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Garcia IS, Silva-Vignato B, Cesar ASM, Petrini J, da Silva VH, Morosini NS, Goes CP, Afonso J, da Silva TR, Lima BD, Clemente LG, Regitano LCDA, Mourão GB, Coutinho LL. Novel putative causal mutations associated with fat traits in Nellore cattle uncovered by eQTLs located in open chromatin regions. Sci Rep 2024; 14:10094. [PMID: 38698200 PMCID: PMC11066111 DOI: 10.1038/s41598-024-60703-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 04/26/2024] [Indexed: 05/05/2024] Open
Abstract
Intramuscular fat (IMF) and backfat thickness (BFT) are critical economic traits impacting meat quality. However, the genetic variants controlling these traits need to be better understood. To advance knowledge in this area, we integrated RNA-seq and single nucleotide polymorphisms (SNPs) identified in genomic and transcriptomic data to generate a linkage disequilibrium filtered panel of 553,581 variants. Expression quantitative trait loci (eQTL) analysis revealed 36,916 cis-eQTLs and 14,408 trans-eQTLs. Association analysis resulted in three eQTLs associated with BFT and 24 with IMF. Functional enrichment analysis of genes regulated by these 27 eQTLs revealed noteworthy pathways that can play a fundamental role in lipid metabolism and fat deposition, such as immune response, cytoskeleton remodeling, iron transport, and phospholipid metabolism. We next used ATAC-Seq assay to identify and overlap eQTL and open chromatin regions. Six eQTLs were in regulatory regions, four in predicted insulators and possible CCCTC-binding factor DNA binding sites, one in an active enhancer region, and the last in a low signal region. Our results provided novel insights into the transcriptional regulation of IMF and BFT, unraveling putative regulatory variants.
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Affiliation(s)
- Ingrid Soares Garcia
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Bárbara Silva-Vignato
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Aline Silva Mello Cesar
- Department of Agroindustry, Food and Nutrition, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Juliana Petrini
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Vinicius Henrique da Silva
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Natália Silva Morosini
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Carolina Purcell Goes
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | | | - Thaís Ribeiro da Silva
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Beatriz Delcarme Lima
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Luan Gaspar Clemente
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | | | - Gerson Barreto Mourão
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil.
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2
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Malheiros JM, Correia BSB, Ceribeli C, Bruscadin JJ, Diniz WJS, Banerjee P, da Silva Vieira D, Cardoso TF, Andrade BGN, Petrini J, Cardoso DR, Colnago LA, Bogusz Junior S, Mourão GB, Coutinho LL, Palhares JCP, de Medeiros SR, Berndt A, de Almeida Regitano LC. Ruminal and feces metabolites associated with feed efficiency, water intake and methane emission in Nelore bulls. Sci Rep 2023; 13:18001. [PMID: 37865691 PMCID: PMC10590413 DOI: 10.1038/s41598-023-45330-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023] Open
Abstract
The objectives of this study were twofold: (1) to identify potential differences in the ruminal and fecal metabolite profiles of Nelore bulls under different nutritional interventions; and (2) to identify metabolites associated with cattle sustainability related-traits. We used different nutritional interventions in the feedlot: conventional (Conv; n = 26), and by-product (ByPr, n = 26). Thirty-eight ruminal fluid and 27 fecal metabolites were significantly different (P < 0.05) between the ByPr and Conv groups. Individual dry matter intake (DMI), residual feed intake (RFI), observed water intake (OWI), predicted water intake (WI), and residual water intake (RWI) phenotypes were lower (P < 0.05) in the Conv group, while the ByPr group exhibited lower methane emission (ME) (P < 0.05). Ruminal fluid dimethylamine was significantly associated (P < 0.05) with DMI, RFI, FE (feed efficiency), OWI and WI. Aspartate was associated (P < 0.05) with DMI, RFI, FE and WI. Fecal C22:1n9 was significantly associated with OWI and RWI (P < 0.05). Fatty acid C14:0 and hypoxanthine were significantly associated with DMI and RFI (P < 0.05). The results demonstrated that different nutritional interventions alter ruminal and fecal metabolites and provided new insights into the relationship of these metabolites with feed efficiency and water intake traits in Nelore bulls.
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Affiliation(s)
| | | | - Caroline Ceribeli
- Institute of Chemistry, University of São Paulo/USP, São Carlos, São Paulo, Brazil
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Wellison J S Diniz
- Departament of Animal Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Priyanka Banerjee
- Departament of Animal Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | | | - Bruno Gabriel Nascimento Andrade
- Embrapa Southeast Livestock, São Carlos, São Paulo, Brazil
- Computer Science Department, Munster Technological University, MTU/ADAPT, Cork, Ireland
| | - Juliana Petrini
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | | | | | - Gerson Barreto Mourão
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
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3
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Buss CE, Afonso J, de Oliveira PSN, Petrini J, Tizioto PC, Cesar ASM, Gustani-Buss EC, Cardoso TF, Rovadoski GA, da Silva Diniz WJ, de Lima AO, Rocha MIP, Andrade BGN, Wolf JB, Coutinho LL, Mourão GB, de Almeida Regitano LC. Bivariate GWAS reveals pleiotropic regions among feed efficiency and beef quality-related traits in Nelore cattle. Mamm Genome 2023; 34:90-103. [PMID: 36463529 DOI: 10.1007/s00335-022-09969-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/16/2022] [Indexed: 12/07/2022]
Abstract
Feed-efficient cattle selection is among the most leading solutions to reduce cost for beef cattle production. However, technical difficulties in measuring feed efficiency traits had limited the application in livestock. Here, we performed a Bivariate Genome-Wide Association Study (Bi-GWAS) and presented candidate biological mechanisms underlying the association between feed efficiency and meat quality traits in a half-sibling design with 353 Nelore steers derived from 34 unrelated sires. A total of 13 Quantitative Trait Loci (QTL) were found explaining part of the phenotypic variations. An important transcription factor of adipogenesis in cattle, the TAL1 (rs133408775) gene located on BTA3 was associated with intramuscular fat and average daily gain (IMF-ADG), and a region located on BTA20, close to CD180 and MAST4 genes, both related to fat accumulation. We observed a low positive genetic correlation between IMF-ADG (r = 0.30 ± 0.0686), indicating that it may respond to selection in the same direction. Our findings contributed to clarifying the pleiotropic modulation of the complex traits, indicating new QTLs for bovine genetic improvement.
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Affiliation(s)
- Carlos Eduardo Buss
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos, São Paulo, Brazil
- Mindflow Genomics, Leuven, Flanders, Belgium
| | - Juliana Afonso
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
| | - Priscila S N de Oliveira
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | - Juliana Petrini
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | - Aline S M Cesar
- Department of Agroindustry, Food and Nutrition, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | - Emanuele Cristina Gustani-Buss
- Mindflow Genomics, Leuven, Flanders, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium
| | - Tainã Figueiredo Cardoso
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
| | - Gregori A Rovadoski
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | - Andressa Oliveira de Lima
- Division of Medical Genetics, Department of Genomics Science, University of Washington, Seattle, WA, USA
| | | | - Bruno Gabriel Nascimento Andrade
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
- Department of Computer Science, Munster Technological University/MTU, Cork, Ireland
| | - Jason B Wolf
- Department of Biology & Biochemistry, Milner Centre for Evolution Bath, University of Bath, Bath, BA2 7AY, UK
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
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Bruscadin JJ, Cardoso TF, da Silva Diniz WJ, de Souza MM, Afonso J, Vieira D, Malheiros J, Andrade BGN, Petrini J, Ferraz JBS, Zerlotini A, Mourão GB, Coutinho LL, de Almeida Regitano LC. Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle. Genes (Basel) 2022; 13:genes13122336. [PMID: 36553605 PMCID: PMC9777870 DOI: 10.3390/genes13122336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Traditional transcriptomics approaches have been used to identify candidate genes affecting economically important livestock traits. Regulatory variants affecting these traits, however, remain under covered. Genomic regions showing allele-specific expression (ASE) are under the effect of cis-regulatory variants, being useful for improving the accuracy of genomic selection models. Taking advantage of the better of these two methods, we investigated single nucleotide polymorphisms (SNPs) in regions showing differential ASE (DASE SNPs) between contrasting groups for beef quality traits. For these analyses, we used RNA sequencing data, imputed genotypes and genomic estimated breeding values of muscle-related traits from 190 Nelore (Bos indicus) steers. We selected 40 contrasting unrelated samples for the analysis (N = 20 animals per contrasting group) and used a beta-binomial model to identify ASE SNPs in only one group (i.e., DASE SNPs). We found 1479 DASE SNPs (FDR ≤ 0.05) associated with 55 beef-quality traits. Most DASE genes were involved with tenderness and muscle homeostasis, presenting a co-expression module enriched for the protein ubiquitination process. The results overlapped with epigenetics and phenotype-associated data, suggesting that DASE SNPs are potentially linked to cis-regulatory variants affecting simultaneously the transcription and phenotype through chromatin state modulation.
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Affiliation(s)
- Jennifer Jessica Bruscadin
- Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos 13560-000, SP, Brazil
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
| | | | | | | | - Juliana Afonso
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
| | - Dielson Vieira
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jessica Malheiros
- Federal University of Latin American Integration-UNILA, Foz do Iguaçu 85851-000, PR, Brazil
| | | | - Juliana Petrini
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, University of São Paulo (FMVZ—USP), Pirassununga 13630-000, SP, Brazil
| | | | - Gerson Barreto Mourão
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
| | - Luiz Lehmann Coutinho
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
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5
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Bruscadin JJ, Cardoso TF, da Silva Diniz WJ, Afonso J, de Souza MM, Petrini J, Nascimento Andrade BG, da Silva VH, Ferraz JBS, Zerlotini A, Mourão GB, Coutinho LL, de Almeida Regitano LC. Allele-specific expression reveals functional SNPs affecting muscle-related genes in bovine. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2022; 1865:194886. [DOI: 10.1016/j.bbagrm.2022.194886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/27/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022]
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Silva-Vignato B, Cesar ASM, Afonso J, Moreira GCM, Poleti MD, Petrini J, Garcia IS, Clemente LG, Mourão GB, Regitano LCDA, Coutinho LL. Integrative Analysis Between Genome-Wide Association Study and Expression Quantitative Trait Loci Reveals Bovine Muscle Gene Expression Regulatory Polymorphisms Associated With Intramuscular Fat and Backfat Thickness. Front Genet 2022; 13:935238. [PMID: 35991540 PMCID: PMC9386181 DOI: 10.3389/fgene.2022.935238] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding the architecture of gene expression is fundamental to unravel the molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These traits are economically important for the beef industry since they affect carcass and meat quality. Our main goal was to identify gene expression regulatory polymorphisms within genomic regions (QTL) associated with IMF and BFT in Nellore cattle. For that, we used RNA-Seq data from 193 Nellore steers to perform SNP calling analysis. Then, we combined the RNA-Seq SNP and a high-density SNP panel to obtain a new dataset for further genome-wide association analysis (GWAS), totaling 534,928 SNPs. GWAS was performed using the Bayes B model. Twenty-one relevant QTL were associated with our target traits. The expression quantitative trait loci (eQTL) analysis was performed using Matrix eQTL with the complete SNP dataset and 12,991 genes, revealing a total of 71,033 cis and 36,497 trans-eQTL (FDR < 0.05). Intersecting with QTL for IMF, we found 231 eQTL regulating the expression levels of 117 genes. Within those eQTL, three predicted deleterious SNPs were identified. We also identified 109 eQTL associated with BFT and affecting the expression of 54 genes. This study revealed genomic regions and regulatory SNPs associated with fat deposition in Nellore cattle. We highlight the transcription factors FOXP4, FOXO3, ZSCAN2, and EBF4, involved in lipid metabolism-related pathways. These results helped us to improve our knowledge about the genetic architecture behind important traits in cattle.
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Affiliation(s)
- Bárbara Silva-Vignato
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Aline Silva Mello Cesar
- Department of Agroindustry, Food, and Nutrition, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | | | | | - Mirele Daiana Poleti
- College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Juliana Petrini
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Ingrid Soares Garcia
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Luan Gaspar Clemente
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | | | - Luiz Lehmann Coutinho
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
- *Correspondence: Luiz Lehmann Coutinho,
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7
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da Silva VH, Goes CP, Trevisoli PA, Lello R, Clemente LG, de Almeida TB, Petrini J, Coutinho LL. Simulation of group testing scenarios can boost COVID-19 screening power. Sci Rep 2022; 12:11854. [PMID: 35831373 PMCID: PMC9277601 DOI: 10.1038/s41598-022-14626-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 06/09/2022] [Indexed: 12/02/2022] Open
Abstract
The COVID-19 has severely affected economies and health systems around the world. Mass testing could work as a powerful alternative to restrain disease dissemination, but the shortage of reagents is a limiting factor. A solution to optimize test usage relies on ‘grouping’ or ‘pooling’ strategies, which combine a set of individuals in a single reaction. To compare different group testing configurations, we developed the poolingr package, which performs an innovative hybrid in silico/in vitro approach to search for optimal testing configurations. We used 6759 viral load values, observed in 2389 positive individuals, to simulate a wide range of scenarios. We found that larger groups (>100) framed into multi-stage setups (up to six stages) could largely boost the power to detect spreaders. Although the boost was dependent on the disease prevalence, our method could point to cheaper grouping schemes to better mitigate COVID-19 dissemination through identification and quarantine recommendation for positive individuals.
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Affiliation(s)
- Vinicius Henrique da Silva
- Department of Animal Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Carolina Purcell Goes
- Department of Animal Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Priscila Anchieta Trevisoli
- Department of Animal Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Raquel Lello
- Department of Animal Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Luan Gaspar Clemente
- Department of Animal Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | | | - Juliana Petrini
- Department of Animal Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil.
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8
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Cardoso TF, Bruscadin JJ, Afonso J, Petrini J, Andrade BGN, de Oliveira PSN, Malheiros JM, Rocha MIP, Zerlotini A, Ferraz JBS, Mourão GB, Coutinho LL, Regitano LCA. EEF1A1 transcription cofactor gene polymorphism is associated with muscle gene expression and residual feed intake in Nelore cattle. Mamm Genome 2022; 33:619-628. [PMID: 35816191 DOI: 10.1007/s00335-022-09959-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/22/2022] [Indexed: 12/01/2022]
Abstract
Cis-acting effects of noncoding variants on gene expression and regulatory molecules constitute a significant factor for phenotypic variation in complex traits. To provide new insights into the impacts of single-nucleotide polymorphisms (SNPs) on transcription factors (TFs) and transcription cofactors (TcoF) coding genes, we carried out a multi-omic analysis to identify cis-regulatory effects of SNPs on these genes' expression in muscle and describe their association with feed efficiency-related traits in Nelore cattle. As a result, we identified one SNP, the rs137256008C > T, predicted to impact the EEF1A1 gene expression (β = 3.02; P-value = 3.51E-03) and the residual feed intake trait (β = - 3.47; P-value = 0.02). This SNP was predicted to modify transcription factor sites and overlaps with several QTL for feed efficiency traits. In addition, co-expression network analyses showed that animals containing the T allele of the rs137256008 SNP may be triggering changes in the gene network. Therefore, our analyses reinforce and contribute to a better understanding of the biological mechanisms underlying gene expression control of feed efficiency traits in bovines. The cis-regulatory SNP can be used as biomarker for feed efficiency in Nelore cattle.
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Affiliation(s)
- T F Cardoso
- Embrapa Southeast Livestock, São Carlos, SP, Brazil
| | - J J Bruscadin
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - J Afonso
- Embrapa Southeast Livestock, São Carlos, SP, Brazil
| | - J Petrini
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
| | - B G N Andrade
- Computer Science Department, Munster Technological University, MTU/ADAPT, Cork, Ireland
| | - P S N de Oliveira
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - J M Malheiros
- Federal University of Latin American Integration, Foz do Iguaçu, Paraná, Brazil
| | - M I P Rocha
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - A Zerlotini
- Embrapa Agricultural Informatics, Campinas, SP, Brazil
| | - J B S Ferraz
- Department of Veterinary Medicine, University of São Paulo/FZEA, Pirassununga, Brazil
| | - G B Mourão
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
| | - L L Coutinho
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
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9
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Andrade BGN, Bressani FA, Cuadrat RRC, Cardoso TF, Malheiros JM, de Oliveira PSN, Petrini J, Mourão GB, Coutinho LL, Reecy JM, Koltes JE, Neto AZ, R de Medeiros S, Berndt A, Palhares JCP, Afli H, Regitano LCA. Stool and Ruminal Microbiome Components Associated With Methane Emission and Feed Efficiency in Nelore Beef Cattle. Front Genet 2022; 13:812828. [PMID: 35656319 PMCID: PMC9152269 DOI: 10.3389/fgene.2022.812828] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/02/2022] [Indexed: 12/27/2022] Open
Abstract
Background: The impact of extreme changes in weather patterns on the economy and human welfare is one of the biggest challenges our civilization faces. From anthropogenic contributions to climate change, reducing the impact of farming activities is a priority since it is responsible for up to 18% of global greenhouse gas emissions. To this end, we tested whether ruminal and stool microbiome components could be used as biomarkers for methane emission and feed efficiency in bovine by studying 52 Brazilian Nelore bulls belonging to two feed intervention treatment groups, that is, conventional and by-product-based diets. Results: We identified a total of 5,693 amplicon sequence variants (ASVs) in the Nelore bulls’ microbiomes. A Differential abundance analysis with the ANCOM approach identified 30 bacterial and 15 archaeal ASVs as differentially abundant (DA) among treatment groups. An association analysis using Maaslin2 software and a linear mixed model indicated that bacterial ASVs are linked to the host’s residual methane emission (RCH4) and residual feed intake (RFI) phenotype variation, suggesting their potential as targets for interventions or biomarkers. Conclusion: The feed composition induced significant differences in both abundance and richness of ruminal and stool microbial populations in ruminants of the Nelore breed. The industrial by-product-based dietary treatment applied to our experimental groups influenced the microbiome diversity of bacteria and archaea but not of protozoa. ASVs were associated with RCH4 emission and RFI in ruminal and stool microbiomes. While ruminal ASVs were expected to influence CH4 emission and RFI, the relationship of stool taxa, such as Alistipes and Rikenellaceae (gut group RC9), with these traits was not reported before and might be associated with host health due to their link to anti-inflammatory compounds. Overall, the ASVs associated here have the potential to be used as biomarkers for these complex phenotypes.
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Affiliation(s)
- Bruno G N Andrade
- Embrapa Southeast Livestock, São Carlos, Brazil.,Department of Computer Science, Munster Technological University, MTU/ADAPT, Cork, Ireland
| | | | - Rafael R C Cuadrat
- Department of Molecular Epidemiology, German Institute of Human Nutrition Potsdam-Rehbrücke (DIfE), Nuthetal, Germany
| | | | | | | | - Juliana Petrini
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Gerson B Mourão
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | | | | | | | | | - Haithem Afli
- Department of Computer Science, Munster Technological University, MTU/ADAPT, Cork, Ireland
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10
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Petrini J, Salgado RM, Rodriguez MAP, Machado PF, Mourão GB. Machine learning methods for the prediction of milk fatty acid content. INT J DAIRY TECHNOL 2022. [DOI: 10.1111/1471-0307.12877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Juliana Petrini
- Department of Animal Science University of São Paulo Piracicaba 13418‐900 Brazil
| | - Ricardo Menezes Salgado
- Department of Computer Science, Institute of Exact Sciences Federal University of Alfenas Alfenas 37130‐001 Brazil
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11
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Bóscollo PP, Dauria BD, Portes JV, Petrini J, da Silva Lopes JE, Ladeira GC, Júnior LFS, Mourão GB. BIOECONOMIC SELECTION INDexes FOR terminal lamb systems in tropical conditions. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Dauria BD, Sigdel A, Petrini J, Bóscollo PP, Pilonetto F, Salvian M, Rezende FM, Pedrosa VB, Bittar CMM, Machado PF, Coutinho LL, Wiggans GR, Mourão GB. Genetic effects of heat stress on milk fatty acids in a Brazilian Holstein cattle. J Dairy Sci 2022; 105:3296-3305. [PMID: 35094861 DOI: 10.3168/jds.2021-20914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/13/2021] [Indexed: 11/19/2022]
Abstract
The present study aimed to estimate covariance components of milk fatty acids (FA) and to compare the genomic estimated breeding values under general and heat-stress effects. Data consisted of 38,762 test-day records from 6,344 Holstein cows obtained from May 2012 through January 2018 on 4 dairy herds from Brazil. Single-trait repeatability test-day models with random regressions as a function of temperature-humidity index values were used for genetic analyses. The models included contemporary groups, parity order (1-6), and days in milk classes as fixed effects, and general and thermotolerance additive genetic and permanent environmental as random effects. Notably, differences in heritability estimates between environments (general and heat stress) increased (0.03 to 0.06) for unsaturated FA traits, such as unsaturated, monounsaturated, and polyunsaturated, at higher heat-stress levels. In contrast, heritability estimated between environments for saturated FA traits, including saturated FA, palmitic acid (C16:0), and stearic acid (C18:0) did not observe significant differences between environments. In addition, our study revealed negative genetic correlations between general and heat-stress additive genetic effects (antagonistic effect) for the saturated FA, C16:0, C18:0, and C18:1, which ranged from -0.007 to -0.32. Spearman's ranking correlation between genomic estimated breeding values ranged from -0.27 to 0.99. Results indicated a moderate to strong interaction of genotype by the environment for most FA traits comparing a heat-stress environment with thermoneutral conditions. Our findings point out novel opportunities to explore the use of FA milk profile and heat-stress models.
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Affiliation(s)
- B D Dauria
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - A Sigdel
- Department of Animal and Dairy Science, University of Wisconsin, Madison 53706
| | - J Petrini
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - P P Bóscollo
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - F Pilonetto
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - M Salvian
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - F M Rezende
- Department of Animal Sciences, University of Florida, Gainesville 32608
| | - V B Pedrosa
- Department of Animal Science, State University of Ponta Grossa, Ponta Grossa, PR 84030-900, Brazil
| | - C M M Bittar
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - P F Machado
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - L L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - G R Wiggans
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - G B Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil.
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13
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Colonia SRR, Oliveira ADC, Pilonetto F, Dauria BD, Mourão GB, Machado PF, Nogueira DA, Beijo LA, Petrini J. Genetic parameters for milk yield, casein percentage, subclinical mastitis incidence and sexual precocity using Bayesian linear and threshold models. Anim Prod Sci 2022. [DOI: 10.1071/an20313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Trevisoli PA, Moreira GCM, Boschiero C, Cesar ASM, Petrini J, Margarido GRA, Ledur MC, Mourão GB, Garrick D, Coutinho LL. A Missense Mutation in the MYBPH Gene Is Associated With Abdominal Fat Traits in Meat-Type Chickens. Front Genet 2021; 12:698163. [PMID: 34456973 PMCID: PMC8386115 DOI: 10.3389/fgene.2021.698163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/09/2021] [Indexed: 12/14/2022] Open
Abstract
Chicken is an important source of protein for human nutrition and a model system for growth and developmental biology. Although the genetic architecture of quantitative traits in meat-type chickens has been the subject of ongoing investigation, the identification of mutations associated with carcass traits of economic interest remains challenging. Therefore, our aim was to identify predicted deleterious mutation, which potentially affects protein function, and test if they were associated with carcass traits in chickens. For that, we performed a genome-wide association analysis (GWAS) for breast, thigh and drumstick traits in meat-type chickens and detected 19 unique quantitative trait loci (QTL). We then used: (1) the identified windows; (2) QTL for abdominal fat detected in a previous study with the same population and (3) previously obtained whole genome sequence data, to identify 18 predicted deleterious single nucleotide polymorphisms (SNPs) in those QTL for further association with breast, thigh, drumstick and abdominal fat traits. Using the additive model, a predicted deleterious SNP c.482C > T (SIFT score of 0.4) was associated (p-value < 0.05) with abdominal fat weight and percentage. This SNP is in the second exon of the MYBPH gene, and its allele frequency deviates from Hardy–Weinberg equilibrium. In conclusion, our study provides evidence that the c.482C > T SNP in the MYBPH gene is a putative causal mutation for fat deposition in meat-type chickens.
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Affiliation(s)
- Priscila Anchieta Trevisoli
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Gabriel Costa Monteiro Moreira
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Clarissa Boschiero
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Aline Silva Mello Cesar
- Agri-Food Industry, Food and Nutrition Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Juliana Petrini
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | | | | | - Gerson Barreto Mourão
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Dorian Garrick
- School of Agriculture, Massey University, Wellington, New Zealand
| | - Luiz Lehmann Coutinho
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
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15
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Carrara ER, Petrini J, Salvian M, de Oliveira HR, Rovadoscki GA, Iung LHDS, Miquilini M, Machado PF, Mourão GB. Genetic parameters for milk yield and quality traits of Brazilian Holstein cows as a function of temperature and humidity index. J Anim Breed Genet 2021; 138:643-654. [PMID: 34184799 DOI: 10.1111/jbg.12636] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/11/2021] [Accepted: 06/11/2021] [Indexed: 11/29/2022]
Abstract
Measurements of milk yield (MY), somatic cell score (SCS), percentage of fat (FP), protein (PP), lactose (LP), casein (CP) and percentage of palmitic (C16:0), stearic (C18:0), oleic (C18:1), total saturated (SFA), unsaturated (UFA), monounsaturated (MUFA) and polyunsaturated (PUFA) fatty acids in milk from 5,224 Holstein cows were evaluated as a function of a temperature and humidity index (THI). Legendre orthogonal polynomials from second to seventh order were tested. The best fit order for MY, PP and C18:0 was the third, whereas the second for all other traits. The heritability estimates decreased for MY (0.31 to 0.14), FP (0.28 to 0.16), LP (0.43 to 0.30), SCS (0.14 to 0.09), SFA (0.33 to 0.22) and C16:0 (0.31 to 0.26), whereas increased for CP (0.32 to 0.42), MUFA (0.08 to 0.13), UFA (0.07 to 0.11) and C18:1 (0.07 to 0.11) as the THI level increased. For PP, heritabilities (0.26 to 0.39) presented larger values in intermediate THI. For PUFA and C18:0, heritabilities were approximately constant (0.13 to 0.14 and 0.15, respectively). However, the greatest variations may have been the result of the limitations of Legendre polynomials at the extreme points of the curve, and the pattern of heritabilities curves was approximately constant for the evaluated traits. Spearman's rank correlations between breeding values in extreme THI levels were greater than 0.80 for all traits considering all animals, only cows and only bulls. When considering the top 1% and the top 50% animals (only cows, only bulls and all), Spearman correlations smaller than 0.70 were found, suggesting reranking of the animals. Although there was little variation in the variance components over THI, it is possible that there is no heat stress in the animals studied, because, on average, there was no great impact of the thermal load on the traits. One possible explanation is the use of herds with little climatic difference among herds, as well as the use of fans and sprinklers into the barns. However, the THI levels may be important factors in the selection process, as reranking of animals was verified.
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Affiliation(s)
| | - Juliana Petrini
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - Mayara Salvian
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - Hinayah Rojas de Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Canada
| | | | | | - Marina Miquilini
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
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16
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Afonso J, Fortes MRS, Reverter A, Diniz WJDS, Cesar ASM, Lima AOD, Petrini J, de Souza MM, Coutinho LL, Mourão GB, Zerlotini A, Gromboni CF, Nogueira ARA, Regitano LCDA. Genetic regulators of mineral amount in Nelore cattle muscle predicted by a new co-expression and regulatory impact factor approach. Sci Rep 2020; 10:8436. [PMID: 32439843 PMCID: PMC7242321 DOI: 10.1038/s41598-020-65454-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/04/2020] [Indexed: 12/11/2022] Open
Abstract
Mineral contents in bovine muscle can affect meat quality, growth, health, and reproductive traits. To better understand the genetic basis of this phenotype in Nelore (Bos indicus) cattle, we analysed genome-wide mRNA and miRNA expression data from 114 muscle samples. The analysis implemented a new application for two complementary algorithms: the partial correlation and information theory (PCIT) and the regulatory impact factor (RIF), in which we included the estimated genomic breeding values (GEBVs) for the phenotypes additionally to the expression levels, originally proposed for these methods. We used PCIT to determine putative regulatory relationships based on significant associations between gene expression and GEBVs for each mineral amount. Then, RIF was adopted to determine the regulatory impact of genes and miRNAs expression over the GEBVs for the mineral amounts. We also investigated over-represented pathways, as well as pieces of evidences from previous studies carried in the same population and in the literature, to determine regulatory genes for the mineral amounts. For example, NOX1 expression level was positively correlated to Zinc and has been described as Zinc-regulated in humans. Based on our approach, we were able to identify genes, miRNAs and pathways not yet described as underlying mineral amount. The results support the hypothesis that extracellular matrix interactions are the core regulator of mineral amount in muscle cells. Putative regulators described here add information to this hypothesis, expanding the knowledge on molecular relationships between gene expression and minerals.
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Affiliation(s)
- Juliana Afonso
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Marina Rufino Salinas Fortes
- School of Chemistry and Molecular Biosciences, Faculty of Sciences, The University of Queensland, Brisbane, Australia
| | - Antonio Reverter
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia
| | | | - Aline Silva Mello Cesar
- Department of Agroindustry, Food and Nutrition, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Andressa Oliveira de Lima
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Juliana Petrini
- Department of Statistics, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, Brazil
| | | | | | - Gerson Barreto Mourão
- Department of Agroindustry, Food and Nutrition, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Adhemar Zerlotini
- Bioinformatic Multi-user Laboratory, Embrapa Informática Agropecuária, Campinas, São Paulo, Brazil
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17
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de Lima AO, Koltes JE, Diniz WJS, de Oliveira PSN, Cesar ASM, Tizioto PC, Afonso J, de Souza MM, Petrini J, Rocha MIP, Cardoso TF, Neto AZ, Coutinho LL, Mourão GB, Regitano LCA. Potential Biomarkers for Feed Efficiency-Related Traits in Nelore Cattle Identified by Co-expression Network and Integrative Genomics Analyses. Front Genet 2020; 11:189. [PMID: 32194642 PMCID: PMC7064723 DOI: 10.3389/fgene.2020.00189] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Feed efficiency helps to reduce environmental impacts from livestock production, improving beef cattle profitability. We identified potential biomarkers (hub genes) for feed efficiency, by applying co-expression analysis in Longissimus thoracis RNA-Seq data from 180 Nelore steers. Six co-expression modules were associated with six feed efficiency-related traits (p-value ≤ 0.05). Within these modules, 391 hub genes were enriched for pathways as protein synthesis, muscle growth, and immune response. Trait-associated transcription factors (TFs) ELF1, ELK3, ETS1, FLI1, and TCF4, were identified with binding sites in at least one hub gene. Gene expression of CCDC80, FBLN5, SERPINF1, and OGN was associated with multiple feed efficiency-related traits (FDR ≤ 0.05) and were previously related to glucose homeostasis, oxidative stress, fat mass, and osteoblastogenesis, respectively. Potential regulatory elements were identified, integrating the hub genes with previous studies from our research group, such as the putative cis-regulatory elements (eQTLs) inferred as affecting the PCDH18 and SPARCL1 hub genes related to immune system and adipogenesis, respectively. Therefore, our analyses contribute to a better understanding of the biological mechanisms underlying feed efficiency in bovine and the hub genes disclosed can be used as biomarkers for feed efficiency-related traits in Nelore cattle.
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Affiliation(s)
- Andressa O de Lima
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Wellison J S Diniz
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | | | - Aline S M Cesar
- Department of Agroindustry, Food and Nutrition, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Juliana Afonso
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Marcela M de Souza
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Juliana Petrini
- Exact Sciences Institute, Federal University of Alfenas, Alfenas, Brazil
| | - Marina I P Rocha
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Tainã F Cardoso
- Embrapa Pecuária Sudeste, Empresa Brazileira de Pesquisa Agropecuária, São Carlos, Brazil
| | - Adhemar Zerlotini Neto
- Embrapa Informática Agropecuária, Empresa Brazileira de Pesquisa Agropecuária, Campinas, Brazil
| | - Luiz L Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Gerson B Mourão
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Luciana C A Regitano
- Embrapa Pecuária Sudeste, Empresa Brazileira de Pesquisa Agropecuária, São Carlos, Brazil
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Carrara ER, de Genova Gaya L, de Paiva JT, Petrini J, Salvian M, Rovadoscki GA, Chaves Zanetti Reis A, Machado PF, Barreto Mourão G. Impact of inbreeding on milk fatty acids of a Brazilian Holstein cattle. Anim Prod Sci 2020. [DOI: 10.1071/an19240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Reproductive technologies may either contribute to the increase of genetic gains or inbreeding levels in dairy cattle breeding programs and herds. In general, studies have evaluated the impacts of inbreeding on traditional traits, such as production and reproduction. However, studies on novel traits, such as milk fatty acids profile, are scarce in the literature.
Aim
We aimed to evaluate the impact of inbreeding levels on milk fatty acids profile measured in a Brazilian Holstein cattle population.
Methods
Monthly records of the percentages (%) of palmitic, stearic, oleic, total saturated, unsaturated, monounsaturated and polyunsaturated fatty acids in milk were collected from 2047 Holstein cows between May and December 2012. The pedigree file contained 7963 animals over seven generations. The inbreeding trend was evaluated by linear regression of inbreeding coefficients on generations. The inbreeding impacts on breeding and phenotypic values were evaluated by linear regression of breeding values and phenotypic values on generations respectively. Breeding values were obtained by a Bayesian approach based on an animal model that included the systematic effect of contemporary group, cubic effect of days in milk as a covariate, and the random direct additive genetic and animal permanent environmental effects.
Key results
The average inbreeding coefficient was 0.28% for all animals, and 1.39% for inbred animals. Inbreeding tended to increase 0.24% per generation (P-value <0.0001). The regression coefficients of phenotypic values on inbreeding were not significant for saturated, unsaturated, monounsaturated, palmitic, stearic and oleic fatty acids (P-values >0.18, 0.10, 0.16, 0.26, 0.51 and 0.09 respectively); whereas for polyunsaturated fatty acids, they were significant (P-value <0.04), with an increase of –0.000978% on phenotypic values for each 1% increase in inbreeding. The regression coefficients of breeding values on inbreeding were not significant for unsaturated, monounsaturated, polyunsaturated, stearic and oleic fatty acids (P-values >0.33, 0.78, 0.48, 0.32 and 0.07 respectively). However, they were significant for saturated and palmitic fatty acids (P-values <0.03 and 0.0001 respectively), presenting an increase of 0.000689% and 0.000283% respectively on breeding values for each 1% increase in inbreeding.
Conclusions
There was a significant increase in inbreeding coefficients over the studied generations; however, the impacts on both breeding and phenotypic values were small, when significant.
Implications
Our study may contribute to the understanding of how inbreeding levels may affect the fatty acids profile in a Brazilian Holstein cattle population, as well as encourage future research on this subject.
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Santos MMG, Beijo LA, Avelar FG, Petrini J. Statistical methods for identification of golden ratio. Biosystems 2019; 189:104080. [PMID: 31812721 DOI: 10.1016/j.biosystems.2019.104080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 08/07/2019] [Accepted: 11/28/2019] [Indexed: 01/06/2023]
Abstract
Several biological systems such as the biomechanics of human heart, locomotion, and phyllotaxis of plants present a harmonic behavior because their fractal structure are associated to the golden ratio. The golden ratio (Φ = 1.618033988749…), also known as Phi, golden mean, golden section or divine proportion, is an irrational constant found in various forms in nature and recently has been used in many health areas. However, there is no literature on a specific statistical test to identify the golden ratio structures. To validate the results from each survey, it is necessary that statistical techniques be correctly selected and implemented, and the absence of a test to identify the golden ratio may undermines the scientific papers which have this goal. Since the golden number is a ratio, some tests have been wrongly applied in its identification. The objective of this paper is to present and to evaluate methods for identification of golden ratio. Four tests were evaluated: t-Student with ratio statistic (TR), with delta statistic (TΔ), with difference statistic (TED), and Wilcoxon test with statistic difference (WD). Data simulating different samples sizes (n = 2-200) and variability scenarios were used. The tests were assessed regarding type I error rate and power. For TΔ, type I error rate increased along with sample size and variability, achieving 50% in the scenario of relative standard deviation of 12.5% and 20.0% for line segments of lengths a and b, and sample size equal 200. This test also showed lower power when compared to the others in all scenarios. Similarly, for TR, the type I error rate was sensitive to the increasing in sample size, varying from 5 to 60%. On the other hand, WD and TED were associated to low type I error rates (around 5%) and high power (6.1% for sample size equal 2-100% for sample size equal 200). The TΔ and TR were inadequate to identify the golden ratio, since they did not controlled the type I error rate and/or presented low power, leading to possible erroneous conclusions. Therefore WD and TED, both with statistical of difference, appeared as the most appropriate methods to test golden ratio structures.
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Affiliation(s)
| | - Luiz Alberto Beijo
- Department of Statistics, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, MG, 37130-001, Brazil.
| | - Fabricio Goecking Avelar
- Department of Statistics, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, MG, 37130-001, Brazil
| | - Juliana Petrini
- Department of Statistics, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, MG, 37130-001, Brazil
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20
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Petrini J, Souza Iung LH, Petersen Rodriguez MA, Salvian M, Alberto Rovadoscki G, Colonia SRR, Cassoli LD, Lehmann Coutinho L, Fernando Machado P, Wiggans G, Mourão GB. Assessing the accuracy of prediction for milk fatty acids by using a small reference population of tropical Holstein cows. J Anim Breed Genet 2019; 136:453-463. [DOI: 10.1111/jbg.12434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Juliana Petrini
- Department of Animal Science University of São Paulo Piracicaba Brazil
- Department of Statistics, Institute of Exact Sciences Federal University of Alfenas Alfenas Brazil
| | | | | | - Mayara Salvian
- Department of Animal Science University of São Paulo Piracicaba Brazil
| | | | | | | | | | | | - George Wiggans
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA Beltsville Maryland
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21
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Iung LHS, Petrini J, Ramírez-Díaz J, Salvian M, Rovadoscki GA, Pilonetto F, Dauria BD, Machado PF, Coutinho LL, Wiggans GR, Mourão GB. Genome-wide association study for milk production traits in a Brazilian Holstein population. J Dairy Sci 2019; 102:5305-5314. [PMID: 30904307 DOI: 10.3168/jds.2018-14811] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 10/19/2018] [Indexed: 12/19/2022]
Abstract
Advances in the molecular area of selection have expanded knowledge of the genetic architecture of complex traits through genome-wide association studies (GWAS). Several GWAS have been performed so far, but confirming these results is not always possible due to several factors, including environmental conditions. Thus, our objective was to identify genomic regions associated with traditional milk production traits, including milk yield, somatic cell score, fat, protein and lactose percentages, and fatty acid composition in a Holstein cattle population producing under tropical conditions. For this, 75,228 phenotypic records from 5,981 cows and genotypic data of 56,256 SNP from 1,067 cows were used in a weighted single-step GWAS. A total of 46 windows of 10 SNP explaining more than 1% of the genetic variance across 10 Bos taurus autosomes (BTA) harbored well-known and novel genes. The MGST1 (BTA5), ABCG2 (BTA6), DGAT1 (BTA14), and PAEP (BTA11) genes were confirmed within some of the regions identified in our study. Potential novel genes involved in tissue damage and repair of the mammary gland (COL18A1), immune response (LTTC19), glucose homeostasis (SLC37A1), synthesis of unsaturated fatty acids (LTBP1), and sugar transport (SLC37A1 and MFSD4A) were found for milk yield, somatic cell score, fat percentage, and fatty acid composition. Our findings may assist genomic selection by using these regions to design a customized SNP array to improve milk production traits on farms with similar environmental conditions.
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Affiliation(s)
- L H S Iung
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - J Petrini
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - J Ramírez-Díaz
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - M Salvian
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - G A Rovadoscki
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - F Pilonetto
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - B D Dauria
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - P F Machado
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - L L Coutinho
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - G R Wiggans
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - G B Mourão
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil.
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Alvarenga AB, Rovadoscki GA, Petrini J, Coutinho LL, Morota G, Spangler ML, Pinto LFB, Carvalho GGP, Mourão GB. Linkage disequilibrium in Brazilian Santa Inês breed, Ovis aries. Sci Rep 2018; 8:8851. [PMID: 29892085 PMCID: PMC5995818 DOI: 10.1038/s41598-018-27259-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 05/25/2018] [Indexed: 11/13/2022] Open
Abstract
For genomic selection to be successful, there must be sufficient linkage disequilibrium between the markers and the causal mutations. The objectives of this study were to evaluate the extent of LD in ovine using the Santa Inês breed and to infer the minimum number of markers required to reach reasonable prediction accuracy. In total, 38,168 SNPs and 395 samples were used. The mean LD between adjacent marker pairs measured by r2 and |D′| were 0.166 and 0.617, respectively. LD values between adjacent marker pairs ranged from 0.135 to 0.194 and from 0.568 to 0.650 for r2 for |D′| across all chromosomes. The average r2 between all pairwise SNPs on each chromosome was 0.018. SNPs separated by between 0.10 to 0.20 Mb had an estimated average r2 equal to 0.1033. The identified haplotype blocks consisted of 2 to 21 markers. Moreover, estimates of average coefficients of inbreeding and effective population size were 0.04 and 96, respectively. LD estimated in this study was lower than that reported in other species and was characterized by short haplotype blocks. Our results suggest that the use of a higher density SNP panel is recommended for the implementation of genomic selection in the Santa Inês breed.
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Affiliation(s)
- Amanda Botelho Alvarenga
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Gregori Alberto Rovadoscki
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Juliana Petrini
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Gota Morota
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | | | | | | | - Gerson Barreto Mourão
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil.
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Rovadoscki GA, Pertile SFN, Alvarenga AB, Cesar ASM, Pértille F, Petrini J, Franzo V, Soares WVB, Morota G, Spangler ML, Pinto LFB, Carvalho GGP, Lanna DPD, Coutinho LL, Mourão GB. Estimates of genomic heritability and genome-wide association study for fatty acids profile in Santa Inês sheep. BMC Genomics 2018; 19:375. [PMID: 29783944 PMCID: PMC5963081 DOI: 10.1186/s12864-018-4777-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 05/10/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Despite the health concerns and nutritional importance of fatty acids, there is a relative paucity of studies in the literature that report genetic or genomic parameters, especially in the case of sheep populations. To investigate the genetic architecture of fatty acid composition of sheep, we conducted genome-wide association studies (GWAS) and estimated genomic heritabilities for fatty acid profile in Longissimus dorsi muscle of 216 male sheep. RESULTS Genomic heritability estimates for fatty acid content ranged from 0.25 to 0.46, indicating that substantial genetic variation exists for the evaluated traits. Therefore, it is possible to alter fatty acid profiles through selection. Twenty-seven genomic regions of 10 adjacent SNPs associated with fatty acids composition were identified on chromosomes 1, 2, 3, 5, 8, 12, 14, 15, 16, 17, and 18, each explaining ≥0.30% of the additive genetic variance. Twenty-three genes supporting the understanding of genetic mechanisms of fat composition in sheep were identified in these regions, such as DGAT2, TRHDE, TPH2, ME1, C6, C7, UBE3D, PARP14, and MRPS30. CONCLUSIONS Estimates of genomic heritabilities and elucidating important genomic regions can contribute to a better understanding of the genetic control of fatty acid deposition and improve the selection strategies to enhance meat quality and health attributes.
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Affiliation(s)
- G A Rovadoscki
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - S F N Pertile
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - A B Alvarenga
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - A S M Cesar
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - F Pértille
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - J Petrini
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - V Franzo
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - W V B Soares
- Institute of Zootechny (IZ), Nova Odessa, SP, Brazil
| | - G Morota
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - M L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - L F B Pinto
- Department of Animal Science, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - G G P Carvalho
- Department of Animal Science, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - D P D Lanna
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - L L Coutinho
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - G B Mourão
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil.
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Wassmuth R, Hristova K, Monney P, Olander RFW, Rodriguez Munoz D, Huayan X, Pagourelias E, Loardi C, Moreno J, Miljkovic T, Takase H, Latet SC, Henquin R, America R, Carter-Storch R, Panelo ML, Fernandez-Golfin C, Cho IJ, Petrini J, Buonauro A, Liu B, Mapelli M, Tamulenaite E, De Chiara B, Minden H, Kostova V, Nesheva N, Katova TZ, Bojadzhiev L, Crisinel V, Reverdin S, Conti L, Mach F, Mueller H, Jeanrenaud X, Bochud M, Ehret G, Sundholm JKM, Ojala T, Andersson S, Sarkola T, Moya Mur JL, Berlot B, Fernandez-Golfin C, Moreno Planas J, Casas Rojo E, Garcia Martin A, Jimenez Nacher JJ, Hernandez-Madrid A, Franco Diez E, Matia Frances R, Zamorano JL, Zhigang YANG, Yingkun GUO, Jing CHEN, Duchenne J, Mirea O, Triantafyllis A, Michalski B, Vovas G, Delforge M, Van Cleemput J, Bogaert J, Voigt JU, Saccocci M, Tamborini G, Veglia F, Pepi M, Alamanni F, Zanobini M, Zuniga Sedano JJ, Alexanderson E, Martinez C, Bjelobrk M, Pavlovic K, Ilic A, Colakovic S, Dodic S, Tanaka T, Machii M, Nonaka D, Van Herck PL, Claeys MJ, Haine SE, Miljoen HP, Segers VF, Vandendriessche TR, De Winter BY, Hoymans VY, Vrints CJ, Lombardero M, Perea G, Miele MM, De Amicis DAV, Mannacio VAM, Dahl JS, Christensen NL, Soendergaard EV, Marcussen N, Moeller JE, Fernandez-Palomeque C, Garcia-Vega D, Mont-Girbau L, Pardo A, Izurieta C, Boretti I, Hinojar R, Gonzalez-Gomez A, Garcia Martin A, Casas E, Salido L, Barrios V, Ruiz S, Moya JL, Hernandez Antolin R, Jimenez Nacher JL, Zamorano JL, Chang HJ, Choi HH, Lee SY, Shim CY, Ha JW, Chung N, Ring M, Caidahl K, Eriksson MJ, Esposito R, Santoro C, Monteagudo JM, Trimarco B, Galderisi M, Zamorano JL, Baig S, Hayer M, Steeds R, Edwards N, Fusini L, Zagni P, Muratori M, Agostoni P, Tamborini G, Gripari P, Ghulam Ali S, Pepi M, Fiorentini C, Valuckiene Z, Jurkevicius R, Peritore A, Botta L, Belli O, Musca F, Casadei F, Russo C, Giannattasio C, Moreo A. Poster Session 6Assessment of morphology and functionP1222Multimodality imaging for left atrial appendage occluder sizingP1223Longitudinal left atrial strain is a main predictor for long term prognosis on atrial fibrillation after CABG operation patientsP1224Comparison of 2D and 3D left ventricular volumes measurements: results from the SKIPOGH II studyP1225Adjusting for thoracic circumference is superior to body surface area in the assessment of neonatal cardiac dimensions in foetal growth abnormalityP1226Maximal vortex suction pressure: an equivocal marker for optimization of atrio-ventricular delayP1227Volume-time curve of cardiac magnetic resonance assessed left ventricular dysfunction in coronary artery disease patients with type 2 diabetes mellitusP1228Thickness matters, but not in the same way for all strain parametersP1229Digging deeper in postoperative modifications of right ventricular function: impact of pericardial approach and cardioplegiaP1230Left atrial function evaluated by 2D-speckle tracking echocardiography in diabetes mellitus populationP1231The influence of arterial hypertension duration on left ventricular diastolic parameters in patients with well regulated arterial blood pressureP1232Investigation of factors affecting left ventricular diastolic dysfunction determined using mitral annulus velocityP1233High regulatory T-lymphocytes after ST-elevation myocardial infarction relate with adverse left ventricular remodelling assessed by 3D-echocardiographyP1234Prevalence of paradoxical low flow/low gradient severe aortic stenosis measure with 3 dimensional transesophageal echocardiographyP1235Coronary microvascular and diastolic dysfunctions after aortic valve replacement: comparison between mechanical and biological prosthesesP1236Normal-flow, low gradient aortic stenosis is common in a population of patients with severe aortic valve stenosis undergoing aortic valve replacementP1237Analysis of validity and reproducibility of calcium burden visual estimation by echocardiographyP12383D full automatic software in the evaluation of aortic stenosis severity in TAVI patients. Preliminary resultsP1239Differential impact of net atrioventricular compliance on clinical outcomes in patients with mitral stenosis according to cardiac rhythmP1240Aortic regurgitation affects the intima-media thickness of the right and left common carotid artery differentlyP1241Global longitudinal strain: an hallmark of cardiac damage in mitral valve regurgitation. Experience from the european registry of mitral regurgitationP1242Echocardiographic characterisation of Barlow's disease versus fibroelastic deficiencyP1243Echocardiographic screening for rheumatic heart disease in a ugandan orphanage - feasibility and outcomesP1244Alterations in right ventricular mechanics upon follow-up period in patients with persistent ischemic mitral regurgitation after inferoposterior myocardial infarctionP1245Ten-years conventional mitral surgery in patients with mitral regurgitation and left ventricular dysfunction: clinical and echocardiographic outcomes. Eur Heart J Cardiovasc Imaging 2016. [DOI: 10.1093/ehjci/jew266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Petrini J, Ring M, Eriksson P, Franco-Cereceda A, Caidahl K, Eriksson M. Intima-media thickness of the descending aorta is influenced by aortic valve disease. Atherosclerosis 2016. [DOI: 10.1016/j.atherosclerosis.2016.07.798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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26
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Rovadoscki GA, Petrini J, Ramirez-Diaz J, Pertile SFN, Pertille F, Salvian M, Iung LHS, Rodriguez MAP, Zampar A, Gaya LG, Carvalho RSB, Coelho AAD, Savino VJM, Coutinho LL, Mourão GB. Genetic parameters for growth characteristics of free-range chickens under univariate random regression models. Poult Sci 2016; 95:1989-98. [PMID: 27208151 DOI: 10.3382/ps/pew167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2016] [Indexed: 11/20/2022] Open
Abstract
Repeated measures from the same individual have been analyzed by using repeatability and finite dimension models under univariate or multivariate analyses. However, in the last decade, the use of random regression models for genetic studies with longitudinal data have become more common. Thus, the aim of this research was to estimate genetic parameters for body weight of four experimental chicken lines by using univariate random regression models. Body weight data from hatching to 84 days of age (n = 34,730) from four experimental free-range chicken lines (7P, Caipirão da ESALQ, Caipirinha da ESALQ and Carijó Barbado) were used. The analysis model included the fixed effects of contemporary group (gender and rearing system), fixed regression coefficients for age at measurement, and random regression coefficients for permanent environmental effects and additive genetic effects. Heterogeneous variances for residual effects were considered, and one residual variance was assigned for each of six subclasses of age at measurement. Random regression curves were modeled by using Legendre polynomials of the second and third orders, with the best model chosen based on the Akaike Information Criterion, Bayesian Information Criterion, and restricted maximum likelihood. Multivariate analyses under the same animal mixed model were also performed for the validation of the random regression models. The Legendre polynomials of second order were better for describing the growth curves of the lines studied. Moderate to high heritabilities (h(2) = 0.15 to 0.98) were estimated for body weight between one and 84 days of age, suggesting that selection for body weight at all ages can be used as a selection criteria. Genetic correlations among body weight records obtained through multivariate analyses ranged from 0.18 to 0.96, 0.12 to 0.89, 0.06 to 0.96, and 0.28 to 0.96 in 7P, Caipirão da ESALQ, Caipirinha da ESALQ, and Carijó Barbado chicken lines, respectively. Results indicate that genetic gain for body weight can be achieved by selection. Also, selection for body weight at 42 days of age can be maintained as a selection criterion.
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Affiliation(s)
- Gregori A Rovadoscki
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13.418-900, Brazil
| | - Juliana Petrini
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13.418-900, Brazil
| | - Johanna Ramirez-Diaz
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13.418-900, Brazil
| | - Simone F N Pertile
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13.418-900, Brazil
| | - Fábio Pertille
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13.418-900, Brazil
| | - Mayara Salvian
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13.418-900, Brazil
| | - Laiza H S Iung
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13.418-900, Brazil
| | - Mary Ana P Rodriguez
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13.418-900, Brazil
| | - Aline Zampar
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13.418-900, Brazil
| | - Leila G Gaya
- Department of Basic Sciences, University of São Paulo, Pirassununga, SP, 13.635-900, Brazil
| | - Rachel S B Carvalho
- Department of Basic Sciences, University of São Paulo, Pirassununga, SP, 13.635-900, Brazil
| | - Antonio A D Coelho
- Department of Genetics, University of São Paulo, Piracicaba, SP, 13.418-900, Brazil
| | - Vicente J M Savino
- Department of Genetics, University of São Paulo, Piracicaba, SP, 13.418-900, Brazil
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13.418-900, Brazil
| | - Gerson B Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13.418-900, Brazil
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Petrini J, Iung LHS, Rodriguez MAP, Salvian M, Pértille F, Rovadoscki GA, Cassoli LD, Coutinho LL, Machado PF, Wiggans GR, Mourão GB. Genetic parameters for milk fatty acids, milk yield and quality traits of a Holstein cattle population reared under tropical conditions. J Anim Breed Genet 2016; 133:384-95. [PMID: 26968150 DOI: 10.1111/jbg.12205] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/30/2016] [Indexed: 12/19/2022]
Abstract
Information about genetic parameters is essential for selection decisions and genetic evaluation. These estimates are population specific; however, there are few studies with dairy cattle populations reared under tropical and sub-tropical conditions. Thus, the aim was to obtain estimates of heritability and genetic correlations for milk yield and quality traits using pedigree and genomic information from a Holstein population maintained in a tropical environment. Phenotypic records (n = 36 457) of 4203 cows as well as the genotypes for 57 368 single nucleotide polymorphisms from 755 of these cows were used. Covariance components were estimated using the restricted maximum likelihood method under a mixed animal model, considering a pedigree-based relationship matrix or a combined pedigree-genomic matrix. High heritabilities (around 0.30) were estimated for lactose and protein content in milk whereas moderate values (between 0.19 and 0.26) were obtained for percentages of fat, saturated fatty acids and palmitic acid in milk. Genetic correlations ranging from -0.38 to -0.13 were determined between milk yield and composition traits. The smaller estimates compared to other similar studies can be due to poor environmental conditions, which may reduce genetic variability. These results highlight the importance in using genetic parameters estimated in the population under evaluation for selection decisions.
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Affiliation(s)
- J Petrini
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - L H S Iung
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - M A P Rodriguez
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - M Salvian
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - F Pértille
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - G A Rovadoscki
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - L D Cassoli
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - L L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - P F Machado
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - G R Wiggans
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - G B Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil.
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Petrini J, Pertile SFN, Eler JP, Ferraz JBS, Mattos EC, Figueiredo LGG, Mourão GB. Genetic grouping strategies in selection efficiency of composite beef cattle ( × ). J Anim Sci 2016; 93:541-52. [PMID: 26020743 DOI: 10.2527/jas.2014-8088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The inclusion of genetic groups in sire evaluation has been widely used to represent genetic differences among animals not accounted for by the absence of parentage data. However, the definition of these groups is still arbitrary, and studies assessing the effects of genetic grouping strategies on the selection efficiency are rare. Therefore, the aim in this study was to compare genetic grouping strategies for animals with unknown parentage in prediction of breeding values (EBV). The total of 179,302 records of weaning weight (WW), 29,825 records of scrotal circumference (SC), and 70,302 records of muscling score (MUSC) from Montana Tropical animals, a Brazilian composite beef cattle population, were used. Genetic grouping strategies involving year of birth, sex of the unknown parent, birth farm, breed composition, and their combinations were evaluated. Estimated breeding values were predicted for each approach simulating a loss of genealogy data. Thereafter, these EBV were compared to those obtained in an analysis involving a real relationship matrix to estimate selection efficiency and correlations between EBV and animal rankings. The analysis model included the fixed effects of contemporary groups and class of the dam age at calving, the covariates of additive and nonadditive genetic effects, and age, and the additive genetic effect of animal as random effects. A second model also included the fixed effects of genetic group. The use of genetic groups resulted in means of selection efficiency and correlation of 70.4 to 97.1% and 0.51 to 0.94 for WW, 85.8 to 98.8% and 0.82 to 0.98 for SC, and 85.1 to 98.6% and 0.74 to 0.97 for MUSC, respectively. High selection efficiencies were observed for year of birth and breed composition strategies. The maximum absolute difference in annual genetic gain estimated through the use of complete genealogy and genetic groups were 0.38 kg for WW, 0.02 cm for SC, and 0.01 for MUSC, with lower differences obtained when year of birth was adopted as a genetic group criterion. Grouping strategy must consider selection decisions and the number of genetic groups formed, in the way that genetic groups represent the genetic differences in population and allow an adequate prediction of EBV.
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Peertile SFN, Zampar A, Petrini J, Gaya LDG, Rovadoscki GA, Ramírez-Díaz J, Ferraz JBS, Michelan Filho T, Mourão GB. Correlated responses and genetic parameters for performance and carcass traits in a broiler line. Rev bras saúde prod anim 2014. [DOI: 10.1590/s1519-99402014000400008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The growth rate of broilers has triplicated in the last decades. The body weight is used as one of the selection criteria whereas the carcass traits are valuable market requirements. Thus, the meat industry like animals with high weights at slaughter and better carcass traits. However, the genetic relation of carcass traits with several body weights is unknown. Therefore, we established genetic associations among performance and carcass traits in a broiler chicken line and estimated genetic gain and trends. We also evaluated what age of selection would lead to a more efficient indirect selection of carcass traits. The data set with information of weights in different ages and carcass traits of 128,459 chickens was used. The pedigree data used contained 132,442 chickens. Genetic analysis were realized using ASREML® software applied a restricted maximum likelihood method. Heritability estimates ranged from moderate to high, which indicates that these traits can have high selection response. Genetic correlations between performance and carcass traits varied from moderate to high, which indicates the presence of a genetic association whereas genetic trends indicated that direct selection is occurring for body weight at different ages. Theselection at 30 and 38 days should be considered instead of the slaughter weight, as it anticipates selection in around 12 days.
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Rodriguez MAP, Petrini J, Ferreira EM, Mourão LRMB, Salvian M, Cassoli LD, Pires AV, Machado PF, Mourão GB. Concordance analysis between estimation methods of milk fatty acid content. Food Chem 2014; 156:170-5. [PMID: 24629954 DOI: 10.1016/j.foodchem.2014.01.092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 01/09/2014] [Accepted: 01/26/2014] [Indexed: 10/25/2022]
Abstract
Considering the milk fatty acid influence on human health, the aim of this study was to compare gas chromatography (GC) and Fourier transform infrared (FTIR) spectroscopy for the determination of these compounds. Fatty acid content (g/100g of fat) were obtained by both methods and compared through Pearson's correlation, linear Bayesian regression, and the Bland-Altman method. Despite the high correlations between the measurements (r=0.60-0.92), the regression coefficient values indicated higher measures for palmitic acid, oleic acid, unsaturated and monounsaturated fatty acids and lower values for stearic acid, saturated and polyunsaturated fatty acids estimated by GC in comparison to FTIR results. This inequality was confirmed in the Bland-Altman test, with an average bias varying from -8.65 to 6.91g/100g of fat. However, the inclusion of 94% of the samples into the concordance limits suggested that the variability of the differences between the methods was constant throughout the range of measurement. Therefore, despite the inequality between the estimates, the methods displayed the same pattern of milk fat composition, allowing similar conclusions about the milk samples under evaluation.
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Affiliation(s)
| | - Juliana Petrini
- University of São Paulo, PO Box 9, CEP 13418-900 Piracicaba, SP, Brazil
| | | | | | - Mayara Salvian
- University of São Paulo, PO Box 9, CEP 13418-900 Piracicaba, SP, Brazil
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Oliveira Júnior GAD, Eler JP, Ferraz JBS, Petrini J, Mattos ECD, Mourão GB. Definição de grupos genéticos aditivos visando melhor predição de valores genéticos em bovinos de corte. Rev bras saúde prod anim 2013. [DOI: 10.1590/s1519-99402013000200003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
O objetivo do estudo foi avaliar a estrutura de grupos genéticos aditivos como uma alternativa para melhor ajuste de animais com paternidade desconhecida nas avaliações genéticas. As características estudadas foram: peso a desmama; peso ao sobreano; ganho de peso pós-desmama em 345 dias; perímetro escrotal ao sobreano e o escore visual de musculosidade ao sobreano. Um banco em que todos os animais tinham paternidade conhecida foi utilizado como grupo controle. A partir deste, três cenários foram criados em que 30; 50 ou 70% dos indivíduos foram aleatoriamente assumidos como animais com paternidade desconhecida. As estratégias consideradas de grupos genéticos aditivos foram: ano de nascimento do animal com paternidade desconhecida; fazenda de nascimento do animal com paternidade desconhecida; ano de nascimento e fazenda de nascimento do animal e um grupo controle negativo que manteve os animais com pais desconhecidos. A estratégia adequada de grupo genético aditivo foi escolhida como sendo aquela que resultou em um maior coeficiente de regressão e com valor genético aditivo mais próximos ao predito para os animais do grupo controle. Os resultados que incluíram a estratégia de grupo genético aditivo nos modelos de predição dos valores genéticos mostraram maior coerência com o grupo controle, frente a não inclusão destes nas análises. Dentre as estratégias propostas, ano de nascimento e fazenda de nascimento do animal e apenas ano de nascimento do animal com paternidade desconhecida obtiveram os melhores resultados.
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Dias RAP, Petrini J, Ferraz JBS, Eler JP, Bueno RS, da Costa ALL, Mourão GB. Multicollinearity in genetic effects for weaning weight in a beef cattle composite population. Livest Sci 2011. [DOI: 10.1016/j.livsci.2011.07.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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STT, Locorotondo G, Porto I, Paraggio L, Fedele E, Barchetta S, De Caterina AR, Rebuzzi AG, Crea F, Galiuto L, Lipiec P, Szymczyk E, Michalski B, Wozniakowski B, Stefanczyk L, Rotkiewicz A, Shim A, Kasprzak JD, Vainer J, Habets J, Lousberg A, Pont De C, Waltenberger J, Farouk H, Heshmat H, Adel A, El Chilali K, Baghdady Y, Sorour K, Gustafsson U, Larsson M, Bjallmark A, Lindqvist P, A'roch R, Haney M, Waldenstrom A, Mladenovic Z, Tavciovski D, Mijailovic Z, Djordjevic - Dikic A, Obradovic S, Matunovic R, Jovic Z, Djuric P, Torp H, Aase S, Dalen H, Sarkola T, Redington AN, Keeley F, Bradley T, Jaeggi E, Sahlen H, Winter R, Brodin L, Sahlen A, Olsen NT, Risum N, Jons C, Mogelvang R, Valeur N, Fritz-Hansen T, Sogaard P. Poster session IV * Friday 10 December 2010, 14:00-18:00. European Journal of Echocardiography 2010. [DOI: 10.1093/ejechocard/jeq146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Kuznetsov VA, Kozhurina AO, Plusnin AV, Szulik M, Sredniawa B, Streb W, Lenarczyk R, Stabryla-Deska J, Sedkowska A, Kowalski O, Kalarus Z, Kukulski T, Katova TM, Nesheva A, Simova I, Hristova K, Kostova V, Boiadjiev L, Dimitrov N, Papamichalis Michalis MP, Sitafidis George SG, Dimopoulos Basilios BD, Kelepesis Glafkos GK, Economou Dimitrios DE, Skoularigis John JS, Triposkiadis Filippos FT, Attenhofer Jost CH, Pfyffer M, Naegeli B, Levis P, Faeh-Gunz A, Brunner-Larocca HP, Velasco Del Castillo MS, Cacicedo A, Onaindia JJ, Gonzalez Ruiz J, Subinas A, Alarcon JA, Quintana O, Rodriguez I, Laraudogoitia E, Lam YY, Henein MY, Mazzone A, Vianello A, Perlini S, Corciu AI, Cappelli S, Cerillo A, Chiappino D, Berti S, Glauber M, Herrmann S, Niemann M, Stoerk S, Strotmann J, Voelker W, Ertl G, Weidemann F, Yong ZY, Boerlage - Van Dijk K, Koch KT, Vis MM, Bouma BJ, Henriques JPS, Cocchieri R, De Mol BAJM, Piek JJ, Baan J, Keenan NGJ, Cueff C, Cimadevilla C, Brochet E, Lepage L, Detaint D, Iung B, 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Dahle G, Bugge JF, Bendz B, Aaberge L, Rein KA, Fiane A, Bergsland J, Fosse E, Aakhus S, Koopman LP, Chahal N, Slorach C, Hui W, Sarkola T, Manlhiot C, Bradley TJ, Jaeggi ET, Mccrindle BW, Mertens L, Di Salvo G, Pacileo G, Castaldi B, Gala S, Baldini L, D'aiello FA, Mormilw A, Rea A, Russo MG, Calabro R, Calin A, Rosca M, O'Connor K, Romano G, Magne J, Beladan CC, Ginghina C, Pierard L, Lancellotti P, Popescu BA, Arita T, Ando K, Isotani A, Soga Y, Iwabuchi M, Nobuyoshi M, Hammerstingl C, Momcilovic D, Wiesen M, Nickenig G, Skowasch D, Mornos C, Cozma D, Rusinaru D, Ionac A, Pescariu S, Dragulescu SI, Niemann M, Breunig F, Beer M, Herrmann S, Strotmann J, Hu K, Voelker W, Ertl G, Wanner C, Weidemann F, Morel MA, Bernard YF, Descotes-Genon V, Meneveau N, Schiele F, Vitarelli A, Bernardi M, Scarno A, Caranci F, Padella V, Dettori O, Capotosto L, Vitarelli M, De Cicco V, Bruno P, Bajraktari G, Lindqvist P, Gustafsson U, Holmgren A, Henein MY, Hassan M, Said K, Baligh E, Farouk H, Osama D, Elmahdy MF, Elfaramawy A, Sorour K, Luckie M, Zaidi A, Fitzpatrick A, Khattar RS, Schwartz J, Huttin O, Popovic B, Zinzius PY, Christophe C, Marcon O, Groben L, Juilliere Y, Chabot F, Selton-Suty C, Krastev B, Kinova ETK, Zlatareva NIZ, Goudev ARG, Teske AJ, De Boeck BW, Mohames Hoesein FA, Van Driel V, Loh P, Cramer MJ, Doevendans PA, Dillenburg F, Mertens L, Abd El Salam KM, Ho EMM, Hall M, Hemeryck L, Bennett K, Scott K, King G, Murphy RT, Mahmud A, Brown AS, Dalen H, Thorstensen A, Romundstad PR, Aase SA, Stoylen A, Vatten L, Bochenek T, Wita K, Tabor Z, Doruchowska A, Lelek M, Trusz-Gluza M, Hamodraka E, Paraskevaidis I, Karamanou A, Michalakeas C, Vrettou H, Kapsali E, Tsiapras D, Lekakis I, Anastasiou-Nana M, Kremastinos D, Sirugo L, Bottari VE, Licciardi S, Blundo A, Atanasio A, Monte IP, Park CS, Kim JH, Cho JS, Kim MJ, Cho EJ, Ihm SH, Jung HO, Jeon HK, Youn HJ, Kim KS, Fontana A, Taravella L, Zambon A, Trocino G, Giannattasio C, Kalinin A, Alekhin M, Bahs G, Lejnieks A, Kalvelis A, Kalnins A, Shipachovs P, Zakharova E, Blumentale G, Trukshina M, Biering-Sorensen T, Mogelvang R, Haahr-Pedersen S, Schnohr P, Sogaard P, Skov Jensen J, Gargani L, Agoston G, Capati E, Badano L, Moreo A, Costantino MF, Caputo ML, Mondillo S, Sicari R, Picano E, Malev EG, Timofeev EV, Reeva SV, Zemtsovsky EV, Piazza R, Enache R, Roman-Pognuz A, Muraru D, Popescu BA, Leiballi E, Pecoraro R, Antonini-Canterin F, Ginghina C, Nicolosi GL, Sadeghian H, Lotfi_Tokaldany M, Rezvanfard M, Kasemisaeid A, Majidi S, Montazeri M, Saber-Ayad M, Nassar YS, Farhan A, Moussa A, El-Sherif A, Cooper RM, Somauroo JD, Shave RE, Williams KL, Forster J, George C, Bett T, Gaze DC, George KP, Mansencal N, Dupland A, Caille V, Perrot S, Bouferrache K, Vieillard-Baron A, Jouffroy R, Cioroiu SG, Alexe OS, Bobescu E, Rus H, Schiano Lomoriello V, Esposito R, Santoro A, Raia R, Farina F, Ippolito R, Galderisi M, Aburawi EH, Malcus P, Thuring A, Maxedius A, Pesonen E, Nair SV, Joyce E, Lee L, Shrimpton J, Newman E, James PR, Jurcut C, Caraiola S, Jurcut RO, Giusca S, Nitescu D, Amzulescu MS, Copaci I, Popescu BA, Tanasescu C, Ginghina C, Silva Marques J, Silva D, Ferreira F, Ferreira PC, Almeida AG, Martim Martins J, Lopes MG, Bergenzaun L, Chew M, Ersson A, Gudmundsson P, Ohlin H, Borowiec A, Dabrowski R, Wozniak J, Jasek S, Chwyczko T, Kowalik I, Musiej-Nowakowska E, Szwed H, Wen YL, Tian J, Yan L, Cheng H, Yang H, Luo B, Wang J, Kozman H, Villarreal D, Liu K, Karavidas A, Tsiachris D, Lazaros G, Matzaraki V, Xylomenos G, Levendopoulos G, Arapi S, Perpinia A, Matsakas E, Pyrgakis V, Liu YW, Su CT, Tsai WC, Huang JW, Hung KY, Chen JH, Larsson M, Kremer F, Kouznetsova T, Bjallmark A, Lind B, Brodin LA, D'hooge J, Santoro A, Caputo M, Antonelli G, Lisi M, Giacomin E, Mondillo S, Moustafa S, Alharthi M, Kansal M, Deng Y, Chandrasekaran K, Mookadam F, Hayashi SY, Bjallmark A, Larsson M, Nascimento MM, Lindholm B, Lind B, Seeberger A, Nowak J, Riella MC, Brodin LA, Theodosis A, Fousteris E, Tsiaousis G, Krommydas A, Margetis P, Katidis Z, Beldekos D, Argirakis S, Melidonis A, Foussas S, Khaleva O, Onyshchenko O, Lukaschuk E, Sherwi N, Nikitin N, Cleland JGF, Risum N, Jons C, Olsen NT, Valeur N, Kronborg MB, Jensen MT, Fritz-Hansen T, Bruun NE, Hojgaard MV, Sogaard P, Petrini J, Yousry M, Rickenlund A, Liska J, Franco-Cereceda A, Hamsten A, Eriksson P, Caidahl K, Eriksson MJ, Elmstedt N, Lind B, Ferm-Widlund K, Westgren M, Brodin LA, Szymczyk E, Kasprzak JD, Wozniakowski B, Rotkiewicz A, Szymczyk K, Stefanczyk L, Michalski B, Lipiec P, Ring L, Eller T, Deegan P, Rusk R, Urbano Moral JA, Arias JA, Kuvin JT, Patel AR, Pandian NG, Bellsham-Revell H, Bell AJ, Miller O, Greil GF, Simpson J, Moustafa S, Kansal M, Alharthi M, Deng Y, Chandrasekaran K, Mookadam F, Ancona R, Comenale Pinto S, Caso P, Severino S, Nunziata L, Roselli T, Calabro R, Dussault C, Donal E, Lafitte S, Habib G, Reant P, Derumeaux G, Thibault H, Gueret P, Lim P, Kaladaridis A, Agrios IA, Pamboucas CP, Mesogitis SM, Vasiladiotis NV, Bramos DB, Toumanidis STT, Martiniello AR, Santangelo G, Caso P, Pedrizzetti G, Tonti G, Cioppa C, Cavallaro M, Calvi V, Chianese R, Calabro R. Poster session I * Thursday 9 December 2010, 08:30-12:30. European Journal of Echocardiography 2010. [DOI: 10.1093/ejechocard/jeq136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Levran O, Attwooll C, Henry RT, Milton KL, Neveling K, Rio P, Batish SD, Kalb R, Velleuer E, Barral S, Ott J, Petrini J, Schindler D, Hanenberg H, Auerbach AD. Addendum: The BRCA1-interacting helicase BRIP1 is deficient in Fanconi anemia. Nat Genet 2005. [DOI: 10.1038/ng1105-1296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Davis P, Petrini J. Program addresses surgical nursing needs. Aust Nurs J 2001; 9:39. [PMID: 11908205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- P Davis
- Department of Nursing Education and Research, Royal Melbourne Hospital
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Affiliation(s)
- D R Mattison
- March of Dimes Birth Defects Foundation, 1272 Mamaroneck Ave., White Plains, NY, USA.
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Girard PM, Foray N, Stumm M, Waugh A, Riballo E, Maser RS, Phillips WP, Petrini J, Arlett CF, Jeggo PA. Radiosensitivity in Nijmegen Breakage Syndrome cells is attributable to a repair defect and not cell cycle checkpoint defects. Cancer Res 2000; 60:4881-8. [PMID: 10987302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Cells derived from Nijmegen Breakage Syndrome (NBS) patients display radiosensitivity and cell cycle checkpoint defects. Here, we examine whether the radiosensitivity of NBS cells is the result of a repair defect or whether it can be attributed to impaired checkpoint arrest. We report a small increased fraction of unrejoined double strand breaks and, more significantly, increased chromosome breaks in noncycling NBS cells at 24 h after irradiation. One of the NBS lines examined (347BR) was atypical in showing a nearly normal checkpoint response. In contrast to the mild checkpoint defect, 347BR displays marked y-ray sensitivity similar to that shown by other NBS lines. Thus, the gamma-ray sensitivity correlates with the repair defect rather than impaired checkpoint control. Taken together, the results provide direct evidence for a repair defect in NBS cells and are inconsistent with the suggestion that the radiosensitivity is attributable only to impaired checkpoint arrest. 347BR also displays elevated spontaneous damage that cannot be attributed to impaired G2-M arrest, suggesting a function of Nbsl in decreasing or limiting the impact of spontaneously arising double strand breaks.
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Affiliation(s)
- P M Girard
- Medical Research Council Cell Mutation Unit, University of Sussex, Falmer, Brighton, United Kingdom
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Kirby R, Petrini J, Alter C. Collecting and interpreting birth defects surveillance data by hispanic ethnicity: a comparative study. The Hispanic Ethnicity Birth Defects Workgroup. Teratology 2000; 61:21-7. [PMID: 10603199 DOI: 10.1002/(sici)1096-9926(200001/02)61:1/2<21::aid-tera5>3.0.co;2-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- R Kirby
- Department of Obstetrics and Gynecology, Milwaukee Clinical Campus, University of Wisconsin Medical School, Milwaukee Wisconsin 53201-0342, USA.
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Petrini J, Damus K, Roy S, Johnson K, Johnston RB. The effect of using "race of child" instead of "race of mother" on the black-white gap in infant mortality due to birth defects. Public Health Rep 1998; 113:263-7. [PMID: 9633874 PMCID: PMC1308680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE For at least 20 years, birth defects have been the leading cause of infant mortality in the United States. Some studies have reported higher rates for black infants than white infants of mortality due to birth defects, while other studies have reported no black-white differences. The authors analyzed the effect on these rates of a change in the way the National Center for Health Statistics (NCHS) tabulates "race" for newborns. METHODS The authors calculated infant mortality rates due to birth defects for 1980-1993 using two standard methods of assigning newborns to "racial" categories: a "race of child" algorithm and the "race of mother" approach currently used by NCHS. RESULTS From 1980 through 1993, birth defect-specific infant mortality rates (BD-IMRs) were significantly higher for black infants than white infants 12 of the 14 years by "race of mother" and only 5 of 14 years by "race of child." Calculation of BD-IMRs by "race of mother" reduced the rate for white infants and increased the rate for black infants in each of the 14 years. The choice of method for assigning newborns to "racial" categories had a progressively greater effect over time on the black-white gap in BD-IMRs. CONCLUSIONS Calculations of trends in "race"-specific BD-IMRs by may vary substantially by whether "race of mother" or "race of child" is used. Identifying the method of tabulation is imperative for appropriate comparisons and interpretations.
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Affiliation(s)
- J Petrini
- National Office of the March of Dimes Birth Defects Foundation, White Plains, NY 10605, USA.
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41
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Affiliation(s)
- J Petrini
- March of Dimes Birth Defects Foundation, White Plains, New York 10605, USA
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Vivier E, Rochet N, Ackerly M, Petrini J, Levine H, Daley J, Anderson P. Signaling function of reconstituted CD16: zeta: gamma receptor complex isoforms. Int Immunol 1992; 4:1313-23. [PMID: 1472481 DOI: 10.1093/intimm/4.11.1313] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Natural killer cells express an Fc receptor for IgG (CD16) in association with disulfide-linked dimers composed of two homologous subunits: the zeta chain of the T cell antigen receptor complex and the gamma chain of the mast cell/basophil Fc receptor for IgE. The ability of zeta and gamma to transduce CD16-mediated activation signals was compared by reconstituting distinct CD16 receptor isoforms composed of various combinations of zeta- and gamma-containing dimers. Stably transformed non-hematopoietic and hematopoietic cell lines were established that expressed chimeric molecules comprising the extracellular domain of CD16 joined to the transmembrane and intracellular domains of zeta or gamma. Reconstituted CD16 receptor complexes triggered Ca2+ influx, tyrosine phosphorylation, and IL-2 production in stable transformants of the Jurkat T cell line. However, cross-linking of the CD16/gamma chimera induced a specific pattern of tyrosine phosphorylation and was more efficient at signal transduction than a CD16, zeta-zeta complex, suggesting that zeta and gamma cytoplasmic domains may be coupled to distinct tyrosine kinase pathways that differentially regulate CD16-mediated activation signals. By contrast, both CD16/zeta and CD16/gamma chimeric molecules were not functional in stable transformants of the fibroblast Chinese Hamster Ovary cell line, indicating a requirement for downstream signaling components present in hematopoietic cells. Finally, the zeta transmembrane domain appears to preferentially associate with CD16 rather than the CD3:TCR complex, suggesting that a hierarchy of molecular interactions governs NK and T cell differentiation.
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MESH Headings
- Animals
- Base Sequence
- CHO Cells
- Calcium/metabolism
- Cricetinae
- Cricetulus
- Humans
- Interleukin-2/metabolism
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lymphocyte Activation
- Membrane Proteins/physiology
- Molecular Sequence Data
- Phosphorylation
- Protein Processing, Post-Translational
- Protein-Tyrosine Kinases/metabolism
- Receptors, Antigen, T-Cell/physiology
- Receptors, Antigen, T-Cell, gamma-delta/physiology
- Receptors, IgG/physiology
- Recombinant Fusion Proteins
- Signal Transduction
- T-Lymphocytes
- Transfection
- Tumor Cells, Cultured
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Affiliation(s)
- E Vivier
- Division of Tumor Immunology, Dana-Farber Cancer Institute, Boston, MA 02115
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Schultz C, Petrini J, Collins J, Claflin JL, Denis KA, Gearhart P, Gritzmacher C, Manser T, Shulman M, Dunnick W. Patterns and extent of isotype-specificity in the murine H chain switch DNA rearrangement. The Journal of Immunology 1990. [DOI: 10.4049/jimmunol.144.1.363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
We have analyzed the configuration of the H chain locus of 41 hybridomas by Southern blot analysis. Each H chain switch region was determined to be germ line, rearranged, or deleted. Including 13 previously analyzed hybridomas, 60% of those with rearrangements on both alleles showed a correlation of the two alleles, i.e., both the expressed and the nonexpressed alleles have rearranged to the same H chain constant region gene segment. When the two H chain alleles did not rearrange to the same gene, they often rearranged to neighboring H chain genes. These results support a role for isotype-specific factors in H chain switch recombination. The action of these isotype-specific factors may be propagated to some extent along the chromosome, which would lead to rearrangements to neighboring genes.
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Affiliation(s)
- C Schultz
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
| | - J Petrini
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
| | - J Collins
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
| | - J L Claflin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
| | - K A Denis
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
| | - P Gearhart
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
| | - C Gritzmacher
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
| | - T Manser
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
| | - M Shulman
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
| | - W Dunnick
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
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Schultz C, Petrini J, Collins J, Claflin JL, Denis KA, Gearhart P, Gritzmacher C, Manser T, Shulman M, Dunnick W. Patterns and extent of isotype-specificity in the murine H chain switch DNA rearrangement. J Immunol 1990; 144:363-70. [PMID: 2104891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have analyzed the configuration of the H chain locus of 41 hybridomas by Southern blot analysis. Each H chain switch region was determined to be germ line, rearranged, or deleted. Including 13 previously analyzed hybridomas, 60% of those with rearrangements on both alleles showed a correlation of the two alleles, i.e., both the expressed and the nonexpressed alleles have rearranged to the same H chain constant region gene segment. When the two H chain alleles did not rearrange to the same gene, they often rearranged to neighboring H chain genes. These results support a role for isotype-specific factors in H chain switch recombination. The action of these isotype-specific factors may be propagated to some extent along the chromosome, which would lead to rearrangements to neighboring genes.
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Affiliation(s)
- C Schultz
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
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Petrini J, Dunnick WA. Products and implied mechanism of H chain switch recombination. J Immunol 1989; 142:2932-5. [PMID: 2495330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Ig H chain switch is a DNA recombination event. The recombination occurs between two or more switch regions, areas of tandem sequence duplication that lie upstream of the corresponding H chain C region genes. We have determined the DNA sequence at four recombination sites in three molecularly cloned, rearranged switch regions. All eight donor and recipient recombination sites are at the common pentamers GGGGT, GAGCT, and GGTGG. One of the switch recombination events is an inversion of S gamma 3 sequences. Another of the recombinational events is an internal S gamma 1 deletion, which may be switch enzyme mediated. These results, together with other switch recombination site sequences, suggest that switch recombination is mediated by cutting enzymes with modest specificity and religation enzymes with no specificity.
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Affiliation(s)
- J Petrini
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
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Petrini J, Dunnick WA. Products and implied mechanism of H chain switch recombination. The Journal of Immunology 1989. [DOI: 10.4049/jimmunol.142.8.2932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
The Ig H chain switch is a DNA recombination event. The recombination occurs between two or more switch regions, areas of tandem sequence duplication that lie upstream of the corresponding H chain C region genes. We have determined the DNA sequence at four recombination sites in three molecularly cloned, rearranged switch regions. All eight donor and recipient recombination sites are at the common pentamers GGGGT, GAGCT, and GGTGG. One of the switch recombination events is an inversion of S gamma 3 sequences. Another of the recombinational events is an internal S gamma 1 deletion, which may be switch enzyme mediated. These results, together with other switch recombination site sequences, suggest that switch recombination is mediated by cutting enzymes with modest specificity and religation enzymes with no specificity.
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Affiliation(s)
- J Petrini
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
| | - W A Dunnick
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor 48109-0620
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Abstract
FACS analysis showed that the incidence of leaky T cells increases with age, such that virtually all old scid mice (greater than 1 year) contain detectable CD3+ cells. The number of detectable T cells remained very low; individual old scid mice generally contained less than 10(5) CD3+ cells. When CD3+ populations in individual leaky mice were analyzed for expression of the T cell subset markers, CD4 and CD8, the ratios of CD4/CD8 were found to be markedly skewed relative to normal mice. This suggested the presence of very few T cell clones. Indeed, the analysis of TCR gene rearrangements in polyclonally stimulated T cell cultures revealed only 1-5 clones in the pooled spleen and lymph nodes of individual old scid mice. These studies also indicated that TCR gene rearrangements in the majority of the stimulated T cell cultures did not contain abnormal J-associated deletions that are characteristic of antigen receptor genes of scid lymphomas. Four of five alloreactive T cell clones from leaky scid mice also apparently lacked abnormal J-associated deletions in their rearranged TCR alleles. Therefore, most leaky lymphocytes appear to derive from progenitors with normal or near-normal scid recombinase activity. However, one of five leaky T cell clones (S1233) and one Con A stimulated monoclonal culture (8706) contained both normally and abnormally rearranged TCR genes. The configuration of TCR loci in such clones may reflect the ability of the defective scid recombinase to mediate normal rearrangements at a low frequency.
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Abstract
In a multicenter pilot study, a prototype bipolar electrocoagulation tumor probe was employed for palliation of obstructing circumferential esophageal cancer in 20 patients. Mean number of initial treatment sessions was 1.7. Dysphagia and tumor channel size improved significantly after treatment. Mean treatment interval before repeat treatment was 7.6 weeks. Major complications included delayed hemorrhage (two patients) and esophageal-pulmonary fistula (two patients). This new device may provide a less expensive alternative to laser or surgery for palliation of malignant esophageal obstruction.
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Affiliation(s)
- J H Johnston
- Department of Gastroenterology, University of Mississippi Medical Center, Jackson
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49
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Petrini J, Shell B, Hummel M, Dunnick W. The immunoglobulin heavy chain switch: structural features of gamma 1 recombinant switch regions. The Journal of Immunology 1987. [DOI: 10.4049/jimmunol.138.6.1940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Abstract
The immunoglobulin heavy chain isotype switch is mediated by a DNA rearrangement involving specific genomic segments referred to as switch regions. Switch regions are composed of tandemly repeated simple sequences. The role of the tandemly repeated structure of switch regions in the switch recombination process is not understood. We mapped eight recombination sites--six in the gamma 1 and two in the gamma 3 tandem arrays. In addition, we obtained molecular clones representing three of the six gamma 1 rearrangements, and determined the nucleotide sequences of the recombination sites in each. In general, the rearrangements are confined to the tandem repeat units, and are not clustered in a particular portion of either the gamma 3 or gamma 1 switch region. Nucleotide sequence analysis of one of the recombinant clones, gamma M35, reveals evidence for a successive switch event wherein a recombination between S mu and S gamma 3 was followed by recombination 57 bp downstream with S gamma 1. gamma 1 sequence data from the molecular clones we obtained, together with similar data from other investigators regarding the gamma 1, gamma 2b, and gamma 2a switch regions, reveals that recombinations tend to occur at homologous positions of the respective gamma-unit repeats, adjacent to the elements AGCT and GGGG found in each. This finding suggests that the cutting and religation step of the recombination process is mediated by a recombinase common to the four gamma-isotypes.
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Petrini J, Shell B, Hummel M, Dunnick W. The immunoglobulin heavy chain switch: structural features of gamma 1 recombinant switch regions. J Immunol 1987; 138:1940-6. [PMID: 3029225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The immunoglobulin heavy chain isotype switch is mediated by a DNA rearrangement involving specific genomic segments referred to as switch regions. Switch regions are composed of tandemly repeated simple sequences. The role of the tandemly repeated structure of switch regions in the switch recombination process is not understood. We mapped eight recombination sites--six in the gamma 1 and two in the gamma 3 tandem arrays. In addition, we obtained molecular clones representing three of the six gamma 1 rearrangements, and determined the nucleotide sequences of the recombination sites in each. In general, the rearrangements are confined to the tandem repeat units, and are not clustered in a particular portion of either the gamma 3 or gamma 1 switch region. Nucleotide sequence analysis of one of the recombinant clones, gamma M35, reveals evidence for a successive switch event wherein a recombination between S mu and S gamma 3 was followed by recombination 57 bp downstream with S gamma 1. gamma 1 sequence data from the molecular clones we obtained, together with similar data from other investigators regarding the gamma 1, gamma 2b, and gamma 2a switch regions, reveals that recombinations tend to occur at homologous positions of the respective gamma-unit repeats, adjacent to the elements AGCT and GGGG found in each. This finding suggests that the cutting and religation step of the recombination process is mediated by a recombinase common to the four gamma-isotypes.
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