dbEST‐derived microsatellite markers in celery (Apium graveolens L. var. dulce)

We report on the development of 11 (from database expressed sequence tags) dbEST‐derived microsatellite markers in celery (Apium graveolens L. var. dulce). The sequences were obtained from DNA accessions available from GenBank and contained di‐, tri‐ and pentanucleotidic motifs. All the microsatellites were found in expressed sequence tags and they are expected to become useful tools for ecological, genetic and evolutionary studies, as well as for celery breeding. Polymorphism was explored in 16 celery commercial varieties, and marker transferability was tested on three accessions of celeriac (A. graveolens var. rapaceum). Primers and PCR conditions for microsatellite amplification are reported.     

Metabolic Enzyme Alterations and Astrocyte Dysfunction in a Murine Model of Alexander Disease With Severe Reactive Gliosis

Alexander disease (AxD) is a rare and fatal neurodegenerative disorder caused by mutations in the gene encoding glial fibrillary acidic protein (GFAP). In this report, a mouse model of AxD (GFAP^Tg;Gfap^+/R236H) was analyzed that contains a heterozygous R236H point mutation in murine Gfap as well as a transgene with a GFAP promoter to overexpress human GFAP. Using label-free quantitative proteomic comparisons of brain tissue from GFAP^Tg;Gfap^+/R236H versus wild-type mice confirmed upregulation of the glutathione metabolism pathway and indicated proteins were elevated in the peroxisome proliferator-activated receptor (PPAR) signaling pathway, which had not been reported previously in AxD. Relative protein-level differences were confirmed by a targeted proteomics assay, including proteins related to astrocytes and oligodendrocytes. Of particular interest was the decreased level of the oligodendrocyte protein, 2-hydroxyacylsphingosine 1-beta-galactosyltransferase (Ugt8), since Ugt8-deficient mice exhibit a phenotype similar to GFAP^Tg;Gfap^+/R236H mice (e.g., tremors, ataxia, hind-limb paralysis). In addition, decreased levels of myelin-associated proteins were found in the GFAP^Tg;Gfap^+/R236H mice, consistent with the role of Ugt8 in myelin synthesis. Fabp7 upregulation in GFAP^Tg;Gfap^+/R236H mice was also selected for further investigation due to its uncharacterized association to AxD, critical function in astrocyte proliferation, and functional ability to inhibit the anti-inflammatory PPAR signaling pathway in models of amyotrophic lateral sclerosis (ALS). Within Gfap⁺ astrocytes, Fabp7 was markedly increased in the hippocampus, a brain region subjected to extensive pathology and chronic reactive gliosis in GFAP^Tg;Gfap^+/R236H mice. Last, to determine whether the findings in GFAP^Tg;Gfap^+/R236H mice are present in the human condition, AxD patient and control samples were analyzed by Western blot, which indicated that Type I AxD patients have a significant fourfold upregulation of FABP7. However, immunohistochemistry analysis showed that UGT8 accumulates in AxD patient subpial brain regions where abundant amounts of Rosenthal fibers are located, which was not observed in the GFAP^Tg;Gfap^+/R236H mice.     

CLIX: a search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure.

A computer algorithm, CLIX, capable of searching a crystallographic data-base of small molecules for candidates which have both steric and chemical likelihood of binding a protein of known three-dimensional structure is presented. The algorithm is a significant advance over previous strategies which consider solely steric or chemical requirements for binding. The algorithm is shown to be capable of predicting the correct binding geometry of sialic acid to a mutant influenza-virus hemagglutinin and of proposing a number of potential new ligands to this protein.     

A 5.8S nuclear ribosomal RNA gene sequence database: applications to ecology and evolution

We compiled a 5.8S nuclear ribosomal gene sequence database for animals, plants, and fungi using both newly generated and GenBank sequences. We demonstrate the utility of this database as an internal check to determine whether the target organism and not a contaminant has been sequenced, as a diagnostic tool for ecologists and evolutionary biologists to determine the placement of asexual fungi within larger taxonomic groups, and as a tool to help identify fungi that form ectomycorrhizae.     

Characterization of rabbit DNA micros extracted from the EMBL nucleotide sequence database

Microsatellite polymorphisms are invaluable for mapping vertebrate genomes. In order to estimate the occurrence of microsatellites in the rabbit genome and to assess their feasibility as markers in rabbit genetics, a survey on the presence of all types of mononucleotide, dinucleotide, trinucleotide and tetranucleotide repeats, with a length of about 20 bp or more, was conducted by searching the published rabbit DNA sequences in the EMBL nucleotide database (version 32). A total of 181 rabbit microsatellites could be extracted from the present database. The estimated frequency of microsatellites in the rabbit genome was one microsatellite for every 2–3 kb of DNA. Dinucleotide repeats constituted the prevailing class of microsatellites, followed by trinucleotide, mononucleotide and tetranucleotide repeats, respectively. The average length of the microsatellites, as found in the database, was 26, 23, 23 and 22 bp for mono-, di-, tri- and tetranucleotide repeats, respectively. The most common repeat motif was AG, followed by A, AC, AGG and CCG. This group comprised about 70% of all extracted rabbit microsatellites. About 61% of the microsatellites were found in non-coding regions of genes, whereas 15% resided in (protein) coding regions. A significant fraction of rabbit microsatellites (about 22%) was found within interspersed repetitive DNA sequences.     

Developmental status of the French consumer home product information database

Summary The purpose of this study is, first, to perform a national data bank cellecting as many data as possible for various household products with attention to the frequency of their use and, secondly, to determine their volatile organic compound (VOC) emissions.     

Open exchange of scientific knowledge and European copyright: The case of biodiversity information

Background. The 7^th Framework Programme for Research and Technological Development is helping the European Union to prepare for an integrative system for intelligent management of biodiversity knowledge. The infrastructure that is envisaged and that will be further developed within the Programme “Horizon 2020” aims to provide open and free access to taxonomic information to anyone with a requirement for biodiversity data, without the need for individual consent of other persons or institutions. Open and free access to information will foster the re-use and improve the quality of data, will accelerate research, and will promote new types of research. Progress towards the goal of free and open access to content is hampered by numerous technical, economic, sociological, legal, and other factors. The present article addresses barriers to the open exchange of biodiversity knowledge that arise from European laws, in particular European legislation on copyright and database protection rights.We present a legal point of view as to what will be needed to bring distributed information together and facilitate its re-use by data mining, integration into semantic knowledge systems, and similar techniques. We address exceptions and limitations of copyright or database protection within Europe, and we point to the importance of data use agreements. We illustrate how exceptions and limitations have been transformed into national legislations within some European states to create inconsistencies that impede access to biodiversity information.Conclusions. The legal situation within the EU is unsatisfactory because there are inconsistencies among states that hamper the deployment of an open biodiversity knowledge management system. Scientists within the EU who work with copyright protected works or with protected databases have to be aware of regulations that vary from country to country. This is a major stumbling block to international collaboration and is an impediment to the open exchange of biodiversity knowledge. Such differences should be removed by unifying exceptions and limitations for research purposes in a binding, Europe-wide regulation.     

Minority of mammalian orthologs can be regarded as physiologically closest genes

Orthologs are genes from different genomes that originate from a common ancestor gene by speciation event. They are most similar by the structure of encoded proteins and therefore should have a similar function. Here I apply the principle used for detection of structural orthology for a genome-wide analysis of gene expression. For this purpose, I determine the mutual similarity rank in all-by-all comparison of among-tissues expression patterns. The expression of most part of human–mouse orthologs in homologous tissues is poorly correlated (average mutual coexpression rank is only 4835 out of 18,092). Genes from evolutionarily labile gene families, which experience rapid turnover of family composition, are among those with the strongest expression change. However, the revealed phenomenon is not limited to them. There is no or very weak relationship between protein sequence divergence and mutual coexpression rank. Also, generally there is no relationship between the ratio of nonsynonymous to synonymous nucleotide substitutions and coexpression rank. This relationship is tangible only within evolutionarily labile gene families. These results indicate that despite of a similar biochemical function of orthologs reflected in the conserved protein sequence, the physiological (systemic) context of this function can be changed. Also, these results suggest that gene biochemical function and its physiological role in the organism can evolve independently.