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

Recommended Readings: Paul Cohen, M.D., Ph.D. June 24

Special Seminar 
Tuesday, June 24, 2014
4:00 p.m., Carson Family Auditorium

Paul Cohen, M.D., Ph.D.
Postdoctoral Fellow, Dana Farber Cancer Institute
Attending Cardiologist, Brigham and Women’s Hospital
Instructor in Medicine, Harvard Medical School

Transcriptional Determinants of Subcutaneous and Visceral Adipose Tissue: Towards Engineering Healthier Fat

Recommended Readings:

Empirical Articles

Cohen, P., Levy, J. D., Zhang, Y., Frontini, A., Kolodin, D. P., Svensson, K. J., … Spiegelman, B. M. (2014). Ablation of PRDM16 and beige adipose causes metabolic dysfunction and a subcutaneous to visceral fat switch. Cell, 156(1-2), 304–16. doi:10.1016/j.cell.2013.12.021

Seale, P., Conroe, H. M., Estall, J., Kajimura, S., Frontini, A., Ishibashi, J., … Spiegelman, B. M. (2011). Prdm16 determines the thermogenic program of subcutaneous white adipose tissue in mice. The Journal of Clinical Investigation, 121(1), 53–56. doi:10.1172/JCI44271.96

Review Papers

Wu, J., Cohen, P., & Spiegelman, B. M. (2013). Adaptive thermogenesis in adipocytes: is beige the new brown? Genes & Development, 27(3), 234–50. doi:10.1101/gad.211649.112

Recommended Readings: Thomas Walz, Ph.D. June 23

Special Seminar 
Monday, June 23, 2014
4:00 p.m., Carson Family Auditorium

Thomas Walz, Ph.D
Professor, Department of Cell Biology
Harvard Medical School
Investigator, Howard Hughes Medical Institute

Using Two-dimensional Crystals of Aquaporin-0 to Investigate Lipid-Protein Interactions

Recommended Readings:

Empirical Articles

Aponte-Santamaría, C., Briones, R., Schenk, A. D., Walz, T., & de Groot, B. L. (2012). Molecular driving forces defining lipid positions around aquaporin-0. Proceedings of the National Academy of Sciences, 109(25), 9887–9892. doi:10.1073/pnas.1121054109

Gonen, T., Cheng, Y., Sliz, P., Hiroaki, Y., Fujiyoshi, Y., Harrison, S. C., & Walz, T. (2005). Lipid-protein interactions in double-layered two-dimensional AQP0 crystals. Nature, 438(7068), 633–638. doi:10.1038/nature04321

Gonen, T., Sliz, P., Kistler, J., Cheng, Y., & Walz, T. (2004). Aquaporin-0 membrane junctions reveal the structure of a closed water pore. Nature, 429(6988), 193–197. doi:10.1038/nature02503

Hite, R. K., Li, Z., & Walz, T. (2010). Principles of membrane protein interactions with annular lipids deduced from aquaporin-0 2D crystals. The EMBO Journal, 29(10), 1652–1658. doi:10.1038/emboj.2010.68

Review Papers

Gonen, T., & Walz, T. (2006). The structure of aquaporins. Quarterly Reviews of Biophysics, 39(4), 361–396. doi:10.1017/S0033583506004458

Raunser, S., & Walz, T. (2009). Electron crystallography as a technique to study the structure on membrane proteins in a lipidic environment. Annual Review of Biophysics, 38, 89–105. doi:10.1146/annurev.biophys.050708.133649

Recommended Readings: Daniel Finley, Ph.D. May 30

Friday Lecture Series
Friday, May 30, 2014
3:45 p.m., Caspary Auditorium

Daniel Finley, Ph.D.
Professor
Department of Cell Biology
Harvard Medical School

Regulation of Proteasome Activity by Ubiquitin Chain Editing

Recommended Readings:

Empirical Articles

Crosas, B., Hanna, J., Kirkpatrick, D. S., Zhang, D. P., Tone, Y., Hathaway, N. a, … Finley, D. (2006). Ubiquitin chains are remodeled at the proteasome by opposing ubiquitin ligase and deubiquitinating activities. Cell, 127(7), 1401–1413. doi:10.1016/j.cell.2006.09.051

Hanna, J., Hathaway, N. a, Tone, Y., Crosas, B., Elsasser, S., Kirkpatrick, D. S., … Finley, D. (2006). Deubiquitinating enzyme Ubp6 functions noncatalytically to delay proteasomal degradation. Cell, 127(1), 99–111. doi:10.1016/j.cell.2006.07.038

Lee, B.-H., Lee, M. J., Park, S., Oh, D.-C., Elsasser, S., Chen, P.-C., … Finley, D. (2010). Enhancement of proteasome activity by a small-molecule inhibitor of USP14. Nature, 467(7312), 179–184. doi:10.1038/nature09299

Leggett, D. S., Hanna, J., Borodovsky, A., Crosas, B., Schmidt, M., Baker, R. T., … Finley, D. (2002). Multiple associated proteins regulate proteasome structure and function. Molecular Cell, 10(3), 495–507.

Review Papers

Finley, D. (2009). Recognition and Processing of Ubiquitin-Protein Conjugates by the Proteasome. Annual Review of Biochemistry, 78(1), 477–513. doi:10.1146/annurev.biochem.78.081507.101607

Schmidt, M., & Finley, D. (2014). Regulation of proteasome activity in health and disease. Biochimica et Biophysica Acta, 1843(1), 13–25. doi:10.1016/j.bbamcr.2013.08.012

 

Recommended Readings: Craig B. Thompson, M.D. May 23

Friday Lecture Series
Friday, May 23, 2014
3:45 p.m., Caspary Auditorium

Craig B. Thompson, M.D.
President and CEO
Memorial Sloan Kettering Cancer Center

What Cancer Is Teaching Us about Cellular Metabolism

Recommended Readings:

Empirical Papers

Buzzai, M., Bauer, D. E., Jones, R. G., Deberardinis, R. J., Hatzivassiliou, G., Elstrom, R. L., & Thompson, C. B. (2005). The glucose dependence of Akt-transformed cells can be reversed by pharmacologic activation of fatty acid beta-oxidation. Oncogene, 24(26), 4165–4173. doi:10.1038/sj.onc.1208622

Lum, J. J., Bauer, D. E., Kong, M., Harris, M. H., Li, C., Lindsten, T., & Thompson, C. B. (2005). Growth factor regulation of autophagy and cell survival in the absence of apoptosis. Cell, 120(2), 237–248. doi:10.1016/j.cell.2004.11.046

Selak, M. a, Armour, S. M., MacKenzie, E. D., Boulahbel, H., Watson, D. G., Mansfield, K. D., … Gottlieb, E. (2005). Succinate links TCA cycle dysfunction to oncogenesis by inhibiting HIF-alpha prolyl hydroxylase. Cancer Cell, 7(1), 77–85. doi:10.1016/j.ccr.2004.11.022

Ye, J., Mancuso, A., Tong, X., Ward, P. S., Fan, J., & Rabinowitz, J. D. (2012). Pyruvate kinase M2 promotes de novo serine synthesis to sustain mTORC1 activity and cell proliferation. Proceedings of the National Academy of Sciences, 109(18), 2–7. doi:10.1073/pnas.1204176109

Review Papers

DeBerardinis, R. J., Lum, J. J., Hatzivassiliou, G., & Thompson, C. B. (2008). The biology of cancer: metabolic reprogramming fuels cell growth and proliferation. Cell Metabolism, 7(1), 11–20. doi:10.1016/j.cmet.2007.10.002

Vander Heiden, M. G., Cantley, L. C., & Thompson, C. B. (2009). Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science, 324(5930), 1029–1033. doi:10.1126/science.1160809

Ward, P. S., & Thompson, C. B. (2012). Metabolic reprogramming: a cancer hallmark even Warburg did not anticipate. Cancer Cell, 21(3), 297–308. doi:10.1016/j.ccr.2012.02.014

Recommended Readings: Allan C Spradling, Ph.D. May 16

Friday Lecture Series
Friday, May 16, 2014
3:45 p.m., Caspary Auditorium

Allan C Spradling, Ph.D.
Director, Department of Embryology
Carnegie Institution for Science

Investigator, Howard Hughes Medical Institute

Epigenetic and genetic programing of Drosophila development

Recommended Readings:

Empirical Articles

Morris, L. X., & Spradling, A. C. (2011). Long-term live imaging provides new insight into stem cell regulation and germline-soma coordination in the Drosophila ovary. Development, 138(11), 2207–2215. doi:10.1242/dev.065508

Nystul, T., & Spradling, A. (2007). An epithelial niche in the Drosophila ovary undergoes long-range stem cell replacement. Cell Stem Cell, 1(3), 277–285. doi:10.1016/j.stem.2007.07.009

Skora, A. D., & Spradling, A. C. (2010). Epigenetic stability increases extensively during Drosophila follicle stem cell differentiation. Proceedings of the National Academy of Sciences, 107(16), 7389–7394. doi:10.1073/pnas.1003180107

Xie, T., & Spradling, A. C. (2000). A niche maintaining germ line stem cells in the Drosophila ovary. Science, 290(5490), 328–330. doi:10.1126/science.290.5490.328

Review Papers

Losick, V. P., Morris, L. X., Fox, D. T., & Spradling, A. (2011). Drosophila stem cell niches: a decade of discovery suggests a unified view of stem cell regulation. Developmental Cell, 21(1), 159–171. doi:10.1016/j.devcel.2011.06.018

Morrison, S. J., & Spradling, A. C. (2008). Stem cells and niches: mechanisms that promote stem cell maintenance throughout life. Cell, 132(4), 598–611. doi:10.1016/j.cell.2008.01.038

Recommended Readings: Sangeeta Bhatia, M.D., Ph.D. May 12

SPECIAL SEMINAR
Monday, May 12, 2014
4:00 p.m., Carson Family Auditorium

Sangeeta Bhatia, M.D., Ph.D.
John J. and Dorothy Wilson Professor of Health Sciences & Technology
Institute for Medical Engineering and Science
Director, Laboratory for Multiscale Regenerative Technologies
Massachusetts Institute of Technology
Investigator, Howard Hughes Medical Institute

Tiny Technologies for Studying Tissue Microenvironments

Recommended Readings:

Empirical Papers

Chen, A., & Thomas, D. (2011). Humanized mice with ectopic artificial liver tissues. Proceedings of the National Academy of Sciences, 108(29), 11842–11847. doi:10.1073/pnas.1101791108

Hui, E. E., & Bhatia, S. N. (2007). Micromechanical control of cell-cell interactions. Proceedings of the National Academy of Sciences, 104(14), 5722–5726. doi:10.1073/pnas.0608660104

Khetani, S. R., & Bhatia, S. N. (2008). Microscale culture of human liver cells for drug development. Nature Biotechnology, 26(1), 120–126. doi:10.1038/nbt1361

Review Papers

Underhill, G. H., Galie, P., Chen, C. S., & Bhatia, S. N. (2012). Bioengineering methods for analysis of cells in vitro. Annual Review of Cell and Developmental Biology, 28, 385–410. doi:10.1146/annurev-cellbio-101011-155709

Wong, I. Y., Bhatia, S. N., & Toner, M. (2013). Nanotechnology: emerging tools for biology and medicine. Genes & Development, 27(22), 2397–2408. doi:10.1101/gad.226837.113