DNA Of Uncultured Organisms Sequenced Using Novel Single-cell Approach

ScienceDaily (Apr. 28, 2009) — Scientists from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Bigelow Laboratory for Ocean Sciences have assembled high quality, contamination-free draft genomes of uncultured biodegrading microorganisms using a novel single cell genome sequencing approach.  This proof of principle study, published in the April 23 edition of the journal PLoS One, offers researchers a new method to access and decipher the information embedded in genomes of interest with only minute quantities of DNA.

Inter’l Congress of Biochemistry and Molecular Biology 2009


21st IUBMB and 12th FAOBMB

International Congress of Biochemistry and Molecular Biology

August 2-7, 2009, Shanghai, China 

Congress Major Themes:
1, Genome Dynamics and Gene Regulation
2, Protein Structure, Dynamics and Proteomics
3, Cell Signaling and Network 4, Molecular Basis of Diseases

About 200 confirmed invited speakers from around the world

Biomedical Researchers Invited To Design Experiments For Space Station

 The NIH announced its willingness to fund highly meritorious biomedical experiments that could utilize the unique environment in space and produce breakthroughs to improve human health on Earth.  The International Space Station provides a special microgravity and radiological environment that Earth-based laboratories cannot replicate. Congress opened the U.S. portion of the International Space Station to other federal agencies and university and private sector researchers when it designated the U.S. resources as a National Laboratory in 2005.

The NIH solicitation is the next step in a new partnership to apply the National Laboratory to research that complements NASA’s space exploration efforts.   Biomedical experiments already conducted on the International Space Station have addressed how bone and muscle deteriorate, how humans fight infectious disease, and how cancers grow and spread.

Click here for more information on the NIH-NASA partnership and the funding opportunity announcement.

Click here for more information on the National Laboratory at the International Space Station.

Recommended Readings: William Bialek, Ph.D. April 13, 2009

Monday Lecture Series

“Optimization Principles and the Physical Limits to Biological Function”

William Bialek, Ph.D.

Professor, Lewis-Sigler Institute for Integrative Genomics, Princeton University 

Visiting Professor, Rockefeller University

Monday, April 13, 2009

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

Second Floor, Welch Hall

Recommended Articles:

Tkacik G, Callan CG, and  Bialek Wm.  2008. Information flow and optimization in transcriptional regulation.  PNAS  105 (34):12265-12270    

Tkacik G, Callan CG, and Bialek Wm.  2008.  Information capacity of genetic regulatory elements. PHYSICAL REVIEW E . 78 (issue 1, part 1): Article Number: 011910  

 

Bialek Wm. and Setayeshgar S.   2008.  Cooperativity, sensitivity, and noise in biochemical signaling.  PHYSICAL REVIEW LETTERS . 100(25): Article number 258101

 

Gregor T, Tank DW, Wieschaus EF, et al.   2007.  Probing the limits to positional information.  CELL .  130(1): 153-164   

 

Schneidman E,  Berry MJ, and  Segev R, et al.   2006.  Weak pairwise correlations imply strongly correlated network states in a neural population.  NATURE .   440(7087):1007-1012

 

Bialek Wm, and Setayeshgar S.   2005.  Physical limits to biochemical signaling. PNAS. 102(29):10040-10045   

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

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.

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

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.

Recommended Readings: Alejandro Sanchez Alvarado, Ph.D.; May 1

Friday Lecture Series

“Dying Young as Late as Possible: Regeneration, Planarians and Stem Cells”

Alejandro Sanchez Alvarado, Ph.D.

University of Utah

May 1, 2009

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

Caspary Auditorium

Recommended Articles:

Sanchez Alvarado, A. 2008. Stem cells: time to check our premises. Cell stem cell. 3(1):25-29.

 

Sanchez Alvarado, A. 2007. Stem cells and the Planarian Schmidtea mediterranea. Comptes Rendus – Biologies. 330(6-7):498-503. (Request a copy from the Markus Library librequest@rockefeller.edu)

 

Sanchez Alvarado, A. 2006. Planarian regeneration: Its end is its beginning. Cell. 124(2):241-245.

 

Reddien, P.W., Oviedo, N.J., Jennings, J.R., Jenkin, J.C., Sanchez Alvarado, A. 2005. Developmental biology: SMEDWI-2 is a PIWI-like protein that regulates planarian stem cells. Science. 310(5752):1327-1330.

 

Reddien, P.W., Bermange, A.L., Murfitt, K.J., Jennings, J.R., Sanchez Alvarado, A. 2005. Identification of genes needed for regeneration, stem cell function, and tissue homeostasis by systematic gene perturbation in planaria. Developmental Cell. 8(5):635-649.

 

Reddien, P.W., Sanchez Alvarado, A. 2004. Fundamentals of planarian regeneration. Annual Review of Cell and Developmental Biology. (20):725-757.

 

Sanchez Alvarado, A. 2004. Regeneration and the need for simpler model organisms. Philosophical Transactions of the Royal Society B: Biological Sciences. 359(1445):759-763.

Recommended Readings: Arthur Horwich, M.D.; April 24

Friday Lecture Series

“Chaperone Machines and Involvement in a Form of ALS”

Weisbach Memorial Lecture

Arthur Horwich, M.D.

Yale University

April 24, 2009

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

Caspary Auditorium

Recommended Articles:

Bukau, B., J. Weissman, and A. Horwich. 2006. Molecular chaperones and protein quality control. Cell. 125(3):443-451.

 

Wang, J., G. W. Farr, D. H. Hall, F. Li, K. Furtak, L. Dreier, and A. L. Horwich. 2009. An ALS-linked mutant SOD1 produces a locomotor defect associated with aggregation and synaptic dysfunction when expressed in neurons of Caenorhabditis elegans. PLoS Genetics. 5(1), art. no. e1000350.

 

Wang, J., G. W. Farr, C. J. Zeiss, D. J. Rodriguez-Gil, J. H. Wilson, K. Furtak, D. T. Rutkowski, et al. 2009. Progressive aggregation despite chaperone associations of a mutant SOD1-YFP in transgenic mice that develop ALS. Proceedings of the National Academy of Sciences of the United States of America. 106(5):1392-1397.

 

Grantcharova, V., E. J. Alm, D. Baker, and A. L. Horwich. 2001. Mechanisms of protein folding. Current opinion in structural biology. 11(1): 70-82.

 

Horwich, A. L., Fenton, W. A., Chapman, E., and Farr, G. W. 2007.  Two families of chaperonin: Physiology and mechanism. Annual Review of Cell and Developmental Biology. 23:115-145 .

 

Recommended Readings: Harvey F. Lodish, Ph.D.; Friday April 17

Friday Lecture Series

“Expansion of Human and Mouse Hematopoietic Stem Cells by Novel Cytokines: Their Expression by a Newly Identified Stromal Cell Population”

Detlev W. Bronk Alumni Lecture

Harvey F. Lodish, Ph.D.

Member, Whitehead Institute for Biomedical Research; Professor of Biology and Bioengineering, Massachusetts Institute of Technology

April 17, 2009

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

Caspary Auditorium

Recommended Articles:

Cheng, C. Z., M. Kaba, G. Ge, K. Xie, W. Tong, C. Hug, and H. F. Lodish. 2006. Angiopoietin-like proteins stimulate ex vivo expansion of hematopoietic stem cells. Nature Medicine. 12(2): 240-245.

 

Huynh, H., S. Iizuka, M. Kaba, O. Kirak, J. Zheng, H. F. Lodish, and C. Z. Cheng. 2008. Insulin-like growth factor-binding protein 2 secreted by a tumorigenic cell line supports ex vivo expansion of mouse hematopoietic stem cells. Stem Cells. 26(6): 1628-1635.
(Contact the Markus Library to request a copy of this article librequest@rockefeller.edu)

 

Socolovsky, M., H. F. Lodish, and G. Q. Daley. 1998. Control of hematopoietic differentiation: Lack of specificity in signaling by cytokine receptors. Proceedings of the National Academy of Sciences of the United States of America. 95(12):6573-6575.

 

Watowich, S. S., Wu, H., Socolovsky, M., Klingmuller, U., Constantinescu, S. N., and Lodish, H. F. 1996. Cytokine receptor signal transduction and the control of hematopoietic cell development. Annual Review of Cell and Developmental Biology. (12):91-128.

 

Zhang, C. C., M. Kaba, S. Iizuka, H. Huynh, and H. F. Lodish. 2008. Angiopoietin-like 5 and IGFBP2 stimulate ex vivo expansion of human cord blood hematopoietic stem cells as assayed by NOD/SCID transplantation. Blood. 111 (7): 3415-3423.

 

Zhang, C. C., and H. F. Lodish. 2008. Cytokines regulating hematopoietic stem cell function. Current Opinion in Hematology. 15(4): 307-311.
(Contact the Markus Library to request a copy of this article librequest@rockefeller.edu)

 

Zhang, C.C., and H. F. Lodish. 2004. Insulin-like growth factor 2 expressed in a novel fetal liver cell population is a growth factor for hematopoietic stem cells. Blood. 103(7): 2513-2521.