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1.
Bioinformatics ; 2019 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-31647543

RESUMO

MOTIVATION: Whole-genome regressions methods represent a key framework for genome-wide prediction, cross-validation studies, and association analysis. The bWGR offers a compendium of Bayesian methods with various priors available, allowing users to predict complex traits with different genetic architectures. RESULTS: Here we introduce bWGR, an R package that enables users to efficient fit and cross-validate Bayesian and likelihood whole-genome regression methods. It implements a series of methods referred to as the Bayesian alphabet under the traditional Gibbs sampling and optimized Expectation-Maximization. The package also enables fitting efficient multivariate models and complex hierarchical models. The package is user-friendly and computational efficient. AVAILABILITY AND IMPLEMENTATION: bWGR is an R package available in the CRAN repository. It can be installed in R by typing: install.packages("bWGR"). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

2.
PLoS Genet ; 12(8): e1006178, 2016 08.
Artigo em Inglês | MEDLINE | ID: mdl-27490364

RESUMO

Investigations on the influence of nature vs. nurture on Alcoholism (Alcohol Use Disorder) in human have yet to provide a clear view on potential genomic etiologies. To address this issue, we sequenced a replicated animal model system bidirectionally-selected for alcohol preference (AP). This model is uniquely suited to map genetic effects with high reproducibility, and resolution. The origin of the rat lines (an 8-way cross) resulted in small haplotype blocks (HB) with a corresponding high level of resolution. We sequenced DNAs from 40 samples (10 per line of each replicate) to determine allele frequencies and HB. We achieved ~46X coverage per line and replicate. Excessive differentiation in the genomic architecture between lines, across replicates, termed signatures of selection (SS), were classified according to gene and region. We identified SS in 930 genes associated with AP. The majority (50%) of the SS were confined to single gene regions, the greatest numbers of which were in promoters (284) and intronic regions (169) with the least in exon's (4), suggesting that differences in AP were primarily due to alterations in regulatory regions. We confirmed previously identified genes and found many new genes associated with AP. Of those newly identified genes, several demonstrated neuronal function involved in synaptic memory and reward behavior, e.g. ion channels (Kcnf1, Kcnn3, Scn5a), excitatory receptors (Grin2a, Gria3, Grip1), neurotransmitters (Pomc), and synapses (Snap29). This study not only reveals the polygenic architecture of AP, but also emphasizes the importance of regulatory elements, consistent with other complex traits.


Assuntos
Alcoolismo/genética , Estudo de Associação Genômica Ampla , Seleção Genética , Alcoolismo/fisiopatologia , Álcoois/toxicidade , Animais , Modelos Animais de Doenças , Éxons/genética , Frequência do Gene , Genômica , Haplótipos , Humanos , Íntrons/genética , Herança Multifatorial/genética , Neurônios/efeitos dos fármacos , Fenótipo , Ratos
3.
BMC Bioinformatics ; 18(1): 191, 2017 Mar 24.
Artigo em Inglês | MEDLINE | ID: mdl-28340551

RESUMO

BACKGROUND: Genome-wide assisted selection is a critical tool for the genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each round of a Markov Chain Monte Carlo. We evaluated the effect of subsampling bootstrap on prediction and computational parameters. RESULTS: Across datasets, we observed an optimal subsampling proportion of observations around 50% with replacement, and around 33% without replacement. Subsampling provided a substantial decrease in computation time, reducing the time to fit the model by half. On average, losses on predictive properties imposed by subsampling were negligible, usually below 1%. For each dataset, an optimal subsampling point that improves prediction properties was observed, but the improvements were also negligible. CONCLUSION: Combining subsampling with Gibbs sampling is an interesting ensemble algorithm. The investigation indicates that the subsampling bootstrap Markov chain algorithm substantially reduces computational burden associated with model fitting, and it may slightly enhance prediction properties.


Assuntos
Teorema de Bayes , Estudo de Associação Genômica Ampla/métodos , Genômica/métodos , Animais , Humanos , Estudos de Amostragem
4.
Development ; 141(15): 3003-12, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-25053433

RESUMO

talpid(2) is an avian autosomal recessive mutant with a myriad of congenital malformations, including polydactyly and facial clefting. Although phenotypically similar to talpid(3), talpid(2) has a distinct facial phenotype and an unknown cellular, molecular and genetic basis. We set out to determine the etiology of the craniofacial phenotype of this mutant. We confirmed that primary cilia were disrupted in talpid(2) mutants. Molecularly, we found disruptions in Hedgehog signaling. Post-translational processing of GLI2 and GLI3 was aberrant in the developing facial prominences. Although both GLI2 and GLI3 processing were disrupted in talpid(2) mutants, only GLI3 activator levels were significantly altered in the nucleus. Through additional fine mapping and whole-genome sequencing, we determined that the talpid(2) phenotype was linked to a 1.4 Mb region on GGA1q that contained the gene encoding the ciliary protein C2CD3. We cloned the avian ortholog of C2CD3 and found its expression was ubiquitous, but most robust in the developing limbs and facial prominences. Furthermore, we found that C2CD3 is localized proximal to the ciliary axoneme and is important for docking the mother centriole to the ciliary vesicle and cell membrane. Finally, we identified a 19 bp deletion in talpid(2) C2CD3 that produces a premature stop codon, and thus a truncated protein, as the likely causal allele for the phenotype. Together, these data provide insight into the cellular, molecular and genetic etiology of the talpid(2) phenotype. Our data suggest that, although the talpid(2) and talpid(3) mutations affect a common ciliogenesis pathway, they are caused by mutations in different ciliary proteins that result in differences in craniofacial phenotype.


Assuntos
Anormalidades Craniofaciais/genética , Proteínas Hedgehog/genética , Proteínas Hedgehog/metabolismo , Fatores de Transcrição Kruppel-Like/genética , Mutação , Alelos , Animais , Membrana Celular/metabolismo , Núcleo Celular , Centríolos/metabolismo , Embrião de Galinha , Mapeamento Cromossômico , Cílios/metabolismo , Códon de Terminação , Fibroblastos/metabolismo , Proteínas Hedgehog/fisiologia , Heterozigoto , Fenótipo , Polimorfismo Genético , Processamento de Proteína Pós-Traducional , Análise de Sequência de DNA , Transdução de Sinais , Proteína Gli2 com Dedos de Zinco
5.
Vet Anaesth Analg ; 44(6): 1303-1312, 2017 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-29113716

RESUMO

OBJECTIVE: To examine the accuracy of plethysmography variability index (PVI) as a noninvasive indicator of fluid responsiveness in hypovolaemic dogs. STUDY DESIGN: Prospective experimental study. ANIMALS: Six adult healthy sevoflurane-anaesthetized Beagle dogs. METHODS: Dogs were anaesthetized with 1.3-fold their individual minimum alveolar concentration of sevoflurane. The lungs were mechanically ventilated after neuromuscular blockade with vecuronium bromide. Cardiopulmonary variables including mean arterial blood pressure (MAP), central venous pressure (CVP), transpulmonary thermodilution cardiac output (TPTDCO), stroke volume (SV), perfusion index (PI), pulse pressure variation (PPV), stroke volume variation (SVV) and PVI were determined during six stages of graded venous blood withdrawal (5 mL kg-1 increments) and six stages of graded blood infusion (5 mL kg-1 increments). The cardiopulmonary variables were analysed using paired t test or Wilcoxon signed rank test. Correlations between PPV and SVV or PVI were analysed by linear regression. The accuracy of PPV, SVV and PVI for predicting fluid responsiveness was examined by using receiver operating characteristic curve analysis. A value of p < 0.05 was considered statistically significant. RESULTS: Blood withdrawal resulted in significant increases in PPV and PVI and decreases in MAP, CVP, TPTDCO, SV and PI. Blood infusion resulted in significant increases in MAP, CVP, TPTDCO, SV and PI and decreases in PPV and PVI. PPV and PVI showed a relevant correlation (p < 0.001, r2 = 0.62) and threshold values of PPV ≥ 16% (sensitivity 71%, specificity 82%) and PVI ≥ 12% (sensitivity 78%, specificity 72%) for identifying fluid responsiveness. SVV did not change. CONCLUSIONS AND CLINICAL RELEVANCE: Noninvasive measurement of PVI predicted fluid responsiveness with moderate accuracy equal to PPV in sevoflurane-anaesthetized mechanically ventilated dogs. Provisional threshold values for identification of fluid responsiveness were PPV ≥ 16% and PVI ≥ 12%. Clinical trials are needed to confirm these threshold values in dogs.


Assuntos
Anestésicos Inalatórios , Pressão Sanguínea , Transfusão de Sangue/veterinária , Hidratação/veterinária , Hemorragia/veterinária , Éteres Metílicos , Pletismografia/veterinária , Respiração Artificial/veterinária , Animais , Transfusão de Sangue/métodos , Débito Cardíaco , Doenças do Cão/fisiopatologia , Cães , Feminino , Hidratação/métodos , Hemorragia/fisiopatologia , Masculino , Pletismografia/instrumentação , Respiração Artificial/métodos , Sevoflurano , Resultado do Tratamento
6.
BMC Bioinformatics ; 17: 55, 2016 Feb 02.
Artigo em Inglês | MEDLINE | ID: mdl-26830693

RESUMO

BACKGROUND: Success in genome-wide association studies and marker-assisted selection depends on good phenotypic and genotypic data. The more complete this data is, the more powerful will be the results of analysis. Nevertheless, there are next-generation technologies that seek to provide genotypic information in spite of great proportions of missing data. The procedures these technologies use to impute genetic data, therefore, greatly affect downstream analyses. This study aims to (1) compare the genetic variance in a single-nucleotide polymorphism panel of soybean with missing data imputed using various methods, (2) evaluate the imputation accuracy and post-imputation quality associated with these methods, and (3) evaluate the impact of imputation method on heritability and the accuracy of genome-wide prediction of soybean traits. The imputation methods we evaluated were as follows: multivariate mixed model, hidden Markov model, logical algorithm, k-nearest neighbor, single value decomposition, and random forest. We used raw genotypes from the SoyNAM project and the following phenotypes: plant height, days to maturity, grain yield, and seed protein composition. RESULTS: We propose an imputation method based on multivariate mixed models using pedigree information. Our methods comparison indicate that heritability of traits can be affected by the imputation method. Genotypes with missing values imputed with methods that make use of genealogic information can favor genetic analysis of highly polygenic traits, but not genome-wide prediction accuracy. The genotypic matrix captured the highest amount of genetic variance when missing loci were imputed by the method proposed in this paper. CONCLUSIONS: We concluded that hidden Markov models and random forest imputation are more suitable to studies that aim analyses of highly heritable traits while pedigree-based methods can be used to best analyze traits with low heritability. Despite the notable contribution to heritability, advantages in genomic prediction were not observed by changing the imputation method. We identified significant differences across imputation methods in a dataset missing 20 % of the genotypic values. It means that genotypic data from genotyping technologies that provide a high proportion of missing values, such as GBS, should be handled carefully because the imputation method will impact downstream analysis.


Assuntos
Variação Genética/genética , Genoma de Planta , Glycine max/genética , Modelos Genéticos , Polimorfismo de Nucleotídeo Único/genética , Algoritmos , Estudo de Associação Genômica Ampla , Genômica , Linhagem , Fenótipo , Locos de Características Quantitativas , Análise de Sequência de DNA
7.
Bioinformatics ; 31(23): 3862-4, 2015 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-26243017

RESUMO

MOTIVATION: Mixed linear models provide important techniques for performing genome-wide association studies. However, current models have pitfalls associated with their strong assumptions. Here, we propose a new implementation designed to overcome some of these pitfalls using an empirical Bayes algorithm. RESULTS: Here we introduce NAM, an R package that allows user to take into account prior information regarding population stratification to relax the linkage phase assumption of current methods. It allows markers to be treated as a random effect to increase the resolution, and uses a sliding-window strategy to increase power and avoid double fitting markers into the model. AVAILABILITY AND IMPLEMENTATION: NAM is an R package available in the CRAN repository. It can be installed in R by typing install.packages ('NAM'). CONTACT: krainey@purdue.edu. SUPPLEMENTARY INFORMATION: Supplementary date are available at Bioinformatics online.


Assuntos
Estudo de Associação Genômica Ampla/métodos , Software , Algoritmos , Teorema de Bayes , Ligação Genética , Modelos Lineares
8.
Theor Appl Genet ; 129(10): 1933-49, 2016 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-27435734

RESUMO

KEY MESSAGE: The main statistical procedures in plant breeding are based on Gaussian process and can be computed through mixed linear models. Intelligent decision making relies on our ability to extract useful information from data to help us achieve our goals more efficiently. Many plant breeders and geneticists perform statistical analyses without understanding the underlying assumptions of the methods or their strengths and pitfalls. In other words, they treat these statistical methods (software and programs) like black boxes. Black boxes represent complex pieces of machinery with contents that are not fully understood by the user. The user sees the inputs and outputs without knowing how the outputs are generated. By providing a general background on statistical methodologies, this review aims (1) to introduce basic concepts of machine learning and its applications to plant breeding; (2) to link classical selection theory to current statistical approaches; (3) to show how to solve mixed models and extend their application to pedigree-based and genomic-based prediction; and (4) to clarify how the algorithms of genome-wide association studies work, including their assumptions and limitations.


Assuntos
Melhoramento Vegetal/métodos , Plantas/genética , Estatística como Assunto , Algoritmos , Alelos , Genômica/métodos , Modelos Lineares , Modelos Genéticos , Distribuição Normal , Fenótipo , Seleção Genética
9.
Genet Sel Evol ; 48(1): 68, 2016 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-27623765

RESUMO

BACKGROUND: Mortality due to cannibalism causes both economic and welfare problems in laying hens. To limit mortality due to cannibalism, laying hens are often beak-trimmed, which is undesirable for animal welfare reasons. Genetic selection is an alternative strategy to increase survival and is more efficient by taking heritable variation that originates from social interactions into account, which are modelled as the so-called indirect genetic effects (IGE). Despite the considerable heritable variation in survival time due to IGE, genetic improvement of survival time in laying hens is still challenging because the detected heritable variation of the trait with IGE is still limited, ranging from 0.06 to 0.26, and individuals that are still alive at the end of the recording period are censored. Furthermore, survival time records are available late in life and only on females. To cope with these challenges, we tested the hypothesis that genomic prediction increases the accuracy of estimated breeding values (EBV) compared to parental average EBV, and increases response to selection for survival time compared to a traditional breeding scheme. We tested this hypothesis in two lines of brown layers with intact beaks, which show cannibalism, and also the hypothesis that the rate of inbreeding per year is lower for genomic selection than for the traditional breeding scheme. RESULTS AND DISCUSSION: The standard deviation of genomic prediction EBV for survival time was around 22 days for both lines, indicating good prospects for selection against mortality in laying hens with intact beaks. Genomic prediction increased the accuracy of the EBV by 35 and 32 % compared to the parent average EBV for the two lines. At the current reference population size, predicted response to selection was 91 % higher when using genomic selection than with the traditional breeding scheme, as a result of a shorter generation interval in males and greater accuracy of selection in females. The predicted rate of inbreeding per generation with truncation selection was substantially lower for genomic selection than for the traditional breeding scheme for both lines. CONCLUSIONS: Genomic selection for socially affected traits is a promising tool for the improvement of survival time in laying hens with intact beaks.


Assuntos
Canibalismo , Galinhas/genética , Animais , Comportamento Animal/fisiologia , Feminino , Testes Genéticos/métodos , Genômica/métodos , Linhagem , Fenótipo , Seleção Genética
10.
BMC Genomics ; 16: 816, 2015 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-26481588

RESUMO

BACKGROUND: Marek's disease (MD) is a lymphoproliferative disease of poultry induced by Marek's disease virus (MDV), a highly oncogenic alphaherpesvirus. Identifying the underlying genes conferring MD genetic resistance is desired for more efficacious control measures including genomic selection, which requires accurately identified genetic markers throughout the chicken genome. METHODS: Hypothesizing that variants located in transcriptional regulatory regions are the main mechanism underlying this complex trait, a genome-wide association study was conducted by genotyping a ~1,000 bird MD resource population derived from experimental inbred layers with SNPs containing 1,824 previously identified allele-specific expression (ASE) SNPs in response to MDV infection as well as 3,097 random SNPs equally spaced throughout the chicken genome. Based on the calculated associations, genomic predictions were determined for 200 roosters and selected sires had their progeny tested for Marek's disease incidence. RESULTS: Our analyses indicate that these ASE SNPs account for more than 83 % of the genetic variance and exhibit nearly all the highest associations. To validate these findings, 200 roosters had their genetic merit predicted from the ASE SNPs only, and the top 30 and bottom 30 ranked roosters were reciprocally mated to random hens. The resulting progeny showed that after only one generation of bidirectional selection, there was a 22 % difference in MD incidence and this approach gave a 125 % increase in accuracy compared to current pedigree-based estimates. CONCLUSIONS: We conclude that variation in transcriptional regulation is the major driving cause for genetic resistance to MD, and ASE SNPs identify the underlying genes and are sufficiently linked to the causative polymorphisms that they can be used for accurate genomic prediction as well as help define the underlying molecular basis. Furthermore, this approach should be applicable to other complex traits.


Assuntos
Resistência à Doença/genética , Estudo de Associação Genômica Ampla , Doença de Marek/genética , Locos de Características Quantitativas/genética , Alelos , Animais , Galinhas/genética , Feminino , Expressão Gênica , Genótipo , Herpesvirus Galináceo 2/patogenicidade , Masculino , Doença de Marek/virologia , Fenótipo , Polimorfismo de Nucleotídeo Único , Elementos Reguladores de Transcrição/genética
11.
J Surg Res ; 194(2): 679-687, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25586331

RESUMO

BACKGROUND: Fibrocaps, a ready-to-use, dry-powder fibrin sealant containing human plasma-derived thrombin and fibrinogen, is being developed as an adjunct for surgical hemostasis. MATERIALS AND METHODS: Safety and efficacy of Fibrocaps applied directly or by spray device, in combination with gelatin sponge, was compared with that of gelatin sponge-alone in two randomized, single-blind controlled trials: FC-002 US (United States) and FC-002 NL (the Netherlands). A total of 126 adult patients were randomized (Fibrocaps: n = 47 [FC-002 US], n = 39 [FC-002 NL]; gelatin sponge alone: n = 23 [FC-002 US], n = 17 [FC-002 NL). One bleeding site was treated during a surgical procedure (n = 125). Time to hemostasis (primary end point) was measured, with a 28-d safety follow-up. Four surgical indications included hepatic resection (n = 58), spinal procedures (n = 37), peripheral vascular procedures (n = 30), and soft tissue dissection (n = 1). RESULTS: Mean (standard deviation) time to hemostasis was significantly shorter after Fibrocaps treatment than after gelatin sponge alone (FC-002 US: 1.9 [1.3] versus 4.8 min [3.1], P < 0.001; FC-002 NL: 2.2 [1.3] versus 4.4 min [3.1], P = 0.004). The incidence of hemostasis was greater after Fibrocaps compared with that of gelatin sponge alone within 3 min (FC-002 US: 83% versus 35%, P < 0.001; FC-002 NL: 77% versus 53%, P = 0.11), 5 min (94% versus 61%, P = 0.001; 95% versus 71%, P = 0.022), and 10 min (100% versus 78%, P = 0.003; 100% versus 82%, P = 0.025). Adverse events were consistent with surgical procedures performed and patients' underlying diseases and generally similar between treatment arms; most were mild or moderate in severity. Non-neutralizing antithrombin antibodies were detected in 5% of Fibrocaps-treated patients on day 29. CONCLUSIONS: Fibrocaps had good safety and efficacy profiles, supporting continuing clinical development as a novel fibrin sealant.


Assuntos
Perda Sanguínea Cirúrgica/prevenção & controle , Adesivo Tecidual de Fibrina/uso terapêutico , Hemostasia Cirúrgica/instrumentação , Hemostáticos/uso terapêutico , Adulto , Idoso , Idoso de 80 Anos ou mais , Feminino , Adesivo Tecidual de Fibrina/imunologia , Esponja de Gelatina Absorvível , Hemostáticos/imunologia , Humanos , Masculino , Pessoa de Meia-Idade , Resultado do Tratamento , Adulto Jovem
12.
Genet Sel Evol ; 46: 43, 2014 Jul 07.
Artigo em Inglês | MEDLINE | ID: mdl-25001618

RESUMO

BACKGROUND: Antimicrobial peptides (AMP) are important elements of the first line of defence against pathogens in animals. NK-lysin is a cationic AMP that plays a critical role in innate immunity. The chicken NK-lysin gene has been cloned and its antimicrobial and anticancer activity has been described but its location in the chicken genome remains unknown. Here, we mapped the NK-lysin gene and examined the distribution of a functionally significant single nucleotide polymorphism (SNP) among different chicken inbred lines and heritage breeds. RESULTS: A 6000 rad radiation hybrid panel (ChickRH6) was used to map the NK-lysin gene to the distal end of chromosome 22. Two additional genes, the adipocyte enhancer-binding protein 1-like gene (AEBP1) and the DNA polymerase delta subunit 2-like (POLD2) gene, are located in the same NW_003779909 contig as NK-lysin, and were thus indirectly mapped to chromosome 22 as well. Previously, we reported a functionally significant SNP at position 271 of the NK-lysin coding sequence in two different chicken breeds. Here, we examined this SNP and found that the A allele appears to be more common than the G allele in these heritage breeds and inbred lines. CONCLUSIONS: The chicken NK-lysin gene mapped to the distal end of chromosome 22. Two additional genes, AEBP1 and POLD2, were indirectly mapped to chromosome 22 also. SNP analyses revealed that the A allele, which encodes a peptide with a higher antimicrobial activity, is more common than the G allele in our tested inbred lines and heritage breeds.


Assuntos
Proteínas Aviárias/genética , Galinhas/genética , Mapeamento Cromossômico , Proteolipídeos/genética , Alelos , Animais , Cruzamento , Carboxipeptidases/genética , Mapeamento Cromossômico/veterinária , Cromossomos/genética , DNA Polimerase III/genética , Frequência do Gene , Marcadores Genéticos , Genoma , Genótipo , Fenótipo , Polimorfismo de Nucleotídeo Único , Proteínas Repressoras/genética , Análise de Sequência de DNA/veterinária
13.
J Equine Vet Sci ; 139: 105130, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38879096

RESUMO

Horses are the most challenging of the common companion animals to anesthetize. Induction of anesthesia in the horse is complicated by the fact that it is accompanied by a transition from a conscious standing position to uncconconscious recumbency. The purpose of this article is to review the literature on induction of anesthesia with a focus on the behavioral and physiologic/pharmacodynamic responses and the actions and interactions of the drugs administered to induce anesthesia in the healthy adult horse with the goal of increasing consistency and predictability.


Assuntos
Anestesia , Anestésicos , Cavalos , Animais , Anestesia/veterinária , Anestesia/métodos , Anestésicos/farmacologia
14.
BMC Genomics ; 14: 64, 2013 Jan 30.
Artigo em Inglês | MEDLINE | ID: mdl-23363372

RESUMO

BACKGROUND: Marek's disease (MD) is a commercially important neoplastic disease of chickens caused by the Marek's disease virus (MDV), a naturally occurring oncogenic alphaherpesvirus. Enhancing MD genetic resistance is desirable to augment current vaccines and other MD control measures. High throughput sequencing was used to profile splenic transcriptomes from individual F1 progeny infected with MDV at 4 days of age from both outbred broilers (meat-type) and inbred layer (egg-type) chicken lines that differed in MD genetic resistance. The resulting information was used to identify SNPs, genes, and biological pathways exhibiting allele-specific expression (ASE) in response to MDV infection in each type of chicken. In addition, we compared and contrasted the results of pathway analyses (ASE and differential expression (DE)) between chicken types to help inform on the biological response to MDV infection. RESULTS: With 7 individuals per line and treatment group providing high power, we identified 6,132 single nucleotide polymorphisms (SNPs) in 4,768 genes and 4,528 SNPs in 3,718 genes in broilers and layers, respectively, that exhibited ASE in response to MDV infection. Furthermore, 548 and 434 genes in broilers and layers, respectively, were found to show DE following MDV infection. Comparing the datasets, only 72 SNPs and 850 genes for ASE and 20 genes for DE were common between the two bird types. Although the chicken types used in this study were genetically different, at the pathway level, both TLR receptor and JAK/STAT signaling pathways were enriched as well as exhibiting a high proportion of ASE genes, especially at the beginning of both above mentioned regulatory pathways. CONCLUSIONS: RNA sequencing with adequate biological replicates is a powerful approach to identify high confidence SNPs, genes, and pathways that are associated with transcriptional response to MDV infection. In addition, the SNPs exhibiting ASE in response to MDV infection provide a strong foundation for determining the extent to which variation in expression influences MD incidence plus yield genetic markers for genomic selection. However, given the paucity of overlap among ASE SNP sets (broilers vs. layers), it is likely that separate screens need to be incorporated for each population. Finally, comparison of gene lists obtained between these two diverse chicken types indicate the TLR and JAK/STAT signaling are conserved when responding to MDV infection and may be altered by selection of genes exhibiting ASE found at the start of each pathway.


Assuntos
Alelos , Galinhas/genética , Perfilação da Expressão Gênica , Herpesvirus Galináceo 2/fisiologia , Doença de Marek/genética , Carne , Oviposição , Animais , Galinhas/imunologia , Galinhas/fisiologia , Galinhas/virologia , Resistência à Doença/genética , Genômica , Doença de Marek/imunologia , Polimorfismo de Nucleotídeo Único , Análise de Sequência de RNA , Especificidade da Espécie
15.
Plant Physiol ; 159(1): 418-32, 2012 May.
Artigo em Inglês | MEDLINE | ID: mdl-22452853

RESUMO

In Arabidopsis (Arabidopsis thaliana), the ATP-dependent chromatin remodeler PICKLE (PKL) determines expression of genes associated with developmental identity. PKL promotes the epigenetic mark trimethylation of histone H3 lysine 27 (H3K27me3) that facilitates repression of tissue-specific genes in plants. It has previously been proposed that PKL acts indirectly to promote H3K27me3 by promoting expression of the POLYCOMB REPRESSIVE COMPLEX2 complex that generates H3K27me3. We undertook expression and chromatin immunoprecipitation analyses to further characterize the contribution of PKL to gene expression and developmental identity. Our expression data support a critical and specific role for PKL in expression of H3K27me3-enriched loci but do not support a role for PKL in expression of POLYCOMB REPRESSIVE COMPLEX2. Moreover, our chromatin immunoprecipitation data reveal that PKL protein is present at the promoter region of multiple H3K27me3-enriched loci, indicating that PKL directly acts on these loci. In particular, we find that PKL is present at LEAFY COTYLEDON1 and LEAFY COTYLEDON2 during germination, which is when PKL acts to repress these master regulators of embryonic identity. Surprisingly, we also find that PKL is present at the promoters of actively transcribed genes that are ubiquitously expressed such as ACTIN7 and POLYUBIQUITIN10 that do not exhibit PKL-dependent expression. Taken together, our data contravene the previous model of PKL action and instead support a direct role for PKL in determining levels of H3K27me3 at repressed loci. Our data also raise the possibility that PKL facilitates a common chromatin remodeling process that is not restricted to H3K27me3-enriched regions.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Histonas/metabolismo , Actinas/genética , Actinas/metabolismo , Arabidopsis/genética , Arabidopsis/crescimento & desenvolvimento , Proteínas de Arabidopsis/genética , Montagem e Desmontagem da Cromatina , Imunoprecipitação da Cromatina , DNA Helicases , Regulação da Expressão Gênica no Desenvolvimento , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Loci Gênicos , Germinação , Lisina/genética , Lisina/metabolismo , Metilação , Folhas de Planta/genética , Folhas de Planta/metabolismo , Brotos de Planta/genética , Brotos de Planta/crescimento & desenvolvimento , Brotos de Planta/metabolismo , Complexo Repressor Polycomb 2 , Poliubiquitina/genética , Poliubiquitina/metabolismo , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Sementes/genética , Sementes/metabolismo
16.
Poult Sci ; 92(9): 2530-4, 2013 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-23960138

RESUMO

Genomic selection can be implemented based on the genomic relationship matrix (GBLUP) and can be combined with phenotypes from nongenotyped animals through the use of best linear unbiased prediction (BLUP). A common method to combine both sources of information involves multiple steps, but is difficult to use with complicated models and is nonoptimal. A simpler method, termed single-step GBLUP, or ssGBLUP, integrates the genomically derived relationships (G) with population-based pedigree relationships (A) into a combined relationship matrix (H) and allows for genomic selection in a single step. The ssGBLUP method is easy to implement and uses standard BLUP-based programs. Experiences with field data in chickens, pigs, and dairy indicate that ssGBLUP is more accurate yet much simpler than multi-step methods. The current limits of ssGBLUP are approximately 100,000 genotypes and 18 traits. Models involving 10 million animals have been run successfully. The inverse of H can also be used in existing programs for parameter estimationm, but a properly scaled G is needed for unbiased estimation. Also, as genomic predictions can be converted to SNP effects, ssGBLUP is useful for genomic-wide association studies. The single-step method for genomic selection translates the use of genomic information into standard BLUP, and variance-component estimation programs become a routine.


Assuntos
Galinhas/genética , Genoma , Genômica/métodos , Gado/genética , Sus scrofa/genética , Animais , Simulação por Computador , Modelos Genéticos , Linhagem , Polimorfismo de Nucleotídeo Único , Análise de Regressão
17.
J Am Vet Med Assoc ; 261(10): 1539-1546, 2023 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-37315940

RESUMO

The primary purpose of perioperative IV fluid administration is to preserve tissue perfusion by maintaining or restoring the effective circulating intravascular volume. Fluids are drugs that produce beneficial or harmful effects dependent upon their composition, osmotic potential, kinetics, and dose. Appropriate dosing requires an understanding of body fluid compartments, fluid balance, and the administered fluids' behavior in the body. Anesthetic drugs and general anesthesia produce CNS, neuroendocrine, and macro-/microvascular hemodynamic effects. These effects modulate the response to IV fluid administration and promote interstitial fluid accumulation, third-space fluid loss, and fluid overload. This narrative review discusses current knowledge regarding anesthesia-associated physiologic and IV fluid kinetic changes that influence the efficacy of IV fluid administration during the intraoperative period. A rationale for intraoperative fluid dosing that addresses intraoperative hypotension, blood loss, and practices that promote fluid overload is provided. Intraoperative IV fluid administration should be individualized and monitored by dynamic goal-directed methods that evaluate fluid responsiveness.


Assuntos
Anestésicos , Insuficiência Cardíaca , Animais , Hidratação/veterinária , Hemodinâmica , Anestesia Geral/veterinária , Assistência Perioperatória/veterinária , Insuficiência Cardíaca/veterinária
18.
Alcohol Clin Exp Res (Hoboken) ; 47(8): 1478-1493, 2023 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-37336636

RESUMO

BACKGROUND: The basis for familial alcohol use disorder (AUD) remains an enigma due to various biological and societal confounds. The present study used three of the most adopted and documented rat models, combining the alcohol-preferring/non-alcohol-preferring (P/NP) lines and high alcohol-drinking/low alcohol-drinking (HAD/LAD) replicated lines, of AUD as examined through the lens of whole genomic analyses. METHODS: We used complete genome sequencing of the P/NP lines and previously published sequences of the HAD/LAD replicates to enhance the discovery of variants associated with AUD and to remove confounding with genetic background and random genetic drift. Specifically, we used high-order statistical methods to search for genetic variants whose frequency changes in whole sets of gene ontologies corresponded with phenotypic changes in the direction of selection, that is, ethanol-drinking preference. RESULTS: Our first finding was that in addition to variants causing translational changes, the principal genetic changes associated with drinking predisposition were silent mutations and mutations in the 3' untranslated regions (3'UTR) of genes. Neither of these types of mutations alters the amino acid sequence of the translated protein but they influence both the rate and conformation of gene transcription, including its stability and posttranslational events that alter gene efficacy. This finding argues for refocusing human genomic studies on changes in gene efficacy. Among the key ontologies identified were the central genes associated with the Na+ voltage-gated channels of neurons and glia (including the Scn1a, Scn2a, Scn2b, Scn3a, Scn7a, and Scn9a subtypes) and excitatory glutamatergic secretion (including Grm2 and Myo6), both of which are essential in neuroplasticity. In addition, we identified "Nociception or Sensory Perception of Pain," which contained variants in nociception (Arrb1, Ccl3, Ephb1) and enlist sodium (Scn1a, Scn2a, Scn2b, Scn3a, Scn7a), pain activation (Scn9a), and potassium channel (Kcna1) genes. CONCLUSION: The multi-model analyses used herein reduced the confounding effects of random drift and the "founders" genetic background. The most differentiated bidirectionally selected genes across all three animal models were Scn9a, Scn1a, and Kcna, all of which are annotated in the nociception ontology. The complexity of neuroplasticity and nociception adds strength to the hypothesis that neuroplasticity and pain (physical or psychological) are prominent phenotypes genetically linked to the development of AUD.

20.
BMC Genomics ; 13: 509, 2012 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-23009705

RESUMO

BACKGROUND: The events leading to sepsis start with an invasive infection of a primary organ of the body followed by an overwhelming systemic response. Intra-abdominal infections are the second most common cause of sepsis. Peritoneal fluid is the primary site of infection in these cases. A microarray-based approach was used to study the temporal changes in cells from the peritoneal cavity of septic mice and to identify potential biomarkers and therapeutic targets for this subset of sepsis patients. RESULTS: We conducted microarray analysis of the peritoneal cells of mice infected with a non-pathogenic strain of Escherichia coli. Differentially expressed genes were identified at two early (1 h, 2 h) and one late time point (18 h). A multiplexed bead array analysis was used to confirm protein expression for several cytokines which showed differential expression at different time points based on the microarray data. Gene Ontology based hypothesis testing identified a positive bias of differentially expressed genes associated with cellular development and cell death at 2 h and 18 h respectively. Most differentially expressed genes common to all 3 time points had an immune response related function, consistent with the observation that a few bacteria are still present at 18 h. CONCLUSIONS: Transcriptional regulators like PLAGL2, EBF1, TCF7, KLF10 and SBNO2, previously not described in sepsis, are differentially expressed at early and late time points. Expression pattern for key biomarkers in this study is similar to that reported in human sepsis, indicating the suitability of this model for future studies of sepsis, and the observed differences in gene expression suggest species differences or differences in the response of blood leukocytes and peritoneal leukocytes.


Assuntos
Infecções Intra-Abdominais/genética , Infecções Intra-Abdominais/microbiologia , Peritônio/microbiologia , Sepse/genética , Sepse/microbiologia , Animais , Células Cultivadas , Proteínas de Ligação a DNA/biossíntese , Proteínas de Ligação a DNA/genética , Modelos Animais de Doenças , Fatores de Transcrição de Resposta de Crescimento Precoce/biossíntese , Fatores de Transcrição de Resposta de Crescimento Precoce/genética , Escherichia coli , Infecções por Escherichia coli/microbiologia , Feminino , Expressão Gênica , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Marcadores Genéticos , Fator 1-alfa Nuclear de Hepatócito , Fatores de Transcrição Kruppel-Like/biossíntese , Fatores de Transcrição Kruppel-Like/genética , Camundongos , Camundongos Endogâmicos C3H , Camundongos Endogâmicos C57BL , Análise de Sequência com Séries de Oligonucleotídeos , Proteínas de Ligação a RNA/biossíntese , Proteínas de Ligação a RNA/genética , Proteínas Repressoras/biossíntese , Proteínas Repressoras/genética , Fator 1 de Transcrição de Linfócitos T/biossíntese , Fator 1 de Transcrição de Linfócitos T/genética , Transativadores/biossíntese , Transativadores/genética , Fatores de Transcrição/biossíntese , Fatores de Transcrição/genética , Transcrição Gênica , Transcriptoma
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