Category Archives: Methods

Use this category for science related methods posts.

Recommended Readings: Leslie M Turner PhD Oct 22, 2012

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Genomic Networks of Hybrid Sterility

Leslie M Turner  PhD

Postdoctoral Fellow

Laboratory of Genetics, University of Wisconsin – Madison

Monday, October 22,  2012

4 p.m. , Caspary Auditorium.   Refreshments 3:45 p.m.

Recommended Readings:

Janousek, V; Wang, LY; Luzynski, K; et al.  2012.  Genome-wide architecture of reproductive isolation in naturally occurring hybrid zone between Mus musculus musculus and M. m. domesticus.   Molecular Ecology.  21(12):3032-3047.  DOI:10.111/j.1365-294X.2012.05583.x

White, MA; Steffy, B; Wiltshire, T; et al.  2011.  Genetic dissection of a key reproductive barrier between nascent species of house mice.  Genetics. 189(1):289-U988.  DOI:10.1534/genetics.111.129171

Turner, LM; Schwahn, DJ; Harr, B.  2012.  Reduced male fertility is common but highly variable in form and severity in a natural house mouse hybrid zone.   Evolution.  66(2):443-458.  DOI:10.1111/j.1558-5646.2011.01445.x

Turner, LM; Young, AR; Roempler, H; et al.  2010.  Monogamy evolves through multiple mechanisms: evidence from V1aR in deer mice.  Molecular Biology and Evolution.  27(6)1269-1278.  DOI:10.1093/molbev/msq013

Harr, B; Turner, LM.  2010.  Genome-wide analysis of alternative splicing evolution among Mus subspecies.  Molecular Ecology.  19(suppl 1):228-239.  DOI:10.1111/j.1365-294X.04490.x

Gompert, Z; Buerkle, CA.  2009.  A powerful regression-based method for admixture mapping of isolation across the genome of hybrids.  Molecular Ecology.  18(6):1207-1224.  DOI:10.1111/j.1365-0294X.04098.x

Elliott, RW; Miller, DR; Pearsall, RS; et al.  2001.  Genetic analysis of testis weight and fertility in an interspecies hybrid congenic strain for chromosome X.   Mammalian Genome.  12(1):45-51.  DOI:10.1007/s003350010234

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Recommended Readings: Marco Tripodi PhD Oct 8 2012

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Spatiotemporal Control of Motor Circuit Assembly and Function

 Marco Tripodi, Ph.D.

Postdoctoral Fellow

Biozentrum

University of Basel and

Friedrich Miescher Institute for Biomedical Research

 Monday, October 8, 2012

4:00 p.m., Caspary Auditorium

Recommended Readings:

Arber, Silvia.  2012.  Motor circuits in action: specification, connectivity and function.  Neuron.  74(6):975-969  DOI: 10.1016/j.neuron.2012.05.011

Martin, John H.  2012.  Systems neurobiology of restorative neurology and future directions for repair of the damaged motor systems.  Clinical Neurobiology and Neurosurgery.  114(5, Sp.Issue S1):515-523.  DOI: 10.1016/j.clineuro.2012.01.011  Please request from Markus Library.

Denk, W.; K.L. Briggman; M. Helmstaedter.  2012.  Structural neurobiology: missing link t o a mechanistic understanding of neural computation.  Nature Reviews Neuroscience.  13(5):351-358.  DOI: 10.1038/nrn3169

Tripodi, M.; A. E. Stepien; and S. Arber.   2011.  Motor antagonism exposed by spatial segregation and timing of neurogenesis.  Nature.  479:7371:61-U84.  DOI:10.1038/nature1038

Simon, M.A.; S. J. Fusillo; K. Colman, et al. 2010.  Motor patterns associated with crawling in a soft-bodied arthropod.  Journal of Experimental Biology.  213(13):2302-2309.  DOI:10.1242/jeb.039206

Ugolini, G.  2010.  Advances in viral transneuronal tracing.  7th FENS Meeting on Neuroanatomical Tracing and Systems. Amsterdam, Netherlands, July 3, 2010.  Journal of Neuroscience Methods.  194(1):2-20.  DOI:10.1016/j.jneumeth.2009.12.001

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New Method Improves Accuracy of Whole Genome Sequencing

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July 11, 2012  NATURE has published a research article detailing a new methodology to  dramatically improve the accuracy of whole genome sequencing.  The work was done by a company called Complete Genomics.   The NATURE paper describes the Company’s “Long Fragment Read” technology (LFR) that not only improves the accuracy, but also reduces the amount of DNA needed, for analysis.  This technology is expected to accelerate the clinical adoption of whole genome sequencing.

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Recommended Readings: Howard C Hang, PhD.

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Chemical Reporters for Exploring Posttranslational

Modifications in Innate Immunity

Howard C Hang, Ph.D.

Laboratory of Chemical Biology and Microbial Pathogenesis

The Rockefeller University

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

Caspary Auditorium

Recommended Readings

Yount JS, Charron G, Hang HC.   2012.  Bioorthogonal proteomics of 15-hexadecynyloxyacetic acid chemical reporter reveals preferential targeting of fatty acid modified proteins and biosynthetis enzymes.    Bioorganic & Medicinal Chemistry.  20(2, S1):650-654.  DOI: 0.1016/j.bmc.2011.03.062

Lei YL, Xie K. et al.  2012.  Chemistry-based functional proteomics to identify novel deubiquitylating enzymes involved in viral infection.   Combinatorial Chemistry & High Throughput Screening.  15(4):316-327.   Please request from Markus Library.

Grammel M, Dossa PD, Taylor-Salmon E, et al.  2012.  II-selective labeling of bacterial proteomes with an  orthogonal phenylalanine amino acid reporter.   Chemical Communications.  48(10):1473-1474.  DOI: 10.1039/c1cc14939c

Aguera-Gonzales S, Gross CC, Fernandez-Messina L, et al.  2011.  Palmitoylation of MICA, a ligand for NKG2D, mediates its recruitment to membrane microdomains and promotes its shedding.    European Journal of Immunology.  41(12):3667-3676.   DOI: 10.1002/eji.20114165

Hao ZY, Hong SL, Chen X, et al.  2011.  Introducing bioorthogonal functionalities into proteins in living cells.  Accounts of Chemical Research   44(9, S1):742-751.   DOI: 10.1021/ar200067r

Hang HC, Linder ME.  2011.  Exploring protein lipidation with chemical biology.  Chemical Reviews.  111(10):6341-6358.   DOI:  10.1021/cr2001977

Yang YY, Hang HC.  2011.  Chemical approaches for the detection and synthesis of acetylated proteins.  Chembiochem.   12(2):314-322.   DOI: 10.1002/cbc.201000558

 

 

 

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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: Jeannie T. Lee, M.D., Ph.D.

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Friday Lecture Series

Richard M. Furlaud Distinguished Lecture

X-Chromosome Inactivation as a Model for Epigenomic Regulation by Long

Noncoding RNAs

Jeannie T. Lee, M.D., Ph.D., professor of genetics and pathology,

Harvard Medical School, investigator,

Howard Hughes Medical Institute

January 27, 2012

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

Caspary Auditorium

Recommended Readings:

Lengner, C. J., A. A. Gimelbrant, J. A. Erwin, A. W. Cheng, M. G. Guenther, G. G. Welstead, R. Alagappan, et al. 2010. Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations. Cell 141, (5): 872-883

Namekawa, S. H., B. Payer, K. D. Huynh, R. Jaenisch, and J. T. Lee. 2010. Two-step imprinted X inactivation: Repeat versus genic silencing in the mouse. Molecular and cellular biology 30, (13): 3187-3205

Sarma, K., P. Levasseur, A. Aristarkhov, and J. T. Lee. 2010. Locked nucleic acids (LNAs) reveal sequence requirements and kinetics of xist RNA localization to the X chromosome. Proceedings of the National Academy of Sciences of the United States of America 107, (51): 22196-22201

Tian, D., S. Sun, and J. T. Lee. 2010. The long noncoding RNA, jpx, is a molecular switch for X chromosome inactivation. Cell 143, (3): 390-403

Zhou, D., C. Conrad, F. Xia, J. -S Park, B. Payer, Y. Yin, G. Y. Lauwers, et al. 2009. Mst1 and Mst2 maintain hepatocyte quiescence and Suppress hepatocellular carcinoma development through inactivation of the Yap1 oncogene. Cancer Cell 16, (5): 425-438

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Yale Scientists Develop Synthetic Biology Approach for Generating Phosphoproteins

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Yale researchers have devised a technique for expressing activated phosphoproteins in Escherichia coli, using it to generate phosphorylated versions of the protein MEK1, a key molecule in cell proliferation, development, differentiation, and oncogenesis. 

According to Yale assistant professor Jesse Rinehart, one of the leaders of the study – which was published in Science – the technique could prove an important source of reagents for phosphoproteomic research and provides an early glimpse of synthetic biology’s potential to aid proteomics more generally.

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Cancer Drug Candidate Leads to Proteomics Method

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Scientists at Memorial Sloan-Kettering Cancer Center and Weill Cornell Medical have devised an affinity capture-based proteomics technique that could be used to identify and map dysregulated protein pathways in a number of different cancers.

The technique, which was detailed in a paper published Nature Chemical Biology, relies on the inhibitor PU-H71 – a small molecule that selectively binds tumor-enriched Hsp90 proteins, enabling pulldown of Hsp90-bound oncogenic client proteins. According to MSK researcher Gabriela Chiosis ― one of the developers of the method ― measurement of these captured proteins combined with bioinformatic analysis could provide a better understanding of tumor biology.

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