The Much Maligned Tick: Key to a New Class of Antibiotics?

Yale researchers have discovered a glycoprotein in ticks (Ixodidae) that kicks in during winter to protect them from the cold also fights infection.  This protein may be the key to a new class of an antibiotics to help  in the battle against dangers pathogens such as MRSA.
Read more at: http://phys.org/news/2014-10-protein-infection.html#jCp

Recommended Readings: Stephen Quake, Ph.D. November 10

Monday Lecture Series
Monday, November 10, 2014,
4:00 p.m., Carson Family Auditorium (CRC)

Shai Shaham, Ph.D.
Professor and Head,
Laboratory of Developmental Genetics,
The Rockefeller University

Glial Control of Neuronal Receptive Ending Form and Function

Recommended Readings

Empirical Papers

Bacaj, T., Tevlin, M., Lu, Y., & Shaham, S. (2008). Glia are essential for sensory organ function in C. elegans. Science, 322(5902), 744–747. doi:10.1126/science.1163074

Heiman, M. G., & Shaham, S. (2009). DEX-1 and DYF-7 establish sensory dendrite length by anchoring dendritic tips during cell migration. Cell, 137(2), 344–355. doi:10.1016/j.cell.2009.01.057

Procko, C., Lu, Y., & Shaham, S. (2011). Glia delimit shape changes of sensory neuron receptive endings in C. elegans. Development, 138(7), 1371–1381. doi:10.1242/dev.058305

Yoshimura, S., Murray, J. I., Lu, Y., Waterston, R. H., & Shaham, S. (2008). mls-2 and vab-3 Control glia development, hlh-17/Olig expression and glia-dependent neurite extension in C. elegans. Development, 135(13), 2263–2275. doi:10.1242/dev.019547

Review Papers

Oikonomou, G., & Shaham, S. (2011). The glia of Caenorhabditis elegans. Glia, 59(9), 1253–1263. doi:10.1002/glia.21084

Procko, C., & Shaham, S. (2010). Assisted morphogenesis: glial control of dendrite shapes. Current Opinion in Cell Biology, 22(5), 560–565. doi:10.1016/j.ceb.2010.07.005

Recommended Readings: Stephen Quake, Ph.D. November 12

Special Seminar Series
Wednesday, November 12, 2014,
4:00 p.m., Carson Family Auditorium (CRC)

Stephen Quake, Ph.D.
Lee Otterson Professor,
Bioengineering and Applied Physics,
Stanford University
Investigator,
Howard Hughes Medical Institute

Single Cell Genomics

Recommended Readings

Empirical Papers

Ashley, E. a, Butte, A. J., Wheeler, M. T., Chen, R., Klein, T. E., Dewey, F. E., … Altman, R. B. (2010). Clinical assessment incorporating a personal genome. Lancet, 375(9725), 1525–1535. doi:10.1016/S0140-6736(10)60452-7

Fan, H. C., Gu, W., Wang, J., Blumenfeld, Y. J., El-Sayed, Y. Y., & Quake, S. R. (2012). Non-invasive prenatal measurement of the fetal genome. Nature, 487(7407), 320–324. doi:10.1038/nature11251

Pushkarev, D., Neff, N. F., & Quake, S. R. (2009). Single-molecule sequencing of an individual human genome. Nature Biotechnology, 27(9), 847–850. doi:10.1038/nbt.1561

Wang, J., Fan, H. C., Behr, B., & Quake, S. R. (2012). Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell, 150(2), 402–412. doi:10.1016/j.cell.2012.06.030

Review Papers

Kalisky, T., Blainey, P., & Quake, S. R. (2011). Genomic analysis at the single-cell level. Annual Review of Genetics, 45, 431–445. doi:10.1146/annurev-genet-102209-163607

Melin, J., & Quake, S. R. (2007). Microfluidic large-scale integration: the evolution of design rules for biological automation. Annual Review of Biophysics and Biomolecular Structure, 36, 213–231. doi:10.1146/annurev.biophys.36.040306.132646

NIH: without budget cuts, we’d have Ebola vaccine

By Fiona Barry, 22-Oct-2014

The head of the US National Institutes of Health has said the organisation would have developed a finished Ebola vaccine by now if its funding had not been slashed over the last decade.

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
Investigator,
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.