Recommended Readings: Erich Jarvis, Ph.D., September 28th

Special Lecture
Monday, September 28th, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Erich Jarvis, Ph.D.
Associate Professor,
Department of Neurobiology,
Duke University Medical Center
Investigator, Howard Hughes Medical Institute

Dissecting the Molecular Mechanisms of Vocal Learning and Spoken Language

Recommended Readings

Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., … & Samaniego, J. A. (2014). Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215), 1320-1331. doi:10.1126/science.1253451.

Jarvis, E. D., Mirarab, S., Aberer, A. J., Li, B., Houde, P., Li, C., … & Avian Phylogenomics Consortium. (2015). Phylogenomic analyses data of the avian phylogenomics project. GigaScience, 4(1), 1-9. doi:10.1186/s13742-014-0038-1.

Pfenning, A. R., Hara, E., Whitney, O., Rivas, M. V., Wang, R., Roulhac, P. L., … & Jarvis, E. D. (2014). Convergent transcriptional specializations in the brains of humans and song-learning birds. Science, 346(6215), 1256846. doi:10.1126/science.1256846.

Whitney, O., Pfenning, A. R., Howard, J. T., Blatti, C. A., Liu, F., Ward, J. M., … & Jarvis, E. D. (2014). Core and region-enriched networks of behaviorally regulated genes and the singing genome. Science, 346(6215), 1256780. doi: 10.1126/science.1256780.

Zhang, G., Li, C., Li, Q., Li, B., Larkin, D. M., Lee, C., … & Ganapathy, G. (2014). Comparative genomics reveals insights into avian genome evolution and adaptation. Science, 346(6215), 1311-1320. doi:10.1126/science.1251385.

Recommended Readings: Marc Kirschner, Ph.D., May 8th

Friday Lecture Series
Friday, May 8, 2015
3:45 p.m., Caspary Auditorium

Marc W. Kirschner, Ph.D.
John Franklin Enders University Professor,
Professor and Chair,
Department of Systems Biology,
Harvard Medical School

The Origin of Specificity in Regulated Protein Degradation

Recommended Readings

Empirical Articles

Gujral, T. S., Chan, M., Peshkin, L., Sorger, P. K., Kirschner, M. W., & MacBeath, G. (2014). A noncanonical frizzled2 pathway regulates epithelial-mesenchymal transition and metastasis. Cell, 159(4), 844-856. doi: 10.1016/j.cell.2014.10.032.

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.

Zhao, R., Deibler, R. W., Lerou, P. H., Ballabeni, A., Heffner, G. C., Cahan, P., … & Daley, G. Q. (2014). A nontranscriptional role for Oct4 in the regulation of mitotic entry. Proceedings of the National Academy of Sciences, 111(44), 15768-15773. doi: 10.1073/pnas.1417518111

Review Papers

Kirschner, M. W. (2005). The meaning of systems biology. Cell, 121(4), 503-504.

Recommended Readings: Joan Strassmann, Ph.D. & David Queller, Ph.D., January 30

Friday Lecture Series
Friday, January 30, 2015
3:45 p.m., Caspary Auditorium

Joan E. Strassmann, Ph.D.
Charles Rebstock Professor of Biology,
Washington University in St. Louis
David C. Queller, Ph.D.
Spencer T. Olin Professor,
Washington University in St. Louis

Altruism, Cheating, and Mutualism in Social Amoebas: Evolution and Mechanisms

Recommended Readings

Brock, D. a, Read, S., Bozhchenko, A., Queller, D. C., & Strassmann, J. E. (2013). Social amoeba farmers carry defensive symbionts to protect and privatize their crops. Nature Communications, 4, 2385. doi:10.1038/ncomms3385

Kuzdzal-Fick, J., Fox, S., Strassmann, J., & Queller, D. (2011). High relatedness is necessary and sufficient to maintain multicellularity in Dictyostelium. Science, 334(6062), 1548–1552. doi:10.3334/ORNLDAAC/797

Stallforth, P., Brock, D. a, Cantley, A. M., Tian, X., Queller, D. C., Strassmann, J. E., & Clardy, J. (2013). A bacterial symbiont is converted from an inedible producer of beneficial molecules into food by a single mutation in the gacA gene. Proceedings of the National Academy of Sciences, 110(36), 14528–14533. doi:10.1073/pnas.1308199110

Strassmann, J. E., & Queller, D. C. (2011). Evolution of cooperation and control of cheating in a social microbe. Proceedings of the National Academy of Sciences, 108 Suppl, 10855–10862. doi:10.1073/pnas.1102451108

Recommended Readings: Thomas Südhof, M.D. December 5

Friday Lecture Series
Friday, December 5, 2014
3:45 p.m., Caspary Auditorium

Thomas Südhof, M.D.
Avram Goldstein Professor,
Department of Molecular and Cellular Physiology,
Stanford School of Medicine
Howard Hughes Medical Institute

Cracking the Neurexin Code – Towards a Molecular Logic of Neural Circuits

Recommended Readings

Empirical Articles

Gokce, O., & Südhof, T. C. (2013). Membrane-tethered monomeric neurexin LNS-domain triggers synapse formation. The Journal of Neuroscience, 33(36), 14617–14628. doi:10.1523/JNEUROSCI.1232-13.2013

Rothwell, P. E., Fuccillo, M. V, Maxeiner, S., Hayton, S. J., Gokce, O., Lim, B. K., … Südhof, T. C. (2014). Autism-associated neuroligin-3 mutations commonly impair striatal circuits to boost repetitive behaviors. Cell, 158(1), 198–212. doi:10.1016/j.cell.2014.04.045

Treutlein, B., Gokce, O., Quake, S. R., & Südhof, T. C. (2014). Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing. Proceedings of the National Academy of Sciences, 111(13), E1291–E1299. doi:10.1073/pnas.1403244111

Tsetsenis, T., Boucard, a. a., Arac, D., Brunger, a. T., & Sudhof, T. C. (2014). Direct visualization of trans-synaptic neurexin-neuroligin interactions during synapse formation. Journal of Neuroscience, 34(45), 15083–15096. doi:10.1523/JNEUROSCI.0348-14.2014

Review Articles

Südhof, T. C. (2008). Neuroligins and neurexins link synaptic function to cognitive disease. Nature, 455(7215), 903–911. doi:10.1038/nature07456

Südhof, T. C. (2014). The molecular machinery of neurotransmitter release (Nobel Lecture). Angewandte Chemie, 53(47), 12696–12717. doi:10.1002/anie.201406359

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: 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

Elsevier Offers Free Access to 2012 Nobel Laureates Most Cited Papers

Elsevier congratulates the 2012 Nobel Laureates and is proud to honor their revolutionary research in the fields of Medicine, Physics, Chemistry and Economics.  All eight Nobel scientists have connections with Elsevier, publishing journal articles and book chapters and serving as journal editors or members of editorial boards.  In recognition of these extraordinary scholars and their contributions to science, we are pleased to provide free access on ScienceDirect to their most-cited ground-breaking research published in Elsevier journals.

Dr. John Gurdon and Dr. Shinya Yamanaka share the award in physiology or medicine for discovering that mature, specialized cells can be reprogrammed into immature cells capable of developing into all tissues of the body. Their key individual research findings into so-called stem cells were separated by 50 years.


Recommended Readings: Laurie Glimcher, M.D.

Friday Lecture Series

Close to the Bone: Novel Genes that Remodel the Skeleton

Laurie Glimcher, M.D., Stephen and Suzanne Weiss Dean,

Weill Cornell Medical College

 November 9, 2012

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

Caspary Auditorium

Recommended Readings

Greenblatt, M. B., Shim, J. -., Zou, W., Sitara, D., Schweitzer, M., Hu, D., . . . Glimcher, L. H. (2010). The p38 MAPK pathway is essential for skeletogenesis and bone homeostasis in mice. Journal of Clinical Investigation, 120(7), 2457-2473

Jones, D., Glimcher, L. H., & Aliprantis, A. O. (2011). Osteoimmunology at the nexus of arthritis, osteoporosis, cancer, and infection. Journal of Clinical Investigation, 121(7), 2534-2542

Jones, D. C., Wein, M. N., Oukka, M., Hofstaetter, J. G., Glimcher, M. J., & Glimcher, L. H. (2006). Regulation of adult bone mass by the zinc finger adapter protein schnurri-3. Science, 312(5777), 1223-1227

Wein, M. N., Jones, D. C., Shim, J. -., Aliprantis, A. O., Sulyanto, R., Lazarevic, V., . . . Glimcher, L. H. (2012). Control of bone resorption in mice by schnurri-3. Proceedings of the National Academy of Sciences of the United States of America, 109(21), 8173-8178


Recommended Readings: Olaf Schneewind, M.D., Ph.D.

Friday Lecture Series

Ernst A.H. Friedheim Memorial Lecture

Envelope Assembly and Function in Bacterial Pathogens

Olaf Schneewind, M.D., Ph.D.,

Louis Block Professor and chair, department of microbiology,

University of Chicago

November 11,  2011

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

Caspary Auditorium

Recommended Readings:

Cheng, A. G., M. McAdow, H. K. Kim, T. Bae, D. M. Missiakas, and O. Schneewind. 2010. Contribution of coagulases towards staphylococcus aureus disease and protective immunity. PLoS Pathogens 6, (8): 19-20

Hendrickx, A. P. A., J. M. Budzik, S. -Y Oh, and O. Schneewind. 2011. Architects at the bacterial surface-sortases and the assembly of pili with isopeptide bonds. Nature Reviews Microbiology 9, (3): 166-171

Kern, J., and O. Schneewind. 2010. BslA, the S-layer adhesin of B. anthracis, is a virulence factor for anthrax pathogenesis. Molecular microbiology 75, (2): 324-332

Kim, H. K., A. G. Cheng, H. -Y Kim, D. M. Missiakas, and O. Schneewind. 2010. Nontoxigenic protein A vaccine for methicillin-resistant staphylococcus aureus infections in mice. Journal of Experimental Medicine 207, (9): 1863-1870

Kim, H. K., A. DeDent, A. G. Cheng, M. McAdow, F. Bagnoli, D. M. Missiakas, and O. Schneewind. 2010. IsdA and IsdB antibodies protect mice against staphylococcus aureus abscess formation and lethal challenge. Vaccine 28, (38): 6382-6392

Schneewind, O., and D. Missiakas. 2011. Structural vaccinology to thwart antigenic variation in microbial pathogens. Proceedings of the National Academy of Sciences of the United States of America 108, (25): 10029-10030

Thammavongsa, V., J. W. Kern, D. M. Missiakas, and O. Schneewind. 2009. Staphylococcus aureus synthesizes adenosine to escape host immune responses. Journal of Experimental Medicine 206, (11): 2417-2427

NAS Report Calls for Creation of a Biomedical Research and Patient Data Network

WASHINGTON — A new data network that integrates emerging research on the molecular makeup of diseases with clinical data on individual patients could drive the development of a more accurate classification of disease and ultimately enhance diagnosis and treatment, says a new report from the National Research Council.  The “new taxonomy” that emerges would define diseases by their underlying molecular causes and other factors in addition to their traditional physical signs and symptoms.  The report adds that the new data network could also improve biomedical research by enabling scientists to access patients’ information during treatment while still protecting their rights.  This would allow the marriage of molecular research and clinical data at the point of care, as opposed to research information continuing to reside primarily in academia.