Energy balance of dairy cows predicted by mid-infrared spectra data of milk using Bayesian approaches.

Information on dry matter intake (DMI) and energy balance (EB) at the animal and herd level is important for management and breeding decisions. However, routine recording of these traits at commercial farms can be challenging and costly. Fourier-transform mid-infrared (FT-MIR) spectroscopy is a noninvasive technique applicable to a large cohort of animals that is routinely used to analyze milk components and is convenient for predicting complex phenotypes that are typically difficult and expensive to obtain on a large scale. We aimed to develop prediction models for EB and use the predicted phenotypes for genetic analysis. First, we assessed prediction equations using 4,485 phenotypic records from 167 Holstein cows from an experimental station. The phenotypes available were body weight (BW), milk yield (MY) and milk components, weekly-averaged DMI, and FT-MIR data from all milk samples available. We implemented mixed models with Bayesian approaches and assessed them through 50 randomized replicates of a 5-fold cross-validation. Second, we used the best prediction models to obtain predicted phenotypes of EB (EBp) and DMI (DMIp) on 5 commercial farms with 2,365 phenotypic records of MY, milk components and FT-MIR data, and BW from 1,441 Holstein cows. Third, we performed a GWAS and estimated heritability and genetic correlations for energy content in milk (EnM), BW, DMIp, and EBp using the genomic information available on the cows from commercial farms. The highest correlation between the predicted and observed phenotype (ry,y^) was obtained with DMI (0.88) and EB (0.86), while predicting BW was, as anticipated, more challenging (0.69). In our study, models that included FT-MIR information performed better than models without spectra information in the 3 traits analyzed, with increments in prediction correlation ranging from 5% to 10%. For the predicted phenotypes calculated by the prediction equations and data from the commercial farms the heritability ranged between 0.11 and 0.16 for EnM, DMIp and EBp, and 0.42 for BW. The genetic correlation between EnM and BW was -0.17, with DMIp was 0.40 and with EBp was -0.39. From the GWAS, we detected one significant QTL region for EnM, and 3 for BW, but none for DMIp and EBp. The results obtained in our study support previous evidence that FT-MIR information from milk samples contribute to improve the prediction equations for DMI, BW, and EB, and these predicted phenotypes may be used for herd management and contribute to the breeding strategy for improving cow performance.

The Effect of Human and Bovine Milk Osteopontin on Intestinal Caco-2 Cells: A Transcriptome Comparison.

Osteopontin (OPN) is a multifunctional protein abundantly present in human milk, whereas the concentration is significantly lower in bovine milk. Human and bovine milk OPN are structurally similar and both proteins resist gastric digestion and reach the intestines in a bioactive form. Intervention studies have indicated the beneficial effects of supplementing infant formula with bovine milk OPN and several in vivo and in vitro studies have shown that bovine milk OPN positively influences intestinal development. To investigate the functional relationship, we compared the effect of simulated gastrointestinal digested human and bovine milk OPN on gene expression in Caco-2 cells. After incubation, total RNA was extracted and sequenced and transcripts were mapped to the human genome. Human and bovine milk OPN regulated the expression of 239 and 322 genes, respectively. A total of 131 genes were similarly regulated by the OPNs. As a control, a whey protein fraction with a high content of alpha-lactalbumin had a very limited transcriptional impact on the cells. Enrichment data analysis showed that biological processes related to the ubiquitin system, DNA binding, and genes associated with transcription and transcription control pathways were affected by the OPNs. Collectively, this study shows that human and bovine milk OPN have a significant and highly comparable effect on the intestinal transcriptome.

Factors influencing milk osteopontin concentration based on measurements from Danish Holstein cows.

Our objective was to determine the content of the bioactive protein osteopontin (OPN) in bovine milk and identify factors influencing its concentration. OPN is expressed in many tissues and body fluids, with by far the highest concentrations in milk. OPN plays a role in immunological and developmental processes and it has been associated with several milk production traits and lactation persistency in cows. In the present study, we report the development of an enzyme linked immunosorbent assay (ELISA) for measurement of OPN in bovine milk. The method was used to determine the concentration of OPN in milk from 661 individual Danish Holstein cows. The median OPN level was determined to 21.9 mg/l with a pronounced level of individual variation ranging from 0.4 mg/l to 67.8 mg/l. Breeding for increased OPN in cow's milk is of significant interest, however, the heritability of OPN in milk was found to be relatively low, with an estimated value of 0.19 in the current dataset. The variation explained by the herd was also found to be low suggesting that OPN levels are not affected by farm management or feeding. Interestingly, the concentration of OPN was found to increase with days in milk and to decrease with parity.

Indomethacin Increases the Efficacy of Oxygen Utilization of Colonic Mitochondria and Uncouples Hepatic Mitochondria in Tissue Homogenates From Healthy Rats.

Background: Studies suggest that indomethacin (Indo) exhibits detrimental changes in the small intestine (microvascular disorder, villus shortening, and epithelial disruption), mainly due to mitochondrial uncoupling. The effects of Indo on colon and liver tissue are unclear. The aim of this study was to determine the effects of Indo on mitochondrial respiration in colonic and hepatic tissue. Methods: Mitochondrial oxygen consumption was assessed in colon and liver homogenates from healthy rats. Homogenates were incubated without drug (control) or Indo (colon: 0.36, 1, 30, 179, 300, 1,000, 3,000 µM; liver: 0.36, 1, 3, 10, 30, 100, 179 µM; n = 6). State 2 (substrate-dependent) and state 3 (ADP-dependent respiration) were evaluated with respirometry. The respiratory control index (RCI) was derived and the ADP/O ratio was calculated. Statistics: Data presented as % of control, min/median/max, Kruskal-Wallis+Dunn's correction, * p < 0.05 vs. control. Results: Indo had no effect on RCI of colonic mitochondria. ADP/O ratio increased in complex I at concentrations of 1,000 and 3,000 µM (Indo 1,000 µM: 113.9/158.9/166.9%*; Indo 3,000 µM: 151.5/183.0/361.5%*) and in complex II at concentrations of 179 and 3,000 µM vs. control (179 µM: 111.3/73.1/74.9%*; 3,000 µM: 132.4/175.0/339.4%*). In hepatic mitochondria RCI decreased at 179 µM for both complexes vs. control (complex I: 25.6/40.7/62.9%*, complex II: 57.0/73.1/74.9%*). The ADP/O ratio was only altered in complex I at a concentration of 179 µM Indo vs. control (Indo 179 µM: 589.9/993.7/1195.0 %*). Conclusion: Indo affected parameters of mitochondrial function in an organ-specific and concentration-dependent manner. In colonic tissue, RCI remained unaltered whereas the ADP/O ratio increased. Indo at the highest concentration decreased the RCI for both complexes in hepatic mitochondria. The large increase in ADP/O ratio in complex I at the highest concentration likely reflects terminal uncoupling.

Realization of breeding values for milk fatty acids in relation to seasonal variation in organic milk.

Prediction of detailed milk fatty acid (FA) composition by mid-infrared spectroscopy (MIRS) offers possibilities for high-throughput indirect measurements of detailed milk compositional parameters through the milk testing system, which can be used to differentiate the FA profile by genetics or specific management or on dairies for milk quality evaluation. Since 2015, milk samples from all Danish dairy cows under milk testing have been recorded using MIRS. The MIRS software from the FOSS Application Note 64 was used to predict contents of 7 FA groups and 4 individual FA. Data generated from the application note have been used to estimate breeding values for sires for percentage of saturated fat (SFA%) in milk. To investigate whether extreme SFA% breeding values of sires were reflected in the detailed milk FA profile from their daughters, milk samples from 194 cows in 7 organic herds were collected and the detailed FA composition measured by gas chromatography. From each cow, milk samples were collected twice to explore specific seasonal effects of pasture-based diets in relation to sires' estimated breeding value (EBV) for MIRS-predicted SFA% (MIRS-SFA%). The results showed a significant difference in SFA% measured from GC (GC-SFA%) in milk from daughters of sires having high SFA% EBV compared with daughters of sires having low SFA% EBV. The EBV group (low or high) also significantly affected most FA except C13:0, C15:0, C17:0, and C18:1 trans-11. Contents of SFA with even chain-lengths were all higher in the high EBV group, whereas C14:1, C16:1, and the other unsaturated C18 FA had a higher content in the low EBV group. All FA were significantly affected by season. The SFA% decreased from indoor spring feeding to summer pasture, as did FA with chain length ≤16 carbons, whereas long-chain FA (>C17) all increased during summer pasture. The results show that use of MIRS-predicted EBV for SFA% will most likely display a correlated response on the detailed FA composition in milk. In the current study, the combined action of feeding and genetics resulted in a 10 percentage-point difference on average when comparing milk SFA% from daughters of high SFA% EBV sires during indoor spring feeding from one farm to milk SFA% from daughters of low SFA% EBV sires during summer from another farm.

Enteric methane emission from Jersey cows during the spring transition from indoor feeding to grazing.

Organic dairy cows in Denmark are often kept indoors during the winter and outside at least part time in the summer. Consequently, their diet changes by the season. We hypothesized that grazing might affect enteric CH4 emissions due to changes in the nutrition, maintenance, and activity of the cows, and they might differentially respond to these factors. This study assessed the repeatability of enteric CH4 emission measurements for Jersey cattle in a commercial organic dairy herd in Denmark. It also evaluated the effects of a gradual transition from indoor winter feeding to outdoor spring grazing. Further, it assessed the individual-level correlations between measurements during the consecutive feeding periods (phenotype × environment, P × E) as neither pedigrees nor genotypes were available to estimate a genotype by environment effect. Ninety-six mixed-parity lactating Jersey cows were monitored for 30 d before grazing and for 24 d while grazing. The cows spent 8 to 11 h grazing each day and had free access to an in-barn automatic milking system (AMS). For each visit to the AMS, milk yield was recorded and logged along with date and time. Monitoring equipment installed in the AMS feed bins continuously measured enteric CH4 and CO2 concentrations (ppm) using a noninvasive "sniffer" method. Raw enteric CH4 and CO2 concentrations and their ratio (CH4:CO2) were derived from average concentrations measured during milking and per day for each cow. We used mixed models equations to estimate variance components and adjust for the fixed and random effects influencing the analyzed gas concentrations. Univariate models were used to precorrect the gas measurements for diurnal variation and to estimate the direct effect of grazing on the analyzed concentrations. A bivariate model was used to assess the correlation between the 2 periods (in-barn vs. grazing) for each gas concentration. Grazing had a weak P × E interaction for daily average CH4 and CO2 gas concentrations. Bivariate repeatability estimates for average CH4 and CO2 concentrations and CH4:CO2 were 0.77 to 0.78, 0.73 to 0.80, and 0.26, respectively. Repeatability for CH4:CO2 was low (0.26) but indicated some between-animal variation. In conclusion, grazing does not create significant shifts compared with indoor feeding in how animals rank for average CH4 and CO2 concentrations and CH4:CO2. We found no evidence that separate evaluation is needed to quantify enteric CH4 and CO2 emissions from Jersey cows during in-barn and grazing periods.

Introduction of Viral Hemorrhagic Septicemia Virus into Freshwater Cultured Rainbow Trout Is Followed by Bursts of Adaptive Evolution.

Viral hemorrhagic septicemia virus (VHSV), a rhabdovirus infecting teleost fish, has repeatedly crossed the boundary from marine fish species to freshwater cultured rainbow trout. These naturally replicated cross-species transmission events permit the study of general and repeatable evolutionary events occurring in connection with viral emergence in a novel host species. The purpose of the present study was to investigate the adaptive molecular evolution of the VHSV glycoprotein, one of the key virus proteins involved in viral emergence, following emergence from marine species into freshwater cultured rainbow trout. A comprehensive phylogenetic reconstruction of the complete coding region of the VHSV glycoprotein was conducted, and adaptive molecular evolution was investigated using a maximum likelihood approach to compare different codon substitution models allowing for heterogeneous substitution rate ratios among amino acid sites. Evidence of positive selection was detected at six amino acid sites of the VHSV glycoprotein, within the signal peptide, the confirmation-dependent major neutralizing epitope, and the intracellular tail. Evidence of positive selection was found exclusively in rainbow trout-adapted virus isolates, and amino acid combinations found at the six sites under positive selection pressure differentiated rainbow trout- from non-rainbow trout-adapted isolates. Furthermore, four adaptive sites revealed signs of recurring identical changes across phylogenetic groups of rainbow trout-adapted isolates, suggesting that repeated VHSV emergence in freshwater cultured rainbow trout was established through convergent routes of evolution that are associated with immune escape.IMPORTANCE This study is the first to demonstrate that VHSV emergence from marine species into freshwater cultured rainbow trout has been accompanied by bursts of adaptive evolution in the VHSV glycoprotein. Furthermore, repeated detection of the same adaptive amino acid sites across phylogenetic groups of rainbow trout-adapted isolates indicates that adaptation to rainbow trout was established through parallel evolution. In addition, signals of convergent evolution toward the maintenance of genetic variation were detected in the conformation-dependent neutralizing epitope or in close proximity to disulfide bonds involved in the structural conformation of the neutralizing epitope, indicating adaptation to immune response-related genetic variation across freshwater cultured rainbow trout.

Short communication: Genetic variation of riboflavin content in bovine milk.

Riboflavin (vitamin B2) is an essential water-soluble vitamin; elderly people and adolescents in particular can have poor riboflavin status. In Western diets, milk and dairy products are primary sources of riboflavin, but little is known about the natural variation within and among bovine breeds, and how genetic and environmental factors can affect the riboflavin content in milk. As a part of the Danish-Swedish Milk Genomics Initiative, the aim of the study was to quantify milk riboflavin content using reverse-phase HPLC in 2 major Danish dairy breeds. The results showed substantial interbreed differences in milk riboflavin content. Milk from Danish Jersey cows contained significantly higher levels of riboflavin (1.93mg/L of milk) than milk from Danish Holstein cows (1.40mg/L of milk). Furthermore, genetic analyses revealed high heritabilities in both breeds (0.52 for Danish Holstein and 0.31 for Danish Jersey). A genomic association study found 35 significant single nucleotide polymorphisms (false discovery rate<0.10) to be associated with riboflavin content in milk in Jersey cows (all on BTA14 and BTA17), and 511 significant single nucleotide polymorphisms in Holstein cows spread over 25 different autosomes with BTA13 and BTA14 having the most promising quantitative trait loci. The best candidate gene found within the identified quantitative trait loci was SLC52A3, a riboflavin transporter gene, which was among the significant markers on BTA13 in Holstein cows.