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This study examined the effects of frequency of feeding high-solids milk and milk replacer (MMR) blend combined with dry matter (DM) content of starter feed on the performance of dairy calves. Forty-eight Holstein calves (40.2 ± 3.33 kg of body weight) were randomly assigned to 1 of 4 treatments in a completely randomized design. Based on a combination of 2 MMR feeding frequencies (once versus twice daily) and 2 starter DM levels (91.1 and 50% DM), 4 treatments were designed as (1) once daily + dry starter feed (OD), (2) once daily + wet starter feed (OW), (3) twice daily + dry starter feed (TD), and (4) twice daily + wet starter feed (TW). The amount of milk replacer powder added to whole milk was adjusted at each feeding frequency to ensure that calves received similar solids from the MMR blend via the twice-daily (total solids = 18.6%) or once-daily (total solids = 31.0%) programs. Starter intake in the preweaning period did not differ between treatments (average 0.39 kg of DM/d), but the postweaning starter intake was greater in calves fed the wet starter (OW and TW) than in those fed the dry starter (OD and TD). Calves receiving the high-solids MMR blend twice versus once daily grew faster before weaning, which was reflected by a greater weaning weight in the TD and TW groups (88.9 kg) than in the OD and OW groups (83.2 kg). The daily growth rate after weaning did not differ between treatments and averaged 1.15 kg/d. Gain-to-feed ratio during the preweaning period was greater in calves from TD and TW (mean 0.67) than in calves from the OD or OW groups (mean 0.58). Postweaning gain-to-feed ratio was not different among treatments and averaged 0.38. Days to first diarrhea and duration of diarrhea (4.66 ± 0.38), as well as days that animals were treated with antibiotics, remained unaffected with treatments. Although preweaning body weight gain was lower with once-daily milk feeding, calves were twice as heavy at weaning as at birth in both milk feeding programs regardless of starter moisture content, which may qualify the once-daily milk feeding program as a cost-effective management strategy in commercial calf-rearing operations. Feeding solutions with a high solids content (above 15%) may be associated with an increased risk of abomasal bloat and should be used with caution.

Greenhouse gas (GHG) emissions from livestock are an important consideration in environmental science. Estimating GHG production can be problematic at a farm or animal level, and requires controlled conditions to produce real data. An in vitro gas production technique (IVGPT) was developed to evaluate forage-based total mixed rations in digestion kinetics and GHG production. Two hundred and sixty samples of complete mixed rations (MR), which included a pasture component used in commercial lactating dairy herds, were collected around NZ across three calendar years, 2017-2019. Twenty of the 260 samples were 100% total mixed rations (TMR) with no pasture content. The samples were submitted for proximate analysis as well as IVGPT to generate GHG production figures. The results showed an average total gas production (TGP) of 129.82 ml/g dry matter (DM), 78.6% true digestibility (TDMD), 125.06 mg/g DM microbial biomass (MB), 20.16 g CH4/kg DM, and 12.8 MJME/kg DM. The average nutrient composition was dry matter (DM) 31.55%, crude protein (CP) 21.85%, neutral detergent fibre (NDF) 44.35%, and starch 7.03%. The IVGPT CH4 production was negatively correlated to NDF (r=-0.312), ADF (r=-0.193), TGP (r=-0.216), and was positively correlated with TDMD (r=0.250), apparent digestibility (ADMD) (r=0.614), starch (r=0.117) and volatile fatty acids (r=0.538). The MR diet showed a strong positive relationship with ADMD digestibility (P=0.01) and a negative relationship with fibre content (NDF, P=0.01 and ADF, P=0.01). However, CH4 production reduced linearly with increasing TGP (P=0.01). The results indicated that a greater CH4 production may be related to higher digestibility of mixed ration.

This study was conducted to evaluate the effect of substitution of soybean meal (SBM) for formaldehyde-treated sesame meal (FTSM) on nutrient intake and digestibility, ruminal and blood parameters and milk production and composition in lactating Murciano-Granadina goats. Forty lactating goats were randomly assigned to one of the following four treatments: (1) diet with 16.5% CP, containing SBM (CON); (2) diet with 16.5% CP, containing untreated SM (USM); (3) diet with 16.5% CP, containing FTSM (FT); and (4) diet with 14.5% CP containing FTSM (LPFT). The results showed that nutrient intake was highest in the FT group ( p  < 0.001), while it was similar between the CON and LPFT groups, except for the intake of CP, which was higher in the CON group. The FT and LPFT had lower ruminal pH compared to CON and USM groups ( p  < 0.001), with goats in group FT having the highest volatile fatty acids (VFA) production ( p  < 0.001). The highest propionate concentration was observed in the LPFT treatment ( p  < 0.001), followed by the FT, CON, and USM treatments. Goats offered USM and LPFT treatments presented the highest and lowest acetate: propionate values, respectively, among the experimental groups ( p  < 0.001). The results also showed that LPFT goats had the lowest blood urea nitrogen (BUN) level ( p  = 0.004), while FT goats presented a lower non-esterified FA (NEFA) level compared with CON and LPFT goats ( p  = 0.01). Goats offered the FT diet had the highest milk yield ( p  = 0.002) and energy-corrected milk yield ( p  < 0.001) among all dietary groups. The highest milk fat ( p  < 0.001), protein ( p  = 0.001), lactose ( p  = 0.007), total solids ( p  = 0.003), and solids-not-fat (SNF) ( p  = 0.003) contents were observed in FT goats, which didn't differ from USM goats. The inclusion of formaldehyde-treated SM increased the percentage of C18:3 ( p  < 0.001) and C20:1 ( p  = 0.04) FAs compared with USM and CON treatments. Milk from USM, FT, and LPFT goats had lower levels of saturated ( p  < 0.001) and medium-chain FAs ( p  = 0.014) compared with CON goats, whereas milk from CON goats had lower levels of unsaturated, monounsaturated, and long-chain FAs compared to other groups ( p  < 0.001). The lowest and the highest concentrations of polyunsaturated FAs were observed in CON and LPFT goats, respectively ( p  = 0.001). It can be concluded that SBM can be advantageously replaced by formaldehyde-treated SM in the diet as a feasible alternative to improve feed intake and production performance of dairy goats.

Background: In this study, we aimed to investigate functional mechanisms underlying coronary artery disease (CAD) loci and find molecular biomarkers for CAD., Methods: We devised a multiomics data analysis approach based on Mendelian randomization and utilized it to search for molecular biomarkers causally associated with the risk of CAD within genomic regions known to be associated with CAD., Results: Through our CAD-centered multiomics data analysis approach, we identified 33 molecular biomarkers (probes) that were causally associated with the risk of CAD. The majority of these (N=19) were methylation probes; moreover, methylation was often behind the causal effect of expression/protein probes. We identified a number of novel loci that have a causal impact on CAD including C5orf38 , SF3A3 , DHX36 , and MRPL33 . Furthermore, by integrating the risk factors of CAD in our analysis, we were able to investigate the clinical pathways whereby several of our probes exert their effect. We found that the SELE protein level in the blood is under the trans-regulatory impact of methylation sites within the ABO gene and that SELE exerts its effect on CAD through immune, glycemic, and lipid metabolism, making it a candidate of interest for therapeutic interventions. We found the methylation site, cg05126514 within the BSN gene exert its effect on CAD through central nervous system-lifestyle risk factors. Finally, genes with a transcriptional regulatory role ( SF3A3 , ILF3 , and N4BP2L2 ) exert their effect on CAD through height., Conclusions: We demonstrate that multiomics data analysis is a powerful approach to unravel the functional mechanisms underlying CAD loci and to identify novel molecular biomarkers. Our results indicate epigenetic modifications are important in the pathogenesis of CAD and identifying and targeting these sites is of potential therapeutic interest to address the detrimental effects of both environmental and genetic factors.

Background: The industrial de-hulling of fresh pistachio generates a large quantity of pistachio by-products (PBP). The present study aimed to investigate the effects of treating soybean meal (SBM) and canola meal (CM) with tannin extracts derived from PBP on the protein fractions according to the Cornell Net Carbohydrates and Protein System (CNCPS), rumen degradability, and ruminal and post-ruminal crude protein (CP) disappearance in an in situ trials using three fistulated steers. The extracts of PBP were obtained via different solvents and then added to SBM and CM, so that the final concentrations of added tannins were 0, 5 and 10 g kg -1 dry matter., Results: The CNCPS soluble proteins (fractions A + B 1 ) of CP and B 1 fraction of CP were lower (P < 0.01) in SBM and CM treated with PBP extracts than untreated meals. Treating SBM with different PBP extracts (except 5 g kg -1 tannin water extract) and CM with 5 g kg -1 tannin water extract and 10 g kg -1 tannin ethanol extract decreased (P < 0.01) ruminal disappearance of CP. From the in situ results, the rapidly degradable fraction (a) of CP decreased (P < 0.01) by treating SBM with different PBP extracts and CM with 5 and 10 g kg -1 tannin water extracts, whereas the slowly degradable fraction (b) of CP remained unchanged in SBM. Treatment of SBM and CM with PBP extracts decreased (P < 0.01) the effective degradability of crude protein estimated with different outflow rates., Conclusion: Some of the tannin extracts derived from PBP by water, ethanol and methanol could be effective with respect to protein protection of SBM and CM from degradation in the rumen; however, the use of tannin from water extracts can be more economical and practical. © 2020 Society of Chemical Industry., (© 2020 Society of Chemical Industry.)

We report the genome sequence of Sporanaerobacter acetigenes strain F-12, isolated from the rumen of a steer grazing on Rhodes grass in Townsville (Lansdown Research Station), Queensland, Australia. This draft genome consists of 2,866,191 bp, with 31.23% G+C content and 2,889 predicted coding sequences., (Copyright © 2019 Kang et al.)

Heritability is a fundamental parameter in genetics. Traditional estimates based on family or twin studies can be biased due to shared environmental or non-additive genetic variance. Alternatively, those based on genotyped or imputed variants typically underestimate narrow-sense heritability contributed by rare or otherwise poorly tagged causal variants. Identical-by-descent (IBD) segments of the genome share all variants between pairs of chromosomes except new mutations that have arisen since the last common ancestor. Therefore, relating phenotypic similarity to degree of IBD sharing among classically unrelated individuals is an appealing approach to estimating the near full additive genetic variance while possibly avoiding biases that can occur when modeling close relatives. We applied an IBD-based approach (GREML-IBD) to estimate heritability in unrelated individuals using phenotypic simulation with thousands of whole-genome sequences across a range of stratification, polygenicity levels, and the minor allele frequencies of causal variants (CVs). In simulations, the IBD-based approach produced unbiased heritability estimates, even when CVs were extremely rare, although precision was low. However, population stratification and non-genetic familial environmental effects shared across generations led to strong biases in IBD-based heritability. We used data on two traits in ~120,000 people from the UK Biobank to demonstrate that, depending on the trait and possible confounding environmental effects, GREML-IBD can be applied to very large genetic datasets to infer the contribution of very rare variants lost using other methods. However, we observed apparent biases in these real data, suggesting that more work may be required to understand and mitigate factors that influence IBD-based heritability estimates.

Multiple methods have been developed to estimate narrow-sense heritability, h 2 , using single nucleotide polymorphisms (SNPs) in unrelated individuals. However, a comprehensive evaluation of these methods has not yet been performed, leading to confusion and discrepancy in the literature. We present the most thorough and realistic comparison of these methods to date. We used thousands of real whole-genome sequences to simulate phenotypes under varying genetic architectures and confounding variables, and we used array, imputed, or whole genome sequence SNPs to obtain 'SNP-heritability' estimates. We show that SNP-heritability can be highly sensitive to assumptions about the frequencies, effect sizes, and levels of linkage disequilibrium of underlying causal variants, but that methods that bin SNPs according to minor allele frequency and linkage disequilibrium are less sensitive to these assumptions across a wide range of genetic architectures and possible confounding factors. These findings provide guidance for best practices and proper interpretation of published estimates.

Asaluyeh is one of the most heavily industrialised areas in the world where gas, petrochemical, and many downstream industries are located. This study aims to survey the biomonitoring of four metals and one metalloid in children living in the vicinity of Asaluyeh area. To do this, we analysed the creatinine-adjusted urinary levels of arsenic (As), cadmium (Cd), vanadium (V), manganese (Mn), and nickel (Ni) in 184 elementary schoolchildren (99 boys and 85 girls) living in Asaluyeh and compared them with a reference population. The comparisons were done for two seasons (spring and fall). The results showed that in the case area (Asaluyeh), the levels of As, V, Mn, and Ni were significantly higher and that of Cd was not significantly higher than the reference city for both seasons. The mean concentration of metal(loid)s in Asaluyeh (case) and Sadabad (reference) area as μg g -1 creatinine was As 2.90 and 2.24, V 0.06 and 0.03, Mn 0.28 and 0.25, Ni 0.54 and 0.29, and Cd 0.31 and 0.28 in spring and As 3.08 and 2.28, V 0.07 and 0.03, Mn 0.30 and 0.26, Ni 0.91 and 0.30, and Cd 0.36 and 0.31 in the fall. Seasonal variations played a key role in determining urinary metal(loid) concentration, as we saw the significant level of As, Cd, V, and Ni in fall than in spring. With regard to the impact of gender on the absorption and accumulation of urinary metal(loid)s, boys showed higher levels of the studied elements, especially for As, than girls as outdoor activities are more popular among boys. Due to the values being lower than those reported in literature, more research is needed on various population groups and other exposure sources in order to judge whether living in the vicinity of the gas and petrochemical industries in Asaluyeh is a threat to nearby residents.

This study was conducted to evaluate the effect of feeding ensiled alfalfa with waste date on ruminal fermentation characteristics, microbial protein synthesis, protozoa population and blood parameters in sheep. Eight rams were used in a 2 × 2 change over design. Each experimental period consisted of 21 days including 16 days for adaptation and 5 days for sampling. For ensiling, fresh alfalfa (Medicago sativa L.) with different levels of waste date (Phoenix dactylifera L.) were mixed together and ensiled in 100-l containers for 45 days. Chemical composition of silages such as dry matter (DM), crude protein, NH 3 -N, organic matter, NDF, ADF and pH were determined. Then, it was used as 30% (DM basis) in diets. The experimental diets were as follows: (i) control (diet containing alfalfa silage without waste date), (ii) diet containing alfalfa silage with 5 g waste date/95 g DM, (iii) diet containing alfalfa silage with 10 g waste date/90 g DM, and (iv) diet containing alfalfa silage with 15 g waste date/85 g DM. The results of this experiment showed that adding waste date to alfalfa during ensiling, improved silage quality, DM and energy level. Total protozoa population and all of holotrich, cellulolytic and entodinia in rumen fluid were increased linearly by increasing the level of waste date. Nitrogen (N) intake, urinary N excretion and nitrogen retention were affected by dietary treatments. Also, allantoin, uric acid, total purine derivatives, microbial protein synthesis, cholesterol level and blood urea nitrogen were significantly different. In conclusion, direct ensilage of alfalfa can be attained by mixing 15 g waste date/85 g DM and positive associative effects such as increased metabolizable energy (ME) and silage quality occurred., (Journal of Animal Physiology and Animal Nutrition © 2016 Blackwell Verlag GmbH.)

This study was conducted to evaluate the effects of increasing levels of wasted date (WD) in sheep (initial body weight 50 ± 2.3 kg) diets on apparent diet digestibility, rumen fermentation and microbial protein synthesis. The experimental diets contained 0 (0 WD), 9% (9 WD), 18% (18 WD) or 27% (27 WD) of wasted dates. These diets were evaluated through a 4 × 4 Latin square design with four 28-day periods. Sheep were individually housed in metabolic cages and were fed diets ad libitum. To keep the diets isoenergetic and isonitrogenous, increasing partial replacement of WD for barley grain was used with increasing levels of soya bean meal. Increasing the amount of WD in diets of sheep did not influence (p > 0.05) diet intake and digestibility of nutrients. Inclusion of WD in diets of sheep did not affect (p > 0.05) ruminal pH but decreased (p < 0.05) NH 3 -N concentration and blood urea nitrogen. Also there was no effect (p > 0.05) of the WD provision on N intake and faecal N loss of experimental animals, but urinary nitrogen excretion and retained nitrogen were affected (p < 0.05) by dietary treatments. Purine derivatives and microbial protein synthesis increased (p < 0.05) linearly with the level of WD in the diet. In conclusion, the increase in microbial protein synthesis and concomitant reduction in ruminal NH 3 -N concentration and blood urea nitrogen in response to wasted date supply suggest improved efficiency of ruminal nitrogen metabolism without adverse effects on fermentation characteristics and animal performance., (Journal of Animal Physiology and Animal Nutrition © 2016 Blackwell Verlag GmbH.)

Motivation: Computer simulations are excellent tools for understanding the evolutionary and genetic consequences of complex processes that cannot be analytically predicted and for creating realistic genetic data. There are many software packages that simulate genetic data, but they are typically not fast or memory efficient enough to simulate realistic, individual-level genome-wide SNP/sequence data., Results: GeneEvolve is a user-friendly and efficient population genetics simulator that handles complex evolutionary and life history scenarios and generates individual-level phenotypes and realistic whole-genome sequence or SNP data. GeneEvolve runs forward-in-time, which allows it to provide a wide range of scenarios for mating systems, selection, population size and structure, migration, recombination and environmental effects. The software is designed to use as input data from real or previously simulated phased haplotypes, allowing it to mimic very closely the properties of real genomic data., Availability and Implementation: GeneEvolve is freely available at https://github.com/rtahmasbi/GeneEvolve CONTACT: Rasool.Tahmasbi@Colorado.eduSupplementary information: Supplementary data are available at Bioinformatics online., (© The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)

Background: Vitiligo is an acquired idiopathic hypomelanotic disorder characterized by circumscribed depigmented macules resulting from the loss of cutaneous melanocytes., Objective: In order to evaluate the immune system of Iranian patients with vitiligo, this study was accomplished., Methods: Fifty-five Iranian patients with vitiligo and 60 healthy persons as control were investigated in this study. The laboratory techniques were included: antimelanocyte antibody (AMA) and antinuclear antibody (ANA) with indirect immunoflorescent test, C3 and C4 levels with single radial immunodiffusion (SRID), and rheumatoid factor (RF) with enzyme-linked immunosorbent assay (ELISA)., Results: AMA was positive in 17 patients (30.9%) and was negative in the entire control group (P < 0.0001). ANA was positive in 4 patients (7.3%), which was insignificantly higher than control group (1.7%). IgM-RF was positive in 6 patients (10.8%) while it was negative in the entire control group (P = 0.027). C3 and C4 values decreased in 14 patients (25.5%), which was significantly higher than control group (P < 0.001)., Conclusion: The important role of the immune system in the pathogenesis of vitiligo could be suggested. In addition, the autoimmune hypothesis of vitiligo could be confirmed based on the results of this study.