Identificação e avaliação de estratégias de desenvolvimento territorial em áreas de cafeicultura familiar do sul de Minas Gerais.

Este texto se refere a uma pesquisa (?Identificação e avaliação de estratégias de desenvolvimento rural sustentável para a cafeicultura do Sul de Minas?, subprojeto componente do projeto ?Estratégias, modelos e geotecnologias para a caracterização e monitoramento de agroecossistemas cafeeiros de Minas Gerais?, coordenado pela Embrapa Café) em andamento que analisa as relações sócio-ambientais do espaço rural, mais especificamente as que tratam do processo de desenvolvimento rural sustentável das famílias produtoras de café dos de Machado, Campestre e Poço Fundo, Sul de Minas Gerais. A pesquisa optou por uma combinação de métodos científicos que foca o uso eficaz dos recursos naturais e valoriza o conhecimento e cultura locais. De maneira abrangente, três preocupações estruturam o subprojeto: 1) a caracterização de territórios, sob os aspectos físico-ambiental, técnico, comercial, cultural e socioeconômico; 2) a análise da qualidade do café e 3) apoio às dinâmicas sociais e territoriais valorizando ativos específicos da região da cultura cafeeira

Identificação e avaliação de estratégias de desenvolvimento territorial em áreas de cafeicultura familiar do sul de Minas Gerais.

Este texto se refere a uma pesquisa (?Identificação e avaliação de estratégias de desenvolvimento rural sustentável para a cafeicultura do Sul de Minas?, subprojeto componente do projeto ?Estratégias, modelos e geotecnologias para a caracterização e monitoramento de agroecossistemas cafeeiros de Minas Gerais?, coordenado pela Embrapa Café) em andamento que analisa as relações sócio-ambientais do espaço rural, mais especificamente as que tratam do processo de desenvolvimento rural sustentável das famílias produtoras de café dos de Machado, Campestre e Poço Fundo, Sul de Minas Gerais. A pesquisa optou por uma combinação de métodos científicos que foca o uso eficaz dos recursos naturais e valoriza o conhecimento e cultura locais. De maneira abrangente, três preocupações estruturam o subprojeto: 1) a caracterização de territórios, sob os aspectos físico-ambiental, técnico, comercial, cultural e socioeconômico; 2) a análise da qualidade do café e 3) apoio às dinâmicas sociais e territoriais valorizando ativos específicos da região da cultura cafeeira

The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

The 19th annual Database Issue of Nucleic Acids Research features descriptions of 92 new online databases covering various areas of molecular biology and 100 papers describing recent updates to the databases previously described in NAR and other journals. The highlights of this issue include, among others, a description of neXtProt, a knowledgebase on human proteins; a detailed explanation of the principles behind the NCBI Taxonomy Database; NCBI and EBI papers on the recently launched BioSample databases that store sample information for a variety of database resources; descriptions of the recent developments in the Gene Ontology and UniProt Gene Ontology Annotation projects; updates on Pfam, SMART and InterPro domain databases; update papers on KEGG and TAIR, two universally acclaimed databases that face an uncertain future; and a separate section with 10 wiki-based databases, introduced in an accompanying editorial. The NAR online Molecular Biology Database Collection, available at http://www.oxfordjournals.org/nar/database/a/, has been updated and now lists 1380 databases. Brief machine-readable descriptions of the databases featured in this issue, according to the BioDBcore standards, will be provided at the http://biosharing.org/biodbcore web site. The full content of the Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/)

Site-Specific mRNA Cleavage for Selective and Quantitative Profiling of Alternative Splicing with Label-Free Optical Biosensors

Alternative splicing of mRNA precursors is a key process in gene regulation, contributing to the diversity of proteomes by the alternative selection of exonic sequences. Alterations in this mechanism are associated with most cancers, enhancing their proliferation and survival, and can be employed as cancer biomarkers. Label-free optical biosensors are ideal tools for the highly sensitive and label-free analysis of nucleic acids. However, their application for alternative splicing analysis has been hampered due to the formation of complex and intricate long-range base-pairing interactions which make the direct detection in mRNA isoforms difficult. To solve this bottleneck, we introduce a methodology for the generation of length-controlled RNA fragments from purified total RNA, which can be easily detected by the biosensor. The methodology seizes RNase H enzyme activity to degrade the upstream and downstream RNA segments flanking the target sequence upon hybridization to specific DNA oligos. It allows the fast and direct monitoring of Fas gene alternative splicing in real time, employing a surface plasmon resonance biosensor. We demonstrate the selective and specific detection of mRNA fragments in the pM-nM concentration range, reducing quantification errors and showing 81% accuracy when compared to RT-qPCR. The site-specific cleavage outperformed random RNA hydrolysis by increasing the detection accuracy by 20%, making this methodology particularly appropriate for label-free quantification of alternative splicing events in complex samples

BioRuby: bioinformatics software for the Ruby programming language

Summary: The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser

miRiadne : a web tool for consistent integration of miRNA nomenclature

The miRBase is the official miRNA repository which keeps the annotation updated on newly discovered miRNAs: it is also used as a reference for the design of miRNA profiling platforms. Nomenclature ambiguities generated by loosely updated platforms and design errors lead to incompatibilities among platforms, even from the same vendor. Published miRNA lists are thus generated with different profiling platforms that refer to diverse and not updated annotations. This greatly compromises searches, comparisons and analyses that rely on miRNA names only without taking into account the mature sequences, which is particularly critic when such analyses are carried over automatically. In this paper we introduce miRiadne, a web tool to harmonize miRNA nomenclature, which takes into account the original miRBase versions from 10 up to 21, and annotations of 40 common profiling platforms from nine brands that we manually curated. miRiadne uses the miRNA mature sequence to link miRBase versions and/or platforms to prevent nomenclature ambiguities. miRiadne was designed to simplify and support biologists and bioinformaticians in re-annotating their own miRNA lists and/or data sets. As Ariadne helped Theseus in escaping the mythological maze, miRiadne will help the miRNA researcher in escaping the nomenclature maze. miRiadne is freely accessible from the URL http://www.miriadne.org