Recommended Readings: Neil H. Shubin, Ph.D. November 5

Special Seminar Series
Wednesday, November 5, 2014,
4:00 p.m., Carson Family Auditorium (CRC)

Neil H. Shubin, Ph.D.
Robert R. Bensley Distinguished Service Professor,
Senior Advisor to the President,
Department of Organismal Biology and Anatomy,
The University of Chicago

Organogenesis in Deep Time

Recommended Readings

Empirical Papers

Amemiya, C. T., Alföldi, J., Lee, A. P., Fan, S., Philippe, H., Maccallum, I., … Lindblad-Toh, K. (2013). The African coelacanth genome provides insights into tetrapod evolution. Nature, 496(7445), 311–316. doi:10.1038/nature12027

Dahn, R. D., Davis, M. C., Pappano, W. N., & Shubin, N. H. (2007). Sonic hedgehog function in chondrichthyan fins and the evolution of appendage patterning. Nature, 445(7125), 311–314. doi:10.1038/nature05436

Davis, M. C., Dahn, R. D., & Shubin, N. H. (2007). An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish. Nature, 447(7143), 473–476. doi:10.1038/nature05838

Shubin, N. H., Daeschler, E. B., & Jenkins, F. a. (2006). The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb. Nature, 440(7085), 764–771. doi:10.1038/nature04637

Review Articles

Schneider, I., & Shubin, N. H. (2013). The origin of the tetrapod limb: from expeditions to enhancers. Trends in Genetics, 29(7), 419–426. doi:10.1016/j.tig.2013.01.012

Shubin, N., Tabin, C., & Carroll, S. (2009). Deep homology and the origins of evolutionary novelty. Nature, 457(7231), 818–823. doi:10.1038/nature07891

Recommended Readings: Adrienne Fairhall, Ph.D. October 22

Special Seminar Series
Wednesday, October 22, 2014
4 p.m., Carson Family Auditorium

Adrienne Fairhall, Ph.D.
Associate Professor,
Department of Physiology and Biophysics,
University of Washington

Variability and Learning in Birdsong

Recommended Readings

Empirical Articles

Mease, R. A, Famulare, M., Gjorgjieva, J., Moody, W. J., & Fairhall, A. L. (2013). Emergence of adaptive computation by single neurons in the developing cortex. The Journal of Neuroscience, 33(30), 12154–12170. doi:10.1523/JNEUROSCI.3263-12.2013

Schnell, B., Weir, P. T., Roth, E., Fairhall, A. L., & Dickinson, M. H. (2014). Cellular mechanisms for integral feedback in visually guided behavior. Proceedings of the National Academy of Sciences, 111(15), 5700–5. doi:10.1073/pnas.1400698111

Review Papers

Fairhall, A. (2014). The receptive field is dead. Long live the receptive field? Current Opinion in Neurobiology, 25, ix–xii. doi:10.1016/j.conb.2014.02.001

Fairhall, A., Shea-Brown, E., & Barreiro, A. (2012). Information theoretic approaches to understanding circuit function. Current Opinion in Neurobiology, 22(4), 653–9. doi:10.1016/j.conb.2012.06.005

Recommended Readings: James Rothman, Ph.D. November 7

Friday Lecture Series
Friday, November 7, 2014
3:45 p.m., Caspary Auditorium

James Rothman, Ph.D.
Fergus F. Wallace Professor Biomedical Sciences and Chemistry,
Professor and Chair,
Department of Cell Biology,
Professor of Chemistry,
Yale School of Medicine

The Regulation of Neurotransmitter Release

Recommended Readings

Empirical Articles

McNew, J. A., Parlati, F., Fukuda, R., Johnston, R. J., Paz, K., Paumet, F., … Rothman, J. E. (2000). Compartmental specificity of cellular membrane fusion encoded in SNARE proteins. Nature, 407(6801), 153–159. doi:10.1038/35025000

Söllner, T., Whiteheart, S. W., Brunner, M., Erdjument-Bromage, H., Geromanos, S., Tempst, P., & Rothman, J. E. (1993). SNAP receptors implicated in vesicle targeting and fusion. Nature, 362(6418), 318–324. doi:10.1038/362318a0

Weber, T., Zemelman, B. V, McNew, J. a, Westermann, B., Gmachl, M., Parlati, F., … Rothman, J. E. (1998). SNAREpins: Minimal Machinery for Membrane Fusion. Cell, 92(6), 759–772. doi:10.1016/S0092-8674(00)81404-X

Wilson, D. W., Wilcox, C. A., Flynn, G. C., Chen, E., Kuang, W. J., Henzel, W. J., … Rothman, J. E. (1989). A fusion protein required for vesicle-mediated transport in both mammalian cells and yeast. Nature, 339(6223), 355–359. doi:10.1038/339355a0

Review Papers

Rothman, J. E. (2014). The principle of membrane fusion in the cell (Nobel lecture). Angewandte Chemie, 2–21. doi:10.1002/anie.201402380

Südhof, T. C., & Rothman, J. E. (2009). Membrane fusion: grappling with SNARE and SM proteins. Science, 323(5913), 474–477. doi:10.1126/science.1161748

Recommended Readings: Elaine Fuchs, Ph.D. November 3

Monday Lecture Series
Monday, November 3, 2014
4:00 p.m., Carson Family Auditorium

Elaine Fuchs, Ph.D.
Rebecca C. Lancefield Professor and Head,
Laboratory of Mammalian Cell Biology and Development,
The Rockefeller University
Howard Hughes Medical Institute

Stem Cells in Silence, Action and Cancer

Recommended Readings

Empirical Articles

Blanpain, C., Lowry, W., & Geoghegan, A. (2004). Self-renewal, multipotency, and the existence of two cell populations within an epithelial stem cell niche. Cell, 118(5), 635–648. doi:10.1016/j.cell.2004.08.012

Lechler, T., & Fuchs, E. (2005). Asymmetric cell divisions promote stratification and differentiation of mammalian skin. Nature, 437(7056), 275–280. doi:10.1038/nature03922

Yi, R., Poy, M. N., Stoffel, M., & Fuchs, E. (2008). A skin microRNA promotes differentiation by repressing “stemness”. Nature, 452(7184), 225–9. doi:10.1038/nature06642

Review Papers

Fuchs, E., Tumbar, T., & Guasch, G. (2004). Socializing with the neighbors: stem cells and their niche. Cell, 116(6), 769–778. doi:10.1016/S0092-8674(04)00255-7

Hsu, Y.-C., Li, L., & Fuchs, E. (2014). Emerging interactions between skin stem cells and their niches. Nature Medicine, 20(8), 847–856. doi:10.1038/nm.3643

Was the Cerebellum the Center of Evolutionary Change That Makes Us Human?

When we search for the seat of humanity, are we looking at the wrong part of the brain? Most neuroscientists assume that the neocortex, the brain’s distinctive folded outer layer, is the thing that makes us uniquely human. But a new study suggests that another part of the brain, the cerebellum, grew much faster in our ape ancestors.

Read more on this new research in Current Biology.


Nobel Prizes 2014 – Announcement Date Monday Oct 6

The Nobel Prizes: What you should know ahead of time

By: Ben P. Stein, Director, Inside Science

It’s actually quite remarkable how well the Nobel committees keep the prizes and recipients secret until the announcements. (Update: In the earlier version of this blog, I wrote we were unaware of any leaks of prize information prior to the official announcements. But I have now found that Time had reported one for the 2013 Nobel Peace Prize shortly before it was announced. And bookmakers reported an abrupt increase in the odds for poet Tomas Tranströmer to win shortly before he was named the recipient of the 2011 Nobel Prize in Literature, according to Sweden’s The Local newspaper; Swedish authorities investigated the matter and eventually came to no conclusions, according to the Wall Street Journal. Nonetheless, the Nobel committees’ overall track record seems excellent for keeping the prize information under wraps.)

The Nobel committees contact the often bleary-eyed recipients in the very early morning before announcing the prizes. Last year’s physics announcement was delayed because of the committee’s difficulty in reaching recipient Peter Higgs. He was traveling and doesn’t own a cellphone. For the 2012 Nobel Prize in physiology or medicine, one of the recipients, Ralph Steinman, died the Friday before the prize was announced, unbeknownst to the Nobel committee. Nobel Prizes can only be given to living individuals, based on the conditions set forth by the Nobel Foundation. But in my opinion, the Nobel committee did the right thing in 2011 and kept Steinman as the recipient even though he was deceased.

Read more at the Inside Science blog.



Recommended Readings: Amédée des Georges, Ph.D. October 20

Special Lecture Series
Monday, October 20, 2014
4:00 p.m., Carson Family Auditorium

Amédée des Georges, Ph.D.
Postdoctoral Associate,
Department of Biochemistry and Molecular Biophysics,
Columbia University

Structures of Eukaryotic Translation Initiation Complexes by Single-Particle Cryo-EM, a Powerful Tool for the Study of Heterogeneous Samples

Recommended Readings

Empirical Articles

Hashem, Y., des Georges, A., Dhote, V., Langlois, R., Liao, H. Y., Grassucci, R. a, … Frank, J. (2013). Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit. Nature, 503(7477), 539–543. doi:10.1038/nature12658

Hashem, Y., des Georges, A., Dhote, V., Langlois, R., Liao, H. Y., Grassucci, R. a, … Frank, J. (2013). Structure of the mammalian ribosomal 43S preinitiation complex bound to the scanning factor DHX29. Cell, 153(5), 1108–1119. doi:10.1016/j.cell.2013.04.036

Hashem, Y., des Georges, A., Fu, J., Buss, S. N., Jossinet, F., Jobe, A., … Frank, J. (2013). High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature, 494(7437), 385–389. doi:10.1038/nature11872

Review Papers

Jackson, R. J., Hellen, C. U. T., & Pestova, T. V. (2010). The mechanism of eukaryotic translation initiation and principles of its regulation. Nature Reviews Molecular Cell Biology, 11(2), 113–127. doi:10.1038/nrm2838

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
Whitehead Institute for Biomedical Research
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
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