Recommended Readings: Gary Ruvkun, Ph.D. October 24

Friday Lecture Series
Friday, October 24, 2014
3:45 p.m., Caspary Auditorium

Gary Ruvkun, Ph.D.
Hans-Hermann Schoene Distinguished Investigator and Professor,
Department of Genetics,
Harvard Medical School

C. elegans Surveillance of Conserved Cellular Components to Detect and Defend Pathogen Attacks, Real or Imagined

Recommended Readings

Empirical Articles

Liu, Y., Samuel, B. S., Breen, P. C., & Ruvkun, G. (2014). Caenorhabditis elegans pathways that surveil and defend mitochondria. Nature, 508(7496), 406–410. doi:10.1038/nature13204

Melo, J. A, & Ruvkun, G. (2012). Inactivation of conserved C. elegans genes engages pathogen- and xenobiotic-associated defenses. Cell, 149(2), 452–466. doi:10.1016/j.cell.2012.02.050

Shore, D. E., Carr, C. E., & Ruvkun, G. (2012). Induction of cytoprotective pathways is central to the extension of lifespan conferred by multiple longevity pathways. PLoS Genetics, 8(7), e1002792. doi:10.1371/journal.pgen.1002792

Review Papers

Shore, D. E., & Ruvkun, G. (2013). A cytoprotective perspective on longevity regulation. Trends in Cell Biology, 23(9), 409–420. doi:10.1016/j.tcb.2013.04.007

Recommended Readings: Susan Lindquist, Ph.D. October 17

Friday Lecture Series
Friday, October 17, 2014
3:45 p.m., Caspary Auditorium

Susan Lindquist, Ph.D.
Professor of Biology,
Massachussetts Institute of Technology
Member,
Whitehead Institute for Biomedical Research
Investigator,
Howard Hughes Medical Institute

From Yeast to Patient Neurons and Back Again: Powerful Discovery Platforms Combatting Neurodegenerative Disease

Recommended Readings

Empirical Articles

Chung, C. Y., Khurana, V., Auluck, P. K., Tardiff, D. F., Mazzulli, J. R., Soldner, F., … Lindquist, S. (2013). Identification and rescue of α-synuclein toxicity in Parkinson patient-derived neurons. Science, 342(6161), 983–987. doi:10.1126/science.1245296

Tardiff, D. F., Jui, N. T., Khurana, V., Tambe, M. A, Thompson, M. L., Chung, C. Y., … Lindquist, S. (2013). Yeast reveal a “druggable” Rsp5/Nedd4 network that ameliorates α-synuclein toxicity in neurons. Science, 342(6161), 979–983. doi:10.1126/science.1245321

Treusch, S., Hamamichi, S., Goodman, J. L., Matlack, K. E. S., Chung, C. Y., Baru, V., … Lindquist, S. (2011). Functional links between Aβ toxicity, endocytic trafficking, and Alzheimer’s disease risk factors in yeast. Science, 334(6060), 1241–1245. doi:10.1126/science.1213210

Review Papers

Khurana, V., & Lindquist, S. (2010). Modelling neurodegeneration in Saccharomyces cerevisiae: why cook with baker’s yeast? Nature Reviews Neuroscience, 11(6), 436–449. doi:10.1038/nrn2809

Tardiff, D. F., Khurana, V., Chung, C. Y., & Lindquist, S. (2014). From yeast to patient neurons and back again: A powerful new discovery platform. Movement Disorders, 29(10), 1231–1240. doi:10.1002/mds.25989

Recommended Readings: Xiaowei Zhuang, Ph.D. October 16

Harvey Society Lecture Series
Thursday, October 16, 2014
8:00 p.m., Caspary Auditorium

Xiaowei Zhuang, Ph.D.
Professor of Chemistry and Chemical Biology
Professor of Physics,
Harvard University
Investigator,
Howard Hughes Medical Institute

Illuminating Biology at the Nanoscale with Single-Molecule and Super-Resolution Fluorescence Microscopy

Recommended Readings

Empirical Articles

Bates, M., Huang, B., Dempsey, G. T., & Zhuang, X. (2007). Multicolor super-resolution imaging with photo-switchable fluorescent probes. Science, 317(5845), 1749–1753. doi:10.1126/science.1146598

Huang, B., Wang, W., Bates, M., & Zhuang, X. (2008). Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science, 319(5864), 810–813. doi:10.1126/science.1153529

Xu, K., Babcock, H. P., & Zhuang, X. (2012). Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton. Nature Methods, 9(2), 185–188. doi:10.1038/nmeth.1841

Xu, K., Zhong, G., & Zhuang, X. (2013). Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. Science, 339(6118), 452–456. doi:10.1126/science.1232251

Review Papers

Alivisatos, a P., Andrews, A. M., Boyden, E. S., Chun, M., Church, G. M., Deisseroth, K., … Zhuang, X. (2013). Nanotools for neuroscience and brain activity mapping. ACS Nano, 7(3), 1850–1866. doi:10.1021/nn4012847

Huang, B., Babcock, H., & Zhuang, X. (2010). Breaking the diffraction barrier: super-resolution imaging of cells. Cell, 143(7), 1047–1058. doi:10.1016/j.cell.2010.12.002

Recommended Readings: Sohail Tavazoie, Ph.D. October 6

Monday Lecture Series
Monday, October 6, 2014
3:45 p.m., Caspary Auditorium

Sohail Tavazoie, Ph.D.
Leon Hess Assistant Professor and Head,
Elizabeth and Vincent Meyer Laboratory of Systems Cancer Biology,
The Rockefeller University
Senior Attending Physician,
The Rockefeller University Hospital

Molecular Control of Cancer Metastasis

Recommended Readings

Empirical Articles

Pencheva, N., Tran, H., Buss, C., Huh, D., Drobnjak, M., Busam, K., & Tavazoie, S. F. (2012). Convergent multi-miRNA targeting of ApoE drives LRP1/LRP8-dependent melanoma metastasis and angiogenesis. Cell, 151(5), 1068–1082. doi:10.1016/j.cell.2012.10.028

Png, K. J., Halberg, N., Yoshida, M., & Tavazoie, S. F. (2012). A microRNA regulon that mediates endothelial recruitment and metastasis by cancer cells. Nature, 481(7380), 190–194. doi:10.1038/nature10661

Png, K. J., Yoshida, M., Zhang, X. H.-F., Shu, W., Lee, H., Rimner, A., … Tavazoie, S. F. (2011). MicroRNA-335 inhibits tumor reinitiation and is silenced through genetic and epigenetic mechanisms in human breast cancer. Genes & Development, 25(3), 226–231. doi:10.1101/gad.1974211

Tavazoie, S. F., Alarcón, C., Oskarsson, T., Padua, D., Wang, Q., Bos, P. D., … Massagué, J. (2008). Endogenous human microRNAs that suppress breast cancer metastasis. Nature, 451(7175), 147–52. doi:10.1038/nature06487

Review Papers

Pencheva, N., & Tavazoie, S. F. (2013). Control of metastatic progression by microRNA regulatory networks. Nature Cell Biology, 15(6), 546–54. doi:10.1038/ncb2769

Recommended Readings: John Mekalanos, Ph.D. October 10

Friday Lecture Series
Friday, October 10, 2014
3:45 p.m., Caspary Auditorium

John Mekalanos, Ph.D.
Adele H. Lehman Professor of Microbiology
Chair, Department of Microbiology and Immunobiology,
Harvard Medical School

The Ghost in the Machine: Understanding Bacterial Secretion Systems Through Defining Their Effectors

Recommended Readings

Empirical Articles

Basler, M., Ho, B. T., & Mekalanos, J. J. (2013). Tit-for-tat: type VI secretion system counterattack during bacterial cell-cell interactions. Cell, 152(4), 884–894. doi:10.1016/j.cell.2013.01.042

Basler, M., Pilhofer, M., Henderson, G. P., Jensen, G. J., & Mekalanos, J. J. (2012). Type VI secretion requires a dynamic contractile phage tail-like structure. Nature, 483(7388), 182–186. doi:10.1038/nature10846

Ma, A. T., McAuley, S., Pukatzki, S., & Mekalanos, J. J. (2009). Translocation of a Vibrio cholerae type VI secretion effector requires bacterial endocytosis by host cells. Cell Host & Microbe, 5(3), 234–243. doi:10.1016/j.chom.2009.02.005

Ma, A. T., & Mekalanos, J. J. (2010). In vivo actin cross-linking induced by Vibrio cholerae type VI secretion system is associated with intestinal inflammation. Proceedings of the National Academy of Sciences, 107(9), 4365–4370. doi:10.1073/pnas.0915156107

Review Papers

Ho, B. T., Dong, T. G., & Mekalanos, J. J. (2014). A view to a kill: the bacterial type VI secretion system. Cell Host & Microbe, 15(1), 9–21. doi:10.1016/j.chom.2013.11.008

Recommended Readings: Camilla Sjögren, Ph.D. October 31

Friday Lecture Series
Friday, October 31, 2014
3:45 p.m., Caspary Auditorium

Camilla Sjögren, Ph.D.
Professor, Department of Cell and Molecular Biology
Karolinska Institutet

Connecting chromosome replication and segregation: DNA topology and SMC complexes

Recommended Readings

Empirical Articles

Kegel, A., Betts-Lindroos, H., Kanno, T., Jeppsson, K., Ström, L., Katou, Y., … Sjögren, C. (2011). Chromosome length influences replication-induced topological stress. Nature, 471(7338), 392–6. doi:10.1038/nature09791

Lindroos, H. B., Ström, L., Itoh, T., Katou, Y., Shirahige, K., & Sjögren, C. (2006). Chromosomal association of the Smc5/6 complex reveals that it functions in differently regulated pathways. Molecular Cell, 22(6), 755–67. doi:10.1016/j.molcel.2006.05.014

Review Papers

Carter, S. D., & Sjögren, C. (2012). The SMC complexes, DNA and chromosome topology: right or knot? Critical Reviews in Biochemistry and Molecular Biology, 47(1), 1–16. doi:10.3109/10409238.2011.614593

Jeppsson, K., Kanno, T., Shirahige, K., & Sjögren, C. (2014). The maintenance of chromosome structure: positioning and functioning of SMC complexes. Nature Reviews Molecular Cell Biology, 15(9), 601–614. doi:10.1038/nrm3857

Recommended Readings: Tiffany Reese, Ph.D. October 1

Special Seminar
Wednesday, October 1, 2014
4:00 p.m., Carson Family Auditorium

Tiffany Reese, Ph.D.
Instructor,
Department of Pathology and Immunology,
Washington University School of Medicine

Cytokine Regulation of Gammaherpesvirus Reactivation During Helminth Co-Infection

Recommended Readings

Empirical Articles

Osborne, L. C., Monticelli, L. a., Nice, T. J., Sutherland, T. E., Siracusa, M. C., Hepworth, M. R., … Artis, D. (2014). Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation. Science, 345(6196), 578–582. doi:10.1126/science.1256942

Reese, T. A, Wakeman, B. S., Choi, H. S., Hufford, M. M., Huang, S. C., Zhang, X., … Virgin, H. W. (2014). Helminth infection reactivates latent γ-herpesvirus via cytokine competition at a viral promoter. Science, 345(6196), 573–577. doi:10.1126/science.1254517

Review Papers

Virgin, H. W. (2014). The virome in mammalian physiology and disease. Cell, 157(1), 142–150. doi:10.1016/j.cell.2014.02.032

Recommended Readings: Shixin Liu, Ph.D. September 29

Special Seminar
Monday, September 29, 2014
4:00 p.m., Carson Family Auditorium

Shixin Liu, Ph.D.
Postdoctoral Fellow,
California Institute for Quantitative Biosciences (QB3),
University of California, Berkeley

Visualization and Manipulation of Single Biomolecular Machines

Recommended Readings

Empirical Articles

Chistol, G., Liu, S., Hetherington, C. L., Moffitt, J. R., Grimes, S., Jardine, P. J., & Bustamante, C. (2012). High degree of coordination and division of labor among subunits in a homomeric ring ATPase. Cell, 151(5), 1017–1028. doi:10.1016/j.cell.2012.10.031

Liu, S., Abbondanzieri, E., & Rausch, J. (2008). Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates. Science, 322(5904):1092-1097. doi: 10.1126/science.1163108.

Liu, S., Chistol, G., Hetherington, C. L., Tafoya, S., Aathavan, K., Schnitzbauer, J., … Bustamante, C. (2014). A viral packaging motor varies its DNA rotation and step size to preserve subunit coordination as the capsid fills. Cell, 157(3), 702–713. doi:10.1016/j.cell.2014.02.034

Liu, S., Harada, B. T., Miller, J. T., Le Grice, S. F. J., & Zhuang, X. (2010). Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription. Nature Structural & Molecular Biology, 17(12), 1453–60. doi:10.1038/nsmb.1937

Review Papers

Liu, S., Chistol, G., & Bustamante, C. (2014). Mechanical operation and intersubunit coordination of ring-shaped molecular motors: insights from single-molecule studies. Biophysical Journal, 106(9), 1844–58. doi:10.1016/j.bpj.2014.03.029

Recommended Readings: Zhijian ‘James’ Chen, Ph.D. September 26

Friday Lecture Series
Friday, September 26, 2014
3:45 p.m., Caspary Auditorium

Zhijian “James” Chen, Ph.D.
George L. MacGregor Distinguished Chair in Biomedical Sciences,
Director, Center for Inflammation,
Research Professor, Department of Molecular Biology,

The University of Texas Southwestern Medical Center
Investigator, Howard Hughes Medical Institute

Enemy Within – Immune and Autoimmune Responses to cytosolic DNA and RNA

Recommended Readings

Empirical Articles

Gao, D., Wu, J., Wu, Y.-T., Du, F., Aroh, C., Yan, N., … Chen, Z. J. (2013). Cyclic GMP-AMP synthase is an innate immune sensor of HIV and other retroviruses. Science, 341(6148), 903–906. doi:10.1126/science.1240933

Li, X.-D., Wu, J., Gao, D., Wang, H., Sun, L., & Chen, Z. J. (2013). Pivotal roles of cGAS-cGAMP signaling in antiviral defense and immune adjuvant effects. Science, 341(6152), 1390–1394. doi:10.1126/science.1244040

Sun, L., Wu, J., Du, F., Chen, X., & Chen, Z. J. (2013). Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway. Science, 339(6121), 786–791. doi:10.1126/science.1232458

Zeng, W., Sun, L., Jiang, X., Chen, X., Hou, F., Adhikari, A., … Chen, Z. J. (2010). Reconstitution of the RIG-I pathway reveals a signaling role of unanchored polyubiquitin chains in innate immunity. Cell, 141(2), 315–330. doi:10.1016/j.cell.2010.03.029

Review Papers

Cai, X., Chiu, Y.-H., & Chen, Z. J. (2014). The cGAS-cGAMP-STING pathway of cytosolic DNA sensing and signaling. Molecular Cell, 54(2), 289–296. doi:10.1016/j.molcel.2014.03.040

Wu, J., & Chen, Z. J. (2014). Innate immune sensing and signaling of cytosolic nucleic acids. Annual Review of Immunology, 32, 461–88. doi:10.1146/annurev-immunol-032713-120156

Recommended Readings: Jennifer Doudna, Ph.D. September 19

Friday Lecture Series
Friday, September 19, 2014
3:45 p.m., Caspary Auditorium

Jennifer Doudna, Ph.D.
Li Ka Shing Chancellor’s Chair in Biomedical and Health Sciences,
Professor of Biochemistry, Biophysics and Structural Biology,
Departments of Molecular and Cell Biology and Chemistry,
University of California, Berkeley
Investigator, Howard Hughes Medical Institute

CRISPR Systems: A Revolution in Basic Science and Biotechnology

Recommended Readings

Empirical Articles

Haurwitz, R. E., Jinek, M., Wiedenheft, B., Zhou, K., & Doudna, J. a. (2010). Sequence- and structure-specific RNA processing by a CRISPR endonuclease. Science, 329(5997), 1355–1358. doi:10.1126/science.1192272

Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C., & Doudna, J. a. (2014). DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature, 507(7490), 62–67. doi:10.1038/nature13011

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

Review Papers

Bhaya, D., Davison, M., & Barrangou, R. (2011). CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annual Review of Genetics, 45, 273–97. doi:10.1146/annurev-genet-110410-132430

Hsu, P. D., Lander, E. S., & Zhang, F. (2014). Development and Applications of CRISPR-Cas9 for Genome Engineering. Cell, 157(6), 1262–1278. doi:10.1016/j.cell.2014.05.010