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The objectives of this study were to investigate heterogeneity in the variance of and the association between milk yield (MY) and pregnancy outcome (PO) in dairy cows, formally separating the within-herd (i.e., cow-level residual effects) from the between-herd (i.e., herd-level random effects) components. Based on a recently developed extension to bivariate generalized hierarchical linear mixed models, we specified functions of residual and random effect variances and covariances as linear combinations of fixed and random effects to infer upon heterogeneity in the variation of and the association between MY and PO at first postpartum insemination. As potential sources of heterogeneity, we evaluated various management practices and herd attributes of interest by assessing model fit using the deviance information criterion. Our data consisted of 89,105 Dairy Herd Improvement Association cow records from 379 dairy herds in Michigan. Within herds, no evidence of a cow-level (residual) association between MY and PO was observed, as the corresponding association parameter did not significantly depart from zero. However, the herd-level (random effects) relationship between MY and PO was antagonistic and depended on management practices that determine the baseline level of fertility for a herd. In other words, herds with greater average MY at the time of first postpartum insemination had lower pregnancy rates, but within such herds, cows with higher daily yields did not seem to be any more or less likely to become pregnant than lower-yielding herdmates. Nevertheless, Michigan counties differed in the magnitude of the herd-level association between MY and PO, thus indicating that regional environmental conditions or management practices may partially alleviate the herd-level antagonism between MY and PO. The heterogeneity in variability of MY was substantial and primarily explained at the cow level by management conditions and other herd-specific attributes. In summary, the nature of the variability of and the association between MY and PO in dairy cows is complex due to the heterogeneous contributions of both cow- and herd-level components. Further research should be pursued to investigate additional management scenarios that ameliorate or even enhance the association between MY and PO in commercial dairy cows during first postpartum insemination.

The augmentation of categorical outcomes with underlying Gaussian variables in bivariate generalized mixed effects models has facilitated the joint modeling of continuous and binary response variables. These models typically assume that random effects and residual effects (co)variances are homogeneous across all clusters and subjects, respectively. Motivated by conflicting evidence about the association between performance outcomes in dairy production systems, we consider the situation where these (co)variance parameters may themselves be functions of systematic and/or random effects. We present a hierarchical Bayesian extension of bivariate generalized linear models whereby functions of the (co)variance matrices are specified as linear combinations of fixed and random effects following a square-root-free Cholesky reparameterization that ensures necessary positive semidefinite constraints. We test the proposed model by simulation and apply it to the analysis of a dairy cattle data set in which the random herd-level and residual cow-level effects (co)variances between a continuous production trait and binary reproduction trait are modeled as functions of fixed management effects and random cluster effects.

A general belief across the dairy community, both scientific and commercial, is that of an antagonistic association between milk production and reproductive performance of dairy cows. In this article, we critically review the evidence supporting this belief and discuss some of its limitations. Based on the fundamental principles of experimental design and inference, we consider relevant issues that, although critical to the very foundation of the perceived production-reproduction antagonism, seem to have been previously misrepresented or overlooked. In particular, we focus on issues of confounding, randomization, nature of inference, single- versus multiple-trait modeling, cow- versus herd-level modeling, and scope of inference, all within the context of dairy production systems. Taken together, these issues indicate that the production-reproduction antagonism may not be as pervasive as previously believed, suggesting the need for more rigorous methods of scientific investigation on this matter. We revisit the association between milk production and reproductive performance using a novel interdisciplinary approach based on cutting-edge statistical methods that accommodate some of the unique and previously ignored features of this problem. In fact, recent work supports a highly heterogeneous association between milk production and reproductive performance, whereby heterogeneity is partitioned across several scales and driven by many contributing factors, both physiological and managerial. We conclude that the relationship between milk production and reproductive performance is not necessarily that of a universal homogeneous antagonism and suggest better ways to study and even manage this association. A more comprehensive assessment that draws expertise from multiple scientific disciplines will be required to elicit management recommendations targeted to effectively optimize overall performance of dairy cows and commercial herds.

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The objective of this study was to compare linear (LM) with Poisson (PM) mixed models for genetic evaluation of litter size in Iberian pigs. Number born alive and total number born in 8056 litters were analyzed. The LM included effects of year-season of farrowing, strain and parity of sow as fixed factors; random effects were animal and permanent environmental effects, plus the residuals. The PM had the same structure, but the residual distribution was Poisson rather than normal. Endpoints in comparisons were: (1) goodness of fit of the model, and (2) predictive ability. Predictive ability was studied by splitting the data into two parts, and then predicting the deleted records using location parameters estimated from the remaining records. Mean squared errors and correlations between observed and fitted or predicted records were computed. The performance of LM and PM was similar for both traits. A Poisson model does not seem to improve upon the mixed linear model for analysis of litter size in Iberian pigs.

Mycobacterium avium subspecies paratuberculosis (MAP) is a significant concern to the American and European dairy industries and possibly to human health. MAP possesses the rare ability to survive and replicate in infected macrophages, cells that are typically able to destroy pathogens. Little is known about what changes occur in MAP-infected macrophages that prevent phagosome maturation and lead to intracellular survival of the bacteria. In this study, a bovine immunologically specific cDNA microarray was used to study genes whose expression was altered in monocyte-derived macrophages (MDM) when these cells were infected with 10 different strains of MAP bacteria. Although we used MAP strains isolated from four different host species, cluster analysis of each strains influence in infected MDMs showed no species of origin specific MAP alterations in the host transcriptome. However, MAP strain K10 was observed as a clear outlier in the cluster analysis. Additionally, we observed two SuperShedder MAP strains clustering very closely together compared to the other strains in this study. Overall, microarray analysis yielded 78 annotated genes whose expression was altered by MAP infection, regardless of strain. Few of these genes have been previously studied in the context of Johne’s disease or other mycobacterium-caused diseases. Large groups of apoptosis genes, transcription factors and cytokines were found to be differentially expressed in infected monocyte-derived macrophages as well as several genes not previously linked to MAP-host interactions. Identifying novel host genes affected by MAP infection of macrophages may lead to a more complete picture of this complex host^ pathogen interaction.

Two of the most important broad classifications of phenotypes for successful dairy production are milk yield and fertility. The nature of the relationship between milk production and reproductive performance of dairy cows is uncertain due to conflicting results reported in many studies. A common deficiency in many such studies is an underappreciation of the dual dimension of the production-reproduction relationship, as defined by herd (random or u) level and cow (residual or e) level sources of (co)variation. Our overall hypothesis is that the eand ulevel relationships between milk production and reproduction in dairy cows are heterogeneous and depend upon various herd-related and management factors. Our objective is to develop hierarchical Bayesian extensions that capture heterogeneity in the relationships between traits by mixed effects modeling of u level and e level covariances between traits of interest. We specify a bivariate Bayesian model to jointly model two continuous traits and we apply a square-root free Cholesky decomposition to the variance-covariance matrices of the residuals (cow-level) and random effects (herd-level). As a result, the eand u-level covariances among the traits are reparameterized into unconstrained and easily interpretable eand uregression parameters, respectively. These regression parameters specify the cowand herd-level relationships, respectively, between the traits and can be easily modeled as functions of relevant fixed and random effects, thereby providing a mixed model extension of Pourahmadi’s method. We validate our method using a simulation study and apply it to data on 305-day milk yield and calving interval of Michigan dairy cows.

Background Recent evidence suggests that some sex differences in brain and behavior might result from direct genetic effects, and not solely the result of the organizational effects of steroid hormones. The present study examined the potential role for sex-biased gene expression during development of sexually dimorphic singing behavior and associated song nuclei in juvenile zebra finches. Results A microarray screen revealed more than 2400 putative genes (with a false discovery rate less than 0.05) exhibiting sex differences in the telencephalon of developing zebra finches. Increased expression in males was confirmed in 12 of 20 by qPCR using cDNA from the whole telencephalon; all of these appeared to be located on the Z sex chromosome. Six of the genes also showed increased expression in one or more of the song control nuclei of males at post-hatching day 25. Although the function of half of the genes is presently unknown, we have identified three as: 17-beta-hydroxysteroid dehydrogenase type IV, methylcrotonyl-CoA carboxylase, and sorting nexin 2. Conclusion The data suggest potential influences of these genes in song learning and/or masculinization of song system morphology, both of which are occurring at this developmental stage.

Best linear unbiased estimation, or equivalently maximum likelihood under normality, is the method most frequently used in animal breeding for estimation of fixed effects. James and Stein found that maximum likelihood is inadmissible under the mean squared error criterion and proposed a nonlinear, biased estimator that has smaller mean squared error than maximum likelihood throughout the parameter space in normal linear models with more than two uniquely estimable fixed effects. In this paper, several biased estimators of fixed effects in the mixed linear model are considered. Dispersion parameters are assumed to be known. An estimator that minimizes mean squared error in a certain class is derived. Because this estimator regresses the maximum likelihood estimates toward zero, an alternative estimator that “shrinks” these estimates to their mean value is also considered. The two estimators require knowledge of the true values of the fixed effects, so approximations to these are presented, including an extension of the James and Stein estimator to the mixed model. These estimators were compared with maximum likelihood in a simulation study involving a balanced group (fixed) plus sire (random) model. The James and Stein and “minimum mean squared error” estimators gave estimates of group effects with slightly smaller mean squared error than maximum likelihood. Improvement was minimal when the true group effects were far from zero. However, shrinkage of group effects toward their mean value substantially reduced mean squared error of group estimates. Genetic trend (the regression of group effects on time) was considerably underestimated using this type of shrinkage. Care must be exercised when these “improved” statistics are used for estimating some functions of fixed effects.

Background Zinc (Zn) is an essential trace element. However, Zn bioavailability from commonly consumed plants may be reduced due to phytic acid. Zn supplementation has been used to treat diarrheal disease in children, and in the U.S. swine industry at pharmacological levels to promote growth and fecal consistency, but underlying mechanisms explaining these beneficial effects remain unknown. Moreover, adding supplemental phytase improves Zn bioavailability. Thus, we hypothesized that benefits of pharmacological Zn supplementation result from changes in gene expression that could be further affected by supplemental phytase. The goal of this study was to investigate the effects of feeding newly weaned pigs dietary Zn (150, 1,000, or 2,000 mg Zn/kg) as Zn oxide with or without phytase [500 phytase units (FTU)/kg] for 14 d on hepatic gene expression. Liver RNA from pigs fed 150, 1,000, or 2,000 mg Zn/kg, or 1,000 mg Zn/kg with phytase (n = 4 per treatment) was reverse transcribed and examined using the differential display reverse transcription polymerase chain reaction technique. Liver RNA from pigs fed 150 or 2,000 mg Zn/kg (n = 4 per treatment) was also evaluated using a 70-mer oligonucleotide microarray. Results Expressed sequence tags for 61 putatively differentially expressed transcripts were cloned and sequenced. In addition, interrogation of a 13,297 element oligonucleotide microarray revealed 650 annotated transcripts (FDR ≤ 0.05) affected by pharmacological Zn supplementation. Seven transcripts exhibiting differential expression in pigs fed pharmacological Zn with sequence similarities to genes encoding GLO1, PRDX4, ACY1, ORM1, CPB2, GSTM4, and HSP70.2 were selected for confirmation. Relative hepatic GLO1 (P < 0.0007), PRDX4 (P < 0.009) and ACY1 (P < 0.01) mRNA abundances were confirmed to be greater in pigs fed 1,000 (n = 8) and 2,000 (n = 8) mg Zn/kg than in pigs fed 150 (n = 7) mg Zn/kg. Relative hepatic HSP70.2 (P < 0.002) mRNA abundance was confirmed to be lower in pigs fed 2,000 mg Zn/kg than in pigs fed 150 or 1,000 mg Zn/kg. Conclusion Results suggest that feeding pharmacological Zn (1,000 or 2,000 mg Zn/kg) affects genes involved in reducing oxidative stress and in amino acid metabolism, which are essential for cell detoxification and proper cell function.

Background: Cashew nut allergy is an emerging food allergy with a high risk of systemic anaphylaxis. Currently, an adjuvant-free animal model to study cashew nut allergy is not available. Methods: BALB/c mice were exposed to cashew nut protein using a transdermal sensitization protocol that does not use adjuvant. Systemic IgE antibody response, systemic anaphylaxis to oral challenge and allergen-driven, spleen-cell, type-2 cytokine responses were studied. Results: Transdermal exposure to cashew nut resulted in a significant dose-dependent allergic response. Oral challenge of sensitized mice with cashew resulted in severe signs of systemic anaphylaxis and a significant hypothermia. Spleen cell culture with cashew nut protein resulted in allergen-driven IL-4, IL-5 and IL-13 responses only in sensitized but not in saline control mice. Conclusions: These data demonstrate that (i) transdermal exposure to cashew nut protein elicits a robust IgE response leading to clinical sensitization of mice for systemic anaphylaxis to oral cashew nut challenge; (ii) cashew nut is a potent activator of type-2 cytokines, thus explaining the mechanism of cashew allergy, and (iii) this mouse model may be useful for further basic and preclinical studies on cashew nut allergy.

Additive and dominance genetic variances for nine conformation traits in the Canadian Holstein population were estimated by REML using the derivative-free algorithm. All traits were analyzed under two sire and dam models differing in assumptions on the data structure. Within-herd relationships due to dam were defined first to be nested within sire in order to estimate both genetic variances, assuming unimportant biases on the estimates. The potential impact of some of these biases was estimated as the difference between the two parental variance components under a cross-classified model. Heritabilities were similar to those previously computed for Canadian Holsteins and ranged from .10 to .30. Results from the hierarchical dam-within-sire model suggest dominance genetic variation, as a proportion of the total variation, to be important for final score (.15), capacity (.16), and mammary system (.13). However, estimates of dam components, as a proportion of the total variance, were significantly greater than sire components for final score (.019), general appearance (.020), and feet and legs (.018) under the cross-classified model. Therefore, the significant dominance genetic parameter estimated for final score under the hierarchical model may have been biased upward.

Stress and its association with altered immune function and incidence of respiratory diseases in cattle have lead to concerns over animal health and welfare during truck transportation. Previously, bulls subjected to transportation stress displayed altered expression of candidate neutrophil genes, warranting a broader investigation of the neutrophil transcriptome and possible associations with fluctuations in circulating steroid hormones. In the current study, blood was collected from six Belgian BluexFriesian bulls at -24, 0, 4.5, 9.75, 14.25, 24, and 48h relative to initiation of 9h of truck transportation. Plasma concentrations of cortisol, dehydroepiandrosterone (DHEA), progesterone, and testosterone were measured; cortisol:DHEA ratios were computed. Neutrophil gene expression was monitored by microarray analysis using bovine immunobiology (BOTL-5) microarrays. Eighty-eight genes were identified as being differentially expressed at P0.05. Putatively affected genes were grouped into ontological clusters; those of greatest interest for qRT-PCR validation were involved in immune response, apoptosis, wound healing, and several of currently unknown function. Confirmed gene expression changes supported the dramatic effects of transportation stress on the bovine neutrophil transcriptome. Temporal correlations between gene expression profiles and circulating total leukocyte and neutrophil counts were apparent. However, few relationships between gene expression and plasma steroid profiles were detected, possibly due to the biological time-lag between these variables not captured by the blood collection schedule. Further investigation into the factors underlying neutrophil gene expression changes and validations at the protein and cell behavior levels will lead to a better understanding of altered innate immunity in cattle during transportation stress.

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.

To define dietary indispensable amino acid (IAA) needs for milk synthesis by the mammary glands (MG), 16 lactating sows were fed 1 of 4 isocaloric diets varying in protein concentrations (from 78 to 235 g/kg) with an ideal amino acid (AA) pattern. On d 9, 13, 17, and 21 of lactation, blood samples were obtained simultaneously from a carotid artery and the main mammary vein every 30 min over 6 h. A quadratic regression model of the log mammary arteriovenous difference (AVD) of plasma IAA (ŷ) against daily intake of dietary IAA (X) was established. First, the reverse log intercept, defined as the mammary AVD at zero dietary AA supply, was used to quantify the contribution of endogenous IAA. The quantification was validated by body N balance coupled with AA composition analysis. Then, the estimated vertex (ŷ(max), X(i)) was used in 2 aspects: 1) The maximal mammary uptake of plasma IAA, quantified by multiplying the maximal mammary AVD and plasma flow rate, was considered the physiological IAA need for milk synthesis. 2) Corresponding to the ŷ(max), dietary IAA intake (X(i)) would represent the total dietary IAA requirement, i.e., the sum of maintenance need and milk synthesis need after adjustment for body weight loss. Thus, dietary IAA needs for milk synthesis were derived. Moreover, the estimate of lysine need for milk synthesis in this study was identical to an estimate obtained from multiple regression analysis of feeding trial data. We conclude that dietary IAA needs for milk synthesis can be quantified by the maximal uptakes of plasma IAA by porcine MG.

Insemination of sows with frozen-thawed spermatozoa results in lower fertility, in part due to spermatozoa having undergone a capacitation-like reaction. The present study employed chlortetracycline (CTC) staining analysis to investigate the effect of adding 20% (v/v) boar seminal plasma (SP) to boar spermatozoa on the temporal progress of capacitation and the acrosome reaction in spermatozoa cooled to 5 degrees C or incubated at 39 degrees C. Based on CTC staining patterns, seminal plasma appeared to reverse capacitation in spermatozoa that had undergone capacitation while incubated at 39 degrees C in a capacitation-supporting medium from 59.7 to 36.6% capacitated (P0.001). Similarly, the addition of SP to boar spermatozoa cooled to 5 degrees C resulted in both the prevention of the capacitation-like reaction, and the reversal of an established capacitation-like reaction from 63.3 to 34.2% capacitated (P0.001). These observations indicated that some constituent(s) of boar SP both prevent spermatozoa from undergoing capacitation as well as reverse capacitation in spermatozoa that have already undergone the process.

Studies over roughly the last decade have emphasized the importance of gene expression in the development of structure and function of the songbird forebrain. However, few tools have been available to efficiently identify the critical factors. To that end, we have produced a normalized cDNA library from juvenile zebra finch telencephalon, and have spotted inserts from 2400 randomly selected cDNA clones on microarrays (1664 unique sequences). We have also added several previously cloned cDNAs of interest, including three representing genes encoded on sex chromosomes. Hybridizations comparing Cy3- and Cy5-labeled cDNA from the telencephalon of day 25 male and female zebra finches confirmed sexually dimorphic expression of the Z- and W-linked genes, demonstrating the utility of these microarrays for detecting differential expression and providing information about the relative expression of these genes in the brains of juveniles of this age.

A cDNA microarray resource enhanced for transcripts specific to the bovine mammary gland (BMAM) has been developed and used in pilot studies to examine gene expression profiles in the mammary gland. One goal driving development of this resource was to shed some light on the pathways and mechanisms specifically related to bovine mammary gland growth and development. To accomplish this, gene expression patterns from bovine adipose, liver, adrenal, lymph, spleen, thymus, gut, and developing mammary tissue were compared using the BMAM microarray. We have thus identified a putative set of 16 genes being preferentially expressed in developing mammary gland. Another of our long-term goals is to elucidate the genes and pathways associated with bovine lactation and involution and to use these as a model for human mammary gland development as it relates to human breast cancer risks. To begin this process, we conducted a pilot study, comparing gene expression profiles of lactating bovine mammary tissue against nonlactating tissue on the BMAM microarray. Our results have yielded many novel and interesting genes exhibiting differential expression in lactating mammary tissue, including oncogenes (VAV3, C-myc), mediators of apoptosis (Caspase 8), and cell cycle regulators (LASP1).

The U.S. Fish and Wildlife Service required a chronic dosing study that assessed the health and reproductive effects of tungsten-iron and tungsten-polymer shot in adult game-farm mallards (Anas platyrhynchos) prior to granting permanent approval of the shot for waterfowl hunting. Herein, we present the effects of tungsten-iron and tungsten-polymer shot on various hematologic parameters and metal residue concentrations in the femur, liver, kidneys, and gonads. Thirty-two-bird groups (sexes equal) of adult mallards were dosed orally with eight #4 steel shot (control), eight #4 tungsten-iron shot, or eight #4 tungsten-polymer shot on days 0, 30, 60, 90, and 120 of a 150 day trial (26 January 1998 to 25 June 1998). An additional 12 mallards (sexes equal) received eight #4 lead shot (positive control) on day 0 of the study. Lead-dosed mallards had significantly decreased hematocrit, hemoglobin concentration, and whole-blood delta aminolevulinic acid dehydratase activity on day 7, as well as significant changes in a number of plasma chemistry parameters compared to ducks in the control, tungsten-iron, or tungsten-polymer groups. Mallards dosed with tungsten-iron or tungsten-polymer shot had occasional significant differences in hematocrit and plasma chemistry values when compared to control mallards over the 150 day period, but these changes were not considered to be indicative of deleterious effects. Low concentrations of tungsten were detected in gonad and kidney samples from males and females and in liver samples from females dosed with tungsten-polymer shot. Tungsten was also detected in femur samples from tungsten-polymer-dosed mallards. Higher concentrations of tungsten were detected in femur, liver, kidney, and gonad samples from tungsten-iron-dosed ducks. Tungsten-iron or tungsten-polymer shot repeatedly administered to adult mallards did not cause adverse hematological effects during the 150 day trial. Concentrations of tungsten in the femur, liver, kidneys, and gonads were generally higher in tungsten-iron-dosed ducks when compared to tungsten-polymer-dosed ducks.

Sixteen yearling Holstein steers were fed for 210 or 60% of maintenance requirements to impose positive or negative energy balance, respectively. Blood was collected and analyzed for serum concentration of nonesterified fatty acids (NEFA), and leukocytes were isolated and counted. Isolated leukocytes were then analyzed for expression of the adhesion molecules L-selectin (CD62L), Mac-1 (CD11b and CD18), and major histocompatability complex (MHC) class I and class II molecules with immunostaining and flow cytometric analysis. Negative energy balance increased the concentration of NEFA in serum (P < 0.0001). Expression of CD62L on neutrophils was increased 14% during negative energy balance (P = 0.03). Energy balance did not affect expression of CD62L on any other cell types or expression of CD11b or CD18. Negative energy balance did not affect MHC class I expression but resulted in a small but significant increase in the expression of MHC class II (P = 0.03). The results of this study provide little evidence that nutritionally created negative energy balance impairs expression of CD62L, CD11b, and CD18 or expression of MHC class I or MHC class II molecules by resting bovine blood leukocytes.

Cortisol-activated glucocorticoid receptors modulate cellular responses to stress by translocating from the cytosol to the nucleus and enhancing or repressing the transcription of target genes. The functional capacity of mononuclear leukocytes is inhibited in parturient dairy cows at a time when blood cortisol concentrations are high. Because the glucocorticoid receptor is autoregulatory in many cell types, the hypothesis of the current study was that glucocorticoid receptor expression by mononuclear leukocytes is altered around parturition in association with elevated blood cortisol. If true, the glucocorticoid receptor could be involved in suppressed functions of mononuclear leukocytes in parturient cows. The objectives of this study were to determine effects of parturition on lymphocyte and monocyte glucocorticoid receptor expression and to correlate expression with serum cortisol concentrations. Objectives were achieved by using fluorescence staining and flow cytometric analyses to monitor glucocorticoid receptors in peripheral blood mononuclear leukocytes collected multiple times from 13 periparturtient test cows (eight multi- and five primiparous) and 10 midgestation control cows (five multi- and five primiparous). Serum cortisol concentrations were determined by radioimmunoassay. Based on intensity of the fluorescent glucocorticoid receptor stain, parturition caused 42 and 47% reductions in lymphocyte and monocyte glucocorticoid receptor expression, respectively, compared with mean expression in corresponding cells from control cows. When mean prepartum values were compared with nadir values at parturition in the test cows, glucocorticoid receptor expression was reduced by 67% in lymphocytes and by 54% in monocytes. Mononuclear cell expression of glucocorticoid receptors was negatively correlated with serum cortisol concentrations. Results suggest that glucocorticoid receptors are down-regulated in bovine mononuclear leukocytes in association with increased adrenal secretion of cortisol at calving. It is possible that glucocorticoid receptor down-regulation is also associated with altered phenotype or function (or both) of lymphocytes and monocytes. This possibility should be substantiated because it could explain increased disease susceptibility in periparturient dairy cows.

Objective—To determine effects of parturition on glucocorticoid receptor (GR) expression in neutrophils, serum cortisol concentration, and total blood leukocyte and neutrophil counts in periparturient dairy cows. Animals—23 Holstein cows. Procedure—Blood samples were collected from 8 multiparous and 5 primiparous periparturient cows at various times from 28 days before parturition until 14 days after parturition. Glucocorticoid receptor expression in neutrophils, serum cortisol concentration, and total blood leukocyte and neutrophil counts were determined. Results were compared with results from control samples obtained from 5 multiparous and 5 primiparous Holstein cows in midpregnancy. Results—Neutrophils from periparturient cows had 49% reduction in GR expression at calving, compared with GR expression 2 to 4 weeks before calving, and 39% reduction, compared with neutrophils from cows in midpregnancy. Reduction in neutrophil GR expression began 1 week before calving and was most severe at calving and 24 hours after calving; a significant difference in GR expression was detected between primiparous and multiparous cows. Serum cortisol concentrations and total leukocyte and neutrophil counts were significantly increased at calving and returned to baseline values by 24 hours after calving. Significant negative correlations were detected between neutrophil GR expression and serum cortisol concentration, total leukocyte count, and neutrophil count. Conclusions and Clinical Relevance—Reduced GR expression in blood neutrophils of periparturient dairy cows was associated with increased serum cortisol concentrations, leukocytosis, and neutrophilia. Thus, GR down-regulation in neutrophils may be involved in periparturient neutrophil dysregulation and may cause increased susceptibility to mastitis. (Am J Vet Res 2000;61:14–19)

Two negative binomial mixed models with different dispersion specifications were compared for analysis of dairy reproduction count data. The first model was developed previously and had heterogeneous overdispersion in an associated logarithmic scale, assigning greater uncertainty to observations with smaller conditional expectations. The second model postulated homogeneous overdispersion across all data. A simulation study was used to compare marginal modal estimates of additive genetic variance, based on these two negative binomial models, with analogous estimates computed by an overdispersed Poisson mixed model. Estimators from the second negative binomial and overdispersed Poisson models had better frequentist properties than did those from the first negative binomial model. Nevertheless, application to a data set of number of artificial inseminations until conception in Holstein heifers suggested a slightly better fit of the first negative binomial model. A marginal likelihood ratio test indicated that the additive genetic variance was significant. Cross-validation analyses suggested that the two negative binomial mixed models had slightly better predictive ability than a linear mixed model.

The misty ( m) coat color mutation is commonly maintained in linkage disequilibrium with the obesity mutation diabetes ( Leprdb) to serve as a marker for Leprdbgenotype. Comparisons among Leprdbgenotypes are made under the untested assumption that m has no effects on traits under investigation. We tested this assumption in a population segregating m in the absence of db. Analysis of growth curves revealed that m/m mice are smaller than M/M mice by the 2nd wk of life and remain smaller through the 5th wk of life. Analysis of variance of three traits measured at 35 days of age revealed that m/m mice are 8% shorter than M/M mice, weigh 15% less, and have 21% less inguinal adipose mass. These results indicate that m affects growth traits. Therefore, when m and Leprdbsegregate in the same cross, interpretation of their effects is confounded by linkage. More accurate estimates of Leprdbgenotype effects can be made by removing m from populations segregating Leprdband using a direct assay to measure Leprdbgenotype.

Fitness and fertility traits of dairy cattle are of increasing importance and are often measured on a discrete scale. The development and application of generalized linear mixed models to the genetic analysis of these traits are reviewed. Because current genetic evaluation systems are predominantly based on animal models, the inferential challenges of highly parameterized generalized linear mixed models are discussed. Development and adoption of new methods for drawing appropriate inferences on dispersion parameters are essential. Recent hierarchical extensions have been proposed for generalized linear mixed models, allowing for complex dispersion patterns that accommodate heteroscedasticity and outlier robustness. Steady advances in available computing power have facilitated multiple-trait analyses involving continuous and discrete measures. Full Bayesian inference via the development of Markov Chain Monte Carlo methods will continue to allow even greater generality and dimensions in the genetic model.

Repeated records on fertility, litter size, and ovulation rate of Rambouillet ewes and on fertility and litter size of Finnsheep ewes were used to estimate heritabilities and repeatabilities with linear and nonlinear sire and animal models. Linear sire (LSM) and animal models were used with all traits. Nonlinear models were the threshold, Poisson, and negative binomial. Threshold sire (TSM) and animal models were used with all traits. Litter size and ovulation rate were analyzed also with Poisson sire and animal models and with negative binomial sire and animal models. Variance components for linear models were estimated using REML; in the threshold, Poisson, and negative binomial, they were estimated using approximate marginal maximum likelihood. Poisson and negative binomial analyses yielded results difficult to interpret due to problems in variance component estimation. Animal models resulted in slightly greater estimates of heritability for fertility than did sire models, but ovulation rate heritability estimates from sire models were much greater than estimates from animal models. Differ- ences between sire and animal models for heritability estimates for litter size were not consistent. Threshold models resulted in higher heritability estimates for all traits in both breeds and with both sire and animal models. In general, repeatabilities were consistent across models. For example, LSM (TSM) repeatabili- ties were .10 (.14) for fertility, .20 (.25) for litter size, and .25 ( .29) for ovulation rate in the Rambouillet, and .17 ( .17) for fertility and .11 (.13) for litter size in the Finnsheep.

The influence of slaframine (SF), a parasympathomimetic compound isolated from the fungus Rizoctonia leguminicola, on circulating metabolic hormone concentrations was investigated in goats. In Exp. 1, SF was administered i.v. at 0 (CONT), 50 (LSF), 100 (MSF), or 150 (HSF) microgram/kg.75 BW in four mature Spanish-cross does (average BW 36 +/- 7 kg) fitted with indwelling jugular vein catheters in a 4 x 4 Latin square design. Plasma glucose peaked (P.06) at 120 min with LSF and at 180 min with HSF and was higher (P.06) than the CONT at these times. Glucose exhibited a quadratic response (P.03) to SF. Area under the response curve for glucose differed (P.02) in HSF from CONT and MSF. Insulin peaked (P.01) at 240 min with MSF and at 180 min with HSF. Plasma triiodothyronine was maintained at a higher level (P.03) with HSF. Thyroxine peaked (P.06) at 120 min with MSF and 300 min with HSF. Plasma NEFA and somatotropin concentrations were not affected (P.10) by SF. In Exp. 2, four mature Spanish-cross wethers (average BW 27 +/- 2 kg) fitted with jugular vein catheters were administered SF (0 and 114 micrograms/kg.75 BW) and 4-diphenylacetoxy-N-methylpiperidine methiodide (4DAMP; 0 and 258 micrograms/kg.75 BW), a M3-muscarinic receptor antagonist, i.v. in a 4 x 4 Latin square design with a 2 x 2 factorial arrangement of treatments. With SF, glucose peaked (P.06) at 60 min and insulin peaked (P.05) at 180 min. Plasma triiodothyronine levels were maintained (P.05) with SF but declined with other treatments. Plasma NEFA and thyroxine concentrations remained unchanged regardless of treatment. Slaframine administration induced hyperglycemia and hyperinsulinemia in goats; however, these changes were blocked by preadministration of isomolar quantities of the M3-muscarinic receptor antagonist, 4DAMP.

Expression of a single copy of the rat obesity fatty (fa) gene may affect energy balance. To test this hypothesis, the effects of zero, one, and two copies of fa on early growth were evaluated, using a molecular genetic method for counting fa alleles inherited by 7- and 14-day-old F2 offspring of a BN/Crl x Crl:ZUC-fa F1 intercross. Litter and sex effects were controlled by multiple-regression analysis, allowing genotype effects on the weights of body, inguinal adipose pads, interscapular brown adipose tissue, and liver to be isolated. At 7 days of age, the fa copy number had linear effects on body and inguinal adipose pads weight. At 14 days of age, the fa copy number had linear effects on body, inguinal adipose pads, and interscapular brown adipose tissue weights and an additional quadratic effect on inguinal adipose pads weight. Thus fa has codominant effects on growth during the first week of life. The recessive effects of fa on growth appear during the second week of life.

Background Nearly 6,000 QTL have been reported for 588 different traits in pigs, more than in any other livestock species. However, this effort has translated into only a few confirmed causative variants. A powerful strategy for revealing candidate genes involves expression QTL (eQTL) mapping, where the mRNA abundance of a set of transcripts is used as the response variable for a QTL scan. Methodology/Principal Findings We utilized a whole genome expression microarray and an F2 pig resource population to conduct a global eQTL analysis in loin muscle tissue, and compared results to previously inferred phenotypic QTL (pQTL) from the same experimental cross. We found 62 unique eQTL (FDR

We propose a general Bayesian approach to heteroskedastic error modeling for generalized linear mixed models (GLMM) in which linked functions of conditional means and residual variances are specified as separate linear combinations of fixed and random effects. We focus on the linear mixed model (LMM) analysis of birth weight (BW) and the cumulative probit mixed model (CPMM) analysis of calving ease (CE). The deviance information criterion (DIC) was demonstrated to be useful in correctly choosing between homoskedastic and heteroskedastic error GLMM for both traits when data was generated according to a mixed model specification for both location parameters and residual variances. Heteroskedastic error LMM and CPMM were fitted, respectively, to BW and CE data on 8847 Italian Piemontese first parity dams in which residual variances were modeled as functions of fixed calf sex and random herd effects. The posterior mean residual variance for male calves was over 40% greater than that for female calves for both traits. Also, the posterior means of the standard deviation of the herd-specific variance ratios (relative to a unitary baseline) were estimated to be 0.60 ± 0.09 for BW and 0.74 ± 0.14 for CE. For both traits, the heteroskedastic error LMM and CPMM were chosen over their homoskedastic error counterparts based on DIC values.

Count data models are developed for animal breeding applications to account for more variability than in a Poisson mixed effects model. A gamma distribution is assigned to Poisson parameters, thereby leading to a negative binomial model. The natural log of the expected value of the Poisson parameter is expressed as a linear function of fixed and random polygenic effects. The negative binomial and Poisson mixed models were compared in two simulations. In the first, marginal maximum likelihood (MML) estimates of genetic variances obtained under a Poisson "sire" model (PSM) and under a Poisson "animal" model (PAM), accounting for half-sib relationships, were different, contrary to what occurs in a Gaussian mixed linear model. MML estimates of genetic variance under a negative binomial "sire" model were less biased than estimates under a PSM, and had a slightly smaller mean squared error (MSE). The second simulation compared "animal" models in which the variance of the residuals was larger than the genetic variance. Empirical relative bias and MSE of MML estimates of genetic variance were larger under a PAM that ignored the residuals than under a negative binomial animal model. Differences in performance widened as genetic variance increased. An application to the analysis of number of artificial inseminations until conception in dairy heifers is presented to illustrate potential differences in genetic variance estimates under the two animal models.

Background Skeletal muscle growth and development from embryo to adult consists of a series of carefully regulated changes in gene expression. Understanding these developmental changes in agriculturally important species is essential to the production of high quality meat products. For example, consumer demand for lean, inexpensive meat products has driven the turkey industry to unprecedented production through intensive genetic selection. However, achievements of increased body weight and muscle mass have been countered by an increased incidence of myopathies and meat quality defects. In a previous study, we developed and validated a turkey skeletal muscle-specific microarray as a tool for functional genomics studies. The goals of the current study were to utilize this microarray to elucidate functional pathways of genes responsible for key events in turkey skeletal muscle development and to compare differences in gene expression between two genetic lines of turkeys. To achieve these goals, skeletal muscle samples were collected at three critical stages in muscle development: 18d embryo (hyperplasia), 1d post-hatch (shift from myoblast-mediated growth to satellite cell-modulated growth by hypertrophy), and 16wk (market age) from two genetic lines: a randombred control line (RBC2) maintained without selection pressure, and a line (F) selected from the RBC2 line for increased 16wk body weight. Array hybridizations were performed in two experiments: Experiment 1 directly compared the developmental stages within genetic line, while Experiment 2 directly compared the two lines within each developmental stage. Results A total of 3474 genes were differentially expressed (false discovery rate; FDR < 0.001) by overall effect of development, while 16 genes were differentially expressed (FDR < 0.10) by overall effect of genetic line. Ingenuity Pathways Analysis was used to group annotated genes into networks, functions, and canonical pathways. The expression of 28 genes involved in extracellular matrix regulation, cell death/apoptosis, and calcium signaling/muscle function, as well as genes with miscellaneous function was confirmed by qPCR. Conclusions The current study identified gene pathways and uncovered novel genes important in turkey muscle growth and development. Future experiments will focus further on several of these candidate genes and the expression and mechanism of action of their protein products.

A cDNA microarray resource has been developed with the goal of providing integrated functional genomics resources for cattle. The National Bovine Functional Genomics Consortium’s (NBFGC) expressed sequence tag (EST) collection was established in 2001 to develop resources for functional genomics research. The NBFGC EST collection and microarray contains 18,263 unique transcripts, derived from many different tissue types and various physiologically important states within these tissues. The NBFGC microarray has been tested for false-positive rates using self-self hybridizations and was shown to yield robust results in test microarray experiments. A web-accessible database has been established to provide pertinent data related to NBFGC clones, including sequence data, BLAST results, and ontology information. The NBFGC microarray represents the largest cDNA microarray for a livestock species prepared to date and should prove to be a valuable tool in studying genome-wide gene expression in cattle.

Sixteen-bird groups (sexes equal) of adult mallards (Anas platyrhynchos) were orally dosed with eight #4 steel short, eight #4 lead shot, eight BB-size tungsten-iron shot, eight BB-size tungsten-polymer shot, or were sham-dosed and maintained for 30 days (16 January 1996 to 15 February 1996). Half of the lead-dosed ducks (five males, three females) died during the study, whereas no ducks died in the other dosage groups. For lead-dosed ducks, hematocrit and hemoglobin concentration were decreased on day 15 of the trial, but not on day 30. Delta aminolevulinic acid dehydratase activity in lead-dosed ducks was lower when compared to steel-dosed ducks only. Plasma activities of selected enzymes were elevated in lead-dosed ducks when compared to enzyme activities of ducks in the other groups. For lead-dosed ducks, relative heart, liver, and kidney weights increased in comparison to relative weights of those organs of ducks in other groups. Histology of tissues indicated that renal nephrosis accompanied by biliary stasis was present in the eight lead-dosed ducks that died. For the eight lead-dosed ducks that survived, six had mild to severe biliary stasis. Mild biliary stasis was noted in five tungsten-iron dosed ducks and three tungsten-polymer dosed ducks. Amounts of lead in the femur, liver, and kidneys were higher in lead-dosed ducks than in ducks of the other four groups. Small amounts of tungsten were detected in the femur and kidneys of two tungsten-polymer dosed ducks. Higher concentrations of tungsten were detected in the femur, liver, and kidneys of all tungsten-iron dosed ducks. The rate of shot erosion was highest (80%) for the tungsten-polymer shot, followed by tungsten-iron (55%), lead (50%), and steel shot (33%). Results indicated that tungsten-iron or tungsten-polymer shot (8 shot/duck) orally administered to mallards did not adversely affect them during a 30-day trial.

International audience; BackgroundThe cattle tick is a parasite that adversely affects livestock performance in tropical areas. Although countries such as Australia and Brazil have developed genetic evaluations for tick resistance, these evaluations have not considered genotype by environment (G*E) interactions. Genetic gains could be adversely affected, since breedstock comparisons are environmentally dependent on the presence of G*E interactions, particularly if residual variability is also heterogeneous across environments. The objective of this study was to infer upon the existence of G*E interactions for tick resistance of cattle based on various models with different assumptions of genetic and residual variability.MethodsData were collected by the Delta G Connection Improvement program and included 10,673 records of tick counts on 4363 animals. Twelve models, including three traditional animal models (AM) and nine different hierarchical Bayesian reaction norm models (HBRNM), were investigated. One-step models that jointly estimate environmental covariates and reaction norms and two-step models based on previously estimated environmental covariates were used to infer upon G*E interactions. Model choice was based on the deviance criterion information.ResultsThe best-fitting model specified heterogeneous residual variances across 10 subclasses that were bounded by every decile of the contemporary group (CG) estimates of tick count effects. One-step models generally had the highest estimated genetic variances. Heritability estimates were normally higher for HBRNM than for AM. One-step models based on heterogeneous residual variances also usually led to higher heritability estimates. Estimates of repeatability varied along the environmental gradient (ranging from 0.18 to 0.45), which implies that the relative importance of additive and permanent environmental effects for tick resistance is influenced by the environment. Estimated genetic correlations decreased as the tick infestation level increased, with negative correlations between extreme environmental levels, i.e., between more favorable (low infestation) and harsh environments (high infestation).ConclusionsHBRNM can be used to describe the presence of G*E interactions for tick resistance in Hereford and Braford beef cattle. The preferred model for the genetic evaluation of this population for tick counts in Brazilian climates was a one-step model that considered heteroscedastic residual variance. Reaction norm models are a powerful tool to identify and quantify G*E interactions and represent a promising alternative for genetic evaluation of tick resistance, since they are expected to lead to greater selection efficiency and genetic progress.

In this study, a hierarchical threshold mixed model based on a cumulative t-link specification for the analysis of ordinal data or more, specifically, calving ease scores, was developed. The validation of this model and the Markov chain Monte Carlo (MCMC) algorithm was carried out on simulated data from normally and t4 (i.e. a t-distribution with four degrees of freedom) distributed populations using the deviance information criterion (DIC) and a pseudo Bayes factor (PBF) measure to validate recently proposed model choice criteria. The simulation study indicated that although inference on the degrees of freedom parameter is possible, MCMC mixing was problematic. Nevertheless, the DIC and PBF were validated to be satisfactory measures of model fit to data. A sire and maternal grandsire cumulative t-link model was applied to a calving ease dataset from 8847 Italian Piemontese first parity dams. The cumulative t-link model was shown to lead to posterior means of direct and maternal heritabilities (0.40 ± 0.06, 0.11 ± 0.04) and a direct maternal genetic correlation (-0.58 ± 0.15) that were not different from the corresponding posterior means of the heritabilities (0.42 ± 0.07, 0.14 ± 0.04) and the genetic correlation (-0.55 ± 0.14) inferred under the conventional cumulative probit link threshold model. Furthermore, the correlation (> 0.99) between posterior means of sire progeny merit from the two models suggested no meaningful rerankings. Nevertheless, the cumulative t-link model was decisively chosen as the better fitting model for this calving ease data using DIC and PBF.

The cattle tick is a parasite that adversely affects livestock performance in tropical areas. Although countries such as Australia and Brazil have developed genetic evaluations for tick resistance, these evaluations have not considered genotype by environment (G*E) interactions. Genetic gains could be adversely affected, since breed-stock comparisons are environmentally dependent on the presence of G*E interactions, particularly if residual vari-ability is also heterogeneous across environments. The objective of this study was to infer upon the existence of G*E interactions for tick resistance of cattle based on various models with different assumptions of genetic and residual variability. Article 3.

Background: Nearly 6,000 QTL have been reported for 588 different traits in pigs, more than in any other livestock species. However, this effort has translated into only a few confirmed causative variants. A powerful strategy for revealing candidate genes involves expression QTL (eQTL) mapping, where the mRNA abundance of a set of transcripts is used as the response variable for a QTL scan. Methodology/Principal Findings: We utilized a whole genome expression microarray and an F2 pig resource population to conduct a global eQTL analysis in loin muscle tissue, and compared results to previously inferred phenotypic QTL (pQTL) from the same experimental cross. We found 62 unique eQTL (FDR ,10%) and identified 3 gene networks enriched with genes subject to genetic control involved in lipid metabolism, DNA replication, and cell cycle regulation. We observed strong evidence of local regulation (40 out of 59 eQTL with known genomic position) and compared these eQTL to pQTL to help identify potential candidate genes. Among the interesting associations, we found aldo-keto reductase 7A2 (AKR7A2) and thioredoxin domain containing 12 (TXNDC12) eQTL that are part of a network associated with lipid metabolism and in turn overlap with pQTL regions for marbling, % intramuscular fat (% fat) and loin muscle area on Sus scrofa (SSC) chromosome 6. Additionally, we report 13 genomic regions with overlapping eQTL and pQTL involving 14 local eQTL. Conclusions/Significance: Results of this analysis provide novel candidate genes for important complex pig phenotypes.