iScience, Vol. 322, No. 5907. (5 December 2008), pp. 1535-1539./ibr /br /Cryptochromes (CRY) are photolyase-like blue-light receptors that mediate light responses in plants and animals. How plant cryptochromes act in response to blue light is not well understood. We report here the identification and characterization of the Arabidopsis CIB1 (cryptochrome-interacting basic-helix-loop-helix) protein. CIB1 interacts with CRY2 (cryptochrome 2) in a blue light-specific manner in yeast and Arabidopsis cells, and it acts together with additional CIB1-related proteins to promote CRY2-dependent floral initiation. CIB1 binds to G box (CACGTG) in vitro with a higher affinity than its interaction with other E-box elements (CANNTG). However, CIB1 stimulates FT messenger RNA expression, and it interacts with chromatin DNA of the FT gene that possesses various E-box elements except G box. We propose that the blue light-dependent interaction of cryptochrome(s) with CIB1 and CIB1-related proteins represents an early photoreceptor signaling mechanism in plants. 10.1126/science.1163927br /iHongtao Liu, Xuhong Yu, Kunwu Li, John Klejnot, Hongyun Yang, Dominique Lisiero, Chentao Lin/i

Publication Date: 2008 Dec 2 PMID: 19050035br/Authors: Wabnik, K. - Hvidsten, T. R. - Kedzierska, A. - Van Leene, J. - De Jaeger, G. - Beemster, G. T. - Komorowski, J. - Kuiper, M. T.br/Journal: Bioinformaticsbr/br/MOTIVATION: Genome-scale 'omics' data constitutes a potentially rich source of information about biological systems and their function. There is a plethora of tools and methods available to mine omics data. However, the diversity and complexity of different omics data types is a stumbling block for multi-data integration, hence there is a dire need for additional methods to exploit potential synergy from integrated orthogonal data. Rough Sets provide an efficient means to use complex information in classification approaches. Here, we set out to explore the possibilities of Rough Sets to incorporate diverse information sources in a functional classification of unknown genes. RESULTS: We explored the use of Rough Sets for a novel data integration strategy where gene expression data, protein features, and GO annotations were combined to describe general and biologically relevant patterns represented by If-Then rules. The descriptive rules were used to predict the function of unknown genes in Arabidopsis thaliana and Schizosaccharomyces pombe. The If-Then rule models showed success rates of up to 0.89 (discriminative and predictive power for both modeled organisms) whereas models built solely of one data type (protein features or gene expression data) yielded success rates varying from 0.68 to 0.78. Our models were applied to generate classifications for many unknown genes, of which a sizeable number were confirmed either by PubMed literature reports or electronically interfered annotations. Finally, we studied cell cycle protein-protein interactions derived from both tandem affinity purification (TAP) experiments and in silico experiments in the BioGRID interactome database and found strong experimental evidence for the predictions generated by our models. The results show that our approach can be used to build very robust models that create synergy from integrating gene expression data and protein fea-tures. AVAILABILITY: The Rough Set-based method is implemented in the Rosetta toolkit kernel version 1.0.1 available at: http://rosetta.lcb.uu.se/ CONTACT: kuiper@nt.ntnu.no; krwab@psb.ugent.be SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19050035title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Nov 20 PMID: 19046974br/Authors: Pathuri, P. - Nguyen, E. T. - Ozorowski, G. - Svard, S. G. - Luecke, H.br/Journal: J Mol Biolbr/br/Alpha-14 giardin (annexin E1), a member of the alpha giardin family of annexins, has been shown to localize to the flagella of the intestinal protozoan parasite Giardia lamblia. Alpha giardins show a common ancestry with the annexins, a family of proteins most of which bind to phospholipids and cellular membranes in a Ca(2+)-dependent manner and are implicated in numerous membrane-related processes including cytoskeletal rearrangements and membrane organization. It has been proposed that alpha-14 giardin may play a significant role during the cytoskeletal rearrangement during differentiation of Giardia. To gain a better understanding of alpha-14 giardin's mode of action and its biological role, we have determined the three-dimensional structure of alpha-14 giardin and its phospholipid-binding properties. Here, we report the apo crystal structure of alpha-14 giardin determined in two different crystal forms as well as the Ca(2+)-bound crystal structure of alpha-14 giardin, refined to 1.9, 1.6 and 1.65 A, respectively. Although the overall fold of alpha-14 giardin is similar to that of alpha-11 giardin, multiwavelength anomalous dispersion phasing was required to solve the alpha-14 giardin structure, indicating significant structural differences between these two members of the alpha giardin family. Unlike most annexin structures, which typically possess N-terminal domains, alpha-14 giardin is composed of only a core domain, followed by a C-terminal extension that may serve as a ligand for binding to cytoskeletal protein partners in Giardia. In the Ca(2+)-bound structure we detected five bound calcium ions, one of which is a novel, highly coordinated calcium-binding site not previously observed in annexin structures. This novel high-affinity calcium-binding site is composed of seven protein donor groups, a feature rarely observed in crystal structures. In addition, phospholipid-binding assays suggest that alpha-14 giardin exhibits calcium-dependent binding to phospholipids that coordinate cytoskeletal disassembly/assembly during differentiation of the parasite.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19046974title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Nov 20 PMID: 19046973br/Authors: Synowsky, S. A. - van Wijk, M. - Raijmakers, R. - Heck, A. J.br/Journal: J Mol Biolbr/br/Here we combined tandem affinity purification with several mass-spectrometry-based approaches to gain more insight into the composition and structure of the yeast nuclear-cytoplasmic exosome protein complex. The yeast exosome fulfills several different functions in RNA metabolism and can be localized in both the cytoplasm and the nucleus. These two exosome complexes differ in protein composition, although they share several constituents. We focused on these differences in composition by selecting a nuclear-specific exosome protein (Rrp6) and a cytoplasmic-specific protein (Ski7) as the tandem-affinity-purification-tagged affinity bait protein. First, we investigated both these purified exosome assemblies by macromolecular mass spectrometry (MS) to determine the stability and mass of the intact protein complexes and to obtain information on composition and core constituents. We used tandem MS on these intact protein complexes to further probe the composition and to obtain insight into the peripheral nature of some of the constituents. Finally, we combine stable isotope labeling with MS to quantitate differences in exosome composition and their posttranslational modifications. We identified a few phosphorylation sites that are differentially regulated between the cytoplasmic exosome and the nuclear exosome. From all of these data, we conclude that the yeast nuclear exosome and the cytoplasmic exosome share a common stable core complex, but are decorated with quite a few differing peripheral proteins. We show that the nuclear exosome selectively copurifies with the alpha/beta importin heterodimer, which is known to be involved in the transport of proteins across the nuclear membrane.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19046973title=Entrez+PubmedCiteULike/a

Publication Date: 2008 Dec 1 PMID: 19046422br/Authors: Naiser, T. - Kayser, J. - Mai, T. - Michel, W. - Ott, A.br/Journal: BMC Bioinformaticsbr/br/ABSTRACT: BACKGROUND: The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR. Yet our understanding of oligonucleotide hybridization, in particular in presence of surfaces, is rather limited. Here we use oligonucleotide microarrays made in-house by optically controlled DNA synthesis to produce probe sets comprising all possible single base mismatches and base bulges for each of 20 sequence motifs under study. RESULTS: We observe that mismatch discrimination is mostly determined by the defect position (relative to the duplex ends) as well as by the sequence context. We investigate the thermodynamics of the oligonucleotide duplexes on the basis of double-ended molecular zipper. Theoretical predictions of defect positional influence as well as long range sequence influence agree well with the experimental results. CONCLUSIONS: Molecular zipping at thermodynamic equilibrium explains the binding affinity of mismatched DNA duplexes on microarrays well. The position dependent nearest neighbor model (PDNN) can be inferred from it. Quantitative understanding of microarray experiments from first principles is in reach.br/br/post to: a href = http://www.citeulike.org/posturl?url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Fcmd%3DRetrieve%26db%3DPubMed%26dopt%3DAbstract%26list_uids%3D19046422title=Entrez+PubmedCiteULike/a

pFiled under: a href="http://www.autoblog.com/category/etc/" rel="tag"Etc./a, a href="http://www.autoblog.com/category/green/" rel="tag"Green/a, a href="http://www.autoblog.com/category/tech/" rel="tag"Tech/a/pa href="http://ecomodder.com/blog/a-672-electric-car/"img vspace="4" hspace="4" border="0" alt="" src="http://www.blogcdn.com/www.autoblog.com/media/2008/11/forkenswift_spark.jpg" //abr /br /Don't want to wait for the Chevrolet Volt? Don't feel like spending tens of thousands of dollars on a new green car? Combine your thrift, environmental consciousness and affinity for wrench turning by building your own electric car. Canadians Darin Cosgrove and Ivan Limburg have electrified a Geo Metro for less than $1,000 and you can too! Starting with a Metro helps set expectations, as the converted car is not fast and suitable only for low speed in-town tripping, but the original was no paragon of performance anyway. a href="http://www.autobloggreen.com/tag/forkenswift/"AutoblogGreen covered some of the ForkenSwift's construction/a, but we thought it'd be a good thing to revisit. The winter months are upon us, and building an EV in the garage is a nice way to stay out of the snow. br /br /After stripping out the gas engine and its associated plumbing, the duo sold the engine and fuel tank; we're amazed that there's a market for Metro engines. A $500 used forklift provided the DC motors and control systems, and the carcass provided good scrap value once the vital organs were harvested, helping offset costs. A used bank of batteries were donated by another EV owner, though new batteries would boost performance and range. But hey, nothing's as cheap as free. Finding a Metro for cheap might be a neat trick now that prices have a href="http://www.autoblog.com/2008/05/16/geo-metros-going-for-big-money-on-high-gas-prices/"been inflated/a, but any old light thing will work. For a total tally of $672, who can complain with the results? emThanks for the tip, Maxim. /embr /br /[Source: a href="http://ecomodder.com/blog/a-672-electric-car/"Ecomodder/a]p style="padding:5px;background:#ddd;border:1px solid #ccc;clear:both;"a href="http://www.autoblog.com/2008/12/03/cheapskate-greenies-canadians-build-sub-1k-diy-electric-car/"Cheapskate Greenies! Canadians build sub-$1K DIY electric car/a originally appeared on a href="http://www.autoblog.com"Autoblog/a on Wed, 03 Dec 2008 19:00:00 EST. Please see our a href="http://www.weblogsinc.com/feed-terms/"terms for use of feeds/a./ph6 style="clear: both; padding: 8px 0 0 0; height: 2px; font-size: 1px; border: 0; margin: 0; padding: 0;"/h6a href=http://ecomodder.com/blog/a-672-electric-car/Read/anbsp;|nbsp;a href="http://www.autoblog.com/2008/12/03/cheapskate-greenies-canadians-build-sub-1k-diy-electric-car/" rel="bookmark" title="Permanent link to this entry"Permalink/anbsp;|nbsp;a href="http://www.autoblog.com/forward/1386671/" title="Send this entry to a friend via email"Email this/anbsp;|nbsp;a href="http://www.autoblog.com/2008/12/03/cheapskate-greenies-canadians-build-sub-1k-diy-electric-car/#comments" title="View reader comments on this entry"Comments/a pa href="http://feedads.googleadservices.com/~at/IdVH6drY6x-YEVAjlseYc99FthA/a"img src="http://feedads.googleadservices.com/~at/IdVH6drY6x-YEVAjlseYc99FthA/i" border="0" ismap="true"/img/a/pdiv class="feedflare" a href="http://feedproxy.google.com/~f/weblogsinc/autoblog?a=QIkqojKy"img src="http://feedproxy.google.com/~f/weblogsinc/autoblog?i=QIkqojKy" border="0"/img/a a href="http://feedproxy.google.com/~f/weblogsinc/autoblog?a=lRZwTieC"img src="http://feedproxy.google.com/~f/weblogsinc/autoblog?i=lRZwTieC" border="0"/img/a /divimg src="http://feedproxy.google.com/~r/weblogsinc/autoblog/~4/kTOlOFTVQ2s" height="1" width="1"/