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At least 235 records · Page 13Linked to original sources
PubMed2006

Multitrait quantitative trait Loci mapping for milk production traits in danish Holstein cattle.

The aims of this study were (1) to confirm previously identified quantitative trait loci (QTL) on bovine chromosomes 6, 11, 14, and 23 in the Danish Holstein cattle population, (2) to assess the pleiotropic nature of each QTL on milk production traits by building multitrait and multi-QTL models, and (3) to include pedigree information on nongenotyped individuals to improve the estimation of genetic parameters underlying the random QTL model. Nineteen grandsire families were analyzed by single-trait (ST) and multitrait (MT) QTL mapping methods. The variance component-based QTL mapping model was implemented via restricted maximum likelihood (REML) to estimate QTL position and parameters. Segregation of the previously identified QTL was confirmed on bovine chromosomes 6, 11, and 14, but not on 23. A highly significant (1% chromosome-wise level) QTL was found on chromosome 6, between 37 and 73 cM. This QTL had a strong effect on protein percentage (PP) and fat percentage (FP) according to ST analyses, and effects on PP, FP, milk yield (MY), fat yield (FY), and protein yield (PY) in MT analyses. A QTL affecting PP was detected on chromosome 11 (at 70 cM) using ST analysis. The MT analysis revealed a second QTL (at 67 cM) approaching significance with an effect on MY. The ST analysis identified a QTL for MY and FP on chromosome 14, between 10 and 24 cM. The extended pedigree (nongenotyped animals) was included to estimate genetic parameters underlying the random QTL model; that is, additive polygenic and QTL variances. In general, the estimates of the QTL variance components were smaller but more precise when the extended pedigree was considered in the analysis.

Animals↗
PubMedDate not supplied

Bayesian estimation in animal breeding using the Dirichlet process prior for correlated random effects.

In the case of the mixed linear model the random effects are usually assumed to be normally distributed in both the Bayesian and classical frameworks. In this paper, the Dirichlet process prior was used to provide nonparametric Bayesian estimates for correlated random effects. This goal was achieved by providing a Gibbs sampler algorithm that allows these correlated random effects to have a nonparametric prior distribution. A sampling based method is illustrated. This method which is employed by transforming the genetic covariance matrix to an identity matrix so that the random effects are uncorrelated, is an extension of the theory and the results of previous researchers. Also by using Gibbs sampling and data augmentation a simulation procedure was derived for estimating the precision parameter M associated with the Dirichlet process prior. All needed conditional posterior distributions are given. To illustrate the application, data from the Elsenburg Dormer sheep stud were analysed. A total of 3325 weaning weight records from the progeny of 101 sires were used.

Algorithms↗
PubMed2006

Color reversion of the albino medaka fish associated with spontaneous somatic excision of the Tol-1 transposable element from the tyrosinase gene.

The medaka fish albino mutant, i(1) is one of the Tomita collection of medaka pigmentation mutants which exhibits a complete albino phenotype, because of inactivation of the tyrosinase gene due to insertion of a transposable element, Tol-1. Recently, mosaic black-pigmented i(1) medaka fish have arisen in one of our laboratory breeding populations. Their pigmented cells have been observed in all of the tissues, including the eye and skin, in which melanin is detectable in the wild type. In this study, we analyzed the tyrosinase gene of revertants and showed Tol-1 to have been precisely excised from the gene, suggesting a causal relationship. Mosaic patterns of pigmentation indicate spontaneous somatic excision of the element from the tyrosinase gene. To our knowledge, this is the first transposable element with somatic excision activity demonstrated phenotypically in vertebrates. The pattern of pigmentation in mosaic revertants indicates frequencies of melanin pigments to be consistent with the numbers of melanophores per unit area of body sites, such as the eyes, head and dorsal trunk.

Albinism↗
PubMed1986

Use of progesterone 11-glucuronide-alkaline phosphatase conjugate in a sensitive microtitre-plate enzymeimmunoassay of progesterone in milk and its application to pregnancy testing in dairy cattle.

A simple direct-addition microtitre plate enzymeimmunoassay (EIA) for progesterone in whole milk is described. The assay used antiserum raised against 11 alpha-hydroxyprogesterone 11-hemisuccinate (progesterone 11-hemisuccinate) and a heterologous label prepared by conjugation of 11 alpha-hydroxyprogesterone 11-glucuronide (progesterone 11-glucuronide) with alkaline phosphatase using an active ester procedure. The sensitivity, analytical recovery, linearity of response and precision of the assay compared favourably with radioimmunoassay (RIA). Results from EIA of milk samples were compared with determinations made after isolation of progesterone by HPLC (r = 0.910). Milk samples (200) were assayed by RIA at both the Milk Marketing Board and the Cattle Breeding Centre and the results were correlated with EIA performed at the Cattle Breeding Centre (r = 0.890 and r = 0.833 respectively). Calving data were obtained from a further 110 cows for which the milk progesterone EIA had provided a pregnancy test 24 days after AI; 46 cows were correctly identified as non-pregnant and 58 as pregnant and there were 4 false positive and 2 inconclusive results.

Alkaline Phosphatase↗
PubMed1993

[Follicular growth and dynamics before and during ovulation in the mare: review for the practitioner].

Few scientists predicted the impact that echography would have on the equine breeding industry. The aim of this practical review is to give the practitioner the ability to be familiar with the ovarian echographic exam. He should be able to recognize different stages of estrous cycle in the mare, status of preovulatory follicles and to predict precisely the time of ovulation. Various specific criteria and details regarding the equine echography are studied and illustrated, using the last scientific data published after the Fifth International Symposium on Equine Reproduction in Deauville.

Animals↗
PubMed1995

Effects of prerace exercise, frusemide, sex and ambient temperature on blood sodium, bicarbonate and pH values in standardbred horses.

Analysis of data collected at racetracks showed that temperature, the diuretic drug, frusemide, exercise, temperature/exercise interaction and sex/age had significant (P < 0.05) effects on pH and bicarbonate ion concentration (P < 0.01). Sodium concentrations were significantly (P < 0.001) affected by temperature and frusemide. We suggest that the normal range limits for blood sodium, bicarbonate and pH used in prerace testing procedures should be adjusted for ambient temperature and for horses given frusemide and/or prerace exercise. These adjustments should improve the precision of detecting illegal alkalogenic agents and incidence of false positive and false negative test results.

Animals↗
PubMed2006

Accounting for outliers and heteroskedasticity in multibreed genetic evaluations of postweaning gain of Nelore-Hereford cattle.

The objectives of this study were to demonstrate the utility of hierarchical Bayesian models combining residual heteroskedasticity with robustness for outlier detection and muting and to evaluate the effects of such joint modeling in multibreed genetic evaluations. A 3 x 2 factorial specification of 6 residual variance models based on several distributional (Gaussian, Student's t, or Slash) and variability (homoskedastic or heteroskedastic) assumptions was used to analyze 22,717 postweaning gain records from a Nelore-Hereford population (40,082 animals in the pedigree). To illustrate the utility of the 2 robust distributional specifications (Student's t and Slash) for outlier detection and muting, 3 records from the same contemporary group (an extreme residual outlier, a mild residual outlier, and a near-zero residual) were chosen for further study. The posterior densities of the corresponding weighting variables of these records were used to assess their degree of Gaussian outlyingness and the ability of the robust models to mute the effects of deviant records. The Student's t heteroskedastic provided the best-fit model among the 6 specifications and was preferred for genetic merit inference. Kendall rank correlations of the posterior means of the additive genetic effects of the animals, used to compare the selection order of the Student's t and Gaussian models, were reasonably high across all animals within the most frequent genotypes, ranging from 0.83 to 0.91 and from 0.89 to 0.95 for the homoskedastic and the heteroskedastic versions, respectively. However, when considering only animals ranked in the top 10% by the customary Gaussian homoskedastic model, these rank correlations were reduced considerably, ranging from 0.29 to 0.57 and from 0.72 to 0.85 between the 2 residual densities within the homoskedastic and heteroskedastic versions, respectively. Rank correlations between the homoskedastic and heteroskedastic versions within each of the Gaussian and Student's t error models tended to be smaller, with a range from 0.68 to 0.90 across all animals and from 0.28 to 0.67 for animals ranked in the top 10%. These results support the implementation of robust models accounting for sources of heteroskedasticity to increase the precision and stability of multibreed genetic evaluations with proper statistical treatment of deviant records.

Analysis of Variance↗
PubMed2003

Role of the thymus in the development of tolerance and autoimmunity towards the neuroendocrine system.

The thymus is the unique lymphoid organ inside which a confrontation occurs throughout life between neuroendocrine self-antigens and a recently evolved system with original recombination machinery driving random generation of immune response diversity. Through transcription of neuroendocrine genes in the thymus stromal network and expression of cognate receptors by immature T cells, the neuroendocrine system regulates early T cell differentiation. In addition and more specifically, intrathymic presentation of neuroendocrine self-antigens by, or in close association with, major histocompatibility complex (MHC) proteins is responsible for the establishment of central immune self-tolerance of neuroendocrine principles. All members of the insulin gene (INS) family are expressed in the thymus stroma according to a precise hierarchy and cell topography: IGF2 (thymic epithelial cells) > IGF1 (thymic macrophages) >> INS (thymic medullary epithelial cells and/or dendritic cells). Given this hierarchical pattern in gene expression, the protein IGF-2 is more tolerated than INS. Igf2 transcription is defective in the thymus of bio-breeding (BB) rat, one animal model of type 1 diabetes (T1DM). This thymus-specific defect in Igf2 expression may explain both the absence of central tolerance to INS-secreting beta cells and the lymphopenia (including lack of regulatory RT6(+) T cells) in diabetes-prone BB rats. INS B:9-23 and the homologous sequence of IGF-2 compete for binding to DQ8, an MHC class II allele conferring major susceptibility to T1DM. In young DQ8(+) T1DM patients, INS B:9-23 presentation by DQ8 elicits a dominant IFN-gamma secretion by isolated PBMCs, whereas presentation of the IGF-2 self-antigen promotes a dominant regulatory interleukin-10 secretion. These data demonstrate that opposite immune responses are driven by MHC presentation of a self-antigen (here, IGF-2) and an autoantigen (INS, as "altered" self). The important tolerogenic properties of thymic self-antigens deserve now to be exploited for prevention and/or cure of devastating autoimmune diseases such as T1DM.

Animals↗
PubMed2002

[Animal welfare-conforming fallow deer farming in Germany--a review].

Fallow deer farming for venison production on pasture and fallow land has gained importance in Germany during recent years. As fallow deer farming constitutes a relatively young farming practice, many questions concerning a welfare-conforming and ecologically sound keeping of fallow deer are still open. Based on the recommendations on the keeping of fallow deer in enclosures for the purpose of venison meat production including by-products from 2 November 1979, a critical comparative review considering the current knowledge from research and practical deer farming experience was conducted. Recommendations on measures for breeding management and administration (statistics on farms and stocks, security and control of enclosures, training and experience of stockperson, practical skills for immobilisation and killing) are proposed. The cultivation goals for the care of landscape by fallow deer farming in protected areas need to be defined precisely. Due to infection risk, mixed herds with domesticated ruminants are not recommended. Potential progress can be foreseen in preventive health measures (control of endoparasites) and by appropriate feeding and water supply, considering feeding and drinking place design, feeding behaviour and water needs. The knowledge on handling and immobilisation methods should also be applied to small herd sizes. More research is needed on transportation of fallow deer.

Animal Husbandry↗
PubMed1978

Serum hydrocortisone (cortisol) values in normal and adrenopathic dogs as determined by radioimmunoassay.

Using a specific radioimmunoassay, serum hydrocortisone values were measured in dogs. Between 9:00 AM and 10:00 AM, the base-line hydrocortisone value for 56 clinically normal dogs ranged from 6.0 to 28.5 ng/ml, with a mean value of 17.8 +/- 1.32 ng/ml (mean +/- SEM). Marked differences due to age, sex, body weight, or breed were not observed in the hydrocortisone values. In 11 dogs with definitive hyperadrenocorticism, serum hydrocortisone values were from 32 to 148 ng/ml. In 2 dogs with hyperadrenocorticism, the values were 4.5 and 3.1 ng/ml. The estimation of serum hydrocortisone values by radioimmunoassay is simple and precise, and can be utilized to aid in the diagnosis of adrenopathy in dogs.

Adrenocortical Hyperfunction↗
PubMed2000

[Estimates of breeding value of Inner Mongolia cashmere goats using animal model BLUP method].

In this study, single trait animal model of best linear unbiased prediction (BLUP) procedures was used to obtain estimates of 3,981 Inner Mongolia cashmere goats' breeding value for body weight and cashmere yield. The data were collected during 1989-1998 at Arbas cashmere goats farm, Etuoke banner, Inner Mongolia. Multiple traits of BLUP were used to get estimates of total breeding values (TBV) of all goats. The model included age and sex-herd-year as fixed effects, and individual additive effect and individual permanent environment as random effects. The selection based on breeding value and phenotypic value was compared. The results showed as following: (1) There was a large difference between weaning weight selection and TBV selection of ram lamb; (2) The difference between phenotypic selection and TBV selection of gimmer hogg reached a significant level (P < 0.01); (3) The difference between phenotypic selection and TBV selection of ram hogg reached a significant level (P < 0.01); (4) Rank correlation between body weight selection and body weight' EBV selection and that between cashmere yield selection and cashmere yield' EBV selection were not significant (P > 0.05). The study concluded precision of individual phenotypic selection was low and animal model BLUP was suitable to select Inner Mongolia cashmere goats. At last, this study gave a series of methods of selecting sires based on objective reality.

Animals↗
PubMed2001

Weighting factors of sire daughter information in international genetic evaluations.

International genetic evaluations of dairy bulls are currently based on national genetic evaluation results. Total number of daughters in a country is used to weight national information, but may not optimally reflect the precision of a sire's daughter contribution to international genetic evaluations. This study investigates the impact of alternative weighting factors on international evaluation results. A conventional progeny test scheme was simulated for two dairy cattle populations, with semen exchange at a fixed rate after each generation. True breeding values for both populations were generated as bivariate normal deviates. Each cow had three lactation records in one country only. After 10 generations of selection, all records were used in national breeding value prediction. National breeding values of bulls were used as input to international evaluations. Seven different weighting factors were evaluated: 1) total number of daughters; 2) total number of lactations; 3) as (one) also adjusted for finite contemporary group size; 4) as (three) also adjusted for distribution of daughters over contemporary groups; 5) effective daughter contribution considering finite contemporary group size and correlation between repeated records; 6) as (five) also considering the reliability of the daughter dam evaluation; and 7) as (five) also considering the reliability of the daughter female ancestors' evaluations. Using the last two weighting factors yielded empirically unbiased estimates of sire variance. Using total number of daughters overestimated genetic variance by up to 7%. In general, international breeding values were marginally affected by choice of weighting factor. The effect was larger when different national evaluation models had been applied in the two countries. International reliabilities for the last two weighting factors were close to expectation, whereas using total number of daughters resulted in 1 to 4% negative bias. In practice, different countries apply a wide range of national evaluation models, and genetic ties may be weak between some populations, thereby increasing the potential effect of weighting factors on international comparisons. The weighting factor developed in this study, which considers contemporary group structure, correlation between repeated records, and reliability of dams of daughters, should replace total number of daughters in international genetic evaluations of dairy sires.

Animals↗
PubMed2003

Accuracy and precision of a point-of-care hemoglobinometer for measuring hemoglobin concentration and estimating packed cell volume in horses.

OBJECTIVE: To determine accuracy and precision of a point-of-care hemoglobinometer for measuring hemoglobin concentration and estimating PCV in horses. DESIGN: Prospective trial. ANIMALS: 55 horses. PROCEDURE: Blood samples were obtained from 43 horses examined at a veterinary teaching hospital. Hemoglobin concentration was measured with the hemoglobinometer and by means of the standard cyanmethemoglobin method; PCV was measured by centrifugation. Blood samples were also obtained from 12 healthy horses, and PCV of aliquots of these samples was altered to approximately 5 to 80% by removing or adding plasma. Hemoglobin concentration and PCV were then measured. RESULTS: For samples from the clinic patients, hemoglobin concentrations obtained with the hemoglobinometer were less than concentrations obtained with the cyanmethemoglobin method; however, there was a linear relationship between concentrations obtained with the 2 methods. Breed, sex, body weight, and duration of sample storage did not significantly affect the difference between hemoglobin concentrations obtained with the 2 methods. There was a significant linear relationship between PCV and hemoglobinometer hemoglobin concentration (PCV = [2.83 x hemoglobin concentration] - 0.62). For samples from the healthy horses, a substantial negative bias was evident with the hemoglobinometer when hemoglobin concentration exceeded 16 g/dL. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggest that this hemoglobinometer is reasonably accurate and precise when used to measure hemoglobin concentration in blood samples from horses with a hemoglobin concentration < 16 g/dL.

Animals↗
PubMed2026

Integrative machine learning and transcriptomic analysis reveals molecular mechanisms underlying low survival rate in larval Chinese Bahaba (Bahaba taipingensis).

Chinese Bahaba (Bahaba taipingensis) is a Class I protected marine fish endemic to China. Low larvae survival during artificial breeding severely hinder population recovery. To investigate the molecular mechanism of high mortality in larval fish, this study performed RNA-seq on liver from naturally deceased (ND) and mass-dead (MD) individuals, combined with least absolute shrinkage and selection operator (LASSO) regression and random forest (RF) algorithms to screen for core signature genes. A total of 873 differentially expressed genes (DEGs) were identified, including 112 upregulated and 761 downregulated genes. GO and KEGG enrichment analyses revealed significant enrichment in amino acid metabolism disorders, one&#x2011;carbon folate pool impairment, PPAR signaling abnormalities, ECM-receptor interaction, focal adhesion pathway, indicating widespread metabolic suppression accompanied by extracellular matrix remodeling and signaling disturbances in the livers of MD fish. MAD pre-filtering combined with dual machine learning algorithms yielded 18 robust core signature genes, among which SLC38A4, MMP1, FADD, FKBP5, and APOB were consistently identified as high-frequency core genes by both algorithms. SLC38A4 exhibited the highest importance score in the RF model and was significantly downregulated, making it the primary molecule distinguishing ND from MD phenotypes. ROC curve analysis showed that both models achieved an AUC of 1.000 (95% CI lower bound: 0.610), confirming the precise discriminatory ability of the core genes. GSEA further demonstrated significant enrichment of this core gene set in ND samples. This study provides the first systematic elucidation of the molecular mechanisms underlying liver dysfunction in low survival rate B. taipingensis, characterized by amino acid transport impairment, metabolic reprogramming, and structural remodeling, offering theoretical foundations for health assessment, early mortality risk warning, and artificial breeding conservation of this species.

Animals↗
PubMed2006

[Establishment of transgenic mouse model of familial amyotrophic lateral sclerosis and identification of the filial generation].

OBJECTIVE: To establish transgenic mouse models of familial amyotrophic lateral sclerosis (FALS) and identify the genotype of the first filial generation. METHODS: Six male B6SJL SOD1G93A/+ hemizygote mice were mated with 6 female B6SJLF1/J+/+ mice to produce the filial generation. The genomic DNA was extracted from the tail vein blood of the first filial generation mice and PCR was performed to amplify the hmSOD1 gene fragment. The genotype of the mice was determined by electrophoresis, and the PCR product was purified for further gene sequence analysis and detection of mutation loci. RESULTS: Fifty-three progeny mice were born and the survival rate before ALS onset was 98% (52/53), and among the survived mice, the positivity rate for hmSOD1 gene was 44.2% (23/52). Electrophoresis result showed that the PCR product of 236 bp was consistent with the hmSOD1 gene fragment, and the sequence of the PCR product was identical with hmSOD1 gene sequence of G93A mutant. CONCLUSION: Transgenic mouse models of ALS can be established in the first filial generation of male B6SJL SOD1G93A/+ mice mated with female B6SJLF1/J+/+. PCR technique can precisely identify the genotype of the filial generation.

Amyotrophic Lateral Sclerosis↗
PubMed2004

A Bayesian approach to prediction of stallion daily sperm output.

In equine breeding, the number of spermatozoa ejaculated is considered an important factor in fertility. Methods for predicting the number of spermatozoa have been derived from semen collection procedures. A once-daily collection period for 10 days is a standard recommendation to predict long-term daily sperm output (DSO). The first objective of this study was to determine the precision or repeatability of these DSO predictions. Semen was collected and evaluated daily during four periods for 10 days, for 15 different stallions. The analytical methods utilized hierarchal Bayesian modeling as implemented by Gibbs Sampling. The overall population model showed an initial decline in total sperm number of 1.54 billion spermatozoa per day until the observed mean change point of 4.71 days, at which time mean DSO was estimated at 5.28 billion spermatozoa per day. The hierarchal model showed standard deviations in DSO within-stallion of 0.67 billion spermatozoa per day and among-stallion of 1.86 billion spermatozoa per day. The study's second objective was to determine how testicular size affected DSO models. When the model was extended to include testicular size, the optimal prediction of DSO was that DSO = 0.79 + 0.018 x testicular size (in milliliters). Testicular size explained 36.5% of the among-stallion standard deviation in DSO, but was not significantly related to the mean number of collection-days required to reach DSO.

Animals↗
PubMed1993

Assessment of protein quality in heat-treated soybean products using the growth responses of lambs and calves and a nylon bag-rooster assay.

Three studies were conducted to evaluate N and amino acid (AA) availability from processed soybean (SB) products. In Exp. 1 and 2, treatments consisted of corn-cottonseed hull basal diets plus SB products including SB meal (SBM); ground, raw SB (RSB); or extruded SB (ESB). In Exp. 1, 15 Suffolk (28.6 kg) and 15 Louisiana native breed (16.3 kg) ewe lambs were used in a 35-d growth trial. Although breed affected (P < .10) DMI and ADG of lambs, the diets did not (P > .10). In Exp. 2, 12 Suffolk wether lambs (34.0 kg) were used in a 3 x 3 multiple-square Latin square design N metabolism trial. Lambs fed RSB tended (P = .13) to retain more N than those fed ESB, but N retained by lambs fed RSB and ESB was similar (P > .10) to that of lambs fed SBM. In Exp. 3, four crossbred steer calves (240 kg) were used in a 4 x 4 Latin square design N metabolism trial with the above treatments plus heat-damaged SB (HDSB). Calves fed RSB and ESB retained similar (P > .10) amounts of N. Compared with calves fed RSB and ESB, calves fed SBM retained more (P < .10) N. Calves fed HDSB retained less (P < .10) N than those fed other diets. The individual SB products and the total mixed diets used in Exp. 3 were incubated intraruminally in nylon bags and the residual DM recovered and precision-fed to cecectomized roosters to estimate its intestinal AA digestibility. Digestibility of residual AA seemed to be relatively uniform across AA.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acids↗
PubMed1994

Method R variance components procedure: application on the simple breeding value model.

An algorithm for estimating variance components (Method R) based on the linear regression coefficient (R) of recent (more accurate) on previous (less accurate) individual genetic predictions is presented. The previous prediction is obtained by analyzing a subsample of the whole data set. First raw moment of R equals 1 regardless of the distribution of observations and predictions. A condition such as the use of inappropriate variance components ratio (VC) can cause this regression to deviate from its expectation. If the computed R (Rc) is greater than 1, then VC ratio has been underestimated, and if Rc is less than 1, then VC ratio has been overestimated. Several iterations are performed, changing the VC ratio at each iteration, until Rc approximately equal to 1. When an Rc is obtained that is acceptably close to 1 (precision is reached), then the appropriate VC has been used. Method R does not require computation of the inverse of the coefficient matrix and has desirable properties of convergence, precision, and computing feasibility. Additional sampling variance in the estimate of VC is expected due to the requirement of taking a subsample of the entire data set to obtain the lower accuracy predictions. This sampling variance is shown to be small for simulated datasets of size n = 10,000 with no selection.

Algorithms↗