Author Archives: layne

Recommended Readings: Arun Mehra, Ph.D.; September 9, 2009

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Monday Lecture Series

Temperature Compensation in Fungal and Bacterial Oscillators

Arun Mehra, Ph.D.

Postdoctoral Fellow, Department of Genetics,

Dartmouth Medical School

Wednesday, September 9, 2009

4:00 p.m.-5:00 p.m.

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

Second Floor, Welch Hall

Recommended Articles:

Dunlap, J. C., J. J. Loros, H. V. Colot, A. Mehra, W. J. Belden, M. Shi, C. I. Hong, et al. 2007. A circadian clock in Neurospora: How genes and proteins cooperate to produce a sustained, entrainable, and compensated biological oscillator with a period of about a day. Cold Spring Harbor symposia on quantitative biology. 72:57-68.

Gooch, V. D., A. Mehra, L. F. Larrondo, J. Fox, M. Touroutoutoudis, J. J. Loros, and J. C. Dunlap. 2008. Fully codon-optimized luciferase uncovers novel temperature characteristics of the Neurospora clock. Eukaryotic Cell. 7(1):28-37.

Loros, J. J., J. C. Dunlap, L. F. Larrondo, M. Shi, W. J. Belden, V. D. Gooch, C. H. Chen, et al. 2007. Circadian output, input, and intracellular oscillators: Insights into the circadian systems of single cells. Cold Spring Harbor symposia on quantitative biology. 72:201-214. Contact Markus Library by sending article request to librequest@rockefeller.edu or fax request to ext. 7840.

Mehra, A., C. I. Hong, M. Shi, J. J. Loros, J. C. Dunlap, and P. Ruoff. 2006. Circadian rhythmicity by autocatalysis. PLoS Computational Biology. 2(7):0816-0823.

Mehra, A., Hong, C.I., Shi, M., Loros, J.J., Dunlap, J.C., Ruoff, P. 2006. Circadian rhythmicity by autocatalysis. PLoS computational biology. 2(7).

Mehra, A., M. Shi, C. L. Baker, H. V. Colot, J. J. Loros, and J. C. Dunlap. 2009. A role for casein kinase 2 in the mechanism underlying circadian temperature compensation. Cell. 137(4):749-760.

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New Method Kills Rare, Aggressive Breast Cancer Stem Cells

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ScienceDaily, August 17th, 2009.  A team of Boston-area researchers has discovered a chemcial that kills mouse breast concer stem cells.  Researchers do not know whether the chemical holds therapeutic potential in humans.  The finding is significant because it demonstrates that it is possible to identify chemicals that specifically kill cancer stem cells.  The results appear in the August 13 advance issue of Cell.

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Recommended Readings: Alexander Soukas, M.D., Ph.D.; July 20, 2009

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Monday Lecture Series

Genetics of lipid storage: lessons learned from C. elegans

Alexander Soukas, M.D., Ph.D.

Instructor, Dept. of Medicine, Massachusetts General Hospital, Harvard Medical School

Monday, July 20, 2009

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

Second Floor, Welch Hall

Recommended Articles:

Soukas, A. A., E. A. Kane, C. E. Carr, J. A. Melo, and G. Ruvkun. 2009. Rictor/TORC2 regulates fat metabolism, feeding, growth, and life span in Caenorhabditis elegans. Genes and Development. 23(4):496-511.

 

Greer, E. R., C. L. Pérez, M. R. Van Gilst, B. H. Lee, and K. Ashrafi. 2008. Neural and molecular dissection of a C. elegans sensory circuit that regulates fat and feeding. Cell Metabolism. 8(2):118-131.

 

Srinivasan, S., L. Sadegh, I. C. Elle, A. G. L. Christensen, N. J. Faergeman, and K. Ashrafi. 2008. Serotonin regulates C. elegans fat and feeding through independent molecular mechanisms. Cell Metabolism. 7(6): 533-544.

 

Wang, M. C., E. J. O’Rourke, and G. Ruvkun. 2008. Fat metabolism links germline stem cells and longevity in C. elegans. Science. 322(5903):957-960.

 

Xie, T. 2008. Physiology: Burn fat, live longer. Science. 322(5903):865-866.

 

Zhang, J., C. Yang, C. Brey, M. Rodriguez, Y. Oksov, R. Gaugler, E. Dickstein, C. -H Huang, and S. Hashmi. 2009. Mutation in Caenorhabditis elegans krüppel-like factor, KLF-3 results in fat accumulation and alters fatty acid composition. Experimental Cell Research (article in Press).

 

 

 

 

 

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Recommended Readings; Kevin Eggan, Ph.D., Wednesday, May 27, 2009

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Special Seminar Series

“Using Stem Cells and Reprogramming to Understand Neural Degeneration”

Kevin Eggan, Ph.D.,

Assistant professor, Department of Stem Cell and Regenerative Biology, and Principal Investigator, Harvard Stem Cell Institute, Harvard University; Assistant Investigator, Stowers Medical Institute

Wednesday, May 27, 2009

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

Second Floor, Welch Hall

Recommended Articles:

Di Giorgio, F. P., G. L. Boulting, S. Bobrowicz, and K. C. Eggan. 2008. Human embryonic stem cell-derived motor neurons are sensitive to the toxic effect of glial cells carrying an ALS-causing mutation. Cell Stem Cell. 3(6):637-648.

Di Giorgio, F. P., M. A. Carrasco, M. C. Siao, T. Maniatis, and K. Eggan. 2007. Non-cell autonomous effect of glia on motor neurons in an embryonic stem cell-based ALS model. Nature Neuroscience. 10(5):608-614.

Dimos, J. T., K. T. Rodolfa, K. K. Niakan, L. M. Weisenthal, H. Mitsumoto, W. Chung, G. F. Croft, et al. 2008. Induced pluripotent stem cells generated from patients with ALS can be differentiated into motor neurons. Science. 321(5893):1218-1221.

Eggan, K. 2008. Using stem cells and reprogramming to understand disease. Regenerative Medicine. 3(6):799-801.

Egli, D., G. Birkhoff, and K. Eggan. 2008. Mediators of reprogramming: Transcription factors and transitions through mitosis. Nature Reviews Molecular Cell Biology. 9(7):505-516.

Okarma, T., and K. Eggan. 2008. A seismic shift for stem cell research. Science. 319(5863):560-561+563.

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Recommended Readings; Gregory J. Hannon, Ph.D., Friday, May 29th

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Friday Lecture Series

Richard M. Furlaud Distinguished Lecture

“Conserved Roles of Small RNAs in Genome Defense”

Gregory J. Hannon, Ph.D., professor and chair, program in genetics and bioinformatics, Cold Spring Harbor Laboratory; investigator, Howard Hughes Medical Institute

May 29, 2009

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

Caspary Auditorium

Recommended Articles:

Malone, C. D., J. Brennecke, M. Dus, A. Stark, W. R. McCombie, R. Sachidanandam, and G. J. Hannon. 2009. Specialized piRNA pathways act in germline and somatic tissues of the drosophila ovary. Cell. 137:522–535.

 

Czech, B., C. D. Malone, R. Zhou, A. Stark, C. Schlingeheyde, M. Dus, N. Perrimon, et al. 2008. An endogenous small interfering RNA pathway in Drosophila. Nature. 453(7196):798-802.

 

Tam, O. H., A. A. Aravin, P. Stein, A. Girard, E. P. Murchison, S. Cheloufi, E. Hodges, et al. 2008. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature. 453(7194):534-538.

 

Zhou, R., I. Hotta, A. M. Denli, P. Hong, N. Perrimon, and G. J. Hannon. 2008. Comparative analysis of argonaute-dependent small RNA pathways in Drosophila. Molecular Cell. 32(4):592-599.

 

Aravin, A. A., G. J. Hannon, and J. Brennecke. 2007. The piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science. 318(5851): 761-764.

 

Brennecke, J., C. D. Malone, A. A. Aravin, R. Sachidanandam, A. Stark, and G. J. Hannon. 2008. An epigenetic role for maternally inherited piRNAs in transposon silencing. Science. 322(5906): 1387-1392.

 

Girard, A., and G. J. Hannon. 2008. Conserved themes in small-RNA-mediated transposon control. Trends in Cell Biology. 18(3)136-148.

 

Reviews

 

Kim, V. N., J. Han, and M. C. Siomi. 2009. Biogenesis of small RNAs in animals. Nature Reviews Molecular Cell Biology. 10(2):126-139.

Siomi, H., and M. C. Siomi. 2009. On the road to reading the RNA-interference code. Nature. 457(7228):396-404.

Malone, C. D., and G. J. Hannon. 2009. Small RNAs as guardians of the genome. Cell. 136(4):656-668.

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Recommended Readings: Gerald Crabtree, M.D.; June 5, 2009

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Friday Lecture Series

“Understanding the Words of Chromatin Remodeling”

Gerald Crabtree, M.D.

Stanford University

June 5, 2009

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

Caspary Auditorium

Recommended Articles:

Wu, J. I., J. Lessard, and G. R. Crabtree. 2009. Understanding the words of chromatin regulation. Cell. 136(2):200-206.

 

Lessard, J., J. I. Wu, J. A. Ranish, M. Wan, M. M. Winslow, B. T. Staahl, H. Wu, R. Aebersold, I. A. Graef, and G. R. Crabtree. 2007. An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron. 55(2):201-215.

 

Chi, T. H., M. Wan, P. P. Lee, K. Akashi, D. Metzger, P. Chambon, C. B. Wilson, and G. R. Crabtree. 2003. Sequential roles of brg, the ATPase subunit of BAF chromatin remodeling complexes, in thymocyte development. Immunity. 19(2):169-182.

 

Rando, O. J., T. H. Chi, and G. R. Crabtree. 2003. Second messenger control of chromatin remodeling. Nature structural biology. 10(2):81-83.

 

Wu, J. I., J. Lessard, I. A. Olave, Z. Qiu, A. Ghosh, I. A. Graef, and G. R. Crabtree. 2007. Regulation of dendritic development by neuron-specific chromatin remodeling complexes. Neuron. 56(1):94-108.

 

Olave, I. A., Reck-Peterson, S. L., and Crabtree, G. R. 2002. Nuclear actin and actin-related proteins in chromatin remodeling. Annual Review of Biochemistry. 71:755-781.

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Recommended Readings: Robert D. Schreiber, Ph.D.; May 15, 2009

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Friday Lecture Series

“Cancer Immunoediting: Immunologic Control and Sculpting”

Robert D. Schreiber, Ph.D., Alumni Endowed Professor of Pathology and Immunology, professor of molecular microbiology and program leader, tumor immunology, affiliate, Ludwig Institute for Cancer Research

Siteman Cancer Center, Washington University School of Medicine

May 15, 2009

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

Caspary Auditorium

Recommended Articles:

Bui, J. D., and R. D. Schreiber. 2007. Cancer immunosurveillance, immunoediting and inflammation: Independent or interdependent processes? Current opinion in immunology. 19(2):203-208.

 

Dunn, G. P., A. T. Bruce, H. Ikeda, L. J. Old, and R. D. Schreiber. 2002. Cancer immunoediting: From immunosurveillance to tumor escape. Nature immunology. 3(11):991-998.

 

Dunn, G. P., C. M. Koebel, and R. D. Schreiber. 2006. Interferons, immunity and cancer immunoediting. Nature Reviews Immunology. 6(11):836-848.

 

Dunn, G. P., L. J. Old, and R. D. Schreiber. 2004. The immunobiology of cancer immunosurveillance and immunoediting. Immunity. 21(2):137-148.

 

Dunn, G.P., L. J. Old, and R. D. Schreiber. The three Es of cancer immunoediting. 2004. Annual Review of Immunology. 22:329-360.

 
Koebel, C. M., W. Vermi, J. B. Swann, N. Zerafa, S. J. Rodig, L. J. Old, M. J. Smyth, and R. D. Schreiber. 2007. Adaptive immunity maintains occult cancer in an equilibrium state. Nature. 450(7171):903-907.

 

Smyth, M. J., Dunn, G. P., and Schreiber, R. D. Cancer immunosurveillance and immunoediting: The roles of immunity in suppressing tumor development and shaping tumor immunogenicity. 2006. Advances in Immunology. 90:1-50.

 

Swann, J. B., M. D. Vesely, A. Silva, J. Sharkey, S. Akira, R. D. Schreiber, and M. J. Smyth. 2008. Demonstration of inflammation-induced cancer and cancer immunoediting during primary tumorigenesis. Proceedings of the National Academy of Sciences of the United States of America. 105(2):652-656.

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Recommended Readings: Jennifer A. Doudna, Ph.D.; May 8, 2009

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Friday Lecture Series

“Dicer and Beyond: Regulatory RNA Processing and Function”

Jennifer A. Doudna, Ph.D., professor, departments of molecular and cell biology and of chemistry; investigator, Howard Hughes Medical Institute

University of California, Berkeley

May 8, 2009

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

Caspary Auditorium

Recommended Articles:

Aggarwal, A. K., and J. A. Doudna. 2005. Protein-nucleic acid interactions: Unlocking mysteries old and new. Current opinion in structural biology. 15(1 SPEC. ISS.):65-67.

 

Fukunaga, R., and J. A. Doudna. 2009. dsRNA with 5′ overhangs contributes to endogenous and antiviral RNA silencing pathways in plants. EMBO Journal. 28(5):545-555.

 

Jinek, M., and J. A. Doudna. 2009. A three-dimensional view of the molecular machinery of RNA interference. Nature. 457(7228):405-412.

 

Ma, E., I. J. MacRae, J. F. Kirsch, and J. A. Doudna. 2008. Autoinhibition of human dicer by its internal helicase domain. Journal of Molecular Biology. 380(1):237-243.

 

MacRae, I. J., and J. A. Doudna. 2007. Ribonuclease revisited: Structural insights into ribonuclease III family enzymes. Current opinion in structural biology. 17(1):138-145.

 

MacRae, I. J., K. Zhou, and J. A. Doudna. 2007. Structural determinants of RNA recognition and cleavage by dicer. Nature Structural and Molecular Biology. 14(10):934-940.

 

MacRae, I. J., K. Zhou, F. Li, A. Repic, A. N. Brooks, W. Z. Cande, P. D. Adams, and J. A. Doudna. 2006. Structural basis for double-stranded RNA processing by dicer. Science. 311(5758):195-198.

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Recommended Readings: Eduardo Groisman, Ph.D., April 22, 2009

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Special Seminar Series

“Differential Control of Bacterial Gene Expression”

Eduardo Groisman, Ph.D.

Professor, Department of Molecular Microbiology, Washington University School of Medicine/HHMI

Wednesday, April 22, 2009

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

Second Floor, Welch Hall

Recommended Articles:

 

Christian Perez, J., T. Latifi, and E. A. Groisman. 2008. Overcoming H-NS-mediated transcriptional silencing of horizontally acquired genes by the PhoP and SlyA proteins in Salmonella enterica. Journal of Biological Chemistry. 283(16):10773-10783.

Coppins, R. L., K. B. Hall, and E. A. Groisman. 2007. The intricate world of riboswitches. Current opinion in microbiology. 10(2):176-181.

Delgado, M. A., C. Mouslim, and E. A. Groisman. 2006. The PmrA/PmrB and RcsC/YojN/RcsB systems control expression of the Salmonella O-antigen chain length determinant. Molecular microbiology. 60(1):39-50.

Kato, A., A. Y. Mitrophanov, and E. A. Groisman. 2007. A connector of two-component regulatory systems promotes signal amplification and persistence of expression. Proceedings of the National Academy of Sciences of the United States of America. 104(29):12063-12068.

Mitrophanov, A. Y., and E. A. Groisman. 2008. Signal integration in bacterial two-component regulatory systems. Genes and Development. 22(19):2601-2611.

Mitrophanov, A. Y., M. W. Jewett, T. J. Hadley, and E. A. Groisman. 2008. Evolution and dynamics of regulatory architectures controlling polymyxin B resistance in enteric bacteria. PLoS Genetics. 4(10) art. no. e1000233.

Perez, J. C., and E. A. Groisman. 2007. Acid pH activation of the PmrA/PmrB two-component regulatory system of Salmonella enterica. Molecular microbiology. 63(1):283-293.

Tu, X., T. Latifi, A. Bougdour, S. Gottesman, and E. A. Groisman. 2006. The PhoP/PhoQ two-component system stabilizes the alternative sigma factor RpoS in Salmonella enterica. Proceedings of the National Academy of Sciences of the United States of America. 103(36):13503-13508..

Winfield, M. D., and E. A. Groisman. 2004. Phenotypic differences between Salmonella and Escherichia coli resulting from the disparate regulation of homologous genes. Proceedings of the National Academy of Sciences of the United States of America. 101(49):17162-17167.

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Recommended Readings: Andre Hoelz, Ph.D.; May 13, 2009

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Special Seminar Series

            ”Building the Gatekeeper of the Innermost Sanctuary of the Cell Piece by Piece”

Andre Hoelz, Ph.D.

Research Associate, Laboratory of Cell Biology

The Rockefeller University

Wednesday, May 13, 2009

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

Second Floor, Welch Hall

Recommended Articles:

Debler, E. W., Y. Ma, H. -S Seo, K. -C Hsia, T. R. Noriega, G. Blobel, and A. Hoelz. 2008. A fence-like coat for the nuclear pore membrane. Molecular cell. 32(6):815-826.

Hoelz, A., and G. Blobel. 2004. Popping out of the nucleus. Nature. 432(7019):815-816.

Hsia, K. -C, P. Stavropoulos, G. Blobel, and A. Hoelz. 2007. Architecture of a coat for the nuclear pore membrane. Cell. 131(7):1313-1326.

Melcak, I., A. Hoelz, and G. Blobel. 2007. Structure of Nup58/45 suggests flexible nuclear pore diameter by intermolecular sliding. Science. 315(5819):1729-1732.

Napetschnig, J., G. Blobel, and A. Hoelz. 2007. Crystal structure of the N-terminal domain of the human protooncogene Nup214/CAN. Proceedings of the National Academy of Sciences of the United States of America. 104(6):1783-1788.

Stavropoulos, P., V. Nagy, G. Blobel, and A. Hoelz. 2008. Molecular basis for the autoregulation of the protein acetyl transferase Rtt109. Proceedings of the National Academy of Sciences of the United States of America. 105(34):12236-12241.

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