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.

Recommended Readings: Jonas Frisén, M.D., Ph.D., October 16th

Friday Lecture Series
Friday, October 16, 2015
3:45 p.m., Caspary Auditorium

Jonas Frisén, M.D., Ph.D.
Tobias Foundation Professor of Stem Cell Research,
Department of Cell and Molecular Biology,
Karolinska Institutet, Stockholm, Sweden

Cellular Plasticity in the Intact and Injured Central Nervous System

Recommended Readings

Empirical Articles

Ernst, A., Alkass, K., Bernard, S., Salehpour, M., Perl, S., Tisdale, J., … & Frisén, J. (2014). Neurogenesis in the striatum of the adult human brain. Cell, 156(5), 1072-1083. doi: 10.1016/j.cell.2014.01.044

Magnusson, J. P., Göritz, C., Tatarishvili, J., Dias, D. O., Smith, E. M., Lindvall, O., … & Frisén, J. (2014). A latent neurogenic program in astrocytes regulated by Notch signaling in the mouse. Science, 346(6206), 237-241. doi: 10.1126/science.346.6206.237.

Sabelström, H., Stenudd, M., Réu, P., Dias, D. O., Elfineh, M., Zdunek, S., … & Frisén, J. (2013). Resident neural stem cells restrict tissue damage and neuronal loss after spinal cord injury in mice. Science, 342(6158), 637-640. doi: 10.1126/science.1242576

Review Paper

Bergmann, O., Spalding, K. L., & Frisén, J. (2015). Adult neurogenesis in humans. Cold Spring Harbor Perspectives in Biology, 7(7), a018994. doi: 10.1101/cshperspect.a018994

Recommended Readings: Gulcin Pekkurnaz, Ph.D., September 21

Special Lecture
Monday, September 21, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Gulcin Pekkurnaz, Ph.D.,
Postdoctoral Fellow,
Department of Neurobiology,
Harvard Medical School
Boston Children’s Hospital

Metabolic Regulation of Mitochondrial Function in the Nervous System

Recommended Readings

Empirical Articles

Pekkurnaz, G., Trinidad, J. C., Wang, X., Kong, D., & Schwarz, T. L. (2014). Glucose regulates mitochondrial motility via Milton modification by O-GlcNAc transferase. Cell, 158(1), 54-68. doi: 10.1016/j.cell.2014.06.007

Teodoro, R. O., Pekkurnaz, G., Nasser, A., Higashi‐Kovtun, M. E., Balakireva, M., McLachlan, I. G., … & Schwarz, T. L. (2013). Ral mediates activity‐dependent growth of postsynaptic membranes via recruitment of the exocyst. The EMBO Journal, 32(14), 2039-2055. doi: 10.1038/emboj.2013.147

Review Papers

Schwarz, T. L. (2013). Mitochondrial trafficking in neurons. Cold Spring Harbor Perspectives in Biology, 5(6), a011304. doi: 10.1101/cshperspect.a011304

Recommended Readings: Frank Grosveld, Ph.D., June 5th

Friday Lecture Series
Friday, June 5, 2015
3:45 p.m., Caspary Auditorium

Frank Grosveld, Ph.D.
Professor and Head,
Department of Cell Biology
Chair, Research School MGC,
Erasmus MC

Transcription Factors and Genomic Architecture

Recommended Readings

Empirical Articles

Ghamari, A., van de Corput, M. P., Thongjuea, S., van Cappellen, W. A., van IJcken, W., van Haren, J., … & Grosveld, F. G. (2013). In vivo live imaging of RNA polymerase II transcription factories in primary cells. Genes & Development, 27(7), 767-777. doi:10.1101/gad.216200.113

Mylona, A., Andrieu-Soler, C., Thongjuea, S., Martella, A., Soler, E., Jorna, R., … & Grosveld, F. (2013). Genome-wide analysis shows that Ldb1 controls essential hematopoietic genes/pathways in mouse early development and reveals novel players in hematopoiesis. Blood, 121(15), 2902-2913. doi:10.1182/blood-2012-11-467654

Nuez, B., Michalovich, D., Bygrave, A., Ploemacher, R., & Grosveld, F. (1995). Defective haematopoiesis in fetal liver resulting from inactivation of the EKLF gene. Nature, 375(6529), 316-318.

Soler, E., Andrieu-Soler, C., de Boer, E., Bryne, J. C., Thongjuea, S., Stadhouders, R., … & Grosveld, F. (2010). The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation. Genes & Development, 24(3), 277-289. doi:10.1101/gad.551810

Stadhouders, R., Thongjuea, S., Andrieu‐Soler, C., Palstra, R. J., Bryne, J. C., van den Heuvel, A., … & Soler, E. (2012). Dynamic long‐range chromatin interactions control Myb proto‐oncogene transcription during erythroid development. The EMBO Journal, 31(4), 986-999. doi:10.1038/emboj.2011.450

Review Papers

Kolovos, P., Knoch, T. A., Grosveld, F. G., Cook, P. R., & Papantonis, A. (2012). Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin, 5(1). doi:10.1186/1756-8935-5-1

Recommended Readings: W. Ian Lipkin, M.D., May 29th

Friday Lecture Series
Friday, May 29, 2015
3:45 p.m., Caspary Auditorium

W. Ian Lipkin, M.D.
John Snow Professor of Epidemiology,
Mailman School of Public Health
Professor of Neurology and Pathology,
College of Physicians and Surgeons
Director, Center for Infection and Immunity, C
Columbia University

Small Game Hunting

Recommended Readings

Empirical Articles

Cox-Foster, D. L., Conlan, S., Holmes, E. C., Palacios, G., Evans, J. D., Moran, N. A., … & Lipkin, W. I. (2007). A metagenomic survey of microbes in honey bee colony collapse disorder. Science, 318(5848), 283-287.

Memish, Z. A., Mishra, N., Olival, K. J., Fagbo, S. F., Kapoor, V., Epstein, J. H., … & Lipkin, W. I. (2013). Middle East respiratory syndrome coronavirus in bats, Saudi Arabia. Emerging Infectious Diseases, 19(11), 1819-1823. doi:10.3201/eid1911.131172

Negredo, A., Palacios, G., Vázquez-Morón, S., González, F., Dopazo, H., Molero, F., … & Tenorio, A. (2011). Discovery of an ebolavirus-like filovirus in europe. PLoS Pathogens, 7(10), e1002304. doi:10.1371/journal.ppat.1002304

Palacios, G., Druce, J., Du, L., Tran, T., Birch, C., Briese, T., … & Lipkin, W. I. (2008). A new arenavirus in a cluster of fatal transplant-associated diseases. New England Journal of Medicine, 358(10), 991-998. doi:10.1056/NEJMoa073785

Review Papers

Lipkin, W. I. (2013). The changing face of pathogen discovery and surveillance. Nature Reviews Microbiology, 11(2), 133-141. doi:10.1038/nrmicro2949

Lipkin, W. I. (2010). Microbe hunting. Microbiology and Molecular Biology Reviews, 74(3), 363-377. doi:10.1128/MMBR.00007-10

Lipkin, W. I., & Anthony, S. J. (2015). Virus hunting. Virology. doi:10.1016/j.virol.2015.02.006

Recommended Readings: Carl H. June, M.D., May 22nd

Friday Lecture Series
Friday, May 22, 2015
3:45 p.m., Caspary Auditorium

Carl H. June, M.D.
Director, Translational Research Program,
Abramson Family Cancer Research Institute
Richard W. Vague Professor in Immunotherapy,
Perelman School of Medicine,
University of Pennsylvania

Adoptive Cell Therapy with Engineered T Cells

Recommended Readings

Empirical Articles

Grupp, S. A., Kalos, M., Barrett, D., Aplenc, R., Porter, D. L., Rheingold, S. R., … & June, C. H. (2013). Chimeric antigen receptor–modified T cells for acute lymphoid leukemia. New England Journal of Medicine, 368(16), 1509-1518.  doi:10.1056/NEJMoa1215134

Kalos, M., Levine, B. L., Porter, D. L., Katz, S., Grupp, S. A., Bagg, A., & June, C. H. (2011). T cells with chimeric antigen receptors have potent antitumor effects and can establish memory in patients with advanced leukemia. Science Translational Medicine, 3(95), 95ra73-95ra73. doi:10.1126/scitranslmed.3002842

Porter, D. L., Levine, B. L., Kalos, M., Bagg, A., & June, C. H. (2011). Chimeric antigen receptor–modified T cells in chronic lymphoid leukemia. New England Journal of Medicine, 365(8), 725-733. doi:10.1056/NEJMoa1103849

Review Papers

June, C. H., Maus, M. V., Plesa, G., Johnson, L. A., Zhao, Y., Levine, B. L., … & Porter, D. L. (2014). Engineered T cells for cancer therapy. Cancer Immunology, Immunotherapy, 63(9), 969-975. doi:10.1007/s00262-014-1568-1

Maus, M. V., Fraietta, J. A., Levine, B. L., Kalos, M., Zhao, Y., & June, C. H. (2014). Adoptive immunotherapy for cancer or viruses. Annual Review of Immunology, 32, 189-225. doi:10.1146/annurev-immunol-032713-120136

Recommended Readings: John Stamatoyannopoulos, M.D., May 11th

Special Lecture
Monday, May 11, 2015
4:00 p.m., Carson Family Auditorium (CRC)

John Stamatoyannopoulos, M.D.
Associate Professor of Genome Sciences and Medicine,
University Washington School of Medicine

New Insights into Human Genome Function

Recommended Readings

Empirical Articles

ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57-74. doi:10.1038/nature11247

Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., … & Kulkarni, A. (2015). Integrative analysis of 111 reference human epigenomes. Nature, 518(7539), 317-330. doi:10.1038/nature14248

Mayer, A., di Iulio, J., Maleri, S., Eser, U., Vierstra, J., Reynolds, A., … & Churchman, L. S. (2015). Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell, 161(3), 541-554. doi:10.1016/j.cell.2015.03.010

Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., … & Morrissey, C. S. (2014). A comparative encyclopedia of DNA elements in the mouse genome. Nature, 515(7527), 355-364. doi:10.1038/nature13992

Review Paper

Kellis, M., Wold, B., Snyder, M. P., Bernstein, B. E., Kundaje, A., Marinov, G. K., … & Hardison, R. C. (2014). Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences, 111(17), 6131-6138. doi:10.1073/pnas.1318948111

Recommended Readings: Marc Kirschner, Ph.D., May 8th

Friday Lecture Series
Friday, May 8, 2015
3:45 p.m., Caspary Auditorium

Marc W. Kirschner, Ph.D.
John Franklin Enders University Professor,
Professor and Chair,
Department of Systems Biology,
Harvard Medical School

The Origin of Specificity in Regulated Protein Degradation

Recommended Readings

Empirical Articles

Gujral, T. S., Chan, M., Peshkin, L., Sorger, P. K., Kirschner, M. W., & MacBeath, G. (2014). A noncanonical frizzled2 pathway regulates epithelial-mesenchymal transition and metastasis. Cell, 159(4), 844-856. doi: 10.1016/j.cell.2014.10.032.

Lu, Y., Lee, B. H., King, R. W., Finley, D., & Kirschner, M. W. (2015). Substrate degradation by the proteasome: A single-molecule kinetic analysis.Science, 348(6231), 1250834. doi: 10.1126/science.1250834

Lu, Y., Wang, W., & Kirschner, M. W. (2015). Specificity of the anaphase-promoting complex: A single-molecule study. Science, 348(6231), 1248737. doi: 10.1126/science.1248737.

Zhao, R., Deibler, R. W., Lerou, P. H., Ballabeni, A., Heffner, G. C., Cahan, P., … & Daley, G. Q. (2014). A nontranscriptional role for Oct4 in the regulation of mitotic entry. Proceedings of the National Academy of Sciences, 111(44), 15768-15773. doi: 10.1073/pnas.1417518111

Review Papers

Kirschner, M. W. (2005). The meaning of systems biology. Cell, 121(4), 503-504.