Monthly Archives: October 2011

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

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Monday Lecture Series

JAK-STAT at 20: Where The Pathway Came From and Some Things I Still Hope to See Happen

James E. Darnell Jr., M.D., Vincent Astor Professor Emeritus and head,

Laboratory of Molecular Cell Biology,

The Rockefeller University

October 31,  2011

4:00 p.m.-5:00 p.m. (Refreshments, 3:45 p.m.-4:00 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings:

Bromberg, J., and J. E. Darnell Jr. 2000. The role of STATs in transcriptional control and their impact on cellular function. Oncogene 19, (21): 2468-2473

Bromberg, J. F., M. H. Wrzeszczynska, G. Devgan, Y. Zhao, R. G. Pestell, C. Albanese, and J. E. Darnell Jr. 1999. Stat3 as an oncogene. Cell 98, (3): 295-303

Darnell Jr., J. E. 2005. Validating Stat3 in cancer therapy. Nature medicine 11, (6): 595-596

Levy, D. E., and J. E. Darnell Jr. 2002. STATs: Transcriptional control and biological impact. Nature Reviews Molecular Cell Biology 3, (9): 651-662

Mertens, C., and J. E. Darnell Jr. 2007. SnapShot: JAK-STAT signaling. Cell 131, (3): 612.e1-612.e2

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Recommended Readings: Rob Knight, Ph.D.

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Friday Lecture Series

Tools for Understanding the Human Microbiome

Rob Knight, Ph.D., early career scientist, Howard Hughes Medical Institute;

associate professor, department of chemistry and biochemistry,

University of Colorado, Boulder

October 28,  2011

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

Caspary Auditorium

Recommended Readings:

Costello, E. K., C. L. Lauber, M. Hamady, N. Fierer, J. I. Gordon, and R. Knight. 2009. Bacterial community variation in human body habitats across space and time. Science 326, (5960): 1694-1697

Dominguez-Bello, M. G., E. K. Costello, M. Contreras, M. Magris, G. Hidalgo, N. Fierer, and R. Knight. 2010. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences of the United States of America 107, (26): 11971-11975

Kuczynski, J., Z. Liu, C. Lozupone, D. McDonald, N. Fierer, and R. Knight. 2010. Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nature Methods 7, (10): 813-819

Turnbaugh, P. J., C. Quince, J. J. Faith, A. C. McHardy, T. Yatsunenko, F. Niazi, J. Affourtit, et al. 2010. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proceedings of the National Academy of Sciences of the United States of America 107, (16): 7503-7508

Turnbaugh, P. J., V. K. Ridaura, J. J. Faith, F. E. Rey, R. Knight, and J. I. Gordon. 2009. The effect of diet on the human gut microbiome: A metagenomic analysis in humanized gnotobiotic mice. Science translational medicine 1, (6)

Vijay-Kumar, M., J. D. Aitken, F. A. Carvalho, T. C. Cullender, S. Mwangi, S. Srinivasan, S. V. Sitaraman, R. Knight, R. E. Ley, and A. T. Gewirtz. 2010. Metabolie syndrome and altered gut microbiota in mice lacking toll-like receptor 5. Science 328, (5975): 228-231

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Recommended Readings: Sanford M. Simon, Ph.D.

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Monday Lecture Series

The Nuclear Pore: The Search for the Holey Grail

Sanford M. Simon, Ph.D.,

professor and head, Laboratory of Cellular Biophysics,

The Rockefeller University

October 24,  2011

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

Caspary Auditorium

Recommended Readings:

Jouvenet, N., P. D. Bieniasz, and S. M. Simon. 2008. Imaging the biogenesis of individual HIV-1 virions in live cells. Nature 454, (7201): 236-240

Jouvenet, N., M. Zhadina, P. D. Bieniasz, and S. M. Simon. 2011. Dynamics of ESCRT protein recruitment during retroviral assembly. Nature cell biology 13, (4): 394-402

Kampmann, M., C. E. Atkinson, A. L. Mattheyses, and S. M. Simon. 2011. Mapping the orientation of nuclear pore proteins in living cells with polarized fluorescence microscopy. Nature Structural and Molecular Biology 18, (6): 643-649

Mattheyses, A. L., M. Kampmann, C. E. Atkinson, and S. M. Simon. 2010. Fluorescence anisotropy reveals order and disorder of protein domains in the nuclear pore complex. Biophysical journal 99, (6): 1706-1717

Mincer, J. S., and S. M. Simon. 2011. Simulations of nuclear pore transport yield mechanistic insights and quantitative predictions. Proceedings of the National Academy of Sciences of the United States of America 108, (31): E351-E358

Simon, S. M. 2009. Partial internal reflections on total internal reflection fluorescent microscopy. Trends in cell biology 19, (11): 661-668

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1000 Genomes Project Releases Integrated Phase 1 Data Set

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Analyses of data for nearly 1,100 individuals assessed through phase 1 of the 1000 Genomes Project have uncovered more than 40 million genetic variants in the human genome, including almost 30 million SNPs not detected previously.

At the International Congress of Human Genetics here this week, University of Oxford researcher and 1000 Genomes Project Consortium representative Gil McVean described findings from integrated analyses of the SNPs, small insertions and deletions, and large deletions identified through low coverage genome data and deeper coverage exome sequence information for 1,092 individuals.

Data from this integrated analysis of 1000 Genomes Project data, variant discovery, variant integration, and haplotype integration were released this week.

Overall, the researchers identified some 37.9 million SNPs in the dataset, including 29.7 million new SNPs. In addition, the team tracked down 3.8 million short indels and 14,000 large deletions. McVean noted that this set represents highly conservative indels and deletions taken through integrated analyses.

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NCI Awards $9.6M for Research into Therapy-Resistant Prostate Cancer

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The National Cancer Institute has awarded a five-year, $9.6 million grant to a multidisciplinary team of researchers who will study the molecular underpinnings of prostate cancers that progress to a therapy-resistant state.

The funding is for three projects. One will be directed at determining how hypoxic signals affect gene expression. Another will create new transgenic mouse models to better understand how kinases cooperate “to drive tumorigenesis.” The third project will focus on how microRNAs regulate cell proliferation and prostate cancer progression.

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Understanding The Relationship Between Inflammation and Cancer

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The relationship between cancer and inflammation—the immune system’s response to infection, irritation, or injury—is a bit like that between the chicken and the egg. The two seem to occur together, but scientists aren’t really sure which comes first or whether one causes the other.  

A recent discovery by a team of researchers in the tumor biology section at the NIDCD, and scientists at SUNY Buffalo and the U.S. Food and Drug Administration (FDA) in Bethesda, Md., could help shine a welcome light on this quandary. The finding is the first to show that inflammatory factors produced during the development of head and neck tumors play an active role in coordinating a series of cellular events that allow cancer cells to grow and multiply unimpeded. Their findings are published in the September 20 early online edition of Cancer Research.

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Latest Complete Genome: The Naked Mole Rat

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Biologists have a tool for unraveling the odd collection of traits — including apparent complete resistance to cancer – in this odd rodent from South Africa.    They find may clues that will prove useful to human medicine.   A team of 36 scientists working on three continents published the genome this week, the latest and perhaps most exotic organism to have its entire DNA sequence transcribed.

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Recommended Readings: Michael P Rout PhD Monday Oct 17, 2011

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Monday Lecture Series

The Architecture and Transport Mechanism of the Nuclear Pore Complex

Michael P. Rout  Ph.D. 

Laboratory of Cellular and Structural Biology

The Rockefeller University

October 17,  2011

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

Caspary Auditorium

 

Recommended Readings:

Sampathkumar P; Gheyi T; Miller SA; et al.  2011.  Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex.   Proteins-Structure Function and Bioinformatics,  79(5):1672-1677.      Request from Markus Library .

Cohem S; Au S; Pante, N.  2011.  How viruses access the nucleus.  Biochimica et Biophysica Acta – Molecular Cell Research,  1813(9; Spcl Iss. 1):1634-1645.

Hoelz, A; Debler EW; Blobel G. 2011.  The Structure of the nuclear pore complex.   Annual Review of Biochemistry,   80:613-643.

Strambio-de-Castillia C; Niepel M; Rout MP.  2010.  The nuclear pore complex: bridging nuclear transport and gene regulation.   Nature Reviews Molecular Biology,  11(7):490-501.

Wente SR; Rout MP.  2010.  The nuclear pore comlex and nuclear transport.   Cold Spring Harbor Perspectives in Biology,  2(10):a000562

Cook, A; Bono F; Jinek M; et al.   2007.  Structural biology of nucleocytoplasmic transport.   Annual Review of Biochemistry, 76:647-671.

D’Angelo MA; Hetzer MW.   2008.  Structure, dynamics and function of nuclear pore complexes.  Trends in Cell Biology, 18(10):456-466.

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New Drug Target for Alzheimer’s, Stroke Discovered

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A tiny piece of a critical receptor that fuels the brain and without which sentient beings cannot live has been discovered by University at Buffalo scientists as a promising new drug target for Alzheimer’s and other neurodegenerative diseases.

The research on the NMDA (N-methyl-D-aspartate) receptor was being published online  in Nature Communications.

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Stem Cells, Signaling Pathways Identified in Lung Repair

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Researchers at National Jewish Health have identified cells and signaling molecules that trigger the repair of injured lungs. Stijn De Langhe, PhD, and his colleagues report October 10, 2011, online in the Journal of Clinical Investigation, that destruction of lung tissue in mice induces smooth muscle cells surrounding the airways to secrete a protein known as fibroblast growth factor 10 (FGF10), which induces surviving epithelial cells in the airways to revert to a stem-cell state, proliferate, repair and repopulate the lining of the lungs.

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