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Transcriptome and gene expression profile of ovarian follicle tissue of the triatomine bug Rhodnius prolixus

MEDEIROS, Marcelo N.; LOGULLO, Raquel; RAMOS, Isabela B.; SORGINE, Marcos H. F.; PAIVA-SILVA, Gabriela O.; MESQUITA, Rafael D.; MACHADO, Ednildo Alcantara; COUTINHO, Maria Alice; MASUDA, Hatisaburo; CAPURRO, Margareth L.; RIBEIRO, Jose M. C.; BRAZ, Gloria
Fonte: PERGAMON-ELSEVIER SCIENCE LTD Publicador: PERGAMON-ELSEVIER SCIENCE LTD
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
36.6%
Insect oocytes grow in close association with the ovarian follicular epithelium (OFE), which escorts the oocyte during oogenesis and is responsible for synthesis and secretion of the eggshell. We describe a transcriptome of OFE of the triatomine bug Rhodnius prolixus, a vector of Chagas disease, to increase our knowledge of the role of FE in egg development. Random clones were sequenced from a cDNA library of different stages of follicle development. The transcriptome showed high commitment to transcription, protein synthesis, and secretion. The most abundant cDNA was a secreted (S) small, proline-rich protein with maximal expression in the vitellogenic follicle, suggesting a role in oocyte maturation. We also found Rp45, a chorion protein already described, and a putative chitin-associated cuticle protein that was an eggshell component candidate. Six transcripts coding for proteins related to the unfolded-protein response (UPR) by were chosen and their expression analyzed. Surprisingly, transcripts related to UPR showed higher expression during early stages of development and downregulation during late stages, when transcripts coding for S proteins participating in chorion formation were highly expressed. Several transcripts with potential roles in oogenesis and embryo development are also discussed. We propose that intense protein synthesis at the FE results in reticulum stress (RS) and that lowering expression of a set of genes related to cell survival should lead to degeneration of follicular cells at oocyte maturation. This paradoxical suppression of UPR suggests that ovarian follicles may represent an interesting model for studying control of RS and cell survival in professional S cell types. (C) 2011 Elsevier Ltd. All rights reserved.; Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq); Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES); Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ); Fundacao de Amparo a Pesquisa de Estado do Rio de Janeiro (FAPERJ); Fundacao Universitaria Jose Bonifacio (FUJB); Fundacao Universitaria Jose Bonifacio (FUJB); INCT-Entomologia Molecular; INCT-Entomologia Molecular; Howard Hughes Medical Institute (HHMI); Howard Hughes Medical Institute (HHMI); Division of Intramural Research...

Comparative transcriptome analysis of early somatic embryo formation and seed development in Brazilian pine, Araucaria angustifolia (Bertol.) Kuntze; Comparative transcriptome analysis of early somatic embryo formation and seed development in Brazilian pine, Araucaria angustifolia (Bertol.) Kuntze

Elbl, Paula Maria; Lira, Bruno Silvestre; Andrade, Sonia Cristina da Silva; Jo, Leonardo; Santos, André Luis Wendt dos; Coutinho, Luiz Lehmann; Floh, Eny Iochevet Segal; Rossi, Maria Magdalena
Fonte: Springer; Dordrecht Publicador: Springer; Dordrecht
Tipo: Artigo de Revista Científica
ENG
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Somatic embryogenesis (SE) is a method for producing embryos in vitro and is considered a highly promising approach for micropropagation and germplasm conservation. However, the application of SE for genetic breeding and ex situ conservation of certain species, such as Brazilian pine, faces several technical challenges, including the difficulty of inducing embryogenic cultures using tissues of mature trees, the loss of embryogenic competence of cell cultures and incomplete development of somatic embryos. In order to understand the genetic factors governing embryogenesis, a comparative transcriptome analysis was performed to elucidate differences between distinct cell cultures, early zygotic and somatic embryos and, unorthodox seed developmental stages. A total of 64 GB of sequence derived from high-throughput Illumina RNA-seq profiling was used for de novo transcriptome assembly. The reference transcriptome resulted in 112,772 predicted unigenes with an average length of 825 bp and an N50 of 1,638 bp. Sequence similarity searches using a public protein database revealed 19,947 unigenes that could be annotated with gene descriptions and gene ontology terms. Analysis of differential gene expression allowed pinpointing of genes whose products are predicted to be involved in cell line embryogenic potential...

Transcriptome analysis of Gossypium hirsutum flower buds infested by cotton boll weevil (Anthonomus grandis) larvae

Artico, Sinara; Ribeiro-Alves, Marcelo; Oliveira-Neto, Osmundo B; Macedo, Leonardo L P; Silveira, Sylvia; Grossi-de-Sa, Maria F; Martinelli, Adriana P; Alves-Ferreira, Marcio
Fonte: Biomed Central Publicador: Biomed Central
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
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Background Cotton is a major fibre crop grown worldwide that suffers extensive damage from chewing insects, including the cotton boll weevil larvae (Anthonomus grandis). Transcriptome analysis was performed to understand the molecular interactions between Gossypium hirsutum L. and cotton boll weevil larvae. The Illumina HiSeq 2000 platform was used to sequence the transcriptome of cotton flower buds infested with boll weevil larvae. Results The analysis generated a total of 327,489,418 sequence reads that were aligned to the G. hirsutum reference transcriptome. The total number of expressed genes was over 21,697 per sample with an average length of 1,063 bp. The DEGseq analysis identified 443 differentially expressed genes (DEG) in cotton flower buds infected with boll weevil larvae. Among them, 402 (90.7%) were up-regulated, 41 (9.3%) were down-regulated and 432 (97.5%) were identified as orthologues of A. thaliana genes using Blastx. Mapman analysis of DEG indicated that many genes were involved in the biotic stress response spanning a range of functions, from a gene encoding a receptor-like kinase to genes involved in triggering defensive responses such as MAPK...

Análise, via RNAseq, do transcritoma da cana-de-açúcar e identificação de genes expressos em resposta a Sporisorium scitamineum, o agente causal do carvão; RNAseq based transcriptome analysis and identification of sugarcane genes expressed in response to Sporisorium scitamineum, the causal agent of smut

Palhares, Alessandra Carolina
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 09/09/2014 PT
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A cana-de-açúcar (Saccharum spp.) é uma importante cultura agrícola, sendo hospedeira de vários patógenos, incluindo o fungo biotrófico Sporisorium scitamineum, agente causal do carvão. A doença reduz a produtividade das lavouras de cana e a qualidade de seus produtos, sendo reconhecida pelo desenvolvimento de uma estrutura em forma de chicote, onde os teliósporos são produzidos. O objetivo deste estudo foi analisar o transcritoma da interação cana-de-açúcar - S. scitamineum, visando a identificação de genes do hospedeiro diferencialmente expressos em resposta à infecção fúngica. Gemas da variedade tolerante 'RB92-5345' foram inoculadas com S. scitamineum e mantidas em casa de vegetação para a coleta das amostras, em dois momentos: 120 h após a inoculação, e no momento da emissão do chicote, aos 200 dias após a inoculação. Foram construídas 12 bibliotecas com base na abordagem RNAseq. Três estratégias computacionais foram utilizadas nas etapas de mapeamento e análise da expressão diferencial de genes da cana: (i) STAR e DESeq, tomando como referência o genoma do sorgo; (ii) Bowtie 2 e DESeq, e (iii) CLC Genomics Workbench, tomando como referência as sequências codificadoras (CDS) do sorgo. Diagramas de Venn foram construídos para identificar genes diferencialmente expressos comuns às três estratégias computacionais...

Transcriptome variability in yeast strains

Carreto, Laura; Schuller, Dorit; Santos, Manuel A. S.
Fonte: Universidade do Minho Publicador: Universidade do Minho
Tipo: Conferência ou Objeto de Conferência
Publicado em /10/2008 ENG
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In order to understand yeast natural genome and transcriptome variability and evaluate whether such variability correlates with phenotypic diversity, we have isolated approximately 1000 yeast strains from Portuguese vineyards, namely from the Bairrada and Minho wine regions, genotyped them and selected the most divergent ones for genome and transcriptome characterization, using comparative genome hybridization on array (aCGH) and mRNA profiling, respectively. For comparative purposes, strains isolated from opportunistic clinical infections and commercial strains used by the wine industry were also included in the study. Approximately 3 % of the ORFeome showed copy number alterations relative to the reference strain S288C, which was associated with sub-telomeric instability and Ty element transposition. Interestingly, one third of the Ty elements identified in the genome of the reference laboratory strain (S288C) were absent in the wine strains, but were present in the clinical isolates. Distinct gene functional classes were affected by copy number changes in wine and clinical strains. However, no correlation was found between genome alterations and geographical origin. Transcriptome profiling of the same strains grown in synthetic must...

Transcriptome signature of the adult mouse choroid plexus

Marques, Fernanda Cristina Gomes de Sousa; Sousa, João Carlos; Coppola, Giovanni; Gao, Fuying; Puga, Renato; Brentani, Helena; Geschwind, Daniel H.; Sousa, Nuno; Neves, Margarida Correia; Palha, Joana Almeida
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em /01/2011 ENG
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Background: Although the gene expression profile of several tissues in humans and in rodent animal models has been explored, analysis of the complete choroid plexus (CP) transcriptome is still lacking. A better characterization of the CP transcriptome can provide key insights into its functions as one of the barriers that separate the brain from the periphery and in the production of cerebrospinal fluid. Methods: This work extends further what is known about the mouse CP transcriptome through a microarray analysis of CP tissue from normal mice under physiological conditions. Results: We found that the genes most highly expressed are those implicated in energy metabolism (oxidative phosphorylation, glycolysis/gluconeogenesis) and in ribosomal function, which is in agreement with the secretory nature of the CP. On the other hand, genes encoding for immune mediators are among those with lower expression in basal conditions. In addition, we found genes known to be relevant during brain development, and not previously identified to be expressed in the CP, including those encoding for various axonal guidance and angiogenesis molecules and for growth factors. Some of these are known to influence the neural stem cell niche in the subventricular zone...

Developmental Gene Discovery in a Hemimetabolous Insect: De Novo Assembly and Annotation of a Transcriptome for the Cricket Gryllus Bimaculatus

Extavour, Cassandra G.; Zeng, Victor; Ewen-Campen, Benjamin Scott; Horch, Hadley W.; Roth, Siegfried; Mito, Taro
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
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Most genomic resources available for insects represent the Holometabola, which are insects that undergo complete metamorphosis like beetles and flies. In contrast, the Hemimetabola (direct developing insects), representing the basal branches of the insect tree, have very few genomic resources. We have therefore created a large and publicly available transcriptome for the hemimetabolous insect Gryllus bimaculatus (cricket), a well-developed laboratory model organism whose potential for functional genetic experiments is currently limited by the absence of genomic resources. cDNA was prepared using mRNA obtained from adult ovaries containing all stages of oogenesis, and from embryos samples on each day of embryogenesis. Using 454 Titanium pyrosequencing, we sequenced over four million raw reads, and assembled them into 21,512 isotigs (predicted transcripts) and 120,805 singletons with an average coverage per base pair of 51.3. We annotated the transcriptome manually for over 400 conserved genes involved in embryonic patterning, gametogenesis, and signaling pathways. BLAST comparison of the transcriptome against the NCBI non-redundant protein database (nr) identified significant similarity to nr sequences for 55.5% of transcriptome sequences...

Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes

Farkas, Michael H; Grant, Gregory R; White, Joseph A; Sousa, Maria E; Consugar, Mark B; Pierce, Eric A
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
EN_US
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Background: The retina is a complex tissue comprised of multiple cell types that is affected by a diverse set of diseases that are important causes of vision loss. Characterizing the transcripts, both annotated and novel, that are expressed in a given tissue has become vital for understanding the mechanisms underlying the pathology of disease. Results: We sequenced RNA prepared from three normal human retinas and characterized the retinal transcriptome at an unprecedented level due to the increased depth of sampling provided by the RNA-seq approach. We used a non-redundant reference transcriptome from all of the empirically-determined human reference tracks to identify annotated and novel sequences expressed in the retina. We detected 79,915 novel alternative splicing events, including 29,887 novel exons, 21,757 3′ and 5′ alternate splice sites, and 28,271 exon skipping events. We also identified 116 potential novel genes. These data represent a significant addition to the annotated human transcriptome. For example, the novel exons detected increase the number of identified exons by 3%. Using a high-throughput RNA capture approach to validate 14,696 of these novel transcriptome features we found that 99% of the putative novel events can be reproducibly detected. Further...

A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines

Zhang, Qu; Hill, Geoffrey E; Edwards, Scott V; Backström, Niclas
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
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Background: With its plumage color dimorphism and unique history in North America, including a recent population expansion and an epizootic of Mycoplasma gallisepticum (MG), the house finch (Haemorhous mexicanus) is a model species for studying sexual selection, plumage coloration and host-parasite interactions. As part of our ongoing efforts to make available genomic resources for this species, here we report a transcriptome assembly derived from genes expressed in spleen. Results: We characterize transcriptomes from two populations with different histories of demography and disease exposure: a recently founded population in the eastern US that has been exposed to MG for over a decade and a native population from the western range that has never been exposed to MG. We utilize this resource to quantify conservation in gene expression in passerine birds over approximately 50 MY by comparing splenic expression profiles for 9,646 house finch transcripts and those from zebra finch and find that less than half of all genes expressed in spleen in either species are expressed in both species. Comparative gene annotations from several vertebrate species suggest that the house finch transcriptomes contain ~15 genes not yet found in previously sequenced vertebrate genomes. The house finch transcriptomes harbour ~85...

Comparative transcriptome analyses of Pseudomonas aeruginosa

Balasubramanian, Deepak; Mathee, Kalai
Fonte: FIU Digital Commons Publicador: FIU Digital Commons
Tipo: Artigo de Revista Científica Formato: application/pdf
Relevância na Pesquisa
36.68%
One of the hallmarks of bacterial survival is their ability to adapt rapidly to changing environmental conditions. Niche adaptation is a response to the signals received that are relayed, often to regulators that modulate gene expression. In the post-genomic era, DNA microarrays are used to study the dynamics of gene expression on a global scale. Numerous studies have used Pseudomonas aeruginosa--a Gram-negative environmental and opportunistic human pathogenic bacterium--as the model organism in whole-genome transcriptome analysis. This paper reviews the transcriptome studies that have led to immense advances in our understanding of the biology of this intractable human pathogen. Comparative analysis of 23 P. aeruginosa transcriptome studies has led to the identification of a unique set of genes that are signal specific and a core set that is differentially regulated. The 303 genes in the core set are involved in bacterial homeostasis, making them attractive therapeutic targets.

Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat

Schreiber, A.; Hayden, M.; Forrest, K.; Kong, S.; Langridge, P.; Baumann, U.
Fonte: BioMed Central Ltd. Publicador: BioMed Central Ltd.
Tipo: Artigo de Revista Científica
Publicado em //2012 EN
Relevância na Pesquisa
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Background: Bread wheat is one of the world’s most important food crops and considerable efforts have been made to develop genomic resources for this species. This includes an on-going project by the International Wheat Genome Sequencing Consortium to assemble its large and complex genome, which is hexaploid and contains three closely related ‘homoeologous’ copies for each chromosome. This multi-national effort avoids the complications polyploidy entails for correct assembly of the genome by sequencing flow-sorted chromosome arms one at a time. Here we report on an alternate approach, a direct homoeolog-specific assembly of the expressed portion of the genome, the transcriptome. Results: After assessment of the ability of various assemblers to generate homoeolog-specific assemblies, we employed a two-stage assembly process to produce a high-quality assembly of the transcriptome of hexaploid wheat from Roche-454 and Illumina GAIIx paired-end sequence reads. The assembly process made use of a rapid partitioning of expressed sequences into homoeologous clusters, followed by a parallel high-fidelity assembly of each cluster on a 1150-processor compute cloud. We assessed assembly quality through comparison to known wheat gene sequences and found that in ca. 98.5% of cases the assembly was sufficiently accurate for homoeologous triplets to be cleanly separated into either two or three separate contigs. Comparison to publicly available transcript collections suggests that the assembly covers ~75-80% of the complete transcriptome. Conclusions: This work therefore describes the first homoeolog-specific sequence assembly of the wheat transcriptome and provides a reference transcriptome for future wheat research. Furthermore...

Genome-wide methylation and transcriptome analysis in penile carcinoma: uncovering new molecular markers

Kuasne, Hellen; Syllos Colus, Ilce Mara de; Busso, Ariane Fidelis; Hernandez-Vargas, Hector; Barros-Filho, Mateus Camargo; Marchi, Fabio Albuquerque; Scapulatempo-Neto, Cristovam; Faria, Eliney Ferreira; Lopes, Ademar; Guimaraes, Gustavo Cardoso; Herceg,
Fonte: Biomed Central Ltd Publicador: Biomed Central Ltd
Tipo: Artigo de Revista Científica Formato: 10
ENG
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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq); Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP); Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Processo FAPESP: 2009/52088-3; Processo FAPESP: 2010/51601-6; Background: Despite penile carcinoma (PeCa) being a relatively rare neoplasm, it remains an important public health issue for poor and developing countries. Contrary to most tumors, limited data are available for markers that are capable of assisting in diagnosis, prognosis, and treatment of PeCa. We aimed to identify molecular markers for PeCa by evaluating their epigenomic and transcriptome profiles and comparing them with surrounding non-malignant tissue (SNT) and normal glans (NG).Results: Genome-wide methylation analysis revealed 171 hypermethylated probes in PeCa. Transcriptome profiling presented 2,883 underexpressed and 1,378 overexpressed genes. Integrative analysis revealed a panel of 54 genes with an inverse correlation between methylation and gene expression levels. Distinct methylome and transcriptome patterns were found for human papillomavirus (HPV)-positive (38.6%) and negative tumors. Interestingly, grade 3 tumors showed a distinct methylation profile when compared to grade 1. In addition...

Transcriptome Assembly and Molecular Evolutionary Analysis of Sex-Biased Genes in the Guppy (Poecilia reticulata)

Sharma, Eshita
Fonte: Universität Tübingen Publicador: Universität Tübingen
Tipo: Dissertation; info:eu-repo/semantics/doctoralThesis
EN
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It is a phenomenon universally seen that males and females of a species show phenotypic differences as they evolve under often diverging sex-specific selection pressures. The evolution and maintenance of their sexual dimorphism is generally associated with gene expression divergence between the sexes. Genes that show enriched expression in one sex, also called sex-biased genes, often show rapid molecular evolution. Furthermore, sex-biased genes have also been found to be over-represented on X or Z chromosomes in several species with differentiated sex chromosomes or neo-sex chromosomes. While research on sex-biased genes in drosophilids, mammals and birds has developed in the last decade, there is relatively little known about sex-biased genes in teleost species with largely undifferentiated sex-chromosomes of recent origin. A case in point is that of the Trinidadian guppy, Poecilia reticulata, which is the focal species of my thesis. In this dissertation, I investigate sex-biased gene expression in guppy, a fresh-water fish with XY sex-determination and Y-linked inheritance of male-advantageous traits. Guppies display sexual dimorphism in size, ornaments, and behavior, traits that are shaped by both natural and sexual selection in the wild. My first task was to assemble a transcriptome reference using deep sequencing of cDNA. I compared several methods of assembly with RNA sequencing (RNA-seq) data and assembled and annotated a reference transcriptome combining a genome-independent and a genome-guided assembly. Subsequently...

Comparative transcriptome analyses of Pseudomonas aeruginosa

Balasubramanian, Deepak; Mathee, Kalai
Fonte: SelectedWorks Publicador: SelectedWorks
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
36.68%
One of the hallmarks of bacterial survival is their ability to adapt rapidly to changing environmental conditions. Niche adaptation is a response to the signals received that are relayed, often to regulators that modulate gene expression. In the post-genomic era, DNA microarrays are used to study the dynamics of gene expression on a global scale. Numerous studies have used Pseudomonas aeruginosa--a Gram-negative environmental and opportunistic human pathogenic bacterium--as the model organism in whole-genome transcriptome analysis. This paper reviews the transcriptome studies that have led to immense advances in our understanding of the biology of this intractable human pathogen. Comparative analysis of 23 P. aeruginosa transcriptome studies has led to the identification of a unique set of genes that are signal specific and a core set that is differentially regulated. The 303 genes in the core set are involved in bacterial homeostasis, making them attractive therapeutic targets.

Étude du transcriptome des cellules non tumorales de l’épithélium de surface de l’ovaire des femmes porteuses d’une mutation des gènes BRCA1 et BRCA2

Abd Rabbo, Diala
Fonte: Université de Montréal Publicador: Université de Montréal
Tipo: Thèse ou Mémoire numérique / Electronic Thesis or Dissertation
FR
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36.68%
Nous avons étudié le transcriptome de neuf échantillons d'ARN extraits de cultures primaires de cellules non tumorales de l’épithélium de surface de l’ovaire (NOSE) provenant de quatre donneuses non porteuses de mutation, deux mutées sur BRCA1 et trois sur BRCA2, ainsi que de quatre échantillons d’ARN extraits de cultures primaires de cellules tumorales de l’ovaire (TOV) provenant de trois donneuses porteuses de mutation sur BRCA1 et une sur BRCA2. Nous avons identifié, pour la première fois, les signatures moléculaires associées à la présence d’une mutation de BRCA1 et BRCA2 dans les cellules NOSEs ainsi que la signature associée à la transformation tumorale des cellules NOSEs en TOVs chez les porteuses de mutation de BRCA1. Nous avons également localisé les domaines chromosomiques comportant des gènes corégulés en association avec la présence d’une mutation de BRCA1 dans les cellules NOSEs. Les allèles sauvage et muté de BRCA2 étaient exprimés dans les cellules TOVs provenant des porteuses de la mutation 8765delAG sur BRCA2. Nous avons observé que le niveau d’expression des transcrits de BRCA2 était plus élevé dans les cellules provenant des tumeurs ovariennes les plus agressives chez les femmes porteuses de la mutation 8765delAG sur BRCA2...

Construção de um atlas transcriptômico para o estudo da doença vassoura de bruxa do cacaueiro; A comprehensive transcriptome atlas for the study of the witches` broom disease of cacao

Paulo José Pereira Lima Teixeira
Fonte: Biblioteca Digital da Unicamp Publicador: Biblioteca Digital da Unicamp
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 26/02/2013 PT
Relevância na Pesquisa
36.68%
O cacaueiro se destaca como uma das principais culturas perenes na agricultura, sendo economicamente relevante por fornecer a matéria prima para a fabricação do chocolate, um produto que movimenta bilhões de dólares no mercado mundial a cada ano. Apesar de sua importância, o cacaueiro é drasticamente atacado por diversas doenças que diminuem sua produtividade e reduzem a qualidade das amêndoas do cacau. Dentre estas, a vassoura de bruxa, causada pelo basidiomiceto Moniliophthora perniciosa, é um importante fator limitante da produção cacaueira nas Américas. Utilizando tecnologias de sequenciamento de DNA de nova geração, realizamos uma abrangente análise transcriptômica da vassoura de bruxa neste trabalho. Um banco de dados denominado Atlas Transcriptômico da Vassoura de Bruxa foi construído, o qual compreende aproximadamente 60 bibliotecas de RNA-seq representativas dos mais variados estágios de desenvolvimento, condições de crescimento e respostas a estresse do fungo M. perniciosa sob condições in vitro e in planta. O primeiro capítulo desta tese apresenta uma análise global do Atlas Transcriptômico da vassoura de bruxa. Este conjunto de dados tem suportado uma série de estudos específicos relacionados a variados aspectos da doença...

Whole transcriptome organisation in the dehydrated supraoptic nucleus

Hindmarch,C.C.T.; Franses,P.; Goodwin,B.; Murphy,D.
Fonte: Associação Brasileira de Divulgação Científica Publicador: Associação Brasileira de Divulgação Científica
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/12/2013 EN
Relevância na Pesquisa
36.68%
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 previously published euhydrated and dehydrated SON data to observe this trend and how it changes following dehydration. In accordance with other studies, our whole transcriptome data fit well with this model in the euhydrated SON microarrays, but interestingly, fit better in the dehydrated arrays. This trend was observed in a subset of differentially regulated genes and also following network reconstruction using a third-party database that mines public data. We make use of language as a metaphor that helps us philosophise about the role of the whole transcriptome in providing a suitable environment for the delivery of Avp following a survival threat like dehydration.

Cyberinfrastructure resources enabling creation of the loblolly pine reference transcriptome

Wu, Le-Shin; Ganote, Carrie; Doak, Thomas; Barnett, William K.; Mockaitis, Keithanne; Stewart, Craig A.
Fonte: ACM, New York, NY Publicador: ACM, New York, NY
Tipo: Artigo de Revista Científica
EN_US
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This paper was presented at XSEDE 15 conference.; Today's genomics technologies generate more sequence data than ever before possible, and at substantially lower costs, serving researchers across biological disciplines in transformative ways. Building transcriptome assemblies from RNA sequencing reads is one application of next-generation sequencing (NGS) that has held a central role in biological discovery in both model and non- model organisms, with and without whole genome sequence references. A major limitation in effective building of transcriptome references is no longer the sequencing data generation itself, but the computing infrastructure and expertise needed to assemble, analyze and manage the data. Here we describe a currently available resource dedicated to achieving such goals, and its use for extensive RNA assembly of up to 1.3 billion reads representing the massive transcriptome of loblolly pine, using four major assembly software installations. The Mason cluster, an XSEDE second tier resource at Indiana University, provides the necessary fast CPU cycles, large memory, and high I/O throughput for conducting large-scale genomics research. The National Center for Genome Analysis Support, or NCGAS, provides technical support in using HPC systems...

Strategies for wheat stripe rust pathogenicity identified by transcriptome sequencing

Garnica, Diana P.; Upadhyaya, Narayana M.; Dodds, Peter N.; Rathjen, John P.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica Formato: 17 pages
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Stripe rust caused by the fungus Puccinia striiformis f.sp. tritici (Pst) is a major constraint to wheat production worldwide. The molecular events that underlie Pst pathogenicity are largely unknown. Like all rusts, Pst creates a specialized cellular structure within host cells called the haustorium to obtain nutrients from wheat, and to secrete pathogenicity factors called effector proteins. We purified Pst haustoria and used next-generation sequencing platforms to assemble the haustorial transcriptome as well as the transcriptome of germinated spores. 12,282 transcripts were assembled from 454-pyrosequencing data and used as reference for digital gene expression analysis to compare the germinated uredinospores and haustoria transcriptomes based on Illumina RNAseq data. More than 400 genes encoding secreted proteins which constitute candidate effectors were identified from the haustorial transcriptome, with two thirds of these up-regulated in this tissue compared to germinated spores. RT-PCR analysis confirmed the expression patterns of 94 effector candidates. The analysis also revealed that spores rely mainly on stored energy reserves for growth and development, while haustoria take up host nutrients for massive energy production for biosynthetic pathways and the ultimate production of spores. Together...

Selective inhibition of yeast regulons by daunorubicin: A transcriptome-wide analysis

Rojas, Marta; Casado, Marta; Portugal, José; Piña, Benjamín
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artículo Formato: 1033037 bytes; application/pdf
ENG
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16 páginas, 6 figuras, 9 tablas.; Background The antitumor drug daunorubicin exerts some of its cytotoxic effects by binding to DNA and inhibiting the transcription of different genes. We analysed this effect in vivo at the transcriptome level using the budding yeast Saccharomyces cerevisiae as a model and sublethal (IC40) concentrations of the drug to minimise general toxic effects. Results Daunorubicin affected a minor proportion (14%) of the yeast transcriptome, increasing the expression of 195 genes and reducing expression of 280 genes. Daunorubicin down-regulated genes included essentially all genes involved in the glycolytic pathway, the tricarboxylic acid cycle and alcohol metabolism, whereas transcription of ribosomal protein genes was not affected or even slightly increased. This pattern is consistent with a specific inhibition of glucose usage in treated cells, with only minor effects on proliferation or other basic cell functions. Analysis of promoters of down-regulated genes showed that they belong to a limited number of transcriptional regulatory units (regulons). Consistently, data mining showed that daunorubicin-induced changes in expression patterns were similar to those observed in yeast strains deleted for some transcription factors functionally related to the glycolysis and/or the cAMP regulatory pathway...