Vishvanath Nene,* Jennifer R. Wortman, Daniel Lawson, Brian Haas, Chinnappa Kodira, Zhijian (Jake) Tu, Brendan Loftus, Zhiyong Xi, Karyn Megy, Manfred Grabherr, Quinghu Ren, Evgeny M. Zdobnov, Neil F. Lobo, Kathryn S. Campbell, Susan E. Brown, Maria F. Bonaldo, Jingsong Zhu, Steven P. Sinkins, David G. Hogenkamp, Paolo Amedo, Peter Arensburger, Peter W. Atkinson, Shelby Bidwell, Jim Biedler, Ewan Birney, Robert V. Bruggner, Javier Costas, Monique R. Coy, Jonathan Crabtree, Matt Crawford, Becky deBruyn, David DeCaprio, Karin Eiglmeier, Eric Eisenstadt, Hamza El-Dorry, William M. Gelbart, Suely L. Gomes, Martin Hammond, Linda I. Hannick, James R. Hogan, Michael H. Holmes, David Jaffe, J. Spencer Johnston, Ryan C. Kennedy, Hean Koo, Saul Kravitz, Evgenia V. Kriventseva, David Kulp, Kurt LaButti, Eduardo Lee, Song Li, Diane D. Lovin, Chunhong Mao, Evan Mauceli, Carlos F. M. Menck, Jason R. Miller, Philip Montgomery, Akio Mori, Ana L. Nascimento, Horacio F. Naveira, Chad Nusbaum, Sinead O’Leary, Joshua Orvis, Mihaela Pertea, Hadi Quesneville, Kyanne R. Reidenbach, Yu-Hui Rogers, Charles W. Roth, Jennifer R. Schneider, Michael Schatz, Martin Shumway, Mario Stanke, Eric O. Stinson, Jose M. C. Tubio, Janice P. VanZee, Sergio VerjovskiAlmeida, Doreen Werner, Owen White, Stefan Wyder, Qiandong Zeng, Qi Zhao, Yongmei Zhao, Catherine A. Hill, Alexander S. Raikhel, Marcelo B. Soares, Dennis L. Knudson, Norman H. Lee, James Galagan, Steven L. Salzberg, Ian T. Paulsen, George Dimopoulos, Frank H. Collins, Bruce Birren, Claire M. Fraser-Liggett, David W. Severson*
Leopard Complex spotting occurs in several breeds of horses and is caused by an incompletely dominant allele (LP). Homozygosity for LP is also associated with congenital stationary night blindness (CSNB) in Appaloosa horses. Previously, LP was mapped to a 6 cm region on ECA1 containing the candidate gene TRPM1 (Transient Receptor Potential Cation Channel, Subfamily M, Member 1) and decreased expression of this gene, measured by qRT–PCR, was identified as the likely cause of both spotting and ocular phenotypes. This study describes investigations for a mutation causing or associated with the Leopard Complex and CSNB phenotype in horses. Re-sequencing of the gene and associated splice sites within the 105 624 bp genomic region of TRPM1 led to the discovery of 18 SNPs. Most of the SNPs did not have a predictive value for the presence of LP. However, one SNP (ECA1:108,249,293 C>T) found within intron 11 had a strong (P < 0.0005), but not complete, association with LP and CSNB and thus is a good marker but unlikely to be causative. To further localize the association, 70 SNPs spanning over two Mb including the TRPM1 gene were genotyped in 192 horses from three different breeds segregating for LP. A single 173 kb haplotype associated with LP and CSNB (ECA1: 108,197,355- 108,370,150) was identified. Illumina sequencing of 300 kb surrounding this haplotype revealed 57 SNP variants. Based on their localization within expressed sequences or regions of high sequence conservation across mammals, six of these SNPs were considered to be the most likely candidate mutations. While the precise function of TRPM1 remains to be elucidated, this work solidifies its functional role in both pigmentation and night vision. Further, this work has identified several potential regulatory elements of the TRPM1 gene that should be investigated further in this and other species.
The passage of cosmic rays has been observed to excite mechanical vibrations in the resonant gravitational wave detector NAUTILUS operating at temperature of 100 mK. A very significant correlation (more than 10 standard deviations) is found.
We discuss the data acquisition and analysis procedures used on the Allegro gravity wave detector, including a full description of the filtering used for bursts of gravity waves. The uncertainties introduced into timing and signal strength estimates due to stationary noise are measured, giving the windows for both quantities in coincidence searches.
We report on the operation of the resonant gravitational wave (g.w.) detector Explorer of the Rome group ( kg, K, located at CERN) at the time of the gamma-ray burst GRB 980425 (April 25.90915 UT, 1998), which is probably associated with the supernova SN 1998bw. We present the data of the detector (with sensitivity for a 1 ms pulse), and use the BeppoSAX data to estimate the initial time of the GRB: a basic parameter for any correlation analysis. The g.w. data exhibit no significant time signature around the GRB 980425. We wish to remark the importance to make use, in spite of the present low sensitivity, of the data collected with g.w. detectors, that can be regarded as active observatories, in coincidence with the BeppoSAX data.
Today large sequencing centers are producing genomic data at the rate of 10 terabytes a day and require complicated processing to transform massive amounts of noisy raw data into biological information. To address these needs, we develop a system for end-to-end processing of genomic data, including alignment of short read sequences, variation discovery, and deep analysis. We also employ a range of quality control mechanisms to improve data quality and parallel processing techniques for performance. In the demo, we will use real genomic data to show details of data transformation through the workflow, the usefulness of end results (ready for use as testable hypotheses), the effects of our quality control mechanisms and improved algorithms, and finally performance improvement.
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