Recommended Readings: Talking Science, Monday, December 30

Talking Science
Caspary Auditorium
Monday, December 30, 2013
10:30 a.m.-2:30 p.m.

C. David Allis, Ph.D.
Joy and Jack Fishman Professor
Laboratory of Chromatin Biology and Epigenetics
The Rockefeller University

Epigenetics: Inheriting More Than Genes

Recommended Reading:

Epigenetics Basics

Simmons, D. (2008) Epigenetic influence and diseaseNature Education 1(1):6

In-Depth Reading

Feinberg, A. P. (2008). Epigenetics at the epicenter of modern medicine. JAMA : The Journal of the American Medical Association, 299(11), 1345–1350. doi:10.1001/jama.299.11.1345

Goldberg, A. D., Allis, C. D., & Bernstein, E. (2007). Epigenetics: a landscape takes shape. Cell, 128(4), 635–638. doi:10.1016/j.cell.2007.02.006

Recommended Readings: Lei Stanley Qi, Ph.D. Monday, January 13

Monday, January 13, 2014
4:00 p.m., Carson Family Auditorium

Lei Stanley Qi, Ph.D.
UCSF Systems Biology Fellow
Department of Cellular and Molecular Pharmacology and
UCSF Center for Systems and Synthetic Biology
University of California, San Francisco

Repurposing CRISPR/Cas as a versatile platform for genome engineering and imaging

Recommended Readings:

Empirical Articles

Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., … Zhang, F. (2013). Multiplex genome engineering using CRISPR/Cas systems. Science, 339(6121), 819–823. doi:10.1126/science.1231143

Gilbert, L. a, Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., … Qi, L. S. (2013). CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell, 154(2), 442–451. doi:10.1016/j.cell.2013.06.044

Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096), 816–21. doi:10.1126/science.1225829

Qi, L., Haurwitz, R. E., Shao, W., Doudna, J. A., & Arkin, A. P. (2012). RNA processing enables predictable programming of gene expression. Nature Biotechnology, 30(10), 1002–6. doi:10.1038/nbt.2355

Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013). Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell, 152(5), 1173–83. doi:10.1016/j.cell.2013.02.022

Review Articles

Gaj, T., Gersbach, C. A., & Barbas, C. F. (2013). ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends in Biotechnology, 31(7), 397–405. doi:10.1016/j.tibtech.2013.04.004

Makarova, K. S., Haft, D. H., Barrangou, R., Brouns, S. J. J., Charpentier, E., Horvath, P., … Koonin, E. V. (2011). Evolution and classification of the CRISPR-Cas systems. Nature Reviews Microbiology, 9(6), 467–477. doi:10.1038/nrmicro2577

Wiedenheft, B., Sternberg, S. H., & Doudna, J. A. (2012). RNA-guided genetic silencing systems in bacteria and archaea. Nature, 482(7385), 331–338. doi:10.1038/nature10886

Recommended Readings: Diana Libuda, Ph.D. Wednesday, January 22

Wednesday, January 22, 2014
4:00 p.m., Carson Family Auditorium

Diana Libuda, Ph.D.
Postdoctoral Fellow
Department of Developmental Biology
Stanford University School of Medicine

Making the right decision: repairing DNA breaks during meiosis

Recommended Readings:

Empirical Articles

Libuda, D. E., Uzawa, S., Meyer, B. J., & Villeneuve, A. M. (2013). Meiotic chromosome structures constrain and respond to designation of crossover sites. Nature, 502(7473), 703–706. doi:10.1038/nature12577

Martinez-Perez, E., & Villeneuve, A. M. (2005). HTP-1-dependent constraints coordinate homolog pairing and synapsis and promote chiasma formation during C . elegans meiosisGenes & Development, 19(22), 2727–2743. doi:10.1101/gad.1338505.recombination

Rosu, S., Libuda, D. E., & Villeneuve, A. M. (2011). Robust crossover assurance and regulated interhomolog access maintain meiotic crossover number. Science, 334(6060), 1286–1289. doi:10.1126/science.1212424

Yokoo, R., Zawadzki, K. A., Nabeshima, K., Drake, M., Arur, S., & Villeneuve, A. M. (2012). COSA-1 reveals robust homeostasis and separable licensing and reinforcement steps governing meiotic crossovers. Cell, 149(1), 75–87. doi:10.1016/j.cell.2012.01.052

Review Papers

Martinez-Perez, E., & Colaiácovo, M. P. (2009). Distribution of meiotic recombination events: talking to your neighbors. Current Opinion in Genetics & Development, 19(2), 105–112. doi:10.1016/j.gde.2009.02.005

Page, S. L., & Hawley, R. S. (2003). Chromosome choreography: the meiotic ballet. Science, 301(5634), 785–789. doi:10.1126/science.1086605

Recommended Readings: Scott Lowe, Ph.D.

Friday Lecture Series

Cancer Initiation and Maintenance Genes

Scott Lowe, Ph.D., chair, Geoffrey Beene Cancer Research Center,

Memorial Sloan Kettering Cancer Center;

investigator, Howard Hughes Medical Institute

January 3, 2014

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

Caspary Auditorium

Recommended Readings

Chicas, A., Kapoor, A., Wang, X., Aksoy, O., Evertts, A. G., Zhang, M. Q., . . . Lowe, S. W. (2012). H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence. Proceedings of the National Academy of Sciences of the United States of America, 109(23), 8971-8976

Dow, L. E., & Lowe, S. W. (2012). Life in the fast lane: Mammalian disease models in the genomics era. Cell, 148(6), 1099-1109

Premsrirut, P. K., Dow, L. E., Kim, S. Y., Camiolo, M., Malone, C. D., Miething, C., . . . Lowe, S. W. (2011). A rapid and scalable system for studying gene function in mice using conditional RNA interference. Cell, 145(1), 145-158

Sawey, E., Chanrion, M., Cai, C., Wu, G., Zhang, J., Zender, L., . . . Powers, S. (2011). Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by oncogenomic screening. Cancer Cell, 19(3), 347-358

Xue, W., Kitzing, T., Roessler, S., Zuber, J., Krasnitz, A., Schultz, N., . . . Lowe, S. W. (2012). A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proceedings of the National Academy of Sciences of the United States of America, 109(21), 8212-8217

Zuber, J., Rappaport, A. R., Luo, W., Wang, E., Chen, C., Vaseva, A. V., . . . Lowe, S. W. (2011). An integrated approach to dissecting oncogene addiction implicates a myb-coordinated self-renewal program as essential for leukemia maintenance. Genes and Development, 25(15), 1628-1640


Recommended Readings: Dan R. Littman, M.D., Ph.D.

Friday Lecture Series

Shaping of the Systemic Immune Repertoire by the Intestinal Microbiota

Dan R. Littman, M.D., Ph.D., Helen L. and Martin S. Kimmel Professor of Molecular

Immunology; professor of pathology and microbiology, program in molecular pathogenesis,

Skirball Institute of Biomolecular Medicine, New York University Medical Center;

investigator, Howard Hughes Medical Institute

December 20, 2013

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

Caspary Auditorium

Recommended Readings

Diehl, G. E., Longman, R. S., Zhang, J. -., Breart, B., Galan, C., Cuesta, A., . . . Littman, D. R. (2013). Microbiota restricts trafficking of bacteria to mesenteric lymph nodes by CX 3 CR1 hi cells. Nature, 494(7435), 116-120

Honda, K., & Littman, D. R. (2012). The microbiome in infectious disease and inflammation. Annual Review of Immunology,  30 , pp. 759-795

Hooper, L. V., Littman, D. R., & Macpherson, A. J. (2012). Interactions between the microbiota and the immune system. Science, 336(6086), 1268-1273

Kinnebrew, M. A., Buffie, C. G., Diehl, G. E., Zenewicz, L. A., Leiner, I., Hohl, T. M., . . . Pamer, E. G. (2012). Interleukin 23 production by intestinal CD103 +CD11b + dendritic cells in response to bacterial flagellin enhances mucosal innate immune defense. Immunity, 36(2), 276-287

Littman, D. R., & Pamer, E. G. (2011). Role of the commensal microbiota in normal and pathogenic host immune responses. Cell Host and Microbe, 10(4), 311-323


Recommended Readings: Angeline Lyon, Ph.D. Monday, January 6

Monday, January 6, 2014
4:00 p.m., Carson Family Auditorium

Angeline Lyon, Ph.D.
American Heart Association Postdoctoral Fellow
Life Sciences Institute, University of Michigan

Molecular Mechanisms of Phospholipase Cβ Regulation

Recommended Readings:

Empirical Articles

Hicks, S. N., Jezyk, M. R., Gershburg, S., Seifert, J. P., Harden, T. K., & Sondek, J. (2008). General and versatile autoinhibition of PLC isozymes. Molecular Cell, 31(3), 383–394. doi:10.1016/j.molcel.2008.06.018

Lyon, A. M., Dutta, S., Boguth, C. A., Skiniotis, G., & Tesmer, J. J. G. (2013). Full-length Gα(q)-phospholipase C-β3 structure reveals interfaces of the C-terminal coiled-coil domain. Nature: Structural & Molecular Biology, 20(3), 355–362. doi:10.1038/nsmb.2497

Lyon, A. M., Tesmer, V. M., Dhamsania, V. D., Thal, D. M., Gutierrez, J., Chowdhury, S., … Tesmer, J. J. G. (2011). An autoinhibitory helix in the C-terminal region of phospholipase C-β mediates Gαq activation. Nature: Structural & Molecular Biology, 18(9), 999–1005. doi:10.1038/nsmb.2095

Tadano, M., Edamatsu, H., Minamisawa, S., Yokoyama, U., Ishikawa, Y., Suzuki, N., … Kataoka, T. (2005). Congenital semilunar valvulogenesis defect in mice deficient in phospholipase C epsilon. Molecular and Cellular Biology, 25(6), 2191–2199. doi:10.1128/MCB.25.6.2191-2199.2005

Wang, H., Oestreich, E. A., Maekawa, N., Bullard, T. A., Vikstrom, K. L., Dirksen, R. T., … Smrcka, A. V. (2005). Phospholipase C epsilon modulates beta-adrenergic receptor-dependent cardiac contraction and inhibits cardiac hypertrophy. Circulation Research, 97(12), 1305–13. doi:10.1161/

Review Papers

Gresset, A., Sondek, J., & Harden, T. K. (2012). The phospholipase C isozymes and their regulationSub-Cellular Biochemistry58, 61–94. doi:10.1007/978-94-007-3012-0_3

Suh, P.-G., Park, J.-I., Manzoli, L., Cocco, L., Peak, J. C., Katan, M., … Ryu, S. H. (2008). Multiple roles of phosphoinositide-specific phospholipase C isozymesBMB Reports41(6), 415–434.

Woodcock, E. a, Kistler, P. M., & Ju, Y.-K. (2009). Phosphoinositide signalling and cardiac arrhythmiasCardiovascular Research82(2), 286–295. doi:10.1093/cvr/cvn283

Breakthrough Prize in Life Science Foundation Announces Six Recipients for 2014

The Breakthrough Prizes recognize pioneering work in physics and genetics, cosmology, and neurology and mathematics. Each prize carries an award of $3 million.   The six winners for 2014 announced today are:

•    James Allison, MD Anderson Cancer Center, for the discovery of T cell checkpoint blockade as effective cancer therapy.

•    Mahlon DeLong, Emory University, for defining the interlocking circuits in the brain that malfunction in Parkinson’s disease. This scientific foundation underlies the circuit-based treatment of Parkinson’s disease by deep brain stimulation.

•    Michael Hall, University of Basel, for the discovery of Target of Rapamycin (TOR) and its role in cell growth control.

•    Robert Langer, David H. Koch Institute Professor at the Massachusetts Institute of Technology, for discoveries leading to the development of controlled drug-release systems and new biomaterials.

•    Richard Lifton, Yale University; Howard Hughes Medical Institute, for the discovery of genes and biochemical mechanisms that cause hypertension.

•    Alexander Varshavsky, California Institute of Technology, for discovering critical molecular determinants and biological functions of intracellular protein degradation.

Prize recipients are invited to serve on the selection committee to select recipients of future prizes. Last year, HHMI investigators Cornelia I. Bargmann at the Rockefeller University, Charles L. Sawyers at Memorial Sloan-Kettering Cancer Center and Bert Vogelstein at Johns Hopkins University School of Medicine were awarded the Breakthrough Prize in Life Sciences.

Founded in 2013, the Breakthrough Prize in Life Sciences Foundation is a not-for-profit corporation dedicated to advancing breakthrough research, celebrating scientists and generating excitement about the pursuit of science as a career. The Foundation was founded by Sergey Brin and Anne Wojcicki, Mark Zuckerberg and Priscilla Chan, Jack Ma and Cathy Zhang, and Yuri and Julia Milner, and is chaired by Arthur Levinson, who is also chairman of Genentech and Apple.


Recommended Readings: Harmit S. Malik, Ph.D.

Friday Lecture Series

Genetic Conflicts: Beyond the Usual Suspects

Harmit S. Malik, Ph.D., principal investigator, basic sciences division,

Fred Hutchinson Cancer Research Center;

early career scientist, Howard Hughes Medical Institute

December 13, 2013

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

Caspary Auditorium

Recommended Readings

Malik, H. S. (2009). Evolution of TRIM antiviral genes in primate genomes. Retrovirology, 6(SUPPL. 2)

Malik, H. S., & Bayes, J. J. (2006). Genetic conflicts during meiosis and the evolutionary origins of centromere complexity. Biochemical Society Transactions, 34(4), 569-573

Malik, H. S., & Henikoff, S. (2002). Conflict begets complexity: The evolution of centromeres. Current Opinion in Genetics and Development, 12(6), 711-718

Moran, J. V., & Malik, H. S. (2009). Diamonds and rust: How transposable elements influence mammalian genomes. conference on mobile elements in mammalian genomes. EMBO Reports, 10(12), 1306-1310

Oliver, P. L., Goodstadt, L., Bayes, J. J., Birtle, Z., Roach, K. C., Phadnis, N., . . . Ponting, C. P. (2009). Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genetics, 5(12)

Vermaak, D., & Malik, H. S. (2009). Multiple roles for heterochromatin protein 1 genes in drosophila. Annual Review of Genetic 43 , pp. 467-492


The Pearl Meister Greengard Prize: Praising Pioneers in Biomedical Research

Dr. Huda Zoghbi, 2013 PMG Prize Recipient (image courtesy of The Rockefeller University)
There is nothing particularly remarkable about a woman doing science. Any person — man or woman — who shows an intellectual curiosity combined with a strong work ethic, good decision making, and a little bit of luck can be successful in science. What is remarkable, however, is the severe underrepresentation of women in science, technology, engineering, and math (STEM) fields. And for the few women who pursue these career endeavors, their achievements, however great, often go unsung.

To help counteract the inequitable distribution of scientific recognition specifically in biomedical research, Dr. Paul Greengard used the entirety of his 2000 Nobel Prize winnings to establish the Pearl Meister Greengard (PMG) Prize, which spotlights the extraordinary achievements of women in science and hopefully inspires future generations of women scientists in their pursuit of scientific careers. Named after his mother, Pearl Meister, who died while giving birth to him, Dr. Greengard also uses this prize for a very personal reason: to help make the idea of his mother seem less abstract.

Now in its 10th iteration, the Pearl Meister Greengard Prize has been awarded to an outstanding array of pioneering scientists, honoring their contributions to the advancement of biomedical research.

Ceremony is this Thursday, Thursday, December 5, 2013 at 6:30 p.m. (Caspary Auditorium)