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Ghiasi H.,University of Tehran | Pakdel A.,University of Tehran | Nejati-Javaremi A.,University of Tehran | Mehrabani-Yeganeh H.,University of Tehran | And 4 more authors.
Livestock Science | Year: 2011

Linear and threshold animal models were used to estimate genetic parameters for reproductive traits in Iranian Holstein cows. Reproductive traits included: days from calving to first service (DFS), number of inseminations to conception (INS), calving interval (CI), days open (DO), and interval between first and last insemination (IFL), pregnancy rate (PR), and success to first insemination (SF). A total of 72,124 records in parity 1 to 6 from 27,113 cows from 1981 to 2007 were used. Estimated heritabilities for reproductive traits were low (below 0.1); SF (0.029) had the lowest and DO and PR had the highest (0.076) heritability. Heritabilities obtained for interval traits were higher than those for categorical and binary traits. Strong genetic correlations were estimated between fertility traits. The results from current study show that fertility is a complex trait and several measurements related to fertility should be combined in a fertility index for selection purposes. © 2011 Elsevier B.V.


Gonzalez-Recio O.,Instituto Nacional Of Investigaciones Agrarias | Weigel K.A.,University of Wisconsin - Madison | Gianola D.,University of Wisconsin - Madison | Gianola D.,Norwegian University of Life Sciences | And 2 more authors.
Genetics Research | Year: 2010

The L2-Boosting algorithm is one of the most promising machine-learning techniques that has appeared in recent decades. It may be applied to high-dimensional problems such as whole-genome studies, and it is relatively simple from a computational point of view. In this study, we used this algorithm in a genomic selection context to make predictions of yet to be observed outcomes. Two data sets were used: (1) productive lifetime predicted transmitting abilities from 4702 Holstein sires genotyped for 32 611 single nucleotide polymorphisms (SNPs) derived from the Illumina BovineSNP50 BeadChip, and (2) progeny averages of food conversion rate, pre-corrected by environmental and mate effects, in 394 broilers genotyped for 3481 SNPs. Each of these data sets was split into training and testing sets, the latter comprising dairy or broiler sires whose ancestors were in the training set. Two weak learners, ordinary least squares (OLS) and non-parametric (NP) regression were used for the L2-Boosting algorithm, to provide a stringent evaluation of the procedure. This algorithm was compared with BL [Bayesian LASSO (least absolute shrinkage and selection operator)] and BayesA regression. Learning tasks were carried out in the training set, whereas validation of the models was performed in the testing set. Pearson correlations between predicted and observed responses in the dairy cattle (broiler) data set were 065 (033), 053 (037), 066 (026) and 063 (027) for OLS-Boosting, NP-Boosting, BL and BayesA, respectively. The smallest bias and mean-squared errors (MSEs) were obtained with OLS-Boosting in both the dairy cattle (008 and 108, respectively) and broiler (0011 and 0006) data sets, respectively. In the dairy cattle data set, the BL was more accurate (bias=010 and MSE=110) than BayesA (bias=126 and MSE=281), whereas no differences between these two methods were found in the broiler data set. L2-Boosting with a suitable learner was found to be a competitive alternative for genomic selection applications, providing high accuracy and low bias in genomic-assisted evaluations with a relatively short computational time. © 2010 Cambridge University Press.


Costa e Silva V.T.,University of Sao Paulo | Liano F.,Hospital Universitario Ramon y Cajal | Muriel A.,Hospital Universitario Ramon y Cajal | Diez R.,Instituto Nacional Of Investigaciones Agrarias | And 2 more authors.
PLoS ONE | Year: 2013

Background:Delayed nephrology consultation (NC) seems to be associated with worse prognosis in critically ill acute kidney injury (AKI) patients.Design, Setting, Participants, & Measurements:The aims of this study were to analyze factors related with timing of NC and its relation with AKI patients' outcome in intensive care units of a tertiary hospital. AKI was defined as an increase ≥50% in baseline serum creatinine (SCr). Early NC and delayed NC were defined as NC performed before and two days after AKI diagnosis day. Multivariable logistic regression and propensity scores (PS) were used to adjust for confounding and selection biases. Hospital mortality and dialysis dependence on hospital discharge were the primary outcomes.Results:A total of 366 AKI patients were analyzed and NCs were carried out in 53.6% of the patients. Hospital mortality was 67.8% and dialysis required in 31.4% patients (115/366). Delayed NCs (34%) occurred two days after AKI diagnosis day. This group presented higher mortality (OR: 4.04/CI: 1.60-10.17) and increased dialysis dependence (OR: 3.00/CI: 1.43-6.29) on hospital discharge. Four variables were retained in the PS model for delayed NC: diuresis (1000 ml/24 h - OR: 1.92/CI: 1.27-2.90), SCr (OR: 0.49/CI: 0.32-0.75), surgical AKI (OR: 3.67/CI: 1.65-8.15), and mechanical ventilation (OR: 2.82/CI: 1.06-7.44). After correction by PS, delayed NC was still associated with higher mortality (OR: 3.39/CI: 1.24-9.29) and increased dialysis dependence (OR: 3.25/CI: 1.41-7.51). Delayed NC was associated with increased mortality either in dialyzed patients (OR: 1.54/CI: 1.35-1.78) or non-dialyzed patients (OR: 2.89/CI: 1.00-8.35).Conclusion:Delayed NC was associated with higher mortality and increased dialysis dependence rates in critically ill AKI patients at hospital discharge. Further studies are necessary to ascertain whether this effect is due to delayed nephrology intervention or residual confounding factors. © 2013 Costa e Silva et al.


Toro M.A.,Technical University of Madrid | Meuwissen T.H.E.,Norwegian University of Life Sciences | Fernandez J.,Instituto Nacional Of Investigaciones Agrarias | Shaat I.,Mtt Agrifood Research Finland | And 2 more authors.
Animal | Year: 2011

Genetic variation is vital for the populations to adapt to varying environments and to respond to artificial selection; therefore, any conservation and development scheme should start from assessing the state of variation in the population. There are several marker-based and pedigree-based parameters to describe genetic variation. The most suitable ones are rate of inbreeding and effective population size, because they are not dependent on the amount of pedigree records. The acceptable level for effective population size can be considered from different angles leading to a conclusion that it should be at least 50 to 100. The estimates for the effective population size can be computed from the genealogical records or from demographic and marker information when pedigree data are not available. Marker information could also be used for paternity analysis and for estimation of coancestries. The sufficient accuracy in marker-based parameters would require typing thousands of markers. Across breeds, diversity is an important source of variation to rescue problematic populations and to introgress new variants. Consideration of adaptive variation brings new aspects to the estimation of the variation between populations. © 2011 The Animal Consortium.


Fernandez J.,Instituto Nacional Of Investigaciones Agrarias | Meuwissen T.H.E.,Norwegian University of Life Sciences | Toro M.A.,Technical University of Madrid | Maki-Tanila A.,Mtt Agrifood Research Finland
Animal | Year: 2011

Many local breeds of farm animals have small populations and, consequently, are highly endangered. The correct genetic management of such populations is crucial for their survival. Managing an animal population involves two steps: first, the individuals who will be permitted to leave descendants are to be chosen and the number offspring they will be permitted to produce has to be determined; second, the mating scheme has to be identified. Strategies dealing with the first step are directed towards the maximisation of effective population size and, therefore, act jointly on the reduction in the loss of genetic variation and in the increase of inbreeding. In this paper, the most relevant methods are summarised, including the so-called 'Optimum Contribution' methodology (contributions are proportional to the coancestry of each individual with the rest), which has been shown to be the best. Typically, this method is applied to pedigree information, but molecular marker data can be used to complete or replace the genealogy. When the population is subjected to explicit selection on any trait, the above methodology can be used by balancing the response to selection and the increase in coancestry/inbreeding. Different mating strategies also exist. Some of the mating schemes try to reduce the level of inbreeding in the short term by preventing mating between relatives. Others involve regular (circular) schemes that imply higher levels of inbreeding within populations in the short term, but demonstrate better performance in the long term. In addition, other tools such as cryopreservation and reproductive techniques aid in the management of small populations. In the future, genomic marker panels may replace the pedigree information in measuring the coancestry. The paper also includes the results of several experiments and field studies on the effectiveness and on the consequences of the use of the different strategies. © 2011 The Animal Consortium.


Garcia M.J.,Autonomous University of Madrid | Nunez M.C.,Autonomous University of Madrid | Nunez M.C.,Instituto Nacional Of Investigaciones Agrarias | Cox R.A.,UK National Institute for Medical Research
PLoS ONE | Year: 2010

Background: Except for the ribosomal protein L12 (rplL), ribosomal proteins are present as one copy per ribosome; L12 (rplL) is unusual because it is present as four copies per ribosome. Thus, the strategies used by Mycobacterium fortuitum to regulate ribosomal protein synthesis were investigated, including evaluations of the rates of chain elongations of 16S rRNA, rplL and ribosomal protein S12 (rpsL). Methodology: RNA was isolated from cell cultures and cDNA was prepared. The numbers of cDNA copies of 16S rRNA, precursor-16S rRNA and transcripts of rpsL and rplL were quantified by qRT-PCR and then related to the rates of 16S rRNA, rpsL and rplL chain elongations by means of a mathematical framework for coupled transcription/translation. Principal Findings: The rates of synthesis of 16S rRNA, rpsL and rplL respectively were found to be approximately 50×103 nucleotides h-1, 1.6×103 amino acid residues h-1 and 3.4×103 amino acid residues h-1. The number of transcripts of rplL was approximately twice that of rpsL. These data account for the presence of one copy of rpsL and four copies of rplL per ribosome, and reveal that the rate of M. fortuitum ribosome synthesis was closer to that of M. tuberculosis than to E. coli. Except for rplJ, the elongation rate obtained for rpsL was inferred to be appropriate for all other proteins present as one copy per ribosome. Significance: The results obtained provide the basis for a comprehensive view of the kinetics of ribosome synthesis, and of the ways that bacterial cells utilize genes encoding ribosomal proteins. The methodology also applies to proteins involved in transcription, energy generation and to bacterial proteins in general. The method proposed for measuring the fidelity of cDNA preparations is intrinsically much more sensitive than procedures that measure the integrity of 16S rRNA. © 2010 Garcia et al.


Lupulovic D.,Scientific Veterinary Institute Novi Sad | Martin-Acebes M.A.,Instituto Nacional Of Investigaciones Agrarias | Lazic S.,Scientific Veterinary Institute Novi Sad | Alonso-Padilla J.,Instituto Nacional Of Investigaciones Agrarias | And 4 more authors.
Vector-Borne and Zoonotic Diseases | Year: 2011

West Nile virus (WNV), the most widely distributed flavivirus worldwide, has lately reemerged in Europe, causing worrisome outbreaks in humans and horses. Serological analysis by enzyme-linked immunoassay and plaque reduction neutralization test showed for the first time in Serbia that 12% of 349 horses presented specific neutralizing WNV antibodies, which in one case also cross-neutralized Usutu virus (USUV). This is the first time that anti-USUV high neutralizing antibody titers are reported in horses. All these data indicate that WNV and USUV are circulating in the region and advise on the convenience of implementing surveillance programs. © Copyright 2011, Mary Ann Liebert, Inc.


Munoz M.,Instituto Nacional Of Investigaciones Agrarias | Alves E.,Instituto Nacional Of Investigaciones Agrarias | Corominas J.,Autonomous University of Barcelona | Folch J.M.,Autonomous University of Barcelona | And 4 more authors.
Frontiers in Genetics | Year: 2012

Fatty acid composition is a critical aspect of pork because it affects sensorial and technological aspects of meat quality and it is relevant for human health. Previous studies identified significant QTLs in porcine chromosome 12 for fatty acid profile of back fat (BF) and intramuscular fat (IMF). In the present study, 374 SNPs mapped in SSC12 from the 60K Porcine SNP Beadchip were used. We have combined linkage and association analyses with expression data analysis in order to identify regions of SSC12 that could affect fatty acid composition of IMF in longissimus muscle. The QTL scan showed a region around the 60-cM position that significantly affects palmitic fatty acid and two related fatty acid indexes. The Iberian QTL allele increased the palmitic content (+2.6% of mean trait). This QTL does not match any of those reported in the previous study on fatty acid composition of BF, suggesting different genetic control acting at both tissues. The SNP association analyses showed significant associations with linolenic and palmitic acids besides several indexes. Among the polymorphisms that affect palmitic fatty acid and match the QTL region at 60 cM, there were three that mapped in the Phosphatidylcholine transfer protein (PCTP) gene and one in the Acetyl-CoA Carboxylase α gene (ACACA). Interestingly one of the PCTP SNPs also affected significantly unsaturated and double bound indexes and the ratio between polyunsaturated/monounsaturated fatty acids. Differential expression was assessed on longissimus muscle conditional on the genotype of the QTL and on the most significant SNPs, according to the results obtained in the former analyses. Results from the microarray expression analyses, validated by RT-qPCR, showed that PCTP expression levels significantly vary depending on the QTL as well as on the own PCTP genotype. The results obtained with the different approaches point out the PCTP gene as a powerful candidate underlying the QTL for palmitic content. © 2012 Muñoz, Alves, Corominas, Folch, Casellas, Noguera, Silió and Fernández.


Gomez-Brunet A.,Instituto Nacional Of Investigaciones Agrarias | Santiago-Moreno J.,Instituto Nacional Of Investigaciones Agrarias | Chemineau P.,CNRS Physiology of Reproduction and Behaviors | Malpaux B.,CNRS Physiology of Reproduction and Behaviors | Lopez-Sebastian A.,Instituto Nacional Of Investigaciones Agrarias
Animal Reproduction Science | Year: 2010

This study examines the patterns of melatonin secretion during postnatal development in wild (mouflon; n = 7) and domestic (Spanish Merino; n = 6) female lambs under their natural photoperiod conditions. The aim was to determine whether these types of sheep which differ in the timing of puberty, also differ in the establishment of daily melatonin secretory rhythms and/or in the nocturnal plasma melatonin secretion. In addition, the time when the lambs first reached nocturnal levels of melatonin similar to adults was also evaluated. For this purpose, the melatonin secretion in lambs was compared with those of their mothers. A day/night (D/N) difference in plasma melatonin concentration was noticed as early as 1 day after birth in the Merino female lambs (D: 5.9 ± 1.0 pg/ml compared to N: 22.0 ± 3.3 pg/ml; p < 0.05), and by 1 week after birth in the mouflon female lambs (D: 4.9 ± 0.3 pg/ml compared to N: 56.9 ± 15.3 pg/ml; p < 0.05). An effect of the genotype (p < 0.05) and age (p < 0.01) was detected on mean nocturnal plasma melatonin concentrations, which were lower in the Merino than in the mouflon lambs. Night-time plasma concentration of melatonin was also high in mouflon than in Merino mothers (p < 0.05). No differences were detected between the wild genotype and the domestic one in the time when the lambs first reached nocturnal levels of melatonin similar to those of their mothers. © 2009 Elsevier B.V. All rights reserved.


PubMed | Institute Investigacion en Recursos Cinegeticos and Instituto Nacional Of Investigaciones Agrarias
Type: Journal Article | Journal: Veterinary pathology | Year: 2016

After the introduction of West Nile virus (WNV) into North America, bird mortalities associated with West Nile disease have dramatically increased in this continent and, to a lesser extent, in Europe. The different West Nile disease incidence in birds in these 2 continents demands an explanation, and experimental studies can provide important information. The authors inoculated thirteen 9-week-old red-legged partridges (Alectoris rufa) with 10(7)plaque-forming units of a WNV strain isolated in New York in 1999. The objective was to study the pathogenesis of the infection in a native Euro-Mediterranean bird species with a WNV strain known to be highly pathogenic for numerous native American bird species. Additionally, the authors evaluated the dynamics of inflammatory cell activation and recruitment into the brain. WNV was detected in tissues 3 days postinoculation (dpi), and the birds developed macroscopic and microscopic lesions. Two partridges succumbed to the disease. The most affected tissues were the heart, brain, and spinal cord. The main microscopic findings were the presence of mononuclear infiltrates in the heart and brain, gliosis, and degeneration and necrosis of cardiomyocytes and neurons. These lesions were aggravated in the birds that died or were euthanized 7 dpi or later. In the brain, there was an upregulation of microglial cells and astrocytes and an increase in the number of T cells, especially after 7 dpi. These results show that this WNV strain is of moderate virulence for the red-legged partridge and that WNV-infected red-legged partridges develop an immune cell response in the brain similar to that of mammals.

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