Recommended Readings: David A. Relman, M.D., February 19

Friday Lecture Series
The Detlev W. Bronk Alumni Lecture, Ph.D. Recruitment Lecture
Friday, February 26
3:45 p.m., Caspary Auditorium

Vanessa Ruta, Ph.D.
Gabrielle H. Reem and Herbert J. Kayden Assistant Professor,
Laboratory of Neurophysiology and Behavior,
The Rockefeller University

Neural Circuits for Adaptive Behaviors

Recommended Readings

Caron, S. J., Ruta, V., Abbott, L. F., & Axel, R. (2013). Random convergence of olfactory inputs in the Drosophila mushroom body. Nature, 497(7447), 113-117. doi: 10.1038/nature12063.

Clowney, E. J., Iguchi, S., Bussell, J. J., Scheer, E., & Ruta, V. (2015). Multimodal chemosensory circuits controlling male courtship in Drosophila. Neuron, 87(5), 1036-1049. doi: 10.1016/j.neuron.2015.07.025.

Cohn, R., Morantte, I., & Ruta, V. (2015). Coordinated and compartmentalized neuromodulation shapes sensory processing in Drosophila. Cell, 163(7), 1742-1755. doi: 10.1016/j.cell.2015.11.019.

Recommended Readings: David A. Relman, M.D., February 19

Friday Lecture Series
Friday, February 19
3:45 p.m., Caspary Auditorium

David A. Relman, M.D.
Thomas C. and Joan M. Merigan Professor,
Department of Medicine,
Department of Microbiology and Immunology,
Stanford University

The Human Microbiome Across Space and Time

Recommended Readings

Empirical Article

DiGiulio, D. B., Callahan, B. J., McMurdie, P. J., Costello, E. K., Lyell, D. J., Robaczewska, A., … & Stevenson, D. K. (2015). Temporal and spatial variation of the human microbiota during pregnancy. Proceedings of the National Academy of Sciences, 112(35), 11060-11065. doi: 10.1073/pnas.1502875112.

Hoy, Y. E., Bik, E. M., Lawley, T. D., Holmes, S. P., Monack, D. M., Theriot, J. A., & Relman, D. A. (2015). Variation in taxonomic composition of the fecal microbiota in an inbred mouse strain across individuals and time. PLOS ONE, 10(11), e0142825. doi: 10.1371/journal.pone.0142825.

Lin, A., Bik, E. M., Costello, E. K., Dethlefsen, L., Haque, R., Relman, D. A., & Singh, U. (2013). Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLOS ONE, 8(1), e53838. doi: 10.1371/journal.pone.0053838.

Review Paper

Costello, E. K., Stagaman, K., Dethlefsen, L., Bohannan, B. J., & Relman, D. A. (2012). The application of ecological theory toward an understanding of the human microbiome. Science, 336(6086), 1255-1262. doi: 10.1126/science.1224203.

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: Franziska Bleichert, Ph.D., March 21

Special Lecture Series
Monday, March 21, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Franziska Bleichert, Ph.D.
Postdoctoral Fellow,
Department of Biophysics and Biophysical Chemistry,
Johns Hopkins University School of Medicine

Molucular Mechanisms for Initiating DNA Replication in Eukaryotes

Recommended Reading

Bleichert, F., Balasov, M., Chesnokov, I., Nogales, E., Botchan, M. R., & Berger, J. M. (2013). A Meier-Gorlin syndrome mutation in a conserved C-terminal helix of Orc6 impedes origin recognition complex formation. Elife, 2, e00882. doi: 10.7554/eLife.00882.

Bleichert, F., Botchan, M. R., & Berger, J. M. (2015). Crystal structure of the eukaryotic origin recognition complex. Nature. 519(7543):321-326. doi: 10.1038/nature14239

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: Julie Segre, Ph.D., February 12

Friday Lecture Series
Friday, February 12, 2016
3:45 p.m., Caspary Auditorium

Julie Segre, Ph.D.,
Senior Investigator, Microbial Genomics Section,
Chief, Translational and Functional Genomics Branch,
National Human Genome Research Institute,
National Institutes of Health

Human Skin Microbiome in Health and Disease

Recommended Reading

Empirical Papers

Conlan, S., Thomas, P. J., Deming, C., Park, M., Lau, A. F., Dekker, J. P., … & Segre, J. A. (2014). Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Science Translational Medicine, 6(254), 254ra126-254ra126. doi: 10.1126/scitranslmed.3009845.

Naik, S., Bouladoux, N., Linehan, J. L., Han, S. J., Harrison, O. J., Wilhelm, C., … & Belkaid, Y. (2015). Commensal-dendritic-cell interaction specifies a unique protective skin immune signature. Nature, 520(7545), 104-108. doi: 10.1038/nature14052.

Oh, J., Byrd, A. L., Deming, C., Conlan, S., Kong, H. H., Segre, J. A., & NISC Comparative Sequencing Program. (2014). Biogeography and individuality shape function in the human skin metagenome. Nature, 514(7520), 59-64. doi: 10.1038/nature13786.

Review Article

Belkaid, Y., & Segre, J. A. (2014). Dialogue between skin microbiota and immunity. Science, 346(6212), 954-959. doi: 10.1126/science.1260144.

Recommended Readings: Gregory Alushin, Ph.D., February 24

Special Lecture Series
Wednesday, February 24, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Gregory Alushin, Ph.D.
Early Independent Scientist,
National Heart Lung and Blood Institute

Cytoskeletal Structural Plasticity in Force Generation and Mechanosensation

Recommended Reading

Alushin, G. M., Lander, G. C., Kellogg, E. H., Zhang, R., Baker, D., & Nogales, E. (2014). High-resolution microtubule structures reveal the structural transitions in αβ-tubulin upon GTP hydrolysis. Cell, 157(5), 1117-1129. doi: 10.1016/j.cell.2014.03.053.

Kim, L. Y., Thompson, P. M., Lee, H. T., Pershad, M., Campbell, S. L., & Alushin, G. M. (2015). The structural basis of actin organization by vinculin and metavinculin. Journal of Molecular Biology. doi: 10.1016/j.jmb.2015.09.031.

Zhang, R., Alushin, G. M., Brown, A., & Nogales, E. (2015). Mechanistic origin of microtubule dynamic instability and its modulation by EB proteins. Cell, 162(4), 849-859. doi: 10.1016/j.cell.2015.07.012.

Recommended Readings: Li Zhao, Ph.D., March 2

Special Lecture Series
Wednesday, March 2, 2016
4:00 p.m., Carson Family Auditorium (CRC)

Li Zhao, Ph.D.
Postdoctoral Researcher,
Department of Evolution and Ecology,
University of California Davis

Evolution of Genetic Novelties in Drosophila

Recommended Reading

Li, X., Fan, D., Zhang, W., Liu, G., Zhang, L., Zhao, L., … & Ding, Y. (2015). Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies. Nature Communications, 6(8212). doi:10.1038/ncomms9212

Zhao, L., Saelao, P., Jones, C. D., & Begun, D. J. (2014). Origin and spread of de novo genes in Drosophila melanogaster populations. Science, 343(6172), 769-772. doi: 10.1126/science.1248286.

Zhao, L., Wit, J., Svetec, N., & Begun, D. J. (2015). Parallel gene expression differences between low and high latitude populations of Drosophila melanogaster and D. simulans. PLOS Genetics, 11(5), e1005184. doi: 10.1371/journal.pgen.1005184.

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: Xiaoliang “Sunney” Xie, Ph.D, January 15

Friday Lecture Series
Friday, January 15, 2016
3:45 p.m., Caspary Auditorium

Xiaoliang “Sunney” Xie, Ph.D.
Mallinckrodt Professor of Chemistry and Chemical Biology,
Harvard University

Life at the Single Molecule Level: From Single Molecule  Enzymology to MALBAC Babies

Recommended Reading

Empirical Articles

Hou, Y., Fan, W., Yan, L., Li, R., Lian, Y., Huang, J., … & Qiao, J. (2013). Genome analyses of single human oocytes. Cell, 155(7), 1492-1506. doi: 10.1016/j.cell.2013.11.040.

Lu, S., Zong, C., Fan, W., Yang, M., Li, J., Chapman, A. R., … & Bai, F. (2012). Probing meiotic recombination and aneuploidy of single sperm cells by whole-genome sequencing. Science, 338(6114), 1627-1630. doi: 10.1126/science.1229112.

Taniguchi, Y., Choi, P. J., Li, G. W., Chen, H., Babu, M., Hearn, J., … & Xie, X. S. (2010). Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science, 329(5991), 533-538. doi: 10.1126/science.1188308.

Zong, C., Lu, S., Chapman, A. R., & Xie, X. S. (2012). Genome-wide detection of single-nucleotide and copy-number variations of a single human cell. Science, 338(6114), 1622-1626. doi: 10.1126/science.1229164.

Review Papers

Li, G. W., & Xie, X. S. (2011). Central dogma at the single-molecule level in living cells. Nature, 475(7356), 308-315. doi: 10.1038/nature10315.

Xie, X. S. (2010). Enzymology and life at the single molecule level. In Single Molecule Spectroscopy in Chemistry, Physics and Biology (pp. 435-448). Springer Berlin Heidelberg.