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Capra E, Lazzari B, Milanesi M, Nogueira GP, Garcia JF, Utsunomiya YT, Ajmone-Marsan P, Stella A. Comparison between indicine and taurine cattle DNA methylation reveals epigenetic variation associated to differences in morphological adaptive traits. Epigenetics 2023; 18:2163363. [PMID: 36600398 PMCID: PMC9980582 DOI: 10.1080/15592294.2022.2163363] [Citation(s) in RCA: 1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Indicine and taurine subspecies present distinct morphological traits as a consequence of environmental adaptation and artificial selection. Although the two subspecies have been characterized and compared at genome-wide level and at specific loci, their epigenetic diversity has not yet been explored. In this work, Reduced Representation Bisulphite Sequencing (RRBS) profiling of the taurine Angus (A) and indicine Nellore (N) cattle breeds was applied to identify methylation differences between the two subspecies. Genotyping by sequencing (GBS) of the same animals was performed to detect single nucleotide polymorphisms (SNPs) at cytosines in CpG dinucleotides and remove them from the differential methylation analysis. A total of 660,845 methylated cytosines were identified within the CpG context (CpGs) across the 10 animals sequenced (5 N and 5 A). A total of 25,765 of these were differentially methylated (DMCs). Most DMCs clustered in CpG stretches nearby genes involved in cellular and anatomical structure morphogenesis. Also, sequences flanking DMC were enriched in SNPs compared to all other CpGs, either methylated or unmethylated in the two subspecies. Our data suggest a contribution of epigenetics to the regulation and divergence of anatomical morphogenesis in the two subspecies relevant for cattle evolution and sub-species differentiation and adaptation.
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Affiliation(s)
- E Capra
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, Lodi, Italy
| | - B Lazzari
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, Lodi, Italy
| | - M Milanesi
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil.,Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - G P Nogueira
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil
| | - J F Garcia
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | - Y T Utsunomiya
- School of Veterinary Medicine, Araçatuba, Department of Production and Animal Health, São Paulo State University (Unesp), Araçatuba, Brazil
| | - P Ajmone-Marsan
- Department of Animal Science, Food and Nutrition - DIANA, and Nutrigenomics and Proteomics Research Center - PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - A Stella
- Institute of Agricultural Biology and Biotechnology, National Research Council IBBA CNR, Lodi, Italy
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Milanesi M, Obrien AMP, Utsunomiya AT, Feres LF, Sonstegard TS, Garcia JF. Genomic breed composition of pure registered Brazilian Gir. Trop Anim Health Prod 2022; 54:310. [PMID: 36123551 DOI: 10.1007/s11250-022-03299-0] [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: 01/03/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION Gir is a Bos indicus breed originally from India, first imported to Brazil in 1850. High-performance Dairy Gir has been systematically selected in Brazil from its arrival. Since the major phenotypic difference between Gir in India and Brazil is a higher milk production in the former, it is speculated that Brazilian Gir was strategically crossed with Holstein or another Bos taurus to improve milk yield. This study evaluated the purity of Brazilian Gir breed stocks from BASA Farms in Brazil, trying to identify possible admixture events with other cattle breeds based on DNA analysis. MATERIALS AND METHODS The population included 1061 pure registered individuals genotyped using two commercial platforms with 37 k and 25 k SNPs. Admixture analysis was performed individually to estimate levels of genomic composition derived from six different reference populations, three indicine and three taurine breeds. RESULTS A Gir ancestry of 99% or higher was found for 94.2% of the population, while the remaining showed levels of non-Gir ancestry up to 6.8%. Only five individuals were identified with possible taurine ancestry, all of them exhibiting levels lower than 2%. The remaining non-Gir ancestry identified was derived from indicine breeds. The levels of admixture observed in the population were from low to non-detectable. No consistent patterns of admixture were observed indicating sustained introgression of taurine lines as means of genetic improvement. CONCLUSION According to these results, genetic improvement achieved by Brazilian Gir breeders is the result of within-breed selection methods applied intensively over the past five decades, rather than the result from sustained introgression.
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Affiliation(s)
- M Milanesi
- AgroPartners Consulting, Araçatuba, SP, Brazil. .,Department of Animal Production and Health, School of Veterinary Medicine of Araçatuba, São Paulo State University (UNESP), Araçatuba, SP, Brazil. .,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, Brazil.
| | - A M Pérez Obrien
- BASA Farms, Leopoldina, MG, Brazil.,Acceligen, Eagan, MN, 55121, USA
| | - A T Utsunomiya
- AgroPartners Consulting, Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, Brazil
| | | | | | - J F Garcia
- Department of Animal Production and Health, School of Veterinary Medicine of Araçatuba, São Paulo State University (UNESP), Araçatuba, SP, Brazil.,International Atomic Energy Agency (IAEA) Collaborating Centre On Animal Genomics and Bioinformatics, Araçatuba, Brazil
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3
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Utsunomiya YT, Fortunato AAAD, Milanesi M, Trigo BB, Alves NF, Sonstegard TS, Garcia JF. Bos taurus haplotypes segregating in Nellore (Bos indicus) cattle. Anim Genet 2021; 53:58-67. [PMID: 34921423 DOI: 10.1111/age.13164] [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] [Accepted: 12/10/2021] [Indexed: 11/29/2022]
Abstract
Brazil is the largest exporter of beef in the world, and most of that beef derives from Nellore cattle. Although considered a zebu breed (Bos indicus), the history of Nellore cattle in Brazil is marked by the importation of bulls from India, the use of a Creole taurine (Bos taurus) maternal lineage to quickly expand the herds and backcrossing to Nellore bulls to recover zebu ancestry. As a consequence, the current Brazilian Nellore population carries an average taurine ancestry of approximately 1%. Although that percentage seems small, some taurine variants deviate substantially from that average, with the better-known cases being the PLAG1-Q haplotype involved with body size variation and the Guarani (PG ) polled variant producing hornless animals. Here, we report taurine haplotypes in 9074 Nellore animals genotyped for 539 657 imputed SNP markers. Apart from PLAG1-Q and PG , our analysis further revealed common taurine haplotypes (>3%) spanning genes related to immunity, growth, reproduction and hair and skin phenotypes. Using data from 22 economically important traits, we showed that many of the major QTL previously reported in the breed are at least partially driven by taurine haplotypes. As B. taurus and B. indicus haplotypes are highly divergent, presenting widely different sets of functional variants, our results provide promising targets for future scrutiny in Nellore cattle.
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Affiliation(s)
- Y T Utsunomiya
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,AgroPartners Consulting. R. Floriano Peixoto, 120 - Sala 43A - Centro, Araçatuba, SP, 16010-220, Brazil
| | - A A A D Fortunato
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,Personal-PEC. R. Sebastião Lima, 1336 - Centro, Campo Grande, MS, 79004-600, Brazil
| | - M Milanesi
- AgroPartners Consulting. R. Floriano Peixoto, 120 - Sala 43A - Centro, Araçatuba, SP, 16010-220, Brazil.,Department for Innovation in Biological, Agro-Food and Forest Systems, Università Della Tuscia, Via S. Camillo de Lellis snc, Viterbo, 01100, Italy
| | - B B Trigo
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil
| | - N F Alves
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil
| | | | - J F Garcia
- Department of Production and Animal Health, School of Veterinary Medicine of Araçatuba, São Paulo State University, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,AgroPartners Consulting. R. Floriano Peixoto, 120 - Sala 43A - Centro, Araçatuba, SP, 16010-220, Brazil.,Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University, 14884-900 Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, Brazil
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Bonfiglio F, Bruscaggin A, Guidetti F, Terzi di Bergamo L, Faderl M, Spina V, Condoluci A, Bonomini L, Forestieri G, Koch R, Piffaretti D, Pini K, Pirosa MC, Cittone MG, Arribas A, Lucioni M, Ghilardi G, Wu W, Arcaini L, Baptista MJ, Bastidas G, Bea S, Boldorini R, Broccoli A, Canzonieri V, Cascione L, Ceriani L, Cogliatti S, Derenzini E, Devizzi L, Dietrich S, Elia AR, Facchetti F, Gaidano G, Garcia JF, Gerber B, Ghia P, Silva MG, Gritti G, Guidetti A, Hitz F, Inghirami G, Ladetto M, Lopez‐Guillermo A, Lucchini E, Maiorana A, Marasca R, Matutes E, Meignin V, Merli M, Moccia A, Mollejo M, Montalban C, Novak U, Oscier DG, Passamonti F, Piazza F, Pizzolitto S, Sabattini E, Salles G, Santambrogio E, Scarfó L, Stathis A, Stüssi G, Geyer JT, Tapia G, Thieblemont C, Tousseyn T, Tucci A, Visco C, Vitolo U, Zenz T, Zinzani PL, Khiabanian H, Calcinotto A, Bertoni F, Bhagat G, Campo E, Leval L, Dirnhofer S, Pileri SA, Piris MÁ, Traverse‐Glehen A, Tzankov A, Paulli M, Ponzoni M, Mazzucchelli L, Cavalli F, Zucca E, Rossi D. GENETIC AND PHENOTYPIC ATTRIBUTES OF SPLENIC MARGINAL ZONE LYMPHOMA. Hematol Oncol 2021. [DOI: 10.1002/hon.43_2879] [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: 11/05/2022]
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Ferraz JBS, Wu XL, Li H, Xu J, Ferretti R, Simpson B, Walker J, Silva LR, Garcia JF, Tait Jr RG, Bauck S. Development and evaluation of a low-density single-nucleotide polymorphism chip specific to Bos indicus cattle. Anim Prod Sci 2020. [DOI: 10.1071/an19396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Genomic selection has been of increasing interest in the genetic improvement of Zebu cattle, particularly for quantitative traits that are difficult or expensive to measure, such as carcass traits and meat tenderness. The success of genomic selection depends on several factors, and at its core is the availability of single-nucleotide polymorphism (SNP) chips that are appropriately designed for Bos indicus cattle. However, the currently available commercial bovine SNP chips are mostly designed for Bos taurus cattle. There are two commercial Bos indicus SNP chips; namely, GeneSeek genomic profiler high-density Bos indicus (GGP-HDi) SNP chip and a low-density (LD) Bos indicus SNP chip (Z chip), but these two Bos indicus SNP chips were built with mixed contents of SNPs for Bos indicus and Bos taurus cattle, due to limited availability of genotype data from Bos indicus cattle.
Aims
To develop a new GGP indicus 35000 SNP chip specifically for Bos indicus cattle, which has a low cost, but high accuracy of imputation to Illumina BovineHD chips.
Methods
The design of the chip consisted of 34000 optimally selected SNPs, plus 1000 SNPs pre-reserved for those on the Y chromosome, ‘causative’ mutations for a variety of economically relevant traits, genetic health conditions and International Society for Animal Genetics globally recognised parentage markers for those breeds of cattle.
Key results
The present results showed that this new indicus LD SNP chip had considerably increased minor allele frequencies in indicus breeds than the previous Z-chip. It demonstrated with high imputation accuracy to HD SNP genotypes in five indicus breeds, and with considerable predictability on 14 growth and reproduction traits in Nellore cattle.
Conclusions
This new indicus LD chip represented a successful effort to leverage existing knowledge and genotype resources towards the public release of a cost-effective LD SNP chip specifically for Bos indicus cattle, which is expected to replace the previous GGP indicus LD chip and to supplement the existing GGP-HDi 80000 SNP chip.
Implications
A new SNP chip specifically designed for Bos indicus, with high power of imputation to Illumina BovineHD technology and with excellent coverage of the whole genome, is now available on the market for Bos indicus cattle, and Bos indicus and Bos taurus crosses.
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6
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Torrecilha RBP, Milanesi M, Wade CM, Gallana M, Falbo AK, Reichler IM, Hug P, Jagannathan V, Trigo BB, Paulan SC, Bruno DB, Garcia SD, Scaramele NF, Lopes FL, Dolf G, Leeb T, Sölkner J, Garcia JF, Pieńkowska-Schelling A, Schelling C, Utsunomiya YT. Association of missense variants in GDF9 with litter size in Entlebucher Mountain dogs. Anim Genet 2019; 51:78-86. [PMID: 31802524 DOI: 10.1111/age.12882] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2019] [Indexed: 12/28/2022]
Abstract
In the past two decades, average litter size (ALS) in Entlebucher Mountain dogs decreased by approximately 0.8 puppies. We conducted a GWAS for ALS using the single-step methodology to take advantage of 1632 pedigree records, 892 phenotypes and 372 genotypes (173 662 markers) for which only 12% of the dogs had both phenotypes and genotypes available. Our analysis revealed associations towards the growth differentiation factor 9 gene (GDF9), which is known to regulate oocyte maturation. The trait heritability was estimated at 43.1%, from which approximately 15% was accountable by the GDF9 locus alone. Therefore, markers flanking GDF9 explained approximately 6.5% of the variance in ALS. Analysis of WGSs revealed two missense substitutions in GDF9, one of which (g.11:21147009G>A) affected a highly conserved nucleotide in vertebrates. The derived allele A was validated in 111 dogs and shown to be associated with decreased ALS (-0.75 ± 0.22 puppies per litter). The variant was further predicted to cause a proline to serine substitution. The affected residue was immediately followed by a six-residue deletion that is fixed in the canine species but absent in non-canids. We further confirmed that the deletion is prevalent in the Canidae family by sequencing three species of wild canids. Since canids uniquely ovulate oocytes at the prophase stage of the first meiotic division, requiring maturation in the oviduct, we conjecture that the amino acid substitution and the six-residue deletion of GDF9 may serve as a model for insights into the dynamics of oocyte maturation in canids.
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Affiliation(s)
- R B P Torrecilha
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agriculture and Veterinarian Sciences, São Paulo State University (Unesp), Via de acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, São Paulo, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - M Milanesi
- International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | | | - M Gallana
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Eschikon 27, Lindau, 8315, Switzerland
| | - A-K Falbo
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Eschikon 27, Lindau, 8315, Switzerland
| | - I M Reichler
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Winterthurerstr. 260, Zürich, 8057, Switzerland
| | - P Hug
- Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - V Jagannathan
- Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - B B Trigo
- International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - S C Paulan
- International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - D B Bruno
- Department of Clinics, Surgery and Animal Reproduction, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793,, 16050-680, Araçatuba, São Paulo, Brazil
| | - S D Garcia
- Department of Clinics, Surgery and Animal Reproduction, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793,, 16050-680, Araçatuba, São Paulo, Brazil
| | - N F Scaramele
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - F L Lopes
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - G Dolf
- Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - T Leeb
- Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - J Sölkner
- Division of Livestook Sciences, Department of Sustainable Agriculture System, BOKU - University of Natural Resource and Live Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - J F Garcia
- Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agriculture and Veterinarian Sciences, São Paulo State University (Unesp), Via de acesso Prof. Paulo Donato Castellane s/n, 14884-900, Jaboticabal, São Paulo, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
| | - A Pieńkowska-Schelling
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Eschikon 27, Lindau, 8315, Switzerland.,Institute of Genetics, Vetsuisse-Faculty University of Bern, Bremgartenstrasse 109A, Bern, 3012, Switzerland
| | - C Schelling
- Clinic of Reproductive Medicine, Vetsuisse-Faculty University of Zurich, Eschikon 27, Lindau, 8315, Switzerland
| | - Y T Utsunomiya
- International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil.,Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), Clóvis Pestana, 793, 16050-680, Araçatuba, São Paulo, Brazil
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7
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Khayatzadeh N, Mészáros G, Utsunomiya YT, Schmitz-Hsu F, Seefried F, Schnyder U, Ferenčaković M, Garcia JF, Curik I, Sölkner J. Genome-wide mapping of the dominance effects based on breed ancestry for semen traits in admixed Swiss Fleckvieh bulls. J Dairy Sci 2019; 102:11217-11224. [PMID: 31548062 DOI: 10.3168/jds.2019-16899] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 05/03/2019] [Accepted: 08/01/2019] [Indexed: 11/19/2022]
Abstract
Heterosis is the beneficial deviation of crossbred progeny from the average of parental lines for a particular trait. Heterosis is due to nonadditive genetic effects with dominance and epistatic components. Recent advances in genotyping technology have encouraged researchers to estimate and scan heterosis components for a range of traits in crossbred populations, applying various definitions of such components. In this study, we defined the intralocus (dominance) component of heterosis using local genetic ancestry and performed genome-wide association analysis for admixed Swiss Fleckvieh bulls and their parental populations, Red Holstein Friesian and Swiss Simmental, for semen traits. A linear mixed model for 41,824 SNP, including SNP additive genetic, breed additive, and breed dominance effects on 1,178 bulls (148 Red Holstein Friesian, 213 Swiss Simmental, and 817 Swiss Fleckvieh) with a total of 43,782 measurements was performed. In total, 19 significant regions for breed dominance were identified for volume (2 regions on Bos taurus autosome 10 and 22) and percentage of live spermatozoa (17 regions on Bos taurus autosome 3, 4, 5, 7, 13, 14, and 17), and genes associated with spermatogenesis, sperm motility, and male fertility traits were located there. No significant region for breed dominance was detected for total number of spermatozoa. The signals for breed dominance were relatively wide, most likely due to limited numbers of recombination events in a small number of generations (10-15 generations) of crossbreeding in the recent Swiss Fleckvieh composite.
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Affiliation(s)
- N Khayatzadeh
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Strasse 33, A-1180 Vienna, Austria.
| | - G Mészáros
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Strasse 33, A-1180 Vienna, Austria
| | - Y T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Cinêcias Agrárias Veterinárias, UNESP-Univ Estadual Paulista, Araçatuba, São Paulo, Brazil 16050-680
| | - F Schmitz-Hsu
- Swissgenetics, Meielenfeldweg 12, Postfach, 3052 Zollikofen, Switzerland
| | - F Seefried
- Qualitas AG, Chamerstrasse 56, Ch-6300, Zug, Switzerland
| | - U Schnyder
- Qualitas AG, Chamerstrasse 56, Ch-6300, Zug, Switzerland
| | - M Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - J F Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Cinêcias Agrárias Veterinárias, UNESP-Univ Estadual Paulista, Araçatuba, São Paulo, Brazil 16050-680; Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP-Univ Estadual Paulista, Araçatuba, São Paulo, Brazil 16050-680
| | - I Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - J Sölkner
- Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences Vienna (BOKU), Gregor-Mendel-Strasse 33, A-1180 Vienna, Austria
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8
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Utsunomiya YT, Milanesi M, Fortes MRS, Porto-Neto LR, Utsunomiya ATH, Silva MVGB, Garcia JF, Ajmone-Marsan P. Genomic clues of the evolutionary history of Bos indicus cattle. Anim Genet 2019; 50:557-568. [PMID: 31475748 DOI: 10.1111/age.12836] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [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: 06/19/2019] [Indexed: 01/08/2023]
Abstract
Together with their sister subspecies Bos taurus, zebu cattle (Bos indicus) have contributed to important socioeconomic changes that have shaped modern civilizations. Zebu cattle were domesticated in the Indus Valley 8000 years before present (YBP). From the domestication site, they expanded to Africa, East Asia, southwestern Asia and Europe between 4000 and 1300 YBP, intercrossing with B. taurus to form clinal variations of zebu ancestry across the landmass of Afro-Eurasia. In the past 150 years, zebu cattle reached the Americas and Oceania, where they have contributed to the prosperity of emerging economies. The zebu genome is characterized by two mitochondrial haplogroups (I1 and I2), one Y chromosome haplogroup (Y3) and three major autosomal ancestral groups (Indian-Pakistani, African and Chinese). Phenotypically, zebu animals are recognized by their hump, large ears and excess skin. They are rustic, resilient to parasites and capable of bearing the hot and humid climates of the tropics. Many resources are available to study the zebu genome, including commercial arrays of SNP, reference assemblies and publicly available genotypes and whole-genome sequences. Nevertheless, many of these resources were initially developed to support research and subsidize industrial applications in B. taurus, and therefore they can produce bias in data analysis. The combination of genomics with precision agriculture holds great promise for the identification of genetic variants affecting economically important traits such as tick resistance and heat tolerance, which were naturally selected for millennia and played a major role in the evolution of B. indicus cattle.
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Affiliation(s)
- Y T Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M Milanesi
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, Chemistry Bld, 68 Cooper Rd, Brisbane, 4072, Qld, Australia
| | - L R Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia QLD, Brisbane, 4067, Qld, Australia
| | - A T H Utsunomiya
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil
| | - M V G B Silva
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Gado de Leite, Juiz de Fora, MG, 360381330, Brazil
| | - J F Garcia
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University (Unesp), 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency, Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793-Dona Amelia, Araçatuba, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Reproduction, School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), 14884-900 Via de Acesso Prof. Paulo Donato Castellane s/n, Jaboticabal, SP, Brazil
| | - P Ajmone-Marsan
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti-DIANA and BioDNA, Centro di Ricerca sulla Biodiversità e sul DNA Antico, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, Piacenza, 29122, Italy
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9
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Khayatzadeh N, Mészáros G, Utsunomiya YT, Schmitz-Hsu F, Seefried F, Schnyder U, Ferenčaković M, Garcia JF, Curik I, Sölkner J. Effects of breed proportion and components of heterosis for semen traits in a composite cattle breed. J Anim Breed Genet 2017; 135:45-53. [PMID: 29164741 DOI: 10.1111/jbg.12304] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 07/25/2017] [Accepted: 10/22/2017] [Indexed: 11/30/2022]
Abstract
The aim of this study was to estimate the non-additive genetic effects of the dominance component of heterosis as well as epistatic loss on semen traits in admixed Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF) cattle. Heterosis is the additional gain in productivity or fitness of cross-bred progeny over the mid-purebred parental populations. Intralocus gene interaction usually has a positive effect, while epistatic loss generally reduces productivity or fitness due to lack of evolutionarily established interactions of genes from different breeds. Genotypic data on 38,205 SNP of 818 admixed, as well as 148 RHF and 213 SI bulls as the parental breeds were used to predict breed origin of alleles. The genomewide locus-specific breed ancestries of individuals were used to calculate effects of breed difference as well as the dominance component of heterosis, while proxies for two definitions of epistatic loss were derived from 100,000 random pairs of loci. The average Holstein Friesian ancestry in admixed bulls was estimated 0.82. Results of fitting different linear mixed models showed including the dominance component of heterosis considerably improved the model adequacy for three of the four traits. Inclusion of epistatic loss increased the accuracy of the models only for our new definition of the epistatic effect for two traits, while the other definition was so highly correlated with the dominance component that statistical separation was impossible.
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Affiliation(s)
- N Khayatzadeh
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - G Mészáros
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Y T Utsunomiya
- Faculdade de Cinêcias Agrárias Veterinárias, Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | | | | | | | - M Ferenčaković
- Faculty of Agriculture, Department of Animal Science, University of Zagreb, Zagreb, Croatia
| | - J F Garcia
- Faculdade de Cinêcias Agrárias Veterinárias, Departamento de Medicina Veterinária Preventiva e Reprodução Animal, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, Brazil.,Faculdade de Medicina Veterinária de Araçatuba, Departamento de Apoio, Saúde e Produção Animal, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - I Curik
- Faculty of Agriculture, Department of Animal Science, University of Zagreb, Zagreb, Croatia
| | - J Sölkner
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria
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10
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Smith CE, Van Rompay MI, Mattei J, Garcia JF, Garcia-Bailo B, Lichtenstein AH, Tucker KL, Ordovás JM. Dietary fat modulation of hepatic lipase variant -514 C/T for lipids: a crossover randomized dietary intervention trial in Caribbean Hispanics. Physiol Genomics 2017; 49:592-600. [PMID: 28939642 DOI: 10.1152/physiolgenomics.00036.2017] [Citation(s) in RCA: 7] [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: 05/08/2017] [Revised: 08/01/2017] [Accepted: 08/01/2017] [Indexed: 11/22/2022] Open
Abstract
The hepatic lipase (LIPC) locus is a well-established determinant of high-density lipoprotein cholesterol (HDL-C) concentrations, an association that is modified by dietary fat in observational studies. Dietary interventions are lacking. We investigated dietary modulation of LIPC rs1800588 (-514 C/T) for lipids and glucose using a randomized crossover design comparing a high-fat Western diet and a low-fat traditional Hispanic diet in individuals of Caribbean Hispanic descent (n = 42, 4 wk/phase). No significant gene-diet interactions were observed for HDL-C. However, differences in dietary response according to LIPC genotype were observed. In major allele carriers (CC/CT), HDL-C (mmol/l) was higher following the Western diet compared with the Hispanic diet: phase 1 (Western: 1.3 ± 0.03; Hispanic: 1.1 ± 0.04; P = 0.0004); phase 2 (Western: 1.4 ± 0.03; Hispanic: 1.2 ± 0.03; P = 0.0003). In contrast, HDL-C in TT individuals did not differ by diet. Only major allele carriers benefited from the higher-fat diet for HDL-C. Secondarily, we explored dietary fat quality and rs1800588 for HDL-C and triglycerides (TG) in a Boston Puerto Rican Health Study (BPRHS) subset matched for diabetes and obesity status (subset n = 384). In the BPRHS, saturated fat was unfavorably associated with HDL-C and TG in rs1800588 TT carriers. LIPC rs1800588 appears to modify plasma lipids in the context of dietary fat. This new evidence of genetic modulation of dietary responses may inform optimal and personalized dietary fat advice and reinforces the importance of studying genetic markers in diet and cardiometabolic health.
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Affiliation(s)
- C E Smith
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts; .,Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts
| | - M I Van Rompay
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts.,Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts
| | - J Mattei
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts.,Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts
| | - J F Garcia
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts
| | - B Garcia-Bailo
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts
| | - A H Lichtenstein
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts.,Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts
| | - K L Tucker
- Biomedical & Nutritional Sciences, University of Massachusetts Lowell, Lowell, Massachusetts
| | - J M Ordovás
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts.,Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts.,Department of Epidemiology, Centro Nacional Investigaciones Cardiovasculares, Madrid, Spain; and.,Instituto Madrileño de Estudios Avanzados en Alimentación (IMDEA-FOOD), Madrid, Spain
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11
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Nogueira G, Ajmone-Marsan P, Milanesi M, Zavarez L, Aguiar TS, Sandre D, Maioli MA, Ferreira G, Bispo G, Stabile S, Caputo R, Toyama C, Garcia JF, Lima JCP. 1283 Understanding behavior patterns of cattle adaptation to heat stress. J Anim Sci 2016. [DOI: 10.2527/jam2016-1283] [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: 11/13/2022] Open
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12
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Bickhart DM, Xu L, Hutchison JL, Cole JB, Null DJ, Schroeder SG, Song J, Garcia JF, Sonstegard T, VanTassell CP, Schnabel RD, Taylor JF, Liu GE. 0306 Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments. J Anim Sci 2016. [DOI: 10.2527/jam2016-0306] [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: 11/13/2022] Open
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13
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Affiliation(s)
- John A Linfoot
- Donner Laboratory and Donner Pavilion, University of California, Berkeley, California, USA
| | - J F Garcia
- Donner Laboratory and Donner Pavilion, University of California, Berkeley, California, USA
| | - S A Hoye
- Donner Laboratory and Donner Pavilion, University of California, Berkeley, California, USA
| | - J Schmitt
- Donner Laboratory and Donner Pavilion, University of California, Berkeley, California, USA
| | - J H Lawrence
- Donner Laboratory and Donner Pavilion, University of California, Berkeley, California, USA
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14
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Khayatzadeh N, Mészáros G, Utsunomiya YT, Garcia JF, Schnyder U, Gredler B, Curik I, Sölkner J. Locus-specific ancestry to detect recent response to selection in admixed Swiss Fleckvieh cattle. Anim Genet 2016; 47:637-646. [PMID: 27435758 DOI: 10.1111/age.12470] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 05/30/2016] [Indexed: 01/08/2023]
Abstract
Identification of selection signatures is one of the current endeavors of evolutionary genetics. Admixed populations may be used to infer post-admixture selection. We calculated local ancestry for Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF), to infer such signals. Illumina Bovine SNP50 BeadChip data for 300 admixed, 88 SI and 97 RHF bulls were used. The average RHF ancestry across the whole genome was 0.70. To identify regions with high deviation from average, we considered two significance thresholds, based on a permutation test and extreme deviation from normal distribution. Regions on chromosomes 13 (46.3-47.3 Mb) and 18 (18.7-25.9 Mb) passed both thresholds in the direction of increased SI. Extended haplotype homozygosity within (iHS) and between (Rsb) populations was calculated to explore additional patterns of pre- and post-admixture selection signals. The Rsb score of admixed and SI was significant in a wide region of chromosome 18 (6.6-24.6 Mb) overlapped with one area of strong local ancestry deviation. FTO, with pleiotropic effect on milk and fertility, NOD2 on dairy and NKD1 and SALL1 on fertility traits are located there. Genetic differentiation of RHF and SI (Fst ), an alternative indicator of pre-admixture selection in pure populations, was calculated. No considerable overlap of peaks of local ancestry deviations and Fst was observed. We found two regions with significant signatures of post-admixture selection in this very young composite, applying comparatively stringent significance thresholds. The signals cover relatively large genomic areas and did not allow pinpointing of the gene(s) responsible for the apparent shift in ancestry proportions.
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Affiliation(s)
- N Khayatzadeh
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, A-1180, Vienna, Austria
| | - G Mészáros
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, A-1180, Vienna, Austria.
| | - Y T Utsunomiya
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - J F Garcia
- Departamento de Medicina Veterinária Preventiva e Reprodução Animal, Faculdade de Ciências Agrárias e Veterinárias, UNESP - Univ Estadual Paulista, Jaboticabal, São Paulo, Brazil.,Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista, Araçatuba, São Paulo, Brazil
| | - U Schnyder
- Qualitas AG, Chamerstrasse 56, CH-6300, Zug, Switzerland
| | - B Gredler
- Qualitas AG, Chamerstrasse 56, CH-6300, Zug, Switzerland
| | - I Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - J Sölkner
- Division of Livestock Science, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, A-1180, Vienna, Austria
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15
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Nascimento AV, Matos MC, Seno LO, Romero ARS, Garcia JF, Grisolia AB. Genome wide association study on early puberty in Bos indicus. Genet Mol Res 2016; 15:gmr7548. [PMID: 26909970 DOI: 10.4238/gmr.15017548] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The aim of this study was to evaluate a genome wide association study (GWAS) approach to identify single nucleotide polymorphisms (SNPs) associated with fertility traits (early puberty) in Nellore cattle (Bos indicus). Fifty-five Nellore cows were selected from a herd monitored for early puberty onset (positive pregnancy at 18 months of age). Extremes of this phenotype were selected; 30 and 25 individuals were pregnant and non-pregnant, respectively, at that age. DNA samples were genotyped using a high-density SNP chip (>777.000 SNP). GWAS using a case-control strategy highlighted a number of significant markers based on their proximity with the Bonferroni correction line. Results indicated that chromosomes 5, 6, 9, 10, and 22 were associated with the traits of interest. The most significant SNPs on these chromosomes were rs133039577, rs110013280, rs134702839, rs109551605, and rs41639155. Candidate genes, as well as quantitative trait loci (QTL) previously reported in the Ensembl and Cattle QTLdb databases, were further investigated. Analysis of the regions close to the SNP on chromosomes 9 and 10 revealed that four QTL had been previously classified under the reproduction category. In conclusion, we have identified SNPs in close proximity to genes associated with reproductive traits. Moreover, U6 spliceosomal RNA was present on three different chromosomes, which is possibly associated with age at first calving, suggesting that it might be a strong candidate for future studies.
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Affiliation(s)
- A V Nascimento
- Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados, Dourados, MS, Brasil
| | - M C Matos
- Centro Universitário da Grande Dourados, Dourados, MS, Brasil
| | - L O Seno
- Faculdade de Ciências Agrárias, Universidade Federal da Grande Dourados, Dourados, MS, Brasil
| | - A R S Romero
- Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados, Dourados, MS, Brasil
| | - J F Garcia
- Departamento de Apoio, Saúde e Produção Animal, Faculdade de Medicina Veterinária, Universidade Estadual Paulista
| | - A B Grisolia
- Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados, Dourados, MS, Brasil
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16
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Santana MHA, Ventura RV, Utsunomiya YT, Neves HHR, Alexandre PA, Oliveira Junior GA, Gomes RC, Bonin MN, Coutinho LL, Garcia JF, Silva SL, Fukumasu H, Leme PR, Ferraz JBS. A genomewide association mapping study using ultrasound-scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle. J Anim Breed Genet 2015; 132:420-7. [PMID: 26016521 DOI: 10.1111/jbg.12167] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 10/21/2014] [Accepted: 02/11/2015] [Indexed: 01/02/2023]
Abstract
The aim of this study was to identify candidate genes and genomic regions associated with ultrasound-derived measurements of the rib-eye area (REA), backfat thickness (BFT) and rumpfat thickness (RFT) in Nellore cattle. Data from 640 Nellore steers and young bulls with genotypes for 290 863 single nucleotide polymorphisms (SNPs) were used for genomewide association mapping. Significant SNP associations were explored to find possible candidate genes related to physiological processes. Several of the significant markers detected were mapped onto functional candidate genes including ARFGAP3, CLSTN2 and DPYD for REA; OSBPL3 and SUDS3 for BFT; and RARRES1 and VEPH1 for RFT. The physiological pathway related to lipid metabolism (CLSTN2, OSBPL3, RARRES1 and VEPH1) was identified. The significant markers within previously reported QTLs reinforce the importance of the genomic regions, and the other loci offer candidate genes that have not been related to carcass traits in previous investigations.
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Affiliation(s)
- M H A Santana
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil
| | - R V Ventura
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil.,Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada.,Beef Improvement Opportunties (BIO), Guelph, ON, Canada
| | - Y T Utsunomiya
- Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, Brazil
| | - H H R Neves
- Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, Brazil.,GenSys Consultores Associados S/C Ltda, Porto Alegre, Brazil
| | - P A Alexandre
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil
| | - G A Oliveira Junior
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil
| | - R C Gomes
- Empresa Brasileira de Pesquisa Agropecuária, CNPGC/EMBRAPA, Campo Grande, Brazil
| | - M N Bonin
- Empresa Brasileira de Pesquisa Agropecuária, CNPGC/EMBRAPA, Campo Grande, Brazil
| | - L L Coutinho
- Escola Superior de Agricultura Luiz de Queiroz, USP, Piracicaba, Brazil
| | - J F Garcia
- Faculdade de Ciências Agrárias e Veterinárias, UNESP, Jaboticabal, Brazil
| | - S L Silva
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil
| | - H Fukumasu
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil
| | - P R Leme
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil
| | - J B S Ferraz
- Faculdade de Zootecnia e Engenharia de Alimentos - USP, Pirassununga, Brazil
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17
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Santana MHA, Gomes RC, Utsunomiya YT, Neves HHR, Novais FJ, Bonin MN, Fukumasu H, Garcia JF, Alexandre PA, Oliveira Junior GA, Coutinho LL, Ferraz JBS. Genome-wide association with residual body weight gain in Bos indicus cattle. Genet Mol Res 2015; 14:5229-33. [PMID: 26125717 DOI: 10.4238/2015.may.18.14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Weight gain is a key performance trait for beef cat-tle; however, attention should be given to the production costs for better profitability. Therefore, a feed efficiency trait based on per-formance can be an interesting approach to improve performance without increasing food costs. To identify candidate genes and ge-nomic regions associated with residual body weight gain (RWG), we conducted a genome-wide association study (GWAS) with 720 Nellore cattle using the GRAMMAR-Gamma association test. We identified 30 significant single nucleotide polymorphisms (SNPs), especially on chromosomes 2, 8, 12, and 17. Several genes and quantitative train loci (QTLs) present in the regions identified were appointed; we highlight DMRT2 (doublesex and mab-3 related tran-scription factor 2), IFFO2 (intermediate filament family orphan 2), LNX2 (ligand of numb-protein X 2), MTIF3 (mitochondrial transla-tional initiation factor 3), and TRNAG-CCC (transfer RNA glycine anticodon CCC). The metabolic pathways that can explain part of the phenotypic variation in RWG are related to oxidative stress and muscle control.
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Affiliation(s)
- M H A Santana
- Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP, Brasil
| | - R C Gomes
- Empresa Brasileira de Pesquisa Agropecuária, Campo Grande, MS, Brasil
| | - Y T Utsunomiya
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - H H R Neves
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - F J Novais
- Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP, Brasil
| | - M N Bonin
- Empresa Brasileira de Pesquisa Agropecuária, Campo Grande, MS, Brasil
| | - H Fukumasu
- Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP, Brasil
| | - J F Garcia
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, SP, Brasil
| | - P A Alexandre
- Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP, Brasil
| | | | - L L Coutinho
- Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brasil
| | - J B S Ferraz
- Faculdade de Zootecnia e Engenharia de Alimentos, Pirassununga, SP, Brasil
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18
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Mur P, de Lope AR, Hernandez-Iglesias T, Diaz F, Ribalta T, Fiano C, Garcia JF, Rey JA, Mollejo M, Melendez B. P04.18 * PROGNOSIS IMPACT OF THE REGIONAL DISTRIBUTION OF MGMT GENE METHYLATION ACCORDING TO THE CPGISLAND METHYLATOR PHENOTYPE AND AGE IN HIGH-GRADE GLIOMAS. Neuro Oncol 2014. [DOI: 10.1093/neuonc/nou174.150] [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: 11/13/2022] Open
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19
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Santiago LM, Bagán H, Tarancón A, Garcia JF. Synthesis of plastic scintillation microspheres: alpha/beta discrimination. Appl Radiat Isot 2014; 93:18-28. [PMID: 24837324 DOI: 10.1016/j.apradiso.2014.04.002] [Citation(s) in RCA: 13] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 02/17/2014] [Accepted: 04/01/2014] [Indexed: 11/17/2022]
Abstract
Plastic scintillation microspheres (PSm) have been developed as an alternative for liquid scintillation cocktails due to their ability to avoid the mixed waste, besides other strengths in which the possibility for alpha/beta discrimination is included. The aim of this work was to evaluate the capability of PSm containing two combinations of fluorescence solutes (PPO/POPOP and pT/Bis-MSB) and variable amounts of a second organic solvent (naphthalene) to enhance the alpha/beta discrimination. Two commercial detectors with different Pulse Shape Discrimination performances (Quantulus and Triathler) were used to evaluate the alpha/beta discrimination. An optimal discrimination of alpha/beta particles was reached, with very low misclassification values (2% for beta particles and 0.5% for alpha particles), when PSm containing PPO/POPOP and between 0.6 and 2.0 g of naphthalene were evaluated using Triathler and the appropriate programme for data processing.
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Affiliation(s)
- L M Santiago
- Department of Analytical Chemistry of the University of Barcelona, Diagonal 645, E-08028 Barcelona, Spain
| | - H Bagán
- Department of Analytical Chemistry of the University of Barcelona, Diagonal 645, E-08028 Barcelona, Spain
| | - A Tarancón
- Department of Analytical Chemistry of the University of Barcelona, Diagonal 645, E-08028 Barcelona, Spain.
| | - J F Garcia
- Department of Analytical Chemistry of the University of Barcelona, Diagonal 645, E-08028 Barcelona, Spain
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20
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Santana MHA, Utsunomiya YT, Neves HHR, Gomes RC, Garcia JF, Fukumasu H, Silva SL, Leme PR, Coutinho LL, Eler JP, Ferraz JBS. Genome-wide association study for feedlot average daily gain in Nellore cattle (Bos indicus). J Anim Breed Genet 2014; 131:210-6. [PMID: 24906027 DOI: 10.1111/jbg.12084] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [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: 11/13/2013] [Accepted: 01/23/2014] [Indexed: 02/05/2023]
Abstract
The genome-wide association study (GWAS) results are presented for average daily gain (ADG) in Nellore cattle. Phenotype of 720 male Bos indicus animals with information of ADG in feedlots and 354,147 single-nucleotide polymorphisms (SNPs) obtained from a database added by information from Illumina Bovine HD (777,962 SNPs) and Illumina BovineSNP50 (54,609) by imputation were used. After quality control and imputation, 290,620 SNPs remained in the association analysis, using R package Genome-wide Rapid Association using Mixed Model and Regression method GRAMMAR-Gamma. A genomic region with six significant SNPs, at Bonferroni-corrected significance, was found on chromosome 3. The most significant SNP (rs42518459, BTA3: 85849977, p = 9.49 × 10(-8)) explained 5.62% of the phenotypic variance and had the allele substitution effect of -0.269 kg/day. Important genes such as PDE4B, LEPR, CYP2J2 and FGGY are located near this region, which is overlapped by 12 quantitative trait locus (QTLs) described for several production traits. Other regions with markers with suggestive effects were identified in BTA6 and BTA10. This study showed regions with major effects on ADG in Bos indicus in feedlots. This information may be useful to increase the efficiency of selecting this trait and to understand the physiological processes involved in its regulation.
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Affiliation(s)
- M H A Santana
- Faculdade de Zootecnia e Engenharia de Alimentos, USP - Univ. de São Paulo, Pirassununga, Brazil
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Lenstra JA, Groeneveld LF, Eding H, Kantanen J, Williams JL, Taberlet P, Nicolazzi EL, Sölkner J, Simianer H, Ciani E, Garcia JF, Bruford MW, Ajmone-Marsan P, Weigend S. Molecular tools and analytical approaches for the characterization of farm animal genetic diversity. Anim Genet 2012; 43:483-502. [DOI: 10.1111/j.1365-2052.2011.02309.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2011] [Indexed: 12/30/2022]
Affiliation(s)
- J. A. Lenstra
- Faculty of Veterinary Medicine; Utrecht University; Utrecht; The Netherlands
| | - L. F. Groeneveld
- Institute of Farm Animal Genetics; Friedrich-Loeffler-Institut; Hoeltystr. 10; 31535; Neustadt; Germany
| | - H. Eding
- Animal Evaluations Unit; CRV; Arnhem; The Netherlands
| | - J. Kantanen
- Biotechnology and Food Research; MTT Agrifood Research Finland; FI-31600; Jokioinen; Finland
| | - J. L. Williams
- Parco Tecnologico Padano; via Einstein; 2600; Lodi; Italy
| | - P. Taberlet
- Laboratoire d'Ecologie Alpine; Université Joseph Fourier; BP 53; Grenoble; France
| | - E. L. Nicolazzi
- Istituto di Zootecnica and BioDNA Research Centre; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | - J. Sölkner
- Department of Sustainable Agricultural Systems; Animal Breeding Group; BOKU - University of Natural Resources and Life Sciences; Vienna; Austria
| | - H. Simianer
- Department of Animal Sciences; Animal Breeding and Genetics Group; Georg-August-University Göttingen; 37075; Göttingen; Germany
| | - E. Ciani
- Department of General and Environmental Physiology; University of Bari “Aldo Moro”; Bari; Italy
| | - J. F. Garcia
- Universidade Estadual Paulista; Araçatuba; Brazil
| | - M. W. Bruford
- Organisms and Environment Division; School of Biosciences; Cardiff University; Cardiff; UK
| | - P. Ajmone-Marsan
- Istituto di Zootecnica and BioDNA Research Centre; Università Cattolica del Sacro Cuore; Piacenza; Italy
| | - S. Weigend
- Institute of Farm Animal Genetics; Friedrich-Loeffler-Institut; Hoeltystr. 10; 31535; Neustadt; Germany
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Silva MVB, Sonstegard TS, Hanotte O, Mugambi JM, Garcia JF, Nagda S, Gibson JP, Iraqi FA, McClintock AE, Kemp SJ, Boettcher PJ, Malek M, Van Tassell CP, Baker RL. Identification of quantitative trait loci affecting resistance to gastrointestinal parasites in a double backcross population of Red Maasai and Dorper sheep. Anim Genet 2011; 43:63-71. [PMID: 22221026 DOI: 10.1111/j.1365-2052.2011.02202.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A genome-wide scan for quantitative trait loci (QTL) affecting gastrointestinal nematode resistance in sheep was completed using a double backcross population derived from Red Maasai and Dorper ewes bred to F(1) rams. This design provided an opportunity to map potentially unique genetic variation associated with a parasite-tolerant breed like Red Maasai, a breed developed to survive East African grazing conditions. Parasite indicator phenotypes (blood packed cell volume - PCV and faecal egg count - FEC) were collected on a weekly basis from 1064 lambs during a single 3-month post-weaning grazing challenge on infected pastures. The averages of last measurements for FEC (AVFEC) and PCV (AVPCV), along with decline in PCV from challenge start to end (PCVD), were used to select lambs (N = 371) for genotyping that represented the tails (10% threshold) of the phenotypic distributions. Marker genotypes for 172 microsatellite loci covering 25 of 26 autosomes (1560.7 cm) were scored and corrected by Genoprob prior to qxpak analysis that included Box-Cox transformed AVFEC and arcsine transformed PCV statistics. Significant QTL for AVFEC and AVPCV were detected on four chromosomes, and this included a novel AVFEC QTL on chromosome 6 that would have remained undetected without Box-Cox transformation methods. The most significant P-values for AVFEC, AVPCV and PCVD overlapped the same marker interval on chromosome 22, suggesting the potential for a single causative mutation, which remains unknown. In all cases, the favourable QTL allele was always contributed from Red Maasai, providing support for the idea that future marker-assisted selection for genetic improvement of production in East Africa will rely on markers in linkage disequilibrium with these QTL.
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Affiliation(s)
- M V B Silva
- Bovine Functional Genomics Laboratory, Agricultural Research Service, USDA Beltsville, 10300 Baltimore Ave., Beltsville, MD 20705, USA
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23
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Joost S, Colli L, Baret PV, Garcia JF, Boettcher PJ, Tixier-Boichard M, Ajmone-Marsan P. Integrating geo-referenced multiscale and multidisciplinary data for the management of biodiversity in livestock genetic resources. Anim Genet 2010; 41 Suppl 1:47-63. [PMID: 20500755 DOI: 10.1111/j.1365-2052.2010.02037.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In livestock genetic resource conservation, decision making about conservation priorities is based on the simultaneous analysis of several different criteria that may contribute to long-term sustainable breeding conditions, such as genetic and demographic characteristics, environmental conditions, and role of the breed in the local or regional economy. Here we address methods to integrate different data sets and highlight problems related to interdisciplinary comparisons. Data integration is based on the use of geographic coordinates and Geographic Information Systems (GIS). In addition to technical problems related to projection systems, GIS have to face the challenging issue of the non homogeneous scale of their data sets. We give examples of the successful use of GIS for data integration and examine the risk of obtaining biased results when integrating datasets that have been captured at different scales.
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Affiliation(s)
- S Joost
- Laboratory of Geographic Information Systems, School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Bâtiment GC, Station 18, 1015 Lausanne, Switzerland.
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Abstract
The myostatin gene, also known as GDF8 (growth differentiation factor 8), is located on bovine chromosome 2 (BTA2); it has three exons and two introns. Myostatin is specifically expressed during embryonic development and in adult skeletal muscle, functioning as a negative regulatory protein. Several cattle breeds (Piedmontese, Belgian Blue and Blond'Aquitaine, and others) show polymorphisms in this gene; these polymorphisms are directly related to the double muscling phenotype. We looked for polymorphisms in the Nellore cattle myostatin gene and compared them with those known for taurine breeds. Seven regions, covering the three exons of this gene, were amplified by polymerase chain reaction and sequenced, including the untranslated region. DNA from 30 adult Nellore animals was collected; DNA sequencing revealed three, seven and four polymorphisms in exons 1, 2 and 3, respectively. We found previously reported polymorphisms, as well as several new ones; for instance, 37 polymorphisms were found in the untranslated region segment, and in introns 1 and 2 there were one and three polymorphisms, respectively. The high degree of allelic heterogeneity in the myostatin gene could be related to its high mutation rate; it also could be the result of a long history of artificial selection for meat production, which has probably favored such modifications and maintained them in cattle populations. These polymorphisms identified in Nellore cattle could be useful for breeding programs.
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Affiliation(s)
- A B Grisolia
- Departamento de Apoio, Produção e Saúde Animal, Laboratório de Bioquímica e Biologia Molecular Animal, Universidade Estadual Paulista, Araçatuba, SP, Brasil.
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25
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Alonso RV, Hellú JAA, Perri SHV, Visintin JA, Garcia JF. 258 FACTORS AFFECTING COMMERCIAL SEXING PROGRAM AND MULTIPLE GENETIC ANALYSIS PERSPECTIVES OF IN VITRO-PRODUCED BOVINE EMBRYOS. Reprod Fertil Dev 2009. [DOI: 10.1071/rdv21n1ab258] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The present study aimed to evaluate the interactions among different factors on the viability and sex ratio of in vitro-produced (IVP) bovine embryos, submitted to a large scale sexing program. Additionally, whole genome amplification (WGA) technology was used to amplify genomic DNA from IVP bovine embryo biopsies, in order to perform multiple genetic analyses. The survey was performed in a 4650 IVP bovine sexed embryo database. Embryos were biopsied by a microaspiration technique and sex was determined by PCR of DNA from the biopsy. Only female embryos were transferred to synchronized recipients. Pregnancy diagnosis and fetal sex determination were carried out by ultrasound. The variables were classified in accordance with embryo sex (male, female, and indeterminate), five laboratories (A, B, C, D, and E), six bovine breeds (Nellore, Brahman, Girolando, Simmental, Holstein, and Jersey), embryo stage (MO, EB, BL, XB, and HB), embryo quality (1, 2, and 3) and biopsy quality (“standard” and “nonstandard”). The statistical analysis was carried out by association chi-square test, chi-square for a 1:1 ratio, and logistic regression analysis (PROC LOGISTIC) of SAS. PCR showed 93.3% efficiency, 93.2% accuracy, and male and female rates of 52.9% and 47.1%, respectively. Mortality rate of biopsied embryos was 10.3% and pregnancy rate was 31.7%. Significant differences were not observed between male and female viability, although indeterminate embryos resulted in more death after micromanipulation. For quality 2 and 3 embryos, the mortality rate after biopsy was 3.19 and 11.37 fold higher, respectively, than for quality 1 embryos. For embryos whose biopsies were classified as nonstandard, the embryonic mortality rate was 3.6-fold higher than standard ones. Mortality rate was not affected by embryo stage at biopsy (P > 0.05). Although sex ratio was significantly skewed to male embryos, differences were not observed among laboratories (P > 0.05) and breeds (P > 0.05) on the sex ratio of IVP bovine embryos. To test the feasibility of using WGA method for multiple genetic analysis, biopsies from 28 IVP embryos were submitted to the GenomePlex Single Cell System (Sigma-Aldrich, St. Louis, MO, USA). Aliquots from each DNA sample were purified using column chromatography and submitted to PCR using sexing primers BRY4a, SRY, UMN0920, and S4B. PCR was successful and in agreement among tested DNA aliquots from each single biopsy. The WGA strategy used herein was a useful tool for applications involving restricted amounts of starting genetic material (DNA), such as in preimplantation genetic diagnosis using IVP bovine embryos.
To FAPESP and UNESP.
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Simonato LE, Garcia JF, Sundefeld MLMM, Mattar NJ, Veronese LA, Miyahara GI. Detection of HPV in mouth floor squamous cell carcinoma and its correlation with clinicopathologic variables, risk factors and survival. J Oral Pathol Med 2008; 37:593-8. [DOI: 10.1111/j.1600-0714.2008.00704.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Tracey L, Aggarwal M, Garcia-Cosio M, Villuendas R, Algara P, Sanchez-Beato M, Sanchez-Aguilera A, Garcia JF, Rodriguez A, Camacho FI, Martinez N, Ruiz-Ballesteros E, Mollejo M, Piris MA. Somatic hypermutation signature in B-cell low-grade lymphomas. Haematologica 2008; 93:1186-94. [DOI: 10.3324/haematol.12999] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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28
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Rodrigues FP, Garcia JF, Ramos PRR, Bortolozzi J, Duarte JMB. Genetic diversity of two Brazilian populations of the Pampas deer (Ozotoceros bezoarticus, Linnaeus 1758). BRAZ J BIOL 2008; 67:805-11. [PMID: 18278346 DOI: 10.1590/s1519-69842007000500002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2007] [Accepted: 10/10/2007] [Indexed: 11/22/2022] Open
Abstract
The Pampas deer (Ozotoceros bezoarticus) is one of the most endangered Neotropical cervid with populations that have been drastically reduced to small and isolated ones, mainly because of its habitat destruction. Random amplified polymorphic DNA (RAPD) markers were used to analyze population divergence and genetic variation within and between two populations corresponding to distinct subspecies. The RAPD markers displayed substantial genetic variation with all animals possessing unique RAPD phenotypes over 105 polymorphic bands produced by 15 primers. An analysis of molecular variance (AMOVA) and a neighbor-joining cluster analysis were performed to assess levels of differentiation between populations. No differentiation was recorded and about 96.0% (P<0.00001) of the total variance was attributable to variation within populations. This result is quite distinct from data obtained by the analysis of the mtDNA control region, and is discussed on the basis of genetic differences between the different markers and the male-biased dispersal patterns generally observed in the mammal species. The data presented herein are potentially useful for future taxonomic and genetic studies in this species, for the monitoring of the genetic variation observed within these populations, and for the development of management guidelines for its conservation.
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Affiliation(s)
- F P Rodrigues
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Botucatu, SP, Brazil.
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Grisolia AB, Moreno VR, Campagnari F, Milazzotto MP, Garcia JF, Adania CH, Souza EB. Genetic diversity of microsatellite loci in Leopardus pardalis, Leopardus wiedii and Leopardus tigrinus. Genet Mol Res 2007; 6:382-9. [PMID: 17624861] [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: 05/16/2023]
Abstract
The microsatellite loci FCA045, FCA077, FCA008, and FCA096 are highly variable molecular markers which were used to determine the genetic diversity in 148 captive Leopardus sp. The PCR-amplified products of microsatellite loci were characterized in ABI Prism 310 Genetic Analyzer. Allele numbers, heterozygosity, polymorphism information content, exclusive allele number, and shared alleles were calculated. Sixty-five alleles were found and their sizes ranged from 116 to 216 bp in four microsatellite loci. The heterozygosity ranged from 0.36 to 0.81 in Leopardus pardalis, 0.57 to 0.67 in L. tigrinus and 0.80 to 0.92 in L. wiedii. The polymorphism information content was from 0.80 to 0.88 in L. pardalis, 0.76 to 0.88 in L. tigrinus and 0.77 to 0.90 in L. wiedii. The margay (L. wiedii) showed the highest index of polymorphism among the three species in this study. These results imply that microsatellite DNA markers can help in the study of the genetic diversity of Leopardus specimens.
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Affiliation(s)
- A B Grisolia
- Departamento de Genética, Instituto de Biociências, UNESP, Botucatu, SP, Brasil.
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30
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Moreira MAB, Luvizotto MCR, Garcia JF, Corbett CEP, Laurenti MD. Comparison of parasitological, immunological and molecular methods for the diagnosis of leishmaniasis in dogs with different clinical signs. Vet Parasitol 2007; 145:245-52. [PMID: 17257764 DOI: 10.1016/j.vetpar.2006.12.012] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2006] [Revised: 11/23/2006] [Accepted: 12/18/2006] [Indexed: 11/15/2022]
Abstract
Aiming to improve the diagnosis of canine leishmaniasis (CanL) in an endemic area of the Northwest region of São Paulo State, Brazil, the efficacy of parasitological, immunological and molecular diagnostic methods were studied. Dogs with and without clinical signs of the disease and positive for Leishmania, by direct parasite identification on lymph node smears and/or specific antibody detection by ELISA, were selected for the study. According to the clinical signs, 89 dogs attending the Veterinary Hospital of UNESP in Araçatuba (SP, Brazil) were divided into three groups: symptomatic (36%), oligosymptomatic (22%) and asymptomatic (22%). Twenty-six dogs from an area non-endemic for CanL were used as negative controls (20%). Fine-needle aspiration biopsies (FNA) of popliteal lymph nodes were collected and Diff-Quick-stained for optical microscopy. Direct immunofluorescence, immunocytochemistry and parasite DNA amplification by PCR were also performed. After euthanasia, fragments of popliteal lymph nodes, spleen, bone marrow and liver were collected and processed for HE and immunohistochemistry. Parasite detection by both HE and immunohistochemistry was specifically more effective in lymph nodes, when compared with the other organs. Immunolabeling provided higher sensitivity for parasite detection in the tissues. In the symptomatic group, assay sensitivity was 75.61% for direct parasite search on Diff-Quick-stained FNAs, 92.68% for direct immunofluorescence, 92.68% for immunocytochemistry and 100% for PCR; the corresponding values in the other clinical groups were: 32, 60, 76 and 96% (oligosymptomatic), and 39.13, 73.91, 100 and 95.65% (asymptomatic). Results of the control animals from the CanL non-endemic area were all negative, indicating that the methods used were 100% specific.
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Affiliation(s)
- M A B Moreira
- Laboratory of Infectious Diseases Pathology, Department of Pathology, Medical School, University of São Paulo, São Paulo, Brazil
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31
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Evans PAS, Pott C, Groenen PJTA, Salles G, Davi F, Berger F, Garcia JF, van Krieken JHJM, Pals S, Kluin P, Schuuring E, Spaargaren M, Boone E, González D, Martinez B, Villuendas R, Gameiro P, Diss TC, Mills K, Morgan GJ, Carter GI, Milner BJ, Pearson D, Hummel M, Jung W, Ott M, Canioni D, Beldjord K, Bastard C, Delfau-Larue MH, van Dongen JJM, Molina TJ, Cabeçadas J. Significantly improved PCR-based clonality testing in B-cell malignancies by use of multiple immunoglobulin gene targets. Report of the BIOMED-2 Concerted Action BHM4-CT98-3936. Leukemia 2006; 21:207-14. [PMID: 17170731 DOI: 10.1038/sj.leu.2404479] [Citation(s) in RCA: 244] [Impact Index Per Article: 13.6] [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: 11/09/2022]
Abstract
Polymerase chain reaction (PCR) assessment of clonal immunoglobulin (Ig) and T-cell receptor (TCR) gene rearrangements is an important diagnostic tool in mature B-cell neoplasms. However, lack of standardized PCR protocols resulting in a high level of false negativity has hampered comparability of data in previous clonality studies. In order to address these problems, 22 European laboratories investigated the Ig/TCR rearrangement patterns as well as t(14;18) and t(11;14) translocations of 369 B-cell malignancies belonging to five WHO-defined entities using the standardized BIOMED-2 multiplex PCR tubes accompanied by international pathology panel review. B-cell clonality was detected by combined use of the IGH and IGK multiplex PCR assays in all 260 definitive cases of B-cell chronic lymphocytic leukemia (n=56), mantle cell lymphoma (n=54), marginal zone lymphoma (n=41) and follicular lymphoma (n=109). Two of 109 cases of diffuse large B-cell lymphoma showed no detectable clonal marker. The use of these techniques to assign cell lineage should be treated with caution as additional clonal TCR gene rearrangements were frequently detected in all disease categories. Our study indicates that the BIOMED-2 multiplex PCR assays provide a powerful strategy for clonality assessment in B-cell malignancies resulting in high Ig clonality detection rates particularly when IGH and IGK strategies are combined.
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MESH Headings
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 14
- Chromosomes, Human, Pair 18
- Gene Rearrangement
- Genes, Immunoglobulin
- Genotype
- Humans
- Immunoglobulin Heavy Chains/genetics
- Leukemia, B-Cell/diagnosis
- Leukemia, B-Cell/genetics
- Leukemia, B-Cell/immunology
- Lymphoma, B-Cell/diagnosis
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/immunology
- Polymerase Chain Reaction/methods
- Receptors, Antigen, T-Cell/genetics
- Translocation, Genetic
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Affiliation(s)
- P A S Evans
- Haematological Malignancy Diagnostic Service, The General Infirmary at Leeds, Leeds, UK
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van Krieken JHJM, Langerak AW, Macintyre EA, Kneba M, Hodges E, Sanz RG, Morgan GJ, Parreira A, Molina TJ, Cabeçadas J, Gaulard P, Jasani B, Garcia JF, Ott M, Hannsmann ML, Berger F, Hummel M, Davi F, Brüggemann M, Lavender FL, Schuuring E, Evans PAS, White H, Salles G, Groenen PJTA, Gameiro P, Pott C, Dongen JJMV. Improved reliability of lymphoma diagnostics via PCR-based clonality testing: — Report of the BIOMED-2 Concerted Action BHM4-CT98-3936. Leukemia 2006; 21:201-6. [PMID: 17170732 DOI: 10.1038/sj.leu.2404467] [Citation(s) in RCA: 240] [Impact Index Per Article: 13.3] [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: 11/08/2022]
Abstract
The diagnosis of malignant lymphoma is a recognized difficult area in histopathology. Therefore, detection of clonality in a suspected lymphoproliferation is a valuable diagnostic criterion. We have developed primer sets for the detection of rearrangements in the B- and T-cell receptor genes as reliable tools for clonality assessment in lymphoproliferations suspected for lymphoma. In this issue of Leukemia, the participants of the BIOMED-2 Concerted Action CT98-3936 report on the validation of the newly developed clonality assays in various disease entities. Clonality was detected in 99% of all B-cell malignancies and in 94% of all T-cell malignancies, whereas the great majority of reactive lesions showed polyclonality. The combined BIOMED-2 results are summarized in a guideline, which can now be implemented in routine lymphoma diagnostics. The use of this standardized approach in patients with a suspect lymphoproliferation will result in improved diagnosis of malignant lymphoma.
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Bates GJ, Fox SB, Han C, Leek RD, Garcia JF, Harris AL, Banham AH. Increased regulatory T-cell numbers distinguish high-risk breast cancer patients and those at risk of late relapse. Breast Cancer Res 2006. [PMCID: PMC3300278 DOI: 10.1186/bcr1586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Blázquez S, Sirvent JJ, Olona M, Aguilar C, Pelegri A, Garcia JF, Palacios J. Caspase-3 and caspase-6 in ductal breast carcinoma: a descriptive study. Histol Histopathol 2006; 21:1321-9. [PMID: 16977583 DOI: 10.14670/hh-21.1321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Caspases are the main point in the apoptotic process. We have collected some information from 210 cases of Ductal breast cancer (pT1 - pT2) such as tumour size, histological differentiation degree, lymph node status and tumor necrosis in the infiltrating component and we have evaluated the number of apoptotic cells or bodies by TUNEL technique as well as immunohistochemical studies to evaluate the expression of caspase 3 and caspase 6, and proliferation index. Our results show that lymph node status and cell atypism are independent prognostic factors for recurrence and mortality and only tumour size is an independent prognostic factor for recurrence. However, the apoptotic index and the immunohistochemical expression of caspases and cell proliferation index have not turned out to be independent prognostic factors neither for recurrence nor mortality. These results show that classic prognostic factors known until now are the most important factors to predict the evolution of the illness.
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Affiliation(s)
- S Blázquez
- Department of Pathology, Sant Pau i Santa Tecla Hospital, Tarragona, Spain.
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35
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Abstract
Introduction Une épidémie de pneumopathies atypiques est apparue en novembre 2002 dans la région Chinoise de Guangdong. Elle a ensuite été décrite sous le nom de syndrome respiratoire aigu sévère (SRAS) à partir de nouveaux foyers survenus à Hanoi et à Hong Kong en février 2003. En France, 5 cas reliés au même patient source ont été rapportés. Observation Nous rapportons l’observation d’un patient de 52 ans contact direct avec un cas probable de SRAS. À l’admission, le patient présente une hyperthermie isolée sans symptomatologie respiratoire associée à une lymphopénie et une cytolyse hépatique. La radiographie thoracique est normale. La tomodensitométrie thoracique objective l’existence d’un aspect en verre dépoli sous pleural. L’étude par PCR des prélèvements naso-pharyngés précoces (36e heure) à la recherche du coronavirus associé au SARS sera négative. La confirmation du cas sera obtenue par l’étude sérologique. Conclusions Cette observation illustre l’existence de présentations cliniques frustres du syndrome respiratoire aigu sévère. La contagiosité des formes pauci symptomatiques n’est pas connue. Des analyses sérologiques permettront de mieux les préciser. Le danger actuel d’une recrudescence saisonnière particulièrement hivernale ne peut être écarté. Dans ce contexte, l’existence et la reconnaissance des formes pauci symptomatiques pour lesquelles la contagiosité ne peut être écartée est primordiale.
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Affiliation(s)
- M André
- Service de pneumologie, HIA Clermont Tonnerre, Brest, France.
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Roncador G, Garcia JF, Garcia JF, Maestre L, Lucas E, Menarguez J, Ohshima K, Nakamura S, Banham AH, Piris MA. FOXP3, a selective marker for a subset of adult T-cell leukaemia/lymphoma. Leukemia 2005; 19:2247-53. [PMID: 16193085 DOI: 10.1038/sj.leu.2403965] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [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: 11/09/2022]
Abstract
FOXP3 is a forkhead transcription factor family member, implicated in T-cell regulation, activation and differentiation. FOXP3 has been shown to be a master control gene for the development and function of CD4+/CD25+ regulatory T-cells (T(reg)). In this study, FOXP3 protein expression has been analysed using a new anti-FOXP3 monoclonal antibody in 172 paraffin-embedded lymphoma samples. FOXP3 expression in tumour cells was confined to adult T-cell leukaemia/lymphoma (ATLL) cases (17/25, 68%), with some variability in the intensity of the staining and the proportion of positive cells. No other lymphoma types studied exhibited FOXP3 expression in the malignant population. The selective expression of FOXP3 by tumour cells in ATLL makes this antibody a potentially useful diagnostic tool.
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Affiliation(s)
- G Roncador
- Monoclonal Antibodies Unit, Biotechnology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain.
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Barc RM, Rousset J, Maignien B, Lu M, Prime-Guitton CH, Garcia JF. [Diverticula of the appendix and their complications: value of sonography (review of 21 cases)]. J Radiol 2005; 86:299-309. [PMID: 15908870 DOI: 10.1016/s0221-0363(05)81359-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
PURPOSE Diverticulosis is defined by the presence of diverticula along any segment of the GI tract. Diverticulosis and its associated complications may involve the appendix. The imaging and histological findings of 21 cases of diverticulitis of the appendix are reviewed. MATERIALS AND METHODS Sonography, because of its high spatial resolution, is an ideal imaging technique to diagnose diverticulitis of the appendix. RESULTS Similar to diverticulosis of the large bowel, diverticula of the appendix correspond to pseudo-diverticula composed of mucosa and sub mucosa herniating through the muscular layer. Chronic inflammatory changes affect the surrounding appendicular wall, as confirmed by histological examination. Clinical symptoms range from chronic right lower quadrant abdominal pain to acute appendicitis and even peritonitis. CONCLUSION Based on this retrospective analysis of 21 cases, it is possible to describe the specific and sensitive imaging findings for diagnosis of simple and complicated forms of diverticulitis of the appendix. Surgery is the treatment of choice because of the high risk of perforation.
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Affiliation(s)
- R M Barc
- Cabinet d'imagerie médicale, 12 place Gambetta, 56000 Vannes
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D'Antonio A, Caleo A, Garcia JF, Marsilia GM, De Dominicis G, Boscaino A. Primary peripheral PNET/Ewing's sarcoma of the dura with FISH analysis. Histopathology 2005; 45:651-4. [PMID: 15569062 DOI: 10.1111/j.1365-2559.2004.01961.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
MESH Headings
- Chromosome Aberrations
- Dura Mater/chemistry
- Dura Mater/metabolism
- Dura Mater/pathology
- Female
- Humans
- Immunohistochemistry
- In Situ Hybridization, Fluorescence
- Ki-67 Antigen/analysis
- Meningeal Neoplasms/genetics
- Meningeal Neoplasms/metabolism
- Meningeal Neoplasms/pathology
- Middle Aged
- Neuroectodermal Tumors, Primitive, Peripheral/genetics
- Neuroectodermal Tumors, Primitive, Peripheral/metabolism
- Neuroectodermal Tumors, Primitive, Peripheral/pathology
- Sarcoma, Ewing/genetics
- Sarcoma, Ewing/metabolism
- Sarcoma, Ewing/pathology
- Vimentin/analysis
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Neto ASC, Sanches BV, Binelli M, Seneda MM, Perri SH, Garcia JF. Improvement in embryo recovery using double uterine flushing. Theriogenology 2005; 63:1249-55. [PMID: 15725433 DOI: 10.1016/j.theriogenology.2004.03.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [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: 02/12/2004] [Accepted: 03/24/2004] [Indexed: 11/22/2022]
Abstract
The objective of the present study was to evaluate the effects of double uterine flushing on the recovery of embryos/ova in cattle. Two hundred and ten embryo recovery procedures were conducted using a double uterine flushing method, and the results were compared with 432 conventional single-flushing procedures. Cyclic Limousin (n = 403) and Guzera (n = 239) donor cows received an intravaginal progesterone releasing device and 2 mg of estradiol benzoate on Day 0. Between Days 5 and 9, donors received decreasing doses of FSH, which ranged from 200 to 300 IU (Bos indicus) and 300 to 500 IU (Bos taurus). On the afternoon of Day 7, donors received an injection of 500 microg cloprostenol and progesterone implants were removed 12 h later (morning of Day 8). Artificial insemination was performed between 14 and 26 h after first detection of behavioral estrus. Cows were randomly assigned to have embryos recovered by a double-flushing method (n = 210) or the conventional single-flushing procedure (n = 432). For the double-flushing procedure, after first flushing the whole uterus with 1L of Dubelco's Phosphate Buffered Saline (DPBS), a Foley catheter was positioned in the uterine body to permit refilling of the uterus with fresh DPBS (80-150 mL). The catheter was closed with the plunger of a disposable 5 mL syringe, and the donors were allowed to rest in a holding area for 30 min. Thereafter, a second flush was performed to recover the solution remaining in the uterus. Animals from the control group were subjected to a single uterine flush. From 210 double-flushing procedures, 1409 viable embryos were recovered. In comparison, from 432 cows receiving the single-flushing procedure, 1993 embryos were recovered. Double flushing increased (P < 0.05) the number of embryos recovered per procedure compared to single flushing (6.7 +/- 0.4 versus 4.6 +/- 0.2, respectively; mean +/- S.E.M.). When double flushing was performed, average recovered embryos/ova increased (P < 0.05) from 8.3 +/- 0.4 to 12.7 +/- 0.7 in Limousin and from 7.9 to 11.5 in Guzera. Also, utilization of double flushing increased (P < 0.05) the number of viable embryos from 4.7 +/- 0.3 to 6.9 +/- 0.5 in Limousin and from 4.5 +/- 0.4 to 6.4 +/- 0.7 in Guzera. Mean total embryos/ova was similar (P > 0.05) between the control group and after the first uterine flushing in the double-flushing group; therefore, both flushings were conducted efficiently. In conclusion, double uterine flushing increased embryo recovery in cattle.
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Santos SEC, Murua Escobar H, Sider LH, Winkler S, Aoki SM, Milazzotto MP, Campagnari F, Vannucchi CI, Bullerdiek J, Nolte I, Garcia JF. DNA sequence, polymorphism, and mapping of luteinizing hormone receptor fragment (LHCGR) gene in Great Dane dogs. Anim Genet 2004; 35:74-5. [PMID: 14731239 DOI: 10.1111/j.0268-9146.2003.01080.x] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S E C Santos
- Department of Animal Health and Production, São Paulo State University, Araçatuba, Brazil
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Mello MRB, Caetano HVA, Marques MG, Padilha MS, Garcia JF, Milazzotto MP, Assumpção MEOA, Lima AS, Nicácio AC, Mendes CM, Oliveira VP, Visintin JA. Production of a cloned calf from a fetal fibroblast cell line. Braz J Med Biol Res 2003; 36:1485-9. [PMID: 14576903 DOI: 10.1590/s0100-879x2003001100006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [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: 11/22/2022] Open
Abstract
The present study examined the in vitro and in vivo development of bovine nuclear-transferred embryos. A bovine fetal fibroblast culture was established and used as nucleus donor. Slaughterhouse oocytes were matured in vitro for 18 h before enucleation. Enucleated oocytes were fused with fetal fibroblasts with an electric stimulus and treated with cytochalasin D and cycloheximide for 1 h followed by cycloheximide alone for 4 h. Reconstructed embryos were cultured for 7-9 days and those which developed to blastocysts were transferred to recipient cows. Of 191 enucleated oocytes, 83 (43.5%) were successfully fused and 24 (28.9%) developed to blastocysts. Eighteen freshly cloned blastocysts were transferred to 14 recipients, 5 (27.8%) of which were pregnant on day 35 and 3 (16.7%) on day 90. Of the three cows that reached the third trimester, one recipient died of hydrallantois 2 months before term, one aborted fetus was recovered at 8 months of gestation, and one delivered by cesarian section a healthy cloned calf. Today, the cloned calf is 15 months old and presents normal body development (378 kg) and sexual behavior (libido and semen characteristics).
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Affiliation(s)
- M R B Mello
- Departamento de Reprodução Animal, Faculdade de Medicina Veterinária, Universidade de São Paulo, São Paulo, SP, Brasil.
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Abstract
In the past years, research in embryo technologies is moving to the establishment of preimplantation genetic typing or also denominated preimplantation genetic diagnosis (PGD). The objectives of these tests are the prevention of genetic diseases transmission and the prediction of phenotypic characteristics, as well as sex determination, genetic disorders and productive and reproductive profiles, prior to the embryo transfer or freezing, during early stages of development. This paper points out the state-of-the-art of PGD, mainly in cattle and discuss the perspectives of multiloci genetic analysis of embryos.
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Affiliation(s)
- J F Garcia
- Department of Animal Health and Production, São Paulo State University, UNESP, Araçatuba, Brazil
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Bressollette L, Nonent M, Oger E, Garcia JF, Larroche P, Guias B, Scarabin PY, Mottier D. Diagnostic accuracy of compression ultrasonography for the detection of asymptomatic deep venous thrombosis in medical patients--the TADEUS project. Thromb Haemost 2001; 86:529-33. [PMID: 11521998] [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: 02/21/2023]
Abstract
We assessed the accuracy of venous compression ultrasonography (CUS) for the detection of asymptomatic deep vein thrombosis in 122 consecutive patients, with a mean age of 69 years, who were hospitalised in an internal medicine unit. All included patients had CUS within 48 h of admission. Twelve out of 17 patients with a positive CUS underwent phlebography, as the others withdrew their consent, whereas the remaining 105 patients with a negative serial CUS testing were clinically followed-up at 3 months. We found that CUS had a sensitivity and a specificity of respectively 1 (95% CI, 0.73 to 1) and 1 (95% CI, 0.96 to 1) for the detection of asymptomatic deep vein thrombosis. Kappa-coefficients for intra-observer and inter-observer agreements were respectively 0.88 and 0.56. We concluded that venous compression ultrasonography, performed as described, fulfils requirements of a screening test that could be available for prophylactic clinical trials or epidemiological researches.
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Affiliation(s)
- L Bressollette
- Department of Internal Medicine and Chest Diseases, Hĵpital de la Cavale Blanche, Brest, France
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Ould-Ahmed M, Mas B, Hautbois E, Garcia JF, Caroff P, Guiavarch M. [Unusual course of a pulmonary artery catheter through a persistent superior vena cava] . Ann Fr Anesth Reanim 2000; 19:745-8. [PMID: 11200762 DOI: 10.1016/s0750-7658(00)00319-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We report the unusual course of a pulmonary artery catheter through a persistent left-sided superior vena cava. After left subclavian vein cannulation and downward left-sided paramediastinum course, the Swan-Ganz catheter enters the right pulmonary artery. Haemodynamic monitoring was consistent with the diagnosis of septic shock developed by this 56-year-old woman, after cephalic duodenopancreatectomy. Persistent left-sided superior vena cava occurs in 0.5% of the population and 5-10% of patients with congenital heart diseases. It drains into the right atrium through the coronary sinus in 92% of cases and is associated with an absent right superior vena cava in 20% of cases. The left-sided superior vena cava persists when the caudal part of the left anterior cardinal vein does not degenerate. A persistent left superior vena cava may be medically relevant during implantation of pacemaker leads or radiofrequency ablation, during cardiac surgery for placement of a retrograde coronary sinus cardioplegia catheter and during transjugular intrahepatic portosystemic shunt placement.
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Affiliation(s)
- M Ould-Ahmed
- Département d'anesthésie-réanimation et urgences, HIA Clermont-Tonnerre, rue du Colonel Fonferrier, BP 41, 29240 Brest-Naval, France
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Renard G, Garcia JF, Cardoso FC, Richter MF, Sakanari JA, Ozaki LS, Termignoni C, Masuda A. Cloning and functional expression of a Boophilus microplus cathepsin L-like enzyme. Insect Biochem Mol Biol 2000; 30:1017-1026. [PMID: 10989288 DOI: 10.1016/s0965-1748(00)00070-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A cysteine proteinase gene homologous to cathepsins L genes was isolated from a B. microplus cDNA library. The precursor protein deduced from the nucleotide sequence contains 332 amino acid residues consisting of a signal sequence (pre-region), a pro-region and a mature proteinase. The DNA fragment coding for the proenzyme was cloned and expressed using the E. coli expression vector pMAL-p. The recombinant protein (MBP+PROCP) once activated is able to hydrolyze synthetic substrates as well as protein substrates like hemoglobin, vitellin and gelatin. Its optimal enzymatic activity on both fluorogenic and protein substrates was found to occur at an acidic pH. Expression of the proteinase gene was tested by RT-PCR with tick larvae RNA. Detection of amplified sequences indicates that the gene is expressed at this stage of the tick life cycle and the molecule is therefore potentially a target for chemotherapy or an immunogen in a vaccine.
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Affiliation(s)
- G Renard
- Centro de Biotecnologia do Estado do Rio Grande do Sul - UFRGS, C.P. 15005 - Campus do Vale, 91501-970 RS, Porto Alegre, Brazil
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Rahal P, Latronico AC, Kohek MBF, De Lucia RFS, Milazzotto MP, Wheeler MB, Ferraz JBS, Eler JP, Garcia JF. Polymorphisms in the bovine follicle-stimulating hormone receptor gene. Anim Genet 2000. [DOI: 10.1111/j.1365-2052.2000.00604.pp.x] [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: 10/19/2022]
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Rahal P, Latronico AC, Kohek MB, de Lucia RF, Milazzotto MP, Wheeler MB, Ferraz JB, Eler JP, Garcia JF. Polymorphisms in the bovine follicle-stimulating hormone receptor gene. Anim Genet 2000; 31:280-1. [PMID: 11086540 DOI: 10.1046/j.1365-2052.2000.00604.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- P Rahal
- Department of Animal Health and Production, UNESP, Araçatuba, Brazil
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Abstract
OBJECTIVE To evaluate the sonographic (US) appearance of digital annular pulley (DAP) tears in high-level rock climbers. DESIGN AND PATIENTS We performed a retrospective analysis of the US examinations of 16 high-level rock climbers with clinical signs of DAP lesions. MRI and surgical evaluation were performed in five and three patients respectively. The normal US and MRI appearances of DAP were evaluated in 40 and three normal fingers respectively. RESULTS Nine of 16 patients presented a DAP tear. In eight subjects (seven with complete tears involving the fourth finger and one the fifth finger), US diagnosis was based on the indirect sign of volar bowstringing of the flexor tendons. Injured pulleys were not appreciated by US. Tears concerned the A2 and A3 in six patients and the A3 and A4 in two patients. A2 pulley thickening and hypoechogenicity compatible with a partial tear was demonstrated in one patient. MRI and surgical data correlated well with the US findings. Four patients had tenosynovitis of the flexor tendons but no evidence of pulley disruption. US examinations of three patients were normal. In the healthy subjects US demonstrated DAP in 16 of 40 digits. CONCLUSION US can diagnose DAP tears and correlates with the MRI and surgical data. Because of its low cost and non-invasiveness we suggest US as the first imaging modality in the evaluation of injuries of the digital pulley.
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Affiliation(s)
- C Martinoli
- Istituto di Radiologia, Università di Genova, Genoa, Italy
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Abstract
BACKGROUND Some studies have reported an increase of atopy in HIV-infected (HIV+) patients, but the cause still remains unclear. OBJECTIVE To determine the prevalence of atopy in HIV+ patients and to investigate its predictors. METHODS Seventy-four HIV+ hospitalized patients (46 of them with AIDS) were studied prospectively for the presence of atopy, based on immediate hypersensitivity to common allergens by prick test. Serum immunoglobulins, specific IgE, lymphocyte subsets, and the expression of low affinity IgE receptor (CD23) on B cells were determined. RESULTS Thirty-one percent of patients presented IgE values greater than 150 ku/L (39% of patients without AIDS and 26% of AIDS patients; P = .23) and 47% showed an increase (> or = 2%) in the percentage of CD23+ B cells. Non-AIDS patients had higher IgE values than AIDS patients (346 +/- 605 versus 175 +/- 276; P = .16). Atopy prevalence was higher in non-AIDS than in AIDS patients (28% versus 11%; P = .06). Specific IgE agreed with positive prick test in 58% of cases. Multivariate analysis showed that a personal history suggestive of allergic disease and IgE > 150 ku/L were predictors of atopy, while gender, risk group, CD4+ T cells, CD23 expression on B cells, and AIDS were not associated. CONCLUSIONS HIV+ patients present a higher prevalence of atopy in early stages of HIV infection than general population. Since allergic reactions could accelerate HIV-infection by increasing type 2 cytokines, it is important to evaluate the atopic state in HIV+ patients with IgE > 150 ku/L or with suggestive allergic history in order to prevent it.
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Affiliation(s)
- M Corominas
- Immunology Service, Ciutat Sanitària i Universitària de Bellvitge, L'Hospitalet de Llobregat, Barcelona, Spain
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Heinemann MB, Garcia JF, Nunes CM, Gregori F, Higa ZM, Vasconcellos SA, Richtzenhain LJ. Detection and differentiation of Leptospira spp. serovars in bovine semen by polymerase chain reaction and restriction fragment length polymorphism. Vet Microbiol 2000; 73:261-7. [PMID: 10781725 DOI: 10.1016/s0378-1135(00)00150-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [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: 11/20/2022]
Abstract
In view of the importance of venereal transmission of bovine leptospirosis, the objective of the present study was to apply the polymerase chain reaction (PCR) to 26 serovars of Leptospira interrogans, L. borgpetersenii, L. santarosai, L. noguchii and L. biflexa, to determine the detection threshold in semen samples and to evaluate the possibility of differentiation among serovars using 19 restriction endonucleases. The results showed that all serovars were amplified and the detection threshold in semen samples of a bull was 100 bacteria/ml. Using endonucleases we could classify the 26 serovars into eight groups. The present results show that PCR is a method of great potential for the detection of Leptospira spp. at bovine artificial insemination centers.
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Affiliation(s)
- M B Heinemann
- Department of Preventive Veterinary Medicine and Animal Health, University of São Paulo, São Paulo, Brazil
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