Recommended Readings: James E. Darnell, Jr., M.D. May 19

Monday Lecture Series
Monday, May 19, 2014
4:00 p.m., Carson Family Auditorium

James E. Darnell, Jr., M.D.
Vincent Astor Professor Emeritus 
Head, Laboratory of Molecular Cell Biology
The Rockefeller University

Then and now – making mRNA: an unbiased (?) look at pre-mRNA synthesis and processing

Recommended Readings:

Empirical Papers

Brenner, S., Jacob, F., & Meselson, M. (1961). An unstable intermediate carrying information from genes to ribosomes for protein synthesis. Nature, 180(4776), 576–581.

Gros, F., Hiatt, H., Gilbert, W., & Kurland, C. (1961). Unstable ribonucleic acid revealed by pulse labelling of Escherichia coli. Nature, 190(4776), 581–585.

Jacob, F., & Monod, J. (1961). Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology, 3, 318–356.

Scherrer, K., Latham, H., & Darnell, J. E. (1963). Demonstration of an unstable RNA and of a precursor to ribosomal RNA in HeLa cells. Proceedings of the National Academy of Sciences, 49(2), 240–248.

Review Articles

Darnell, J. E. (1968). Ribonucleic acids from animal cells. Bacteriological Reviews, 32(3), 262–290.

Darnell, J. E. (2013). Reflections on the history of pre-mRNA processing and highlights of current knowledge: a unified picture. RNA, 19(4), 443–60. doi:10.1261/rna.038596.113

Licatalosi, D. D., & Darnell, R. B. (2010). RNA processing and its regulation: global insights into biological networks. Nature Reviews Genetics, 11(1), 75–87. doi:10.1038/nrg2673

Recommended Readings: David Kingsley, Ph.D. April 18

Friday Lecture Series
Friday, April 18, 2014
3:45 p.m., Caspary Auditorium

David Kingsley, Ph.D.
HHMI and Department of Developmental Biology
Stanford University School of Medicine

Fishing for the secrets of vertebrate evolution

Recommended Readings:

Empirical Papers

Chan, Y. F., Marks, M. E., Jones, F. C., Villarreal, G., Shapiro, M. D., Brady, S. D., … Kingsley, D. M. (2010). Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science, 327(5963), 302–305. doi:10.1126/science.1182213

Colosimo, P. F., Hosemann, K. E., Balabhadra, S., Villarreal, G., Dickson, M., Grimwood, J., … Kingsley, D. M. (2005). Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles. Science, 307(5717), 1928–1933. doi:10.1126/science.1107239

Jones, F. C., Grabherr, M. G., Chan, Y. F., Russell, P., Mauceli, E., Johnson, J., … Kingsley, D. M. (2012). The genomic basis of adaptive evolution in threespine sticklebacks. Nature, 484(7392), 55–61. doi:10.1038/nature10944

Miller, C. T., Beleza, S., Pollen, A. a, Schluter, D., Kittles, R. a, Shriver, M. D., & Kingsley, D. M. (2007). cis-Regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans. Cell, 131(6), 1179–1189. doi:10.1016/j.cell.2007.10.055

Shapiro, M. D., Marks, M. E., Peichel, C. L., Blackman, B. K., Nereng, K. S., Jónsson, B., … Kingsley, D. M. (2004). Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature, 428(6984), 717–723. doi:10.1038/nature02415

Review Articles

McKinnon, J. S., & Rundle, H. D. (2002). Speciation in nature: the threespine stickleback model systems. Trends in Ecology & Evolution, 17(10), 480–488. doi:10.1016/S0169-5347(02)02579-X

Recommended Readings: Hidde Ploegh, Ph.D.

Friday Lecture Series

Host-pathogen Interactions: A Biochemist’s Perspective

Hidde Ploegh, Ph.D., professor of biology and member,

Whitehead Institute for Biomedical Research

March 28, 2014

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Carette, J. E., Guimaraes, C. P., Varadarajan, M., Park, A. S., Wuethrich, I., Godarova, A., . . . Brummelkamp, T. R. (2009). Haploid genetic screens in human cells identify host factors used by pathogens. Science, 326(5957), 1231-1235

Dougan, S. K., Hu, C. -. A., Paquet, M. -., Greenblatt, M. B., Kim, J., Lilley, B. N., . . . Ploegh, H. L. (2011). Derlin-2-deficient mice reveal an essential role for protein dislocation in chondrocytes. Molecular and Cellular Biology, 31(6), 1145-1159

Loureiro, J., & Ploegh, H. L. (2006). Antigen presentation and the ubiquitin-proteasome system in host-pathogen interactions. Advances in Immunology, 92, 225-305

Reiling, J. H., Olive, A. J., Sanyal, S., Carette, J. E., Brummelkamp, T. R., Ploegh, H. L., . . . Sabatini, D. M. (2013). A CREB3-ARF4 signalling pathway mediates the response to golgi stress and susceptibility to pathogens. Nature Cell Biology, 15(12), 1473-1485

Tafesse, F. G., Sanyal, S., Ashour, J., Guimaraes, C. P., Hermansson, M., Somerharju, P., & Ploegh, H. L. (2013). Intact sphingomyelin biosynthetic pathway is essential for intracellular transport of influenza virus glycoproteins. Proceedings of the National Academy of Sciences of the United States of America, 110(16), 6406-6411

Vyas, J. M., Van Der Veen, A. G., & Ploegh, H. L. (2008). The known unknowns of antigen processing and presentation. Nature Reviews Immunology, 8(8), 607-618


Recommended Readings: Ila R. Fiete, Ph.D. April 7

Monday, April 7, 2014
4:00 p.m., Carson Family Auditorium

Ila R. Fiete, Ph.D.
Associate Professor, Department of Neuroscience
Fellow, The Institute for Neuroscience
The University of Texas at Austin

Neural Codes and Dynamics for Representation and Memory

Recommended Readings:

Empirical Papers

Burak, Y., & Fiete, I. R. (2012). Fundamental limits on persistent activity in networks of noisy neurons. Proceedings of the National Academy of Sciences, 109(43), 17645–17650. doi:10.1073/pnas.1117386109

Fiete, I. R., Burak, Y., & Brookings, T. (2008). What grid cells convey about rat location. The Journal of Neuroscience, 28(27), 6858–6871. doi:10.1523/JNEUROSCI.5684-07.2008

Sreenivasan, S., & Fiete, I. (2011). Grid cells generate an analog error-correcting code for singularly precise neural computation. Nature Neuroscience, 14(10), 1330–1337. doi:10.1038/nn.2901

Yoon, K., Buice, M. a, Barry, C., Hayman, R., Burgess, N., & Fiete, I. R. (2013). Specific evidence of low-dimensional continuous attractor dynamics in grid cells. Nature Neuroscience, 16(8), 1077–1084. doi:10.1038/nn.3450

Review Articles

Burak, Y. (2006). Do We Understand the Emergent Dynamics of Grid Cell Activity? Journal of Neuroscience, 26(37), 9352–9354. doi:10.1523/JNEUROSCI.2857-06.2006

Recommended Readings: Diane Mathis, Ph.D.

Friday Lecture Series

The Ernst A.H. Friedheim Memorial Lecture

Aire, a Transcriptional Regulator Critical for Immunological Tolerance

Diane Mathis, Ph.D., professor, division of immunology,

department of microbiology and immunobiology, Harvard Medical School

March 21, 2014

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Abramson, J., Giraud, M., Benoist, C., & Mathis, D. (2010). Aire’s partners in the molecular control of immunological tolerance. Cell, 140(1), 123-135

Burzyn, D., Benoist, C., & Mathis, D. (2013). Regulatory T cells in nonlymphoid tissues. Nature Immunology, 14(10), 1007-1013

D’Alise, A. M., Ergun, A., Hill, J. A., Mathis, D., & Benoist, C. (2011). A cluster of coregulated genes determines TGF-β – induced regulatory T-cell (treg) dysfunction in NOD mice. Proceedings of the National Academy of Sciences of the United States of America, 108(21), 8737-8742

Fu, W., Ergun, A., Lu, T., Hill, J. A., Haxhinasto, S., Fassett, M. S., . . . Benoist, C. (2012). A multiply redundant genetic switch ‘locks in’ the transcriptional signature of regulatory T cells. Nature Immunology, 13(10), 972-980

Giraud, M., Yoshid, H., Abramson, J., Rahl, P. B., Young, R. A., Mathis, D., & Benoist, C. (2012). Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells. Proceedings of the National Academy of Sciences of the United States of America, 109(2), 535-540

Koh, A. S., Kingston, R. E., Benoist, C., & Mathis, D. (2010). Global relevance of aire binding to hypomethylated lysine-4 of histone-3. Proceedings of the National Academy of Sciences of the United States of America, 107(29), 13016-13021

Yang, S., Bansal, K., Lopes, J., Benoist, C., & Mathis, D. (2013). Aire’s plant homeodomain(PHD)-2 is critical for induction of immunological tolerance. Proceedings of the National Academy of Sciences of the United States of America, 110(5), 1833-1838


Recommended Readings: Debora Marks, Ph.D. March 31

Wednesday, March 31, 2014
4:00 p.m., Carson Family Auditorium

Debora Marks, Ph.D.
Department of Systems Biology
Harvard Medical School

Evolutionary Co-variation in Genomic Sequences Gives Protein 3D and Quantitative Mutation Effects

Recommended Readings:

Empirical Articles

Hopf, T. A., Colwell, L. J., Sheridan, R., Rost, B., Sander, C., & Marks, D. S. (2012). Three-dimensional structures of membrane proteins from genomic sequencing. Cell, 149(7), 1607–1621. doi:10.1016/j.cell.2012.04.012

Marks, D. S., Colwell, L. J., Sheridan, R., Hopf, T. a, Pagnani, A., Zecchina, R., & Sander, C. (2011). Protein 3D structure computed from evolutionary sequence variation. PLOS One, 6(12), e28766. doi:10.1371/journal.pone.0028766

Morcos, F., Pagnani, A., Lunt, B., Bertolino, A., Marks, D. S., Sander, C., … Weigt, M. (2011). Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proceedings of the National Academy of Sciences, 108(49), 1293–1301. doi:10.1073/pnas.1111471108

Review Papers

Marks, D. S., Hopf, T. A, & Sander, C. (2012). Protein structure prediction from sequence variation. Nature Biotechnology, 30(11), 1072–1080. doi:10.1038/nbt.2419

Recommended Readings: Torsten Wiesel, Ph.D. March 24

Monday Lecture Series
March 24, 2014
Carson Family Auditorium (CRC)

Torsten Wiesel, M.D.,
President Emeritus
Vincent and Brooke Astor Professor Emeritus
Head of Laboratory of Neurobiology
The Rockefeller University

An homage to David Hubel: Early days in our studies of the visual cortex

Recommended Readings:

Empirical Articles

Hubel, D. (1957). Tungsten microelectrode for recording from single units. Science, 125(3247), 549–550.

Hubel, D., & Wiesel, T. (1959). Receptive fields of single neurons in the cat’s striate cortex. The Journal of Physiology, 148(3), 574–591.

Hubel, D., & Wiesel, T. (1962). Receptive fields, binocular interaction and functional architecture in the cat’s visual cortex. The Journal of Physiology, 160(1), 106–154.

Hubel, D., & Wiesel, T. (1968). Receptive fields and functional architecture of monkey striate cortex. The Journal of Physiology, 195(1), 215–243.

Hubel, D., & Wiesel, T. (1970). The period of susceptibility to the physiological effects of unilateral eye closure in kittens. The Journal of Physiology, 206(2), 419–436.

Review Papers

Hubel, D. (1982). Exploration of the primary visual cortex, 1955–78. Nature, 299(5883), 515–524.

Hubel, D., & Wiesel, T. (1998). Early exploration of the visual cortex. Neuron, 20(3), 401–412.

Wiesel, T. (1982). The postnatal development of the visual cortex and the influence of environment. Nature, 299(5884), 583–591.

Recommended Readings: Zena Werb, Ph.D.

Friday Lecture Series

Detlev Bronk Alumni Lecture

The Cellular Neighborhood: A Master Regulator from Development to Cancer

Zena Werb, Ph.D., professor and vice-chair, department of anatomy, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco

March 14, 2014

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Chou, J., Lin, J. H., Brenot, A., Kim, J. -., Provot, S., & Werb, Z. (2013). GATA3 suppresses metastasis and modulates the tumour microenvironment by regulating microRNA-29b expression. Nature Cell Biology, 15(2), 201-213

Chou, J., Shahi, P., & Werb, Z. (2013). MicroRNA-mediated regulation of the tumor microenvironment. Cell Cycle, 12(20), 3262-3271

Coussens, L. M., & Werb, Z. (2002). Inflammation and cancer. Nature, 420(6917), 860-867

Egeblad, M., Nakasone, E. S., & Werb, Z. (2010). Tumors as organs: Complex tissues that interface with the entire organism. Developmental Cell, 18(6), 884-901

Engelhardt, J. J., Boldajipour, B., Beemiller, P., Pandurangi, P., Sorensen, C., Werb, Z., . . . Krummel, M. F. (2012). Marginating dendritic cells of the tumor microenvironment cross-present tumor antigens and stably engage tumor-specific T cells. Cancer Cell, 21(3), 402-417

Heissig, B., Lund, L. R., Akiyama, H., Ohki, M., Morita, Y., Rømer, J., . . . Hattori, K. (2007). The plasminogen fibrinolytic pathway is required for hematopoietic regeneration. Cell Stem Cell, 1(6), 658-670

Ohki, M., Ohki, Y., Ishihara, M., Nishida, C., Tashiro, Y., Akiyama, H., . . . Hattori, K. (2010). Tissue type plasminogen activator regulates myeloid-cell dependent neoangiogenesis during tissue regeneration. Blood, 115(21), 4302-4312


Recommended Readings: Lora Hooper, Ph.D. April 2

Wednesday, April 2, 2014
4:00 p.m., Carson Family Auditorium

Lora Hooper, Ph.D.
University of Texas Southwestern Medical Center
Investigator, HHMI

Circadian Regulation of Intestinal Immunity

Recommended Readings:

Empirical Articles

Bäckhed, F., Ding, H., Wang, T., Hooper, L. V, Koh, G. Y., Nagy, A., … Gordon, J. I. (2004). The gut microbiota as an environmental factor that regulates fat storage. Proceedings of the National Academy of Sciences, 101(44), 15718–15723. doi:10.1073/pnas.0407076101

Cash, H. L., Whitham, C. V, Behrendt, C. L., & Hooper, L. V. (2006). Symbiotic bacteria direct expression of an intestinal bactericidal lectin. Science, 313(5790), 1126–1130. doi:10.1126/science.1127119

Scheer, F. a J. L., Hilton, M. F., Mantzoros, C. S., & Shea, S. A. (2009). Adverse metabolic and cardiovascular consequences of circadian misalignment. Proceedings of the National Academy of Sciences, 106(11), 4453–4458. doi:10.1073/pnas.0808180106

Yu, X., Rollins, D., Ruhn, K. a, Stubblefield, J. J., Green, C. B., Kashiwada, M., … Hooper, L. V. (2013). TH17 cell differentiation is regulated by the circadian clock. Science, 342(6159), 727–730. doi:10.1126/science.1243884

Review Papers

Arjona, A., Silver, A. C., Walker, W. E., & Fikrig, E. (2012). Immunity’s fourth dimension: approaching the circadian-immune connection. Trends in Immunology, 33(12), 607–612. doi:10.1016/

Hooper, L. V, & Macpherson, A. J. (2010). Immune adaptations that maintain homeostasis with the intestinal microbiota. Nature Reviews Immunology, 10(3), 159–169. doi:10.1038/nri2710

Korn, T., Bettelli, E., Oukka, M., & Kuchroo, V. K. (2009). IL-17 and Th17 cells. Annual Review of Immunology, 27, 485–517. doi:10.1146/annurev.immunol.021908.132710