Related GMR Articles

Abiotic stress; Fatty acids; Proteomics; Transcriptomics; Zea mays

The aim of this study was to characterize maize lines tolerant to cold temperatures during the germination process. Seeds from lines with different levels of tolerance to low temperatures were used; 3 lines were classified as tolerant and 3 as susceptible to low germination temperatures. A field was set up to multiply seeds from selected lines. After the seeds were harvested and ... more

I.C. Silva-Neta; E.V. Pinho; A.D. Veiga; R.G. Pìnho; R.M. Guimarães; F. Caixeta; H.O. Santos; T.L. Marques
Data integration; Sequence Retrieval System; SOAP; Web services; XML

Data integration has become an important task for biological database providers. The current model for data exchange among different sources simplifies the manner that distinct information is accessed by users. The evolution of data representation from HTML to XML enabled programs, instead of humans, to interact with biological databases. We present here SRS.php, a PHP library that can ... more

A. Barbosa-Silva; E. Pafilis; J.M. Ortega; R. Schneider
Cellular function; Data integration; Knowledge data discovery; Ontology

We present the MOlecular NETwork (MONET) ontology as a model to integrate data from different networks that govern cell function. To achieve this, different existing ontologies were analyzed and an integrated ontology was built in a way to make it possible to share and reuse knowledge, support interoperability between systems, and also allow the formulation of hypotheses through ... more

E. Battistella; J.G.C. de Souza; C.K. Barcellos; N. Lemke; J.C.M. Mombach
Data integration; Gene regulatory network; STAT6; Th2 cells; Transcription factors

Data integration has become a useful strategy for uncovering new insights into complex biological networks. We studied whether this approach can help to delineate the signal transducer and activator of transcription 6 (STAT6)-mediated transcriptional network driving T helper (Th) 2 cell fate decisions. To this end, we performed an integrative analysis of publicly available RNA-seq data of ... more

M. Jargosch; S. Kröger; E. Gralinska; U. Klotz; Z. Fang; W. Chen; U. Leser; J. Selbig; D. Groth; R. Baumgrass; M. Jargosch; S. Kröger; E. Gralinska; U. Klotz; Z. Fang; W. Chen; U. Leser; J. Selbig; D. Groth; R. Baumgrass
BLAST; Databases; Driver

There are many bioinformatics tools that deal with input/output (I/O) issues by using filing systems from the most common operating systems, such as Linux or MS Windows. However, as data volumes increase, there is a need for more efficient disk access, ad hoc memory management and specific page-replacement policies. We propose a device driver that can be used by multiple ... more

R.Campos Mauro; S. Lifschitz
FASTA; Functional classification; Genome evolution; Mycobacteria; MySQL; Perl programming

Several databases and computational tools have been created with the aim of organizing, integrating and analyzing the wealth of information generated by large-scale sequencing projects of mycobacterial genomes and those of other organisms. However, with very few exceptions, these databases and tools do not allow for massive and/or dynamic comparison of these data. GenoMycDB ( ... more

M. Catanho; D. Mascarenhas; W. Degrave; A.Basílio de Miranda
Amniotic fluid; Human phosphate binding protein; Proteomics

Human amniotic fluid is of both maternal and fetal origin; it protects the fetus and provides the environment for growth and development of the fetus. We used a proteomics-based approach for targeting and purifying human phosphate binding protein, a member of the DING family of proteins from amniotic fluid, using Blue Sepharose CL-6B, DEAE-Sephacel and gel filtration chroma­tography. The ... more

M. Alam; M. Mahajan; M. Raziuddin; T.P. Singh; S. Yadav
Biomarkers; Non-tumoral breast tissue; Proteomics

Breast cancer is a complex and heterogeneous disease. In spite of the advances made in recent decades, a better understanding of the intrinsic mechanisms of this disease is crucial. The development of new biomarkers is absolutely necessary to improve diagnosis and prognosis. Research using the proteomic approach has generated interesting results; however, the complexity of the mammary ... more

G.G. Costa; R. Kaviski; L.E.R. Souza; C.A. Urban; R.S. Lima; I.J. Cavalli; E.M.S.F. Ribeiro
MALDI-TOF MS; Musa acuminate Colla; Proteomics; Two-dimensional gel electrophoresis

To establish a proteomic reference map of Musa acuminate Colla (banana) leaf, we separated and identified leaf proteins using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Tryptic digests of 44 spots were subjected to peptide mass fingerprinting (PMF) by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. Three ... more

Y. Lu; Y.X. Qi; H. Zhang; H.Q. Zhang; J.J. Pu; Y.X. Xie
Multiple sclerosis; Neuromyelitis optica; Proteomics

This study aimed to identify the proteins that are differentially expressed in sera of multiple sclerosis (MS) patients, neuromyelitis optica (NMO) patients, and normal controls by using a two-dimensional gel electrophoresis (2-DE) assay. Serum samples were collected from the 3 groups, and total proteins were isolated and quantified by using the Bradford assay. The 2-DE and silver ... more

S.F. Jiang; Q.Y. Lu; S. Hu; Y. Chen; X.L. Liu; Y. Yang; M.P. Ding