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Rockville, MD, United States

Saw J.H.W.,University of Hawaii at Manoa | Yuryev A.,Ariadne Genomics Inc. | Kanbe M.,Universiti Sains Malaysia | Hou S.,University of Hawaii at Manoa | And 4 more authors.
Standards in Genomic Sciences | Year: 2012

Saprospira grandis is a coastal marine bacterium that can capture and prey upon other marine bacteria using a mechanism known as 'ixotrophy'. Here, we present the complete genome sequence of Saprospira grandis str. Lewin isolated from La Jolla beach in San Diego, California. The complete genome sequence comprises a chromosome of 4.35 Mbp and a plasmid of 54.9 Kbp. Genome analysis revealed incomplete pathways for the biosynthesis of nine essential amino acids but presence of a large number of peptidases. The genome en-codes multiple copies of sensor globin-coupled rsbR genes thought to be essential for stress response and the presence of such sensor globins in Bacteroidetes is unprecedented. A total of 429 spacer sequences within the three CRISPR repeat regions were identified in the ge-nome and this number is the largest among all the Bacteroidetes sequenced to date.

Ferlini A.,University of Ferrara | Bovolenta M.,University of Ferrara | Neri M.,University of Ferrara | Gualandi F.,University of Ferrara | And 6 more authors.
BMC Medical Genetics | Year: 2010

Background: Multiple sclerosis (MS) is a complex disorder thought to result from an interaction between environmental and genetic predisposing factors which have not yet been characterised, although it is known to be associated with the HLA region on 6p21.32. Recently, a picture of chronic cerebrospinal venous insufficiency (CCSVI), consequent to stenosing venous malformation of the main extra-cranial outflow routes (VM), has been described in patients affected with MS, introducing an additional phenotype with possible pathogenic significance.Methods: In order to explore the presence of copy number variations (CNVs) within the HLA locus, a custom CGH array was designed to cover 7 Mb of the HLA locus region (6,899,999 bp; chr6:29,900,001-36,800,000). Genomic DNA of the 15 patients with CCSVI/VM and MS was hybridised in duplicate.Results: In total, 322 CNVs, of which 225 were extragenic and 97 intragenic, were identified in 15 patients. 234 known polymorphic CNVs were detected, the majority of these being situated in non-coding or extragenic regions. The overall number of CNVs (both extra- and intragenic) showed a robust and significant correlation with the number of stenosing VMs (Spearman: r = 0.6590, p = 0.0104; linear regression analysis r = 0.6577, p = 0.0106).The region we analysed contains 211 known genes. By using pathway analysis focused on angiogenesis and venous development, MS, and immunity, we tentatively highlight several genes as possible susceptibility factor candidates involved in this peculiar phenotype.Conclusions: The CNVs contained in the HLA locus region in patients with the novel phenotype of CCSVI/VM and MS were mapped in detail, demonstrating a significant correlation between the number of known CNVs found in the HLA region and the number of CCSVI-VMs identified in patients. Pathway analysis revealed common routes of interaction of several of the genes involved in angiogenesis and immunity contained within this region. Despite the small sample size in this pilot study, it does suggest that the number of multiple polymorphic CNVs in the HLA locus deserves further study, owing to their possible involvement in susceptibility to this novel MS/VM plus phenotype, and perhaps even other types of the disease. © 2010 Ferlini et al; licensee BioMed Central Ltd.

Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 100.00K | Year: 2003

DESCRIPTION (provided by applicant): This Small Business Innovation and Research Phase I project focuses on the development of the fully automatic system for extraction of the protein function information from MEDLINE abstracts and conversion it into a form of a conceptual graph. All existent protein function databases depend on human experts who cannot keep up with the exponential growth of protein function information freely available in MEDLINE. There is an urgent need for an automatic system capable of extracting protein function information from literature. The system we proposed will be based on advanced natural language processing (NLP) technologies, and uses it as a fast and reliable way to extract information about protein function from human readable sources. To this end, we have developed and tested MedScan - a prototype of such system that parses scientific abstracts and converts protein function information into a form of a conceptual graph. It consists of a preprocessor module selecting candidate sentences from MEDLINE, an NLP module utilizing proprietary linguistic model to parse the selected sentences, and an information extraction module utilizing developed ontology to extract and validate protein function information. The results of MedScan evaluation indicate that it is a feasible candidate for a proposed task. In Phase II, the software system will be developed to assist the researchers to quickly access, search and navigate through the MEDLINE content, and to visualize and analyze the large volumes of protein function data. We will also extend our approach to other areas including pharmacogenomics and extraction of clinically relevant information.

Elsevier and Ariadne Genomics Inc. | Date: 2011-07-28

Computer software for use by others for building and displaying molecular pathways and helping scientists build databases of information in the fields of processing, medical informatics, drug discovery, genetics, molecular biology, and Computer software for use by others for automated extraction of biological facts from biomedical abstracts, and internal text documents; Computer software for use by others that compiles information about molecular interactions in a cell; Computer software for use by others in the field of biotechnology to store, analyze, and manage information about nucleic acids.

Agency: Cordis | Branch: FP7 | Program: CP-FP | Phase: HEALTH-2009-2.4.4-1 | Award Amount: 7.54M | Year: 2009

The rapidly expanding knowledge of NMDs genetic diagnosis, pathogenesis and therapeutic possibilities has provided new targets for disease characterisation, early diagnosis, drug discovery and development as well as has raised many questions about how to translate this knowledge into clinical practice as (initial) clinical trials typically run for such a short time that clinical improvement can hardly be expected within that time frame. This militates for the discovery of surrogate endpoints for establishing the efficacy of clinical trials. The concept of biomarkers represents measurable bio-parameters able to flank the process of diagnosis, functional characterisation and therapy in NMDs. OMIC sciences (genomic, transcriptomics, proteomics) offer opportunities to identify biomarkers for finely defining and tuning the NMDs bases. This approach can make available non-invasive biomarkers, to be used for monitoring disease progression, prognosis and drugs response, therefore optimising the choice of appropriate and often personalised therapies. Validated biomarkers will increase therapy efficiency (meaning optimal dose of drug to get responders) and efficacy (responders vs non responders for example if we will identify genomic biomarkers linked to the lack of any therapeutic effect). In this case we could address a truly efficacious therapy (avoiding inefficacious treatment due to unfavourable genomic contexts). The new genomic and proteomic biomarkers discovered within BIO-NMD will be validated both in animal models and in human samples, before entering into a qualification process at the EMEA. The qualified biomarkers resulting from the BIO-NMD project will be ready for ongoing and further clinical trials for the patient benefit. This will increase the therapy efficacy and efficiency and also reduce adverse effects, with impact on patients quality of life with also economical relevance. The BIO-NMD consortium is led by the University of Ferrara, an internationally recognised university in the field of genomics of hereditary neuromuscular disorders. In addition the consortium is composed of 7 leading European academic partners bringing their expertise in all OMIC sciences as well as in bio-informatics and patient sample collection, 1 SME providing its skills in bio-informatics and 1 global company specialised in the development of patient samples screening.

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