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Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas ArchiMer
Sussarellu, Rossana; Huvet, Arnaud; Lapegue, Sylvie; Quillen, Virgile; Lelong, Christophe; Cornette, Florence; Jensen, Lasse Fast; Bierne, Nicolas; Boudry, Pierre.
Background Originating from Northeast Asia, the Pacific oyster Crassostrea gigas has been introduced into a large number of countries for aquaculture purpose. Following introduction, the Pacific oyster has turned into an invasive species in an increasing number of coastal areas, notably recently in Northern Europe. Methods To explore potential adaptation of reproductive traits in populations with different histories, we set up a common garden experiment based on the comparison of progenies from two populations of Pacific oyster sampled in France and Denmark and their hybrids. Sex ratio, condition index and microarray gene expression in gonads, were analyzed in each progeny (n = 60). Results A female-biased sex-ratio and a higher condition index were...
Tipo: Text Palavras-chave: Crassostrea gigas; Adaptation; Invasiveness; Fertility; Sex-ratio; Transcriptome; Microarray.
Ano: 2015 URL: https://archimer.ifremer.fr/doc/00287/39829/38343.pdf
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Analysis of gene expression profiles in response to Sporisorium reilianum f. sp. zeae in maize (Zea mays L.) Electron. J. Biotechnol.
Yu,Tao; Wang,Zhenhua; Jin,Xiaochun; Liu,Xianjun; Kan,Shuaishuai.
Background Head smut of maize, which is caused by Sporisorium reilianum f. sp. zeae (Kühn), is a serious disease in maize. In order to reveal the molecular mechanism of the resistance to head smut in maize, a microarray containing ~ 14,850 probes was used to monitor the gene expression profiles between a disease resistant near isogenic line (NIL) and a highly susceptible inbred line after S. reilianum was injected with an artificial inoculation method. Results Levels of expression for 3,532 genes accounting for 23.8% of the total probes changed after inoculation. Gene Ontology analysis revealed that the differentially expressed genes participated in physiological and biochemical pathways. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis...
Tipo: Journal article Palavras-chave: Differentially expressed genes; Head smut resistance gene; Maize; Microarray.
Ano: 2014 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582014000500007
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Comparison of inflammatory microRNA expression in healthy and periodontitis tissues Biocell
Wa Lee,Young H; Am Na,Hee S; Jeong,So Y Eon; Jeong,Sung H Ee; Park,Hae R Youn; Chung,Jin.
MicroRNAs (miRNAs) are short RNA molecules that negatively regulate gene expression primarily by degrading target mRNA or inhibit the translation of protein product. Recently, many reports have shown the altered miRNA expression in various diseases. However, there are no reports on miRNA expression related to periodontitis. Thus, this study aimed to compare the miRNAs differentially expressed in healthy and chronic periodontitis tissues and to determine the miRNAs closely associated with chronic periodontitis. To find out the miRNAs differentially induced in healthy and chronic periodontitis tissues, miRNA microarray was carried out and the expression of miRNAs was confirmed by real-time PCR. According to miRNA microarray analyses, six miRNA genes, let-7a,...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Microarray; Real-time PCR; Gingiva.
Ano: 2011 URL: http://www.scielo.org.ar/scielo.php?script=sci_arttext&pid=S0327-95452011000200002
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Contrasting transcriptional programs control postharvest development of apples (Malus x domestica Borkh.) submitted to cold storage and ethylene blockage. Repositório Alice
STORCH, T. T.; FINATTO, T.; BRUNEAU, M; ORSEL-BALDWIN, M.; RENOU, J-P; ROMBALDI, C. V.; QUECINI, V.; LAURENS, F.; GIRARDI, C. L..
Apple is commercially important worldwide. Favorable genomic contexts and postharvest technologies allow year-round availability. Although ripening is considered a unidirectional developmental process toward senescence, storage at low temperatures, alone or in combination with ethylene blockage, is effective in preserving apple properties. Quality traits and genome wide expression were integrated to investigate the mechanisms underlying postharvest changes. Development and conservation techniques were responsible for transcriptional reprogramming and distinct programs associated with quality traits. A large portion of the differentially regulated genes constitutes a program involved in ripening and senescence, whereas a smaller module consists of genes...
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: 1-methylcyclopropene; Firmness; Fruit quality; Gene expression; Microarray.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1077795
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Current genomic resources in melon and other cucurbits National Institute of Agronomic Research
Garcia-Mas, J..
In recent years there has been an effort towards the development of genomic resources in several cucurbit species, mainly in melon, cucumber and watermelon. The number of available sequences for these species in public databases has increased recently. This has allowed the design of microarrays for transcriptome analysis and the discovery of SNP markers for genotyping. Other genomic tools are also available in melon as BAC libraries, mutant populations and saturated genetic maps. Some international initiatives have emerged that will probably lead to the sequencing of the complete genomes of some cucurbit species during the next years.
Tipo: Conference Paper Palavras-chave: Genomic tool; Microarray; EST; Mutants; Physical map; SNP markers; BAC libraries; Genetic maps; EST databases; Genome; QTL.
Ano: 2008 URL: http://hdl.handle.net/2174/213
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De novo assembly, characterization and functional annotation of Senegalese sole (Solea senegalensis) and common sole (Solea solea) transcriptomes: integration in a database and design of a microarray ArchiMer
Benzekri, Hicham; Armesto, Paula; Cousin, Xavier; Rovira, Mireia; Crespo, Diego; Alejandro Merlo, Manuel; Mazurais, David; Bautista, Rocio; Guerrero-fernandez, Dario; Fernandez-pozo, Noe; Ponce, Marian; Infante, Carlos; Zambonino, Jose Luis; Nidelet, Sabine; Gut, Marta; Rebordinos, Laureana; Planas, Josep V.; Begout, Marie-laure; Gonzalo Claros, M.; Manchado, Manuel.
Background Senegalese sole (Solea senegalensis) and common sole (S. solea) are two economically and evolutionary important flatfish species both in fisheries and aquaculture. Although some genomic resources and tools were recently described in these species, further sequencing efforts are required to establish a complete transcriptome, and to identify new molecular markers. Moreover, the comparative analysis of transcriptomes will be useful to understand flatfish evolution. Results A comprehensive characterization of the transcriptome for each species was carried out using a large set of Illumina data (more than 1,800 millions reads for each sole species) and 454 reads (more than 5 millions reads only in S. senegalensis), providing coverages ranging from...
Tipo: Text Palavras-chave: Soles; Transcriptome; Microarray; Orthology; Molecular markers; SoleaDB.
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00238/34918/33626.pdf
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Delineamento de experimentos em genética genômica R. Bras. Zootec.
Rosa,Guilherme Jordão de Magalhães.
Genética genômica é um termo utilizado para representar o estudo de processos genéticos controladores de caracteres fenotípicos de herança complexa, a partir da análise conjunta de informação relativa a fenótipos, estruturas de parentesco, marcadores moleculares e expressão gênica. Estudos de genética genômica são utilizados, por exemplo, para a estimação da herdabilidade de níveis de transcrição, para o mapeamento de locos controladores da expressao gênica (eQTL, do inglês expression Quantitative Trait Loci), e para o estudo de redes regulatórias. Genética genômica geralmente envolve experimentos com microarrays, os quais são ainda bastante caros e trabalhosos, limitando o tamanho amostral e conseqüentemente o poder estatístico de tais estudos. Desta...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Delineamentos ótimos; EQTL; Fenotipagem seletiva; Genética genômica; Microarray.
Ano: 2007 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982007001000019
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D-MaPs - DNA-microarray projects: web-based software for multi-platform microarray analysis Genet. Mol. Biol.
Carazzolle,Marcelo F.; Herig,Taís S.; Deckmann,Ana C.; Pereira,Gonçalo A.G..
The web application D-Maps provides a user-friendly interface to researchers performing studies based on microarrays. The program was developed to manage and process one- or two-color microarray data obtained from several platforms (currently, GeneTAC, ScanArray, CodeLink, NimbleGen and Affymetrix). Despite the availability of many algorithms and many software programs designed to perform microarray analysis on the internet, these usually require sophisticated knowledge of mathematics, statistics and computation. D-maps was developed to overcome the requirement of high performance computers or programming experience. D-Maps performs raw data processing, normalization and statistical analysis, allowing access to the analyzed data in text or graphical...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Microarray; Web service; Software; Affymetrix and nimblegen.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000300030
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Effects of BST and high energy diet on gene expression in mammary parenchyma of dairy heifers R. Bras. Zootec.
Lew,Betina Joyce; Oliveira,Mauro Dal Secco de; Freitas Júnior,José Esler de; Carvalho,Marina Vieira de; Rêgo,Aníbal Coutinho do; Rennó,Francisco Palma.
The objective of this study was to determine the effects of dietary energy and recombinant bovine somatotropin (bST) injection to identify genes that might control mammogenesis. Total RNA was extracted from the parenchymal tissue of 32 heifers randomly assigned to one of four treatments: two diets (a standard diet and a high energy, high protein diet), each with or without bST. To perform microarray experiments, RNA samples were pooled (2 animals/pool) before reverse transcription and labeling with Cy3 or Cy5. A 4-node loop design was used to examine the differential gene expression among treatments using a bovine-specific cDNA microarray (National Bovine Functional Genomics Consortium Library, NBFGC) containing 18,263 unique expressed sequence tags (EST)....
Tipo: Info:eu-repo/semantics/article Palavras-chave: Gene regulation; Mammary gland development; Microarray; Nutrition; Somatotropin.
Ano: 2013 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982013000700008
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Expression and polymorphism of watermelon fruit ESTs National Institute of Agronomic Research
Levi, A.; Wechter, W.P.; Harris, K.R.; Davis, A.R.; Fei, Z.; Giovannoni, J.J.; Trebitsh, T.; Salman, A.; Hernandez, A.; Thimmapuram, J.; Tadmor, Y.; Portnoy, V.; Katzir, N..
Over 8,000 ESTs were generated for watermelon and were assembled into 4,700 EST-unigenes (http://www.icugi.org). Microarray and Real-Time PCR analyses were used to examine differential expression of 832 of these EST-unigenes in developing and ripening watermelon fruit. RNA was isolated from watermelon fruits(in three sequential stages of development and ripening) and from young leaves of field grown plants (during three consecutive years). The microarray analysis identified 335 EST-unigenes differentially expressed (by at least two-fold when compared to leaf) in watermelon fruit during the early, ripening, or mature stage. A considerable number of these watermelon ESTs are associated with vascular system differentiation and development, ethylene...
Tipo: Conference Paper Palavras-chave: Watermelon; Microarray; Polymorphism; PCR analysis; Expressed sequence tag; EST; Gene expression.
Ano: 2008 URL: http://hdl.handle.net/2174/216
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Expression of virulence genes by Listeria monocytogenes J0161 in natural environment BJM
Tirumalai,Prem Saran; Prakash,Soam.
Majority of studies concerning the gene expression of Listeria monocytogenes have been done on pure culture states. Our objective was to study L.monocytogenes in a co-cultured state and to understand if microbes in their natural state of existence are different in their expression than that of the purely cultured lab grown forms. For a long period discussions have been on the expression of prfA, (which is a virulence gene regulator) in a mammalian host and its role in causing the switch from a saprophytic to pathogenic form of L.monocytogenes. We, in this paper for the first time report the expression of prfA and other virulence genes by L.monocytogenes under different extracellular conditions, and also as a pure culture biofilms, that is different from...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Listeria monocytogenes; PrfA; Virulence; Microarray; Biofilms; Co-culture; Gene Expression.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1517-83822012000200050
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Expression profiling using Affymetrix GeneChip Microarrays in sugarcane during leaf senescence. Repositório Alice
MARTINS, N. F.; PATIL, S.; MOLINARI, H. B. C.; DIAS, B. B. A.; MARTINS, M. T. B.; QUIRINO, B. F.; EMMERSON, Z.; AMOS, B.; MAY, S..
2011
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: Microarray; Sugarcane; Senescence.
Ano: 2011 URL: http://www.alice.cnptia.embrapa.br/handle/doc/908739
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Gene chip analyses reveal differential genetic responses to iron deficiency in rat duodenum and jejunum Biol. Res.
FCOLLINS,JAMES.
Previous studies revealed novel genetic changes in the duodenal mucosa of iron-deprived rats during post-natal development. These observations are now extended to compare the genetic response to iron deficiency in the duodenum versus jejunum of 12-wk-old rats. cRNA samples were prepared from the duodenal and jejunal mucosa of three groups each of control and iron-deficient rats and hybridized with RAE 230A and 230B gene chips (Affymetrix). Stringent data reduction strategies were employed. Results showed that several genes were similarly induced in both gut segments, including DMT1, Dcytb, transferrin receptor 1, heme oxygenase 1, metallothionein, the Menkes copper ATPase (ATP7A), tripartitie motif protein 27, and the sodium-dependent vitamin C...
Tipo: Journal article Palavras-chave: ATP7A; Copper transport; Iron-deficiency anemia; Microarray.
Ano: 2006 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602006000100004
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Gene expression patterns during the larval development of European sea bass (Dicentrarchus labrax) by microarray analysis ArchiMer
Darias, Maria J.; Zambonino, Jose-luis; Hugot, K; Cahu, Chantal; Mazurais, David.
During the larval period, marine teleosts undergo very fast growth and dramatic changes in morphology, metabolism, and behavior to accomplish their metamorphosis into juvenile fish. Regulation of gene expression is widely thought to be a key mechanism underlying the management of the biological processes required for harmonious development over this phase of life. To provide an overall analysis of gene expression in the whole body during sea bass larval development, we monitored the expression of 6,626 distinct genes at 10 different points in time between 7 and 43 days post-hatching (dph) by using heterologous hybridization of a rainbow trout cDNA microarray. The differentially expressed genes (n = 485) could be grouped into two categories: genes that were...
Tipo: Text Palavras-chave: Sea bass; Gene expression; Microarray; Development; Fish larvae.
Ano: 2008 URL: http://archimer.ifremer.fr/doc/2008/publication-4344.pdf
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Gene expression profiling in wild-type and metallothionein mutant fibroblast cell lines Biol. Res.
ARMENDÁRIZ,ÁNGELA D; OLIVARES,FELIPE; PULGAR,RODRIGO; LOGUINOV,ALEX; CAMBIAZO,VERÓNICA; VULPE,CHRISTOPHER D; GONZÁLEZ,MAURICIO.
The role of metallothioneins (MT) in copper homeostasis is of great interest, as it appears to be partially responsible for the regulation of intracellular copper levels during adaptation to extracellular excess of the metal. To further investigate a possible role of MTs in copper metabolism, a genomics approach was utilized to evaluate the role of MT on gene expression. Microarray analysis was used to examine the effects of copper overload in fibroblast cells from normal and MT I and II double knock-out mice (MT-/-). As a first step, we compared genes that were significantly upregulated in wild-type and MT-/- cells exposed to copper. Even though wild-type and mutant cells are undistinguishable in terms of their morphological features and rates of growth,...
Tipo: Journal article Palavras-chave: Copper homeostasis; Metallothionein; Microarray.
Ano: 2006 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602006000100015
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Hypoxia-inducible myoglobin expression in nonmuscle tissues. Repositório Alice
FRASER, J.; MELLO, L. V. de; WARD, D.; REES, H. H.; WILLIAMS, D. R.; FANG, Y.; BRASS, A.; GRACEY, A. Y.; COSSINS, A. R..
bitstream/item/177942/1/ID-26551-1.pdf
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Globin expression; Adaptação de hypoxia; Microarray; Proteômica.
Ano: 2006 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/186962
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Identification of molecular markers for oocyte competence in bovine cumulus cells. Repositório Alice
MELO, E. O.; CORDEIRO, D. M.; PELLEGRINO, R.; WEI, Z.; DAYE, Z. J.; NISHIMURA, R. C.; DODE, M. A. N..
bitstream/item/167130/1/Melo-et-al-2017-Animal-Genetics.pdf
Tipo: Artigo em periódico indexado (ALICE) Palavras-chave: Microarray; Oocyte quality; Cattle; Gene expression.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1080229
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Microarray-based genotyping and detection of drug-resistant HBV mutations from 620 Chinese patients with chronic HBV infection BJID
Hua,Wenhao; Zhang,Guanbin; Guo,Shujun; Weijie,Li; Sun,Lanhua; Xiang,Guangxin.
Background: Research has shown that hepatitis B virus (HBV) genotypes are closely linked to the clinical manifestations, treatment, and prognosis of the disease.Objective: To study the association between genotype and drug-resistant HBV mutations in 620 Chinese patients with chronic HBV infection.Methods: HBV DNA levels were determined using real-time quantitative PCR in plasma samples. Microarrays were performed for the simultaneous detection of HBV genotypes (HBV/B, C, and D) and drug-resistance-related hotspot mutations. A portion of the samples analyzed using microarrays was selected randomly and the data were confirmed using direct DNA sequencing.Results: Most samples were genotype C (471/620; 76.0%), followed by genotype B (149/620; 24.0%). Among the...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Chronic HBV; Microarray; Genotyping; Drug-resistance mutations.
Ano: 2015 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1413-86702015000300291
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Phytochip: Development of a DNA-microarray for rapid and accurate identification of Pseudo-nitzschia spp and other harmful algal species ArchiMer
Noyer, Charlotte; Abot, Anne; Trouilh, Lidwine; Leberre, Veronique Anton; Dreanno, Catherine.
Detection of harmful algal blooms has become a challenging concern because of to the direct impacts on public health and economy. The identification of toxic dinoflagellates and diatoms in monitoring programs requires an extensive taxonomic expertise and is time consuming. Advances in molecular biology have allowed the development of new approaches, more rapid, accurate and cost-effective for detecting these microorganisms. In this context, we developed a new DNA microarray (called, Phytochip) for the simultaneous detection of multiple HAB species with a particular emphasis on Pseudo-nitzschia species. Oligonucleotide probes were designed along the rRNA operon. After DNA extraction, the target rDNA genes were amplified and labeled using an asymmetric PCR;...
Tipo: Text Palavras-chave: HAB; Pseudo-nitzschia; Microarray; Ribosomal oligonucleotide probes; Environmental monitoring.
Ano: 2015 URL: https://archimer.ifremer.fr/doc/00254/36554/42346.pdf
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Pipeline for macro- and microarray analyses BJMBR
Vicentini,R.; Menossi,M..
The pipeline for macro- and microarray analyses (PMmA) is a set of scripts with a web interface developed to analyze DNA array data generated by array image quantification software. PMmA is designed for use with single- or double-color array data and to work as a pipeline in five classes (data format, normalization, data analysis, clustering, and array maps). It can also be used as a plugin in the BioArray Software Environment, an open-source database for array analysis, or used in a local version of the web service. All scripts in PMmA were developed in the PERL programming language and statistical analysis functions were implemented in the R statistical language. Consequently, our package is a platform-independent software. Our algorithms can correctly...
Tipo: Info:eu-repo/semantics/other Palavras-chave: Intensity-dependent selection of expression ratios Pipeline BioArray Software Environment Normalization Macroarray; Microarray.
Ano: 2007 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2007000500003
Registros recuperados: 27
Primeira ... 12 ... Última
 

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