Consulta: subjectFacets:"Genomics"
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Bioinformática : Aplicaciones a la proteómica y genómica
Provedor de dados: 32
Autores: 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

In silico identification of coffee genome expressed sequences potentially associated with resistance to diseases
Provedor de dados: 74
Autores: Alvarenga,Samuel Mazzinghy; Caixeta,Eveline Teixeira; Hufnagel,Bárbara; Thiebaut,Flávia; Maciel-Zambolim,Eunize; Zambolimand,Laércio; Sakiyama,Ney Sussumu.
Sequences potentially associated with coffee resistance to diseases were identified by in silico analyses using the database of the Brazilian Coffee Genome Project (BCGP). Keywords corresponding to plant resistance mechanisms to pathogens identified in the literature were used as baits for data mining. Expressed sequence tags (ESTs) related to each of these keywords were identified with tools available in the BCGP bioinformatics platform. A total of 11,300 ESTs were mined. These ESTs were clustered and formed 979 EST-contigs with similarities to chitinases, kinases, cytochrome P450 and nucleotide binding site-leucine rich repeat (NBS-LRR) proteins, as well as with proteins related to disease resistance, pathogenesis, hypersensitivity response (HR) and...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Coffea; Data mining; ESTs; Genomics; In silico; Bioinformatics.
Ano: 2010
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572010000400031

Holobionts and their hologenomes: Evolution with mixed modes of inheritance
Provedor de dados: 74
Autores: Haag,Karen Luisa.
Abstract Symbioses are ubiquitous and have played an influential role in the evolution of life on Earth. Genomic studies are now revealing a huge diversity of associations among hosts and their microbiotas, allowing us to characterize their complex ecological and evolutionary dynamics. The different transmission modes and the asynchronous cell proliferation of the numerous symbionts associated with one host generate a genomic conflict ought to be solved. Two disputing views have been used to model and predict the outcome of such conflicts. The traditional view is based on community ecology, and considers that selection at the level of individuals is sufficient to explain longstanding associations among species. A new perspective considers that the host and...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Genomics; Metagenomics; Microbiota; Symbiosis; Holobiont.
Ano: 2018
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000200189

Signaling pathways in a Citrus EST database
Provedor de dados: 74
Autores: Mehta,Angela; Silva,Marilia Santos; Guidetti-Gonzalez,Simone; Carrer,Helaine; Takita,Marco Aurélio; Martins,Natália F.
Citrus spp. are economically important crops, which in Brazil are grown mainly in the State of São Paulo. Citrus cultures are attacked by several pathogens, causing severe yield losses. In order to better understand this culture, the Millenium Project (IAC Cordeirópolis) was launched in order to sequence Citrus ESTs (expressed sequence tags) from different tissues, including leaf, bark, fruit, root and flower. Plants were submitted to biotic and abiotic stresses and investigated under different development stages (adult vs. juvenile). Several cDNA libraries were constructed and the sequences obtained formed the Citrus ESTs database with almost 200,000 sequences. Searches were performed in the Citrus database to investigate the presence of different...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Citrus; Cell signaling; Genomics.
Ano: 2007
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000500003

Approaches for in silico finishing of microbial genome sequences
Provedor de dados: 74
Autores: Kremer,Frederico Schmitt; McBride,Alan John Alexander; Pinto,Luciano da Silva.
Abstract The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as “drafts”, incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Microbial genetics; Molecular microbiology; Genomics; Microbiology; Draft genomes.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000400553

A study of the distribution of phylogenetically conserved blocks within clusters of mammalian homeobox genes
Provedor de dados: 74
Autores: Stojanovic,Nikola.
Genome sequencing efforts of the last decade have produced a large amount of data, which has enabled whole-genome comparative analyses in order to locate potentially functional elements and study the overall patterns of phylogenetic conservation. In this paper we present a statistically based method for the characterization of these patterns in mammalian DNA sequences. We have applied this approach to the study of exceptionally well conserved homeobox gene clusters (Hox), based on an alignment of six species, and we have constructed a map of Hox cataloguing the conserved fragments, along with their locations in relation to the genes and other landmarks, sometimes showing unexpected layouts.
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Genomics; Phylogenetic conservation; Multiple sequence alignments; Heaviest segments; Hox.
Ano: 2009
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000300034

Genotyping by sequencing approach for autotetraploid Urochloa Ruziziensis genetic breeding.
Provedor de dados: 14
Autores: RESENDE, R. M. S.; MARTINS, F. B.; VILELA, M. de M.; MORAES, A. C. L.; FERREIRA, R. C. U.; DÉO, T. G.; MOREIRA, F. A.; PASTINA, M. M.; NODA, R. W.; SOUZA, A. P.
Although Brazil is the major producer and exporter of beef in the world, the rangelands are cultivated with varieties obtained by selection on germplasm and conventional breeding. Only lately genomic information started to be used in the tropical forage breeding programs mostly because of the genome complexity and costs. Urochloa ruziziensis is a sexual autotetraploid forage that has a significant role in integrated systems that are currently important in the agribusiness in certain regions of Brazil and is essential as female parent in other Urochloa spp. breeding programs. Thus, this work intends to use the Genotyping by Sequencing (GBS) approach to identify SNP markers to construct the first map of the species and estimate breeding values for Genomic...
Tipo: Fôlder / Folheto / Cartilha (INFOTECA-E)
Palavras-chave: Genomics; Genetic markers; Pipelines; Breeding.
Ano: 2019
URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/1120361

Edição genômica em trigo: potencialidades, desafios e conquistas.
Provedor de dados: 14
Autores: LAU, E. Y.
Edição genômica; Aplicações da edição genômica em trigo; A edição genômica e a transgenia; Estratégias alternativas de edição genômica aplicadas ao trigo; Evolução da legislação relativa à edição genômica; Uso comercial de culturas editadas
Tipo: Folhetos
Palavras-chave: Biotecnologia; Triticum Aestivum; Genomics; Gene transfer; Transgenes.
Ano: 2022
URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/1149768

A biologia avançada e o impacto da genômica na produção de caprinos e ovinos.
Provedor de dados: 14
Autores: SIDER, L. H.; ZAROS, L. G.
bitstream/CNPC-2010/21844/1/doc78.pdf
Tipo: Documentos (INFOTECA-E)
Palavras-chave: Genômica; Caprino; Ovino; Biologia molecular; Goats; Sheep; Molecular biology; Genomics.
Ano: 2008
URL: http://www.infoteca.cnptia.embrapa.br/infoteca/handle/doc/534121

Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout
Provedor de dados: 5
Autores: Smith, Seth R.; Amish, Stephen J.; Bernatchez, Louis; Le Luyer, Jeremy; Wilson, Chris; Boeberitz, Olivia; Luikart, Gordon; Scribner, Kim T.
Understanding the genomic basis of adaptative intraspecific phenotypic variation is a central goal in conservation genetics and evolutionary biology. Lake trout (Salvelinus namaycush) are an excellent species for addressing the genetic basis for adaptive variation because they express a striking degree of ecophenotypic variation across their range; however, necessary genomic resources are lacking. Here we utilize recently-developed analytical methods and sequencing technologies to (1) construct a high-density linkage and centromere map for lake trout, (2) identify loci underlying variation in traits that differentiate lake trout ecophenotypes and populations, (3) determine the location of the lake trout sex determination locus, and (4) identify chromosomal...
Tipo: Text
Palavras-chave: Linkage map; Salvelinus; QTL; RAD; Genomics; Lake trout.
Ano: 2020
URL: https://archimer.ifremer.fr/doc/00634/74659/74565.pdf

Estimates of genetic variability and inbreeding in experimentally selected populations of European sea bass
Provedor de dados: 5
Autores: Hillen, J. E. J.; Coscia, I.; Vandeputte, Marc; Herten, K.; Hellemans, B.; Maroso, F.; Vergnet, Alain; Allal, Francois; Maes, G. E.; Volckaert, F. A. M.
The aquaculture industry has increasingly aimed at improving economically important traits like growth, feed efficiency and resistance to infections. Artificial selection represents an important window of opportunity to significantly improve production. However, the pitfall is that selection will reduce genetic diversity and increase inbreeding in the farmed stocks. Genetic tools are very useful in this context as they provide accurate measures of genetic diversity together with many additional insights in the stock status and the selection process. In this study we assessed the level of genetic variability and relatedness over several generations of two lines of experimentally selected European sea bass (Dicentrarchus labrax L.). The first line was...
Tipo: Text
Palavras-chave: Artificial selection; DdRAD; Fish; Genetic diversity; Genomics; Inbreeding.
Ano: 2017
URL: http://archimer.ifremer.fr/doc/00392/50314/50993.pdf

Vide-omics: A Genomics-inspired Paradigm for Video Analysis
Provedor de dados: 5
Autores: Kazantzidis, Ioannis; Florez-revuelta, Francisco; Dequidt, Mickael; Hill, Natasha; Nebel, Jean-christophe.
With the development of applications associated to ego-vision systems, smart-phones, and autonomous cars, automated analysis of videos generated by freely moving cameras has become a major challenge for the computer vision community. Current techniques are still not suitable to deal with real-life situations due to, in particular, wide scene variability and the large range of camera motions. Whereas most approaches attempt to control those parameters, this paper introduces a novel video analysis paradigm, ‘vide-omics’, inspired by the principles of genomics where variability is the expected norm. Validation of this new concept is performed by designing an implementation addressing foreground extraction from videos captured by freely moving cameras....
Tipo: Text
Palavras-chave: Computer vision; Freely moving camera; Genomics; Foreground detection; Segmentation; Scanlines.
Ano: 2018
URL: http://archimer.ifremer.fr/doc/00405/51643/52191.pdf

The ocean sampling day consortium
Provedor de dados: 5
Autores: Kopf, Anna; Bicak, Mesude; Kottmann, Renzo; Schnetzer, Julia; Kostadinov, Ivaylo; Lehmann, Katja; Fernandez-guerra, Antonio; Jeanthon, Christian; Rahav, Eyal; Ullrich, Matthias; Wichels, Antje; Gerdts, Gunnar; Polymenakou, Paraskevi; Kotoulas, Giorgos; Siam, Rania; Abdallah, Rehab Z.; Sonnenschein, Eva C.; Cariou, Thierry; O'Gara, Fergal; Jackson, Stephen; Orlic, Sandi; Steinke, Michael; Busch, Julia; Duarte, Bernardo; Cacador, Isabel; Canning-clode, Joao; Bobrova, Oleksandra; Marteinsson, Viggo; Reynisson, Eyjolfur; Loureiro, Clara Magalhaes; Luna, Gian Marco; Quero, Grazia Marina; Loescher, Carolin R.; Kremp, Anke; Delorenzo, Marie E.; Ovreas, Lise; Tolman, Jennifer; Laroche, Julie; Penna, Antonella; Frischer, Marc; Davis, Timothy; Katherine, Barker; Meyer, Christopher P.; Ramos, Sandra; Magalhaes, Catarina; Jude-lemeilleur, Florence; Leopoldina Aguirre-macedo, Ma; Wang, Shiao; Poulton, Nicole; Jones, Scott; Collin, Rachel; Fuhrman, Jed A.; Conan, Pascal; Alonso, Cecilia; Stambler, Noga; Goodwin, Kelly; Yakimov, Michael M.; Baltar, Federico; Bodrossy, Levente; Van De Kamp, Jodie; Frampton, Dion M. F.; Ostrowski, Martin; Van Ruth, Paul; Malthouse, Paul; Claus, Simon; Deneudt, Klaas; Mortelmans, Jonas; Pitois, Sophie; Wallom, David; Salter, Ian; Costa, Rodrigo; Schroeder, Declan C.; Kandil, Mahrous M.; Amaral, Valentina; Biancalana, Florencia; Santana, Rafael; Pedrotti, Maria Luiza; Yoshida, Takashi; Ogata, Hiroyuki; Ingleton, Tim; Munnik, Kate; Rodriguez-ezpeleta, Naiara; Berteaux-lecellier, Veronique; Wecker, Patricia; Cancio, Ibon; Vaulot, Daniel; Bienhold, Christina; Ghazal, Hassan; Chaouni, Bouchra; Essayeh, Soumya; Ettamimi, Sara; Zaid, El Houcine; Boukhatem, Noureddine; Bouali, Abderrahim; Chahboune, Rajaa; Barrijal, Said; Timinouni, Mohammed; El Otmani, Fatima; Bennani, Mohamed; Mea, Marianna; Todorova, Nadezhda; Karamfilov, Ventzislav; Ten Hoopen, Petra; Cochrane, Guy; L'Haridon, Stephane; Bizsel, Kemal Can; Vezzi, Alessandro; Lauro, Federico M.; Martin, Patrick; Jensen, Rachelle M.; Hinks, Jamie; Gebbels, Susan; Rosselli, Riccardo; De Pascale, Fabio; Schiavon, Riccardo; Dos Santos, Antonina; Villar, Emilie; Pesant, Stephane; Cataletto, Bruno; Malfatti, Francesca; Edirisinghe, Ranjith; Silveira, Jorge A. Herrera; Barbier, Michele; Turk, Valentina; Tinta, Tinkara; Fuller, Wayne J.; Salihoglu, Ilkay; Serakinci, Nedime; Ergoren, Mahmut Cerkez; Bresnan, Eileen; Iriberri, Juan; Nyhus, Paul Anders Fronth; Bente, Edvardsen; Karlsen, Hans Erik; Golyshin, Peter N.; Gasol, Josep M.; Moncheva, Snejana; Dzhembekova, Nina; Johnson, Zackary; Sinigalliano, Christopher David; Gidley, Maribeth Louise; Zingone, Adriana; Danovaro, Roberto; Tsiamis, George; Clark, Melody S.; Costa, Ana Cristina; El Bour, Monia; Martins, Ana M.; Collins, R. Eric; Ducluzeau, Anne-lise; Martinez, Jonathan; Costello, Mark J.; Amaral-zettler, Linda A.; Gilbert, Jack A.; Davies, Neil; Field, Dawn; Gloeckner, Frank Oliver.
Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
Tipo: Text
Palavras-chave: Ocean sampling day; OSD; Biodiversity; Genomics; Health Index; Bacteria; Microorganism; Metagenomics; Marine; Micro B3; Standards.
Ano: 2015
URL: https://archimer.ifremer.fr/doc/00371/48262/48647.pdf

What role for genomics in fisheries management and aquaculture?
Provedor de dados: 5
Autores: Wenne, Roman; Boudry, Pierre; Hemmer-hansen, Jakob; Lubieniecki, Krzysztof P.; Was, Anna; Kause, Antti.
The development and application of genomics has been facilitated in a number of fields by the availability of new methodologies and tools, such as high throughput DNA sequencing and complementary DNA (cDNA) microarrays. Genomic tools are already used in research on commercially important fish and shellfish species. Thousands of expressed sequence tags (EST) are now available for some of these species, and the sequencing of complete genomes of tilapia, cod, salmonids, flatfishes, sea bass and Pacific oyster has been proposed. Microarray technology through simultaneous analysis of the expression of thousands of genes allows the identification of candidate genes involved in the function of multiple physiological, morphological and behavioural traits of...
Tipo: Text
Palavras-chave: Oyster; Fish; Quantitative trait loci; Mariculture; Fisheries; Genetics; Genomics.
Ano: 2007
URL: http://archimer.ifremer.fr/doc/2007/publication-2927.pdf

Variabilité génétique et évaluation génomique de la résistance à la nécrose nerveuse virale de populations sauvages de bar/loup (Dicentrarchus labrax)
Provedor de dados: 5
Autores: Doan, Quoc Khanh.
European seabass is one of the most economic species in aquaculture in Mediterranean areas. Viral nervous necrosis (VNN), a disease affecting at least 70 aquatic species, has become the most serious threat to seabass cultured industry. While numerous studies have been performed in order to control this disease, no simple and effective procedures are available. In this thesis, we question genetic variability and the potential of selective breeding as an opportunity to address thwart this threat.After a general introduction (first chapter) and a deep literature review of nodavirus in aquaculture (second chapter), we explore in the third chapter the genetic variability of resistance of different wild populations of European seabass, namely Northern Atlantic...
Tipo: Text
Palavras-chave: Génétique quantitative; Analyses génomiques; Pathologie; Résistance virale; Aquaculture; Quantitative genetics; Genomics; Pathology; Virus resistance; Aquaculture.
Ano: 2017
URL: https://archimer.ifremer.fr/doc/00498/60971/64379.pdf

Transcriptomic Profiling of Egg Quality in Sea Bass (Dicentrarchus labrax) Sheds Light on Genes Involved in Ubiquitination and Translation
Provedor de dados: 5
Autores: Zarski, Daniel; Thaovi Nguyen,; Le Cam, Aurelie; Montfort, Jerome; Dutto, Gilbert; Vidal, Marie-odile; Fauvel, Christian; Bobe, Julien.
Variable and low egg quality is a major limiting factor for the development of efficient aquaculture production. This stems from limited knowledge on the mechanisms underlying egg quality in cultured fish. Molecular analyses, such as transcriptomic studies, are valuable tools to identify the most important processes modulating egg quality. However, very few studies have been devoted to this aspect so far. Within this study, the microarray-based transcriptomic analysis of eggs (of different quality) of sea bass (Dicentrarchus labrax) was performed. An Agilent oligo microarray experiment was performed on labelled mRNA extracted from 16 batches of eggs (each batch obtained from a different female) of sea bass, in which over 24,000 published probe arrays were...
Tipo: Text
Palavras-chave: Microarray; Genomics; Transcriptomics; Aquaculture; Controlled reproduction.
Ano: 2017
URL: http://archimer.ifremer.fr/doc/00371/48220/48345.pdf

Genetic improvement of fish: Achievements and challenges for tomorrow
Provedor de dados: 5
Autores: Vandeputte, Marc; Baroiller, Jean-francois; Haffray, Pierrick; Quillet, Edwige.
Genetic improvement is a major contributing factor in developing efficient aquaculture, as it is in other forms of animal production. Moreover, as most fish species are only slightly domesticated, the potential gains are very large. Many of the current methods, developed during the XXth century, are classically used in livestock rearing (choice of breeds, crossbreeding, selective breeding). Others are much more specific to aquatic organisms (genetic control of sex, sterilization through triploidization). The spread of selected lines in aquaculture has been effective only since the 1990s, with lines selected essentially on growth and producing some impressive results. Transgenesis, although technically feasible on growth rate, is not used in practice and...
Tipo: Text
Palavras-chave: Selection; Genomics; Fishes; Breeding; Aquaculture.
Ano: 2009
URL: http://archimer.ifremer.fr/doc/2009/publication-6564.pdf

Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network
Provedor de dados: 5
Autores: 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

Genomics and mollusc pathogens: trends and perspective
Provedor de dados: 5
Autores: Renault, Tristan.
Global mollusc production is continuously increasing and reached 12.8 million tonnes in 2004 representing 28.2 percent of the total world production valued at US$ 9.4 billions. However, cultivated molluscs may suffer from severe mortality outbreaks. Among the possible causes is the occurrence of infectious diseases due to a variety of pathogens including protozoan parasites, bacteria and viruses. Preventing and controlling diseases has become a priority for aquaculture sustainability. However, molluscs are unique in terms of health management. Molluscs like other invertebrates, lack a true adaptative immune system. Vaccination can not be used to protect them against pathogens. Moreover, molluscs are usually reared in the open sea which strongly limits the...
Tipo: Text
Palavras-chave: Diagnosis; Phylogeny; Genomics; Mollluscs; Pathogens.
Ano: 2008
URL: http://archimer.ifremer.fr/doc/2008/publication-4574.pdf

The case for sequencing the Pacific oyster genome
Provedor de dados: 5
Autores: Hedgecock, Dennis; Gaffney, Patrick M.; Goulletquer, Philippe; Guo, Ximing; Reece, Kimberly; Warr, Gregory.
An international community of biologists presents the Pacific oyster Crassostrea gigas as a candidate for genome sequencing. This oyster has global distribution and for the past several years the highest annual production of any freshwater or marine organism (4.2 million metric tons, worth $3.5 billion US). Economic and cultural importance of oysters motivates a great deal of biologic research, which provides a compelling rationale for sequencing an oyster genome. Strong rationales for sequencing the oyster genome also come from contrasts to other genomes: membership in the Lophotrochozoa, an understudied branch of the Eukaryotes and high fecundity, with concomitantly high DNA sequence polymorphism and a population biology that is more like plants than any...
Tipo: Text
Palavras-chave: Genomics; Evolutionary and ecological; Nucleotide diversity; Lophotrochozoa; Crassostrea gigas genome sequence; Pacific oyster.
Ano: 2005
URL: http://archimer.ifremer.fr/doc/2005/publication-2128.pdf

Bivalve genomics
Provedor de dados: 5
Autores: 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

Estimation of genetic parameters of feed conversion ratio based on individual phenotypes and genomic data in sea bass
Provedor de dados: 5
Autores: Besson, Mathieu; Allal, Francois; Chatain, Beatrice; Vergnet, Alain; Clota, Frederic; Ferrari, Sebastien; Vandeputte, Marc.
We estimated genetic parameters of feed conversion ratio (FCR) and daily growth coefficient (DGC) using individual phenotypes measured in aquariums under a restricted feeding regime and genomic information on 2,722 SNP markers. The results showed a moderate heritability of both traits (0.26 for FCR and 0.41 for DGC) as well as close to unity negative genetic correlation between them. Thus, FCR of fish in aquariums could be improved by selecting fish for higher DGC. Nevertheless, these results must be taken with caution until we know whether individual FCR measured in aquariums also reflects the FCR of fish reared in groups.    
Tipo: Text
Palavras-chave: Feed efficiency; Fish; Genomics.
Ano: 2018
URL: http://archimer.ifremer.fr/doc/00446/55756/57416.pdf

Detection and evaluation of selection signatures in sheep
Provedor de dados: 86
Autores: Paim,Tiago do Prado; Ianella,Patrícia; Paiva,Samuel Rezende; Caetano,Alexandre Rodrigues; Pimentel,Concepta Margaret McManus.
Abstract: The recent development of genome-wide single nucleotide polymorphism (SNP) arrays made it possible to carry out several studies with different species. The selection process can increase or reduce allelic (or genic) frequencies at specific loci in the genome, besides dragging neighboring alleles in the chromosome. This way, genomic regions with increased frequencies of specific alleles are formed, caracterizing selection signatures or selective sweeps. The detection of these signatures is important to characterize genetic resources, as well as to identify genes or regions involved in the control and expression of important production and economic traits. Sheep are an important species for theses studies as they are dispersed worldwide and have...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Ovis aries; Analysis software; Animal genetic resources; Genetic improvement; Genomics; Molecular genetics; SNP markers.
Ano: 2018
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2018000500527

Validation of a customized subset of SNPs for sheep breed assignment in Brazil
Provedor de dados: 86
Autores: Paim,Tiago do Prado; McManus,Concepta; Vieira,Fábio Danilo; Oliveira,Stanley Robson de Medeiros; Facó,Olivardo; Azevedo,Hymerson Costa; Araújo,Adriana Mello de; Moraes,José Carlos Ferrugem; Yamagishi,Michel Eduardo Beleza; Carneiro,Paulo Luiz Souza; Caetano,Alexandre Rodrigues; Paiva,Samuel Rezende.
Abstract: The objective of this work was to evaluate the usefulness of a subset of 18 single nucleotide polymorphisms (SNPs) for breed identification of Brazilian Crioula, Morada Nova (MN), and Santa Inês (SI) sheep. Data of 588 animals were analyzed with the Structure software. Assignments higher than 90% confidence were observed in 82% of the studied samples. Most of the low-value assignments were observed in MN and SI breeds. Therefore, although there is a high reliability in this subset of 18 SNPs, it is not enough for an unequivocal assignment of the studied breeds, mainly of hair breeds. A more precise panel still needs to be developed for the widespread use in breed assignment.
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Ovis aries; Animal genetic resources; Certification of origin; Genomics; Traceability.
Ano: 2019
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2019000104302

Accuracy of genomic selection predictions for hip height in Brahman cattle using different relationship matrices
Provedor de dados: 86
Autores: Farah,Michel Marques; Fortes,Marina Rufino Salinas; Kelly,Matthew; Porto-Neto,Laercio Ribeiro; Meira,Camila Tangari; Carreño,Luis Orlando Duitama; Fonseca,Ricardo da; Moore,Stephen Stewart.
Abstract: The objective of this work was to evaluate the effects of genomic information on the genetic evaluation of hip height in Brahman cattle using different matrices built from genomic and pedigree data. Hip height measurements from 1,695 animals, genotyped with high-density SNP chip or imputed from 50 K high-density SNP chip, were used. The numerator relationship matrix (NRM) was compared with the H matrix, which incorporated the NRM and genomic relationship (G) matrix simultaneously. The genotypes were used to estimate three versions of G: observed allele frequency (HGOF), average minor allele frequency (HGMF), and frequency of 0.5 for all markers (HG50). For matrix comparisons, animal data were either used in full or divided into calibration (80%...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Bos indicus; Beef cattle; Genomics; Rare alleles.
Ano: 2018
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2018000600717

Biomassza-alapú energiák innovációjának genomikai megközelítései
Provedor de dados: 31
Autores: Marothy,   Gergely; Kondorosi,   Eva; Bíró,   Tibor.
A genomika valódi eszköz a biomassza-alapú energiák innovatív kutatása területén, egyes részterületei (metagenomika, transzkriptomika) ténylegesen alkalmazhatók a biomassza-alapanyag optimalizálása során, illetve a biomassza-konverzió hatékonyságának javításában, ezáltal a megújuló energiatípusok előállítási költségeinek csökkentésében. ------------------------------------------------ Genomics is a useful tool in innovative research into biomass energy. Certain fields of genomics (metagenomics, transcriptomics) have a practical application in biomass optimisation and in improving the efficiency of biomass, and can thus help reduce the costs of renewable energy production.
Tipo: Article
Palavras-chave: Genomika; Biomassza; Kutatás; Innováció; Biomass energy; Genomics; Innovation; Research; Research and Development/Tech Change/Emerging Technologies.
Ano: 2011
URL: http://purl.umn.edu/119937

Dietary histidine requirement of grow-out Nile tilapia (Oreochromis niloticus), based on growth performance, muscle development, expression of muscle-growth-related genes, and blood parameters
Provedor de dados: 96
Autores: Zaminhan-Hassemer,Micheli; Michelato,Mariana; Boscolo,Wilson Rogério; Urbich,Allan Vinnícius; Cruz,Thais Pereira da; Almeida,Fernanda Losi Alves de; Furuya,Valéria Rossetto Barriviera; Furuya,Wilson Massamitu.
ABSTRACT This research was conducted to determine optimal dietary histidine requirement of grow-out Nile tilapia, Oreochromis niloticus, based on muscle development, expression of muscle-growth-related genes, and blood parameters. Fish (n = 288, initial body weight of 64.17±0.53 g) were fed extruded diets with graded levels of histidine (4.23, 5.44, 7.17, 8.91, and 11.57 g kg−1), containing approximately 289 g kg−1 crude protein and 3565 kcal kg−1 digestible energy. The study followed a completely randomized design with five treatments and four replicates each, for 65 days. There was a quadratic effect of dietary histidine on final body weight, feed conversion, and net protein utilization, and the best values were optimized at 8.09, 7.88, and 7.33 g kg−1,...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Amino acids; Aquaculture; Fish nutrition; Genomics.
Ano: 2020
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982020000100201

Genomic dissection of inbreeding depression: a gate to new opportunities
Provedor de dados: 96
Autores: Curik,Ino; Ferenčaković,Maja; Sölkner,Johann.
ABSTRACT Inbreeding depression, reduction in performance of quantitative traits, including reproduction and survival, caused by inbreeding, is a well-known phenomenon observed in almost all experimental, domesticated, and natural populations. In spite of its importance to the fate of a small population and numerous research performed in the last century, the genetic basis of inbreeding depression is still unclear. Recent fast development of molecular techniques has enabled estimation of a genomic inbreeding coefficient (FROH), which reflects realized autozygosity and can be further partitioned to chromosomes and chromosomal segments. In this review, we first describe classical approach used in the estimation of inbreeding in livestock populations, followed...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Autozygosity; Detrimental load; Genomics; Runs of homozygosity.
Ano: 2017
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-35982017000900773

Assessment of the scientific-technological production in molecular biology in Brazil (1996-2007): the contribution of genomics programs
Provedor de dados: 42
Autores: Meneghini,Rogério; Gamba,Estêvão C.
Several genome sequencing programs were launched in Brazil by the end of the nineties and the early 2000s.The most important initiatives were supported by the ONSA program (http://watson.fapesp.br/onsa/Genoma3.htm) and aimed at gaining domain in genomic technology and bringing molecular biology to the state of art. Two mainsets of data were collected in the 1996-2007 period to evaluate the results of these genome programs: the scientific production (Scopus and Web of Science databases) and the register of patents (US Patent and Trademark Office), both related to the progress of molecular biology along this period. In regard to the former, Brazil took a great leap in comparison to 17 other developed and developing countries, being only surpassed by China....
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Science assessment; Genomics; Scientometrics; Molecular biology.
Ano: 2011
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0001-37652011000200031

Plant genomics: an overview
Provedor de dados: 48
Autores: CAMPOS-DE QUIROZ,HUGO.
Recent technological advancements have substantially expanded our ability to analyze and understand plant genomes and to reduce the gap existing between genotype and phenotype. The fast evolving field of genomics allows scientists to analyze thousand of genes in parallel, to understand the genetic architecture of plant genomes and also to isolate the genes responsible for mutations. Furthermore, whole genomes can now be sequenced. This review addresses these issues and also discusses ways to extract biological meaning from DNA data. Although genomic issuesare addressed from a plant perspective, this review provides insights into the genomic analyses of other organisms
Tipo: Journal article
Palavras-chave: Genomics; Plant breeding; Gene discovery.
Ano: 2002
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602002000300013

Genomic Approaches in Marine Biodiversity and Aquaculture
Provedor de dados: 48
Autores: Huete-Pérez,Jorge A; Quezada,Fernando.
Recent advances in genomic and post-genomic technologies have now established the new standard in medical and biotechnological research. The introduction of next-generation sequencing, NGS,has resulted in the generation of thousands of genomes from all domains of life, including the genomes of complex uncultured microbial communities revealed through metagenomics. Although the application of genomics to marine biodiversity remains poorly developed overall, some noteworthy progress has been made in recent years. The genomes of various model marine organisms have been published and a few more are underway. In addition, the recent large-scale analysis of marine microbes, along with transcriptomic and proteomic approaches to the study of teleost fishes,...
Tipo: Journal article
Palavras-chave: Aquaculture; Genomics; Marine biodiversity; Next-generation sequencing; Proteomics.
Ano: 2013
URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602013000400007

Oxidative stress: molecular perception and transduction of signals triggering antioxidant gene defenses
Provedor de dados: 56
Autores: Scandalios,J.G.
Molecular oxygen (O2) is the premier biological electron acceptor that serves vital roles in fundamental cellular functions. However, with the beneficial properties of O2 comes the inadvertent formation of reactive oxygen species (ROS) such as superoxide (O2&lt;FONT FACE=Symbol&gt;·-&lt;/FONT&gt;), hydrogen peroxide, and hydroxyl radical (OH&lt;FONT FACE=Symbol&gt;·&lt;/FONT&gt;). If unabated, ROS pose a serious threat to or cause the death of aerobic cells. To minimize the damaging effects of ROS, aerobic organisms evolved non-enzymatic and enzymatic antioxidant defenses. The latter include catalases, peroxidases, superoxide dismutases, and glutathione S-transferases (GST). Cellular ROS-sensing mechanisms are not well understood, but a number of...
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Catalase; Aging; Telomeres; Gene regulation; Superoxide dismutase; Genomics.
Ano: 2005
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2005000700003

A conceptual and practical overview of cDNA microarray technology: implications for basic and clinical sciences
Provedor de dados: 56
Autores: Mello-Coelho,V. de; Hess,K.L.
cDNA microarray is an innovative technology that facilitates the analysis of the expression of thousands of genes simultaneously. The utilization of this methodology, which is rapidly evolving, requires a combination of expertise from the biological, mathematical and statistical sciences. In this review, we attempt to provide an overview of the principles of cDNA microarray technology, the practical concerns of the analytical processing of the data obtained, the correlation of this methodology with other data analysis methods such as immunohistochemistry in tissue microarrays, and the cDNA microarray application in distinct areas of the basic and clinical sciences.
Tipo: Info:eu-repo/semantics/article
Palavras-chave: Biotechnology; CDNA microarray; Gene expression; Genomics.
Ano: 2005
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2005001000011