Consulta: subjectFacets:"Microarray"
Registros recuperados: 20
Data/hora: 16/06/2024 10:16:48

Analysis of gene expression profiles in response to Sporisorium reilianum f. sp. zeae in maize (Zea mays L.)
Provedor de dados: Electronic Journal of Biotechnology
Autores: 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

Xylella fastidiosa: An in vivo system to study possible survival strategies within citrus xylem vessels based on global gene expression analysis
Provedor de dados: Electronic Journal of Biotechnology
Autores: Federici,María Teresa; Marcondes,Jackson A; Picchi,Simone Cristina; Stuchi,Eduardo S; Fadel,André Luiz; Laia,Marcelo L; Lemos,Manoel Victor F; Lemos,Eliana Gertrudes Macedo.
Xylella fastidiosa inhabits the plant xylem, a nutrient-poor environment, so that mechanisms to sense and respond to adverse environmental conditions are extremely important for bacterial survival in the plant host. Although the complete genome sequences of different Xylella strains have been determined, little is known about stress responses and gene regulation in these organisms. In this work, a DNA microarray was constructed containing 2,600 ORFs identified in the genome sequencing project of Xylella fastidiosa 9a5c strain, and used to check global gene expression differences in the bacteria when it is infecting a symptomatic and a tolerant citrus tree. Different patterns of expression were found in each variety, suggesting that bacteria are responding...
Tipo: Journal article
Palavras-chave: Citrus; Microarray; Xylella fastidiosa.
Ano: 2012
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582012000300004

D-MaPs - DNA-microarray projects: web-based software for multi-platform microarray analysis
Provedor de dados: Genetics and Molecular Biology
Autores: 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

Use of signal thresholds to determine significant changes in microarray data analyses
Provedor de dados: Genetics and Molecular Biology
Autores: Xinmin,Li; Kim,Jaejung; Zhou,Jian; Gu,Weikuan; Quigg,Richard.
The use of a constant fold-change to determine significant changes in gene expression has been widely accepted for its intuition and ease of use in microarray data analysis, but this concept has been increasingly criticized because it does not reflect signal intensity and can result in a substantial number of false positives and false negatives. To resolve this dilemma, we have analyzed 65 replicate Affymetrix chip-chip comparisons and determined a series of user adjustable signal-dependent thresholds which do not require replicates and offer a 95% confidence interval. Quantitative RT-PCR shows that such thresholds significantly improve the power to discriminate biological changes in mRNA from noise and reduce false calls compared to the traditional...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Microarray; Signal threshold; Affymetrix; Data analysis.
Ano: 2005
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572005000200002

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
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: 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

Additive transcriptomic variation associated with reproductive traits suggest local adaptation in a recently settled population of the Pacific oyster, Crassostrea gigas
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: 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

Phytochip: Development of a DNA-microarray for rapid and accurate identification of Pseudo-nitzschia spp and other harmful algal species
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: 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

Transcriptomic Profiling of Egg Quality in Sea Bass (Dicentrarchus labrax) Sheds Light on Genes Involved in Ubiquitination and Translation
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: Zarski, Daniel; Thaovi Nguyen,; Le Cam, Aurelie; Montfort, Jerome; Dutto, Gilbert; Vidal, Marie-odile; Fauvel, Christian; Bobe, Julien.
Variable and low egg quality is a major limiting factor for the development of efficient aquaculture production. This stems from limited knowledge on the mechanisms underlying egg quality in cultured fish. Molecular analyses, such as transcriptomic studies, are valuable tools to identify the most important processes modulating egg quality. However, very few studies have been devoted to this aspect so far. Within this study, the microarray-based transcriptomic analysis of eggs (of different quality) of sea bass (Dicentrarchus labrax) was performed. An Agilent oligo microarray experiment was performed on labelled mRNA extracted from 16 batches of eggs (each batch obtained from a different female) of sea bass, in which over 24,000 published probe arrays were...
Tipo: Text
Palavras-chave: Microarray; Genomics; Transcriptomics; Aquaculture; Controlled reproduction.
Ano: 2017
URL: http://archimer.ifremer.fr/doc/00371/48220/48345.pdf

Gene expression patterns during the larval development of European sea bass (Dicentrarchus labrax) by microarray analysis
Provedor de dados: Institutional Archive of Ifreme (ArchiMer)
Autores: 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

Delineamento de experimentos em genética genômica
Provedor de dados: Revista Brasileira de Zootecnia
Autores: 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

Effects of BST and high energy diet on gene expression in mammary parenchyma of dairy heifers
Provedor de dados: Revista Brasileira de Zootecnia
Autores: 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

Comparison of inflammatory microRNA expression in healthy and periodontitis tissues
Provedor de dados: Biocell
Autores: 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

Gene chip analyses reveal differential genetic responses to iron deficiency in rat duodenum and jejunum
Provedor de dados: Biological Research
Autores: 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

Gene expression profiling in wild-type and metallothionein mutant fibroblast cell lines
Provedor de dados: Biological Research
Autores: 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

Microarray-based genotyping and detection of drug-resistant HBV mutations from 620 Chinese patients with chronic HBV infection
Provedor de dados: Brazilian Journal of Infectious Diseases
Autores: 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

Whole transcriptome organisation in the dehydrated supraoptic nucleus
Provedor de dados: Brazilian Journal of Medical and Biological Research
Autores: Hindmarch,C.C.T.; Franses,P.; Goodwin,B.; Murphy,D.
The supraoptic nucleus (SON) is part of the central osmotic circuitry that synthesises the hormone vasopressin (Avp) and transports it to terminals in the posterior lobe of the pituitary. Following osmotic stress such as dehydration, this tissue undergoes morphological, electrical and transcriptional changes to facilitate the appropriate regulation and release of Avp into the circulation where it conserves water at the level of the kidney. Here, the organisation of the whole transcriptome following dehydration is modelled to fit Zipf's law, a natural power law that holds true for all natural languages, that states if the frequency of word usage is plotted against its rank, then the log linear regression of this is -1. We have applied this model to our...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Transcriptome; Supraoptic nucleus; Dehydration; Zipf; Microarray; Vasopressin.
Ano: 2013
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2013001201000

Rapid, reliable and inexpensive quality assessment of biotinylated cRNA
Provedor de dados: Brazilian Journal of Medical and Biological Research
Autores: Zander,T.; Yunes,J.A.; Cardoso,A.A.; Nadler,L.M.
The interpretation of oligonucleotide array experiments depends on the quality of the target cRNA used. cRNA target quality is assessed by quantitative analysis of the representation of 5' and 3' sequences of control genes using commercially available Test arrays. The Test array provides an economically priced means of determining the quality of labeled target prior to analysis on whole genome expression arrays. This manuscript validates the use of a duplex RT-PCR assay as a faster (6 h) and less expensive (&lt;US$10) but equally accurate alternative to the Test arrays in determining biotinylated cRNA quality. Forty-one different cRNA samples were hybridized to HG-U133A microarrays from Affymetrix. Ten cRNA samples with a ß-actin 3'/5' ratio &gt;6 were...
Tipo: Info:eu-repo/semantics/other
Palavras-chave: Microarray; Biotinylated cRNA; Probe quality; 5' Representation; 3'/5' Ratio.
Ano: 2006
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2006000500004

Pipeline for macro- and microarray analyses
Provedor de dados: Brazilian Journal of Medical and Biological Research
Autores: 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

Expression of virulence genes by Listeria monocytogenes J0161 in natural environment
Provedor de dados: Brazilian Journal of Microbiology
Autores: 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

Exploring the shared genes of hypertension, diabetes and hyperlipidemia based on microarray
Provedor de dados: Brazilian Journal of Pharmaceutical Sciences
Autores: Dong,Wenzhu; Chen,Hangping; Wang,Lu; Cao,Xiaoqian; Bu,Xiawei; Peng,Yan; Dong,Aiqing; Ying,Mengjiang; Chen,Xu; Zhang,Xin; Yao,Li.
Given their relationship with metabolic syndrome and systematic inflammatory diseases, the pathogenesis of hypertension, hyperglycemia, and hyperlipidemia is closely related. To explore the common genes among these three conditions, spontaneous hypertensive rats (SHR), spontaneous diabetic Goto-Kakizaki rats (GK) and hyperlipidemia rats (HMR) were reared for experiments. Gene array was used to identify the genes of SHR, GK and HMR compared with normal Wistar rats using TBtools software. First, real-time PCR was applied to verify these genes, and Cytoscape software was used to construct networks based on the National Center for Biotechnology Information (NCBI) database. Second, Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis was performed...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Hypertension; Diabetes; Hyperlipidemia; Genes; Microarray; Neoplasm.
Ano: 2020
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1984-82502020000100566