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[PMID]:29367480
[Au] Autor:Mingyai S; Srikaeo K; Kettawan A; Singanusong R; Nakagawa K; Kimura F; Ito J
[Ad] Endereço:Department of Agro-Industry, Faculty of Agriculture, Natural Resources and Environment, Naresuan University.
[Ti] Título:Effects of Extraction Methods on Phytochemicals of Rice Bran Oils Produced from Colored Rice.
[So] Source:J Oleo Sci;67(2):135-142, 2018 Feb 01.
[Is] ISSN:1347-3352
[Cp] País de publicação:Japan
[La] Idioma:eng
[Ab] Resumo:Rice bran oil (RBO) especially from colored rice is rich in phytochemicals and has become popular in food, cosmetic, nutraceutical and pharmaceutical applications owing to its offering health benefits. This study determined the contents of phytochemicals including oryzanols, phytosterols, tocopherols (Toc) and tocotrienols (T3) in RBOs extracted using different methods namely cold-press extraction (CPE), solvent extraction (SE) and supercritical CO extraction (SC-CO ). Two colored rice, Red Jasmine rice (RJM, red rice) and Hom-nin rice (HN, black rice), were studied in comparison with the popular Thai fragrant rice Khao Dawk Mali 105 (KDML 105, white rice). RBOs were found to be the rich source of oryzanols, phytosterols, Toc and T3. Rice varieties had a greater effect on the phytochemicals concentrations than extraction methods. HN rice showed the significantly highest concentration of all phytochemicals, followed by RJM and KDML 105 rice, indicating that colored rice contained high concentration of phytochemicals in the oil than non-colored rice. The RBO samples extracted by the CPE method had a greater concentration of the phytochemicals than those extracted by the SC-CO and SE methods, respectively. In terms of phytochemical contents, HN rice extracted using CPE method was found to be the best.
[Mh] Termos MeSH primário: Extração Líquido-Líquido/métodos
Oryza/química
Compostos Fitoquímicos/isolamento & purificação
Óleo de Farelo de Arroz/análise
[Mh] Termos MeSH secundário: Fenilpropionatos/análise
Fenilpropionatos/isolamento & purificação
Compostos Fitoquímicos/análise
Fitosteróis/análise
Fitosteróis/isolamento & purificação
Tocoferóis/análise
Tocoferóis/isolamento & purificação
Tocotrienóis/análise
Tocotrienóis/isolamento & purificação
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Phenylpropionates); 0 (Phytochemicals); 0 (Phytosterols); 0 (Tocotrienols); LZO6K1506A (Rice Bran Oil); R0ZB2556P8 (Tocopherols); SST9XCL51M (gamma-oryzanol)
[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:180126
[St] Status:MEDLINE
[do] DOI:10.5650/jos.ess17122


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[PMID]:29367479
[Au] Autor:Pornputtapitak W; Pantakitcharoenkul J; Panpakdee R; Teeranachaideekul V; Sinchaipanid N
[Ad] Endereço:Department of Chemical Engineering, Faculty of Engineering, Mahidol University.
[Ti] Título:Development of γ-Oryzanol Rich Extract from Leum Pua Glutinous Rice Bran Loaded Nanostructured Lipid Carriers for Topical Delivery.
[So] Source:J Oleo Sci;67(2):125-133, 2018 Feb 01.
[Is] ISSN:1347-3352
[Cp] País de publicação:Japan
[La] Idioma:eng
[Ab] Resumo:Leum Pua is native Thai glutinous rice that contains antioxidants higher than white rice and other colored rice. One of the major antioxidants in rice brans is γ-oryzanol (GO). In this study, Leum Pua glutinous rice bran was extracted by different solvents. Oleic acid (~40 g/100 g extract), linoleic acid (~30 g/100 g extract), and palmitic acid (~20 g/100 g extract) were found to be major lipid components in the extracts. Methanol extract showed less variety of lipid components compared to the others. However, hexane extract showed the highest percent of γ-oryzanol compared to other solvents. Therefore, the hexane extract was selected to prepare nanostructured lipid carriers (NLC). The prepared NLC had small particles in the size range of 142.9 ± 0.4 nm for extract-loaded NLC and 137.1 ± 0.5 nm for GO-loaded NLC with narrow size distribution (PI < 0.1) in both formulations. The release profile of extract-loaded NLC formulation was slightly higher than GO-loaded NLC formulation. However, they did not follow the Higuchi model because of small amounts of γ-oryzanol loaded in NLC particles.
[Mh] Termos MeSH primário: Antioxidantes/isolamento & purificação
Portadores de Fármacos
Nanoestruturas
Oryza/química
Fenilpropionatos/isolamento & purificação
Extratos Vegetais/análise
Extratos Vegetais/isolamento & purificação
[Mh] Termos MeSH secundário: Hexanos
Ácido Linoleico/análise
Ácido Oleico/análise
Ácido Palmítico/análise
Tamanho da Partícula
Fenilpropionatos/análise
Solventes
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Antioxidants); 0 (Drug Carriers); 0 (Hexanes); 0 (Phenylpropionates); 0 (Plant Extracts); 0 (Solvents); 2UMI9U37CP (Oleic Acid); 2V16EO95H1 (Palmitic Acid); 9KJL21T0QJ (Linoleic Acid); SST9XCL51M (gamma-oryzanol)
[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:180126
[St] Status:MEDLINE
[do] DOI:10.5650/jos.ess17113


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[PMID]:29331375
[Au] Autor:Ma L; Wang Q; Yuan M; Zou T; Yin P; Wang S
[Ad] Endereço:National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
[Ti] Título:Xanthomonas TAL effectors hijack host basal transcription factor IIA α and γ subunits for invasion.
[So] Source:Biochem Biophys Res Commun;496(2):608-613, 2018 02 05.
[Is] ISSN:1090-2104
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:The Xanthomonas genus includes Gram-negative plant-pathogenic bacteria, which infect a broad range of crops and wild plant species, cause symptoms with leaf blights, streaks, spots, stripes, necrosis, wilt, cankers and gummosis on leaves, stems and fruits in a wide variety of plants via injecting their effector proteins into the host cell during infection. Among these virulent effectors, transcription activator-like effectors (TALEs) interact with the γ subunit of host transcription factor IIA (TFIIAγ) to activate the transcription of host disease susceptibility genes. Functional TFIIA is a ternary complex comprising α, ß and γ subunits. However, whether TALEs recruit TFIIAα, TFIIAß, or both remains unknown. The underlying molecular mechanisms by which TALEs mediate host susceptibility gene activation require full elucidation. Here, we show that TALEs interact with the α+γ binary subcomplex but not the α+ß+γ ternary complex of rice TFIIA (holo-OsTFIIA). The transcription factor binding (TFB) regions of TALEs, which are highly conserved in Xanthomonas species, have a dominant role in these interactions. Furthermore, the interaction between TALEs and the α+γ complex exhibits robust DNA binding activity in vitro. These results collectively demonstrate that TALE-carrying pathogens hijack the host basal transcription factors TFIIAα and TFIIAγ, but not TFIIAß, to enhance host susceptibility during pathogen infection. The uncovered mechanism widens new insights on host-microbe interaction and provide an applicable strategy to breed high-resistance crop varieties.
[Mh] Termos MeSH primário: Interações Hospedeiro-Patógeno
Oryza/microbiologia
Doenças das Plantas/microbiologia
Proteínas de Plantas/metabolismo
Efetores Semelhantes a Ativadores de Transcrição/metabolismo
Fator de Transcrição TFIIA/metabolismo
Xanthomonas/fisiologia
[Mh] Termos MeSH secundário: Resistência à Doença
Regulação da Expressão Gênica de Plantas
Genes de Plantas
Oryza/genética
Oryza/metabolismo
Doenças das Plantas/genética
Ligação Proteica
Subunidades Proteicas/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Plant Proteins); 0 (Protein Subunits); 0 (Transcription Activator-Like Effectors); 0 (Transcription Factor TFIIA)
[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:180115
[St] Status:MEDLINE


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[PMID]:29202710
[Au] Autor:Parvathaneni RK; DeLeo VL; Spiekerman JJ; Chakraborty D; Devos KM
[Ad] Endereço:Institute of Plant Breeding, Genetics and Genomics, University of Georgia, 30602, Athens, Georgia, United States.
[Ti] Título:Parallel loss of introns in the ABCB1 gene in angiosperms.
[So] Source:BMC Evol Biol;17(1):238, 2017 Dec 04.
[Is] ISSN:1471-2148
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: The presence of non-coding introns is a characteristic feature of most eukaryotic genes. While the size of the introns, number of introns per gene and the number of intron-containing genes can vary greatly between sequenced eukaryotic genomes, the structure of a gene with reference to intron presence and positions is typically conserved in closely related species. Unexpectedly, the ABCB1 (ATP-Binding Cassette Subfamily B Member 1) gene which encodes a P-glycoprotein and underlies dwarfing traits in maize (br2), sorghum (dw3) and pearl millet (d2) displayed considerable variation in intron composition. RESULTS: An analysis of the ABCB1 gene structure in 80 angiosperms revealed that the number of introns ranged from one to nine. All introns in ABCB1 underwent either a one-time loss (single loss in one lineage/species) or multiple independent losses (parallel loss in two or more lineages/species) with the majority of losses occurring within the grass family. In contrast, the structure of the closest homolog to ABCB1, ABCB19, remained constant in the majority of angiosperms analyzed. Using known phylogenetic relationships within the grasses, we determined the ancestral branch-points where the losses occurred. Intron 7, the longest intron, was lost in only a single species, Mimulus guttatus, following duplication of ABCB1. Semiquantitative PCR showed that the M. guttatus ABCB1 gene copy without intron 7 had significantly lower transcript levels than the gene copy with intron 7. We further demonstrated that intron 7 carried two motifs that were highly conserved across the monocot-dicot divide. CONCLUSIONS: The ABCB1 gene structure is highly dynamic, while the structure of ABCB19 remained largely conserved through evolution. Precise removal of introns, preferential removal of smaller introns and presence of at least 2 bp of microhomology flanking most introns indicated that intron loss may have predominantly occurred through non-homologous end-joining (NHEJ) repair of double strand breaks. Lack of microhomology in the exon upstream of lost phase I introns was likely due to release of the selective constraint on the penultimate base (3rd base in codon) of the terminal codon by the splicing machinery. In addition to size, the presence of regulatory motifs will make introns recalcitrant to loss.
[Mh] Termos MeSH primário: Genes de Plantas
Íntrons/genética
Magnoliopsida/genética
Proteínas de Plantas/genética
[Mh] Termos MeSH secundário: Arabidopsis/genética
Sequência de Bases
Sequência Conservada/genética
DNA Complementar/genética
Evolução Molecular
Regulação da Expressão Gênica de Plantas
Mimulus/genética
Motivos de Nucleotídeos/genética
Oryza/genética
Filogenia
Reação em Cadeia da Polimerase
Polimorfismo Genético
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
Reprodutibilidade dos Testes
Análise de Sequência de DNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (DNA, Complementary); 0 (Plant Proteins); 0 (RNA, Messenger)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171206
[St] Status:MEDLINE
[do] DOI:10.1186/s12862-017-1077-x


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[PMID]:28938141
[Au] Autor:Ye X; Li H; Zhang L; Chai R; Tu R; Gao H
[Ad] Endereço:Anhui Province Key Laboratory of Farmland Ecological Conservation and Pollution Prevention, School of Resources and Environment, Anhui Agricultural University, 130 Changjiang West Road, Hefei 230036, China.
[Ti] Título:Amendment damages the function of continuous flooding in decreasing Cd and Pb uptake by rice in acid paddy soil.
[So] Source:Ecotoxicol Environ Saf;147:708-714, 2018 Jan.
[Is] ISSN:1090-2414
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:Combinations of remediation technologies are needed to solve the problem of soil contamination in paddy rice, due to multiple potential toxic elements (PTEs). Two potential mitigation methods, water management and in-situ remediation by soil amendment, have been widely used in treatment of PTE-polluted paddy soil. However, the interactive relationship between soil amendment and water management, and its influence on the accumulation of PTEs in rice are poorly understood. Greenhouse pot experiments were conducted to examine the effects of phosphate amendment on Cd and Pb availability in soil and their influence on Cd and Pb uptake into rice, on Fe and P availability in soil, and on the alteration of Fe amount and compartment on root surface among different water management strategies. Results indicated that Cd and Pb content in the shoot and grain were significantly affected by the different water management strategies in nonamended soils, and followed the order: wetting irrigation > conventional irrigation > continuous flooding. The application of phosphate amendment significantly decreased the variations of Cd and Pb absorption in shoot and grain of rice among different water treatments. The reasons may be attributed to the enhancement of P availability and the decrease of Fe availability in soil, and the decreased variations of Fe /Fe content in root coating after the application of phosphate amendment. These results suggested that the simultaneous use of phosphate amendment and continuous flooding to immobilize Cd and Pb, especially in acid paddy soils, should be avoided.
[Mh] Termos MeSH primário: Irrigação Agrícola/métodos
Cádmio/análise
Recuperação e Remediação Ambiental/métodos
Chumbo/análise
Oryza/química
Poluentes do Solo/análise
Solo/química
[Mh] Termos MeSH secundário: Ácidos
China
Grãos Comestíveis/química
Poluição Ambiental/prevenção & controle
Concentração de Íons de Hidrogênio
Modelos Teóricos
Oryza/crescimento & desenvolvimento
Raízes de Plantas/química
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Acids); 0 (Soil); 0 (Soil Pollutants); 00BH33GNGH (Cadmium); 2P299V784P (Lead)
[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:170923
[St] Status:MEDLINE


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[PMID]:29264911
[Au] Autor:Mania M; Rebeniak M; Szynal T; Starska K; Wojciechowska-Mazurek M; Postupolski J
[Ad] Endereço:National Institute of Public Health-National Institute of Hygiene, Department of Food Safety, Warsaw, Poland
[Ti] Título:Exposure assessment of the population in Poland to the toxic effects of arsenic compounds present in rice and rice based products
[So] Source:Rocz Panstw Zakl Hig;68(4):339-346, 2017.
[Is] ISSN:0035-7715
[Cp] País de publicação:Poland
[La] Idioma:eng
[Ab] Resumo:Background: Rice is a staple food for many people in the world and an important ingredient for production of food for infants and young children. According to European Food Safety Authority (EFSA), cereals, primarily rice and rice products, are an important source of human exposure to inorganic arsenic, which has been classified by the International Agency for Research on Cancer (IARC) as group I carcinogen. Arsenic is present in rice and rice products mainly as an inorganic form being more toxic than organic compounds Objectives: The aim of the study was to determine the total and inorganic arsenic content in rice, rice-based products including food for infants and young children available on the market in Poland and thus to estimate consumer exposure to inorganic arsenic from these groups of foodstuffs Materials and Methods: A total of 62 samples of rice and rice products from trade, including a group of rice products for infants and young children, were tested. Contents of total and inorganic arsenic were determined by using hydride generation atomic absorption spectrometry (HGAAS), after dry mineralization of samples and reduction of arsenic to arsenic hydride with sodium borohydride. To extract the inorganic arsenic forms, the samples were subjected to hydrolysis in concentrated HCl and then reduced in the presence of hydrobromic acid and hydrazine sulphate after which triple chloroform extractions and triple 1M HCl re-extractions were performed. Exposure of different groups of populations (adults and children), was estimated in relation to the Benchmark Dose Lower Confidence Limit (BMDL05) as set by the Joint FAO/WHO Expert Committee on Food Additives (JECFA) that resulted in a 0.5% increase in lung cancer (3.0 µg/kg body weight (b.w.) per day) Results: Mean content of total and inorganic arsenic in investigated rice samples was 0.12 mg/kg (median: 0.09 mg/kg; 90th percentile 0.22 mg/kg) and 0.04 mg/kg (median: 0.03 mg/kg, 90th percentile 0.07 mg/kg). Brown rice was found to be more highly contaminated with both total and inorganic arsenic than white rice. Mean contamination of brown rice with total arsenic and inorganic arsenic was: 0.18 mg/kg (median: 0.12 mg/kg, 90th percentile: 0.32 mg/kg) and 0.05 mg/kg (median: 0.05 mg/kg, 90th percentile: 0.07 mg/kg). In turn for the white rice contamination was lower, mean total arsenic content: 0.10 mg/kg (median: 0.08 mg/kg, 90th percentile: 0.19 mg/kg) and mean inorganic arsenic: 0.03 mg/kg (median: 0.03 mg/kg, 90th percentile: 0.06 mg/kg). Contamination of rice-based products both total and inorganic arsenic was similar to those reported for rice, except rice wafers (mean: 0.24 mg/kg and 0.13 mg/kg). In the group of products for infants and young children obtained results were low ­ mean total arsenic content was 0.06 mg/kg and inorganic arsenic 0.02 mg/kg. The estimated average adult and children's exposure to inorganic arsenic with rice and rice products was less than 1% of the BMDL05. Intake of inorganic arsenic by 12-month-old infants with ricebased products intended for this group of population was at 6% BMDL05 Conclusions: Based on the obtained results, it was found that the content of total and inorganic arsenic in investigated samples of rice and rice products did not pose a health risk even though contamination levels in some individual samples were significant
[Mh] Termos MeSH primário: Arsenicais/análise
Carcinógenos/análise
Exposição Dietética/análise
Contaminação de Alimentos/análise
Oryza/química
[Mh] Termos MeSH secundário: Análise de Alimentos
Inocuidade dos Alimentos
Seres Humanos
Polônia
Medição de Risco
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Arsenicals); 0 (Carcinogens)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171222
[St] Status:MEDLINE


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[PMID]:29194020
[Au] Autor:Zhang J; Yuan J; Zhang WX; Tu F; Jiang Y; Sun CZ
[Ad] Endereço:a Department of Life Science and Food Engineering/Key Laboratory of Fermentation Resource and Application in Sichuan/Department of Library , Yibin University , Yibin , Sichuan , China.
[Ti] Título:Anaerobic detoxification fermentation by Rhodospirillum rubrum for rice straw as feed with moderate pretreatment.
[So] Source:Prep Biochem Biotechnol;48(1):75-83, 2018 Jan 02.
[Is] ISSN:1532-2297
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:A novel and effective process was put forward for converting rice straw into feed by combining diluted acid hydrolysis and ammonization with Rhodospirillum rubrum fermentation. After pretreatment with dilute sulfuric or phosphoric acid (1%, w/w) at 100°C, materials were subjected to fermentation under several gases (N , CO , and air) and different light intensities in a 2-L fermentor. The key indexes of feed for fermented materials were estimated and several toxic substances were investigated during the fermentation. Following sulfuric acid treatment, the true protein of rice straw increased from 29 to 143 g kg and the crude fiber decreased from 359 to 136 g kg after fermentation at 0.3 L min L of N flow and a light intensity of 3400 lux; and following phosphoric acid treatment, the true protein increased by 286% and the crude fiber decreased by 52% after fermentation at 0.4 L min L of N flow and a light intensity of 3000 lux. Other key contents were also improved for use as feed, and some toxic substances (i.e., furfural, hydroxymethylfurfural, acetic acid, phenol, cresol) produced by the pretreatments could be removed at low levels during the fermentations.
[Mh] Termos MeSH primário: Ração Animal/análise
Oryza/metabolismo
Rhodospirillum rubrum/metabolismo
[Mh] Termos MeSH secundário: Ração Animal/toxicidade
Fermentação
Hidrólise
Microbiologia Industrial
Luz
Ácidos Fosfóricos/metabolismo
Ácidos Sulfúricos/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Phosphoric Acids); 0 (Sulfuric Acids); E4GA8884NN (phosphoric acid); O40UQP6WCF (sulfuric acid)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171202
[St] Status:MEDLINE
[do] DOI:10.1080/10826068.2017.1405023


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[PMID]:28985652
[Au] Autor:Zhang BL; Ouyang YN; Xu JY; Liu K
[Ad] Endereço:Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou 434023, China; Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou 434023, China. Electronic address: zhangbl833@hotmail.com.
[Ti] Título:Cadmium remobilization from shoot to grain is related to pH of vascular bundle in rice.
[So] Source:Ecotoxicol Environ Saf;147:913-918, 2018 Jan.
[Is] ISSN:1090-2414
[Cp] País de publicação:Netherlands
[La] Idioma:eng
[Ab] Resumo:The remobilization of cadmium (Cd) from shoots to grain is the key process to determine the Cd accumulation in grain. The apoplastic pH of plants is an important factor and signal in influencing on plant responding to environmental variation and inorganic elements uptake. It is proposed that pH of rice plants responds and influences on Cd remobilization from shoots to grain when rice is exposed to Cd stress. The results of hydroponic experiment showed that: pH of the rice leaf vascular bundles among 3 cultivars was almost increased, pH value of 1 cultivar was slightly increasing when rice plants were treated with Cd. The decrease degree of H concentration in leaf vascular bundles was different among cultivars. The cultivar with higher decreasing in H concentration, showed higher Cd transfer efficiency from shoots to grain. The H concentration of leaf vascular bundles under normal condition was negatively correlated to cadmium accumulation in leaf. Moreover, pH change was related to Cd accumulation in shots and remobilization from shoots to grain. Uncovering the role of pH response is a key component for the understanding Cd uptake and remobilization mechanism for rice production.
[Mh] Termos MeSH primário: Cádmio/metabolismo
Grãos Comestíveis/metabolismo
Oryza/metabolismo
Brotos de Planta/metabolismo
Feixe Vascular de Plantas/química
Poluentes do Solo/metabolismo
[Mh] Termos MeSH secundário: Transporte Biológico
Cádmio/análise
Grãos Comestíveis/química
Concentração de Íons de Hidrogênio
Hidroponia
Modelos Teóricos
Oryza/química
Folhas de Planta/química
Brotos de Planta/química
Poluentes do Solo/análise
Especificidade da Espécie
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Soil Pollutants); 00BH33GNGH (Cadmium)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171008
[St] Status:MEDLINE


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[PMID]:29178822
[Au] Autor:Bowman MJ; Pulman JA; Liu TL; Childs KL
[Ad] Endereço:Department of Plant Biology, Michigan State University, 612 Wilson Rd, Room 166, East Lansing, MI, 48824, USA.
[Ti] Título:A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa.
[So] Source:BMC Bioinformatics;18(1):522, 2017 Nov 25.
[Is] ISSN:1471-2105
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:BACKGROUND: Accurate structural annotation depends on well-trained gene prediction programs. Training data for gene prediction programs are often chosen randomly from a subset of high-quality genes that ideally represent the variation found within a genome. One aspect of gene variation is GC content, which differs across species and is bimodal in grass genomes. When gene prediction programs are trained on a subset of grass genes with random GC content, they are effectively being trained on two classes of genes at once, and this can be expected to result in poor results when genes are predicted in new genome sequences. RESULTS: We find that gene prediction programs trained on grass genes with random GC content do not completely predict all grass genes with extreme GC content. We show that gene prediction programs that are trained with grass genes with high or low GC content can make both better and unique gene predictions compared to gene prediction programs that are trained on genes with random GC content. By separately training gene prediction programs with genes from multiple GC ranges and using the programs within the MAKER genome annotation pipeline, we were able to improve the annotation of the Oryza sativa genome compared to using the standard MAKER annotation protocol. Gene structure was improved in over 13% of genes, and 651 novel genes were predicted by the GC-specific MAKER protocol. CONCLUSIONS: We present a new GC-specific MAKER annotation protocol to predict new and improved gene models and assess the biological significance of this method in Oryza sativa. We expect that this protocol will also be beneficial for gene prediction in any organism with bimodal or other unusual gene GC content.
[Mh] Termos MeSH primário: Genoma de Planta
Anotação de Sequência Molecular/métodos
Oryza/genética
[Mh] Termos MeSH secundário: Composição de Bases
Cadeias de Markov
RNA de Plantas/química
RNA de Plantas/isolamento & purificação
RNA de Plantas/metabolismo
Ribossomos/metabolismo
Análise de Sequência de RNA
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (RNA, Plant)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180306
[Lr] Data última revisão:
180306
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171128
[St] Status:MEDLINE
[do] DOI:10.1186/s12859-017-1942-z


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[PMID]:29295978
[Au] Autor:Jung B; Park J; Kim N; Li T; Kim S; Bartley LE; Kim J; Kim I; Kang Y; Yun K; Choi Y; Lee HH; Ji S; Lee KS; Kim BY; Shon JC; Kim WC; Liu KH; Yoon D; Kim S; Seo YS; Lee J
[Ad] Endereço:Department of Applied Biology, Dong-A University, Busan, 49315, Korea.
[Ti] Título:Cooperative interactions between seed-borne bacterial and air-borne fungal pathogens on rice.
[So] Source:Nat Commun;9(1):31, 2018 01 02.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Bacterial-fungal interactions are widely found in distinct environments and contribute to ecosystem processes. Previous studies of these interactions have mostly been performed in soil, and only limited studies of aerial plant tissues have been conducted. Here we show that a seed-borne plant pathogenic bacterium, Burkholderia glumae (Bg), and an air-borne plant pathogenic fungus, Fusarium graminearum (Fg), interact to promote bacterial survival, bacterial and fungal dispersal, and disease progression on rice plants, despite the production of antifungal toxoflavin by Bg. We perform assays of toxoflavin sensitivity, RNA-seq analyses, lipid staining and measures of triacylglyceride content to show that triacylglycerides containing linolenic acid mediate resistance to reactive oxygen species that are generated in response to toxoflavin in Fg. As a result, Bg is able to physically attach to Fg to achieve rapid and expansive dispersal to enhance disease severity.
[Mh] Termos MeSH primário: Microbiologia do Ar
Burkholderia/fisiologia
Fusarium/fisiologia
Oryza/microbiologia
Sementes/microbiologia
[Mh] Termos MeSH secundário: Burkholderia/metabolismo
Farmacorresistência Fúngica/efeitos dos fármacos
Fusarium/classificação
Fusarium/genética
Perfilação da Expressão Gênica
Regulação Fúngica da Expressão Gênica
Interações Hospedeiro-Patógeno
Interações Microbianas
Mutação
Filogenia
Doenças das Plantas/microbiologia
Pirimidinonas/metabolismo
Pirimidinonas/farmacologia
Triazinas/metabolismo
Triazinas/farmacologia
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Pyrimidinones); 0 (Triazines); 5N5YI4IP1P (toxoflavin)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180104
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02430-2



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