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1.
BMC Res Notes ; 16(1): 248, 2023 Oct 02.
Artigo em Inglês | MEDLINE | ID: mdl-37784104

RESUMO

OBJECTIVE: Black poplar (Populus nigra L.) is a species native to Eurasia with a wide distribution area. It is an ecologically important species from riparian ecosystems, that is used as a parent of interspecific (P. deltoides x P. nigra) cultivated poplar hybrids. Variant detection from transcriptomics sequences of 241 P. nigra individuals, sampled in natural populations from 11 river catchments (in four European countries) is described here. These data provide new valuable resources for population structure analysis, population genomics and genome-wide association studies. DATA DESCRIPTION: We generated transcriptomics data from a mixture of young differentiating xylem and cambium tissues of 480 Populus nigra trees sampled in a common garden experiment located at Orléans (France), corresponding to 241 genotypes (2 clonal replicates per genotype, at maximum) by using RNAseq technology. We launched on the resulting sequences an in-silico pipeline that allowed us to obtain 878,957 biallelic polymorphisms without missing data. More than 99% of these positions are annotated and 98.8% are located on the 19 chromosomes of the P. trichocarpa reference genome. The raw RNAseq sequences are available at the NCBI Sequence Read Archive SPR188754 and the variant dataset at the Recherche Data Gouv repository under https://doi.org/10.15454/8DQXK5 .


Assuntos
Populus , Humanos , Populus/genética , Ecossistema , Estudo de Associação Genômica Ampla , Genótipo , França
2.
New Phytol ; 232(1): 80-97, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34128549

RESUMO

Trees are long-lived organisms that continuously adapt to their environments, a process in which epigenetic mechanisms are likely to play a key role. Via downregulation of the chromatin remodeler DECREASED IN DNA METHYLATION 1 (DDM1) in poplar (Populus tremula × Populus alba) RNAi lines, we examined how DNA methylation coordinates genomic and physiological responses to moderate water deficit. We compared the growth and drought response of two RNAi-ddm1 lines to wild-type (WT) trees under well-watered and water deficit/rewatering conditions, and analyzed their methylomes, transcriptomes, mobilomes and phytohormone contents in the shoot apical meristem. The RNAi-ddm1 lines were more tolerant to drought-induced cavitation but did not differ in height or stem diameter growth. About 5000 differentially methylated regions were consistently detected in both RNAi-ddm1 lines, colocalizing with 910 genes and 89 active transposable elements. Under water deficit conditions, 136 differentially expressed genes were found, including many involved in phytohormone pathways; changes in phytohormone concentrations were also detected. Finally, the combination of hypomethylation and drought led to the mobility of two transposable elements. Our findings suggest major roles for DNA methylation in regulation of genes involved in hormone-related stress responses, and the maintenance of genome integrity through repression of transposable elements.


Assuntos
Populus , Metilação de DNA/genética , Secas , Regulação da Expressão Gênica de Plantas , Meristema , Populus/genética , Interferência de RNA
3.
J Exp Bot ; 69(20): 4821-4837, 2018 09 14.
Artigo em Inglês | MEDLINE | ID: mdl-30107545

RESUMO

Trees have a long lifespan and must continually adapt to environmental pressures, notably in the context of climate change. Epigenetic mechanisms are doubtless involved in phenotypic plasticity and in stress memory; however, little evidence of the role of epigenetic processes is available for trees growing in fields. Here, we analyzed the possible involvement of epigenetic mechanisms in the winter-dormant shoot apical meristem of Populus × euramericana clones in memory of the growing conditions faced during the vegetative period. We aimed to estimate the range of genetic and environmentally induced variations in global DNA methylation and to evaluate their correlation with changes in biomass production, identify differentially methylated regions (DMRs), and characterize common DMRs between experiments. We showed that the variations in global DNA methylation between conditions were genotype dependent and correlated with biomass production capacity. Microarray chip analysis allowed detection of DMRs 6 months after the stressful summer period. The 161 DMRs identified as common to three independent experiments most notably targeted abiotic stress and developmental response genes. Results are consistent with a winter-dormant shoot apical meristem epigenetic memory of stressful environmental conditions that occurred during the preceding summer period. This memory may facilitate tree acclimation.


Assuntos
Metilação de DNA , Epigênese Genética , Dormência de Plantas/genética , Populus/genética , Meristema/genética , Meristema/crescimento & desenvolvimento , Procedimentos Analíticos em Microchip , Brotos de Planta/genética , Brotos de Planta/crescimento & desenvolvimento , Populus/crescimento & desenvolvimento , Estações do Ano , Árvores/genética , Árvores/crescimento & desenvolvimento
4.
J Microbiol Methods ; 61(2): 201-8, 2005 May.
Artigo em Inglês | MEDLINE | ID: mdl-15722146

RESUMO

Rapid and accurate identification and speciation of staphylococci clinical isolates is important for predicting medical pathology. We evaluated the ability of a high-density DNA probe array based on 16S rDNA sequences to identify Staphylococcus species. Correct identification was observed for 185 out of the 201 strains (92%). Of the 33 tested species, the array was able to correctly identify 30 of them. The total time required for identification of 4 isolates was 5 h. Such a tool represents a powerful method for routine microbiological diagnostic as well as for epidemiological studies.


Assuntos
Sondas de DNA/genética , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Staphylococcus/classificação , Animais , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Sondas de DNA/química , DNA Bacteriano/química , DNA Bacteriano/genética , Humanos , Reação em Cadeia da Polimerase/métodos , RNA Ribossômico 16S/química , RNA Ribossômico 16S/genética , Staphylococcus/genética , Staphylococcus/isolamento & purificação , Superóxido Dismutase/química , Superóxido Dismutase/genética
5.
Dermatology ; 210(1): 21-5, 2005.
Artigo em Inglês | MEDLINE | ID: mdl-15604540

RESUMO

BACKGROUND: Fusarium species are isolated from about 3% of onychomycoses in the Swiss native population. On the basis of macroscopic characters and microscopic examination of the cultures, identification of Fusarium often remains difficult or uncertain because of variations from one isolate to another and overlapping characteristics between species. OBJECTIVE: To obtain information about the prevailing species of Fusarium collected from onychomycoses. METHODS: An analysis of the Fusarium specimens isolated in the Department of Dermatology at the University Hospital of Lausanne was conducted during a 2-year period (71 isolates). A 311-bp fragment of the gene encoding 28S rDNA was amplified by PCR and sequenced. DNA sequences were compared to those available for reference strains. RESULTS: Fusarium oxysporum was the most frequently isolated species, accounting for 54% of the isolates. F. proliferatum and 4 taxons belonging to the F. solani species complex were identified with an appreciable frequency ranging from 4 to 14%. CONCLUSION: The Fusarium species identified were the same as those known to cause disseminated fusariosis in immunocompromised patients. The presence of these Fusarium species in onychomycoses warrants that careful attention should be paid to abnormal nails before beginning immunosuppressive treatments in patients.


Assuntos
Fusarium/isolamento & purificação , Onicomicose/epidemiologia , Onicomicose/microbiologia , Sequência de Bases , Primers do DNA , DNA Bacteriano/análise , DNA Ribossômico/análise , Fusarium/classificação , Fusarium/genética , Humanos , Dados de Sequência Molecular , Reação em Cadeia da Polimerase , Prevalência , Suíça/epidemiologia
6.
Dermatology ; 208(3): 244-50, 2004.
Artigo em Inglês | MEDLINE | ID: mdl-15118380

RESUMO

BACKGROUND: Dermatophytes are usually identified on the basis of macroscopic characteristics and microscopic examination of the cultures. Identification of dermatophytes often remains difficult or uncertain because there are variations from one isolate to another and overlapping characteristics between species. OBJECTIVE: To identify dermatophyte species producing numerous microconidia and resembling Trichophyton mentagrophytes by DNA sequence analysis. METHODS: The complete ITS1 + 5.6s + ITS2 rDNA region of various dermatophytes isolated in culture was amplified by PCR and sequenced. RESULTS: Nine isolates of a fast-growing dermatophyte species were identified as Arthroderma benhamiae by DNA sequencing. Retrospective investigations revealed that the isolates were from 8 children and 1 adult suffering from inflammatory dermatophytosis. Eight of the 9 patients had had previous contact with rodents, mostly guinea pigs. CONCLUSION: It is the first time that A. benhamiae is reported in Switzerland. In cases of dermatophytosis attributed to A. benhamiae, a rodent is the most likely cause of infection.


Assuntos
Arthrodermataceae/genética , Arthrodermataceae/isolamento & purificação , Dermatomicoses/diagnóstico , Análise de Sequência de DNA , Adolescente , Adulto , Animais , Animais Domésticos , Criança , DNA Ribossômico/análise , Feminino , Humanos , Filogenia , Reação em Cadeia da Polimerase , Estudos Retrospectivos , Suíça , Trichophyton/genética
7.
J Clin Microbiol ; 41(2): 826-30, 2003 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-12574293

RESUMO

We have shown that dermatophyte species can be easily identified on the basis of a DNA sequence encoding a part of the large-subunit (LSU) rRNA (28S rRNA) by using the MicroSeq D2 LSU rRNA Fungal Sequencing Kit. Two taxa causing distinct dermatophytoses were clearly distinguished among isolates of the Trichophyton mentagrophytes species complex.


Assuntos
Arthrodermataceae/isolamento & purificação , RNA Ribossômico 28S/análise , Animais , Sequência de Bases , Gatos , DNA Fúngico/análise , Cães , Humanos , Dados de Sequência Molecular , Reação em Cadeia da Polimerase , RNA Ribossômico 28S/genética , Kit de Reagentes para Diagnóstico , Homologia de Sequência do Ácido Nucleico
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