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  1 / 3101 MEDLINE  
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PMID:29054811
Autor:Silva SR; Gibson R; Adamec L; Domínguez Y; Miranda VFO
Endereço:Universidade Estadual Paulista (Unesp), Instituto de Biociências, Botucatu, São Paulo, Brazil; Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, Departamento de Biologia Aplicada à Agropecuária, São Paulo, Brazil.. Electronic address: saura.silva@gma
Título:Molecular phylogeny of bladderworts: A wide approach of Utricularia (Lentibulariaceae) species relationships based on six plastidial and nuclear DNA sequences.
Fonte:Mol Phylogenet Evol; 118:244-264, 2018 Jan.
ISSN:1095-9513
País de publicação:United States
Idioma:eng
Resumo:The carnivorous plant genus Utricularia L. (bladderwort) comprises about 240 species distributed worldwide and is traditionally classified into two subgenera (Polypompholyx and Utricularia) and 35 sections, based mainly on general and trap morphology. It is one out of the largest carnivorous genera, representing ca. 30% of all carnivorous plant species, and is also the most widely distributed. According to previous phylogenetic studies, most infrageneric sections are monophyletic, but there are several incongruences considering their relationships and also the dissenting position of some species as a result of a too few (mostly one or two) molecular markers analyzed. Thus, here we present a multilocus phylogeny for Utricularia species with a wide taxonomic sampling (78 species and 115 accessions) based on six plastid (rbcL, matK, rpl20-rps12, rps16, trnL-F) and nuclear DNA (ITS region) sequences. The aim is to reconstruct a well-resolved tree to propose evolutionary and biogeographic hypotheses for the radiation of lineages with inferences about the divergence times of clades using a molecular clock approach.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (DNA, Plant); 0 (Plant Proteins); EC 4.1.1.39 (RbcL protein, plastid); EC 4.1.1.39 (Ribulose-Bisphosphate Carboxylase)


  2 / 3101 MEDLINE  
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PMID:29217555
Autor:Yeates TO; Wheatley NM
Endereço:University of California Los Angeles (UCLA) Department of Chemistry and Biochemistry and UCLA-DOE Institute of Genomics and Proteomics, Los Angeles, CA, USA. yeates@mbi.ucla.edu nwheatley@mbi.ucla.edu.
Título:Putting the RuBisCO pieces together.
Fonte:Science; 358(6368):1253-1254, 2017 12 08.
ISSN:1095-9203
País de publicação:United States
Idioma:eng
Tipo de publicação: JOURNAL ARTICLE; COMMENT
Nome de substância:EC 4.1.1.39 (Ribulose-Bisphosphate Carboxylase)


  3 / 3101 MEDLINE  
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PMID:28938114
Autor:Freeman Rosenzweig ES; Xu B; Kuhn Cuellar L; Martinez-Sanchez A; Schaffer M; Strauss M; Cartwright HN; Ronceray P; Plitzko JM; Förster F; Wingreen NS; Engel BD; Mackinder LCM; Jonikas MC
Endereço:Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
Título:The Eukaryotic CO -Concentrating Organelle Is Liquid-like and Exhibits Dynamic Reorganization.
Fonte:Cell; 171(1):148-162.e19, 2017 Sep 21.
ISSN:1097-4172
País de publicação:United States
Idioma:eng
Resumo:Approximately 30%-40% of global CO fixation occurs inside a non-membrane-bound organelle called the pyrenoid, which is found within the chloroplasts of most eukaryotic algae. The pyrenoid matrix is densely packed with the CO -fixing enzyme Rubisco and is thought to be a crystalline or amorphous solid. Here, we show that the pyrenoid matrix of the unicellular alga Chlamydomonas reinhardtii is not crystalline but behaves as a liquid that dissolves and condenses during cell division. Furthermore, we show that new pyrenoids are formed both by fission and de novo assembly. Our modeling predicts the existence of a "magic number" effect associated with special, highly stable heterocomplexes that influences phase separation in liquid-like organelles. This view of the pyrenoid matrix as a phase-separated compartment provides a paradigm for understanding its structure, biogenesis, and regulation. More broadly, our findings expand our understanding of the principles that govern the architecture and inheritance of liquid-like organelles.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Algal Proteins); 142M471B3J (Carbon Dioxide); EC 4.1.1.39 (Ribulose-Bisphosphate Carboxylase)


  4 / 3101 MEDLINE  
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PMID:28938113
Autor:Mackinder LCM; Chen C; Leib RD; Patena W; Blum SR; Rodman M; Ramundo S; Adams CM; Jonikas MC
Endereço:Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA.
Título:A Spatial Interactome Reveals the Protein Organization of the Algal CO -Concentrating Mechanism.
Fonte:Cell; 171(1):133-147.e14, 2017 Sep 21.
ISSN:1097-4172
País de publicação:United States
Idioma:eng
Resumo:Approximately one-third of global CO fixation is performed by eukaryotic algae. Nearly all algae enhance their carbon assimilation by operating a CO -concentrating mechanism (CCM) built around an organelle called the pyrenoid, whose protein composition is largely unknown. Here, we developed tools in the model alga Chlamydomonas reinhardtii to determine the localizations of 135 candidate CCM proteins and physical interactors of 38 of these proteins. Our data reveal the identity of 89 pyrenoid proteins, including Rubisco-interacting proteins, photosystem I assembly factor candidates, and inorganic carbon flux components. We identify three previously undescribed protein layers of the pyrenoid: a plate-like layer, a mesh layer, and a punctate layer. We find that the carbonic anhydrase CAH6 is in the flagella, not in the stroma that surrounds the pyrenoid as in current models. These results provide an overview of proteins operating in the eukaryotic algal CCM, a key process that drives global carbon fixation.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Algal Proteins); 0 (Luminescent Proteins); 0 (Plant Proteins); 142M471B3J (Carbon Dioxide); EC 4.1.1.39 (Ribulose-Bisphosphate Carboxylase); EC 4.2.1.1 (Cah6 protein, Chlamydomonas reinhardtii); EC 4.2.1.1 (Carbonic Anhydrases)


  5 / 3101 MEDLINE  
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PMID:28859145
Autor:Hermida-Carrera C; Fares MA; Fernández Á; Gil-Pelegrín E; Kapralov MV; Mir A; Molins A; Peguero-Pina JJ; Rocha J; Sancho-Knapik D; Galmés J
Endereço:Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears-INAGEA, Palma, Balearic Islands, Spain.
Título:Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations.
Fonte:PLoS One; 12(8):e0183970, 2017.
ISSN:1932-6203
País de publicação:United States
Idioma:eng
Resumo:Phylogenetic analysis by maximum likelihood (PAML) has become the standard approach to study positive selection at the molecular level, but other methods may provide complementary ways to identify amino acid replacements associated with particular conditions. Here, we compare results of the decision tree (DT) model method with ones of PAML using the key photosynthetic enzyme RuBisCO as a model system to study molecular adaptation to particular ecological conditions in oaks (Quercus). We sequenced the chloroplast rbcL gene encoding RuBisCO large subunit in 158 Quercus species, covering about a third of the global genus diversity. It has been hypothesized that RuBisCO has evolved differentially depending on the environmental conditions and leaf traits governing internal gas diffusion patterns. Here, we show, using PAML, that amino acid replacements at the residue positions 95, 145, 251, 262 and 328 of the RuBisCO large subunit have been the subject of positive selection along particular Quercus lineages associated with the leaf traits and climate characteristics. In parallel, the DT model identified amino acid replacements at sites 95, 219, 262 and 328 being associated with the leaf traits and climate characteristics, exhibiting partial overlap with the results obtained using PAML.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:EC 4.1.1.39 (Ribulose-Bisphosphate Carboxylase)


  6 / 3101 MEDLINE  
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PMID:28813504
Autor:Hu S; Zhou B; Wang Y; Wang Y; Zhang X; Zhao Y; Zhao X; Tang X
Endereço:Department of Marine Ecology, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
Título:Effect of CO2-induced seawater acidification on growth, photosynthesis and inorganic carbon acquisition of the harmful bloom-forming marine microalga, Karenia mikimotoi.
Fonte:PLoS One; 12(8):e0183289, 2017.
ISSN:1932-6203
País de publicação:United States
Idioma:eng
Resumo:Karenia mikimotoi is a widespread, toxic and non-calcifying dinoflagellate, which can release and produce ichthyotoxins and hemolytic toxins affecting the food web within the area of its bloom. Shifts in the physiological characteristics of K. mikimotoi due to CO2-induced seawater acidification could alter the occurrence, severity and impacts of harmful algal blooms (HABs). Here, we investigated the effects of elevated pCO2 on the physiology of K. mikimotoi. Using semi-continuous cultures under controlled laboratory conditions, growth, photosynthesis and inorganic carbon acquisition were determined over 4-6 week incubations at ambient (390ppmv) and elevated pCO2 levels (1000 ppmv and 2000 ppmv). pH-drift and inhibitor-experiments suggested that K. mikimotoi was capable of acquiring HCO3-, and that the utilization of HCO3- was predominantly mediated by anion-exchange proteins, but that HCO3- dehydration catalyzed by external carbonic anhydrase (CAext) only played a minor role in K. mikimotoi. Even though down-regulated CO2 concentrating mechanisms (CCMs) and enhanced gross photosynthetic O2 evolution were observed under 1000 ppmv CO2 conditions, the saved energy did not stimulate growth of K. mikimotoi under 1000 ppmv CO2, probably due to the increased dark respiration. However, significantly higher growth and photosynthesis [in terms of photosynthetic oxygen evolution, effective quantum Yield (Yield), photosynthetic efficiency (α), light saturation point (Ek) and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activity] were observed under 2000 ppmv CO2 conditions. Furthermore, elevated pCO2 increased the photo-inhibition rate of photosystem II (ß) and non-photochemical quenching (NPQ) at high light. We suggest that the energy saved through the down-regulation of CCMs might lead to the additional light stress and photo-damage. Therefore, the response of this species to elevated CO2 conditions will be determined by more than regulation and efficiency of CCMs.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:142M471B3J (Carbon Dioxide); 7440-44-0 (Carbon); EC 4.1.1.39 (Ribulose-Bisphosphate Carboxylase); S88TT14065 (Oxygen)


  7 / 3101 MEDLINE  
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PMID:28803776
Autor:Bhat JY; Milicic G; Thieulin-Pardo G; Bracher A; Maxwell A; Ciniawsky S; Mueller-Cajar O; Engen JR; Hartl FU; Wendler P; Hayer-Hartl M
Endereço:Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
Título:Mechanism of Enzyme Repair by the AAA Chaperone Rubisco Activase.
Fonte:Mol Cell; 67(5):744-756.e6, 2017 Sep 07.
ISSN:1097-4164
País de publicação:United States
Idioma:eng
Resumo:How AAA+ chaperones conformationally remodel specific target proteins in an ATP-dependent manner is not well understood. Here, we investigated the mechanism of the AAA+ protein Rubisco activase (Rca) in metabolic repair of the photosynthetic enzyme Rubisco, a complex of eight large (RbcL) and eight small (RbcS) subunits containing eight catalytic sites. Rubisco is prone to inhibition by tight-binding sugar phosphates, whose removal is catalyzed by Rca. We engineered a stable Rca hexamer ring and analyzed its functional interaction with Rubisco. Hydrogen/deuterium exchange and chemical crosslinking showed that Rca structurally destabilizes elements of the Rubisco active site with remarkable selectivity. Cryo-electron microscopy revealed that Rca docks onto Rubisco over one active site at a time, positioning the C-terminal strand of RbcL, which stabilizes the catalytic center, for access to the Rca hexamer pore. The pulling force of Rca is fine-tuned to avoid global destabilization and allow for precise enzyme repair.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Bacterial Proteins); 0 (Cross-Linking Reagents); 0 (Molecular Chaperones); 0 (Plant Proteins); 0 (Protein Subunits); 0 (rca protein, plant); 8L70Q75FXE (Adenosine Triphosphate); EC 3.4.21.68 (Tissue Plasminogen Activator); EC 4.1.1.39 (Ribulose-Bisphosphate Carboxylase)


  8 / 3101 MEDLINE  
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PMID:28622375
Autor:An SM; Choi DH; Lee JH; Lee H; Noh JH
Endereço:Marine Ecosystem and Biological Research Center, Korea Institute of Ocean Science & Technology, Ansan, Republic of Korea.
Título:Identification of benthic diatoms isolated from the eastern tidal flats of the Yellow Sea: Comparison between morphological and molecular approaches.
Fonte:PLoS One; 12(6):e0179422, 2017.
ISSN:1932-6203
País de publicação:United States
Idioma:eng
Resumo:Benthic diatoms isolated from tidal flats in the west coast of Korea were identified through both traditional morphological method and molecular phylogenetic method for methodological comparison. For the molecular phylogenetic analyses, we sequenced the 18S rRNA and the ribulose bisphosphate carboxylase large subunit coding gene, rbcL. Further, the comparative analysis allowed for the assessment of the suitability as a genetic marker for identification of closely related benthic diatom species and as potential barcode gene. Based on the traditional morphological identification system, the 61 isolated strains were classified into 52 previously known taxa from 13 genera. However, 17 strains could not be classified as known species by morphological analyses, suggesting a hidden diversity of benthic diatoms. The Blast search on NCBI's Genebank indicated that the reference sequences for most of the species were absent for the benthic diatoms. Of the two genetic markers, the rbcL genes were more divergent than the 18S rRNA genes. Furthermore, a long branch attraction artefact was found in the 18S rRNA phylogeny. These results suggest that the rbcL gene is a more appropriate genetic marker for identification and classification of benthic diatoms. Considering their high diversity and simple shapes, and thus the difficulty associated with morphological classification of benthic diatoms, a molecular approach could provide a relatively easy and reliable classification system. However, this study suggests that more effort should be made to construct a reliable database containing polyphasic taxonomic data for diatom classification.
Tipo de publicação: COMPARATIVE STUDY; JOURNAL ARTICLE
Nome de substância:0 (RNA, Ribosomal, 18S); EC 4.1.1.39 (RbcL protein, plastid); EC 4.1.1.39 (Ribulose-Bisphosphate Carboxylase)


  9 / 3101 MEDLINE  
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PMID:28602754
Autor:Loukas CM; McQuillan JS; Laouenan F; Tsaloglou MN; Ruano-Lopez JM; Mowlem MC
Endereço:National Oceanography Centre, European Way, Southampton SO14 3ZH, United Kingdom; Department of Ocean and Earth Science, University of Southampton Waterfront Campus, European Way, Southampton SO14 3ZH, United Kingdom.
Título:Detection and quantification of the toxic microalgae Karenia brevis using lab on a chip mRNA sequence-based amplification.
Fonte:J Microbiol Methods; 139:189-195, 2017 Aug.
ISSN:1872-8359
País de publicação:Netherlands
Idioma:eng
Resumo:Now and again, the rapid proliferation of certain species of phytoplankton can give rise to Harmful Algal Blooms, which pose a serious threat to marine life and human health. Current methods of monitoring phytoplankton are limited by poor specificity or by the requirement to return samples to a highly resourced, centralised lab. The Lab Card is a small, microfluidic cassette which, when used in tandem with a portable Lab Card Reader can be used to sensitively and specifically quantify harmful algae in the field, from nucleic acid extracts using RNA amplification; a sensitive and specific method for the enumeration of potentially any species based on their unique genetic signatures. This study reports the culmination of work to develop a Lab Card-based genetic assay to quantify the harmful algae Karenia brevis using mRNA amplification by the Nucleic Acid Sequence Based Amplification (NASBA) method. K. brevis cells were quantified by amplification of the rbcL gene transcript in nucleic acid extracts of K. brevis cell samples. A novel enzyme dehydration and preservation method was combined with a pre-existing reagent Gelification method to prepare fully preserved Lab Cards with a shelf-life of at least six weeks prior to use. Using an internal control (IC), the Lab Card-based rbcL NASBA was demonstrated for the quantification of K. brevis from cell extracts containing between 50 and 5000 cells. This is the first demonstration of quantitation of K. brevis using IC-NASBA on a Lab Card.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (RNA, Messenger); EC 4.1.1.39 (RbcL protein, plastid); EC 4.1.1.39 (Ribulose-Bisphosphate Carboxylase)


  10 / 3101 MEDLINE  
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PMID:28472730
Autor:Jean N; Dumont E; Herzi F; Balliau T; Laabir M; Masseret E; Mounier S
Endereço:Université de Toulon, PROTEE, EA 3819, 83957 La Garde, France. Electronic address: jean@univ-tln.fr.
Título:Modifications of the soluble proteome of a mediterranean strain of the invasive neurotoxic dinoflagellate Alexandrium catenella under metal stress conditions.
Fonte:Aquat Toxicol; 188:80-91, 2017 Jul.
ISSN:1879-1514
País de publicação:Netherlands
Idioma:eng
Resumo:The soluble proteome of the mediterranean strain ACT03 of the invasive neurotoxic dinoflagellate Alexandrium catenella exposed to lead or zinc at 6, 12 or 18µM (total concentrations), or under control conditions, was characterized by two-dimensional gel electrophoresis (2-DE). Zinc reduced (P<0.05) the total number of protein spots (-41%, -52% and -60%, at 6, 12 or 18µM, respectively). Besides, most of the proteins constituting the soluble proteome were down-regulated in response to lead or zinc stresses. These proteins were involved mainly in photosynthesis (20-37% for lead; 36-50% for zinc) (ribulose-1,5-bisphosphate carboxylase/oxygenase: RUBISCO; ferredoxin-NADP reductase: FNR; peridinin-chlorophyll a-protein: PCP), and in the oxidative stress response (29-34% for lead; 17-36% for zinc) (superoxide dismutase: SOD; proteasome α/ß subunits). These negative effects could be partly compensated by the up-regulation of specific proteins such as ATP-synthase ß subunit (+16.3 fold after exposure to lead at 12µM). Indeed, an increase in the abundance of ATP-synthase could enrich the ATP pool and provide more energy available for the cells to survive under metal stress, and make the ATP-synthase transport of metal cations out of the cells more efficient. Finally, this study shows that exposure to lead or zinc have a harmful effect on the soluble proteome of A. catenella ACT03, but also suggests the existence of an adaptative proteomic response to metal stresses, which could contribute to maintaining the development of this dinoflagellate in trace metal-contaminated ecosystems.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Proteome); 0 (Water Pollutants, Chemical); 2P299V784P (Lead); 36-88-4 (Carotenoids); EC 1.15.1.1 (Superoxide Dismutase); EC 1.18.1.2 (Ferredoxin-NADP Reductase); EC 3.6.3.- (Mitochondrial Proton-Translocating ATPases); EC 4.1.1.39 (Ribulose-Bisphosphate Carboxylase); J41CSQ7QDS (Zinc)



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