B., Pewe, L. L., Kaech, S. M., & Harty, J. T. (2013). Lung airway-surveilling CXCR3 hi memory CD8+ T cells are critical for protection against influenza A virus. Immunity, 39(5), 939-948. doi:10.1016/j.immuni.2013.09.013.

Review Paper

Gray, S. M., Kaech, S. M., & Staron, M. M. (2014). The interface between transcriptional and epigenetic control of effector and memory CD8+ T‐cell differentiation. Immunological Reviews, 261(1), 157-168. doi:10.1111/imr.12205.

Kaech, S. M., & Cui, W. (2012). Transcriptional control of effector and memory CD8+ T cell differentiation. Nature Reviews Immunology, 12(11), 749-761. doi:10.1038/nri3307.