Base de dados : MEDLINE
Pesquisa : B01.650.940.800.575.156.100.666.755 [Categoria DeCS]
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  1 / 1710 MEDLINE  
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[PMID]:28453674
[Au] Autor:Mohamadi H; Khan H; Birol I
[Ad] Endereço:Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada.
[Ti] Título:ntCard: a streaming algorithm for cardinality estimation in genomics data.
[So] Source:Bioinformatics;33(9):1324-1330, 2017 05 01.
[Is] ISSN:1367-4811
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Motivation: Many bioinformatics algorithms are designed for the analysis of sequences of some uniform length, conventionally referred to as k -mers. These include de Bruijn graph assembly methods and sequence alignment tools. An efficient algorithm to enumerate the number of unique k -mers, or even better, to build a histogram of k -mer frequencies would be desirable for these tools and their downstream analysis pipelines. Among other applications, estimated frequencies can be used to predict genome sizes, measure sequencing error rates, and tune runtime parameters for analysis tools. However, calculating a k -mer histogram from large volumes of sequencing data is a challenging task. Results: Here, we present ntCard, a streaming algorithm for estimating the frequencies of k -mers in genomics datasets. At its core, ntCard uses the ntHash algorithm to efficiently compute hash values for streamed sequences. It then samples the calculated hash values to build a reduced representation multiplicity table describing the sample distribution. Finally, it uses a statistical model to reconstruct the population distribution from the sample distribution. We have compared the performance of ntCard and other cardinality estimation algorithms. We used three datasets of 480 GB, 500 GB and 2.4 TB in size, where the first two representing whole genome shotgun sequencing experiments on the human genome and the last one on the white spruce genome. Results show ntCard estimates k -mer coverage frequencies >15× faster than the state-of-the-art algorithms, using similar amount of memory, and with higher accuracy rates. Thus, our benchmarks demonstrate ntCard as a potentially enabling technology for large-scale genomics applications. Availability and Implementation: ntCard is written in C ++ and is released under the GPL license. It is freely available at https://github.com/bcgsc/ntCard. Contact: hmohamadi@bcgsc.ca or ibirol@bcgsc.ca. Supplementary information: Supplementary data are available at Bioinformatics online.
[Mh] Termos MeSH primário: Genômica/métodos
Análise de Sequência de DNA/métodos
Software
[Mh] Termos MeSH secundário: Algoritmos
Tamanho do Genoma
Genoma Humano
Genoma de Planta
Seres Humanos
Modelos Estatísticos
Picea/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1093/bioinformatics/btw832


  2 / 1710 MEDLINE  
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[PMID]:29372791
[Au] Autor:Kiselev KV; Ogneva ZV; Suprun AR; Zhuravlev YN
[Ti] Título:[Expression of the stilbene synthase genes in the needles of spruce Picea jezoensis].
[So] Source:Genetika;52(11):1279-86, 2016 Nov.
[Is] ISSN:0016-6758
[Cp] País de publicação:Russia (Federation)
[La] Idioma:rus
[Ab] Resumo:Stilbenes are valuable plant phytoalexins, the biosynthesis of which is characteristic of different groups of phylogenetically unrelated plants. It is believed that all the stilbenes are the derivatives of resveratrol (3,5,4'-trihydroxy-trans-stilbene) or compounds close to it (pinosylvin or piceatannol). The last stage of the resveratrol biosynthesis takes place with the involvement of stilbene synthase or resveratrol synthase (STS). The family Pinaceae is characterized by the presence of the derivatives of pinosylvin (genus Pinus) and piceatannol (genus Picea), the biosynthetic pathways of which are scarcely examined. Previously, in different species of the genus Picea, only two stilbene synthase genes were described. On the basis of RNA isolated from the needles of spruce Picea jezoensis, the full-length cDNAs of the four stilbene synthase genes, PjSTS1a, PjSTS1b, PjSTS2, and PjSTS3, were obtained. Then, using the clone frequency analysis and real-time PCR, expression of the PjSTS1a, PjSTS1b, PjSTS2, and PjSTS3 genes was examined in the needles of P. jezoensis accessions of different age and sampled in different seasons (spring, summer, autumn, winter). Among the analyzed transcripts, the PjSTS1a and PjSTS1b genes were the most frequent, indicating their higher level of expression compared to other STS genes. The highest level of PjSTS1a and PjSTS1b expression was observed in autumn, while the level of PjSTS2 and PjSTS3 expression was the highest in spring and winter. Moreover, the highest PjSTS expression was detected in the young tissues of P. jezoensis in autumn, which may indicate a higher level of stilbene biosynthesis in these tissues.
[Mh] Termos MeSH primário: Aciltransferases/biossíntese
Regulação Enzimológica da Expressão Gênica/fisiologia
Regulação da Expressão Gênica de Plantas/fisiologia
Picea/enzimologia
Proteínas de Plantas/biossíntese
[Mh] Termos MeSH secundário: Aciltransferases/genética
Picea/genética
Proteínas de Plantas/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Plant Proteins); EC 2.3.- (Acyltransferases); EC 2.3.1.- (stilbene synthase)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180205
[Lr] Data última revisão:
180205
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180127
[St] Status:MEDLINE


  3 / 1710 MEDLINE  
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[PMID]:29372789
[Au] Autor:Kravchenko AN; Ekart AK; Larionova AY
[Ti] Título:[Genetic diversity and differentiation of Siberian spruce populations at nuclear microsatellite loci].
[So] Source:Genetika;52(11):1262-9, 2016 Nov.
[Is] ISSN:0016-6758
[Cp] País de publicação:Russia (Federation)
[La] Idioma:rus
[Ab] Resumo:The results of the study of 21 populations of Siberian spruce (Picea obovata Ledeb.) from different parts of the species natural range by microsatellite (SSR) analysis of nuclear DNA are presented. Using nine loci developed for Picea abies (L.) Karst. and Picea glauca (Moench) Voss and detecting variation in Picea obovata, the parameters of intra- and interpopulation genetic diversity, as well as the degree of population differentiation, were determined. It was demonstrated that the population of Siberian spruce in the study was characterized by a relatively high average level of intrapopulation variability (H o = 0.408; H e = 0.423) and low interpopulation differentiation (F st = 0.048, P = 0.001) at this class of DNA markers. The genetic distance between populations ranged from 0.009 to 0.167, averaging 0.039. The isolated Magadan population, located in the extreme Northeast of Russia at a considerable distance from the main species range and characterized by the lowest genetic diversity among the studied populations, was maximally differentiated from the rest of the spruce populations. In addition, the steppe Ubukun population from Buryatia and the population from the Bogd Khan Uul Biosphere Reserve, Mongolia, were considerably different in the genetic structure from most populations of Siberian spruce, although to a lesser extent than the Magadan population. These findings are consistent with the results of previous studies of this species carried out using allozyme and microsatellite loci of chloroplast DNA and point to the prospects of using nuclear microsatellites as DNA markers to analyze the population genetic structure of Siberian spruce.
[Mh] Termos MeSH primário: Variação Genética
Repetições de Microssatélites
Picea/genética
[Mh] Termos MeSH secundário: Marcadores Genéticos
Picea/enzimologia
Sibéria
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Genetic Markers)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180205
[Lr] Data última revisão:
180205
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180127
[St] Status:MEDLINE


  4 / 1710 MEDLINE  
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[PMID]:28454519
[Au] Autor:Lenz PRN; Beaulieu J; Mansfield SD; Clément S; Desponts M; Bousquet J
[Ad] Endereço:Canadian Wood Fibre Centre, Canadian Forest Service, Natural Resources Canada, Government of Canada, 1055 du PEPS, P.O. Box 10380, Québec, Québec, G1V 4C7, Canada. Patrick.Lenz@canada.ca.
[Ti] Título:Factors affecting the accuracy of genomic selection for growth and wood quality traits in an advanced-breeding population of black spruce (Picea mariana).
[So] Source:BMC Genomics;18(1):335, 2017 04 28.
[Is] ISSN:1471-2164
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Genomic selection (GS) uses information from genomic signatures consisting of thousands of genetic markers to predict complex traits. As such, GS represents a promising approach to accelerate tree breeding, which is especially relevant for the genetic improvement of boreal conifers characterized by long breeding cycles. In the present study, we tested GS in an advanced-breeding population of the boreal black spruce (Picea mariana [Mill.] BSP) for growth and wood quality traits, and concurrently examined factors affecting GS model accuracy. RESULTS: The study relied on 734 25-year-old trees belonging to 34 full-sib families derived from 27 parents and that were established on two contrasting sites. Genomic profiles were obtained from 4993 Single Nucleotide Polymorphisms (SNPs) representative of as many gene loci distributed among the 12 linkage groups common to spruce. GS models were obtained for four growth and wood traits. Validation using independent sets of trees showed that GS model accuracy was high, related to trait heritability and equivalent to that of conventional pedigree-based models. In forward selection, gains per unit of time were three times higher with the GS approach than with conventional selection. In addition, models were also accurate across sites, indicating little genotype-by-environment interaction in the area investigated. Using information from half-sibs instead of full-sibs led to a significant reduction in model accuracy, indicating that the inclusion of relatedness in the model contributed to its higher accuracies. About 500 to 1000 markers were sufficient to obtain GS model accuracy almost equivalent to that obtained with all markers, whether they were well spread across the genome or from a single linkage group, further confirming the implication of relatedness and potential long-range linkage disequilibrium (LD) in the high accuracy estimates obtained. Only slightly higher model accuracy was obtained when using marker subsets that were identified to carry large effects, indicating a minor role for short-range LD in this population. CONCLUSIONS: This study supports the integration of GS models in advanced-generation tree breeding programs, given that high genomic prediction accuracy was obtained with a relatively small number of markers due to high relatedness and family structure in the population. In boreal spruce breeding programs and similar ones with long breeding cycles, much larger gain per unit of time can be obtained from genomic selection at an early age than by the conventional approach. GS thus appears highly profitable, especially in the context of forward selection in species which are amenable to mass vegetative propagation of selected stock, such as spruces.
[Mh] Termos MeSH primário: Cruzamento
Genômica
Picea/crescimento & desenvolvimento
Picea/genética
Madeira
[Mh] Termos MeSH secundário: Ligação Genética
Modelos Genéticos
Fenótipo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[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:170430
[St] Status:MEDLINE
[do] DOI:10.1186/s12864-017-3715-5


  5 / 1710 MEDLINE  
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[PMID]:29049391
[Au] Autor:Sharma RP; Vacek Z; Vacek S; Podrázský V; Jansa V
[Ad] Endereço:Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Suchdol, Czech Republic.
[Ti] Título:Modelling individual tree height to crown base of Norway spruce (Picea abies (L.) Karst.) and European beech (Fagus sylvatica L.).
[So] Source:PLoS One;12(10):e0186394, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Height to crown base (HCB) of a tree is an important variable often included as a predictor in various forest models that serve as the fundamental tools for decision-making in forestry. We developed spatially explicit and spatially inexplicit mixed-effects HCB models using measurements from a total 19,404 trees of Norway spruce (Picea abies (L.) Karst.) and European beech (Fagus sylvatica L.) on the permanent sample plots that are located across the Czech Republic. Variables describing site quality, stand density or competition, and species mixing effects were included into the HCB model with use of dominant height (HDOM), basal area of trees larger in diameters than a subject tree (BAL- spatially inexplicit measure) or Hegyi's competition index (HCI-spatially explicit measure), and basal area proportion of a species of interest (BAPOR), respectively. The parameters describing sample plot-level random effects were included into the HCB model by applying the mixed-effects modelling approach. Among several functional forms evaluated, the logistic function was found most suited to our data. The HCB model for Norway spruce was tested against the data originated from different inventory designs, but model for European beech was tested using partitioned dataset (a part of the main dataset). The variance heteroscedasticity in the residuals was substantially reduced through inclusion of a power variance function into the HCB model. The results showed that spatially explicit model described significantly a larger part of the HCB variations [R2adj = 0.86 (spruce), 0.85 (beech)] than its spatially inexplicit counterpart [R2adj = 0.84 (spruce), 0.83 (beech)]. The HCB increased with increasing competitive interactions described by tree-centered competition measure: BAL or HCI, and species mixing effects described by BAPOR. A test of the mixed-effects HCB model with the random effects estimated using at least four trees per sample plot in the validation data confirmed that the model was precise enough for the prediction of HCB for a range of site quality, tree size, stand density, and stand structure. We therefore recommend measuring of HCB on four randomly selected trees of a species of interest on each sample plot for localizing the mixed-effects model and predicting HCB of the remaining trees on the plot. Growth simulations can be made from the data that lack the values for either crown ratio or HCB using the HCB models.
[Mh] Termos MeSH primário: Fagus/crescimento & desenvolvimento
Modelos Biológicos
Picea/crescimento & desenvolvimento
[Pt] Tipo de publicação:JOURNAL ARTICLE; VALIDATION STUDIES
[Em] Mês de entrada:1711
[Cu] Atualização por classe:171107
[Lr] Data última revisão:
171107
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171020
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0186394


  6 / 1710 MEDLINE  
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[PMID]:28968421
[Au] Autor:Rutledge RG; Stewart D; Overton C; Klimaszewska K
[Ad] Endereço:Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du P.E.P.S., Stn. Sainte-Foy, Québec, Canada.
[Ti] Título:Gene expression analysis of primordial shoot explants collected from mature white spruce (Picea glauca) trees that differ in their responsiveness to somatic embryogenesis induction.
[So] Source:PLoS One;12(10):e0185015, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Within a plantation of clonal somatic embryo-derived white spruce trees that belonged to four genotypes, one genotype (G6) has consistently responded for the last 16 years, to the induction of somatic embryogenesis within primordial shoot explants. Analysis of fourteen individuals within this genotype subsequently revealed a group of clonal trees that were nonresponsive. This in turn provided a unique opportunity to conduct differential gene expression analysis in the absence of genotype-specific factors. Absolute qPCR was first used to expand the analysis of several genes previously identified via microarray analysis to be differentially expressed during SE induction, along with the inclusion of two nonresponsive genotypes. While this demonstrated a high level of repeatability within, and between, responsive and nonresponsive genotypes, it did not support our previous contention that an adaptive stress response plays a role in SE induction responsiveness, at least with respect to the candidate genes we analyzed. RNAseq analysis was then used to compare responsive and nonresponsive G6 primordial shoots during the somatic embryogenesis induction treatment. Although not analyzed in this study, this included samples of callus and embryonal masses previously generated from G6 explants. In addition to revealing a large number of differentially expressed genes, de novo assembly of unmapped reads was used to generate over 25,000 contigs that potentially represent previously unidentified transcripts. This included a MADS-domain gene that was found to be the most highly differentially expressed gene within responsive shoot explants during the first seven days of the induction treatment.
[Mh] Termos MeSH primário: Regulação da Expressão Gênica de Plantas
Picea/genética
Sementes/metabolismo
[Mh] Termos MeSH secundário: Adaptação Fisiológica
Genes de Plantas
Picea/embriologia
Picea/fisiologia
Brotos de Planta/metabolismo
Análise de Sequência de RNA
Estresse Fisiológico
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171026
[Lr] Data última revisão:
171026
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171003
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0185015


  7 / 1710 MEDLINE  
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[PMID]:28837647
[Au] Autor:Carlsson J; Svennerstam H; Moritz T; Egertsdotter U; Ganeteg U
[Ad] Endereço:Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.
[Ti] Título:Nitrogen uptake and assimilation in proliferating embryogenic cultures of Norway spruce-Investigating the specific role of glutamine.
[So] Source:PLoS One;12(8):e0181785, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Somatic embryogenesis is an in vitro system employed for plant propagation and the study of embryo development. Nitrogen is essential for plant growth and development and, hence, the production of healthy embryos during somatic embryogenesis. Glutamine has been shown to increase plant biomass in many in vitro applications, including somatic embryogenesis. However, several aspects of nitrogen nutrition during somatic embryogenesis remain unclear. Therefore, we investigated the uptake and assimilation of nitrogen in Norway spruce pro-embryogenic masses to elucidate some of these aspects. In our study, addition of glutamine had a more positive effect on growth than inorganic nitrogen. The nitrogen uptake appeared to be regulated, with a strong preference for glutamine; 67% of the assimilated nitrogen in the free amino acid pool originated from glutamine-nitrogen. Glutamine addition also relieved the apparently limited metabolism (as evidenced by the low concentration of free amino acids) of pro-embryogenic masses grown on inorganic nitrogen only. The unusually high alanine concentration in the presence of glutamine, suggests that alanine biosynthesis was involved in alleviating these constraints. These findings inspire further studies of nitrogen nutrition during the somatic embryogenesis process; identifying the mechanism(s) that govern glutamine enhancement of pro-embryogenic masses growth is especially important in this regard.
[Mh] Termos MeSH primário: Glutamina/metabolismo
Nitrogênio/metabolismo
Picea/metabolismo
Sementes/metabolismo
[Mh] Termos MeSH secundário: Aminoácidos/metabolismo
Amônia/metabolismo
Biomassa
Linhagem Celular
Picea/embriologia
Sementes/crescimento & desenvolvimento
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Amino Acids); 0RH81L854J (Glutamine); 7664-41-7 (Ammonia); N762921K75 (Nitrogen)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:171019
[Lr] Data última revisão:
171019
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170825
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0181785


  8 / 1710 MEDLINE  
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[PMID]:28676323
[Au] Autor:Jakobsson J; Henze MJ; Svensson GP; Lind O; Anderbrant O
[Ad] Endereço:Department of Biology, Lund University, Sweden. Electronic address: johan.jakobsson@biol.lu.se.
[Ti] Título:Visual cues of oviposition sites and spectral sensitivity of Cydia strobilella L.
[So] Source:J Insect Physiol;101:161-168, 2017 Aug.
[Is] ISSN:1879-1611
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:We investigated whether the spruce seed moth (Cydia strobilella L., Tortricidae: Grapholitini), an important pest in seed orchards of Norway spruce (Picea abies (L.) Karst.), can make use of the spectral properties of its host when searching for flowers to oviposit on. Spectral measurements showed that the flowers, and the cones they develop into, differ from a background of P. abies needles by a higher reflectance of long wavelengths. These differences increase as the flowers develop into mature cones. Electroretinograms (ERGs) in combination with spectral adaptation suggest that C. strobilella has at least three spectral types of photoreceptor; an abundant green-sensitive receptor with maximal sensitivity at wavelength λ =526nm, a blue-sensitive receptor with λ =436nm, and an ultraviolet-sensitive receptor with λ =352nm. Based on our spectral measurements and the receptor properties inferred from the ERGs, we calculated that open flowers, which are suitable oviposition sites, provide detectable achromatic, but almost no chromatic contrasts to the background of needles. In field trials using traps of different spectral properties with or without a female sex pheromone lure, only pheromone-baited traps caught moths. Catches in baited traps were not correlated with the visual contrast of the traps against the background. Thus, visual contrast is probably not the primary cue for finding open host flowers, but it could potentially complement olfaction as a secondary cue, since traps with certain spectral properties caught significantly more moths than others.
[Mh] Termos MeSH primário: Mariposas/fisiologia
Oviposição
Células Fotorreceptoras de Invertebrados/fisiologia
Percepção Visual
[Mh] Termos MeSH secundário: Animais
Sinais (Psicologia)
Feminino
Flores
Masculino
Células Fotorreceptoras de Invertebrados/classificação
Picea
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170928
[Lr] Data última revisão:
170928
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170706
[St] Status:MEDLINE


  9 / 1710 MEDLINE  
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[PMID]:28590734
[Au] Autor:Moraux T; Dumarçay S; Gérardin P; Gérardin-Charbonnier C
[Ad] Endereço:Laboratoire d'Études et de Recherche sur le Matériau Bois, EA4370 USC INRA, Université de Lorraine, Faculté des Sciences et Technologies , Boulevard des Aiguillettes, 54506 VandÅ“uvre-lès-Nancy, France.
[Ti] Título:Derivatives of the Lignan 7'-Hydroxymatairesinol with Antioxidant Properties and Enhanced Lipophilicity.
[So] Source:J Nat Prod;80(6):1783-1790, 2017 Jun 23.
[Is] ISSN:1520-6025
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The lignan 7'-hydroxymatairesinol (1), extracted from the knotwoods of fir (Abies alba), spruce (Picea abies), and Douglas fir (Pseudotsuga menziesii), exhibited unexpected reactivity when esterification reactions were attempted on the hydroxy group at position C-7'. To circumvent the rapid intramolecular cyclization procedure, leading quantitatively to the lignan conidendrin (7), a simple strategy for 7'-esterification of 1 under mild conditions (three steps, up to 80% overall yield) was developed. Compared to hydroxymatairesinol (1) (log K' = 1.49), the derivatives (2-5) had increased lipophilicity with log K' > 3.1, as determined by a UHPLC method. Compounds 1-5 exhibited potent antioxidant properties in the same range as the standards ascorbic acid and α-tocopherol (IC = 20-25 µM) and higher than that of BHT using a DPPH radical-scavenging assay.
[Mh] Termos MeSH primário: Antioxidantes/química
Antioxidantes/farmacologia
Lignanas/química
Lignanas/farmacologia
Picea/química
Pinus/química
Tetra-Hidronaftalenos/química
Tetra-Hidronaftalenos/farmacologia
[Mh] Termos MeSH secundário: Compostos de Bifenilo/farmacologia
Estrutura Molecular
Ressonância Magnética Nuclear Biomolecular
Picratos/farmacologia
Estereoisomerismo
alfa-Tocoferol
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Antioxidants); 0 (Biphenyl Compounds); 0 (Lignans); 0 (Picrates); 0 (Tetrahydronaphthalenes); 0 (hydroxymatairesinol); 518-55-8 (conidendrin); DFD3H4VGDH (1,1-diphenyl-2-picrylhydrazyl); H4N855PNZ1 (alpha-Tocopherol)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:170830
[Lr] Data última revisão:
170830
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170608
[St] Status:MEDLINE
[do] DOI:10.1021/acs.jnatprod.6b01124


  10 / 1710 MEDLINE  
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[PMID]:28486552
[Au] Autor:Li Q; Deng C; Xia Y; Kong L; Zhang H; Zhang S; Wang J
[Ad] Endereço:Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
[Ti] Título:Identification of novel miRNAs and miRNA expression profiling in embryogenic tissues of Picea balfouriana treated by 6-benzylaminopurine.
[So] Source:PLoS One;12(5):e0176112, 2017.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Here, we compared miRNA expression profiles in embryonic cell cultures of the conifer Picea balfouriana following application of the synthetic cytokinin 6-benzylaminopurine (6-BAP). We used next-generation sequencing to analyze three libraries of small RNAs from the treated embryogenic cell cultures and generated 24,000,000 raw reads from each of the libraries. Over 70 differentially regulated micro RNA (miRNA) families (≥2 fold change in expression) were identified between pairs of treatments. A quantitative analysis showed that miR3633 and miR1026 were upregulated in tissues with the highest embryogenic ability. These two miRNAs were predicted to target genes encoding receptor-like protein kinase and GAMYB transcription factors, respectively. In one library, miR1160, miR5638, miR1315, and miR5225 were downregulated. These four miRNAs were predicted to target genes encoding APETALA2, calmodulin-binding protein, and calcium-dependent protein kinase transcription factors. The expression patterns of the miRNAs and their targets were negatively correlated. Approximately 181 potentially novel P. balfouriana miRNAs were predicted from the three libraries, and seven were validated during the quantitative analysis. This study is the first report of differential miRNA regulation in tissues treated with 6-BAP during somatic embryogenesis. The differentially expressed miRNAs will be of value for investigating the mechanisms of embryogenic processes that are responsive to 6-BAP in P. balfouriana.
[Mh] Termos MeSH primário: Compostos de Benzil/farmacologia
Perfilação da Expressão Gênica
MicroRNAs/genética
Picea/embriologia
Purinas/farmacologia
Sementes/genética
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Benzyl Compounds); 0 (MicroRNAs); 0 (Purines); KXG6A989PS (benzylaminopurine)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:170915
[Lr] Data última revisão:
170915
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170510
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0176112



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