SABIIA - Sistema Aberto e Integrado de Informação em Agricultura (Sabiia)

MALUF, M. P.; SILVA, C. C. da; OLIVEIRA, M. de P. A. de; TAVARES, A. G.; SILVAROLLA, M. B.; GUERREIRO FILHO, O..

In this work, we studied the biosynthesis of caffeine by examining the expression of genes involved in this biosynthetic pathway in coffee fruits containing normal or low levels of this substance. The amplification of gene-specific transcripts during fruit development revealed that low-caffeine fruits had a lower expression of the theobromine synthase and caffeine synthase genes and also contained an extra transcript of the caffeine synthase gene. This extra transcript contained only part of exon 1 and all of exon 3. The sequence of the mutant caffeine synthase gene revealed the substitution of isoleucine for valine in the enzyme active site that probably interfered with enzymatic activity. These findings indicate that the absence of caffeine in these...

Tipo: Artigo de periódico

Palavras-chave: Coffee; Naturally decaffeinated.; Differential expression; Cup quality.

Ano: 2009

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/880373

Altered expression of the caffeine synthase gene in a naturally caffeine-free mutant of Coffea arabica

Maluf,Mirian Perez; Silva,Carla Cristina da; Oliveira,Michelle de Paula Abreu de; Tavares,Aline Gomes; Silvarolla,Maria Bernadete; Guerreiro Filho,Oliveiro.

Bioinformatics analysis of the gene expression profile in Bladder carcinoma

Palavras-chave: Coffee; Cup quality; Differential expression; Naturally decaffeinated.

Ano: 2009

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000400023

Xiao,Jing; Yiqing,Qiu.

Bladder carcinoma, which has the ninth highest incidence among malignant tumors in the world, is a complex, multifactorial disease. The malignant transformation of bladder cells results from DNA mutations and alterations in gene expression levels. In this work, we used a bioinformatics approach to investigate the molecular mechanisms of bladder carcinoma. Biochips downloaded from the Gene Expression Omnibus (GEO) were used to analyze the gene expression profile in urinary bladder cells from individuals with carcinoma. The gene expression profile of normal genomes was used as a control. The analysis of gene expression revealed important alterations in genes involved in biological processes and metabolic pathways. We also identified some small molecules...

Changes in fatty acid composition in the giant clam Tridacna maxima in response to thermal stress

Palavras-chave: Bladder carcinoma; Differential expression; Expression profile; Small molecular mimic; Susceptibility forecast.

Ano: 2013

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572013000200021

ArchiMer

Dubousquet, Vaimiti; Gros, Emmanuelle; Berteaux-lecellier, Veronique; Viguier, Bruno; Raharivelomanana, Phila; Bertrand, Cédric; Lecellier, Gael J..

Temperature can modify membrane fluidity and thus affects cellular functions and physiological activities. This study examines lipid remodelling in the marine symbiotic organism, Tridacna maxima, during a time series of induced thermal stress, with an emphasis on the morphology of their symbiont Symbiodinium. First, we show that the French Polynesian giant clams harbour an important proportion of saturated fatty acids (SFA), which reflects their tropical location. Second, in contrast to most marine organisms, the total lipid content in giant clams remained constant under stress, though some changes in their composition were shown. Third, the stress-induced changes in fatty acid (FA) diversity were accompanied by an upregulation of genes involved in lipids...

Tipo: Text

Palavras-chave: Thermal stress; Fatty acids; Differential expression; Antioxidant; Symbiodinium; Tridacna maxima.

Ano: 2016

URL: https://archimer.ifremer.fr/doc/00361/47195/79514.pdf

Coexpression and transcriptome analyses identify active apomixis-related genes in Paspalum notatum leaves.

Differential gene expression profiles in peripheral blood in Northeast Chinese Han people with acute myocardial infarction

OLIVEIRA, F. A. de; VIGNA, B. B. Z.; SILVA, C. C. da; FAVERO, A. P.; MATTA, F. de P.; AZEVEDO, A. L. S.; SOUZA, A. P. de.

RNA sequencing (RNA-seq) is the most effective method for simultaneously predicting new transcripts and identifying differentially expressed genes among distinct tissues, genotypes, abiotic conditions and developmental stages [1]. Conversely, considering the large amount of data generated from RNA-seq, new approaches that efficiently extract meaningful associations from highly multivariate datasets are needed [2]. Transcriptome coexpression studies can show how complex phenotypes depend on the activity of coordinated batteries of genes [3]. Therefore, the construction of coexpression networks based on gene expression data using correlation metrics provides valuable information regarding alterations in biological systems in response to differential gene...

Tipo: Artigo de periódico

Palavras-chave: Differential expression; Gene coexpression network; RNA sequencing; Apomixis; Paspalum.

Ano: 2020

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1121557

Fan,Lin; Meng,Heyu; Guo,Xudong; Li,Xiangdong; Meng,Fanbo.

Abstract This study aimed to use gene chips to investigate differential gene expression profiles in the occurrence and development of acute myocardial infarction (AMI). The study included 12 AMI patients and 12 healthy individuals. Total mRNA of peripheral bloodwas extracted and reversed-transcribed to cDNA for microarray analysis. After establishing two pools with three subjects each (3 AMI patients and 3 healthy individuals), the remaining samples were used for RT-qPCR to confirm the microarray data. From the microarray results, seven genes were randomly selected for RT-qPCR. RT-qPCR results were analyzed by the 2-ΔΔCt method. Microarray analysis showed that 228 genes were up- regulated and 271 were down-regulated (p ≤ 0.05, |logFC| > 1). Gene...

Effects of somatic embryogenesis on gene expression of cloned coffee heterozygous hybrids.

Palavras-chave: Acute myocardial infarction; RNA; Differential expression.

Ano: 2018

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000100059

Gene expression profile during coffee fruit development and identification of candidate markers for phenological stages.

OLIVEIRA, K. C. de; GUIMARÃES, P. de S.; BAZIOLI, J. M.; MARTINATI, J. C.; SANTOS, M. M. dos; PADILHA, L.; GUERREIRO-FILHO, O.; MALUF, M. P..

Cloning of superior coffee plants by somatic embryogenesis can assist breeding programs on reducing the cost and time for launch of new cultivars. This study aimed to evaluate the efficiency of this methodology for cloning coffee trees with high heterozygosity, and to gather evidence that clonal progenies are faithful copies of mother plants. Selected plants IAC1 and IAC 2 from Coffea arabica breeding populations, resistant to leaf rust and leaf miner, respectively, were cloned via indirect somatic embryogenesis. Expression of selected genes involved in biological processes potentially affected by in vitro cultivation was evaluated by quantitative analysis. Genes encoding proteins associated with maintenance of DNA integrity and control of cell cycle...

Tipo: Artigo de periódico

Palavras-chave: In vitro cultivation; Differential expression; Coffea Arábica; Somaclonal variation.

Ano: 2019

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1113261

Gene expression profile during coffee fruit development and identification of candidate markers for phenological stages

GASPARI-PEZZOPANE, C. de; BONTURI, N.; GUERREIRO FILHO, O.; FAVARIN, J. L.; MALUF, M. P..

The objective of this work was to identify genes that could be used as suitable markers for molecular recognition of phenological stages during coffee (Coffea arabica) fruit development. Four cultivars were evaluated as to their differential Expression of genes associated to fruit development and maturation processes. GEne expression was characterized by both semi?quantitative and quantitative RT?PCR, in fruit harvested at seven different developmental stages, during three different seasons. No size polymorphisms or differential expression were observed among the cultivars for the evaluated genes; however, distinct expression profiles along fruit development were determined for each gene. Four out of the 28 evaluated genes exhibited a regular expression...

Tipo: Artigo de periódico

Palavras-chave: Cup quality; Differential expression; Fruit phenology; Qualidade de bebida; Coffea Arábica.; Ripening..

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1044180

PAB

Gaspari-Pezzopane,Cristiana de; Bonturi,Nemailla; Guerreiro Filho,Oliveiro; Favarin,José Laércio; Maluf,Mirian Perez.

The objective of this work was to identify genes that could be used as suitable markers for molecular recognition of phenological stages during coffee (Coffea arabica) fruit development. Four cultivars were evaluated as to their differential expression of genes associated to fruit development and maturation processes. Gene expression was characterized by both semi-quantitative and quantitative RT-PCR, in fruit harvested at seven different developmental stages, during three different seasons. No size polymorphisms or differential expression were observed among the cultivars for the evaluated genes; however, distinct expression profiles along fruit development were determined for each gene. Four out of the 28 evaluated genes exhibited a regular expression...

Gonad transcriptome analysis of pearl oyster Pinctada margaritifera: identification of potential sex differentiation and sex determining genes

Palavras-chave: Coffea arabica; Cup quality; Differential expression; Fruit phenology; Ripening; QRT-PCR.

Ano: 2012

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2012000700014

ArchiMer

Teaniniuraitemoana, Vaihiti; Huvet, Arnaud; Levy, Peva; Klopp, Christophe; Lhuillier, Emeline; Gaertner-mazouni, Nabila; Gueguen, Yannick; Le Moullac, Gilles.

Background Black pearl farming is based on culture of the blacklip pearl oyster Pinctada margaritifera (Mollusca, lophotrochozoa), a protandrous hermaphrodite species. At first maturation, all individuals are males. The female sex appears progressively from two years old, which represents a limitation for broodstock conditioning for aquaculture production. In marine mollusks displaying hermaphroditic features, data on sexual determinism and differentiation, including the molecular sex determining cascade, are scarce. To increase genomic resources and identify the molecular mechanisms whereby gene expression may act in the sexual dimorphism of P. margaritifera, we performed gonad transcriptome analysis. Results The gonad transcriptome of P. margaritifera...

Tipo: Text

Palavras-chave: Pinctada margaritifera; Gametogenesis; Transcriptome; Differential expression; Sex determinism.

Ano: 2014

URL: http://archimer.ifremer.fr/doc/00201/31194/29593.pdf

HIGH EXPRESSION OF HMOX1 IN BLUE-SHELLED CHICKENS IS ASSOCIATED WITH A TG HAPLOTYPE

Rev. Bras. Ciênc. Avic.

Wang,Z; Deng,X; Wang,AI; Liu,R.

ABSTRACTHMOX1 is an important gene in biosynthesis of the eggshell pigment of blue eggs. Previous studies found that HMOX1 is highly expressed in the shell gland of hens laying blue eggs (BlueH) compared with hens laying brown eggs (BrownH); however, the reasons for the differential expression are unclear. In this study five single nucleotide polymorphism (SNP) in HMOX1 were genotyped in 111 BlueH and 115 BrownH. The association of haplotypes of these SNP with the blue egg phenotype was tested. Haplotype-specific expression of HMOX1 was detected in the shell gland. The interaction of sequence variants and transcription factors was analyzed using electrophoretic mobility shift assay (EMSA). A TG haplotype covering upstream 1.4 kb region of HMOX1 was...

Identification of differentially expressed genes of Xanthomonas axonopodis pv. citri by representational difference analysis of cDNA

Palavras-chave: Chicken; Blue egg; Biliverdin; HMOX1; Differential expression.

Ano: 2015

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-635X2015000300267

Mehta,Angela; Rosato,Yoko B..

Xanthomonas axonopodis pv. citri is a phytopathogenic bacterium responsible for citrus canker, a serious disease which causes severe losses in citriculture around the world. In this study we report the differential expression of X. axonopodis pv. citri in response to specific treatments by using Representational Difference Analysis of cDNA (cDNA RDA). cDNAs from X. axonopodis pv. citri cultured in the presence of leaf extract of the host plant (Citrus sinensis), in vivo, as well as in the complex medium were hybridized against cDNA of the bacterium grown in the minimal medium. Sequencing of the difference products obtained after the second and third hybridizations revealed a total of 37 distinct genes identified by homology searches in the genome of X....

Identification of genes associated with shell color in the black-lipped pearl oyster, Pinctada margaritifera

Palavras-chave: Citrus canker; Differential expression; Leaf extract; In vivo.

Ano: 2005

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572005000100024

ArchiMer

Lemer, Sarah; Saulnier, Denis; Gueguen, Yannick; Planes, Serge.

Background: Color polymorphism in the nacre of pteriomorphian bivalves is of great interest for the pearl culture industry. The nacreous layer of the Polynesian black-lipped pearl oyster Pinctada margaritifera exhibits a large array of color variation among individuals including reflections of blue, green, yellow and pink in all possible gradients. Although the heritability of nacre color variation patterns has been demonstrated by experimental crossing, little is known about the genes involved in these patterns. In this study, we identify a set of genes differentially expressed among extreme color phenotypes of P. margaritifera using a suppressive and subtractive hybridization (SSH) method comparing black phenotypes with full and half albino individuals....

Tipo: Text

Palavras-chave: Differential expression; Biomineralization; Nacre; Pearl; Pigmentation; Albino.

Ano: 2015

URL: http://archimer.ifremer.fr/doc/00275/38627/37167.pdf

Identification of host proteins modulated by the virulence factor AC2 of tomato chlorotic mottle virus in Nicotiana benthamiana.

Identification of KCNJ11 as a functional candidate gene for bovine meat tenderness.

CARMO, L. S. T.; RESENDE, R. O.; SILVA, L. P. da; RIBEIRO, S. da G.; MEHTA, A..

Tipo: Separatas

Palavras-chave: Differential expression; Plant proteomics; Plant–virus interaction; ToCMoV..

Ano: 2013

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/979952

In silico evaluation of the Eucalyptus transcriptome

TIZIOTO, P.; GASPARINI, G.; SOUZA, M. M.; MUDADU, M. de A.; COUTINHO, L. L.; MOURÃO, G. B.; THOLON, P.; MEIRELLES, S. L. C.; TULLIO, R. R.; ROSA, A. do N.; ALENCAR, M. M. de; MEDEIROS, S. R.; SIQUEIRA, F.; FEIJO, G. L. D.; NASSU, R. T.; REGITANO, L. C. de A..

The potassium inwardly rectifying channel, subfamily J, member 11 (KCNJ11) gene was investigated as a candidate for meat tenderness based on the effects reported on muscle for KCNJ11 gene knockout in rat models and its position in a quantitative trait locus (QTL) for meat tenderness in the bovine genome. Sequence variations in the KCNJ11 gene were described by sequencing six amplified fragments, covering almost the entire gene. We identified single nucleotide polymorphisms (SNP) and validated them by different approaches, taking advantage of simultaneous projects that are being developed with the same Nelore population. By sequencing the KCNJ11 in Nelore steers representing extreme phenotypes for Warner-Bratzler shear force (WBSF), it was possible to...

Tipo: Artigo de periódico

Palavras-chave: Candidate gene; Bovine; Differential expression; Molecular markers; Warner Bratzler; Shear force; Beef; Meat.

Ano: 2013

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/982035

Vicentini,Renato; Sassaki,Flávio T.; Gimenes,Marcos A.; Maia,Ivan G.; Menossi,Marcelo.

The expressed sequence tags (ESTs) produced in the Forests project provide an invaluable opportunity to assess the Eucalyptus transcriptome. Besides providing information on the different proteins produced by this plant, it is possible to infer gene expression profiles because non-normalized cDNA libraries were used. The EST frequency from any gene is correlated to the transcript levels in the tissues from which the cDNA libraries were constructed. The goal of this work was to identify Eucalyptus genes that showed either differential expression pattern or were ubiquitously expressed in the tissues sampled in the Forests project. Six robust statistical tests and very restrictive rules were applied to gain confidence in the in silico data aiming to avoid...

Integrated omic approaches reveal molecular mechanisms of tolerance during soybean and meloidogyne incognita interactions.

Palavras-chave: Transcriptome; Eucalyptus; Tissue-specific; Statistics; Differential expression.

Ano: 2005

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572005000400002

Introduction of the rd29A: AtDREB2A CA gene into soybean (Glycine max L. Merril) and its molecular characterization in leaves and roots during dehydration

ARRAES, F. B. M.; VASQUEZ, D. D. N.; TAHIR, M.; PINHEIRO, D. H.; FAHEEM, M.; FREITAS-ALVES, N. S.; MOREIRA-PINTO, C. E.; MOREIRA, V. J. V.; PAES-DE-MELO, B.; LISEI-DE-SA, M. E.; MORGANTE, C. V.; MOTA, A. P. Z.; LOURENÇO-TESSUTTI, I. T.; TOGAWA, R. C.; GRYNBERG, P.; FRAGOSO, R. da R.; ALMEIDA-ENGLER, J. de; LARSEN, M. R.; GROSSI-DE-SA, M. F..

The root-knot nematode (RKN), Meloidogyne incognita, is a devastating soybean pathogen worldwide. The use of resistant cultivars is the most effective method to prevent economic losses caused by RKNs. To elucidate the mechanisms involved in resistance to RKN, we determined the proteome and transcriptome profiles from roots of susceptible (BRS133) and highly tolerant (PI595099) Glycine max genotypes 4, 12, and 30 days after RKN infestation. After in silico analysis, we described major defense molecules and mechanisms considered constitutive responses to nematodeinfestation, such as mTOR, PI3K-Akt, relaxin, and thermogenesis. The integrated data allowed us to identify protein families and metabolic pathways exclusively regulated in tolerant soybean...

Tipo: Artigo de periódico

Palavras-chave: Root-knot nematode; Differential expression; Meloidogyne Incognita; Soja; Glycine Max; Transcriptome; Proteome; Phenylpropanoids.

Ano: 2022

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1148619

Engels,Cibelle; Fuganti-Pagliarini,Renata; Marin,Silvana Regina Rockenbach; Marcelino-Guimarães,Francismar Corrêa; Oliveira,Maria Cristina Neves; Kanamori,Norihito; Mizoi,Junya; Nakashima,Kazuo; Yamaguchi-Shinozaki,Kazuko; Nepomuceno,Alexandre Lima.

The loss of soybean yield to Brazilian producers because of a water deficit in the 2011-2012 season was 12.9%. To reduce such losses, molecular biology techniques, including plant transformation, can be used to insert genes of interest into conventional soybean cultivars to produce lines that are more tolerant to drought. The abscisic acid (ABA)-independent Dehydration Responsive Element Binding (DREB) gene family has been used to obtain plants with increased tolerance to abiotic stresses. In the present study, the rd29A:AtDREB2A CA gene from Arabidopsis thaliana was inserted into soybean using biolistics. Seventy-eight genetically modified (GM) soybean lines containing 2-17 copies of the AtDREB2A CA gene were produced. Two GM soybean lines (P1397 and...

Methodological evaluzation of 2-DE to study root proteomics during nematode infection in cotton and coffee plants.

Palavras-chave: Arabidopsis; Differential expression; Genetically modified organism; Water deficit.

Ano: 2013

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572013000400015