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Cucurbitaceae genetic resources in the Czech gene bank. Current status of the collection National Institute of Agronomic Research
Karlová, K..
The Crop Research Institute, Dept. of Vegetables and Special Crops in Olomouc is responsible for the conservation and documentation of genetic resources of vegetable, medicinal, aromatic, and spice plants. Collections maintained by the department in Olomouc include more than 10,000 accessions of about 430 botanical species and the collection of cucurbitaceous genetic resources with 1,713 accessions potentially available is one of the largest. Unfortunately only about 40 % of them is already regenerated. The collection is distributed in 11 species and the biggest part of collection shapes Cucumis sativus L. and Cucurbita sp.
Tipo: Poster Palavras-chave: Cucurbitacea; Regeneration; Storage; Characterization; Safe duplicate; Genetic resources.
Ano: 2008 URL: http://hdl.handle.net/2174/224
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Curating Genetic Association Literature for Common Diseases Nature Precedings
Elana Silver; Eran Halperin; Kord M. Kober; Badri Padhukasahasram; Nila Patil; Michelle Sommargren; Dietrich A. Stephan; Daryl J. Thomas; Heather Trumbower; Michele Cargill.
Papers describing genetic associations with common diseases are currently being published at a rapid rate. These new papers add to an already large body of literature which includes candidate gene studies, genome wide association studies, review papers, and meta-analyses. Related papers describe the basic epidemiology of these common diseases, as well as interactions between genes and environment, other genes, and drugs (pharmacogenomics), all of which may affect disease predisposition and management. 

As the field of personalized genomics continues to grow and mature, this body of literature is being synthesized in various ways. One aspect of utmost importance is to track gene-disease associations over time to see if...
Tipo: Poster Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3174/version/1
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Curation and annotation for BioModels Database, a resource of published quantitative kinetic models Nature Precedings
Chelliah Vijayalakshmi; Lukas Endler; Camille Laibe; Chen Li; Nicolas Le Novère.
BioModels Database ("http://www.ebi.ac.uk/biomodels/":http://www.ebi.ac.uk/biomodels/) is a free resource for storing, viewing and retrieving published, peer-reviewed, quantitative models of biochemical and cellular systems. As a storage format, BioModels Database uses the Systems Biology Markup Language (SBML), but also allows submission and export of models in various other commonly used formats.

To offer scientists reliable information, models are curated to comply with the MIRIAM (Minimal Information Requested In the Annotation of biochemical Models) standard. This curation process involves verification of the model structure, the parameter and variable values and its mathematical relations....
Tipo: Poster Palavras-chave: Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3124/version/1
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Curation at the NCBI: Genomes, Genes, & Sequence Standards Nature Precedings
Garth Brown; Catherine Farrell; Jennifer Hart; Melissa Landrum; Donna Maglott; Bonnie Maidak; Michael Murphy; Terence Murphy; Bhanu Rajput; Kim D. Pruitt; Lillian Riddick; David Webb; Janet Weber; Wendy Wu.
The National Center for Biotechnology Information (NCBI) provides curation support for many genomes, and disseminates information in several resources including Entrez Gene, reference sequences (RefSeq), the Consensus CDS (CCDS) database, and the Genome Reference Consortium (GRC). These projects are supported by several collaborations to provide:1) support to the international consortium maintaining the assemblies for human and mouse (GRC); 2) sequence standards for chromosomes, genes, transcripts and proteins (RefSeq); 3) reports of integrated information including nomenclature, publications, phenotypes and diseases, sequences, ontologies, interactions (Gene); and 4) identification of proteins that are consistently annotated on the human and mouse...
Tipo: Poster Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3287/version/1
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Curation of NISEED, an integrative framework for the digital representation of embryonic development Nature Precedings
Delphine Dauga; Olivier Tassy; Fabrice Daian; Daniel Sobral; Patrick Lemaire.
NISEED (Network for In situ Expression and Embryological Data) is a generic infrastructure for the creation, maintenance and integration of molecular and anatomical information on model organisms. We applied it to ascidians which are marine invertebrate chordates. These animals constitute model organisms of choice for developmental biology because their embryos develop with a small number of cells and an invariant lineage, allowing their study with a cellular level of resolution. In ANISEED (Ascidian NISEED), embryogenesis of ascidian is represented at the level of the genome via functional gene annotations, cis-regulatory elements or gene expression data, at the level of the cell by representing its morphology, fates, lineage, and relations with its...
Tipo: Poster Palavras-chave: Developmental Biology; Genetics & Genomics; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3168/version/1
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Curcumin Functions as a Positive Regulator of miRNA Processing & a Negative Regulator of Cancer Stem Cell Proliferation Nature Precedings
Lakshmanane P. Boominathan.
Identifying agents that inhibit the proliferation of cancer stem cells is of great importance in cancer biology. Curcumin has been shown to function as an anti-cancer agent. One of the tumor suppressors that appear to be induced in response to curcumin treatment is p53. A recent study suggests that curcumin increases the expression of miRNAs, such as miR-22, miR-181a, b, c, miR-34, miR-103, and miR-21. Intriguingly, miR-34, 181b, c, miR-103, miR-21, and miR-24 have been identified as transcriptional targets of the tumor suppressor p53. This data suggests a possibility that curcumin, by inducing the expression of p53, it could increase the expression of these microRNAs. A number of groups have shown that c-Myc, Sox-2, Klf-4, Oct-4, Sox-2, Nanog, and...
Tipo: Poster Palavras-chave: Cancer.
Ano: 2009 URL: http://precedings.nature.com/documents/4110/version/1
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DARPP-32 is a robust integrator of dopamine and glutamate signals Nature Precedings
Nicolas Le Novere; Eric Fernandez; Renaud Schiappa; Jean-Antoine Girault.
Integration of neurotransmitter and neuromodulator signals in the striatum plays a central role in the functions and dysfunctions of the basal ganglia. DARPP-32 is a key actor of this integration in the GABAergic medium-size spiny neurons, in particular in response to dopamine and glutamate. When phosphorylated by cAMP-dependent protein kinase (PKA) DARPP-32 inhibits protein phosphatase-1 (PP1), whereas when phosphorylated by cyclin-dependent kinase 5 (CDK5) it inhibits PKA. DARPP-32 is also regulated by casein kinases and by several protein phosphatases. These complex and intricate regulations make simple predictions of DARPP-32 dynamic behaviour virtually impossible. We used detailed quantitative modelling of the regulation of DARPP-32 phosphorylation to...
Tipo: Poster Palavras-chave: Neuroscience.
Ano: 2006 URL: http://precedings.nature.com/documents/9/version/1
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Data citation in the wild Nature Precedings
Valerie Enriquez; Sarah Walker Judson; Nicholas M. Walker; Suzie Allard; Robert B. Cook; Heather A. Piwowar; Robert J. Sandusky; Todd J. Vision; Bruce E. Wilson.
Consistent attribution of research data upon reuse is necessary to reward the original data-producing investigators, reconstruct provenance, and inform data sharing policies, tool requirements, and funding decisions. Unfortunately, norms for data attribution are varied and often weak. As part of the DataONE 2010 summer internship program, three interns studied the policies, practice, and implications of current data attribution behavior in the environmental sciences. We found that few policies recommend robust data citation practices: in our preliminary evaluation, only one-third of repositories (n=26), 6% of journals (n=307), and 1 of 53 funders suggested a best practice for data citation. We manually reviewed 500 papers published between 2000 and...
Tipo: Poster Palavras-chave: Ecology; Earth & Environment; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5452/version/1
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Data Mining of the Coffee Rust Genome Nature Precedings
David Octavio Botero-Rozo; William Giraldo; Alvaro Gaitan; Marco Cristancho; Diego M. Riaño-Pachon; Silvia Restrepo.
The genomes of nine isolates of _Hemileia vastatrix_, the causal agent of coffee leaf rust were sequenced by Illumina and 454. Quality control, cleaning and _de novo_ assemblies of data were performed. Since isolates were obtained from the field and it is not possible to produce axenic cultures of _H. vastatrix_, MEGAN software was used to evaluate contamination levels and to select contigs with fungal similarities. Mitochondrial contigs were identified and annotated by comparing this assembly against the _Puccinia_ genome. Furthermore, two transcriptomes from isolates of _H. vastatrix_ were assembled to complement the genomic data.
Tipo: Poster Palavras-chave: Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2012 URL: http://precedings.nature.com/documents/7034/version/1
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Data submission and curation for caArray, a standard based microarray data repository system Nature Precedings
X Bian; J Klemm; A Basu; J Hadfield; R Srinivasa; T Parnell; S Miller; W Mason; D Kokotov; M Duncan; P Duvall; L Gurses; T Boal; L Misquitta; D Swan; R Wysong; A Klink; A Johnson; G Fontenay; J Liu; M Colbert; G Komatsoulis.
caArray is an open-source, open development, web and programmatically accessible array data management system developed at National Cancer Institute. It was developed to support the exchange of array data across the Cancer Biomedical Informatics Grid (caBIG™), a collaborative information network that connect scientists and practitioners through a shareable and interoperable infrastructure to share data and knowledge. caArray adopts a federated model of local installations, in which data deposited are shareable across caBIG™. 

Comprehensive in annotation yet easy to use has always been a challenge to any data repository system. To alleviate this difficulty, caArray accepts data upload using the...
Tipo: Poster Palavras-chave: Cancer; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3138/version/1
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DDBJ Activities: Contribution to the Research in Information Biology Nature Precedings
Jun Mashima; Takehide Kosuge; Toshihisa Okido; Yuichi Kodama; Kazuho Ikeo; Hideaki Sugawara; Yoshio Tateno; Takashi Gojobori.
DDBJ (DNA Data Bank of Japan; "http://www.ddbj.nig.ac.jp/":http://www.ddbj.nig.ac.jp/)started its database activities in 1986. From the beginning, DDBJ has been one of INSDC (International Nucleotide Sequence Database Collaboration; "http://www.insdc.org/":http://www.insdc.org/) that is a tripartite collaboration with EMBL-Bank/EBI and GenBank/NCBI.The total base number of the primary nucleotide sequence data collected and distributed by INSDC exceeded 100 Gbases in August 2005. Since then it took only three years for the total base number to be doubled (200 Gbases). Now, the collaboration is being expanded to Traces (DNA sequence chromatograms) and Short Reads (raw reads data from 454, Solexa, SOLiD etc). DDBJ is also...
Tipo: Poster Palavras-chave: Genetics & Genomics; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3211/version/1
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DDBJ Sequence Read Archive / DDBJ Omics Archive Nature Precedings
Yuichi Kodama; Satoshi Saruhashi; Eli Kaminuma; Hideaki Sugawara; Toshihisa Takagi; Kousaku Okubo; Yasukazu Nakamura.
Massively parallel sequencers become widespread and produce unprecedented amounts of sequence reads in many biological fields. DNA Data Bank of Japan (DDBJ) has constructed the international sequence database collaboration (INSDC) together with EBI and NCBI. In 2008, DDBJ has established the DDBJ Read Archive (DRA) to archive raw output data from the new sequencing platforms. DRA archives and provides the raw data sets together with the other two INSDC partners the Sequence Read Archive (SRA) at NCBI and the European Sequence Read Archive (ERA) at EBI. These new sequencing platforms are also used to count DNA/RNA molecules instead of microarray experiment because of their higher accuracy. Since 2004, DDBJ has operated CIBEX as a repository database for...
Tipo: Poster Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010 URL: http://precedings.nature.com/documents/5085/version/1
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Decadal-scale changes in seagrass coverage on the Mississippi barrier islands, northern Gulf of Mexico Nature Precedings
Gregory A. Carter; G. Alan Criss; Gabriel A. Blossom; Patrick D. Biber.
Seagrasses provide habitat for a wide variety of aquatic species, and reduce coastal erosion via sediment stabilization. The areal coverage of seagrass beds on the Mississippi barrier islands appears to have declined substantially since the 1960s. However, difficulties in sampling benthic vegetation, differences among previous studies in survey methods, and a lack of data on year-to-year variation in coverage have impeded quantitative study of this decline. Thus, the goal of the present study was to utilize historical remote sensing data to quantitatively determine changes in seagrass (predominantly Halodule wrightii Ascherson) coverage on the Mississippi barrier islands. Analyses were limited to imagery acquired during late summer through autumn, when...
Tipo: Poster Palavras-chave: Ecology; Earth & Environment; Plant Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/3669/version/1
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Deciphering the phylogenetic history of neuroserpin orthologs across metazoans by analysis of synteny and rare genomic characters Nature Precedings
Abhishek Kumar; Hermann Ragg.
The superfamily of serine proteinase inhibitors (serpins) is involved in wide arrays of fundamental biological processes such as blood coagulation, complement activation, fibrinolysis, angiogenesis, inflammation and tumor suppression. The average protein size of a serpin family member is 350-400 amino acids, but gene structure varies in terms of number and position of exons and introns. All known serpins can be grouped into 16 clades and 10 orphan sequences. Vertebrate serpins can be conveniently classified into six sub-groups, based on three independent biological features - genomic organization, diagnostic amino acid sites and rare indels.
The objective of this study was to elucidate the phylogenetic kinships of serpins involved in...
Tipo: Poster Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/2496/version/1
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Decoding Sequence Classification Models for Acquiring New Biological Insights Nature Precedings
Ulrich Bodenhofer; Andreas Kothmeier; Ingrid G. Abfalter; Carsten C. Mahrenholz; Sepp Hochreiter.
Classifying biological sequences is one of the most important tasks in computational biology. In the last decade, support vector machines (SVMs) in combination with sequence kernels have emerged as a de-facto standard. These methods are theoretically well-founded, reliable, and provide high-accuracy solutions at low computational cost. However, obtaining a highly accurate classifier is rarely the end of the story in many practical situations. Instead, one often aims to acquire biological knowledge about the principles underlying a given classification task. SVMs with traditional sequence kernels do not offer a straightforward way of accessing this knowledge.

In this contribution, we propose a new approach to analyzing...
Tipo: Poster Palavras-chave: Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4708/version/1
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Decomposing CO2 emissions data into a pair of logistic growth pulses Nature Precedings
Gleb G. Alexandrov.
Numerous scenarios of emissions growth presume that it can not grow infinitely: there are certain limits that may not or must not be exceeded. Applying the theory of pulsing logistic growth, I detected two pulses of logistic growth. This led me to the conclusion that constructing a scenario of emissions growth one should pay attention to the fact that limits to their growth do not remain constant.
Tipo: Poster Palavras-chave: Earth & Environment.
Ano: 2010 URL: http://precedings.nature.com/documents/4306/version/1
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Demographic vital rates and population growth: rethinking the relationship in a harvested elk population Nature Precedings
Jonathan M. Conard; Philip S. Gipson.
Understanding the nature of the relationship between demographic vital rates and the rate of population change (λ) is important for determining effective strategies for population management and conservation. We examined the relative impacts of various demographic vital rates on λ within the range of temporal vital rate variability observed in a harvested population to test the hypotheses that adult survival rates in ungulates are relatively invariant when compared to other vital rates and that variability in calf survival has a greater influence on rates of population change than adult survival. Vital rates were estimated for an elk (_Cervus elaphus_) population at Fort Riley, Kansas from October 2003 – February 2007. The...
Tipo: Poster Palavras-chave: Ecology; Earth & Environment.
Ano: 2009 URL: http://precedings.nature.com/documents/3609/version/1
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Denitrification Hotspots and N20 Flux in Fluvial Systems Nature Precedings
Julia Hyman; Arthur Gold; Kelly Addy; Ken Forshay; Paul Mayer; Peter Groffman.
a)	Background/Question/Methods
Watersheds have a profound capacity to retain and remove nitrogen (N) inputs before entering coastal waters thereby minimizing eutrophication and hypoxia in estuarine waters. Research suggests that much of this N cycling occurs within aquatic ecosystems, e.g., lakes, streams and wetlands, which may become “hotspots” of nitrous oxide (N2O) production. We examined the effects of woody debris on nitrate removal and denitrification rates in streams of different N enrichment levels. Three different standardized substrates (fresh wood blocks, bundles of naturally occurring streambed wood, and clay‐fired blocks) that were expected to vary in their pool of labile carbon were...
Tipo: Poster Palavras-chave: Ecology; Earth & Environment.
Ano: 2010 URL: http://precedings.nature.com/documents/5284/version/1
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Design and development of a Europe-wide case specific monitoring method Nature Precedings
Angelika Ziegler; Wenke Mönkemeyer; Ralf Wilhelm; Kerstin Schmidt.
Directive 2001/18 EC demands the cultivation of genetically modified organisms (GMO) to be accompanied by post-market environmental monitoring (PMEM). It is composed of a general surveillance for unanticipated adverse effects and case specific monitoring (CSM), which is set up to reduce substantial uncertainties in relevant risk scenarios identified in the environmental risk assessment. PMEM should also allow early identification of potential long-term effects of cultivating GMOs. It should facilitate decisions in risk management.
In this project, a method for a Europe-wide CSM was to be developed. Starting with critical questions from ERA, exposure scenarios (first for non target organisms, later for all other partitions of the ERA) were...
Tipo: Poster Palavras-chave: Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4472/version/1
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Designing Novel Lead Molecules For Human Ribosomal Protein S6 Kinase Beta-1 Involved In Cancers: Ligand Based Virtual Screening Approach Nature Precedings
Nainaru Ganesh; Dibyabhaba Pradhan; Amineni Umamaheswari.
Protein kinases are clinically relevant and attractive drug targets for most of the cancerous diseases. Ribosomal protein s6 kinase (P70s6 kinase) is a mitogen activated Ser/Thr protein kinase, essential for cell growth, G1 cell cycle progression and cell survival. Human P70s6 kinase is involved in different signaling pathways and phosphorylates the downstream S6 protein of the 40S ribosomal subunit there by controlling the translational activity. Over expression of human P70s6 or rapid amplification of gene (RPS6KB1) leads to rapid cell proliferation causing cancer in various organs of humans like colon, breast, ovary, etc. The over expression is principally due to activation of some phosphorylating sites or ATP binding sites in the domain regions. In the...
Tipo: Poster Palavras-chave: Cancer; Bioinformatics.
Ano: 2010 URL: http://precedings.nature.com/documents/4906/version/1
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