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  1 / 11520 MEDLINE  
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[PMID]:29425202
[Au] Autor:Du M; Li N; Niu B; Liu Y; You D; Jiang D; Ruan C; Qin Z; Song T; Wang W
[Ad] Endereço:Key Lab for Quality, Efficient Cultivation and Security Control of Crops in Colleges and University of Yunnan Province, Honghe University, Mengzi, Yunnan Province, P.R. China.
[Ti] Título:De novo transcriptome analysis of Bagarius yarrelli (Siluriformes: Sisoridae) and the search for potential SSR markers using RNA-Seq.
[So] Source:PLoS One;13(2):e0190343, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The yellow sisorid catfish (Bagarius yarrelli) is a carnivorous freshwater fish that inhabits the Honghe River, Lanchangjiang River and Nujiang River of southern China and other Southeast Asian countries. However, the publicly available genomic data for B. yarrelli are limited. METHODOLOGY AND PRINCIPAL FINDINGS: Illumina Solexa paired-end technology produced 1,706,456 raw reads from muscle, liver and caudal fin tissues of B. yarrelli. Nearly 5 Gb of data were acquired, and de novo assembly generated 14,607 unigenes, with an N50 of 2006 bp. A total of 9093 unigenes showed significant similarities to known proteins in public databases: 4477 and 6391 of B. yarrelli unigenes were mapped to the Gene Ontology (GO) and Clusters of Orthologous Groups (COG) databases, respectively. Moreover, 9635 unigenes were assigned to 242 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. In addition, 8568 microsatellites (simple sequence repeats, SSRs) were detected, and 31 pairs of polymorphic primers were characterized using wild populations of B. yarrelli from the Nujiang River, Yunnan Province, China. CONCLUSION/SIGNIFICANCE: These sequences enrich the genomic resources for B. yarrelli and will benefit future investigations into the evolutionary and biological processes of this and related Bagarius species. The SSR markers developed in this study will facilitate construction of genetic maps, investigations of genetic structures and germplasm polymorphism assessments in B. yarrelli.
[Mh] Termos MeSH primário: Peixes-Gato/genética
Marcadores Genéticos
Análise de Sequência de RNA
Transcriptoma
[Mh] Termos MeSH secundário: Animais
Repetições de Microssatélites/genética
Fases de Leitura Aberta
Reação em Cadeia da Polimerase
Polimorfismo Genético
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Genetic Markers)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180210
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190343


  2 / 11520 MEDLINE  
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[PMID]:29414690
[Au] Autor:Li X; Lin Z; Zhan X; Gao J; Sun L; Cao Y; Qiu H
[Ad] Endereço:Department of Endocrinology, First Affiliated Hospital Harbin Medical University, Harbin, Heilongjiang, PR China; Department of Pharmacology, The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Harbin Medical Un
[Ti] Título:RNA-seq analysis of the transcriptome of the liver of cynomolgus monkeys with type 2 diabetes.
[So] Source:Gene;651:118-125, 2018 Apr 20.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Genetic and environmental factors such as high-fat diet are involved in the development of type 2 diabetes mellitus (T2DM). Cynomolgus monkey shares similar genetic makeup, tissue structures, physiology and metabolic function to human. This study aimed to establish T2DM model in cynomolgus monkey and compare expression profiles of hepatic genes and their associated pathways in normal cynomolgus monkeys and those with T2DM. We employed RNA-seq technique and identified 1451 differentially expressed genes (DEGs) with a false discovery rate (FDR) of 0.1% between normal and T2DM animals. KEGG pathway analysis revealed that DEGs were associated with 12 KEGG pathways (P < 0.05). Two of these pathways were associated with metabolism and five were related to immunity. Unexpected, we found ECM-receptor interaction pathway. In conclusion, our data suggest that three major pathways may be implicated in the development of T2DM, including steroid biosynthesis, immune response and ECM. Further characterization of these pathways may provide new targets for the prevention and therapy of T2DM.
[Mh] Termos MeSH primário: Diabetes Mellitus Tipo 2/veterinária
Fígado/metabolismo
Macaca fascicularis/genética
Doenças dos Macacos/genética
Transcriptoma
[Mh] Termos MeSH secundário: Animais
Diabetes Mellitus Experimental/genética
Diabetes Mellitus Tipo 2/genética
Diabetes Mellitus Tipo 2/imunologia
Diabetes Mellitus Tipo 2/metabolismo
Modelos Animais de Doenças
Ontologia Genética
Masculino
Redes e Vias Metabólicas
Doenças dos Macacos/imunologia
Doenças dos Macacos/metabolismo
Análise de Sequência de RNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180208
[St] Status:MEDLINE


  3 / 11520 MEDLINE  
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[PMID]:29378241
[Au] Autor:Zhang L; Wang MY; Li XP; Wang XT; Jia CL; Yang XZ; Feng RQ; Yuan ML
[Ad] Endereço:State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, People's Republic of China.
[Ti] Título:A small set of differentially expressed genes was associated with two color morphs in natural populations of the pea aphid Acyrthosiphon pisum.
[So] Source:Gene;651:23-32, 2018 Apr 20.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Color polymorphism is an ecologically important trait, which is related to local adaptation and ecological speciation. The pea aphid Acyrthosiphon pisum shows color polymorphism: the red and green color morphs where differences in ecological adaptation have been observed. Here, we measured genome-wide gene expression profiles of two color morphs in natural populations of A. pisum to explore the genetic basis of differentiated ecological adaptation. The results showed that only 32 genes were significantly differentially expressed between the two morphs, of which 18 had functional annotations. Among them, 13 genes were up-regulated [e.g. genes encoding protoheme IX farnesyltransferase (LOC100570971), carotene dehydrogenase (tor) and V-type proton ATPase subunit B (LOC100169462)] and 5 genes were down-regulated in the red morph (e.g. genes encoding transcription factors and heat shock proteins). To assess the functional importance of these differentially expressed genes (DEGs), we selected three highly expressed DEGs (LOC100169462, LOC100570971 and tor) with functional annotations and analyzed their expression levels in the red morph under three low temperatures (1 °C, 4 °C, and 8 °C) for 24 h. These three DEGs showed an interesting expression response to the cold acclimating conditions which resulted in an obvious phenotypic change of the red individuals to be greenish variants. This study suggests a link between gene expressions and body color polymorphisms in the pea aphid and provides important clues for further studying molecular mechanisms of ecological adaptation in aphids.
[Mh] Termos MeSH primário: Afídeos/genética
Genes de Insetos
[Mh] Termos MeSH secundário: Animais
Temperatura Baixa
Regulação Enzimológica da Expressão Gênica
Ontologia Genética
Medicago sativa
Pigmentação/genética
Polimorfismo Genético
Reação em Cadeia da Polimerase em Tempo Real
Análise de Sequência de RNA
Transcriptoma
beta-Caroteno 15,15'-Mono-Oxigenase/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 1.14.99.36 (beta-Carotene 15,15'-Monooxygenase)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180130
[St] Status:MEDLINE


  4 / 11520 MEDLINE  
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[PMID]:29377917
[Au] Autor:Xu FQ; Li A; Lan JJ; Wang YM; Yan MJ; Lian SY; Wu X
[Ad] Endereço:College of Animal Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, People's Republic of China.
[Ti] Título:Study of formation of green eggshell color in ducks through global gene expression.
[So] Source:PLoS One;13(1):e0191564, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The green eggshell color produced by ducks is a threshold trait that can be influenced by various factors, such as hereditary, environment and nutrition. The aim of this study was to investigate the genetic regulation of the formation of eggs with green shells in Youxian ducks. We performed integrative analysis of mRNAs and miRNAs expression profiling in the shell gland samples from ducks by RNA-Seq. We found 124 differentially expressed genes that were associated with various pathways, such as the ATP-binding cassette (ABC) transporter and solute carrier supper family pathways. A total of 31 differentially expressed miRNAs were found between ducks laying green eggs and white eggs. KEGG pathway analysis of the predicted miRNA target genes also indicated the functional characteristics of these miRNAs; they were involved in the ABC transporter pathway and the solute carrier (SLC) supper family. Analysis with qRT-PCR was applied to validate the results of global gene expression, which showed a correlation between results obtained by RNA-seq and RT-qPCR. Moreover, a miRNA-mRNA interaction network was established using correlation analysis of differentially expressed mRNA and miRNA. Compared to ducks that lay white eggs, ducks that lay green eggs include six up-regulated miRNAs that had regulatory effects on 35 down-regulated genes, and seven down-regulated miRNAs which influenced 46 up-regulated genes. For example, the ABC transporter pathway could be regulated by expressing gga-miR-144-3p (up-regulated) with ABCG2 (up-regulated) and other miRNAs and genes. This study provides valuable information about mRNA and miRNA regulation in duck shell gland tissues, and provides foundational information for further study on the eggshell color formation and marker-assisted selection for Youxian duck breeding.
[Mh] Termos MeSH primário: Cor
Casca de Ovo/metabolismo
Expressão Gênica
[Mh] Termos MeSH secundário: Animais
Patos
Reação em Cadeia da Polimerase em Tempo Real
Análise de Sequência de RNA
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180130
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191564


  5 / 11520 MEDLINE  
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[PMID]:28458032
[Au] Autor:Khan A; Al Balwi M; AlAyyar L; AlAbdulkareem I; Albekairy A; Aljumah A
[Ad] Endereço:Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia.
[Ti] Título:Tracing the epidemic history of hepatitis C virus genotypes in Saudi Arabia.
[So] Source:Infect Genet Evol;52:82-88, 2017 Aug.
[Is] ISSN:1567-7257
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:HCV genotype 4 is highly prevalent in many Middle Eastern countries, yet little is known about the genotype's epidemic history at the subtype-level in this region. To address the dearth of data from Saudi Arabia (SA) we genotyped 230 HCV isolates in the core/E- and NS5B-region and analyzed using Bayesian phylogenetic approaches. HCV genotype 4 (HCV/4) was positive in 61.7% (142/230) of isolates belonging to 7 different subtypes with the predominance of 4d (73/142; 51.4%) followed by 4a (51/142; 35.9%). Phylogenetic analysis also revealed a distinct epidemiological cluster of HCV/4d for Saudi Arabia. HCV/1 appeared as the second most prevalent genotype positive in 31.3% (72/230) of isolates with the predominance of 1b (53/72; 73.6%) followed by 1a (16/72; 22.2%), and 1g (3/72; 4.1%). A small proportion of isolates belonged to HCV/3a (12/230; 5.2%), and HCV/2a (4/230; 1.7%). We estimate that the genotype 4 common ancestor existed around 1935 (1850-1985). Genotype 4 originated plausibly in Central Africa and multiple subtypes disseminated across African borders since ~1970, including subtype 4d which dominates current HCV infections in Saudi Arabia. The Bayesian skyline plot (BSP) analysis showed that genotype 4d entered the Saudi population in 1900. The effective number of HCV infections grew gradually until the second half of the 1950s and more rapidly until the early-80s through the use of imported blood units and blood products. Subsequently, the rate of HCV infection in the Saudi Arabian population was stabilized through effective screening of blood and infection control measures.
[Mh] Termos MeSH primário: Hepacivirus/classificação
Hepatite C/virologia
Análise de Sequência de RNA/métodos
[Mh] Termos MeSH secundário: Adolescente
Adulto
Idoso
Idoso de 80 Anos ou mais
Teorema de Bayes
Criança
Pré-Escolar
Feminino
Genoma Viral
Genótipo
Hepacivirus/genética
Hepatite C/epidemiologia
Seres Humanos
Masculino
Meia-Idade
Filogenia
Arábia Saudita/epidemiologia
Adulto Jovem
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE


  6 / 11520 MEDLINE  
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[PMID]:28456663
[Au] Autor:Singh S; Anupriya MG; Sreekumar E
[Ad] Endereço:Molecular Virology Laboratory, Rajiv Gandhi Centre for Biotechnology (RGCB), Thycaud P.O., Thiruvananthapuram 695014, Kerala, India.
[Ti] Título:Comparative whole genome analysis of dengue virus serotype-2 strains differing in trans-endothelial cell leakage induction in vitro.
[So] Source:Infect Genet Evol;52:34-43, 2017 Aug.
[Is] ISSN:1567-7257
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:The role of genetic differences among dengue virus (DENV) in causing increased microvascular permeability is less explored. In the present study, we compared two closely related DENV serotype-2 strains of Cosmopolitan genotype for their in vitro infectivity phenotype and ability to induce trans-endothelial leakage. We found that these laboratory strains differed significantly in infecting human microvascular endothelial cells (HMEC-1) and hepatocytes (Huh7), two major target cells of DENV in in vivo infections. There was a reciprocal correlation in infectivity and vascular leakage induced by these strains, with the less infective strain inducing more trans-endothelial cell leakage in HMEC-1 monolayer upon infection. The cells infected with the strain capable of inducing more permeability were found to secrete more Non-Structural protein (sNS1) into the culture supernatant. A whole genome analysis revealed 37 predicted amino acid changes and changes in the secondary structure of 3' non-translated region between the strains. But none of these changes involved the signal sequence coded by the C-terminal of the Envelope protein and the two glycosylation sites within the NS1 protein critical for its secretion, and the N-terminal NS2A sequence important for surface targeting of NS1. The strain that secreted lower levels of NS1 and caused less leakage had two mutations within the NS1 protein coding region, F103S and T146I that significantly changed amino acid properties. A comparison of the sequences of the two strains with published sequences of various DENV strains known to cause clinically severe dengue identified a number of amino acid changes which could be implicated as possible key genetic differences. Our data supports the earlier observations that the vascular leakage induction potential of DENV strains is linked to the sNS1 levels. The results also indicate that viral genetic determinants, especially the mutations within the NS1 coding region, could affect this critical phenotype of DENV strains.
[Mh] Termos MeSH primário: Vírus da Dengue/fisiologia
Células Endoteliais/virologia
Hepatócitos/virologia
Proteínas não Estruturais Virais/genética
[Mh] Termos MeSH secundário: Regiões 3' não Traduzidas
Animais
Permeabilidade Capilar
Linhagem Celular
Vírus da Dengue/genética
Células Endoteliais/citologia
Variação Genética
Genoma Viral
Hepatócitos/citologia
Seres Humanos
Estrutura Secundária de Proteína
Análise de Sequência de RNA
Proteínas não Estruturais Virais/química
Proteínas não Estruturais Virais/secreção
Replicação Viral/fisiologia
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (3' Untranslated Regions); 0 (NS1 protein, Dengue virus type 2); 0 (Viral Nonstructural Proteins)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170501
[St] Status:MEDLINE


  7 / 11520 MEDLINE  
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[PMID]:28450084
[Au] Autor:Bodnar L; Lorusso E; Di Martino B; Catella C; Lanave G; Elia G; Bányai K; Buonavoglia C; Martella V
[Ad] Endereço:University Aldo Moro of Bari, Valenzano, Italy.
[Ti] Título:Identification of a novel canine norovirus.
[So] Source:Infect Genet Evol;52:75-81, 2017 Aug.
[Is] ISSN:1567-7257
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:By screening a collection of fecal samples from young dogs from different European countries, noroviruses (NoVs) were found in 13/294 (4.4%) animals with signs of enteritis whilst they were not detected in healthy dogs (0/42). An informative portion of the genome (3.4kb at the 3' end) was generated for four NoV strains. In the capsid protein VP1 region, strains 63.15/2015/ITA and FD53/2007/ITA were genetically related to the canine GVI.2 strain C33/Viseu/2007/PRT (97.4-98.6% nt and 90.3-98.6% aa). Strain FD210/2007/ITA displayed the highest identity to the GVI.1 canine strain Bari/91/2007/ITA (88.0% nt and 95.0% aa). Strain 5010/2009/ITA displayed only 66.6-67.6% nt and 75.5-81.6% aa identities to the GVI.1 canine strains FD210/2007/ITA and Bari/91/2007/ITA and the GVI feline strain M49-1/2012/JPN. Identity to the other canine/feline NoVs strains in the VP1 was lower than 67.6% nt and 62.7% aa. Based on the full-length VP1 amino acid sequence and the criteria proposed for distinction of NoV genotypes, the canine NoV 5010/2009/ITA could represent the prototype of a third GVI genotype, thus providing further evidence for the genetic heterogeneity of NoVs in carnivores.
[Mh] Termos MeSH primário: Infecções por Caliciviridae/veterinária
Doenças do Cão/virologia
Gastroenterite/veterinária
Norovirus/classificação
[Mh] Termos MeSH secundário: Animais
Infecções por Caliciviridae/diagnóstico
Infecções por Caliciviridae/epidemiologia
Doenças do Cão/epidemiologia
Cães
Europa (Continente)/epidemiologia
Evolução Molecular
Fezes/virologia
Gastroenterite/virologia
Genoma Viral
Norovirus/genética
Norovirus/isolamento & purificação
Filogenia
Análise de Sequência de RNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE


  8 / 11520 MEDLINE  
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[PMID]:28987404
[Au] Autor:Xu H; Yu C; Xia X; Li M; Li H; Wang Y; Wang S; Wang C; Ma Y; Zhou G
[Ad] Endereço:Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
[Ti] Título:Comparative transcriptome analysis of duckweed (Landoltia punctata) in response to cadmium provides insights into molecular mechanisms underlying hyperaccumulation.
[So] Source:Chemosphere;190:154-165, 2018 Jan.
[Is] ISSN:1879-1298
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Cadmium (Cd) is a detrimental environmental pollutant. Duckweeds have been considered promising candidates for Cd phytoremediation. Although many physiological studies have been conducted, the molecular mechanisms underlying Cd hyperaccumulation in duckweeds are largely unknown. In this study, clone 6001 of Landoltia punctata, which showed high Cd tolerance, was obtained by large-scale screening of over 200 duckweed clones. Subsequently, its growth, Cd flux, Cd accumulation, and Cd distribution characteristics were investigated. To further explore the global molecular mechanism, a comprehensive transcriptome analysis was performed. For RNA-Seq, samples were treated with 20 µM CdCl for 0, 1, 3, and 6 days. In total, 9,461, 9,847, and 9615 differentially expressed unigenes (DEGs) were discovered between Cd-treated and control (0 day) samples. DEG clustering and enrichment analysis identified several biological processes for coping with Cd stress. Genes involved in DNA repair acted as an early response to Cd, while RNA and protein metabolism would be likely to respond as well. Furthermore, the carbohydrate metabolic flux tended to be modulated in response to Cd stress, and upregulated genes involved in sulfur and ROS metabolism might cause high Cd tolerance. Vacuolar sequestration most likely played an important role in Cd detoxification in L. punctata 6001. These novel findings provided important clues for molecular assisted screening and breeding of Cd hyperaccumulating cultivars for phytoremediation.
[Mh] Termos MeSH primário: Araceae/efeitos dos fármacos
Araceae/genética
Biodegradação Ambiental
Cádmio/farmacocinética
Perfilação da Expressão Gênica
[Mh] Termos MeSH secundário: Araceae/metabolismo
Cádmio/metabolismo
Tolerância a Medicamentos/genética
Perfilação da Expressão Gênica/métodos
Genes de Plantas/efeitos dos fármacos
Genes de Plantas/genética
Análise de Sequência de RNA
Estresse Fisiológico/genética
Transcriptoma/efeitos dos fármacos
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Nm] Nome de substância:
00BH33GNGH (Cadmium)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171009
[St] Status:MEDLINE


  9 / 11520 MEDLINE  
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[PMID]:29434199
[Au] Autor:Hayashi T; Ozaki H; Sasagawa Y; Umeda M; Danno H; Nikaido I
[Ad] Endereço:Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, 2-1 Hirosawa Wako, Saitama, 351-0198, Japan.
[Ti] Título:Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs.
[So] Source:Nat Commun;9(1):619, 2018 02 12.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Total RNA sequencing has been used to reveal poly(A) and non-poly(A) RNA expression, RNA processing and enhancer activity. To date, no method for full-length total RNA sequencing of single cells has been developed despite the potential of this technology for single-cell biology. Here we describe random displacement amplification sequencing (RamDA-seq), the first full-length total RNA-sequencing method for single cells. Compared with other methods, RamDA-seq shows high sensitivity to non-poly(A) RNA and near-complete full-length transcript coverage. Using RamDA-seq with differentiation time course samples of mouse embryonic stem cells, we reveal hundreds of dynamically regulated non-poly(A) transcripts, including histone transcripts and long noncoding RNA Neat1. Moreover, RamDA-seq profiles recursive splicing in >300-kb introns. RamDA-seq also detects enhancer RNAs and their cell type-specific activity in single cells. Taken together, we demonstrate that RamDA-seq could help investigate the dynamics of gene expression, RNA-processing events and transcriptional regulation in single cells.
[Mh] Termos MeSH primário: Sequenciamento de Nucleotídeos em Larga Escala/métodos
Células-Tronco Embrionárias Murinas/metabolismo
Processamento de RNA
RNA Longo não Codificante/genética
RNA Mensageiro/genética
Análise de Célula Única/métodos
[Mh] Termos MeSH secundário: Animais
Sequência de Bases
Diferenciação Celular
Elementos Facilitadores Genéticos
Éxons
Histonas/genética
Histonas/metabolismo
Íntrons
Camundongos
Células-Tronco Embrionárias Murinas/citologia
RNA Longo não Codificante/metabolismo
RNA Mensageiro/metabolismo
Análise de Sequência de RNA
Transcrição Genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Histones); 0 (NEAT1 long non-coding RNA, mouse); 0 (RNA, Long Noncoding); 0 (RNA, Messenger)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180214
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-018-02866-0


  10 / 11520 MEDLINE  
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[PMID]:29244011
[Au] Autor:Yu N; Yu Z; Pan Y
[Ad] Endereço:Department of Computing Sciences, The College at Brockport, State University of New York, 350 New Campus Drive, Brockport, 14420, NY, USA. nyu@brockport.edu.
[Ti] Título:A deep learning method for lincRNA detection using auto-encoder algorithm.
[So] Source:BMC Bioinformatics;18(Suppl 15):511, 2017 Dec 06.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: RNA sequencing technique (RNA-seq) enables scientists to develop novel data-driven methods for discovering more unidentified lincRNAs. Meantime, knowledge-based technologies are experiencing a potential revolution ignited by the new deep learning methods. By scanning the newly found data set from RNA-seq, scientists have found that: (1) the expression of lincRNAs appears to be regulated, that is, the relevance exists along the DNA sequences; (2) lincRNAs contain some conversed patterns/motifs tethered together by non-conserved regions. The two evidences give the reasoning for adopting knowledge-based deep learning methods in lincRNA detection. Similar to coding region transcription, non-coding regions are split at transcriptional sites. However, regulatory RNAs rather than message RNAs are generated. That is, the transcribed RNAs participate the biological process as regulatory units instead of generating proteins. Identifying these transcriptional regions from non-coding regions is the first step towards lincRNA recognition. RESULTS: The auto-encoder method achieves 100% and 92.4% prediction accuracy on transcription sites over the putative data sets. The experimental results also show the excellent performance of predictive deep neural network on the lincRNA data sets compared with support vector machine and traditional neural network. In addition, it is validated through the newly discovered lincRNA data set and one unreported transcription site is found by feeding the whole annotated sequences through the deep learning machine, which indicates that deep learning method has the extensive ability for lincRNA prediction. CONCLUSIONS: The transcriptional sequences of lincRNAs are collected from the annotated human DNA genome data. Subsequently, a two-layer deep neural network is developed for the lincRNA detection, which adopts the auto-encoder algorithm and utilizes different encoding schemes to obtain the best performance over intergenic DNA sequence data. Driven by those newly annotated lincRNA data, deep learning methods based on auto-encoder algorithm can exert their capability in knowledge learning in order to capture the useful features and the information correlation along DNA genome sequences for lincRNA detection. As our knowledge, this is the first application to adopt the deep learning techniques for identifying lincRNA transcription sequences.
[Mh] Termos MeSH primário: Algoritmos
Biologia Computacional/métodos
Aprendizado de Máquina
RNA Longo não Codificante/genética
Análise de Sequência de RNA/métodos
[Mh] Termos MeSH secundário: Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Long Noncoding)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180307
[Lr] Data última revisão:
180307
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171216
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1922-3



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