Recommended Readings: Poornima Parameswaran Ph.D. February 10

Monday, February 10, 2014
4:00 p.m., Carson Family Auditorium

Poornima Parameswaran, Ph.D.

Postdoctoral Research Fellow
School of Public Health
University of California, Berkeley

Virome & Immunome Diversity in Dengue & other Infectious Diseases

Recommended Readings:

Empirical Papers

Parameswaran, P., Charlebois, P., Tellez, Y., Nunez, A., Ryan, E. M., Malboeuf, C. M., … Henn, M. R. (2012). Genome-wide patterns of intrahuman dengue virus diversity reveal associations with viral phylogenetic clade and interhost diversity. Journal of Virology, 86(16), 8546–8558. doi:10.1128/JVI.00736-12

Parameswaran, P., Liu, Y., Roskin, K. M., Jackson, K. K. L., Dixit, V. P., Lee, J.-Y., … Fire, A. Z. (2013). Convergent antibody signatures in human dengue. Cell Host & Microbe, 13(6), 691–700. doi:10.1016/j.chom.2013.05.008

Parameswaran, P., Sklan, E., Wilkins, C., Burgon, T., Samuel, M. a, Lu, R., … Fire, A. Z. (2010). Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems. PLoS pathogens, 6(2), e1000764. doi:10.1371/journal.ppat.1000764

Review Articles

Fontana, J. M., Alexander, E., & Salvatore, M. (2012). Translational research in infectious disease: current paradigms and challenges ahead. Translational Research, 159(6), 430–453. doi:10.1016/j.trsl.2011.12.009

Wylie, K. M., Weinstock, G. M., & Storch, G. a. (2012). Emerging view of the human virome. Translational Research, 160(4), 283–290. doi:10.1016/j.trsl.2012.03.006

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: Rob Knight, Ph.D. Wednesday, Oct. 30, 2013

Wednesday, October 30, 2013
4:00 p.m., Carson Family Auditorium

Rob Knight, Ph.D.
HHMI Early Career Scientist and Professor
Department of Chemistry & Biochemistry, Department of Computer Science, and BioFrontiers Institute
University of Colorado at Boulder

Gut Microbes and their Role in Malnutrition and Obesity

Recommended Readings:

Review Papers

Clemente, J. C., Ursell, L. K., Parfrey, L. W., & Knight, R. (2012). The impact of the gut microbiota on human health: an integrative view. Cell, 148(6), 1258–1270. doi:10.1016/j.cell.2012.01.035

Gevers, D., Knight, R., Petrosino, J. F., Huang, K., McGuire, A. L., Birren, B. W., … Huttenhower, C. (2012). The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biology, 10(8), e1001377. doi:10.1371/journal.pbio.1001377

Hamady, M., & Knight, R. (2009). Microbial community profiling for human microbiome projects : Tools , techniques , and challenges, Genome Research, 19(7), 1141–1152. doi:10.1101/gr.085464.108.19

Ley, R. E., Lozupone, C. a, Hamady, M., Knight, R., & Gordon, J. I. (2008). Worlds within worlds: evolution of the vertebrate gut microbiotaNature Reviews Microbiology6(10), 776–788. doi:10.1038/nrmicro1978

Empirical Articles

Costello, E., Lauber, C., & Hamady, M. (2009). Bacterial community variation in human body habitats across space and time. Science, 326, 8–11.

The Human Microbiome Project Consortium. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207–14. doi:10.1038/nature11234

Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A, Knight, R. D., & Gordon, J. I. (2005). Obesity alters gut microbial ecology. Proceedings of the National Academy of Sciences of the United States of America, 102(31), 11070–5. doi:10.1073/pnas.0504978102

Lozupone, C. A., Stombaugh, J., Gonzalez, A., Ackermann, G., Jansson, J. K., Gordon, J. I., … Knight, R. (2013). Meta-analyses of studies of the human microbiota, Genome Research, 23,1704–1714. doi:10.1101/gr.151803.112

Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., … Gordon, J. I. (2009). A core gut microbiome in obese and lean twins. Nature, 457(7228), 480–484. doi:10.1038/nature07540

Turnbaugh, P. J., Ley, R. E., Mahowald, M. a, Magrini, V., Mardis, E. R., & Gordon, J. I. (2006). An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 444(7122), 1027–31. doi:10.1038/nature05414

Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., … Gordon, J. I. (2012). Human gut microbiome viewed across age and geography. Nature, 486(7402), 222–7. doi:10.1038/nature11053

Recommended Readings: Gaby Maimon, Ph.D. Feb 17 2010

Monday Lecture Series

Active Vision and Higher Brain Function in Drosophila melanogaster

Gaby Maimon, Ph.D.,

Post Doctoral Fellow, Division of Biology

California Institute of Technology

February 17, 2010

4:00p.m.-5:00 p.m.

Welch Hall, Level Two

Recommended Articles:

Maimon G, Straw AD, Dickinson MH.  2008.  A simple vision-based algorithm for decision making in flying Drosophila. CURRENT BIOLOGY 18(6): 464-470

Duistermars BJ, Chow DM, Frye MA.  2009.  Flies Require Bilateral Sensory Input to Track Odor Gradients in Flight. CURRENT BIOLOGY 19(15):1301-1307

Nordstrom K, O’Carroll DC.   2009.  Feature detection and the hypercomplex property in insects. TRENDS IN NEUROSCIENCES 32(7): 383-391

Yin Y, Chen NN, Zhang SX, et al.   2009.  Choice strategies in Drosophila are based on competition between olfactory memories. EUROPEAN JOURNAL OF NEUROSCIENCE 30(2): 279-288

Olsen SR, Wilson RI.   2008.  Cracking neural circuits in a tiny brain: new approaches for understanding the neural circuitry of Drosophila. TRENDS IN NEUROSCIENCES 31(10):512-520

Chow DM, Frye MA.  2008.  Context-dependent olfactory enhancement of optomotor flight control in Drosophila. JOURNAL OF EXPERIMENTAL BIOLOGY 211(15): 2478-2485

Recommended Readings: Adam Martin, PhD Jan 13, 2010

Wednesday Lecture Series

Taking Steps to Develop: the Dynamic Forces that Drive Epithelial Invagination

Adam Martin, Ph.D.,

Post Doctoral Fellow, Department of  Molecular Biology

Princeton University

January 13, 2010

4:00p.m.-5:00 p.m.

Welch Hall, Level Two


Recommended articles:

Chesarone MA, DuPage AG, Goode BL.  2010.  Unleashing formins to remodel the actin and microtubule cytoskeletons .   NATURE REVIEWS MOLECULAR CELL BIOLOGY   11(1): 62-74  

Delon I, Brown NH.  2009.  The integrin adhesion complex changes its composition and function during morphogenesis of an epithelium.   JOURNAL OF CELL SCIENCE   122(23):4363-4374  

Fernandez-Gonzalez R, Simoes SD, Roper JC, et al.  2009.   Myosin II Dynamics Are Regulated by Tension in Intercalating Cells.  DEVELOPMENTAL CELL   17(5):736-743

Paluch E, Heisenberg CP.  2009.  Biology and Physics of Cell Shape Changes in Development.  CURRENT BIOLOGY  19(17 Sp. Iss. SI): R790-R799   

T Sawyer JK, Harris NJ, Slep KC, et al.  2009. The Drosophila afadin homologue Canoe regulates linkage of the actin cytoskeleton to adherens junctions during apical constrictionJOURNAL OF CELL BIOLOGY    186(1):57-73

Rauzi M, Lecuit T.  2009.  Closing in on Mechanisms of Tissue Morphogenesis    CELL  137(7):1183-1185   

Blanchard GB, Kabla AJ, Schultz NL, et al.  2009.  Tissue tectonics: morphogenetic strain rates, cell shape change and intercalation.  NATURE METHODS    6(6):458-U86

Mammoto A, Connor KM, Mammoto T, et al.  2009.  A mechanosensitive transcriptional mechanism that controls angiogenesis.   NATURE   457(7233):1103-U57

Mammoto A, Connor KM, Mammoto T, et al.   2008.  Mechanical control of tissue morphogenesis.  CIRCULATION RESEARCH    103(3):234-243   

Quintin S, Gally C, Labouesse M.  2008.  Epithelial morphogenesis in embryos: asymmetries, motors and brakes.  TRENDS IN GENETICS   24(5):221-230

Recommended Readings: Eduardo Groisman, Ph.D., April 22, 2009

Special Seminar Series

“Differential Control of Bacterial Gene Expression”

Eduardo Groisman, Ph.D.

Professor, Department of Molecular Microbiology, Washington University School of Medicine/HHMI

Wednesday, April 22, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Articles:


Christian Perez, J., T. Latifi, and E. A. Groisman. 2008. Overcoming H-NS-mediated transcriptional silencing of horizontally acquired genes by the PhoP and SlyA proteins in Salmonella enterica. Journal of Biological Chemistry. 283(16):10773-10783.

Coppins, R. L., K. B. Hall, and E. A. Groisman. 2007. The intricate world of riboswitches. Current opinion in microbiology. 10(2):176-181.

Delgado, M. A., C. Mouslim, and E. A. Groisman. 2006. The PmrA/PmrB and RcsC/YojN/RcsB systems control expression of the Salmonella O-antigen chain length determinant. Molecular microbiology. 60(1):39-50.

Kato, A., A. Y. Mitrophanov, and E. A. Groisman. 2007. A connector of two-component regulatory systems promotes signal amplification and persistence of expression. Proceedings of the National Academy of Sciences of the United States of America. 104(29):12063-12068.

Mitrophanov, A. Y., and E. A. Groisman. 2008. Signal integration in bacterial two-component regulatory systems. Genes and Development. 22(19):2601-2611.

Mitrophanov, A. Y., M. W. Jewett, T. J. Hadley, and E. A. Groisman. 2008. Evolution and dynamics of regulatory architectures controlling polymyxin B resistance in enteric bacteria. PLoS Genetics. 4(10) art. no. e1000233.

Perez, J. C., and E. A. Groisman. 2007. Acid pH activation of the PmrA/PmrB two-component regulatory system of Salmonella enterica. Molecular microbiology. 63(1):283-293.

Tu, X., T. Latifi, A. Bougdour, S. Gottesman, and E. A. Groisman. 2006. The PhoP/PhoQ two-component system stabilizes the alternative sigma factor RpoS in Salmonella enterica. Proceedings of the National Academy of Sciences of the United States of America. 103(36):13503-13508..

Winfield, M. D., and E. A. Groisman. 2004. Phenotypic differences between Salmonella and Escherichia coli resulting from the disparate regulation of homologous genes. Proceedings of the National Academy of Sciences of the United States of America. 101(49):17162-17167.

Recommended Readings: Andre Hoelz, Ph.D.; May 13, 2009

Special Seminar Series

            “Building the Gatekeeper of the Innermost Sanctuary of the Cell Piece by Piece”

Andre Hoelz, Ph.D.

Research Associate, Laboratory of Cell Biology

The Rockefeller University

Wednesday, May 13, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Articles:

Debler, E. W., Y. Ma, H. -S Seo, K. -C Hsia, T. R. Noriega, G. Blobel, and A. Hoelz. 2008. A fence-like coat for the nuclear pore membrane. Molecular cell. 32(6):815-826.

Hoelz, A., and G. Blobel. 2004. Popping out of the nucleus. Nature. 432(7019):815-816.

Hsia, K. -C, P. Stavropoulos, G. Blobel, and A. Hoelz. 2007. Architecture of a coat for the nuclear pore membrane. Cell. 131(7):1313-1326.

Melcak, I., A. Hoelz, and G. Blobel. 2007. Structure of Nup58/45 suggests flexible nuclear pore diameter by intermolecular sliding. Science. 315(5819):1729-1732.

Napetschnig, J., G. Blobel, and A. Hoelz. 2007. Crystal structure of the N-terminal domain of the human protooncogene Nup214/CAN. Proceedings of the National Academy of Sciences of the United States of America. 104(6):1783-1788.

Stavropoulos, P., V. Nagy, G. Blobel, and A. Hoelz. 2008. Molecular basis for the autoregulation of the protein acetyl transferase Rtt109. Proceedings of the National Academy of Sciences of the United States of America. 105(34):12236-12241.

Recommended Readings: Mitchell Guttman; March 25, 2009

Special Seminar Series

Large Intergenic ncRNAs in the Mammalian Genome:

From Discovery to Mechanism

Mitchell Guttman

Graduate fellow, Department of Biology

Broad Institute of MIT and Harvard/Massachusetts Institute of Technology

Wednesday, March 25, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Articles:

Guttman, M., I. Amit, M. Garber, C. French, M. F. Lin, D. Feldser, M. Huarte, et al. 2009. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, in press.

Guttman, M., C. Mies, K. Dudycz-Sulicz, S. J. Diskin, D. A. Baldwin, C. J. Stoeckert Jr., and G. R. Grant. 2007. Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays. PLoS Genetics. 3(8)e143.

Clamp, M., B. Fry, M. Kamal, X. Xie, J. Cuff, M. F. Lin, M. Kellis, K. Lindblad-Toh, and E. S. Lander. 2007. Distinguishing protein-coding and noncoding genes in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 104(49):19428-19433.

Willingham, A. T., A. P. Orth, S. Batalov, E. C. Peters, B. G. Wen, P. Aza-Blanc, J. B. Hogenesch, and P. G. Schultz. 2005. Molecular biology: A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science. 309(5740):1570-1573.

Rinn, J. L., M. Kertesz, J. K. Wang, S. L. Squazzo, X. Xu, S. A. Brugmann, L. H. Goodnough, et al. 2007. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell. 129(7):1311-1323.

Ponjavic, J., C. P. Ponting, and G. Lunter. 2007. Functionality or transcriptional noise? evidence for selection within long noncoding RNAs. Genome Research. 17(5):556-565.

Recommended Readings: Junying Yuan, Ph.D.


Special Seminar Series

A Quest to Understand the Mechanisms of Neurodegeneration

Junying Yuan, Ph.D.

Professor, Department of Cell Biology

Harvard Medical School

Wednesday, March 18, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Articles:

Panaretakis T, Kepp O, Brockmeier U, Tesniere A, Bjorklund A-, Chapman DC, Durchschlag M, Joza N, Pierron G, van Endert P, Yuan J, Zitvogel L, Madeo F, Williams DB, Kroemer G. Mechanisms of pre-apoptotic calreticulin exposure in immunogenic cell death. EMBO Journal. 2009.

Yi CH, Yuan J. The jekyll and hyde functions of caspases. Developmental Cell. 2009;16(1):21-34.

Yuan J. Neuroprotective strategies targeting apoptotic and necrotic cell death for stroke. Apoptosis. 2009:1-9.
Article in press.

Hitomi J, Christofferson DE, Ng A, Yao J, Degterev A, Xavier RJ, Yuan J. Identification of a molecular signaling network that regulates a cellular necrotic cell death pathway. Cell. 2008;135(7):1311-23.

Zheng W, Degterev A, Hsu E, Yuan J, Yuan C. Structure-activity relationship study of a novel necroptosis inhibitor, necrostatin-7. Bioorganic and Medicinal Chemistry Letters. 2008;18(18):4932-5.

You Z, Savitz SI, Yang J, Degterev A, Yuan J, Cuny GD, Moskowitz MA, Whalen MJ. Necrostatin-1 reduces histopathology and improves functional outcome after controlled cortical impact in mice. Journal of Cerebral Blood Flow and Metabolism 2008;28(9):1564-73.
Contact the Markus Library for a reprint of this article.

Degterev A, Hitomi J, Germscheid M, Ch’en IL, Korkina O, Teng X, Abbott D, Cuny GD, Yuan C, Wagner G, Hedrick SM, Gerber SA, Lugovskoy A, Yuan J. Identification of RIP1 kinase as a specific cellular target of necrostatins. Nature Chemical Biology. 2008;4(5):313-21.

Cuny GD, Degterev A, Yuan J. Necroptosis – A novel cell death mechanism. Drugs of the Future 2008;33(3):225-33.
Contact the Markus Library for a reprint of this article.

Degterev A, Boyce M, Yuan J. A decade of caspases. Oncogene. 2003;22(53 REV. ISS. 7):8543-67.

Recommended Readings: Sandeep R. Datta MD PhD

Monday Lecture Series

From Odors to Behavior: Visualizing Sensory Circuits in Flies and Mice

Sandeep Robert Datta  MD, PhD

Post-doctoral Fellow, Department of Neurobiology

Columbia University, New York

Monday, February 2, 2009

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.)

Second Floor, Welch Hall

Recommended Review Article:


Sato T,  Hirono J,  Hamana H, et al.  2008.  Architecture of odor information processing in the olfactory system.    Anatomical science international    83(4):195-206   



Recommended Readings:

Dickson BJ.  2008.  Wired for Sex: the neurobiology of Drosophila mating decisions .  Science  322(5903): 904-909


Katz DB, Matsunami H, Rinberg D, et al.  2008. Receptors, circuits, and behaviors: new directions in chemical senses.  Journal of neuroscience.   28(46): 11802-11805


Sambandan D, Carbone MA, Anholt RRH, et al.  2008. Phenotypic plasticity and genotype by environment interaction for olfactory behavior in Drosophila melanogaster.
Genetics.   179(2):1079-1088   


Datta SR, Vasconcelos ML  Ruta V, et al.   2008.  The Drosophila pheromone cVA activates a sexually dimorphic neural circuit.   Nature (London). 452(7186):473-477


Schlief ML, Wilson RI.  2007.  Olfactory processing and behavior downstream from highly selective receptor neurons.  Nature Neuroscience.    10(5):623-630   


 Sambandan D, Yamamoto A, Fanara JJ, et al.  2006.  Dynamic genetic interactions determine odor-guided behavior in Drosophila melanogaster.  Genetics.  174(3):1349-1363