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[PMID]:28463571
[Au] Autor:Penaud-Budloo M; Lecomte E; Guy-Duché A; Saleun S; Roulet A; Lopez-Roques C; Tournaire B; Cogné B; Léger A; Blouin V; Lindenbaum P; Moullier P; Ayuso E
[Ad] Endereço:1 INSERM UMR1089, University of Nantes, Centre Hospitalier Universitaire, Nantes, France.
[Ti] Título:Accurate Identification and Quantification of DNA Species by Next-Generation Sequencing in Adeno-Associated Viral Vectors Produced in Insect Cells.
[So] Source:Hum Gene Ther Methods;28(3):148-162, 2017 06.
[Is] ISSN:1946-6544
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Recombinant adeno-associated viral (rAAV) vectors have proven excellent tools for the treatment of many genetic diseases and other complex diseases. However, the illegitimate encapsidation of DNA contaminants within viral particles constitutes a major safety concern for rAAV-based therapies. Moreover, the development of rAAV vectors for early-phase clinical trials has revealed the limited accuracy of the analytical tools used to characterize these new and complex drugs. Although most published data concerning residual DNA in rAAV preparations have been generated by quantitative PCR, we have developed a novel single-strand virus sequencing (SSV-Seq) method for quantification of DNA contaminants in AAV vectors produced in mammalian cells by next-generation sequencing (NGS). Here, we describe the adaptation of SSV-Seq for the accurate identification and quantification of DNA species in rAAV stocks produced in insect cells. We found that baculoviral DNA was the most abundant contaminant, representing less than 2.1% of NGS reads regardless of serotype (2, 8, or rh10). Sf9 producer cell DNA was detected at low frequency (≤0.03%) in rAAV lots. Advanced computational analyses revealed that (1) baculoviral sequences close to the inverted terminal repeats preferentially underwent illegitimate encapsidation, and (2) single-nucleotide variants were absent from the rAAV genome. The high-throughput sequencing protocol described here enables effective DNA quality control of rAAV vectors produced in insect cells, and is adapted to conform with regulatory agency safety requirements.
[Mh] Termos MeSH primário: Dependovirus/genética
Sequenciamento de Nucleotídeos em Larga Escala/métodos
Análise de Sequência de DNA/métodos
[Mh] Termos MeSH secundário: Animais
Baculoviridae/genética
Contaminação por DNA
Células HEK293
Sequenciamento de Nucleotídeos em Larga Escala/normas
Seres Humanos
Análise de Sequência de DNA/normas
Células Sf9
Spodoptera
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Em] Mês de entrada:1710
[Cu] Atualização por classe:180310
[Lr] Data última revisão:
180310
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170503
[St] Status:MEDLINE
[do] DOI:10.1089/hgtb.2016.185


  2 / 141553 MEDLINE  
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[PMID]:29408405
[Au] Autor:Wang H; Park BS; Lim WA; Ki JS
[Ad] Endereço:Department of Biotechnology, Sangmyung University, Seoul 03016, South Korea.
[Ti] Título:CpMCA, a novel metacaspase gene from the harmful dinoflagellate Cochlodinium polykrikoides and its expression during cell death.
[So] Source:Gene;651:70-78, 2018 Apr 20.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Metacaspases (MCAs) are cysteine proteases that share sequence homology with caspases, and may play roles in programmed cell death (PCD). In the present study, we identified a novel MCA gene (CpMCA) from the red tide dinoflagellate Cochlodinium polykrikoides, and examined its molecular characteristics and gene expression in response to algicide-induced cell death. CpMCA cDNA is 1164 bp in length, containing a dinoflagellate spliced leader sequence (dinoSL), an 879-bp open reading frame (ORF), which codes for a 293-aa protein, and a poly (A) tail. Multi-sequence comparison indicated that CpMCA belongs to type I MCA, but it has a different structure at the N-terminal. Phylogenetic analysis showed that C. polykrikoides may have acquired the MCA gene from bacteria by means of horizontal gene transfer (HGT). In addition, expressions of CpMCA significantly increased following exposure to the common algicides copper sulfate and oxidizing chlorine, which trigger cell death in dinoflagellates, suggesting that CpMCA may be involved in cell death.
[Mh] Termos MeSH primário: Caspases/genética
Dinoflagelados/genética
[Mh] Termos MeSH secundário: Morte Celular/efeitos dos fármacos
Morte Celular/genética
DNA Complementar
DNA de Protozoário
Dinoflagelados/efeitos dos fármacos
Dinoflagelados/enzimologia
Expressão Gênica
Transferência Genética Horizontal
Genes Bacterianos
Genes de Protozoários
Herbicidas/farmacologia
Filogenia
Análise de Sequência de DNA
Transcrição Genética/efeitos dos fármacos
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Complementary); 0 (DNA, Protozoan); 0 (Herbicides); EC 3.4.22.- (Caspases)
[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:180207
[St] Status:MEDLINE


  3 / 141553 MEDLINE  
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[PMID]:29408396
[Au] Autor:Wang W; Zhang H; Wei X; Yang L; Yang B; Zhang L; Li J; Jiang YQ
[Ad] Endereço:State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A & F University, Yangling, Shaanxi 712100, China.
[Ti] Título:Functional characterization of calcium-dependent protein kinase (CPK) 2 gene from oilseed rape (Brassica napus L.) in regulating reactive oxygen species signaling and cell death control.
[So] Source:Gene;651:49-56, 2018 Apr 20.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Calcium-dependent protein kinases (CPKs), being Ser/Thr protein kinases found only in plants and some protozoans are calcium sensors that regulate diverse biological processes. However, the function and mode of CPKs in oilseed rape (Brassica napus) remain elusive. In this study, we identified CPK2 from oilseed rape as a novel regulator of reactive oxygen species (ROS) and cell death. BnaCPK2 was identified to be located at the endoplasmic reticulum membrane. Expression of BnaCPK2 was induced during Bax-induced cell death. Overexpression of the constitutively active form of BnaCPK2 led to significantly more accumulation of ROS and cell death than the full-length CPK2, which is supported by various measurements of physiological data. In addition, a quantitative RT-PCR survey revealed that the expression levels of a few marker genes are significantly changed as a result of CPK2 expression. Mating-based split ubiquitin system (mbSUS) and bimolecular fluorescence complementation (BiFC) were used to screen and confirm the BnaCPK2 interacting proteins. We identified and confirmed that CPK2 interacted with NADPH oxidase-like respiratory burst oxidase homolog D (RbohD), but not with RbohF. Based on its function and interacting partners, we propose that BnaCPK2 plays an important role in ROS and cell death control through interacting with RbohD.
[Mh] Termos MeSH primário: Brassica napus/genética
Morte Celular/genética
Proteínas de Plantas/genética
Proteínas Quinases/genética
Espécies Reativas de Oxigênio/metabolismo
[Mh] Termos MeSH secundário: Brassica napus/enzimologia
Clonagem Molecular
DNA de Plantas
Proteínas de Plantas/metabolismo
Proteínas Quinases/metabolismo
Análise de Sequência de DNA
Transdução de Sinais
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Plant); 0 (Plant Proteins); 0 (Reactive Oxygen Species); EC 2.7.- (Protein Kinases); EC 2.7.1.- (calcium-dependent protein kinase)
[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:180207
[St] Status:MEDLINE


  4 / 141553 MEDLINE  
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[PMID]:29378242
[Au] Autor:Wang X; Xue M; Zhao M; He F; Li C; Li X
[Ad] Endereço:Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China; Key Laboratory for Tumor Precision Medicine of Shaanxi Province, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
[Ti] Título:Identification of a novel mutation (Ala66Thr) of SRY gene causes XY pure gonadal dysgenesis by affecting DNA binding activity and nuclear import.
[So] Source:Gene;651:143-151, 2018 Apr 20.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Sex-determining region of the Y chromosome (SRY) gene plays a crucial role in male sexual differentiation and development. Several mutations in the SRY gene have been reported in the high mobility group (HMG) box domain and can cause gonadal dysgenesis symptoms. In this study, we report that a novel missense mutation in the SRY gene, a G to A transition within the HMG box, causes the Ala66Thr amino acid substitution in a female patient presenting 46,XY karyotype with pure gonadal dysgenesis. The G to A base transition was not found in the SRY sequence after the screening of 100 normal males. Furthermore, Ala66Thr mutation drastically reduced the binding capacity of SRY to DNA sequences, whereas wild-type SRY protein showed the normal binding capacity to DNA sequences in vitro. We also found that the mutant SRY protein was partly localized in cytoplasm, whereas wild-type SRY protein was strictly localized in cell nucleus. In addition, we analyzed the three-dimensional structure of SRY protein by homology modeling methods. In conclusion, we identified a novel SRY mutation in a 46,XY female patient with pure gonadal dysgenesis, demonstrating the importance of the Ala66Thr mutation in DNA binding activity and nuclear transport.
[Mh] Termos MeSH primário: Disgenesia Gonadal 46 XY/genética
Mutação de Sentido Incorreto
Proteína da Região Y Determinante do Sexo/genética
[Mh] Termos MeSH secundário: Transporte Ativo do Núcleo Celular
Adolescente
Adulto
Alanina
DNA/metabolismo
Feminino
Células HEK293
Seres Humanos
Cariotipagem
Masculino
Ligação Proteica
Conformação Proteica
Análise de Sequência de DNA
Proteína da Região Y Determinante do Sexo/química
Proteína da Região Y Determinante do Sexo/metabolismo
Treonina
Adulto Jovem
[Pt] Tipo de publicação:CASE REPORTS; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Sex-Determining Region Y Protein); 2ZD004190S (Threonine); 9007-49-2 (DNA); OF5P57N2ZX (Alanine)
[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


  5 / 141553 MEDLINE  
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[PMID]:29202710
[Au] Autor:Parvathaneni RK; DeLeo VL; Spiekerman JJ; Chakraborty D; Devos KM
[Ad] Endereço:Institute of Plant Breeding, Genetics and Genomics, University of Georgia, 30602, Athens, Georgia, United States.
[Ti] Título:Parallel loss of introns in the ABCB1 gene in angiosperms.
[So] Source:BMC Evol Biol;17(1):238, 2017 Dec 04.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The presence of non-coding introns is a characteristic feature of most eukaryotic genes. While the size of the introns, number of introns per gene and the number of intron-containing genes can vary greatly between sequenced eukaryotic genomes, the structure of a gene with reference to intron presence and positions is typically conserved in closely related species. Unexpectedly, the ABCB1 (ATP-Binding Cassette Subfamily B Member 1) gene which encodes a P-glycoprotein and underlies dwarfing traits in maize (br2), sorghum (dw3) and pearl millet (d2) displayed considerable variation in intron composition. RESULTS: An analysis of the ABCB1 gene structure in 80 angiosperms revealed that the number of introns ranged from one to nine. All introns in ABCB1 underwent either a one-time loss (single loss in one lineage/species) or multiple independent losses (parallel loss in two or more lineages/species) with the majority of losses occurring within the grass family. In contrast, the structure of the closest homolog to ABCB1, ABCB19, remained constant in the majority of angiosperms analyzed. Using known phylogenetic relationships within the grasses, we determined the ancestral branch-points where the losses occurred. Intron 7, the longest intron, was lost in only a single species, Mimulus guttatus, following duplication of ABCB1. Semiquantitative PCR showed that the M. guttatus ABCB1 gene copy without intron 7 had significantly lower transcript levels than the gene copy with intron 7. We further demonstrated that intron 7 carried two motifs that were highly conserved across the monocot-dicot divide. CONCLUSIONS: The ABCB1 gene structure is highly dynamic, while the structure of ABCB19 remained largely conserved through evolution. Precise removal of introns, preferential removal of smaller introns and presence of at least 2 bp of microhomology flanking most introns indicated that intron loss may have predominantly occurred through non-homologous end-joining (NHEJ) repair of double strand breaks. Lack of microhomology in the exon upstream of lost phase I introns was likely due to release of the selective constraint on the penultimate base (3rd base in codon) of the terminal codon by the splicing machinery. In addition to size, the presence of regulatory motifs will make introns recalcitrant to loss.
[Mh] Termos MeSH primário: Genes de Plantas
Íntrons/genética
Magnoliopsida/genética
Proteínas de Plantas/genética
[Mh] Termos MeSH secundário: Arabidopsis/genética
Sequência de Bases
Sequência Conservada/genética
DNA Complementar/genética
Evolução Molecular
Regulação da Expressão Gênica de Plantas
Mimulus/genética
Motivos de Nucleotídeos/genética
Oryza/genética
Filogenia
Reação em Cadeia da Polimerase
Polimorfismo Genético
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
Reprodutibilidade dos Testes
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Complementary); 0 (Plant Proteins); 0 (RNA, Messenger)
[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:171206
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1077-x


  6 / 141553 MEDLINE  
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[PMID]:29183283
[Au] Autor:Fraser TA; Shao R; Fountain-Jones NM; Charleston M; Martin A; Whiteley P; Holme R; Carver S; Polkinghorne A
[Ad] Endereço:School of Biological Sciences, University of Tasmania, Sandy Bay, Hobart, TAS, Australia.
[Ti] Título:Mitochondrial genome sequencing reveals potential origins of the scabies mite Sarcoptes scabiei infesting two iconic Australian marsupials.
[So] Source:BMC Evol Biol;17(1):233, 2017 Nov 28.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Debilitating skin infestations caused by the mite, Sarcoptes scabiei, have a profound impact on human and animal health globally. In Australia, this impact is evident across different segments of Australian society, with a growing recognition that it can contribute to rapid declines of native Australian marsupials. Cross-host transmission has been suggested to play a significant role in the epidemiology and origin of mite infestations in different species but a chronic lack of genetic resources has made further inferences difficult. To investigate the origins and molecular epidemiology of S. scabiei in Australian wildlife, we sequenced the mitochondrial genomes of S. scabiei from diseased wombats (Vombatus ursinus) and koalas (Phascolarctos cinereus) spanning New South Wales, Victoria and Tasmania, and compared them with the recently sequenced mitochondrial genome sequences of S. scabiei from humans. RESULTS: We found unique S. scabiei haplotypes among individual wombat and koala hosts with high sequence similarity (99.1% - 100%). Phylogenetic analysis of near full-length mitochondrial genomes revealed three clades of S. scabiei (one human and two marsupial), with no apparent geographic or host species pattern, suggestive of multiple introductions. The availability of additional mitochondrial gene sequences also enabled a re-evaluation of a range of putative molecular markers of S. scabiei, revealing that cox1 is the most informative gene for molecular epidemiological investigations. Utilising this gene target, we provide additional evidence to support cross-host transmission between different animal hosts. CONCLUSIONS: Our results suggest a history of parasite invasion through colonisation of Australia from hosts across the globe and the potential for cross-host transmission being a common feature of the epidemiology of this neglected pathogen. If this is the case, comparable patterns may exist elsewhere in the 'New World'. This work provides a basis for expanded molecular studies into mange epidemiology in humans and animals in Australia and other geographic regions.
[Mh] Termos MeSH primário: Genoma Mitocondrial
Marsupiais/parasitologia
Sarcoptes scabiei/genética
Escabiose/parasitologia
Análise de Sequência de DNA
[Mh] Termos MeSH secundário: Animais
Animais Selvagens/genética
Austrália/epidemiologia
Composição de Bases/genética
Sequência de Bases
Complexo IV da Cadeia de Transporte de Elétrons/genética
Genes Mitocondriais
Tamanho do Genoma
Haplótipos/genética
Seres Humanos
Anotação de Sequência Molecular
Filogenia
Escabiose/epidemiologia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
EC 1.9.3.1 (Electron Transport Complex IV)
[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:171130
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1086-9


  7 / 141553 MEDLINE  
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[PMID]:29178825
[Au] Autor:Abalde S; Tenorio MJ; Afonso CML; Uribe JE; Echeverry AM; Zardoya R
[Ad] Endereço:Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006, Madrid, Spain.
[Ti] Título:Phylogenetic relationships of cone snails endemic to Cabo Verde based on mitochondrial genomes.
[So] Source:BMC Evol Biol;17(1):231, 2017 Nov 25.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Due to their great species and ecological diversity as well as their capacity to produce hundreds of different toxins, cone snails are of interest to evolutionary biologists, pharmacologists and amateur naturalists alike. Taxonomic identification of cone snails still relies mostly on the shape, color, and banding patterns of the shell. However, these phenotypic traits are prone to homoplasy. Therefore, the consistent use of genetic data for species delimitation and phylogenetic inference in this apparently hyperdiverse group is largely wanting. Here, we reconstruct the phylogeny of the cones endemic to Cabo Verde archipelago, a well-known radiation of the group, using mitochondrial (mt) genomes. RESULTS: The reconstructed phylogeny grouped the analyzed species into two main clades, one including Kalloconus from West Africa sister to Trovaoconus from Cabo Verde and the other with a paraphyletic Lautoconus due to the sister group relationship of Africonus from Cabo Verde and Lautoconus ventricosus from Mediterranean Sea and neighboring Atlantic Ocean to the exclusion of Lautoconus endemic to Senegal (plus Lautoconus guanche from Mauritania, Morocco, and Canary Islands). Within Trovaoconus, up to three main lineages could be distinguished. The clade of Africonus included four main lineages (named I to IV), each further subdivided into two monophyletic groups. The reconstructed phylogeny allowed inferring the evolution of the radula in the studied lineages as well as biogeographic patterns. The number of cone species endemic to Cabo Verde was revised under the light of sequence divergence data and the inferred phylogenetic relationships. CONCLUSIONS: The sequence divergence between continental members of the genus Kalloconus and island endemics ascribed to the genus Trovaoconus is low, prompting for synonymization of the latter. The genus Lautoconus is paraphyletic. Lautoconus ventricosus is the closest living sister group of genus Africonus. Diversification of Africonus was in allopatry due to the direct development nature of their larvae and mainly triggered by eustatic sea level changes during the Miocene-Pliocene. Our study confirms the diversity of cone endemic to Cabo Verde but significantly reduces the number of valid species. Applying a sequence divergence threshold, the number of valid species within the sampled Africonus is reduced to half.
[Mh] Termos MeSH primário: Genoma Mitocondrial
Filogenia
Caramujos/classificação
Caramujos/genética
[Mh] Termos MeSH secundário: Animais
Sequência de Bases
Cabo Verde
DNA Mitocondrial/genética
Variação Genética
Análise de Sequência de DNA
Especificidade da Espécie
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Mitochondrial)
[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:171128
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1069-x


  8 / 141553 MEDLINE  
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[PMID]:28465725
[Au] Autor:McEwen LM; Morin AM; Edgar RD; MacIsaac JL; Jones MJ; Dow WH; Rosero-Bixby L; Kobor MS; Rehkopf DH
[Ad] Endereço:Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada.
[Ti] Título:Differential DNA methylation and lymphocyte proportions in a Costa Rican high longevity region.
[So] Source:Epigenetics Chromatin;10:21, 2017.
[Is] ISSN:1756-8935
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The Nicoya Peninsula in Costa Rica has one of the highest old-age life expectancies in the world, but the underlying biological mechanisms of this longevity are not well understood. As DNA methylation is hypothesized to be a component of biological aging, we focused on this malleable epigenetic mark to determine its association with current residence in Nicoya versus elsewhere in Costa Rica. Examining a population's unique DNA methylation pattern allows us to differentiate hallmarks of longevity from individual stochastic variation. These differences may be characteristic of a combination of social, biological, and environmental contexts. METHODS: In a cross-sectional subsample of the Costa Rican Longevity and Healthy Aging Study, we compared whole blood DNA methylation profiles of residents from Nicoya ( = 48) and non-Nicoya (other Costa Rican regions,  = 47) using the Infinium HumanMethylation450 microarray. RESULTS: We observed a number of differences that may be markers of delayed aging, such as bioinformatically derived differential CD8+ T cell proportions. Additionally, both site- and region-specific analyses revealed DNA methylation patterns unique to Nicoyans. We also observed lower overall variability in DNA methylation in the Nicoyan population, another hallmark of younger biological age. CONCLUSIONS: Nicoyans represent an interesting group of individuals who may possess unique immune cell proportions as well as distinct differences in their epigenome, at the level of DNA methylation.
[Mh] Termos MeSH primário: Metilação de DNA
Longevidade/genética
Linfócitos/metabolismo
[Mh] Termos MeSH secundário: Idoso
Idoso de 80 Anos ou mais
Linfócitos T CD4-Positivos/citologia
Linfócitos T CD4-Positivos/metabolismo
Linfócitos T CD8-Positivos/citologia
Linfócitos T CD8-Positivos/metabolismo
Costa Rica
Ilhas de CpG
Estudos Transversais
DNA/química
DNA/isolamento & purificação
DNA/metabolismo
Epigenômica
Feminino
Seres Humanos
Linfócitos/citologia
Masculino
Meia-Idade
Células T Matadoras Naturais/citologia
Células T Matadoras Naturais/metabolismo
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
9007-49-2 (DNA)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180310
[Lr] Data última revisão:
180310
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170504
[St] Status:MEDLINE
[do] DOI:10.1186/s13072-017-0128-2


  9 / 141553 MEDLINE  
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[PMID]:27777629
[Au] Autor:Lau AC; Zhu KP; Brouhard EA; Davis MB; Csankovszki G
[Ad] Endereço:Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University Ave., Ann Arbor, MI 48109-1048 USA ; Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA.
[Ti] Título:An H4K16 histone acetyltransferase mediates decondensation of the X chromosome in males.
[So] Source:Epigenetics Chromatin;9:44, 2016.
[Is] ISSN:1756-8935
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: In , in order to equalize gene expression between the sexes and balance X and autosomal expression, two steps are believed to be required. First, an unknown mechanism is hypothesized to upregulate the X chromosome in both sexes. This mechanism balances the X to autosomal expression in males, but creates X overexpression in hermaphrodites. Therefore, to restore the balance, hermaphrodites downregulate gene expression twofold on both X chromosomes. While many studies have focused on X chromosome downregulation, the mechanism of X upregulation is not known. RESULTS: To gain more insight into X upregulation, we studied the effects of chromatin condensation and histone acetylation on gene expression levels in male . We have found that the H4K16 histone acetyltransferase MYS-1/Tip60 mediates dramatic decondensation of the male X chromosome as measured by FISH. However, RNA-seq analysis revealed that MYS-1 contributes only slightly to upregulation of gene expression on the X chromosome. These results suggest that the level of chromosome decondensation does not necessarily correlate with the degree of gene expression change in vivo. Furthermore, the X chromosome is more sensitive to MYS-1-mediated decondensation than the autosomes, despite similar levels of H4K16ac on all chromosomes, as measured by ChIP-seq. H4K16ac levels weakly correlate with gene expression levels on both the X and the autosomes, but highly expressed genes on the X chromosome do not contain exceptionally high levels of H4K16ac. CONCLUSION: These results indicate that H4K16ac and chromosome decondensation influence regulation of the male X chromosome; however, they do not fully account for the high levels of gene expression observed on the X chromosomes.
[Mh] Termos MeSH primário: Proteínas de Caenorhabditis elegans/metabolismo
Caenorhabditis elegans/metabolismo
Histona Acetiltransferases/metabolismo
Cromossomo X/metabolismo
[Mh] Termos MeSH secundário: Acetilação
Animais
Caenorhabditis elegans/genética
Proteínas de Caenorhabditis elegans/genética
Cromatina/metabolismo
Montagem e Desmontagem da Cromatina
Imunoprecipitação da Cromatina
Compensação de Dosagem (Genética)
Expressão Gênica
Histona Acetiltransferases/genética
Histonas/metabolismo
Hibridização in Situ Fluorescente
Masculino
Análise de Sequência de DNA
Cromossomo X/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (Caenorhabditis elegans Proteins); 0 (Chromatin); 0 (Histones); EC 2.3.1.48 (Histone Acetyltransferases); EC 2.3.1.48 (MYS-1 protein, C elegans)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180310
[Lr] Data última revisão:
180310
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161026
[St] Status:MEDLINE


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[PMID]:29458686
[Au] Autor:Anson LW; Chau K; Sanderson N; Hoosdally S; Bradley P; Iqbal Z; Phan H; Foster D; Oakley S; Morgan M; Peto TEA; Modernizing Medical Microbiology Informatics Group Mmmig; Crook DW; Pankhurst LJ
[Ad] Endereço:1​Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
[Ti] Título:DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing.
[So] Source:J Med Microbiol;67(3):347-357, 2018 Mar.
[Is] ISSN:1473-5644
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:PURPOSE: Speed of bloodstream infection diagnosis is vital to reduce morbidity and mortality. Whole genome sequencing (WGS) performed directly from liquid blood culture could provide single-assay species and antibiotic susceptibility prediction; however, high inhibitor and human cell/DNA concentrations limit pathogen recovery. We develop a method for the preparation of bacterial DNA for WGS-based diagnostics direct from liquid blood culture. METHODOLOGY: We evaluate three commercial DNA extraction kits: BiOstic Bacteraemia, Amplex Hyplex and MolYsis Plus. Differential centrifugation, filtration, selective lysis and solid-phase reversible immobilization bead clean-up are tested to improve human cells/DNA and inhibitor removal. Using WGS (Illumina/MinION), we assess human DNA removal, pathogen recovery, and predict species and antibiotic susceptibility inpositive blood cultures of 44 Gram-negative and 54 Staphylococcus species.Results/Key findings. BiOstic kit extractions yield the greatest mean DNA concentration, 94-301 ng µl , versus 0-2.5 ng µl using Amplex and MolYsis kits. However, we note higher levels of inhibition (260/280 ratio 0.9-2.1) and human DNA (0.0-4.4×10 copies) in BiOstic extracts. Differential centrifugation (2000 g, 1 min) prior to BiOstic extraction reduces human DNA by 63-89 % with selective lysis minimizing by a further 62 %. Post-extraction bead clean-up lowers inhibition. Overall, 67 % of sequenced samples (Illumina MiSeq) contain <10 % human DNA, with >93 % concordance between WGS-based species and susceptibility predictions and clinical diagnosis. If >60 % of sequencing reads are human (7/98 samples) susceptibility prediction becomes compromised. Novel MinION-based WGS (n=9) currently gives rapid species identification but not susceptibility prediction. CONCLUSION: Our method for DNA preparation allows WGS-based diagnosis direct from blood culture bottles, providing species and antibiotic susceptibility prediction in a single assay.
[Mh] Termos MeSH primário: Bacteriemia/diagnóstico
Hemocultura
DNA Bacteriano/isolamento & purificação
Genoma Bacteriano
Sequenciamento Completo do Genoma
[Mh] Termos MeSH secundário: Bacteriemia/microbiologia
Infecções Relacionadas a Cateter/diagnóstico
Infecções Relacionadas a Cateter/microbiologia
DNA Bacteriano/análise
DNA Bacteriano/genética
Escherichia coli/genética
Seres Humanos
Testes de Sensibilidade Microbiana
Técnicas de Diagnóstico Molecular/métodos
Kit de Reagentes para Diagnóstico
Análise de Sequência de DNA/métodos
Staphylococcus aureus/genética
[Pt] Tipo de publicação:EVALUATION STUDIES; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Bacterial); 0 (Reagent Kits, Diagnostic)
[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:180221
[St] Status:MEDLINE
[do] DOI:10.1099/jmm.0.000664



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