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  1 / 2839 MEDLINE  
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[PMID]:27077531
[Au] Autor:Møller HD; Bojsen RK; Tachibana C; Parsons L; Botstein D; Regenberg B
[Ad] Endereço:Department of Biology, University of Copenhagen.
[Ti] Título:Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells.
[So] Source:J Vis Exp;(110):e54239 |, 2016 Apr 04.
[Is] ISSN:1940-087X
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods for detecting eccDNA are needed to clarify how these elements affect genome stability and how environmental and biological factors induce their formation in eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The method encompasses column purification of circular DNA, removal of remaining linear chromosomal DNA, rolling-circle amplification of eccDNA, deep sequencing, and mapping. Extensive exonuclease treatment was required for sufficient linear chromosomal DNA degradation. The rolling-circle amplification step by φ29 polymerase enriched for circular DNA over linear DNA. Validation of the Circle-Seq method on three S. cerevisiae CEN.PK populations of 10(10) cells detected hundreds of eccDNA profiles in sizes larger than 1 kilobase. Repeated findings of ASP3-1, COS111, CUP1, RSC30, HXT6, HXT7 genes on circular DNA in both S288c and CEN.PK suggests that DNA circularization is conserved between strains at these loci. In sum, the Circle-Seq method has broad applicability for genome-scale screening for eccDNA in eukaryotes as well as for detecting specific eccDNA types.
[Mh] Termos MeSH primário: DNA Circular/isolamento & purificação
DNA Fúngico/isolamento & purificação
Herança Extracromossômica/genética
Saccharomyces cerevisiae/genética
[Mh] Termos MeSH secundário: DNA Circular/genética
DNA Fúngico/genética
Células Eucarióticas
Genoma
Genoma Fúngico
[Pt] Tipo de publicação:JOURNAL ARTICLE; VIDEO-AUDIO MEDIA
[Nm] Nome de substância:
0 (DNA, Circular); 0 (DNA, Fungal)
[Em] Mês de entrada:1612
[Cu] Atualização por classe:170601
[Lr] Data última revisão:
170601
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160415
[St] Status:MEDLINE
[do] DOI:10.3791/54239


  2 / 2839 MEDLINE  
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[PMID]:26863962
[Au] Autor:Reardon S
[Ti] Título:US panel greenlights creation of male 'three-person' embryos.
[So] Source:Nature;530(7589):142, 2016 Feb 11.
[Is] ISSN:1476-4687
[Cp] País de publicação:England
[La] Idioma:eng
[Mh] Termos MeSH primário: Pesquisas com Embriões/legislação & jurisprudência
Terapia Genética/legislação & jurisprudência
Terapia Genética/métodos
Doenças Mitocondriais/prevenção & controle
Terapia de Substituição Mitocondrial/legislação & jurisprudência
Terapia de Substituição Mitocondrial/métodos
Segurança do Paciente
[Mh] Termos MeSH secundário: Animais
Herança Extracromossômica/genética
Feminino
Seguimentos
Haplorrinos/genética
Hereditariedade/genética
Hereditariedade/fisiologia
Seres Humanos
Masculino
Doenças Mitocondriais/genética
Terapia de Substituição Mitocondrial/efeitos adversos
Mutação/genética
Fatores Sexuais
Reino Unido
Estados Unidos
United States Food and Drug Administration/legislação & jurisprudência
[Pt] Tipo de publicação:NEWS
[Em] Mês de entrada:1602
[Cu] Atualização por classe:161126
[Lr] Data última revisão:
161126
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:160212
[St] Status:MEDLINE
[do] DOI:10.1038/nature.2016.19290


  3 / 2839 MEDLINE  
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[PMID]:26347561
[Au] Autor:Sharma A
[Ad] Endereço:CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Sukhdev Vihar, Mathura Road, New Delhi 110025, India abhaysharma@igib.res.in.
[Ti] Título:Systems genomics analysis centered on epigenetic inheritance supports development of a unified theory of biology.
[So] Source:J Exp Biol;218(Pt 21):3368-73, 2015 Nov.
[Is] ISSN:1477-9145
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:New discoveries are increasingly demanding integration of epigenetics, molecular biology, genomic networks and physiology with evolution. This article provides a proof of concept for evolutionary transgenerational systems biology, proposed recently in the context of epigenetic inheritance in mammals. Gene set enrichment analysis of available genome-level mammalian data presented here seem consistent with the concept that: (1) heritable information about environmental effects in somatic cells is communicated to the germline by circulating microRNAs (miRNAs) or other RNAs released in physiological fluids; (2) epigenetic factors including miRNA-like small RNAs, DNA methylation and histone modifications are propagated across generations via gene networks; and (3) inherited epigenetic variations in the form of methylated cytosines are fixed in the population as thymines over the evolutionary time course. The analysis supports integration of physiology and epigenetics with inheritance and evolution. This may catalyze efforts to develop a unified theory of biology.
[Mh] Termos MeSH primário: Evolução Biológica
Epigênese Genética
Mamíferos/genética
Biologia de Sistemas
[Mh] Termos MeSH secundário: Animais
Metilação de DNA
Herança Extracromossômica
Redes Reguladoras de Genes
Células Germinativas/fisiologia
Mamíferos/fisiologia
MicroRNAs/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (MicroRNAs)
[Em] Mês de entrada:1612
[Cu] Atualização por classe:161230
[Lr] Data última revisão:
161230
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150909
[St] Status:MEDLINE
[do] DOI:10.1242/jeb.125922


  4 / 2839 MEDLINE  
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[PMID]:26038577
[Au] Autor:Møller HD; Parsons L; Jørgensen TS; Botstein D; Regenberg B
[Ad] Endereço:Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark;
[Ti] Título:Extrachromosomal circular DNA is common in yeast.
[So] Source:Proc Natl Acad Sci U S A;112(24):E3114-22, 2015 Jun 16.
[Is] ISSN:1091-6490
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Examples of extrachromosomal circular DNAs (eccDNAs) are found in many organisms, but their impact on genetic variation at the genome scale has not been investigated. We mapped 1,756 eccDNAs in the Saccharomyces cerevisiae genome using Circle-Seq, a highly sensitive eccDNA purification method. Yeast eccDNAs ranged from an arbitrary lower limit of 1 kb up to 38 kb and covered 23% of the genome, representing thousands of genes. EccDNA arose both from genomic regions with repetitive sequences ≥ 15 bases long and from regions with short or no repetitive sequences. Some eccDNAs were identified in several yeast populations. These eccDNAs contained ribosomal genes, transposon remnants, and tandemly repeated genes (HXT6/7, ENA1/2/5, and CUP1-1/-2) that were generally enriched on eccDNAs. EccDNAs seemed to be replicated and 80% contained consensus sequences for autonomous replication origins that could explain their maintenance. Our data suggest that eccDNAs are common in S. cerevisiae, where they might contribute substantially to genetic variation and evolution.
[Mh] Termos MeSH primário: DNA Circular/genética
DNA Fúngico/genética
Saccharomyces cerevisiae/genética
[Mh] Termos MeSH secundário: Sequência de Bases
DNA Circular/isolamento & purificação
DNA Fúngico/isolamento & purificação
Evolução Molecular
Herança Extracromossômica
Variação Genética
Genoma Fúngico
Modelos Genéticos
Mutação
Origem de Replicação
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (DNA, Circular); 0 (DNA, Fungal)
[Em] Mês de entrada:1510
[Cu] Atualização por classe:161019
[Lr] Data última revisão:
161019
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150604
[St] Status:MEDLINE
[do] DOI:10.1073/pnas.1508825112


  5 / 2839 MEDLINE  
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[PMID]:25922527
[Au] Autor:Djeddi A; Al Rawi S; Deuve JL; Perrois C; Liu YY; Russeau M; Sachse M; Galy V
[Ad] Endereço:Sorbonne Universités, UPMC, Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), UMR7622, Paris F-75005, France CNRS, IBPS, UMR7622, Paris F-75005, France.
[Ti] Título:Sperm-inherited organelle clearance in C. elegans relies on LC3-dependent autophagosome targeting to the pericentrosomal area.
[So] Source:Development;142(9):1705-16, 2015 May 01.
[Is] ISSN:1477-9129
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Macroautophagic degradation of sperm-inherited organelles prevents paternal mitochondrial DNA transmission in C. elegans. The recruitment of autophagy markers around sperm mitochondria has also been observed in mouse and fly embryos but their role in degradation is debated. Both worm Atg8 ubiquitin-like proteins, LGG-1/GABARAP and LGG-2/LC3, are recruited around sperm organelles after fertilization. Whereas LGG-1 depletion affects autophagosome function, stabilizes the substrates and is lethal, we demonstrate that LGG-2 is dispensable for autophagosome formation but participates in their microtubule-dependent transport toward the pericentrosomal area prior to acidification. In the absence of LGG-2, autophagosomes and their substrates remain clustered at the cell cortex, away from the centrosomes and their associated lysosomes. Thus, the clearance of sperm organelles is delayed and their segregation between blastomeres prevented. This allowed us to reveal a role of the RAB-5/RAB-7 GTPases in autophagosome formation. In conclusion, the major contribution of LGG-2 in sperm-inherited organelle clearance resides in its capacity to mediate the retrograde transport of autophagosomes rather than their fusion with acidic compartments: a potential key function of LC3 in controlling the fate of sperm mitochondria in other species.
[Mh] Termos MeSH primário: Autofagia/fisiologia
Proteínas de Caenorhabditis elegans/metabolismo
Caenorhabditis elegans/fisiologia
Proteínas Associadas aos Microtúbulos/metabolismo
Organelas/metabolismo
Espermatozoides/citologia
[Mh] Termos MeSH secundário: Animais
Transporte Biológico
Herança Extracromossômica/fisiologia
Imunofluorescência
Masculino
Microscopia Eletrônica de Transmissão
Interferência de RNA
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Caenorhabditis elegans Proteins); 0 (LGG-1 protein, C elegans); 0 (LGG-2 protein, C elegans); 0 (Microtubule-Associated Proteins)
[Em] Mês de entrada:1507
[Cu] Atualização por classe:150429
[Lr] Data última revisão:
150429
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150430
[St] Status:MEDLINE
[do] DOI:10.1242/dev.117879


  6 / 2839 MEDLINE  
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[PMID]:25416558
[Au] Autor:Lace MJ; Anson JR; Haugen TH; Dierdorff JM; Turek LP
[Ad] Endereço:Veterans Affairs Healthcare System and The Department of Pathology, University of Iowa Roy J. and Lucille A. Carver College of Medicine, Iowa City, IA 52242, USA michael-lace@uiowa.edu.
[Ti] Título:Interferon treatment of human keratinocytes harboring extrachromosomal, persistent HPV-16 plasmid genomes induces de novo viral integration.
[So] Source:Carcinogenesis;36(1):151-9, 2015 Jan.
[Is] ISSN:1460-2180
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Interferons (IFNs) have been used to treat epithelial lesions caused by human papillomavirus (HPV) persistence. Here, we exposed primary human keratinocytes (HFKs) immortalized by persistently replicating HPV-16 plasmid genomes to increasing levels of IFN-γ. While untreated HFKs retained replicating HPV-16 plasmids for up to 60-120 population doublings, IFN led to rapid HPV-16 plasmid loss. However, treated cultures eventually gave rise to outgrowth of clones harboring integrated HPV-16 genomes expressing viral E6 and E7 oncogenes from chimeric virus-cell mRNAs similar to those in cervical and head and neck cancers. Surprisingly, every HPV-16 integrant that arose after IFN exposure stemmed from an independent integration event into a different cellular gene locus, even within parallel cultures started from small cell inocula and cultured separately for ≥ 25 doublings to permit the rise and expansion of spontaneous integrants. While IFN treatment conferred a growth advantage upon preexisting integrants added to mixed control cultures, our results indicate that IFN exposure directly or indirectly induces HPV-16 integration, rather than only selects preexisting, spontaneous integrants that appear to be much less frequent. We estimate that IFN exposure increased integration rates by ≥ 100-fold. IFN-induced HPV-16 integration involved a wide range of chromosomal loci with less apparent selection for recurrent insertions near genes involved in cancer-related pathways. We conclude that IFNs and other potential treatments targeting high-risk HPV persistence that disrupt viral genome replication may promote increased high-risk HPV integration as a step in cancer progression. Therapies against high-risk HPV persistence thus need to be evaluated for their integration-inducing potential.
[Mh] Termos MeSH primário: Herança Extracromossômica
Genoma Viral/efeitos dos fármacos
Papillomavirus Humano 16/genética
Interferon gama/farmacologia
Queratinócitos/efeitos dos fármacos
Infecções por Papillomavirus/genética
Plasmídeos/genética
Integração Viral/genética
[Mh] Termos MeSH secundário: Antivirais/farmacologia
Transformação Celular Viral/efeitos dos fármacos
Células Cultivadas
DNA Viral/genética
Seres Humanos
Queratinócitos/virologia
Infecções por Papillomavirus/virologia
Reação em Cadeia da Polimerase em Tempo Real
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, U.S. GOV'T, NON-P.H.S.
[Nm] Nome de substância:
0 (Antiviral Agents); 0 (DNA, Viral); 82115-62-6 (Interferon-gamma)
[Em] Mês de entrada:1503
[Cu] Atualização por classe:150113
[Lr] Data última revisão:
150113
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:141123
[St] Status:MEDLINE
[do] DOI:10.1093/carcin/bgu236


  7 / 2839 MEDLINE  
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[PMID]:26104369
[Au] Autor:Kado CI
[Ti] Título:Historical Events That Spawned the Field of Plasmid Biology.
[So] Source:Microbiol Spectr;2(5), 2014 Oct.
[Is] ISSN:2165-0497
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:This chapter revisits the historical development and outcome of studies focused on the transmissible, extrachromosomal genetic elements called plasmids. Early work on plasmids involved structural and genetic mapping of these molecules, followed by the development of an understanding of how plasmids replicate and segregate during cell division. The intriguing property of plasmid transmission between bacteria and between bacteria and higher cells has received considerable attention. The utilitarian aspects of plasmids are described, including examples of various plasmid vector systems. This chapter also discusses the functional attributes of plasmids needed for their persistence and survival in nature and in man-made environments. The term plasmid biology was first conceived at the Fallen Leaf Lake Conference on Promiscuous Plasmids, 1990, Lake Tahoe, California. The International Society for Plasmid Biology was established in 2004 (www.ISPB.org).
[Mh] Termos MeSH primário: Biologia/história
Herança Extracromossômica
Genética Microbiana/história
Biologia Molecular/história
Plasmídeos
[Mh] Termos MeSH secundário: Adaptação Biológica
Evolução Molecular
Transferência Genética Horizontal
História do Século XX
História do Século XXI
Seleção Genética
[Pt] Tipo de publicação:HISTORICAL ARTICLE; JOURNAL ARTICLE; REVIEW
[Em] Mês de entrada:1602
[Cu] Atualização por classe:150624
[Lr] Data última revisão:
150624
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150625
[St] Status:MEDLINE
[do] DOI:10.1128/microbiolspec.PLAS-0019-2013


  8 / 2839 MEDLINE  
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[PMID]:26104348
[Au] Autor:Hernández-Arriaga AM; Chan WT; Espinosa M; Díaz-Orejas R
[Ti] Título:Conditional Activation of Toxin-Antitoxin Systems: Postsegregational Killing and Beyond.
[So] Source:Microbiol Spectr;2(5), 2014 Oct.
[Is] ISSN:2165-0497
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Toxin-antitoxin (TA) systems are small genetic modules formed by a stable toxin and an unstable antitoxin that are widely present in plasmids and in chromosomes of Bacteria and Archaea. Toxins can interfere with cell growth or viability, targeting a variety of key processes. Antitoxin inhibits expression of the toxin, interacts with it, and neutralizes its effect. In a plasmid context, toxins are kept silent by the continuous synthesis of the unstable antitoxins; in plasmid-free cells (segregants), toxins can be activated owing to the faster decay of the antitoxin, and this results in the elimination of these cells from the population (postsegregational killing [PSK]) and in an increase of plasmid-containing cells in a growing culture. Chromosomal TA systems can also be activated in particular circumstances, and the interference with cell growth and viability that ensues contributes in different ways to the physiology of the cell. In this article, we review the conditional activation of TAs in selected plasmidic and chromosomal TA pairs and the implications of this activation. On the whole, the analysis underscores TA interactions involved in PSK and points to the effective contribution of TA systems to the physiology of the cell.
[Mh] Termos MeSH primário: Archaea/genética
Bactérias/genética
Herança Extracromossômica
Viabilidade Microbiana
Plasmídeos/metabolismo
Toxinas Biológicas/antagonistas & inibidores
Toxinas Biológicas/metabolismo
[Mh] Termos MeSH secundário: Archaea/metabolismo
Bactérias/metabolismo
Transporte Biológico
Divisão Celular
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T; REVIEW
[Nm] Nome de substância:
0 (Toxins, Biological)
[Em] Mês de entrada:1602
[Cu] Atualização por classe:150624
[Lr] Data última revisão:
150624
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150625
[St] Status:MEDLINE
[do] DOI:10.1128/microbiolspec.PLAS-0009-2013


  9 / 2839 MEDLINE  
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[PMID]:25832746
[Au] Autor:Tsunewaki K; Mori N; Takumi S
[Ad] Endereço:Emeritus Professor, Kyoto University.
[Ti] Título:Genetic effect of the Aegilops caudata plasmon on the manifestation of the Ae. cylindrica genome.
[So] Source:Genes Genet Syst;89(5):195-202, 2014.
[Is] ISSN:1880-5779
[Cp] País de publicação:Japan
[La] Idioma:eng
[Ab] Resumo:In the course of reconstructing Aegilops caudata from its own genome (CC) and its plasmon, which had passed half a century in common wheat (genome AABBDD), we produced alloplasmic Ae. cylindrica (genome CCDD) with the plasmon of Ae. caudata. This line, designated (caudata)-CCDD, was found to express male sterility in its second substitution backcross generation (SB2) of (caudata)-AABBCCDD pollinated three times with the Ae. cylindrica pollen. We repeatedly backcrossed these SB2 plants with the Ae. cylindrica pollen until the SB5 generation, and SB5F2 progeny were produced by self-pollination of the SB5 plants. Thirteen morphological and physiological characters, including pollen and seed fertilities, of the (caudata)-CCDD SB5F2 were compared with those of the euplasmic Ae. cylindrica. The results indicated that the male sterility expressed by (caudata)-CCDD was due to genetic incompatibility between the Ae. cylindrica genome and Ae. caudata plasmon that did not affect any other characters of Ae. cylindrica. Also, we report that the genome integrity functions in keeping the univalent transmission rate high.
[Mh] Termos MeSH primário: Cruzamento/métodos
Cruzamentos Genéticos
Herança Extracromossômica/genética
Hibridização Genética/genética
Poaceae/genética
[Mh] Termos MeSH secundário: Cromossomos de Plantas/genética
Fertilidade/genética
Especificidade da Espécie
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1510
[Cu] Atualização por classe:150402
[Lr] Data última revisão:
150402
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:150403
[St] Status:MEDLINE
[do] DOI:10.1266/ggs.89.195


  10 / 2839 MEDLINE  
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[PMID]:24859414
[Au] Autor:Sharma A
[Ad] Endereço:CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Sukhdev Vihar, Mathura Road, New Delhi 110025, India. Electronic address: abhaysharma@igib.res.in.
[Ti] Título:Bioinformatic analysis revealing association of exosomal mRNAs and proteins in epigenetic inheritance.
[So] Source:J Theor Biol;357:143-9, 2014 Sep 21.
[Is] ISSN:1095-8541
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Transgenerational inheritance of environment induced phenotype requires transmission of epigenetic information through the germline. Whereas several epigenetic factors have been implicated in germline transmission, mediators of information transfer from soma to the germline remain unidentified in mammals. Notably, a recent bioinformatic analysis showed association of extracellular microRNAs (miRNAs) and altered transcriptomes in diverse instances of mammalian epigenetic inheritance involving different environmental factors, tissues, life cycle stages, generations and genders. It was predicted that regulatory non-coding RNAs (ncRNAs) may potentially mediate soma to germline information transfer. Remarkably, the present bioinformatic evidence suggests similar association of exosomal mRNAs and proteins. The differentially expressed genes reported previously in genome level expression profiling studies related to or relevant in epigenetic inheritance showed enrichment for documented set of exosomal mRNAs in a few instances of epigenetic inheritance and of exosomal proteins in a majority of instances. Differentially expressed genes encoding exosomal miRNAs and proteins, directly or indirectly through first and/or second degree interactome networks, overrepresented biological processes related to environmental factors used in these instances as well as to epigenetic alterations, especially chromatin and histone modifications. These findings predict that exosomal mRNAs and proteins, like extracellular miRNAs, may also potentially mediate soma to germline information transfer. A convergent conceptual model is presented wherein extracellular ncRNAs/miRNA, mRNAs and proteins provide the much needed continuum inclusive of epigenetic inheritance. The phrase "transgenerational systems biology" is introduced to signify that the realm of systems biology extends beyond an individual organism and encompasses generations.
[Mh] Termos MeSH primário: Epigênese Genética/fisiologia
Exossomos
Herança Extracromossômica/fisiologia
Modelos Genéticos
Proteínas
[Mh] Termos MeSH secundário: Animais
Biologia Computacional
Exossomos/genética
Exossomos/metabolismo
Proteínas/genética
Proteínas/metabolismo
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
Ratos
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Proteins); 0 (RNA, Messenger)
[Em] Mês de entrada:1503
[Cu] Atualização por classe:140722
[Lr] Data última revisão:
140722
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:140527
[St] Status:MEDLINE



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