Transcriptomic analysis by RNA sequencing reveals that hepatic interferon-induced genes may be associated with feed efficiency in beef heifers.

In beef cattle, production feedstuffs are the largest variable input cost. Beef cattle also have a large carbon footprint, raising concern about their environmental impact. Unfortunately, only a small proportion of dietary energy is directed toward protein deposition and muscle growth whereas the majority supports body maintenance. Improving feed efficiency would, therefore, have important consequences on productivity, profitability, and sustainability of the beef industry. Various measures of feed efficiency have been proposed to improve feed utilization, and currently, residual feed intake (RFI) is gaining popularity. However, the cost associated with measuring RFI and the limited knowledge of the biology underlying improved feed efficiency make its adoption prohibitive. Identifying molecular mechanisms explaining divergence in RFI in beef cattle would lead to the development of early detection methods for the selection of more efficient breeding stock. The objective of this study was to identify hepatic markers of metabolic feed efficiency in replacement beef heifers. A group of 87 heifers were tested for RFI adjusted for off-test backfat thickness (RFIfat). Preprandial liver biopsies were collected from 10 high- and 10 low-RFIfat heifers (7 Hereford­Aberdeen Angus and 3 Charolais­Red Angus­Main Anjou per group) and gene expression analysis was performed using RNA sequencing and quantitative real-time PCR. The heifers used in this study differed in RFIfat averaging 0.438 vs. ­0.584 kg DM/d in high- and low-RFIfat groups, respectively. As expected, DMI was correlated with RFIfat and ADG did not differ between high- and low-RFIfat heifers. Through a combination of whole transcriptome and candidate gene analyses, we identified differentially expressed genes involved in inflammatory processes including hemoglobin ß (HBB), myxovirus resistance 1 interferon-inducible protein p78 (MX1), ISG15 ubiquitin-like modifier (ISG15), hect domain and RLD 6 (HERC6), and interferon-induced protein 44 (IFI44) whose mRNA abundance was lower (HBB) or higher (MX1, ISG15, HERC6, and IFI44) in low-RFIfat heifers. These genes have been shown to be directly or indirectly modulated by interferon signaling and involved with innate immunity. Our results suggest that more efficient heifers respond differently to hepatic proinflammatory stimulus, potentially expending less energy toward combating systemic inflammation and redirecting nutrients toward growth and protein accretion.

A high-resolution radiation hybrid map of the river buffalo major histocompatibility complex and comparison with BoLA.

The major histocompatibility complex (MHC) in mammals codes for antigen-presenting proteins. For this reason, the MHC is of great importance for immune function and animal health. Previous studies revealed this gene-dense and polymorphic region in river buffalo to be on the short arm of chromosome 2, which is homologous to cattle chromosome 23. Using cattle-derived STS markers and a river buffalo radiation hybrid (RH) panel (BBURH5000 ), we generated a high-resolution RH map of the river buffalo MHC region. The buffalo MHC RH map (cR5000 ) was aligned with the cattle MHC RH map (cR12000 ) to compare gene order. The buffalo MHC had similar organization to the cattle MHC, with class II genes distributed in two segments, class IIa and class IIb. Class IIa was closely associated with the class I and class III regions, and class IIb was a separate cluster. A total of 53 markers were distributed into two linkage groups based on a two-point LOD score threshold of ≥8. The first linkage group included 32 markers from class IIa, class I and class III. The second linkage group included 21 markers from class IIb. Bacterial artificial chromosome clones for seven loci were mapped by fluorescence in situ hybridization on metaphase chromosomes using single- and double-color hybridizations. The order of cytogenetically mapped markers in the region corroborated the physical order of markers obtained from the RH map and served as anchor points to align and orient the linkage groups.

Identification of candidate markers on bovine chromosome 14 (BTA14) under milk production trait quantitative trait loci in Holstein.

The objective of this study was to identify single-nucleotide polymorphisms using a bovine chromosome 14 high-density SNP panel after accounting for the effect of DGAT1. Linkage disequilibrium information and sire heterozygosity were used to select markers for linkage analysis on bovine chromosome 14 for milk production traits in 321 Holstein animals. Results show putative milk peaks at 42 and 61 cM, both at p<0.10, a fat yield peak at 42 and 63 cM, both at p<0.05; a protein yield peak at 42 (p<0.01) and 84 cM (p<0.05); fat per cent peaks at 3 (p<0.01) and 29 cM (p<0.05), and a protein per cent peak at 4 cM (p<0.05). Once quantitative trait loci positions were established, allele substitution effects for all markers were evaluated using the same statistical model. Overlaying information between quantitative trait loci (QTL) and allele effect analysis enabled the identification (p<0.01) of 20 SNPs under the milk yield QTL, 2 under both of the fat yield peaks, 8 and 9 under the protein yield peaks, 2 and 6 for the fat per cent peaks and 5 for the protein per cent peak. One SNP in particular, ss61514555:A>C, showed association with 3 of the 5 traits: milk (p=1.59E-04), fat (p=6.88E-05) and protein yields (p=5.76E-05). Overall, combining information from linkage disequilibrium, sire heterozygosity and genetic knowledge of traits enabled the characterization of additional markers with significant associations with milk production traits.

Associations of marker panel scores with feed intake and efficiency traits in beef cattle using preselected single nucleotide polymorphisms.

Because of the moderate heritability and the expense associated with collecting feed intake data, effective selection for residual feed intake would be enhanced if marker-assisted evaluation were used for accurate estimation of genetic merit. In this study, a suite of genetic markers predictive of residual feed intake, DMI, and ADG were preselected using single-marker regression analysis, and the top 100 SNP were analyzed further to provide prediction equations for the traits. The data used consisted of 728 spring-born beef steers, offspring of a cross between a composite dam line and Angus, Charolais, or University of Alberta hybrid bulls. Feed intake data were collected over a 5-yr period, with 2 groups (fall-winter and winter-spring) tested every year. Training and validation data sets were obtained by splitting the data into 2 distinct sets, by randomly splitting the data into training and testing sets based on sire family (split 1) in 5 replicates or by retaining all animals with no known pedigree relationships as the validation set (split 2). A total of 37,959 SNP were analyzed by single-marker regression, of which only the top 100 that corresponded to a P-value <0.002 were retained. The 100 SNP were then analyzed using random regression BLUP, and only SNP that were jointly significant (P < 0.05) were included in the final marker panels. The marker effects from the selected panels were used to derive the molecular breeding values, which were calculated as a weighted sum of the number of copies of the more frequent allele at each SNP locus, with the weights being the allele substitution effects. The correlation between molecular breeding value and phenotype represented the accuracy of prediction. For all traits evaluated, accuracy across breeds was low, ranging between 0.007 and 0.414. Accuracy was least in data split 2, where the validation individuals had no pedigree relationship with animals in the training data. Given the low predictive ability observed, a large number of individuals may be needed for prediction when using such an admixed population. Further, these results suggest that breed composition of the target population in which the marker panels are likely to be used should be an important consideration when developing prediction equations across breeds, especially where an admixed population is used as the training data set.

Comparative RH maps of the river buffalo and bovine Y chromosomes.

Radiation hybrid maps were constructed for river buffalo and cattle Y chromosomes. A total of 41 cattle-derived Y-chromosome molecular markers were selected and tested with 2 previously described 5,000-rad whole-genome radiation hybrid (RH) panels (river buffalo - BBURH(5000) and cattle - BTARH(5000)) for generation of maps. Among the initial 41 selected markers, a subset of 26 markers generated PCR products suitable for scoring with the BBURH(5000) panel. Of these, 19 markers (73%) were distributed in 1 linkage group spanning 341.3 cR. Retention frequencies (RF) for individual markers ranged from 17.8% for SMCY to 56.7% for BTY1, with an average RF of 37.6%. From the selected markers, 37 generated reliable scores using the BTARH(5000) panel. The newly constructed BTAY RH map contains 28 markers distributed within 1 linkage group. Twenty-four of these markers had been previously mapped on BTAY using a 7,000-rad cattle-hamster WG-RH panel and 4 markers were mapped for the first time (ZFY, SeqRep, RepSeqS4 and BTY1). The length of the BTAY RH map was estimated to be 602.4 cR. Retention frequencies for individual mapped markers ranged from 10% (INRA126) to 63.3% (SeqRep), with an average RF of 35.3%. RH marker positions along the Y chromosome were compared between BBUY and BTAY, which revealed differences in the order of some of the markers. The BBUY pseudoautosomal region (PAR) is delineated by 3 BTAY PAR markers (MAF45, TGLA325 and UMN2008). These markers are telomeric in both species but are not found in the same order. Here we have demonstrated the effective use of bovine Y chromosome markers for the development of the first BBUY RH map. Likewise, these set of markers can be used for comparative assessment of Y chromosomes in other members of the Bovidae family.

A whole genome scan to map QTL for milk production traits and somatic cell score in Canadian Holstein bulls.

The detection and mapping of genetic markers linked to quantitative trait loci (QTL) can be utilized to enhance genetic improvement of livestock populations. With the completion of the bovine genome sequence assembly, single nucleotide polymorphisms (SNP) assays spanning the whole bovine genome and research work on large scale identification, validation and analysis of genotypic variation in cattle has become possible. The objective of the present study was to perform a whole genome scan to identify and map QTL affecting milk production traits and somatic cell scores using linkage disequilibrium (LD) regression and 1536 SNP markers. Three and 18 SNP were found to be associated with only milk yield (MY) at a genome and chromosome wise significance (p < 0.05) level respectively. Among the 21 significant SNP, 16 were in a region reported to have QTL for MY in other dairy cattle populations and while the rest five were new QTL finding. Four SNP out of 21 are significant for the milk production traits (MY, fat yield, protein yield (PY), and milk contents) in the present study. Six and nine SNP were associated with PY at a genome and chromosome wise significant (p < 0.05) level respectively. Three and 17 SNP were found to be associated with FY at a genome and chromosome wise significant (p < 0.05) level. Five and seven SNP were mapped with somatic cell score at a genome and chromosome wise significant (p < 0.05) level respectively. The results of this study have revealed QTL for MY, PY, protein percentage, FY, fat percentage, somatic cell score and persistency of milk in the Canadian dairy cattle population. The chromosome regions identified in this study should be further investigated to potentially identify the causative mutations underlying the QTL.

A whole-genome scan to map quantitative trait loci for conformation and functional traits in Canadian Holstein bulls.

Genetic improvement of livestock populations can be achieved through detection and mapping of genetic markers linked to quantitative trait loci (QTL). With the completion of the bovine genome sequence assembly, single nucleotide polymorphism (SNP) assays spanning the whole bovine genome and research work on large-scale identification, validation, and analysis of genotypic variation in cattle has become possible. A total of 462 Canadian Holstein Bulls were used to test the association between SNP and QTL. Single locus linkage disequilibrium regression model was implemented to perform a whole genome scan to identify and map QTL affecting conformation and functional traits. One thousand five hundred thirty-six SNP markers from introns and exons of potential QTL regions for economically important traits across the bovine genome were selected for association analysis. A total of 45 and 151 SNP were found to be associated with 17 conformation and functional traits at a genome- and chromosome-wise significance level, respectively. Among the 196 significant SNP, 169 of them are newly detected in this study, whereas 27 of them have been reported in previous literature and 161 of these were located in genes and are worth further investigating to potentially identify the causative mutations underlying the QTL. The single locus linkage disequilibrium regression method using SNP marker genotypes has proven to be a successful methodology for detecting and mapping QTL in dairy cattle populations.

Human CARD4 protein is a novel CED-4/Apaf-1 cell death family member that activates NF-kappaB.

The nematode CED-4 protein and its human homolog Apaf-1 play a central role in apoptosis by functioning as direct activators of death-inducing caspases. A novel human CED-4/Apaf-1 family member called CARD4 was identified that has a domain structure strikingly similar to the cytoplasmic, receptor-like proteins that mediate disease resistance in plants. CARD4 interacted with the serine-threonine kinase RICK and potently induced NF-kappaB activity through TRAF-6 and NIK signaling molecules. In addition, coexpression of CARD4 augmented caspase-9-induced apoptosis. Thus, CARD4 coordinates downstream NF-kappaB and apoptotic signaling pathways and may be a component of the host innate immune response.

Epitope mapping and immunoneutralization of recombinant human stem-cell factor.

The epitope regions of three anti-[stem-cell factor (SCF)]g have been mapped by characterization of immunoreactivities against truncated forms of SCF in immunoblots and against synthetic peptides in solution-phase competition ELISA. Two of the antibodies, mAb 7H6 and mAb 8H7A, were raised against Escherichia coli-derived human SCF-(1-164) while the third, polyclonal antibody (pAb) 1337, was raised against a peptide corresponding to residues 3-31 of human SCF. The epitopes of mAbs 7H6 and 8H7A have been mapped to residues 61-95 and 95-110, respectively. The epitope of pAb 1337 has been mapped to residues 21-31. The ability of the anti-SCF Ig to recognize E. coli-derived human SCF presented in various formats, i.e. partially denatured (fixed in standard ELISA or on a western blot) or native (in solution), was studied, mAb 7H6 recognized its epitope in partially denatured or native SCF with equally high affinity, while mAb 8H7A and pAb 1337 recognized their epitopes only when SCF was at least partially denatured, mAb 7H6 was found to neutralize in vitro SCF-mediated cell proliferation and SCF binding to its receptor, when present in equimolar concentrations relative to the ligand, suggesting that the epitope region is functionally significant. Evidence that the mAb 7H6 epitope is represented by discontinuous regions (residues within sequences 61-65 and 91-95 are critically involved) is presented. The observation that the mAb 7H6 epitope is discontinuous has implications for the structure of SCF.

Relationship of sexual and physical abuse to pain description, coping, psychological distress, and health-care utilization in a chronic pain sample.

OBJECTIVE: We investigated the association of physical/sexual abuse to pain description, coping, psychological distress, and health-care utilization in a heterogeneous sample of chronic pain patients. DESIGN: A cross-sectional, retrospective design was used. Patients were categorized as abused (n = 22) or nonabused (n = 58) based on responses to a valid and reliable sexual/physical abuse questionnaire. MAIN OUTCOME MEASURES: Pain description (Visual Analog Scale measures of pain intensity and frequency, and the McGill Pain Questionnaire); coping ability and attributional style (Functional Interference Estimate, Self-Control Schedule, Pain Locus of Control Scale); psychological distress (SCL-90-R Global Severity Index); and a Health-care utilization measure. RESULTS AND CONCLUSIONS: No differences between abused and nonabused groups were found for the pain description or functional interference variables. Compared to the nonabused group, the abused group had significantly lower Self-Control Schedule scores, higher Pain Locus of Control Scale Chance Factor scores, and higher SCL-90-R Global Severity Index scores and was more likely to use the emergency room for pain symptoms. These results replicate the findings of previous studies of the effects of abuse in more specific pain samples and underscore the importance of assessment of abuse in patients with chronic pain. The data suggest that interventions which involve coping-skills training or self-control management of pain may be affected by an abuse history via reduced perceptions of efficacy, resourcefulness, and beliefs that external variables are responsible for pain.

Why do women exercise? Factor analysis and further validation of the Reasons for Exercise Inventory.

This investigation examined the factor structure and correlates of the Reasons for Exercise Inventory among 101 exercising women. Subjects completed the 24-item inventory (with one added item), reported their weekly frequency of exercise, and completed two standardized body-image measures. Factor analysis indicated that, with minor modifications, the instrument has an internally consistent structure with four factors of Appearance/Weight Management, Fitness/Health Management, Stress/Mood Management, and Socializing. Appearance/Weight Management was associated with a more negative body image independent of actual body mass and was the only motive related to self-reported frequency of exercise.

Are inaccuracies in self-reported weight motivated distortions?

The accuracy of self-reported weight and the motivation of distorted reporting were studied among 169 female and 101 male college students. Although subjects were moderately accurate in their weight estimates, errors reflected women's underreporting, men's overreporting, and heavier persons' underreporting. With body mass controlled, most motivational variables had little explanatory value.

Ascending spinal pathway for arterial pressor response elicited by ventral root afferent inputs in the cat.

In an attempt to localize the spinal ascending pathway for ventral root afferent inputs, changes in ventral root stimulation-evoked arterial blood pressure responses were observed in anesthetized cats after selective spinal lesions. The results of these experiments indicate that the ascending spinal pathways responsible for the pressor response lie in the dorsal-most part of the lateral funiculus. The pathway was found to be bilateral, and it is likely to occupy the same area throughout the entire length of the spinal cord.

Children's retention of dental hygiene instruction. Report of a pilot study.

Following three days of instruction in dental hygiene regarding correct brushing, plaque control, and nutrition, 23 hospitalized children between 4 and 13 significantly (p less than .05) improved practices in plaque control and brushing.