Recommended Readings: Yi Rao, Ph.D.

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Friday Lecture Series

Molecular Sociophysiology of Sexual Preference

Yi Rao, Ph.D., investigator, National Institute of Biological Sciences;

dean, school of life sciences, Peking University, Beijing

May 11, 2012

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

Caspary Auditorium

 

Recommended Readings

Liu, Y., Y. -A Jiang, Y. Si, J. -Y Kim, Z. -F Chen, and Y. Rao. 2011. Molecular Regulation of Sexual Preference Revealed by Genetic Studies of 5-HT in the Brains of Male Mice. Nature 472 (7341): 95-100

Park, H. T., J. Wu, and Y. Rao. 2002. Molecular Control of Neuronal Migration. BioEssays 24 (9): 821-827

Park, K. W., C. M. Morrison, L. K. Sorensen, C. A. Jones, Y. Rao, C. -B Chien, J. Y. Wu, L. D. Urness, and D. Y. Li. 2003. Robo4 is a Vascular-Specific Receptor that Inhibits Endothelial Migration. Developmental Biology 261 (1): 251-267

Yuan, W., L. Zhou, J. -H Chen, J. Y. Wu, Y. Rao, and D. M. Ornitz. 1999. The Mouse SLIT Family: Secreted Ligands for ROBO Expressed in Patterns that Suggest a Role in Morphogenesis and Axon Guidance. Developmental Biology 212 (2): 290-306

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HHMI News: Janelia Farm’s Newest Addition to HMMER

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A few weeks after its release, the Janelia Farm’s Jackhmmer algorithm — an iterative search method in the HMMER package similar to the NCBI’s PSI-BLAST algorithm — is performing as expected.  The new algorithm takes advantage of the sophisticated probabilistic models that underpin profile Hidden Markov Models (HMMs).

Profile HMMs are the most sensitive tools to use, which is why many protein family databases use them. Bench biologists now have a fast method for discovering the likely structure of a sequence which can allow for the creation of functional hypothesis that can guide experiments.

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Recommended Readings: Anne Ephrussi, Ph.D.

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Friday Lecture Series

RNP Assembly and Transport in the Drosophila Oocyte

Anne Ephrussi, Ph.D., head, Developmental Biology Unit and head,

International Center for Advanced Training,

European Molecular Biology Laboratory

April 20, 2012

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

Caspary Auditorium

 

Recommended Readings:

Chekulaeva, M. and A. Ephrussi. 2004. “Drosophila Development: RNA Interference Ab Ovo.” Current Biology 14 (11): R428-R430

Hachet, O. and A. Ephrussi. 2001. “Drosophila Y14 Shuttles to the Posterior of the Oocyte and is Required for Oskar mRNA Transport.” Current Biology 11 (21): 1666-1674

Jambor, H., C. Brunel, and A. Ephrussi. 2011. “Dimerization of Oskar 3′ UTRs Promotes Hitchhiking for RNA Localization in the Drosophila Oocyte.” RNA 17 (12): 2049-2057

Krauss, J., S. López de Quinto, C. Nüsslein-Volhard, and A. Ephrussi. 2009. “Myosin-V Regulates Oskar mRNA Localization in the Drosophila Oocyte.” Current Biology 19 (12): 1058-1063

Vanzo, N., A. Oprins, D. Xanthakis, A. Ephrussi, and C. Rabouille. 2007. “Stimulation of Endocytosis and Actin Dynamics by Oskar Polarizes the Drosophila Oocyte.” Developmental Cell 12 (4): 543-555

Vanzo, N. F. and A. Ephrussi. 2002. “Oskar Anchoring Restricts Pole Plasm Formation to the Posterior of the Drosophila Oocyte.” Development 129 (15): 3705-3714

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Delivering Paricles Directly Into Cells

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Scientists who developed a technology for identifying and targeting unique protein receptor ZIP Codes on the cellular surface have found a way to penetrate the outer membrane and deliver engineered particles — called iPhage — to organelles inside the cell. 

In a paper recently published online in Nature Communications, the team led by researchers at The University of Texas MD Anderson Cancer Center reports packaging the phage particles with a peptide called penetratin to reach inside the cell.

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Recommended Readings: Bruce Walker, M.D.

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Friday Lecture Series

Immune Control and Immune Failure in HIV Infection

Bruce Walker, M.D., Principal Investigator,

Ragon Institute of MGH, MIT and Harvard

April 13, 2012

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

Caspary Auditorium

 

Recommended Readings:

Huang, J., P. S. Burke, T. D. H. Cung, F. Pereyra, I. Toth, B. D. Walker, L. Borges, M. Lichterfeld, and X. G. Yu. 2010. “Leukocyte Immunoglobulin-Like Receptors Maintain Unique Antigen-Presenting Properties of Circulating Myeloid Dendritic Cells in HIV-1-Infected Elite Controllers.” Journal of Virology 84 (18): 9463-9471

Kawashima, Y., K. Pfafferott, J. Frater, P. Matthews, R. Payne, M. Addo, H. Gatanaga, et al. 2009. “Adaptation of HIV-1 to Human Leukocyte Antigen Class I.” Nature 458 (7238): 641-645

Mahalanabis, M., P. Jayaraman, T. Miura, F. Pereyra, E. M. Chester, B. Richardson, B. Walker, and N. L. Haigwood. 2009. “Continuous Viral Escape and Selection by Autologous Neutralizing Antibodies in Drug-Naïve Human Immunodeficiency Virus Controllers.” Journal of Virology 83 (2): 662-672

Matthews, P. C., A. Prendergast, A. Leslie, H. Crawford, R. Payne, C. Rousseau, M. Rolland, et al. 2008. “Central Role of Reverting Mutations in HLA Associations with Human Immunodeficiency Virus Set Point.” Journal of Virology 82 (17): 8548-8559

Pereyra, F., S. Palmer, T. Miura, B. L. Block, A. Wiegand, A. C. Rothchild, B. Baker, et al. 2009. “Persistent Low-Level Viremia in HIV-1 Elite Controllers and Relationship to Immunologic Parameters.” Journal of Infectious Diseases 200 (6): 984-990

Virgin, H. W. and B. D. Walker. 2010. “Immunology and the Elusive AIDS Vaccine.” Nature 464 (7286): 224-231

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Recommended Readings: Sheetz, M., Kenan, W., Spudich, J., and Vale, R.

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Friday Lecture Series

Wiley Prize in Biomedical Sciences

Biological Motility and Mechanotransduction

Michael Sheetz, Ph.D., William R. Kenan Jr. Professor,Columbia University, 

Myosin Pulling and Mechanotransduction

James Spudich, Ph.D., professor of biochemistry, Stanford School of Medicine, Hypertrophic and Dilated Cardiomyopathies:

Single Molecule Analysis of Human Cardiac Myosin

Ronald Vale, Ph.D., professor, University of California, San Francisco; investigator, Howard Hughes Medical Institute (HHMI),

Structure and Mechanism of the Dynein Motor Protein

April 6, 2012

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

Caspary Auditorium

 

Recommended Readings:

Carter, A. P., C. Cho, L. Jin, and R. D. Vale. 2011. “Crystal Structure of the Dynein Motor Domain.” Science 331 (6021): 1159-1165

Chuan, P., J. A. Spudich, and A. R. Dunn. 2011. “Robust Mechanosensing and Tension Generation by Myosin VI.” Journal of Molecular Biology 405 (1): 105-112

Hartman, M. A., D. Finan, S. Sivaramakrishnan, and J. A. Spudich. 2011. Principles of Unconventional Myosin Function and Targeting. Annual Review of Cell and Developmental Biology. Vol. 27: 133-155

Kardon, J. R. and R. D. Vale. 2009. “Regulators of the Cytoplasmic Dynein Motor.” Nature Reviews Molecular Cell Biology 10 (12): 854-865

Vogel, V. and M. Sheetz. 2006. “Local Force and Geometry Sensing Regulate Cell Functions.” Nature Reviews Molecular Cell Biology 7 (4): 265-275

Vogel, V. and M. P. Sheetz. 2009. “Cell Fate Regulation by Coupling Mechanical Cycles to Biochemical Signaling Pathways.” Current Opinion in Cell Biology 21 (1): 38-46


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Recommended Readings: Hugo Bellen, Ph.D., D.V.M.

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Friday Lecture Series

Mitochondria and Neurodegeneration

Hugo Bellen, Ph.D., D.V.M., investigator, Howard Hughes Medical Institute;

professor, departments of molecular and human

genetics and neuroscience, director, Program in Developmental Biology,

Baylor College of Medicine

March 30, 2012

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

Caspary Auditorium

 

Recommended Readings:

Bibliography

Han, S. M., H. Tsuda, Y. Yang, J. Vibbert, P. Cottee, S. -J Lee, J. Winek, C. Haueter, H. J. Bellen, and M. A. Miller. 2012. “Secreted VAPB/ALS8 Major Sperm Protein Domains Modulate Mitochondrial Localization and Morphology Via Growth Cone Guidance Receptors.” Developmental Cell 22 (2): 348-362

Pesah, Y., T. Pham, H. Burgess, B. Middlebrooks, P. Verstreken, Y. Zhou, M. Harding, H. Bellen, and G. Mardon. 2004. “Drosophila Parkin Mutants have Decreased Mass and Cell Size and Increased Sensitivity to Oxygen Radical Stress.” Development 131 (9): 2183-2194

Romero, E., G. -H Cha, P. Verstreken, C. V. Ly, R. E. Hughes, H. J. Bellen, and J. Botas. 2008. “Suppression of Neurodegeneration and Increased Neurotransmission Caused by Expanded Full-Length Huntingtin Accumulating in the Cytoplasm.” Neuron 57 (1): 27-40

Venken, K. J. T., Y. He, R. A. Hoskins, and H. J. Bellen. 2006. “P[Acman]: A BAC Transgenic Platform for Targeted Insertion of Large DNA Fragments in D. Melanogaster.” Science 314 (5806): 1747-1751

Verstreken, P., C. V. Ly, K. J. T. Venken, T. -W Koh, Y. Zhou, and H. J. Bellen. 2005. “Synaptic Mitochondria are Critical for Mobilization of Reserve Pool Vesicles at Drosophila Neuromuscular Junctions.” Neuron 47 (3): 365-378


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NIH News: IOM Report on the Complexities of Translating “Omics” Into Treatment

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WASHINGTON — Genomics, proteomics, and other branches of molecular bioscience offer the prospect of greater precision in medical care, but some clinical tests based on “omics” research have proved invalid and highlighted the challenges of dealing with complex data.  To enhance the translation of omics-based discoveries to clinical use, a new report by the Institute of Medicine recommends a detailed process to evaluate whether the data and computational steps underlying such tests are sound and the tests are ready to be used in clinical trials.  The proposed process defines responsibilities and best practices for the investigators, research institutions, funders, regulators, and journals involved in development and dissemination of clinical omics-based technologies.

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Recommended Readings: Shai Shaham PH.D. Monday, March 26, 2012

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A New C. elegans Cell Death Program: Implications for

Neurodegeneration and Cancer

Shai Shaham, Ph.D.

Laboratory of Developmental Genetics

The Rockefeller University

4:00 p.m. Monday, March 26, 2012    Refreshments  3:45  Abby Lounge

Caspary Auditorium

Recommended readings:

Blum, E.S., Abraham, M.C., Yoshimura, S., Lu, Y., and S. Shaham.  2012.  Control of nonapoptotic developmental cell death in Caeanorhabditis elegans by a polyglutamic-repeat protein.  Science.  335(6071):970-973.  DOI: 10.1126/science.1215156

 McCall, K.  2010.  Generic control of necrosis – another type of programmed cell death.  Current Opinion in Cell Biology.  22(6):882-888.  DOI: 10.1016/j.ceb.2010.09.002

 Yuan, J. and G. Kroemer.  2010.  Alternative cell death mechanisms in development and beyond.  Genes & Development.  24(23):2592-2602.  DOI: 10.1101/gad.1984410

 Vlachos, M. and  N. Tavernarakis.  2010.  Non-apoptotic cell death in Caenorhabditis elegans.  Developmental Dynamics.  239(5, S1):1337-1351.   DOI: 10.1002/dvdy.22230

 Miguel-Aliaga, I. and T. Stefan.  2009.  Programmed cell death in the nervous system – a programmed cell fate?  Current Opinion in Neurobiology.  19(2):127-133   DOI: 10.1016/j.conb.2009.04.002

Blum, E.S., M. Driscoll, and S. Shaham.  2008.  Noncanonical cell death programs in the nematode Caenorhabditis elegans.  Cell Death and Differeentiation.  15(7):1124-1131.  DOI: 10.1038/cdd.2008.56

 Abraham, M. C., L. Yun, and S. Shaham.  2007.  A morphologically conserved nonapoptotic program promotes linker cell death in Caenorhabiditis elegans.   Development Cell.  12(1):73-86.  DOI:  10.1016/j.devcel.2006.11.012

 

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Erez Lieberman-Aiden Ph.D. Wednesday, April 4, 2012

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How the Genome Folds

Erez Aiden  Ph.D.

Fellow, Harvard Society of Fellows

Prinicpal Investigator, Laboratory-at-Large

Harvard University

Visiting Faculty, Google

4:00 Wednesday, April 4, 2012  Refreshments Abby Lounge 3:45

Caspary Auditorium 

Recommended Readings

Zhang Y; McCord RP, Ho YJ; et al.  2012.  Spatial organization of the mouse genome and its role in recurrent chromosomal translocations.  Cell. 148(5):908-921.  DOI: 10.1016/j.cell.2012.02.002

Sung MH and  GL Hager.  2011.  More to Hi-C than meets the eye.  Nature Genetics.  43(11):1047-1048.  DOI: 10.1038/ng.984

Yaffe E and A Tanay.  2011.  Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nature Genetics.  43(11):1059-U40.  DOI: 10.1038/ng.947

Fudenberg G; Getz G; Meyerson M; et al.  2011.  High order chromatic architecture shapes the landscape of chromosomal alterations in cancer.   Nature Biotechnology. 29(12):1109-U75.  DOI: 10.1038/nbt.2049

Lieberman-Aiden E; van Berkum NL; Williams L; et al.  2009.  Comprehenesive mapping of long-range interactions reveals folding principles of the human genome.  Science.  326(5950):289-293.  DOI: 10.1126/science.1181369

Guelen L; Pagie L; Brasset E; et al.  Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.   Nature.  453(7197):948-U83.  DOI: 10.1038/nature06947

Rada-Iglesias A; Ameur A; Kapronov P; et al.  2008.  Whole-genome maps opf USA and USF2 binding and histone H3 acetylation reveal new aspects of prmotoer structure and candidate genes for common human disorders.  Genome Research.  18(3):380-392.  DOI: 10.1101/gr.6880908

Xiao G; Wang X; and Ab Khodursky.  2011.  Modeling three-dimensional chromosome structures using gene expression data. Journal of the American Statistical Association.  106(493):61-72.  DOI: 10.1198/jasa.2010/ap09504   Please request copy from Markus Library.

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