Recommended Readings: Nicole King Ph.D. October 7 2016

Friday Lecture Series

Friday October 7, 2016   3:45 p.m.

The Fairfield Osborn Memorial Lecture

Caspary Auditorium

Nicole King

Professor, and HHMI Investigator

Dept.of Molecular and Cell Biology, Division of Genetics, Genomics and Development

University of California Berkeley

Bacteria as Master Regulators and Aphrodisiacs

Recommended Readings:

Anderson, Douglas P.; Whitney, Dustin S.; Hanson-Smith, Victor; et al.  Evolution of an ancient protein function involved in organized multicellularity in animals. ELIFE                   5: e10147    JAN 7 2016

Alegado, Rosanna A.; King, Nicole  Bacterial Influences on Animal OriginsCOLD SPRING HARBOR PERSPECTIVES IN BIOLOGY    6(11): a016162  NOV 2014

King, Nicole.  Evolutionary Transitions to Multicellular Life Principles and Mechanisms Forrward.  EVOLUTIONARY TRANSITIONS TO MULTICELLULAR LIFE: PRINCIPLES AND MECHANISMS   Book Series:Advances in Marine Genomics   Volume: 2   Pages: V-VI    2015

King, Nicole; Mueller, Susann.  Environmental microbiology: Revisiting the physiology of microorganisms on the single cell scale. CURRENT OPINION IN MICROBIOLOGY     Volume: 25   Pages: V-VI   Published: JUN 2015

Recommended Readings: Michael Levine Ph.D. Sept 30, 2016

Friday Lecture Series

Norton Zinder Lecture

Michael Levine, Ph.D.

Director, Lewis-Sigler Institute for Integrative Genomics, Princeton Univ.

Anthony B. Evnin Professor, Dept Molecular Biology, Princeton Univ.

Visualization and evolution of transcriptional enhancers

Recommended Readings:

Bothma, J.P., Garcia, H.G., Ng, S., Perry, M.W., Gregor, T., and Levine, M. (2015). Enhancer additivity and nonadditivity are determined by enhancer strength in the Drosophila embryo. eLife 4, 07956.

Farley, E.K., Olson, K.M., Zhang, W., Brandt, A.J., Rokhsar, D.S., and Levine, M. (2015). Suboptimization of developmental enhancers. Science 350, 325-328.

Fukaya, T., Lim, B., and Levine, M. 2016. Enhancer control of transcriptional bursting. Cell 166, 358-368.

Bothma, J., Garcia, H., Gavin, S., Esposito, E., Gregor, T., and Levine, M. (2014). Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos. PNAS 111, 10598-10603.

Evans, Nicole C.; Swanson, Christina I.; Barolo, Scott.  Sparkling Insights into Enhancer Structure, Function, and Evolution.  TRANSCRIPTIONAL SWITCHES DURING DEVELOPMENT   Book Series: Current Topics in Developmental Biology .  98: 97-120   2012

Gordon, Kacy L.; Ruvinsky, Ilya.  Tempo and Mode in Evolution of Transcriptional Regulation.  PLOS GENETICS.   8(1): e1002432    2012

Recommended Readings: Lydia Finley, Ph.D., March 30

Special Lecture
Wednesday, March 30
4:00 p.m., Carson Family Auditorium (CRC)

Lydia Finley, Ph.D.
Jack Sorrell Fellow,
Damon Runyon Cancer Research Foundation,
Cancer Biology and Genetics Program,
Memorial Sloan Kettering Cancer Center

Metabolic Regulation of Cell Fate Decisions

Recommended Readings

Carey, B. W., Finley, L. W., Cross, J. R., Allis, C. D., & Thompson, C. B. (2015). Intracellular [agr]-ketoglutarate maintains the pluripotency of embryonic stem cells. Nature, 518(7539), 413-416.  doi: 10.1038/nature13981.

Intlekofer, A. M., Dematteo, R. G., Venneti, S., Finley, L. W., Lu, C., Judkins, A. R., … & Thompson, C. B. (2015). Hypoxia induces production of L-2-hydroxyglutarate, Cell Metabolism, 22(2), 304-311. doi: 10.1016/j.cmet.2015.06.023.

Jeong, S. M., Xiao, C., Finley, L. W., Lahusen, T., Souza, A. L., Pierce, K., … & Xu, X. (2013). SIRT4 has tumor-suppressive activity and regulates the cellular metabolic response to DNA damage by inhibiting mitochondrial glutamine metabolism. Cancer Cell, 23(4), 450-463. doi: 10.1016/j.ccr.2013.02.024.

Laurent, G., de Boer, V. C., Finley, L. W., Sweeney, M., Lu, H., Schug, T. T., … & Haigis, M. C. (2013). SIRT4 represses peroxisome proliferator-activated receptor α activity to suppress hepatic fat oxidation. Molecular and Cellular Biology, 33(22), 4552-4561. doi: 10.1128/MCB.00087-13.

Recommended Readings: Ying Lu, Ph.D., February 29

Special Lecture Series
Monday, February 29
4:00 p.m., Carson Family Auditorium (CRC)

Ying Lu, Ph.D.,
Postdoctoral Fellow,
Department of Systems Biology,
Harvard Medical School

Specificity, Efficiency and Processivity in the Eukaryotic Protein Degradation System

Recommended Readings

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

Recommended Readings: David Breslow, Ph.D., February 17

Special Lecture Series
Wednesday, March 17, 2016
4:00 p.m., Carson Family Auditorium (CRC)

David Breslow, Ph.D.
Postdoctoral Scholar,
Department of Molecular and Cellular Physiology,
Stanford School of Medicine

Unraveling the Primary Cilium: Insights from New Biochemical and Functional Genomic Tools

Recommended Reading

Breslow, D. K., & Nachury, M. V. (2015). Analysis of soluble protein entry into primary cilia using semipermeabilized cells. Methods in Cell Biology, 127, 203-221. doi: 10.1016/bs.mcb.2014.12.006.

Breslow, D. K., Koslover, E. F., Seydel, F., Spakowitz, A. J., & Nachury, M. V. (2013). An in vitro assay for entry into cilia reveals unique properties of the soluble diffusion barrier. The Journal of Cell Biology, 203(1), 129-147. doi: 10.1083/jcb.201212024.

Recommended Readings: Talia Lerner, Ph.D., March 10

Special Lecture Series
Thursday, March 10, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Talia Lerner, Ph.D.
Postdoctoral Fellow,
Department of Bioengineering,
Stanford University

Distinct Information Encoding in Circuit-Defined Nigrostriatal Dopamine Neuron Subpopulations

Recommended Reading

Adhikari, A., Lerner, T. N., Finkelstein, J., Pak, S., Jennings, J. H., Davidson, T. J., … & Kim, S. Y. (2015). Basomedial amygdala mediates top-down control of anxiety and fear. Nature,  527(7577), 179-185. doi: 10.1038/nature15698

Lerner, T. N., Shilyansky, C., Davidson, T. J., Evans, K. E., Beier, K. T., Zalocusky, K. A., … & Deisseroth, K. (2015). Intact-brain analyses reveal distinct information carried by SNc dopamine subcircuits. Cell, 162(3), 635-647. doi: 10.1016/j.cell.2015.07.014.

Recommended Readings: Elena Gallo MacFarlane, Ph.D., February 8

Special Seminar
Wednesday, February 8, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Elena Gallo MacFarlane, Ph.D.
Postdoctoral and Research Fellow,
Institute of Genetic Medicine,
Johns Hopkins University School of Medicine

The Vessel Wall as a Paracrine Engine in TGF-Beta-Driven Vasculopathies

Recommended Reading:

Chetaille, P., Preuss, C., Burkhard, S., Côté, J. M., Houde, C., Castilloux, J., … & Thibeault, M. (2014). Mutations in SGOL1 cause a novel cohesinopathy affecting heart and gut rhythm. Nature Genetics, 46(11), 1245-1249. doi: 10.1038/ng.3113.

Gallo, E. M., Loch, D. C., Habashi, J. P., Calderon, J. F., Chen, Y., Bedja, D., … & Judge, D. P. (2014). Angiotensin II–dependent TGF-β signaling contributes to Loeys-Dietz syndrome vascular pathogenesis. The Journal of Clinical Investigation, 124(1), 448-460. doi: 10.1172/JCI69666.

Gerber, E. E., Gallo, E. M., Fontana, S. C., Davis, E. C., Wigley, F. M., Huso, D. L., & Dietz, H. C. (2013). Integrin-modulating therapy prevents fibrosis and autoimmunity in mouse models of scleroderma. Nature, 503(7474), 126-130. doi: 10.1038/nature12614.
Chicago

Lindsay, M. E., Schepers, D., Bolar, N. A., Doyle, J. J., Gallo, E., Fert-Bober, J., … & Bjeda, D. (2012). Loss-of-function mutations in TGFB2 cause a syndromic presentation of thoracic aortic aneurysm. Nature Genetics, 44(8), 922-927. doi: 10.1038/ng.2349

Recommended Readings: Brian Liau, Ph.D., February 3

Special Seminar
Wednesday, February 3, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Brian Liau, Ph.D.
Jane Coffins Child Memorial Fund Postdoctoral Fellow,
Department of Pathology,
Massachusetts General Hospital,
Harvard Medical School

Chemical Epigenetics: Discovering Chromatin Mediated Mechanisms in Cancer Using Small Molecules

Recommended Reading

Flavahan, W. A., Drier, Y., Liau, B. B., Gillespie, S. M., Venteicher, A. S., Stemmer-Rachamimov, A. O., … & Bernstein, B. E. (2015). Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature. doi: 10.1038/nature16490

Pelish, H. E., Liau, B. B., Nitulescu, I. I., Tangpeerachaikul, A., Poss, Z. C., Da Silva, D. H., … & Du, K. (2015). Mediator kinase inhibition further activates super-enhancer-associated genes in AML. Nature, 526(7572), 273-276. doi: 10.1038/nature14904

van Galen, P., Viny, A. D., Ram, O., Ryan, R. J., Cotton, M. J., Donohue, L., … & Carroll, K. M. (2015). A Multiplexed system for quantitative comparisons of chromatin landscapes. Molecular Cell. doi: 10.1016/j.molcel.2015.11.003.

Recommended Readings: David Baker, Ph.D., April 29

Special Lecture Series
Wednesday, April 29, 2015
3:45 p.m., Carson Family Auditorium (CRC)

David Baker, Ph.D.,
Professor of Biochemistry,
University of Washington
Investigator, Howard Hughes Medical Institute

Post-Evolutionary Biology: Design of Novel Protein Structures, Functions and Assemblies

Recommended Readings

Empirical Articles

Bradley, P., Misura, K. M., & Baker, D. (2005). Toward high-resolution de novo structure prediction for small proteins. Science, 309(5742), 1868-1871.

Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., … & Popović, Z. (2010). Predicting protein structures with a multiplayer online game. Nature, 466(7307), 756-760. doi:10.1038/nature09304

Eiben, C. B., Siegel, J. B., Bale, J. B., Cooper, S., Khatib, F., Shen, B. W., … & Baker, D. (2012). Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature Biotechnology, 30(2), 190-192. doi:10.1038/nbt.2109

Jiang, L., Althoff, E. A., Clemente, F. R., Doyle, L., Röthlisberger, D., Zanghellini, A., … & Baker, D. (2008). De novo computational design of retro-aldol enzymes. Science, 319(5868), 1387-1391. doi:10.1126/science.1152692

Review Papers

Adams, P. D., Baker, D., Brunger, A. T., Das, R., DiMaio, F., Read, R. J., … & Terwilliger, T. C. (2013). Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annual Review of Biophysics, 42, 265-287.doi: 10.1146/annurev-biophys-083012-130253

Das, R., & Baker, D. (2008). Macromolecular modeling with Rosetta. Annual Review of Biophysics, 77, 363-382. doi:10.1146/annurev.biochem.77.062906.171838

Recommended Readings: Liangcai Gu, Ph.D. January 7

Special Lecture
Wednesday, January 7, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Liangcai Gu, Ph.D.
Research Fellow,
Department of Genetics,
Harvard Medical School

In Situ Sequencing of Molecular Interactomes

Recommended Readings

Empirical Articles

Gu, L., Li, C., Aach, J., Hill, D. E., Vidal, M., & Church, G. M. (2014). Multiplex single-molecule interaction profiling of DNA-barcoded proteins. Nature, 515(7528), 554–557. doi:10.1038/nature13761

Gu, L., Wang, B., Kulkarni, A., Geders, T. W., Grindberg, R. V, Gerwick, L., … Sherman, D. H. (2009). Metamorphic enzyme assembly in polyketide diversification. Nature, 459(7247), 731–735. doi:10.1038/nature07870

Li, J., Gu, L., Aach, J., & Church, G. M. (2014). Improved cell-free RNA and protein synthesis system. PLOS ONE, 9(9), e106232. doi:10.1371/journal.pone.0106232

Review Papers

Jones, A. C., Gu, L., Sorrels, C. M., Sherman, D. H., & Gerwick, W. H. (2009). New tricks from ancient algae: natural products biosynthesis in marine cyanobacteria. Current Opinion in Chemical Biology, 13(2), 216–23. doi:10.1016/j.cbpa.2009.02.019