|
|
|
Registros recuperados: 35 | |
|
|
Riaño Pachón, Diego Mauricio; González Estrada, Elizabeth; Alexa, Adrian; Ramírez, Fidel; Vischi Winck, Flavia; Gómez Merino, Fernando, Coord.; Silva Rojas, Hilda Victoria, Coord.; Pérez Rodríguez, Paulino, Coord.. |
En esta publicación intitulada “Bioinformática: aplicaciones a la genómica y proteómica” se detallan algunos de los avances más sobresalientes de los temas de genómica y proteómica, derivados de un curso internacional sobre el tema, organizado por el Colegio de Postgraduados. Estos avances incluyen aspectos de las dos ciencias ómicas, incluyendo genómica y biología estructural, código R, análisis comparativo y evolución, agrupamiento y minería de datos en R, redes de interacciones entre proteínas y proteómica bioinformática. BIOINFORMATICS : APPLICATIONS TO GENOMICS AND PROTEOMICS. ABSTRACT : In this publication entitled "Bioinformatics: applications to genomics and proteomics" are some of the most salient issues of genomics and proteomics, derived from an... |
Tipo: Libro |
Palavras-chave: Bioinformática; Proteómica; Genómica; ADN; Proteínas; Modelación; Simulación; Análisis de genómas; Biología estructural; Código R; Análisis comparativo; Minería de datos; Computación aplicada; Bioinformatics; Proteomics; DNA; Proteins; Models; Genomics; Simulation; R Code; Data mining; Computing; Genome analysis. |
Ano: 2010 |
URL: http://hdl.handle.net/10521/313 |
| |
|
|
Phonsakhan,Wipada; Kong-Ngern,Kanlaya. |
Background Black glutinous rice contains remarkable levels of anthocyanins, which possess anti-oxidative properties and thus have health benefits. The accumulation of anthocyanins in grains of thirty black glutinous rice varieties was measured, and the results revealed that the accumulated anthocyanin content ranged from 0.262 to 2.539 mg/g. Black glutinous rice Br no. 19 was selected, and its leaf protein expression profile was compared with that of white glutinous rice RD 6 using 2D-PAGE, and the protein spots were then directly analyzed after proteolysis by LC-MS/MS. Results The proteins from the leaves of the two rice varieties were separated using 2D-PAGE and silver stained, and the spots were analyzed using Image Master 2D Platinum version 5... |
Tipo: Journal article |
Palavras-chave: 2D-PAGE; Anthocyanin; LC-MS/MS; Oryza sativa L; Proteomics. |
Ano: 2015 |
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582015000100006 |
| |
|
| |
|
| |
|
|
Jia,Yan-Long; Chen,Hui; Zhang,Chong; Gao,Li-Jie; Wang,Xi-Cheng; Qiu,Le-Le; Wu,Jun-Fang. |
Abstract Dunaliella salina, a single-celled marine alga with extreme salt tolerance, is an important model organism for studying fundamental extremophile survival mechanisms and their potential practical applications. In this study, two-dimensional differential in-gel electrophoresis (2D-DIGE) was used to investigate the expression of halotolerant proteins under high (3 M NaCl) and low (0.75 M NaCl) salt concentrations. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) and bioinformatics were used to identify and characterize the differences among proteins. 2D-DIGE analysis revealed 141 protein spots that were significantly differentially expressed between the two salinities. Twenty-four differentially... |
Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Dunaliella salina; Halotolerant protein; Proteomics; Two-dimensional differential in-gel electrophoresis. |
Ano: 2016 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572016000200239 |
| |
|
|
Yang,Yanhua; Zhu,Keming; Xia,Hengchuan; Chen,Liang; Chen,Keping. |
Indica and japonica are two main subspecies of Asian cultivated rice (Oryza sativa L.) that differ clearly in morphological and agronomic traits, in physiological and biochemical characteristics and in their genomic structure. However, the proteins and genes responsible for these differences remain poorly characterized. In this study, proteomic tools, including two-dimensional electrophoresis and mass spectrometry, were used to globally identify proteins that differed between two sequenced rice varieties (93-11 and Nipponbare). In all, 47 proteins that differed significantly between 93-11 and Nipponbare were identified using mass spectrometry and database searches. Interestingly, seven proteins were expressed only in Nipponbare and one protein was... |
Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Indica and japonica rice; Molecular marker; Proteomics; Quantitative real-time PCR; Unique proteins. |
Ano: 2014 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572014000500008 |
| |
|
| |
|
|
Rodrigues,Elisete Pains; Torres,Adalgisa Ribeiro; Batista,Jesiane Stefânia da Silva; Huergo,Luciano; Hungria,Mariangela. |
Sample preparation is a critical step in two-dimensional gel electrophoresis (2-DE) of plant tissues. Here we describe a phenol/SDS procedure that, although greatly simplified, produced well-resolved and reproducible 2-DE profiles of protein extracts from soybean [Glycine max (L.) Merril] roots. Extractions were made in three replicates using both the original and simplified procedure. To evaluate the quality of the extracted proteins, ten spots were randomly selected and identified by mass spectrometry (MS). The 2-DE gels were equally well resolved, with no streaks or smears, and no significant differences were observed in protein yield, reproducibility, resolution or number of spots. Mass spectra of the ten selected spots were compared with database... |
Tipo: Info:eu-repo/semantics/article |
Palavras-chave: 2-DE; Protein extraction; Proteomics; Soybean roots; Symbiosis. |
Ano: 2012 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000200016 |
| |
|
|
Leprêtre, Maxime; Faury, Nicole; Segarra, Amelie; Claverol, Stéphane; Degremont, Lionel; Palos-ladeiro, Mélissa; Armengaud, Jean; Renault, Tristan; Morga, Benjamin. |
Massive mortality outbreaks affecting Pacific oysters (Crassostrea gigas) spat/juveniles are often associated with the detection of a herpesvirus called ostreid herpesvirus type 1 (OsHV-1). In this work, experimental infection trials of C. gigas spat with OsHV-1 were conducted using two contrasted Pacific oyster families for their susceptibility to viral infection. Live oysters were sampled at 12, 26, and 144 h post infection (hpi) to analyze host-pathogen interactions using comparative proteomics. Shotgun proteomics allowed the detection of seven viral proteins in infected oysters, some of them with potential immunomodulatoy functions. Viral proteins were mainly detected in susceptible oysters sampled at 26 hpi, which correlates with the mortality and... |
Tipo: Text |
Palavras-chave: Proteomics; Interactions; Antiviral response; OsHV-1; Pacific oysters. |
Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00669/78075/80307.pdf |
| |
|
| |
|
|
Smits, M.; Artigaud, Sebastien; Bernay, B.; Pichereau, Vianney; Bargelloni, L.; Paillard, Christine. |
Marine mollusk aquaculture has more than doubled over the past twenty years, accounting for over 15% of total aquaculture production in 2016. Infectious disease is one of the main limiting factors to the development of mollusk aquaculture, and the difficulties inherent to combating pathogens through antibiotic therapies or disinfection have led to extensive research on host defense mechanisms and host-pathogen relationships. It has become increasingly clear that characterizing the functional profiles of response to a disease is an essential step in understanding resistance mechanisms and moving towards more effective disease control. The Manila clam, Ruditapes philippinarum, is a main cultured bivalve species of economic importance which is affected by... |
Tipo: Text |
Palavras-chave: Bivalve; Diseases; Resistance; Manila clam; Vibrio tapetis; Proteomics; Immune response. |
Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00615/72670/71758.pdf |
| |
|
| |
|
|
Barranger, Audrey; Langan, Laura M; Sharma, Vikram; Rance, Graham A; Aminot, Yann; Weston, Nicola J; Akcha, Farida; Moore, Michael N; Arlt, Volker M; Kholbystov, Andrei N; Readman, James W; Jha, Awadhesh N.. |
This study aimed to assess the ecotoxicological effects of the interaction of fullerene (C60) and benzo[a]pyrene (B[a]P) on the marine mussel, Mytilus galloprovincialis. The uptake of nC60, B[a]P and mixtures of nC60 and B[a]P into tissues was confirmed by GC-MS, LC-HRMS and ICP-MS. Biomarkers of DNA damage as well as proteomics analysis were applied to unravel the toxic effect of B[a]P and C60. Antagonistic responses were observed at the genotoxic and proteomic level. Differentially expressed proteins (DEPs) were only identified in the B[a]P single exposure and the B[a]P mixture exposure groups containing 1 mg/L of C60, the majority of which were down-regulated (~52%). No DEPs were identified at any of the concentrations of nC60 (p < 0.05, 1% FDR).... |
Tipo: Text |
Palavras-chave: Trojan Horse effect; B[a]P; NC60; Co-exposure; Mussels; DNA damage; Proteomics. |
Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00498/60946/64340.pdf |
| |
|
|
Hamza, Neila; Silvestre, Frederic; Mhetli, Mohamed; Ben Khemis, Ines; Dieu, Marc; Raes, Martine; Cahu, Chantal; Kestemont, Patrick. |
A comparative proteomic approach was used to assess the protein expression profile in the liver of 34 days old pikeperch larvae fed from day 10 post hatching, with three isoproteic and isolipidic formulated diets varying by their phospholipid (PL) contents (% dry diet weight): 1.4% (PL1), 4.7% (PL5) and 9.5% (PL9). Using 2D-DIGE minimal labelling of liver extracts, we were able to show 56 protein spots with a differential intensity (p<0.05) depending on the dietary PL content. Among these spots, 11 proteins were un-ambiguously identified using nanoLC-MS/MS tandem mass spectrometry. In the PL9 larvae, our results indicate that the glycolytic pathway could be down-regulated due to the under-expression of the fructose biphosphate aldolase B and the... |
Tipo: Text |
Palavras-chave: 2D-DIGE; Metabolism; Phospholipid; Pikeperch; Proteomics. |
Ano: 2010 |
URL: http://archimer.ifremer.fr/doc/00007/11837/8575.pdf |
| |
|
|
Corporeau, Charlotte; Vanderplancke, Gwenaelle; Boulais, Myrina; Suquet, Marc; Quere, Claudie; Boudry, Pierre; Huvet, Arnaud; Madec, Stephanie. |
We used a 2-DE proteomic approach to identify abundant proteins linked to oocyte quality in the Pacific oyster Crassostrea gigas, an economically important bivalve. Oocyte quality of 14 females was estimated by recording fertilisation and early developmental success until D-larval stage under controlled conditions. Proteins that were differentially expressed between females showing high or low oocyte quality were identified by nano-liquid chromatography tandem mass spectrometry. Twelve up-accumulated spots associated with low quality oocytes revealed 10 distinct proteins, including vitellogenin — breakdown products and metabolic enzymes. Eight up-accumulated spots from high quality oocytes revealed 6 distinct proteins, including chaperone molecules and... |
Tipo: Text |
Palavras-chave: Marine bivalves; Crassostrea gigas; Oocyte quality; Proteomics. |
Ano: 2012 |
URL: http://archimer.ifremer.fr/doc/00098/20925/18534.pdf |
| |
|
|
Meng, Arnaud; Corre, Erwan; Probert, Ian; Gutierrez-rodriguez, Andres; Siano, Raffaele; Annamale, Anita; Alberti, Adriana; Da Silva, Corinne; Wincker, Patrick; Le Crom, Stephane; Not, Fabrice; Bittner, Lucie. |
Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core-predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional... |
Tipo: Text |
Palavras-chave: Genomics; Proteomics; Microbial biology; Molecular evolution; Protists; Transcriptomics. |
Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00444/55550/57209.pdf |
| |
|
| |
|
|
Barranger, Audrey; Langan, Laura M.; Sharma, Vikram; Rance, Graham A.; Aminot, Yann; Weston, Nicola J.; Akcha, Farida; Moore, Michael N.; Arlt, Volker M.; Khlobystov, Andrei N.; Readman, James W.; Jha, Awadhesh N.. |
This study aimed to assess the ecotoxicological effects of the interaction of fullerene (C60) and benzo[a]pyrene (B[a]P) on the marine mussel, Mytilus galloprovincialis. The uptake of nC60, B[a]P and mixtures of nC60 and B[a]P into tissues was confirmed by Gas Chromatography–Mass Spectrometry (GC–MS), Liquid Chromatography–High Resolution Mass Spectrometry (LC–HRMS) and Inductively Coupled Plasma Mass Spectrometer (ICP–MS). Biomarkers of DNA damage as well as proteomics analysis were applied to unravel the interactive effect of B[a]P and C60. Antagonistic responses were observed at the genotoxic and proteomic level. Differentially expressed proteins (DEPs) were only identified in the B[a]P single exposure and the B[a]P mixture exposure groups containing 1... |
Tipo: Text |
Palavras-chave: Trojan horse effect; B[a]P; NC(60); Co-exposure; Mussels; DNA damage; Proteomics. |
Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00506/61780/65779.pdf |
| |
|
|
Saavedra, Carlos; Bachere, Evelyne. |
Interest in bivalve genomics has emerged during the last decade, owing to the importance of these organisms in aquaculture and fisheries and to their role in marine environmental science. Knowledge of bivalve genome structure, function and evolution resulting from 20th century "single gene" approaches is limited, but genomic technologies are called to dramatically increase it. Research based on linkage maps, transcriptomics and proteomics is being carried out to study the genetic and molecular bases of traits of interest in bivalve farming industry, mainly disease susceptibility, tolerance to environmental stress, and growth. The Pacific oyster (Crassostrea gigas) is now the focus of an international genome-sequencing consortium. The use of bivalves in... |
Tipo: Text |
Palavras-chave: Shellfish toxins; Feeding; Stress; Proteomics; Genomics; Bivalves. |
Ano: 2006 |
URL: http://archimer.ifremer.fr/doc/2006/publication-1709.pdf |
| |
|
|
Chetouhi, Cherif; Masseret, Estelle; Satta, Cecilia Teodora; Balliau, Thierry; Laabir, Mohamed; Jean, Natacha. |
Over the past decades, the occurrence, distribution and intensity of harmful algal blooms involving the dinoflagellate Alexandrium pacificum have increased in marine coastal areas disturbed by anthropogenic inputs. This invasive species produces saxitoxin, which causes the paralytic shellfish poisoning syndrome in humans upon consumption of contaminated seafood. Blooms of A. pacificum have been reported in metal-contaminated coastal ecosystems, suggesting some ability of these microorganisms to adapt to and/or resist in metal stress conditions. This study seeks to characterize the modifications in membrane proteomes (by 2-D electrophoresis coupled to LC-MS/MS), cell growth and morphometry (measured with an inverted microscope), in response to metal stress... |
Tipo: Text |
Palavras-chave: Alexandrium pacificum; Harmful algal bloom; Proteomics; Membrane pmteome; Trace metals. |
Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00606/71802/70290.pdf |
| |
Registros recuperados: 35 | |
|
|
|