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 | Acesso ao texto completo restrito à biblioteca da Embrapa Gado de Leite. Para informações adicionais entre em contato com cnpgl.biblioteca@embrapa.br. |
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Registro Completo |
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Biblioteca(s): |
Embrapa Gado de Leite. |
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Data corrente: |
23/03/2009 |
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Data da última atualização: |
05/02/2024 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Autoria: |
SANTOS, O. C. S.; BARROS, E. M.; BRITO, M. A. V. P.; BASTOS, M. C. F.; SANTOS, K. R. N.; GIAMBIAGI-DE-MARVAL, M. |
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Afiliação: |
Olinda Cabral da Silva Santos, UFRJ; Elaine Menezes Barros, UFRJ; Maria Aparecida Vasconcelos Paiva Brito, Embrapa Gado de Leite; Maria do Carmo de Freire Bastos, UFRJ; Kátia Regina Netto dos Santos, UFRJ; Marcia Giambiagi-deMarval, UFRJ. |
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Título: |
Identification of coagulase-negative staphylococci from bovine mastitis using RFLP-PCR of the groEL gene. |
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Ano de publicação: |
2008 |
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Fonte/Imprenta: |
Veterinary Microbiology, n. 130, n. 1/2, p. 134-140, 2008. |
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DOI: |
https://doi.org/10.1016/j.vetmic.2007.12.009 |
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Idioma: |
Inglês |
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Conteúdo: |
Coagulase-negative staphylococci (CNS) have become the predominant pathogens causing bovine mastitis in many countries. CNS infections are associated with damage to milk secretory tissue of the mammary gland by increased connective tissue stroma, moderate increases of somatic cells count in milk and significant production decreases. These consequences impose serious economic losses for the farmers and the dairy industry. Routine veterinary laboratories do not usually identify CNS at the species level. Thereby, the aims of this study were to identify the most common staphylococcal pathogens involved in bovine mastitis using PCR-restriction fragment length polymorphism (RFLP) analysis of a partial groEL gene sequence and to compare our results with the identification carried out by the conventional method. A total of 54 isolates of Staphylococcus, involved in bovine mastitis, were analyzed by this method. The size and number of the fragments obtained by either AluI or HindIII/PvuII digestions made possible to form clear patterns differentiating, among the isolates, 11 of the most common species of animal staphylococcal pathogens. Most of the isolates clustered together with the reference strain of Staphylococcus chromogenes (28) and the type strain of Staphylococcus epidermidis (8). Besides, some isolates clustered together with the type strain of Staphylococcus aureus (5). All patterns were confirmed by the conventional biochemical method, showing concordant results. Thus, the PCR-RFLP of the groEL gene constitutes a reliable and reproducible molecular method for identification of CNS species responsible for bovine mastitis. MenosCoagulase-negative staphylococci (CNS) have become the predominant pathogens causing bovine mastitis in many countries. CNS infections are associated with damage to milk secretory tissue of the mammary gland by increased connective tissue stroma, moderate increases of somatic cells count in milk and significant production decreases. These consequences impose serious economic losses for the farmers and the dairy industry. Routine veterinary laboratories do not usually identify CNS at the species level. Thereby, the aims of this study were to identify the most common staphylococcal pathogens involved in bovine mastitis using PCR-restriction fragment length polymorphism (RFLP) analysis of a partial groEL gene sequence and to compare our results with the identification carried out by the conventional method. A total of 54 isolates of Staphylococcus, involved in bovine mastitis, were analyzed by this method. The size and number of the fragments obtained by either AluI or HindIII/PvuII digestions made possible to form clear patterns differentiating, among the isolates, 11 of the most common species of animal staphylococcal pathogens. Most of the isolates clustered together with the reference strain of Staphylococcus chromogenes (28) and the type strain of Staphylococcus epidermidis (8). Besides, some isolates clustered together with the type strain of Staphylococcus aureus (5). All patterns were confirmed by the conventional biochemical method, showing concordant results. Thus, th... Mostrar Tudo |
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Palavras-Chave: |
Coagulase-negative staphylococci; groEL gene. |
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Thesaurus Nal: |
bovine mastitis; Staphylococcus. |
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Categoria do assunto: |
-- |
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Marc: |
LEADER 02440naa a2200241 a 4500
001 1596414
005 2024-02-05
008 2008 bl uuuu u00u1 u #d
024 7 $ahttps://doi.org/10.1016/j.vetmic.2007.12.009$2DOI
100 1 $aSANTOS, O. C. S.
245 $aIdentification of coagulase-negative staphylococci from bovine mastitis using RFLP-PCR of the groEL gene.$h[electronic resource]
260 $c2008
520 $aCoagulase-negative staphylococci (CNS) have become the predominant pathogens causing bovine mastitis in many countries. CNS infections are associated with damage to milk secretory tissue of the mammary gland by increased connective tissue stroma, moderate increases of somatic cells count in milk and significant production decreases. These consequences impose serious economic losses for the farmers and the dairy industry. Routine veterinary laboratories do not usually identify CNS at the species level. Thereby, the aims of this study were to identify the most common staphylococcal pathogens involved in bovine mastitis using PCR-restriction fragment length polymorphism (RFLP) analysis of a partial groEL gene sequence and to compare our results with the identification carried out by the conventional method. A total of 54 isolates of Staphylococcus, involved in bovine mastitis, were analyzed by this method. The size and number of the fragments obtained by either AluI or HindIII/PvuII digestions made possible to form clear patterns differentiating, among the isolates, 11 of the most common species of animal staphylococcal pathogens. Most of the isolates clustered together with the reference strain of Staphylococcus chromogenes (28) and the type strain of Staphylococcus epidermidis (8). Besides, some isolates clustered together with the type strain of Staphylococcus aureus (5). All patterns were confirmed by the conventional biochemical method, showing concordant results. Thus, the PCR-RFLP of the groEL gene constitutes a reliable and reproducible molecular method for identification of CNS species responsible for bovine mastitis.
650 $abovine mastitis
650 $aStaphylococcus
653 $aCoagulase-negative staphylococci
653 $agroEL gene
700 1 $aBARROS, E. M.
700 1 $aBRITO, M. A. V. P.
700 1 $aBASTOS, M. C. F.
700 1 $aSANTOS, K. R. N.
700 1 $aGIAMBIAGI-DE-MARVAL, M.
773 $tVeterinary Microbiology$gn. 130, n. 1/2, p. 134-140, 2008.
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Registro original: |
Embrapa Gado de Leite (CNPGL) |
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Registro Completo
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Biblioteca(s): |
Embrapa Gado de Leite. |
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Data corrente: |
26/12/2018 |
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Data da última atualização: |
24/01/2023 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
B - 3 |
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Autoria: |
RIBEIRO, I. M.; BORGES, C. C. H.; SILVA, B. Z.; ARBEX, W. A. |
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Afiliação: |
WAGNER ANTONIO ARBEX, CNPGL. |
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Título: |
A genetic programming model for association studies to detect epistasis in low heritability data. |
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Ano de publicação: |
2018 |
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Fonte/Imprenta: |
Revista de Informática Teórica e Aplicada, v. 25, n. 2, p. 85-92, 2018. |
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Idioma: |
Inglês |
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Conteúdo: |
Abstract The genome-wide associations studies (GWAS) aims to identify the most influential markers in relation to the phenotype values. One of the substantial challenges is to find a non-linear mapping between genotype and phenotype, also known as epistasis, that usually becomes the process of searching and identifying functional SNPs more complex. Some diseases such as cervical cancer, leukemia and type 2 diabetes have low heritability. The heritability of the sample is directly related to the explanation defined by the genotype, so the lower the heritability the greater the influence of the environmental factors and the less the genotypic explanation. In this work, an algorithm capable of identifying epistatic associations at different levels of heritability is proposed. The developing model is a aplication of genetic programming with a specialized initialization for the initial population consisting of a random forest strategy. The initialization process aims to rank the most important SNPs increasing the probability of their insertion in the initial population of the genetic programming model. The expected behavior of the presented model for the obtainment of the causal markers intends to be robust in relation to the heritability level. The simulated experiments are case-control type with heritability level of 0.4, 0.3, 0.2 and 0.1 considering scenarios with 100 and 1000 markers. Our approach was compared with the GPAS software and a genetic programming algorithm without the initialization step. The results show that the use of an efficient population initialization method based on ranking strategy is very promising compared to other models. MenosAbstract The genome-wide associations studies (GWAS) aims to identify the most influential markers in relation to the phenotype values. One of the substantial challenges is to find a non-linear mapping between genotype and phenotype, also known as epistasis, that usually becomes the process of searching and identifying functional SNPs more complex. Some diseases such as cervical cancer, leukemia and type 2 diabetes have low heritability. The heritability of the sample is directly related to the explanation defined by the genotype, so the lower the heritability the greater the influence of the environmental factors and the less the genotypic explanation. In this work, an algorithm capable of identifying epistatic associations at different levels of heritability is proposed. The developing model is a aplication of genetic programming with a specialized initialization for the initial population consisting of a random forest strategy. The initialization process aims to rank the most important SNPs increasing the probability of their insertion in the initial population of the genetic programming model. The expected behavior of the presented model for the obtainment of the causal markers intends to be robust in relation to the heritability level. The simulated experiments are case-control type with heritability level of 0.4, 0.3, 0.2 and 0.1 considering scenarios with 100 and 1000 markers. Our approach was compared with the GPAS software and a genetic programming algorithm without... Mostrar Tudo |
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Palavras-Chave: |
Computational Modeling; Genetic Programming; GWAS; Mathematical Modeling; Random Forest; SNP. |
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Thesaurus NAL: |
Bioinformatics. |
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Categoria do assunto: |
X Pesquisa, Tecnologia e Engenharia |
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URL: |
https://ainfo.cnptia.embrapa.br/digital/bitstream/item/189322/1/Artigo-RevInfTeorApl.pdf
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Marc: |
LEADER 02397naa a2200241 a 4500
001 2102526
005 2023-01-24
008 2018 bl uuuu u00u1 u #d
100 1 $aRIBEIRO, I. M.
245 $aA genetic programming model for association studies to detect epistasis in low heritability data.$h[electronic resource]
260 $c2018
520 $aAbstract The genome-wide associations studies (GWAS) aims to identify the most influential markers in relation to the phenotype values. One of the substantial challenges is to find a non-linear mapping between genotype and phenotype, also known as epistasis, that usually becomes the process of searching and identifying functional SNPs more complex. Some diseases such as cervical cancer, leukemia and type 2 diabetes have low heritability. The heritability of the sample is directly related to the explanation defined by the genotype, so the lower the heritability the greater the influence of the environmental factors and the less the genotypic explanation. In this work, an algorithm capable of identifying epistatic associations at different levels of heritability is proposed. The developing model is a aplication of genetic programming with a specialized initialization for the initial population consisting of a random forest strategy. The initialization process aims to rank the most important SNPs increasing the probability of their insertion in the initial population of the genetic programming model. The expected behavior of the presented model for the obtainment of the causal markers intends to be robust in relation to the heritability level. The simulated experiments are case-control type with heritability level of 0.4, 0.3, 0.2 and 0.1 considering scenarios with 100 and 1000 markers. Our approach was compared with the GPAS software and a genetic programming algorithm without the initialization step. The results show that the use of an efficient population initialization method based on ranking strategy is very promising compared to other models.
650 $aBioinformatics
653 $aComputational Modeling
653 $aGenetic Programming
653 $aGWAS
653 $aMathematical Modeling
653 $aRandom Forest
653 $aSNP
700 1 $aBORGES, C. C. H.
700 1 $aSILVA, B. Z.
700 1 $aARBEX, W. A.
773 $tRevista de Informática Teórica e Aplicada$gv. 25, n. 2, p. 85-92, 2018.
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