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[PMID]:29409851
[Au] Autor:Tan M; Li G; Qi S; Liu X; Chen X; Ma J; Zhang D; Han M
[Ad] Endereço:College of Horticulture, Northwest A & F University, Yangling, Shaanxi 712100, China.
[Ti] Título:Identification and expression analysis of the IPT and CKX gene families during axillary bud outgrowth in apple (Malus domestica Borkh.).
[So] Source:Gene;651:106-117, 2018 Apr 20.
[Is] ISSN:1879-0038
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Cytokinins (CKs) play a crucial role in promoting axillary bud outgrowth and targeting the control of CK metabolism can be used to enhance branching in plants. CK levels are maintained mainly by CK biosynthesis (isopentenyl transferase, IPT) and degradation (dehydrogenase, CKX) genes in plants. A systematic study of the IPT and CKX gene families in apple, however, has not been conducted. In the present study, 12 MdIPTs and 12 MdCKXs were identified in the apple genome. Systematic phylogenetic, structural, and synteny analyses were performed. Expression analysis of these genes in different tissues was also assessed. MdIPT and MdCKX genes exhibit distinct expression patterns in different tissues. The response of MdIPT, MdCKX, and MdPIN1 genes to various treatments (6-BA, decapitation and Lovastatin, an inhibitor of CKs synthesis) that impact branching were also investigated. Results indicated that most of the MdIPT and MdCKX, and MdPIN1 genes were upregulated by 6-BA and decapitation treatment, but inhibited by Lovastatin, a compound that effectively suppresses axillary bud outgrowth induced by decapitation. These findings suggest that cytokinin biosynthesis is required for the activation of bud break and the export of auxin from buds in apple tree with intact primary shoot apex or decapitated apple tree. MdCKX8 and MdCKX10, however, exhibited little response to decapitation, but were significantly up-regulated by 6-BA and Lovastatin, a finding that warrants further investigation in order to understand their function in bud-outgrowth.
[Mh] Termos MeSH primário: Alquil e Aril Transferases/genética
Genes de Plantas
Malus/genética
Oxirredutases/genética
[Mh] Termos MeSH secundário: Arabidopsis/genética
Compostos de Benzil/farmacologia
Mapeamento Cromossômico
Cromossomos de Plantas
Evolução Molecular
Flores/genética
Perfilação da Expressão Gênica
Regulação da Expressão Gênica de Plantas
Genoma de Planta
Lovastatina/farmacologia
Malus/enzimologia
Malus/crescimento & desenvolvimento
Família Multigênica
Filogenia
Reguladores de Crescimento de Planta
Purinas/farmacologia
Sintenia
Regulação para Cima
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Benzyl Compounds); 0 (Plant Growth Regulators); 0 (Purines); 9LHU78OQFD (Lovastatin); EC 1.- (Oxidoreductases); EC 1.5.99.12 (cytokinin oxidase); EC 2.5.- (Alkyl and Aryl Transferases); EC 2.5.1.27 (adenylate isopentenyltransferase); KXG6A989PS (benzylaminopurine)
[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


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[PMID]:29338040
[Au] Autor:Yang X; Li H; Yang Y; Wang Y; Mo Y; Zhang R; Zhang Y; Ma J; Wei C; Zhang X
[Ad] Endereço:State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, China.
[Ti] Título:Identification and expression analyses of WRKY genes reveal their involvement in growth and abiotic stress response in watermelon (Citrullus lanatus).
[So] Source:PLoS One;13(1):e0191308, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Despite identification of WRKY family genes in numerous plant species, a little is known about WRKY genes in watermelon, one of the most economically important fruit crops around the world. Here, we identified a total of 63 putative WRKY genes in watermelon and classified them into three major groups (I-III) and five subgroups (IIa-IIe) in group II. The structure analysis indicated that ClWRKYs with different WRKY domains or motifs may play different roles by regulating respective target genes. The expressions of ClWRKYs in different tissues indicate that they are involved in various tissue growth and development. Furthermore, the diverse responses of ClWRKYs to drought, salt, or cold stress suggest that they positively or negatively affect plant tolerance to various abiotic stresses. In addition, the altered expression patterns of ClWRKYs in response to phytohormones such as, ABA, SA, MeJA, and ETH, imply the occurrence of complex cross-talks between ClWRKYs and plant hormone signals in regulating plant physiological and biological processes. Taken together, our findings provide valuable clues to further explore the function and regulatory mechanisms of ClWRKY genes in watermelon growth, development, and adaption to environmental stresses.
[Mh] Termos MeSH primário: Citrullus/genética
Citrullus/fisiologia
Regulação da Expressão Gênica de Plantas
Proteínas de Plantas/genética
Estresse Fisiológico/genética
Fatores de Transcrição/genética
[Mh] Termos MeSH secundário: Motivos de Aminoácidos
Sequência de Aminoácidos
Citrullus/efeitos dos fármacos
Sequência Conservada
Evolução Molecular
Duplicação Gênica
Regulação da Expressão Gênica de Plantas/efeitos dos fármacos
Filogenia
Reguladores de Crescimento de Planta/farmacologia
Proteínas de Plantas/química
Alinhamento de Sequência
Estresse Fisiológico/efeitos dos fármacos
Sintenia
Fatores de Transcrição/química
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Plant Growth Regulators); 0 (Plant Proteins); 0 (Transcription Factors)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180226
[Lr] Data última revisão:
180226
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180117
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0191308


  3 / 2336 MEDLINE  
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[PMID]:29304093
[Au] Autor:Schmid-Hempel P; Aebi M; Barribeau S; Kitajima T; du Plessis L; Schmid-Hempel R; Zoller S
[Ad] Endereço:Institute of Integrative Biology (IBZ), ETH Zurich, Zürich, Switzerland.
[Ti] Título:The genomes of Crithidia bombi and C. expoeki, common parasites of bumblebees.
[So] Source:PLoS One;13(1):e0189738, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Trypanosomatids (Trypanosomatidae, Kinetoplastida) are flagellated protozoa containing many parasites of medical or agricultural importance. Among those, Crithidia bombi and C. expoeki, are common parasites in bumble bees around the world, and phylogenetically close to Leishmania and Leptomonas. They have a simple and direct life cycle with one host, and partially castrate the founding queens greatly reducing their fitness. Here, we report the nuclear genome sequences of one clone of each species, extracted from a field-collected infection. Using a combination of Roche 454 FLX Titanium, Pacific Biosciences PacBio RS, and Illumina GA2 instruments for C. bombi, and PacBio for C. expoeki, we could produce high-quality and well resolved sequences. We find that these genomes are around 32 and 34 MB, with 7,808 and 7,851 annotated genes for C. bombi and C. expoeki, respectively-which is somewhat less than reported from other trypanosomatids, with few introns, and organized in polycistronic units. A large fraction of genes received plausible functional support in comparison primarily with Leishmania and Trypanosoma. Comparing the annotated genes of the two species with those of six other trypanosomatids (C. fasciculata, L. pyrrhocoris, L. seymouri, B. ayalai, L. major, and T. brucei) shows similar gene repertoires and many orthologs. Similar to other trypanosomatids, we also find signs of concerted evolution in genes putatively involved in the interaction with the host, a high degree of synteny between C. bombi and C. expoeki, and considerable overlap with several other species in the set. A total of 86 orthologous gene groups show signatures of positive selection in the branch leading to the two Crithidia under study, mostly of unknown function. As an example, we examined the initiating glycosylation pathway of surface components in C. bombi, finding it deviates from most other eukaryotes and also from other kinetoplastids, which may indicate rapid evolution in the extracellular matrix that is involved in interactions with the host. Bumble bees are important pollinators and Crithidia-infections are suspected to cause substantial selection pressure on their host populations. These newly sequenced genomes provide tools that should help better understand host-parasite interactions in these pollinator pathogens.
[Mh] Termos MeSH primário: Abelhas/parasitologia
Crithidia/genética
Crithidia/patogenicidade
Genoma de Protozoário
[Mh] Termos MeSH secundário: Animais
Crithidia/classificação
Evolução Molecular
Interações Hospedeiro-Parasita/genética
Redes e Vias Metabólicas/genética
Anotação de Sequência Molecular
Filogenia
Polissacarídeos/metabolismo
Proteínas de Protozoários/genética
Especificidade da Espécie
Sintenia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Polysaccharides); 0 (Protozoan Proteins)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180210
[Lr] Data última revisão:
180210
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180106
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0189738


  4 / 2336 MEDLINE  
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[PMID]:28464795
[Au] Autor:Marandel L; Panserat S; Plagnes-Juan E; Arbenoits E; Soengas JL; Bobe J
[Ad] Endereço:INRA, UPPA, UMR 1419 Nutrition, Metabolism, Aquaculture, F-64310, Saint Pée sur Nivelle, France. lucie.marandel@inra.fr.
[Ti] Título:Evolutionary history of glucose-6-phosphatase encoding genes in vertebrate lineages: towards a better understanding of the functions of multiple duplicates.
[So] Source:BMC Genomics;18(1):342, 2017 05 02.
[Is] ISSN:1471-2164
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Glucose-6-phosphate (G6pc) is a key enzyme involved in the regulation of the glucose homeostasis. The present study aims at revisiting and clarifying the evolutionary history of g6pc genes in vertebrates. RESULTS: g6pc duplications happened by successive rounds of whole genome duplication that occurred during vertebrate evolution. g6pc duplicated before or around Osteichthyes/Chondrichthyes radiation, giving rise to g6pca and g6pcb as a consequence of the second vertebrate whole genome duplication. g6pca was lost after this duplication in Sarcopterygii whereas both g6pca and g6pcb then duplicated as a consequence of the teleost-specific whole genome duplication. One g6pca duplicate was lost after this duplication in teleosts. Similarly one g6pcb2 duplicate was lost at least in the ancestor of percomorpha. The analysis of the evolution of spatial expression patterns of g6pc genes in vertebrates showed that all g6pc were mainly expressed in intestine and liver whereas teleost-specific g6pcb2 genes were mainly and surprisingly expressed in brain and heart. g6pcb2b, one gene previously hypothesised to be involved in the glucose intolerant phenotype in trout, was unexpectedly up-regulated (as it was in liver) by carbohydrates in trout telencephalon without showing significant changes in other brain regions. This up-regulation is in striking contrast with expected glucosensing mechanisms suggesting that its positive response to glucose relates to specific unknown processes in this brain area. CONCLUSIONS: Our results suggested that the fixation and the divergence of g6pc duplicated genes during vertebrates' evolution may lead to adaptive novelty and probably to the emergence of novel phenotypes related to glucose homeostasis.
[Mh] Termos MeSH primário: Evolução Molecular
Glucose-6-Fosfatase/genética
Vertebrados/genética
[Mh] Termos MeSH secundário: Animais
Encéfalo/efeitos dos fármacos
Encéfalo/metabolismo
Carboidratos da Dieta/farmacologia
Regulação Enzimológica da Expressão Gênica/efeitos dos fármacos
Coração/efeitos dos fármacos
Seres Humanos
Miocárdio/metabolismo
Filogenia
Sintenia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Dietary Carbohydrates); EC 3.1.3.9 (Glucose-6-Phosphatase)
[Em] Mês de entrada:1712
[Cu] Atualização por classe:180104
[Lr] Data última revisão:
180104
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170504
[St] Status:MEDLINE
[do] DOI:10.1186/s12864-017-3727-1


  5 / 2336 MEDLINE  
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[PMID]:29045412
[Au] Autor:Theofanopoulou C; Gastaldon S; O'Rourke T; Samuels BD; Messner A; Martins PT; Delogu F; Alamri S; Boeckx C
[Ad] Endereço:Section of General Linguistics, Universitat de Barcelona, Barcelona, Spain.
[Ti] Título:Self-domestication in Homo sapiens: Insights from comparative genomics.
[So] Source:PLoS One;12(10):e0185306, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:This study identifies and analyzes statistically significant overlaps between selective sweep screens in anatomically modern humans and several domesticated species. The results obtained suggest that (paleo-)genomic data can be exploited to complement the fossil record and support the idea of self-domestication in Homo sapiens, a process that likely intensified as our species populated its niche. Our analysis lends support to attempts to capture the "domestication syndrome" in terms of alterations to certain signaling pathways and cell lineages, such as the neural crest.
[Mh] Termos MeSH primário: Domesticação
Genômica
[Mh] Termos MeSH secundário: Alelos
Animais
Perfilação da Expressão Gênica
Hominidae/genética
Seres Humanos
Seleção Genética
Especificidade da Espécie
Sintenia/genética
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171031
[Lr] Data última revisão:
171031
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171019
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0185306


  6 / 2336 MEDLINE  
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[PMID]:28910296
[Au] Autor:Kirk IK; Weinhold N; Brunak S; Belling K
[Ad] Endereço:Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
[Ti] Título:The impact of the protein interactome on the syntenic structure of mammalian genomes.
[So] Source:PLoS One;12(9):e0179112, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Conserved synteny denotes evolutionary preserved gene order across species. It is not well understood to which degree functional relationships between genes are preserved in syntenic blocks. Here we investigate whether protein-coding genes conserved in mammalian syntenic blocks encode gene products that serve the common functional purpose of interacting at protein level, i.e. connectivity. High connectivity among protein-protein interactions (PPIs) was only moderately associated with conserved synteny on a genome-wide scale. However, we observed a smaller subset of 3.6% of all syntenic blocks with high-confidence PPIs that had significantly higher connectivity than expected by random. Additionally, syntenic blocks with high-confidence PPIs contained significantly more chromatin loops than the remaining blocks, indicating functional preservation among these syntenic blocks. Conserved synteny is typically defined by sequence similarity. In this study, we also examined whether a functional relationship, here PPI connectivity, can identify syntenic blocks independently of orthology. While orthology-based syntenic blocks with high-confident PPIs and the connectivity-based syntenic blocks largely overlapped, the connectivity-based approach identified additional syntenic blocks that were not found by conventional sequence-based methods alone. Additionally, the connectivity-based approach enabled identification of potential orthologous genes between species. Our analyses demonstrate that subsets of syntenic blocks are associated with highly connected proteins, and that PPI connectivity can be used to detect conserved synteny even if sequence conservation drifts beyond what orthology algorithms normally can identify.
[Mh] Termos MeSH primário: Cromatina/genética
Mapeamento Cromossômico/métodos
Mamíferos/genética
Mapas de Interação de Proteínas
[Mh] Termos MeSH secundário: Algoritmos
Animais
Sequência Conservada
Cães
Evolução Molecular
Ordem dos Genes
Ligação Genética
Seres Humanos
Camundongos
Pan troglodytes
Análise de Sequência de DNA/métodos
Suínos
Sintenia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Chromatin)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171012
[Lr] Data última revisão:
171012
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170915
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0179112


  7 / 2336 MEDLINE  
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[PMID]:28856619
[Au] Autor:de Los Ángeles Bivian-Hernández M; López-Tlacomulco J; Mares-Mares E; Ibarra JE; Del Rincón-Castro MC
[Ad] Endereço:Posgrado en Biociencias, División de Ciencias de la Vida, Departamento de Alimentos, Campus Irapuato-Salamanca, Universidad de Guanajuato, Ex Hacienda El Copal Km. 9.0, Carretera Irapuato-León, Irapuato, Guanajuato, Mexico.
[Ti] Título:Genomic analysis of a Trichoplusia ni Betabaculovirus (TnGV) with three different viral enhancing factors and two unique genes.
[So] Source:Arch Virol;162(12):3705-3715, 2017 Dec.
[Is] ISSN:1432-8798
[Cp] País de publicação:Austria
[La] Idioma:eng
[Ab] Resumo:The complete genome of a Trichoplusia ni granulovirus (TnGV) is described and analyzed. The genome contains 175,360 bp (KU752557), becoming the third largest genome within the genus Betabaculovirus, smaller only than the Xestia c-nigrum GV (XecnGV) (178,733 pb) and the Pseudaletia unipuncta GV (PsunGV) (176,677 pb) genomes. The TnGV genome has a 39.81% C+G content and a total of 180 ORFs were identified, 96 of them in the granulin gene direction and 84 in the opposite direction. A total of 94.38% of the ORFs showed high identity with those of ClanGV, HaGV, and SlGV. Eight homologous regions (hrs) were identified as well as one apoptosis inhibitor (IAP-3). Interestingly, three viral enhancing factors (VEFs) were located in TnGV genome: VEF-1 (orf153), VEF-3 (orf155), and VEF-4 (orf164), additional to another metalloprotease (orf37). Two ORFs were unique to TnGV (orf100 and orf101) and another one was shared by only TnGV and AgseGV (orf2). Eleven of the deduced proteins showed high identity with proteins from nucleopolyhedroviruses, three with proteins from ascoviruses, and one with an entomopoxvirus protein. The largest deduced protein contains 1,213 amino acids (orf43) and the smallest deduced protein contains only 50 amino acids (orf143). Sequence identity and phylogenetic analyses showed that the closest related genomes to TnGV are, to date, those of PsunGV and XecnGV. This genome analysis may contribute to functional research on TnGV, and may form the bases for the utilization of this betabaculovirus as a pest control agent.
[Mh] Termos MeSH primário: Baculoviridae/classificação
Baculoviridae/genética
Genoma Viral
Genômica
Lepidópteros/virologia
[Mh] Termos MeSH secundário: Animais
Baculoviridae/isolamento & purificação
Composição de Bases
Fases de Leitura Aberta
Filogenia
Análise de Sequência de DNA
Homologia de Sequência
Sintenia
Proteínas Virais/genética
Fatores de Virulência/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Viral Proteins); 0 (Virulence Factors)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171113
[Lr] Data última revisão:
171113
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170901
[St] Status:MEDLINE
[do] DOI:10.1007/s00705-017-3506-y


  8 / 2336 MEDLINE  
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[PMID]:28852802
[Au] Autor:van Geest G; Bourke PM; Voorrips RE; Marasek-Ciolakowska A; Liao Y; Post A; van Meeteren U; Visser RGF; Maliepaard C; Arens P
[Ad] Endereço:Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, The Netherlands. geert.vangeest@wur.nl.
[Ti] Título:An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis.
[So] Source:Theor Appl Genet;130(12):2527-2541, 2017 Dec.
[Is] ISSN:1432-2242
[Cp] País de publicação:Germany
[La] Idioma:eng
[Ab] Resumo:KEY MESSAGE: We constructed the first integrated genetic linkage map in a polysomic hexaploid. This enabled us to estimate inheritance of parental haplotypes in the offspring and detect multi-allelic QTL. Construction and use of linkage maps are challenging in hexaploids with polysomic inheritance. Full map integration requires calculations of recombination frequency between markers with complex segregation types. In addition, detection of QTL in hexaploids requires information on all six alleles at one locus for each individual. We describe a method that we used to construct a fully integrated linkage map for chrysanthemum (Chrysanthemum × morifolium, 2n = 6x = 54). A bi-parental F1 population of 406 individuals was genotyped with an 183,000 SNP genotyping array. The resulting linkage map consisted of 30,312 segregating SNP markers of all possible marker dosage types, representing nine chromosomal linkage groups and 107 out of 108 expected homologues. Synteny with lettuce (Lactuca sativa) showed local colinearity. Overall, it was high enough to number the chrysanthemum chromosomal linkage groups according to those in lettuce. We used the integrated and phased linkage map to reconstruct inheritance of parental haplotypes in the F1 population. Estimated probabilities for the parental haplotypes were used for multi-allelic QTL analyses on four traits with different underlying genetic architectures. This resulted in the identification of major QTL that were affected by multiple alleles having a differential effect on the phenotype. The presented linkage map sets a standard for future genetic mapping analyses in chrysanthemum and closely related species. Moreover, the described methods are a major step forward for linkage mapping and QTL analysis in hexaploids.
[Mh] Termos MeSH primário: Mapeamento Cromossômico
Chrysanthemum/genética
Ligação Genética
Polimorfismo de Nucleotídeo Único
Locos de Características Quantitativas
[Mh] Termos MeSH secundário: Alelos
Marcadores Genéticos
Genoma de Planta
Técnicas de Genotipagem
Haplótipos
Alface/genética
Fenótipo
Poliploidia
Sintenia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Genetic Markers)
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171117
[Lr] Data última revisão:
171117
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170831
[St] Status:MEDLINE
[do] DOI:10.1007/s00122-017-2974-5


  9 / 2336 MEDLINE  
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[PMID]:28818331
[Au] Autor:Hick PM; Subramaniam K; Thompson PM; Waltzek TB; Becker JA; Whittington RJ
[Ad] Endereço:OIE Reference Laboratory for Epizootic Haematopoietic Necrosis Virus and Ranavirus Infection of Amphibians, Sydney School of Veterinary Science and School of Life and Environmental Sciences, The University Sydney, Werombi Road, Camden 2570, NSW, Australia. Electronic address: paul.hick@sydney.edu.au
[Ti] Título:Molecular epidemiology of Epizootic haematopoietic necrosis virus (EHNV).
[So] Source:Virology;511:320-329, 2017 Nov.
[Is] ISSN:1096-0341
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Low genetic diversity of Epizootic haematopoietic necrosis virus (EHNV) was determined for the complete genome of 16 isolates spanning the natural range of hosts, geography and time since the first outbreaks of disease. Genomes ranged from 125,591-127,487 nucleotides with 97.47% pairwise identity and 106-109 genes. All isolates shared 101 core genes with 121 potential genes predicted within the pan-genome of this collection. There was high conservation within 90,181 nucleotides of the core genes with isolates separated by average genetic distance of 3.43 × 10 substitutions per site. Evolutionary analysis of the core genome strongly supported historical epidemiological evidence of iatrogenic spread of EHNV to naïve hosts and establishment of endemic status in discrete ecological niches. There was no evidence of structural genome reorganization, however, the complement of non-core genes and variation in repeat elements enabled fine scale molecular epidemiological investigation of this unpredictable pathogen of fish.
[Mh] Termos MeSH primário: Surtos de Doenças
Doenças dos Peixes/epidemiologia
Doenças dos Peixes/virologia
Variação Genética
Epidemiologia Molecular
Ranavirus/classificação
Ranavirus/genética
[Mh] Termos MeSH secundário: Animais
Infecções por Vírus de DNA/veterinária
Infecções por Vírus de DNA/virologia
Doenças Endêmicas
Peixes
Genes Virais
Genoma Viral
Doença Iatrogênica/epidemiologia
Doença Iatrogênica/veterinária
Ranavirus/isolamento & purificação
Análise de Sequência de DNA
Homologia de Sequência
Sintenia
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171010
[Lr] Data última revisão:
171010
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170819
[St] Status:MEDLINE


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[PMID]:28800596
[Au] Autor:Sun S; Yadav V; Billmyre RB; Cuomo CA; Nowrousian M; Wang L; Souciet JL; Boekhout T; Porcel B; Wincker P; Granek JA; Sanyal K; Heitman J
[Ad] Endereço:Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America.
[Ti] Título:Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination.
[So] Source:PLoS Biol;15(8):e2002527, 2017 Aug.
[Is] ISSN:1545-7885
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Species within the human pathogenic Cryptococcus species complex are major threats to public health, causing approximately 1 million annual infections globally. Cryptococcus amylolentus is the most closely known related species of the pathogenic Cryptococcus species complex, and it is non-pathogenic. Additionally, while pathogenic Cryptococcus species have bipolar mating systems with a single large mating type (MAT) locus that represents a derived state in Basidiomycetes, C. amylolentus has a tetrapolar mating system with 2 MAT loci (P/R and HD) located on different chromosomes. Thus, studying C. amylolentus will shed light on the transition from tetrapolar to bipolar mating systems in the pathogenic Cryptococcus species, as well as its possible link with the origin and evolution of pathogenesis. In this study, we sequenced, assembled, and annotated the genomes of 2 C. amylolentus isolates, CBS6039 and CBS6273, which are sexual and interfertile. Genome comparison between the 2 C. amylolentus isolates identified the boundaries and the complete gene contents of the P/R and HD MAT loci. Bioinformatic and chromatin immunoprecipitation sequencing (ChIP-seq) analyses revealed that, similar to those of the pathogenic Cryptococcus species, C. amylolentus has regional centromeres (CENs) that are enriched with species-specific transposable and repetitive DNA elements. Additionally, we found that while neither the P/R nor the HD locus is physically closely linked to its centromere in C. amylolentus, and the regions between the MAT loci and their respective centromeres show overall synteny between the 2 genomes, both MAT loci exhibit genetic linkage to their respective centromere during meiosis, suggesting the presence of recombinational suppressors and/or epistatic gene interactions in the MAT-CEN intervening regions. Furthermore, genomic comparisons between C. amylolentus and related pathogenic Cryptococcus species provide evidence that multiple chromosomal rearrangements mediated by intercentromeric recombination have occurred during descent of the 2 lineages from their common ancestor. Taken together, our findings support a model in which the evolution of the bipolar mating system was initiated by an ectopic recombination event mediated by similar repetitive centromeric DNA elements shared between chromosomes. This translocation brought the P/R and HD loci onto the same chromosome, and further chromosomal rearrangements then resulted in the 2 MAT loci becoming physically linked and eventually fusing to form the single contiguous MAT locus that is now extant in the pathogenic Cryptococcus species.
[Mh] Termos MeSH primário: Cryptococcus/citologia
Cryptococcus/genética
Genes Fúngicos Tipo Acasalamento
Genoma Fúngico
Meiose
Translocação Genética
[Mh] Termos MeSH secundário: Imunoprecipitação da Cromatina
Biologia Computacional
Troca Genética
Cryptococcus/crescimento & desenvolvimento
Cryptococcus/fisiologia
Cryptococcus neoformans/citologia
Cryptococcus neoformans/genética
Cryptococcus neoformans/fisiologia
Epistasia Genética
Evolução Molecular
Ligação Genética
Loci Gênicos
Estruturas Genéticas
Desequilíbrio de Ligação
Anotação de Sequência Molecular
Recombinação Genética
Análise de Sequência de RNA
Especificidade da Espécie
Sintenia
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171014
[Lr] Data última revisão:
171014
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170812
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pbio.2002527



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