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A conceptual and practical overview of cDNA microarray technology: implications for basic and clinical sciences BJMBR
Mello-Coelho,V. de; Hess,K.L..
cDNA microarray is an innovative technology that facilitates the analysis of the expression of thousands of genes simultaneously. The utilization of this methodology, which is rapidly evolving, requires a combination of expertise from the biological, mathematical and statistical sciences. In this review, we attempt to provide an overview of the principles of cDNA microarray technology, the practical concerns of the analytical processing of the data obtained, the correlation of this methodology with other data analysis methods such as immunohistochemistry in tissue microarrays, and the cDNA microarray application in distinct areas of the basic and clinical sciences.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Biotechnology; CDNA microarray; Gene expression; Genomics.
Ano: 2005 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2005001000011
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A Floricaula/Leafy gene homolog is preferentially expressed in developing female cones of the tropical pine Pinus caribaea var. caribaea Genet. Mol. Biol.
Dornelas,Marcelo Carnier; Rodriguez,Adriana Pinheiro Martinelli.
In angiosperms, flower formation is controlled by meristem identity genes, one of which, FLORICAULA (FLO)/LEAFY (LFY), plays a central role. It is not known if the formation of reproductive organs of pre-angiosperm species is similarly regulated. Here, we report the cloning of a conifer (Pinus caribaea var. caribaea) FLO/LFY homolog, named PcLFY. This gene has a large C-terminal region of high similarity to angiosperm FLO/LFY orthologs and shorter regions of local similarity. In contrast to angiosperms, conifers have two divergent genes resembling LFY. Gymnosperm FLO/LFY proteins constitute a separate clade, that can be divided into two divergent groups. Phylogenetic analysis of deduced protein sequences has shown that PcLFY belongs to the LFY-like clade....
Tipo: Info:eu-repo/semantics/article Palavras-chave: LEAFY; Plant reproduction; Development; Gene expression; Flowering.
Ano: 2005 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572005000200021
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A microarray-based analysis of oocyte quality in the European clam Ruditapes decussatus ArchiMer
De Sousa, Joana Teixeira; Milan, Massimo; Pauletto, Marianna; Bargelloni, Luca; Joaquim, Sandra; Matias, Domitilia; Matias, Ana Margarete; Quillien, Virgile; Leitao, Alexandra; Huvet, Arnaud.
A microarray-based analysis was performed with the objective of describing genomic features of oocytes and looking for potential markers of oocyte quality in the economically important European clam, Ruditapes decussatus. Oocytes of 25 females from Ria de Aveiro, Western coast of Portugal (40°42′N; 08°40′W) were selected for this study and oocyte quality was estimated by success of D-larval rate under controlled conditions, which appeared to vary from 0 to 95 %. By genome-wide expression profiling with a DNA microarray, 526 probes appeared differentially expressed between two groups representing the largest and smallest value of D larval rates, named good (represented by a mean D-larval yield of 57 ± 22%) and poor (9 ± 5%) quality oocytes. Enrichment...
Tipo: Text Palavras-chave: Ruditapes decussatus; Oocyte; Developmental success; Gene expression; Marine bivalve; Transcriptomics.
Ano: 2015 URL: https://archimer.ifremer.fr/doc/00260/37147/35676.pdf
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A moderate threonine deficiency affects gene expression profile, paracellular permeability and glucose absorption capacity in the ileum of piglets ArchiMer
Hamard, Alice; Mazurais, David; Boudry, Gaelle; Le Huerou-luron, Isabelle; Seve, Bernard; Le Floc'H, Nathalie.
High dietary threonine extraction by the digestive tract suggests that threonine contributes to maintain gut physiology. In the present study, we evaluated the impact of a low (6.5 g of threonine/kg diet; LT group) or a control well-balanced threonine diet (9.3 g of threonine/kg diet; C group) given to piglets for 2 weeks on ileal permeability and Na+-dependant glucose absorption capacity in Ussing chambers. The paracellular permeability was significantly increased in the ileum of LT compared to C piglets (P=.017). The Na+-dependent glucose absorption capacity showed a nonsignificant increase in the LT piglets. In addition, we analysed ileal gene expression profiles in the LT and C groups using porcine multitissue cDNA microarrays. Compared to the C...
Tipo: Text Palavras-chave: Threonine; Small intestine; Paracellular permeability; Gene expression.
Ano: 2010 URL: http://archimer.ifremer.fr/doc/00014/12531/9425.pdf
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A parallel algorithm for finding small sets of genes that are enough to distinguish two biological states Genet. Mol. Biol.
Torres,Martha; Barrera,Junior.
GCLASS is an algorithm which explores small samples of two distinct biological states for finding small sets of genes, which form a feature vector that is enough to separate these two states. A typical sample is a set of 60 microarrays, 30 for each biological state, with several thousand genes. The technique consists of the following: a spreading model defined in the space of small sets of genes studied and centered in each feature vector considered; the designing of optimal linear classifiers under this spreading model; and ranking the designed classifiers, based on their error and robustness relative to the spreading. The feature vectors used in the best classifiers are considered the best feature vectors. Due to the great number of potential feature...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Gene expression; Classification; Parallel processing.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572004000400034
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A possible relationship between gluconeogenesis and glycogen metabolism in rabbits during myocardial ischemia Anais da ABC (AABC)
AGUIAR,RAQUEL R. DE; VALE,DANIELA F.; SILVA,RENATO M. DA; MUNIZ,YOLANDA P.; ANTUNES,FERNANDA; LOGULLO,CARLOS; OLIVEIRA,ANDRÉ L.A.; ALMEIDA,ADRIANA J. DE.
ABSTRACT Ischemia is responsible for many metabolic abnormalities in the heart, causing changes in organ function. One of modifications occurring in the ischemic cell is changing from aerobic to anaerobic metabolism. This change causes the predominance of the use of carbohydrates as an energy substrate instead of lipids. In this case, the glycogen is essential to the maintenance of heart energy intake, being an important reserve to resist the stress caused by hypoxia, using glycolysis and lactic acid fermentation. In order to study the glucose anaerobic pathways utilization and understand the metabolic adaptations, New Zealand white rabbits were subjected to ischemia caused by Inflow occlusion technique. The animals were monitored during surgery by pH and...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Gene expression; Glycogen; Ischemia; Myocardium; Rabbit.
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652017000401683
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A tecnologia de microarranjos na identificação de genes de interesse na bovinocultura. Infoteca-e
GIACHETTO, P. F..
Como ferramenta de análise da expressão gênica, a tecnologia dos microarranjos de DNA permite a investigação de milhares de transcritos de um tecido, de maneira simultânea. Essa metodologia tem revolucionado diversas áreas do conhecimento, por meio do aumento substancial da capacidade analítica dos processos moleculares. Hoje, dentro da ciência animal, a disponibilidade desse método de investigação tem permitido aos pesquisadores identificar variações na expressão de determinados genes que possam ocorrer como respostas biológicas devido à condição experimental (idade, raça, estado fisiológico). Sob um aspecto prático, essa tecnologia tem seu papel na identificação de genes envolvidos na determinação de características fenotípicas de interesse econômico, os...
Tipo: Documentos (INFOTECA-E) Palavras-chave: Tecnologia de microarranjos de DNA; Expressão gênica.; Bovinocultura.; Microarray technology; Gene expression; Cattle.
Ano: 2010 URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/885253
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A web-based bioinformatics interface applied to the GENOSOJA project: databases and pipelines Genet. Mol. Biol.
Nascimento,Leandro Costa do; Costa,Gustavo Gilson Lacerda; Binneck,Eliseu; Pereira,Gonçalo Amarante Guimarães; Carazzolle,Marcelo Falsarella.
The Genosoja consortium is an initiative to integrate different omics research approaches carried out in Brazil. Basically, the aim of the project is to improve the plant by identifying genes involved in responses against stresses that affect domestic production, like drought stress and Asian Rust fungal disease. To do so, the project generated several types of sequence data using different methodologies, most of them sequenced by next generation sequencers. The initial stage of the project is highly dependent on bioinformatics analysis, providing suitable tools and integrated databases. In this work, we describe the main features of the Genosoja web database, including the pipelines to analyze some kinds of data (ESTs, SuperSAGE, microRNAs, subtractive...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Bioinformatics; Database; Gene expression; Soybean; Genosoja.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000200002
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Alterations in gene expression profiles correlated with cisplatin cytotoxicity in the glioma U343 cell line Genet. Mol. Biol.
Carminati,Patricia Oliveira; Mello,Stephano Spano; Fachin,Ana Lucia; Junta,Cristina Moraes; Sandrin-Garcia,Paula; Carlotti,Carlos Gilberto; Donadi,Eduardo Antonio; Passos,Geraldo Aleixo Silva; Sakamoto-Hojo,Elza Tiemi.
Gliomas are the most common tumors in the central nervous system, the average survival time of patients with glioblastoma multiforme being about 1 year from diagnosis, in spite of harsh therapy. Aiming to study the transcriptional profiles displayed by glioma cells undergoing cisplatin treatment, gene expression analysis was performed by the cDNA microarray method. Cell survival and apoptosis induction following treatment were also evaluated. Drug concentrations of 12.5 to 300 μM caused a pronounced reduction in cell survival rates five days after treatment, whereas concentrations higher than 25 μM were effective in reducing the survival rates to ~1%. However, the maximum apoptosis frequency was 20.4% for 25 μM cisplatin in cells analyzed at 72 h,...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Apoptosis; Cisplatin; Gene expression; Glioma.
Ano: 2010 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572010000100027
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Alternagin-C, a disintegrin-like protein from the venom of Bothrops alternatus, modulates alpha2ß1 integrin-mediated cell adhesion, migration and proliferation BJMBR
Selistre-de-Araujo,H.S.; Cominetti,M.R.; Terruggi,C.H.B.; Mariano-Oliveira,A.; De Freitas,M.S.; Crepin,M.; Figueiredo,C.C.; Morandi,V..
The alpha2ß1 integrin is a major collagen receptor that plays an essential role in the adhesion of normal and tumor cells to the extracellular matrix. Alternagin-C (ALT-C), a disintegrin-like protein purified from the venom of the Brazilian snake Bothrops alternatus, competitively interacts with the alpha2ß1 integrin, thereby inhibiting collagen binding. When immobilized in plate wells, ALT-C supports the adhesion of fibroblasts as well as of human vein endothelial cells (HUVEC) and does not detach cells previously bound to collagen I. ALT-C is a strong inducer of HUVEC proliferation in vitro. Gene expression analysis was done using an Affimetrix HU-95A probe array with probe sets of ~10,000 human genes. In human fibroblasts growing on collagen-coated...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Alpha2ß1 integrin; Disintegrin; Snake venom; Adhesion; Gene expression; Extracellular matrix.
Ano: 2005 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2005001000007
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Ammonia determines transcriptional profile of microorganisms in anaerobic digestion BJM
Zhang,Nan; Peng,Huijuan; Li,Yong; Yang,Wenxiu; Zou,Yuneng; Duan,Huiguo.
ABSTRACT Anaerobic digestion is important for the management of livestock manure with high ammonia level. Although ammonia effects on anaerobic digestion have been comprehensively studied, the molecular mechanism underlying ammonia inhibition still remains elusive. In this study, based on metatranscriptomic analysis, the transcriptional profile of microbial community in anaerobic digestion under low (1500 mg L-1) and high NH4 + (5000 mg L-1) concentrations, respectively, were revealed. The results showed that high NH4 + concentrations significantly inhibited methane production but facilitated the accumulations of volatile fatty acids. The expression of methanogenic pathway was significantly inhibited by high NH4 + concentration but most of the other...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Anaerobic digestion; Ammonia; Pathway; Gene expression; Methanogenesis.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822018000400770
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Análise de agrupamento de dados de expressão gênica na Rede Genômica Animal. Infoteca-e
HIGA, R. H.; GIACHETTO, P. F.; YAMAGISHI, M. E. B.; IBELLI, A. M. G.; REGITANO, L. C. de A.; CARDOSO, F. F..
O objetivo deste trabalho é apresentar a análise de agrupamento de dados de expressão gênica, conforme realizada no escopo da ?Rede Genômica Animal?. Na seção 2, são apresentados conceitos básicos sobre análises de agrupamento. Em particular, os algoritmos de agrupamento utilizados nessas análises compreendem aqueles mais conhecidos, como k-means, SOM e agrupamento hierárquico. A plataforma de análise escolhida para realização das análises de agrupamento na ?Rede Genômica Animal? é o ambiente de análise estatística R (R DEVELOPMENT CORE TEAM, 2010) e o projeto Bioconductor (GENTLEMAN et al., 2004). Assim, na seção 3 é apresentado um exemplo completo de análise de agrupamento e seu respectivo script R.
Tipo: Comunicado Técnico (INFOTECA-E) Palavras-chave: Agrupamento de dados; Expressão gênica; Rede Genômica Animal; Análise de componentes principais - PCA.; Análise Estatística.; Gene expression; Algorithms; Statistical analysis; Principal component analysis.
Ano: 2010 URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/883623
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Análise de conjunto de genes de dados de expressão gênica na Rede Genômica Animal. Infoteca-e
HIGA, R. H.; IBELLI, A. M. G.; CARDOSO, F. F.; REGITANO, L. C. de A..
O objetivo deste trabalho é apresentar a análise de conjuntos de genes para dados de experssão gênica, conforme utilizada no escopo da RGA. Na seção 2 é apresentado o procedimento correspondente à análise de GSA proposta por (EFRON; TIBSHIRANI, 2007), utilizado na RGA. Um exemplo completo, incluindo principais comandos do correspondente script R é apresentado na seção 3.
Tipo: Comunicado Técnico (INFOTECA-E) Palavras-chave: Bioinformática; Expressão gênica; Rede Genômica Animal; Análise de genes; Bioinformatics; Gene expression.
Ano: 2011 URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/920185
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Análise de dados de RNA-Seq utilizando o Galaxy. Infoteca-e
ZERLOTINI NETO, A.; CINTRA, L. C..
Neste documento, serão apresentados métodos computacionais para facilitar o processo de análise de dados de RNA-Seq, por meio de ferramentas acessíveis via navegadores. Esta metodologia possibilita o processamento distribuído e o compartilhamento de grandes volumes de dados de RNA-Seq, com o objetivo de efetivamente identificarmos as diferenças de expressão de genes para elucidar mecanismos biológicos ligados à produtividade e a doenças.
Tipo: Documentos (INFOTECA-E) Palavras-chave: Bioinformática; Plataforma Galaxy; RNA-Seq; Expressão gênica; Bioinformatics; Gene expression.
Ano: 2016 URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/1064217
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Analysis of the black-chinned tilapia Sarotherodon melanotheron heudelotii reproducing under a wide range of salinities: from RNA-seq to candidate genes ArchiMer
Avarre, Jean-christophe; Dugue, R.; Alonso, Pascal; Diombokho, A.; Joffrois, C.; Faivre, N.; Cochet, C.; Durand, Jean Dominique.
The black-chinned tilapia Sarotherodon melanotheron heudelotii is an ecologically appealing model as it shows exceptional adaptive capacities, especially with regard to salinity. In spite of this, this species is devoid of genomic resources, which impedes the understanding of such remarkable features. De novo assembly of transcript sequences produced by next-generation sequencing technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. It also facilitates the development of quantitative real-time PCR (qPCR) assays for analysing gene expression under different environmental conditions. Nevertheless, obtaining accurate and reliable qPCR results from such data requires a number of validations prior to interpretation....
Tipo: Text Palavras-chave: Gene expression; Non-model organism; Reference gene; Salinity; Spermatogenesis; Tilapia.
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00171/28255/26625.pdf
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Anoxia- and hypoxia-induced expression of LDH-A* in the Amazon Oscar, Astronotus crassipinis Genet. Mol. Biol.
Almeida-Val,Vera Maria Fonseca; Oliveira,Alice Reis; Silva,Maria de Nazaré Paula da; Ferreira-Nozawa,Monica Stropa; Araújo,Roziete Mendes; Val,Adalberto Luis; Nozawa,Sérgio Ricardo.
Adaptation or acclimation to hypoxia occurs via the modulation of physiologically relevant genes, such as erythropoietin, transferrin, vascular endothelial growth factor, phosphofructokinase and lactate dehydrogenase A. In the present study, we have cloned, sequenced and examined the modulation of the LDH-A gene after an Amazonian fish species, Astronotus crassipinis (the Oscar), was exposed to hypoxia and anoxia. In earlier studies, we have discovered that adults of this species are extremely tolerant to hypoxia and anoxia, while the juveniles are less tolerant. Exposure of juveniles to acute hypoxia and anoxia resulted in increased LDH-A gene expression in skeletal and cardiac muscles. When exposed to graded hypoxia juveniles show decreased LDH-A...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Amazon; Fishes; Gene expression; RT-PCR; LDH-A; Hypoxia; Anoxia.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572011000200025
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Application of the differential display RT-PCR strategy for the identification of inflammation-related mouse genes BJMBR
Silva,A.M.; Pires,E.G.; Abrantes,E.F.; Ferreira,L.R.P.; Gazzinelli,R.T.; Reis,L.F.L..
The inflammatory response elicited by various stimuli such as microbial products or cytokines is determined by differences in the pattern of cellular gene expression. We have used the differential display RT-PCR (DDRT-PCR) strategy to identify mRNAs that are differentially expressed in various murine cell types stimulated with pro-inflammatory cytokines, microbial products or anti-inflammatory drugs. Mouse embryonic fibroblasts (MEFs) were treated with IFNs, TNF, or sodium salicylate. Also, peritoneal macrophages from C3H/Hej mice were stimulated with T. cruzi-derived GPI-mucin and/or IFN-<FONT FACE="Symbol">g</FONT>. After DDRT-PCR, various cDNA fragments that were differentially represented on the sequencing gel were recovered, cloned and...
Tipo: Info:eu-repo/semantics/article Palavras-chave: DDRT-PCR; Gene expression; Inflammation; TNF; Interferon.
Ano: 1999 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X1999000700008
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Applications of genomics to rice breeding International Rice Research Institute
Mackill, D. J..
p.9-15
Palavras-chave: Breeding; Genome analysis; Gene mapping; DNA sequencing; Genetic markers; Genetic markers; Genetic transformation; Gene expression.
Ano: 2003 URL: http://hdl.handle.net/123456789/1307
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Apport des informations moléculaires et cellulaires pour la caractérisation de la résistance de l'huître plate européenne vis-à-vis de la bonamiose, et pour la détection de signatures de la sélection naturelle ArchiMer
Harrang, Estelle.
The European flat oyster, an endemic species from European coasts, has been classified in the category of "endangered and/or declining species" since 2003. Indeed, the natural beds of this oyster, consumed since ancient times, have gradually been decimated by over-exploitation and by successive emergence of parasitic diseases. The parasite that causes the disease called bonamiosis has contributed to drastically reduce the French and European aquacultural production of flat oyster. Marine bivalve molluscs display two specificities that restrict possibilities to fight against diseases: they are grown in an open environment, and possess an innate immune system lacking in adaptive response. In this context, the selection of animaIs naturally resistant to...
Tipo: Text Palavras-chave: Huître plate Européenne; Ostre edulis; Bonamiose; Bonamia ostreae; Marqueurs SNP; Expression génique; Activité hémocytaire; Cartographie de liaison; QTL; EQTL; Populations naturelles; Diversité génétique; Sélection naturelle; European flat oyster; Ostrea edulis; Bonamiosis; Bonamia ostreae; SNP markers; Gene expression; Haemocytic activity; Linkage map; QTL; EQTL; Natural populations; Genetic diversity; Genetic structure; Natural selection.
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00127/23785/21702.pdf
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Approche protéomique de la qualité organoleptique et nutritionnelle de la tomate National Institute of Agronomic Research
Faurobert, Mireille; Pelpoir, Esther; Chaïb, Jamila; Pawlowski, Thomasz; Mihr, Christina; Causse, Mathilde; Tricon, David.
Tipo: Other Palavras-chave: Tomato; Fruit quality; Organoleptic quality; Sensorial quality; Plant proteomic; Gene expression; Qualité du fruit; Tomate; Qualité organoleptique; Qualité sensorielle; Lycopersicon esculentum; Protéomique des plantes; Expression des gènes.
Ano: 2004 URL: http://hdl.handle.net/2174/325
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