Thu, 21 Aug 2008 14:08:00 BST CiteULike: neils's Dong http://www.citeulike.org/user/neils/author/Dong CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/neils/article/2553355 <i>BMC Genomics, Vol. 9, No. 1. (2008)</i><br /><br />BACKGROUND:Songbirds hold great promise for biomedical, environmental and evolutionary research. A complete draft sequence of the zebra finch genome is imminent, yet a need remains for application of genomic resources within a research community traditionally focused on ethology and neurobiological methods. In response, we developed a core set of genomic tools and a novel collaborative strategy to probe gene expression in diverse songbird species and natural contexts.RESULTS:We end-sequenced cDNAs from zebra finch brain and incorporated additional sequences from community sources into a database of 86,784 high quality reads. These assembled into 31,658 non-redundant contigs and singletons, which we annotated via BLAST search of chicken and human databases. The results are publicly available in ESTIMA:Songbird. We produced a spotted cDNA microarray with 20,160 addresses representing 17,214 non-redundant products of an estimated 11,500-15,000 genes, validating it by analysis of immediate-early gene (zenk) gene activation following song exposure and by demonstrating effective cross hybridization to genomic DNAs of other songbird species in the Passerida Parvorder. Our assembly was also used in the design of the "Lund-zfa" Affymetrix array representing ~22,000 non-redundant sequences. When the two arrays were hybridized to cDNAs from the same set of male and female zebra finch brain samples, both arrays detected a common set of regulated transcripts with a Pearson correlation coefficient of 0.895. To stimulate use of these resources by the songbird research community and to maintain consistent technical standards, we devised a aCommunity Collaborationa mechanism whereby individual birdsong researchers develop experiments and provide tissues, but a single individual in the community is responsible for all RNA extractions, labelling and microarray hybridizations.CONCLUSIONS:Immediately, these results set the foundation for a coordinated set of 25 planned experiments by 16 research groups probing fundamental links between genome, brain, evolution and behavior in songbirds. Energetic application of genomic resources to research using songbirds should help illuminate how complex neural and behavioral traits emerge and evolve. The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution Kirstin Replogle Arthur Arnold Gregory Ball Mark Band Staffan Bensch Eliot Brenowitz Shu Dong Jenny Drnevich Margaret Ferris Julia George George Gong Dennis Hasselquist Alvaro Hernandez Ryan Kim Harris Lewin Lei Liu Peter Lovell Claudio Mello Sara Naurin Sandra Zas Jyothi Thimmapuram Juli Wade David Clayton doi:10.1186/1471-2164-9-131 BMC Genomics, Vol. 9, No. 1. (2008) 2008-03-19T00:14:12-00:00 2008 BMC Genomics 9 1 annotation bioinformatics bird genome genomics zebrafinch http://www.citeulike.org/user/neils/article/1962723 <i>Circ Res, Vol. 93, No. 9. (31 October 2003), pp. 805-812.</i><br /><br />Nitrate tolerance (NT) in hypertension is attributed to reduced activity of soluble guanylyl cyclase (sGC). We examined NT in basilar artery vascular smooth muscle cells (VSMCs) from control rats, rats infused with angiotensin II (Ang; 240 microg/kg per hour for 4 days), which were normotensive, and Ang-hypertensive rats (AHR; 240 microg/kg per hour for 28 days). Ca2+-activated K+ (Maxi-K) channels in VSMCs from AHR showed reduced activation by NO donor, consistent with NT. The concentration-response relationship for 8-Br-cGMP was shifted 2.5-fold to the right, indicating that abnormal sGC alone could not account for NT. Inside-out patches from AHR showed normal activation with exogenous cGMP-dependent protein kinase I (cGKI), suggesting no abnormality downstream of cGKI. We hypothesized that the reduction in apparent affinity of 8-Br-cGMP for cGKI in AHR might be due to a change in relative amounts of cGKIalpha versus cGKIbeta, since cGKIbeta is less sensitive to cGMP activators than cGKIalpha. This was substantiated by showing the following in AHR: (1) reduced effect of the cGKIalpha-selective activator 8-APT-cGMP; (2) reduced total cGKI protein (both isoforms), but an increase in cGKIbeta protein in quantitative immunofluorescence and Western blots; (3) similar changes in cGKI isoforms immunoisolated with Maxi-K channels; and (4) a large increase in cGKIbeta mRNA and a decrease in cGKIalpha mRNA in real-time PCR and Northern blots. Upregulation of cytosolic cGKIbeta was evident 4 days after Ang infusion, before development of hypertension. Our data identify a functional role for cGKIbeta in VSMCs previously ascribed exclusively to cGKIalpha. Ang-induced alternative splicing of cGKI represents a novel mechanism for reducing sensitivity to NO/cGMP. Alternative splicing of cGMP-dependent protein kinase I in angiotensin-hypertension: novel mechanism for nitrate tolerance in vascular smooth muscle. V Gerzanich A Ivanov S Ivanova JB Yang H Zhou Y Dong JM Simard doi:10.1161/01.RES.0000097872.69043.A0 Circ Res, Vol. 93, No. 9. (31 October 2003), pp. 805-812. 2007-11-23T01:57:46-00:00 2003 Circ Res 1524-4571 93 9 805 812 article-pka-pkg camp isoform kinase