Base de dados : MEDLINE
Pesquisa : G05.360.325 [Categoria DeCS]
Referências encontradas : 23658 [refinar]
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[PMID]:29385199
[Au] Autor:Schaefer C; Mallela N; Seggewiß J; Lechtape B; Omran H; Dirksen U; Korsching E; Potratz J
[Ad] Endereço:Pediatric Hematology and Oncology, University Hospital Münster, Münster, Germany.
[Ti] Título:Target discovery screens using pooled shRNA libraries and next-generation sequencing: A model workflow and analytical algorithm.
[So] Source:PLoS One;13(1):e0191570, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:In the search for novel therapeutic targets, RNA interference screening has become a valuable tool. High-throughput technologies are now broadly accessible but their assay development from baseline remains resource-intensive and challenging. Focusing on this assay development process, we here describe a target discovery screen using pooled shRNA libraries and next-generation sequencing (NGS) deconvolution in a cell line model of Ewing sarcoma. In a strategy designed for comparative and synthetic lethal studies, we screened for targets specific to the A673 Ewing sarcoma cell line. Methods, results and pitfalls are described for the entire multi-step screening procedure, from lentiviral shRNA delivery to bioinformatics analysis, illustrating a complete model workflow. We demonstrate that successful studies are feasible from the first assay performance and independent of specialized screening units. Furthermore, we show that a resource-saving screen depth of 100-fold average shRNA representation can suffice to generate reproducible target hits despite heterogeneity in the derived datasets. Because statistical analysis methods are debatable for such datasets, we created ProFED, an analysis package designed to facilitate descriptive data analysis and hit calling using an aim-oriented profile filtering approach. In its versatile design, this open-source online tool provides fast and easy analysis of shRNA and other count-based datasets to complement other analytical algorithms.
[Mh] Termos MeSH primário: Descoberta de Drogas/métodos
Avaliação Pré-Clínica de Medicamentos/métodos
Biblioteca Gênica
RNA Interferente Pequeno/genética
[Mh] Termos MeSH secundário: Algoritmos
Linhagem Celular Tumoral
Biologia Computacional
Células HEK293
Sequenciamento de Nucleotídeos em Larga Escala
Seres Humanos
Lentivirus/genética
Interferência de RNA
Sarcoma de Ewing/tratamento farmacológico
Sarcoma de Ewing/genética
Análise de Sequência de RNA
Fluxo de Trabalho
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (RNA, Small Interfering)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180302
[Lr] Data última revisão:
180302
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180201
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191570


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[PMID]:29352242
[Au] Autor:Cottrell KA; Chaudhari HG; Cohen BA; Djuranovic S
[Ad] Endereço:Department of Cell Biology and Physiology, School of Medicine, Washington University, St. Louis, MO, 63110, USA.
[Ti] Título:PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs.
[So] Source:Nat Commun;9(1):301, 2018 01 19.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:RNA binding proteins (RBP) and microRNAs (miRNAs) often bind sequences in 3' untranslated regions (UTRs) of mRNAs, and regulate stability and translation efficiency. With the identification of numerous RBPs and miRNAs, there is an urgent need for new technologies to dissect the function of the cis-acting elements of RBPs and miRNAs. We describe post-transcriptional regulatory element sequencing (PTRE-seq), a massively parallel method for assaying the target sequences of miRNAs and RBPs. We use PTRE-seq to dissect sequence preferences and interactions between miRNAs and RBPs. The binding sites for these effector molecules influenced different aspects of the RNA lifecycle: RNA stability, translation efficiency, and translation initiation. In some cases, post-transcriptional control is modular, with different factors acting independently of each other, while in other cases factors show specific epistatic interactions. The throughput, flexibility, and reproducibility of PTRE-seq make it a valuable tool to study post-transcriptional regulation by 3'UTR elements.
[Mh] Termos MeSH primário: MicroRNAs/genética
Biossíntese de Proteínas
Processamento Pós-Transcricional do RNA
Proteínas de Ligação a RNA/genética
Elementos Reguladores de Transcrição
Fatores de Transcrição/genética
[Mh] Termos MeSH secundário: Regiões 3' não Traduzidas
Sequência de Bases
Sítios de Ligação
Linhagem Celular
Biblioteca Gênica
Células HEK293
Células HeLa
Seres Humanos
MicroRNAs/metabolismo
Ligação Proteica
Estabilidade de RNA
Proteínas de Ligação a RNA/metabolismo
Análise de Sequência de RNA
Termodinâmica
Fatores de Transcrição/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (3' Untranslated Regions); 0 (MicroRNAs); 0 (RNA-Binding Proteins); 0 (Transcription Factors); 0 (mirnlet7 microRNA, human); 0 (pumilio protein, human)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180222
[Lr] Data última revisão:
180222
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180121
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02745-0


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[PMID]:27779108
[Au] Autor:D'Alesio C; Punzi S; Cicalese A; Fornasari L; Furia L; Riva L; Carugo A; Curigliano G; Criscitiello C; Pruneri G; Pelicci PG; Faretta M; Bossi D; Lanfrancone L
[Ad] Endereço:Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy.
[Ti] Título:RNAi screens identify CHD4 as an essential gene in breast cancer growth.
[So] Source:Oncotarget;7(49):80901-80915, 2016 Dec 06.
[Is] ISSN:1949-2553
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Epigenetic regulation plays an essential role in tumor development and epigenetic modifiers are considered optimal potential druggable candidates. In order to identify new breast cancer vulnerabilities and improve therapeutic chances for patients, we performed in vivo and in vitro shRNA screens in a human breast cancer cell model (MCF10DCIS.com cell line) using epigenetic libraries. Among the genes identified in our screening, we deeply investigated the role of Chromodomain Helicase DNA binding Protein 4 (CHD4) in breast cancer tumorigenesis. CHD4 silencing significantly reduced tumor growth in vivo and proliferation in vitro of MCF10DCIS.com cells. Similarly, in vivo breast cancer growth was decreased in a spontaneous mouse model of breast carcinoma (MMTV-NeuT system) and in metastatic patient-derived xenograft models. Conversely, no reduction in proliferative ability of non-transformed mammary epithelial cells (MCF10A) was detected. Moreover, we showed that CHD4 depletion arrests proliferation by inducing a G0/G1 block of cell cycle associated with up-regulation of CDKN1A (p21). These results highlight the relevance of genetic screens in the identification of tumor frailties and the role of CHD4 as a potential pharmacological target to inhibit breast cancer growth.
[Mh] Termos MeSH primário: Neoplasias da Mama/genética
Proliferação Celular
DNA Helicases/genética
Complexo Mi-2 de Remodelação de Nucleossomo e Desacetilase/genética
Interferência de RNA
[Mh] Termos MeSH secundário: Animais
Neoplasias da Mama/enzimologia
Neoplasias da Mama/patologia
Pontos de Checagem do Ciclo Celular
Linhagem Celular Tumoral
Biologia Computacional
Inibidor de Quinase Dependente de Ciclina p21/genética
Inibidor de Quinase Dependente de Ciclina p21/metabolismo
DNA Helicases/metabolismo
Feminino
Regulação Neoplásica da Expressão Gênica
Biblioteca Gênica
Redes Reguladoras de Genes
Predisposição Genética para Doença
Seres Humanos
Complexo Mi-2 de Remodelação de Nucleossomo e Desacetilase/metabolismo
Camundongos Endogâmicos NOD
Camundongos SCID
Transplante de Neoplasias
Fenótipo
Transdução de Sinais
Fatores de Tempo
Carga Tumoral
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (CDKN1A protein, human); 0 (CHD4 protein, human); 0 (Cdkn1a protein, mouse); 0 (Cyclin-Dependent Kinase Inhibitor p21); EC 3.5.1.98 (Mi-2 Nucleosome Remodeling and Deacetylase Complex); EC 3.6.1.3 (Mi-2beta protein, mouse); EC 3.6.4.- (DNA Helicases)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180222
[Lr] Data última revisão:
180222
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161026
[St] Status:MEDLINE
[do] DOI:10.18632/oncotarget.12646


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[PMID]:28470598
[Au] Autor:Mas PJ; Hart DJ
[Ad] Endereço:Integrated Structural Biology Grenoble (ISBG), CNRS, CEA, Université Grenoble Alpes, EMBL, 71Avenue des Martyrs, CS 10090, Grenoble, 38044, France.
[Ti] Título:ESPRIT: A Method for Defining Soluble Expression Constructs in Poorly Understood Gene Sequences.
[So] Source:Methods Mol Biol;1586:45-63, 2017.
[Is] ISSN:1940-6029
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Production of soluble, purifiable domains or multi-domain fragments of proteins is a prerequisite for structural biology and other applications. When target sequences are poorly annotated, or when there are few similar sequences available for alignments, identification of domains can be problematic. A method called expression of soluble proteins by random incremental truncation (ESPRIT) addresses this problem by high-throughput automated screening of tens of thousands of enzymatically truncated gene fragments. Rare soluble constructs are identified by experimental screening, and the boundaries revealed by DNA sequencing.
[Mh] Termos MeSH primário: Clonagem Molecular/métodos
Escherichia coli/genética
Biblioteca Gênica
[Mh] Termos MeSH secundário: Animais
DNA/genética
Expressão Gênica
Vetores Genéticos/genética
Seres Humanos
Plasmídeos/genética
Proteínas Recombinantes/química
Proteínas Recombinantes/genética
Análise de Sequência de DNA/métodos
Solubilidade
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Recombinant Proteins); 9007-49-2 (DNA)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180220
[Lr] Data última revisão:
180220
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170505
[St] Status:MEDLINE
[do] DOI:10.1007/978-1-4939-6887-9_4


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[PMID]:29320569
[Au] Autor:Guo WL; Chen BH; Chen XJ; Guo YY; Yang HL; Li XZ; Wang GY
[Ad] Endereço:School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China.
[Ti] Título:Transcriptome profiling of pumpkin (Cucurbita moschata Duch.) leaves infected with powdery mildew.
[So] Source:PLoS One;13(1):e0190175, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Cucurbit powdery mildew (PM) is one of the most severe fungal diseases, but the molecular mechanisms underlying PM resistance remain largely unknown, especially in pumpkin (Cucurbita moschata Duch.). The goal of this study was to identify gene expression differences in PM-treated plants (harvested at 24 h and 48 h after inoculation) and untreated (control) plants of inbred line "112-2" using RNA sequencing (RNA-Seq). The inbred line "112-2" has been purified over 8 consecutive generations of self-pollination and shows high resistance to PM. More than 7600 transcripts were examined in pumpkin leaves, and 3129 and 3080 differentially expressed genes (DEGs) were identified in inbred line "112-2" at 24 and 48 hours post inoculation (hpi), respectively. Based on the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database and GO (Gene Ontology) database, a complex regulatory network for PM resistance that may involve hormone signal transduction pathways, transcription factors and defense responses was revealed at the transcription level. In addition, the expression profiles of 16 selected genes were analyzed using quantitative RT-PCR. Among these genes, the transcript levels of 6 DEGs, including bHLH87 (Basic Helix-loop-helix transcription factor), ERF014 (Ethylene response factor), WRKY21 (WRKY domain), HSF (heat stress transcription factor A), MLO3 (Mildew Locus O), and SGT1 (Suppressor of G-Two Allele of Skp1), in PM-resistant "112-2" were found to be significantly up- or down-regulated both before 9 hpi and at 24 hpi or 48 hpi; this behavior differed from that observed in the PM-susceptible material (cultivar "Jiujiangjiaoding"). The transcriptome data provide novel insights into the response of Cucurbita moschata to PM stress and are expected to be highly useful for dissecting PM defense mechanisms in this major vegetable and for improving pumpkin breeding with enhanced resistance to PM.
[Mh] Termos MeSH primário: Ascomicetos/fisiologia
Cucurbita/genética
Perfilação da Expressão Gênica
Regulação da Expressão Gênica de Plantas
Genes de Plantas
Doenças das Plantas/genética
Folhas de Planta/metabolismo
[Mh] Termos MeSH secundário: Resistência à Doença
Biblioteca Gênica
Ontologia Genética
Redes e Vias Metabólicas/genética
Fotossíntese/genética
Reguladores de Crescimento de Planta/fisiologia
Folhas de Planta/microbiologia
RNA de Plantas/biossíntese
RNA de Plantas/genética
Análise de Sequência de RNA
Transdução de Sinais/genética
Fatores de Transcrição/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Plant Growth Regulators); 0 (RNA, Plant); 0 (Transcription Factors)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180214
[Lr] Data última revisão:
180214
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180111
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190175


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[PMID]:28448897
[Au] Autor:Ring JD; Sturk-Andreaggi K; Peck MA; Marshall C
[Ad] Endereço:Armed Forces DNA Identification Laboratory, A Division of the Armed Forces Medical Examiner System, 115 Purple Heart Drive, Dover AFB, DE 19902, United States; ARP Sciences, LLC, Contractor Supporting the Armed Forces Medical Examiner System, 9210 Corporate Boulevard, Suite 120, Rockville, MD 20850,
[Ti] Título:A performance evaluation of Nextera XT and KAPA HyperPlus for rapid Illumina library preparation of long-range mitogenome amplicons.
[So] Source:Forensic Sci Int Genet;29:174-180, 2017 07.
[Is] ISSN:1878-0326
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Next-generation sequencing (NGS) facilitates the rapid and high-throughput generation of human mitochondrial genome (mitogenome) data to build population and reference databases for forensic comparisons. To this end, long-range amplification provides an effective method of target enrichment that is amenable to library preparation assays employing DNA fragmentation. This study compared the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA) and the KAPA HyperPlus Library Preparation Kit (Kapa Biosystems, Wilmington, MA) for enzymatic fragmentation and indexing of ∼8500bp mitogenome amplicons for Illumina sequencing. The Nextera XT libraries produced low-coverage regions that were consistent across all samples, while the HyperPlus libraries resulted in uniformly high coverage across the mitogenome, even with reduced-volume reaction conditions. The balanced coverage observed from KAPA HyperPlus libraries enables not only low-level variant calling across the mitogenome but also increased sample multiplexing for greater processing efficiency.
[Mh] Termos MeSH primário: Biblioteca Gênica
Genoma Mitocondrial
Sequenciamento de Nucleotídeos em Larga Escala/métodos
[Mh] Termos MeSH secundário: Seres Humanos
Análise de Sequência de DNA
[Pt] Tipo de publicação:COMPARATIVE STUDY; EVALUATION STUDIES; JOURNAL ARTICLE; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Em] Mês de entrada:1707
[Cu] Atualização por classe:180215
[Lr] Data última revisão:
180215
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170428
[St] Status:MEDLINE


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[PMID]:29323842
[Au] Autor:Kuznetsova TV; Smimova MS; Leonovich OA; Gordeichuk IV; Biriukova IK; Zylkova MV; Tyn'o YY; Belyakova AV; Shevelev AB
[Ti] Título:A new method of producing NS5A antigen of hepatitis C virus.
[So] Source:Vopr Virusol;62(1):17-25, 2017.
[Is] ISSN:0507-4088
[Cp] País de publicação:Russia (Federation)
[La] Idioma:eng
[Ab] Resumo:A task of creating a universal platform for engineering affordable recombinant producers of viral proteins conserving immunogenicity has not been solved yet. High toxicity of the viral proteins for the host cells, low yield and abnormal folding of the products often present severe obstacles to obtaining producers of the viral proteins. In this work, we report a new method of engineering and screening of deletion libraries from the viral antigen genes. This method allows selection of artificial derivatives of these genes adapted for expression in microbial producer cells. The method involves PCR amplification of the gene fragments using a system of randomized and adapter primers, which allows the spontaneous formation of duplexes from the random primers in the absence of the template DNA to be prevented. For selecting variants capable of in vivo expression, the obtained PCR products are cloned to a special vector of a direct phenotypical selection pQL30. It contains E. coli ß-galactosidase gene with an inserted polylinker producing a frame-shift mutation. Using this screening method, an artificial variant of hepatitis C (HCV) NS5a gene with optimal biotechnological properties was established. 27 clinical specimens of 1670 bp long HCV1b NS5a fragments were used as a source gene. A PCR bank of the deletion derivatives was produced. 40 LacZ-positive clones based on pQL30 vector with a 50-700 bp long insertion were selected. The LacZ activity of the cell lysates and the immunogenicity of the products were tested. As a result, a single clone encoding a soluble protein with Mr = 114 kDa was selected. Its yield reached 0.3% of the total cell protein. It was highly reactive with sera of HCV 1b infected patients but not with sera of the healthy donors.
[Mh] Termos MeSH primário: Antígenos Virais/genética
Escherichia coli/genética
Hepacivirus/genética
Hepatite C/diagnóstico
Engenharia de Proteínas/métodos
Proteínas Recombinantes/genética
Proteínas não Estruturais Virais/genética
[Mh] Termos MeSH secundário: Antígenos Virais/biossíntese
Antígenos Virais/imunologia
Antígenos Virais/isolamento & purificação
Proteínas de Bactérias/genética
Proteínas de Bactérias/metabolismo
Primers do DNA/síntese química
Primers do DNA/genética
Escherichia coli/metabolismo
Mutação da Fase de Leitura
Biblioteca Gênica
Vetores Genéticos/química
Vetores Genéticos/metabolismo
Hepacivirus/imunologia
Hepatite C/imunologia
Hepatite C/virologia
Seres Humanos
Soros Imunes/química
Óperon Lac
Proteínas Recombinantes/biossíntese
Proteínas Recombinantes/imunologia
Proteínas Recombinantes/isolamento & purificação
Proteínas não Estruturais Virais/biossíntese
Proteínas não Estruturais Virais/imunologia
Proteínas não Estruturais Virais/isolamento & purificação
beta-Galactosidase/genética
beta-Galactosidase/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Antigens, Viral); 0 (Bacterial Proteins); 0 (DNA Primers); 0 (Immune Sera); 0 (NS-5 protein, hepatitis C virus); 0 (Recombinant Proteins); 0 (Viral Nonstructural Proteins); EC 3.2.1.23 (beta-Galactosidase)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180208
[Lr] Data última revisão:
180208
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180112
[St] Status:MEDLINE


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[PMID]:28923662
[Au] Autor:Kammoonah S; Prasad B; Balaraman P; Mundhada H; Schwaneberg U; Plettner E
[Ad] Endereço:Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.
[Ti] Título:Selecting of a cytochrome P450 SeSaM library with 3-chloroindole and endosulfan - Identification of mutants that dehalogenate 3-chloroindole.
[So] Source:Biochim Biophys Acta;1866(1):68-79, 2018 01.
[Is] ISSN:0006-3002
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Cytochrome P450 (a camphor hydroxylase) from the soil bacterium Pseudomonas putida shows potential importance in environmental applications such as the degradation of chlorinated organic pollutants. Seven P450 mutants generated from Sequence Saturation Mutagenesis (SeSaM) and isolated by selection on minimal media with either 3-chloroindole or the insecticide endosulfan were studied for their ability to oxidize of 3-chloroindole to isatin. The wild-type enzyme did not accept 3-chloroindole as a substrate. Mutant (E156G/V247F/V253G/F256S) had the highest maximal velocity in the conversion of 3-chloroindole to isatin, whereas mutants (T56A/N116H/D297N) and (G60S/Y75H) had highest k /K values. Six of the mutants had more than one mutation, and within this set, mutation of residues 297 and 179 was observed twice. Docking simulations were performed on models of the mutant enzymes; the wild-type did not accommodate 3-chloroindole in the active site, whereas all the mutants did. We propose two potential reaction pathways for dechlorination of 3-chloroindole. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
[Mh] Termos MeSH primário: Proteínas de Bactérias/química
Cânfora 5-Mono-Oxigenase/química
Endossulfano/metabolismo
Biblioteca Gênica
Indóis/metabolismo
Pseudomonas putida/enzimologia
[Mh] Termos MeSH secundário: Motivos de Aminoácidos
Substituição de Aminoácidos
Proteínas de Bactérias/genética
Proteínas de Bactérias/metabolismo
Sítios de Ligação
Biodegradação Ambiental
Cânfora 5-Mono-Oxigenase/genética
Cânfora 5-Mono-Oxigenase/metabolismo
Clonagem Molecular
Endossulfano/química
Escherichia coli/genética
Escherichia coli/metabolismo
Expressão Gênica
Halogenação
Indóis/química
Isatina/química
Isatina/metabolismo
Cinética
Simulação de Acoplamento Molecular
Mutação
Oxirredução
Ligação Proteica
Domínios e Motivos de Interação entre Proteínas
Estrutura Secundária de Proteína
Pseudomonas putida/química
Proteínas Recombinantes/química
Proteínas Recombinantes/genética
Proteínas Recombinantes/metabolismo
Especificidade por Substrato
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Bacterial Proteins); 0 (Indoles); 0 (Recombinant Proteins); 82X95S7M06 (Isatin); EC 1.14.15.1 (Camphor 5-Monooxygenase); OKA6A6ZD4K (Endosulfan)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180208
[Lr] Data última revisão:
180208
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170920
[St] Status:MEDLINE


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[PMID]:29305975
[Au] Autor:Qiu W; Zhu Y; Wu Y; Yuan C; Chen K; Li M
[Ad] Endereço:Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture Shanghai Ocean University, Shanghai 201306, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China; National Demonstrat
[Ti] Título:Identification and expression analysis of microRNAs in medaka gonads.
[So] Source:Gene;646:210-216, 2018 Mar 10.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Gonad development is a highly regulated, coordinated biological process and increasing evidences have indicated that microRNA (miRNA) may be involved in this dynamic program. Medaka (Oryzias latipes) is a good model for reproductive research as it has distinct sex determining genes, however, research in gonadal miRNAs is lacked. In this study, two small RNA libraries from the ovaries and testes were constructed and sequenced. A total of 285 conserved and 388 novel miRNAs were obtained, among which 142 mature miRNAs were significantly (> two-fold change) up or down regulated in the testis compared to the ovary. Quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR) analysis showed that miR-430c, miR-26a and miR-202-5p were expressed in a gonad-specific or sex-biased pattern. Fluorescence in situ hybridization (FISH) indicated that miR-202-5p was present throughout spermatogenesis and was only detected at the early stages of oogenesis, this sex biased expression pattern suggested that miR-202-5p might be a crucial candidate in male differentiation and development. Our study provides the repertoire, a comprehensive annotation of miRNAs from gonads and a reference for functional studies of miRNAs in medaka.
[Mh] Termos MeSH primário: Perfilação da Expressão Gênica/métodos
Gônadas/crescimento & desenvolvimento
MicroRNAs/genética
Oryzias/fisiologia
[Mh] Termos MeSH secundário: Animais
Feminino
Regulação da Expressão Gênica no Desenvolvimento
Biblioteca Gênica
Gônadas/química
Hibridização in Situ Fluorescente
Masculino
Oogênese
Especificidade de Órgãos
Oryzias/genética
Sexismo
Espermatogênese
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (MicroRNAs)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180202
[Lr] Data última revisão:
180202
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180107
[St] Status:MEDLINE


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[PMID]:28457942
[Au] Autor:Orquera-Tornakian GK; Garrido P; Kronmiller B; Hunger R; Tyler BM; Garzon CD; Marek SM
[Ad] Endereço:Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, United States. Electronic address: orquera@okstate.edu.
[Ti] Título:Identification and characterization of simple sequence repeats (SSRs) for population studies of Puccinia novopanici.
[So] Source:J Microbiol Methods;139:113-122, 2017 08.
[Is] ISSN:1872-8359
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Switchgrass (Panicum virgatum L.) can be severely affected by rust disease. Recently switchgrass rust caused by P. emaculata (now confirmed to be Puccinia novopanici) has received most of the attention by the research community because this pathogen is responsible for reducing the biomass production and biofuel feedstock quality of switchgrass. Microsatellite markers found in the literature were either not informative (no allele frequency) or showed few polymorphisms in the target populations, therefore additional markers are needed for future studies of the genetic variation and population structure of P. novopanici. This study reports the development and characterization of novel simple sequence repeat (SSR) markers from a Puccinia emaculata s.l. microsatellite-enriched library and expressed sequence tags (ESTs). Microsatellites were evaluated for polymorphisms on P. emaculata s.l. urediniospores collected in Iowa (IA), Mississippi (MS), Oklahoma (OK), South Dakota (SD) and Virginia (VA). Puccinia novopanici single spore whole genome amplifications were used as templates to validate the SSR reactions protocol and to assess a preliminary population genetics statistics of the pathogen. Eighteen microsatellite markers were polymorphic (average PIC=0.72) on individual urediniospores, with an average of 8.3 alleles per locus (range 3 to 17). Of the 49 SSRs loci initially identified in P. emaculata s.l., 18 were transferable to P. striiformis f. sp. tritici, 23 to P. triticina, 20 to P. sorghi and 31 to P. andropogonis. Thus, these markers could be useful for DNA fingerprinting and population structure analysis for population genetics, epidemiology and ecological studies of P. novopanici and potentially other related Puccinia species.
[Mh] Termos MeSH primário: Basidiomycota/genética
Genoma Fúngico
Repetições de Microssatélites
Reação em Cadeia da Polimerase/métodos
[Mh] Termos MeSH secundário: Basidiomycota/classificação
Basidiomycota/crescimento & desenvolvimento
Basidiomycota/patogenicidade
Etiquetas de Sequências Expressas
Biblioteca Gênica
Marcadores Genéticos
Variação Genética
Iowa
Tipagem Molecular
Polimorfismo Genético
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Genetic Markers)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:180126
[Lr] Data última revisão:
180126
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE



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