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Background: Increasing studies have demonstrated potential disproportionate functional and ecological contributions of rare taxa in a microbial community. However, the study of the microbial rare biosphere is hampered by their inherent scarcity and the deficiency of currently available techniques. Sample-wise cross contaminations might be introduced by sample index misassignment in the most widely used metabarcoding amplicon sequencing approach. Although downstream bioinformatic quality control and clustering or denoising algorithms could remove sequencing errors and non-biological artifact reads, no algorithm could eliminate high quality reads from sample-wise cross contaminations introduced by index misassignment, making it difficult to distinguish between bona fide rare taxa and potential false positives in metabarcoding studies. Results: We thoroughly evaluated the rate of index misassignment of the widely used NovaSeq 6000 and DNBSEQ-G400 sequencing platforms using both commercial and customized mock communities, and observed significant lower (0.08% vs. 5.68%) fraction of potential false positive reads for DNBSEQ-G400 as compared to NovaSeq 6000. Significant batch effects could be caused by stochastically introduced false positive or false negative rare taxa. These false detections could also lead to inflated alpha diversity of relatively simple microbial communities and underestimated that of complex ones. Further test using a set of cow rumen samples reported differential rare taxa by different sequencing platforms. Correlation analysis of the rare taxa detected by each sequencing platform demonstrated that the rare taxa identified by DNBSEQ-G400 platform had a much higher possibility to be correlated with the physiochemical properties of rumen fluid as compared to NovaSeq 6000 platform. Community assembly mechanism and microbial network correlation analysis indicated that false positive or negative rare taxa detection could lead to biased community assembly mechanism and identification of fake keystone species of the community. Conclusions: We highly suggest proper positive/negative/blank controls, technical replicate settings, and proper sequencing platform selection in future amplicon studies, especially when the microbial rare biosphere would be focused. [ABSTRACT FROM AUTHOR]

Microbial ureases catalyze the hydrolysis of urea to ammonia, and inhibition of these enzymes in rumen has the potential to improve urea utilization efficiency and reduce urinary nitrogen excretion. Urease activity is catalyzed by a protein complex encoded by a gene cluster, and its accessory proteins (especially UreE and UreG) play important roles in transferring nickel to the active site for urease maturation. In this study, a predominant urease gene cluster (5290 bp) from the ruminal microbial metagenome was identified. Isothermal titration calorimetry (ITC) and analytical ultracentrifugation (AUC) analyses showed that the reaction of identified UreE with UreG was endothermic, and was dominated by a hydrophobic interaction, in which each UreE dimer bound 2 M equivalents of UreG monomer to form a UreE 2 -2UreG complex. Mutagenesis analyses showed that the UreG residues Glu-23, Asp-41, Glu-46, Glu-66, Cys-70, His-72, Asp-78, and Asp-118 were involved in the GTPase activity of UreG. Furthermore, variants of Cys-70 and His-72 involved in CPH motif of UreG, as well as the nearby Glu-66 and Asp-78, not only prevented interactions with UreE, but also prevented nickel binding. These data provide additional information regarding UreG residues that may be targeted for the design of new urease inhibitors. Unlabelled Image • Identification of a predominant urease gene cluster of an uncultured ruminal bacterium • Characteristic interactions of UreE and UreG from a rumen microorganism • Identification of critical residues in UreG [ABSTRACT FROM AUTHOR]

Abstract In cow mammary epithelial cells (CMECs), cell growth and casein synthesis are regulated by amino acids (AAs), and lysosomes are important organelles in this regulatory process, but the mechanisms remain unclear. Herein, lysosomal membrane proteins (LMPs) in CMECs in the presence (Leu+) and absence (Leu-) of leucine were quantitatively analysed using Sequential Windowed Acquisition of All Theoretical Fragment Ion (SWATH) mass spectrometry. In identified LMPs, Guanine nucleotide-binding protein subunit gamma-12 (GNG12) was a markedly up-regulated protein in Leu+ group. CMECs were treated with Leu+ or Leu−, expression and lysosomal localization of GNG12 were decreased in response to Leu absence. Overexpressing or inhibiting GNG12 demonstrated that cell growth, casein synthesis and activation of the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway were all up-regulated by GNG12. Cell growth, casein synthesis and mTORC1 signaling pathway were decreased in response to Leu absence, but these decreases were partially restored by GNG12 overexpression, and those effects were partially reversed by inhibiting GNG12. Co-immunoprecipitation analysis showed that GNG12 activates the mTORC1 pathway via interaction with Ragulator. Taken together, these results suggest that GNG12 is a positive regulator of the Leu-mediated mTORC1 signaling pathway in CMECs that promotes cell growth and casein synthesis. Highlights • GNG12 controls leucine mediated-cell growth and casein synthesis. • GNG12 controls leucine mediated-mTORC1 pathway. • GNG12 interacts with Ragulator. • GNG12 controls cell growth and casein synthesis though mTORC1 pathway. [ABSTRACT FROM AUTHOR]

The purpose of this study was to evaluate steam explosion as a pretreatment to enhance degradation of corn stover by ruminal microbiome. The steam explosion conditions were first optimized, and then the efficacy of steam explosion was evaluated both in vitro and in vivo . Steam explosion altered the physical and chemical structure of corn stover as revealed by scanning electron microscopy (SEM) and Fourier-transform infrared (FTIR) spectroscopy, respectively, and increased its cellulose content while decreasing hemicellulose content. Steam-exploded corn stover also increased release of reducing sugars, rate of fermentation, and production of volatile fatty acids (VFAs) in vitro . The steam explosion treatment increased microbial colonization and in situ degradation of cellulose and hemicellulose of corn stover in the rumen of dairy cows. Steam explosion may be a useful pretreatment of corn stover to improve its nutritional value as forage for cattle, or as feedstock for biofuel production. [ABSTRACT FROM AUTHOR]

Heat stress (HS) negatively affects various industries that rely on animal husbandry, particularly the dairy industry. A better understanding of metabolic responses in HS dairy cows is necessary to elucidate the physiological mechanisms of HS and offer a new perspective for future research. In this paper, we review the current knowledge of responses of body metabolism (lipid, carbohydrate, and protein), endocrine profiles, and bovine mammary epithelial cells during HS. Furthermore, we summarize the metabolomics and proteomics data that have revealed the metabolite profiles and differentially expressed proteins that are a feature of HS in dairy cows. Analysis of metabolic changes and 'omics' data demonstrated that HS is characterized by reduced lipolysis, increased glycolysis, and catabolism of amino acids in dairy cows. Here, analysis of the impairment of immune function during HS and of the inflammation that arises after long-term HS might suggest new strategies to ameliorate the effects of HS in dairy production. [ABSTRACT FROM AUTHOR]

Analysis of the full-length 18S rRNA gene sequences of rumen ciliates is more reliable for taxonomical classification and diversity assessment than the analysis of partial hypervariable regions only. The objective of this study was to develop new oligonucleotide primers targeting the full-length 18S rRNA genes of rumen ciliates, and to evaluate the effect of different sources of dietary fiber (corn stover or a mixture of alfalfa hay and corn silage) and protein (mixed rapeseed, cottonseed, and/or soybean meals) on rumen ciliate diversity in dairy cows. Primers were designed based on a total of 137 previously reported ciliate 18S rRNA gene sequences. The 3′-terminal sequences of the newly designed primers, P.1747r_2, P.324f, and P.1651r, demonstrated >99 % base coverage. Primer pair D (P.324f and P.1747r_2) was selected for the cloning and sequencing of ciliate 18S rRNA genes because it produced a 1423-bp amplicon, and did not amply the sequences of other eukaryotic species, such as yeast. The optimal species-level cutoff value for distinguishing between the operational taxonomic units of different ciliate species was 0.015. The phylogenetic analysis of full-length ciliate 18S rRNA gene sequences showed that distinct ciliate profiles were induced by the different sources of dietary fiber and protein. Dasytricha and Entodinium were the predominant genera in the ruminal fluid of dairy cattle, and Dasytricha was significantly more abundant in cows fed with corn stover than in cows fed with alfalfa hay and corn silage. [ABSTRACT FROM AUTHOR]

Abstract: Beta-2-microglobulin (β2m) is an integral component of the Fc receptor (FcRn) heterodimer which is involved in IgG transfer across mammary epithelial cells. The aim of this study was to estimate the frequency of alleles of β2m and the association of SNPs genotypes as well as haplotypes with milk IgG1 concentration and mass. Blood DNA from 189 Chinese Holstein dairy cows was extracted, sequenced and genotyping was analyzed. Milk IgG1 concentrations from these cows were determined by ELISA and evaluated with respect to their β2m genotypes. The results showed that two single nucleotide polymorphisms (SNPs) and one insertion/deletion (indel) of two base pairs, assorted into four haplotypes, were identified. The genotypes and haplotypes of β2m were found to be correlated (P <0.05) with milk IgG1 concentration and mass. Dairy cows with homozygous deletion of β2m had the lowest milk IgG1 concentration and mass. These results indicate that β2m genotypes could serve as a marker to identify dairy cows with high IgG1 milk levels. [Copyright &y& Elsevier]

The maximum gasification rate of corn stalk char (CSC) appeared at high conversion range, and its quite different gasification behaviors from other carbonaceous materials are all derived from the catalytic effect of alkali and alkali earth metals (AAEMs), so it is necessary to study the effect of AAEMs and gasification kinetics of such biomass char. However, there are few systematic discussions about this effect and kinetic modeling. Thus, in this study, CSC samples were prepared in a fast pyrolysis fixed-bed reactor, and its gasification experiments were conducted on a pressurized magnetic suspension balance at various total pressures (0.1–0.7 MPa), steam concentrations (10–70 vol.%) and temperatures (725–900 °C). Moreover, a water-leached CSC (H2O-CSC) was also prepared to evaluate the impact of AAEMs on the gasification performance of CSC, and some well-known models were adopted to describe the gasification behaviors. On the basis of these results, the effect of primary AAEMs on the gasification behaviors of CSC and gasification kinetic modeling were obtained. Results showed total pressure had no obvious influence on the gasification rate of CSC, and the reaction order varied at 0.43–0.55 with respect to steam partial pressures. In addition, the modified random pore model (MRPM) and Langmuir–Hinshelwood (L-H) model were satisfactorily applied to predict the gasification behaviors of CSC. The catalytic effect of AAEMs on CSC gasification was weakened due to water-leaching treatment. A random pore model (RPM) could describe the gasification behavior of H2O-CSC well, followed by grain model (GM) and volumetric model (VM). [ABSTRACT FROM AUTHOR]

Altitude is the main external environmental pressure affecting the production performance of Tibetan sheep, and the adaptive evolution of many years has formed a certain response mechanism. However, there are few reports on the response of ruminal microbiota and host genomes of Tibetan sheep to high-altitude environments. Here, we conducted an integrated analysis of volatile fatty acids (VFAs), microbial diversity (16S rRNA), epithelial morphology, and epithelial transcriptome in the rumen of Tibetan sheep at different altitudes to understand the changes in ruminal microbiota–host interaction in response to high altitude. The differences in the nutritional quality of forage at different altitudes, especially the differences in fiber content (ADF/NDF), led to changes in rumen VFAs of Tibetan sheep, in which the A/P value (acetic acid/propionic acid) was significantly decreased (p < 0.05). In addition, the concentrations of IgA and IgG in Middle-altitude (MA) and High-altitude Tibetan sheep (HA) were significantly increased (p < 0.05), while the concentrations of IgM were significantly increased in MA (p < 0.05). Morphological results showed that the width of the rumen papilla and the thickness of the basal layer increased significantly in HA Tibetan sheep (p < 0.05). The 16S rRNA analysis found that the rumen microbial diversity of Tibetan sheep gradually decreased with increasing altitude, and there were some differences in phylum- and genus-level microbes at the three altitudes. RDA analysis found that the abundance of the Rikenellaceae RC9 gut group and the Ruminococcaceae NK4A214 group increased with altitudes. Furthermore, a functional analysis of the KEGG microbial database found the "lipid metabolism" function of HA Tibetan sheep to be significantly enriched. WGCNA revealed that five gene modules were enriched in "energy production and conversion", "lipid transport and metabolism", and "defense mechanisms", and cooperated with microbiota to regulate rumen fermentation and epithelial immune barrier function, so as to improve the metabolism and immune level of Tibetan sheep at high altitude. [ABSTRACT FROM AUTHOR]

Simple Summary: Rumen microorganisms and their hosts have co-evolved over a long period of time, adapting to their environment. This co-evolution not only impacts the host phenotype but also establishes a sophisticated regulatory network with the host to uphold organismal homeostasis. This study's findings indicated that the process of three-way hybridization had a notable impact on the taxonomic characteristics, functions, and metabolites of rumen microbes. Moreover, significant interactions were observed between rumen microbes and metabolites in sheep, with biomarkers playing a significant role in influencing the variation in rumen metabolites. Meanwhile, rumen microbial markers in Hu sheep exhibited a predominantly positive correlation with down-regulated metabolites and a negative correlation with up-regulated metabolites. In contrast, rumen microbial markers in CAH lambs showed an overall negative correlation with down-regulated metabolites and a positive correlation with up-regulated metabolites. The data obtained in this study provide a basis for understanding hybridization advantages from microbial metabolic pathways. The objective of this experiment was to explore the effects of three-way hybridization on rumen microbes and metabolites in sheep using rumen metagenomics and metabolomics. Healthy Hu and CAH (Charolais × Australian White × Hu) male lambs of similar birth weight and age were selected for short-term fattening after intensive weaning to collect rumen fluid for sequencing. Rumen metagenomics diversity showed that Hu and CAH sheep were significantly segregated at the species, KEGG-enzyme, and CAZy-family levels. Moreover, the CAH significantly increased the ACE and Chao1 indices. Further, correlation analysis of the abundance of the top 80 revealed that the microorganisms were interrelated at the species, KEGG-enzyme, and CAZy-family levels. Overall, the microbiome significantly affected metabolites of the top five pathways, with the strongest correlation found with succinic acid. Meanwhile, species-level microbial markers significantly affected rumen differential metabolites. In addition, rumen microbial markers in Hu sheep were overall positively correlated with down-regulated metabolites and negatively correlated with up-regulated metabolites. In contrast, rumen microbial markers in CAH lambs were overall negatively correlated with down-regulated metabolites and positively correlated with up-regulated metabolites. These results suggest that three-way crossbreeding significantly affects rumen microbial community and metabolite composition, and that significant interactions exist between rumen microbes and metabolites. [ABSTRACT FROM AUTHOR]

The Qinghai-Tibet Plateau is a valuable genetic resource pool, and the high-altitude adaptation of Tibetan pigs is a classic example of the adaptive evolution of domestic animals. Here, we report the presence of Darwinian positive selection signatures in Tibetan pigs (TBPs) using 348 genome-wide datasets (127 whole-genome sequence datasets (WGSs) and 221 whole-genome single-nucleotide polymorphism (SNP) chip datasets). We characterized a high-confidence list of genetic signatures related response to high-altitude adaptation in Tibetan pigs, including 4,598 candidate SNPs and 131 candidate genes. Functional annotation and enrichment analysis revealed that 131 candidate genes are related to multiple systems and organs in Tibetan pigs. Notably, eight of the top ten novel genes, RALB, NBEA, LIFR, CLEC17A, PRIM2, CDH7, GK5 and FAM83B, were highlighted and associated with improved adaptive heart functions in Tibetan pigs high-altitude adaptation. Moreover, genome-wide association analysis revealed that 29 SNPs were involved in 13 candidate genes associated with at least one adaptive trait. In particular, among the top ten candidate genes, CLEC17A is related to a reduction in hemoglobin (HGB) in Tibetan pigs. Overall, our study provides a robust SNP/gene list involving genetic adaptation for Tibetan pig high-altitude adaptation, and it will be a valuable resource for future Tibetan pig studies. [ABSTRACT FROM AUTHOR]

Simple Summary: Heat stress negatively impacts the health and milk production of dairy cows, and ruminal microbes play an important role in the animal's milk production. Understanding the link between heat stress and the ruminal microbiome could help to develop strategies to relieve the influence of heat stress by manipulating the ruminal microbial composition. We found that heat-stressed cows had decreased ruminal pH and acetate concentration, whereas the ruminal lactate concentration increased. Heat-stressed cows also had a significantly higher relative abundance of lactate producing bacteria (e.g., Streptococcus and unclassified Enterobacteriaceae), Ruminobacter, Treponema, and unclassified Bacteroidaceae, all of which utilize soluble carbohydrate as an energy source. The relative abundance of the acetate-producing bacterium Acetobacter decreased with heat stress treatment. Therefore, heat stress is associated with changes in ruminal bacterial composition and metabolites, with more lactate and less acetate-producing species in the population, which potentially negatively affects milk production. Heat stress negatively impacts the health and milk production of dairy cows, and ruminal microbial populations play an important role in dairy cattle's milk production. Currently there are no available studies that investigate heat stress-associated changes in the rumen microbiome of lactating dairy cattle. Improved understanding of the link between heat stress and the ruminal microbiome may be beneficial in developing strategies for relieving the influence of heat stress on ruminants by manipulating ruminal microbial composition. In this study, we investigated the ruminal bacterial composition and metabolites in heat stressed and non-heat stressed dairy cows. Eighteen lactating dairy cows were divided into two treatment groups, one with heat stress and one without heat stress. Dry matter intake was measured and rumen fluid from all cows in both groups was collected. The bacterial 16S rRNA genes in the ruminal fluid were sequenced, and the rumen pH and the lactate and acetate of the bacterial metabolites were quantified. Heat stress was associated with significantly decreased dry matter intake and milk production. Rumen pH and rumen acetate concentrations were significantly decreased in the heat stressed group, while ruminal lactate concentration increased. The influence of heat stress on the microbial bacterial community structure was minor. However, heat stress was associated with an increase in lactate producing bacteria (e.g., Streptococcus and unclassified Enterobacteriaceae), and with an increase in Ruminobacter, Treponema, and unclassified Bacteroidaceae, all of which utilize soluble carbohydrates as an energy source. The relative abundance of acetate-producing bacterium Acetobacter decreased during heat stress. We concluded that heat stress is associated with changes in ruminal bacterial composition and metabolites, with more lactate and less acetate-producing species in the population, which potentially negatively affects milk production. [ABSTRACT FROM AUTHOR]

Copy number variations (CNVs) critically influence individual genetic diversity and phenotypic traits. In this study, we employed whole-genome resequencing technology to conduct an in-depth analysis of 50 pigs from five local swine populations [Rongchang pig (RC), Wuzhishan pig (WZS), Tibetan pig (T), Yorkshire (YL) and Landrace (LR)], aiming to assess their genetic potential and explore their prospects in the field of animal model applications. We identified a total of 96,466 CNVs, which were subsequently integrated into 7112 non-redundant CNVRs, encompassing 1.3% of the swine genome. Functional enrichment analysis of the genes within these CNVRs revealed significant associations with sensory perception, energy metabolism, and neural-related pathways. Further selective scan analyses of the local pig breeds RC, T, WZS, along with YL and LR, uncovered that for the RC variety, the genes PLA2G10 and ABCA8 were found to be closely related to fat metabolism and cardiovascular health. In the T breed, the genes NCF2 and CSGALNACT1 were associated with immune response and connective tissue characteristics. As for the WZS breed, the genes PLIN4 and CPB2 were primarily linked to fat storage and anti-inflammatory responses. In summary, this research underscores the pivotal role of CNVs in fostering the diversity and adaptive evolution of pig breeds while also offering valuable insights for further exploration of the advantageous genetic traits inherent to China's local pig breeds. This facilitates the creation of experimental animal models tailored to the specific characteristics of these breeds, contributing to the advancement of livestock and biomedical research. [ABSTRACT FROM AUTHOR]

Simple Summary: Simple Summary: The rumen is the most important digestive organ of ruminants, and its rich microbial co−evolved with the host to play a crucial role in immunomodulation, defense, digestive metabolism, animal productivity, and meat quality control. It also forms a complex regulatory network with host genes and phenotypes that are involved in maintaining organismal homeostasis. In this study, we compared the differences in rumen microorganisms between crossbred progeny of sheep and Hu sheep, identified key biomarkers, and analyzed their relationship with rumen function. The results showed that microbial diversity was significantly higher in crossbred progeny, which was able to alter the microbial community structure to regulate rumen fermentation, promote carbon homeostasis, and enhance amino acid metabolism. In addition, there were significant correlations between biomarkers and key traits. Therefore, we suggest that there is a link between sheep rumen microbes and differential traits in crossbred progeny, which provides new insights for sheep trait improvement. This experiment was conducted to investigate the effect of three–way hybrid sheep and Hu sheep on serum indicators, rumen fermentation, rumen enzyme activity, and microorganisms in sheep. Healthy and similar birth weights from three groups (Hu, n = 11; Charolais × Australian White × Hu, CAH, n = 11; Charolais × Dorper × Hu, CDH, n = 11) were selected to be fed by the ewes until 45 days of age. Subsequently, they were weaned intensively and underwent short–term fattening for 3 months along with selected male lambs fed intensively. During this period, they were fed and watered ad libitum. Blood and rumen fluid were collected and analyzed for serum indicators and rumen fluid microorganisms, enzyme activity, and VFA, respectively, at the end of the fattening period. Compared with Hu lamb, the offspring of the three–way hybrid lamb showed significant improvements in body weight, serum lactate dehydrogenase, and creatinine content. However, there was no significant effect on serum immunity and antioxidant indices. In addition, the rumen fluid volatile fatty acid (VFA) molar concentration and microcrystalline cellulose and lipase content were significantly lower in the three–way hybrid lamb compared to Hu lamb, but β–glucosidase, amylase, pepsin, and VFA molar ratio were not significantly affected. Subsequently, 16S rRNA sequencing diversity analysis revealed that three–way hybrid lamb significantly increased rumen microbial ACE and Chao1 indices compared to Hu lamb. Meanwhile, the abundance of Verrucomicrobiota and Synergistota significantly increased at the phylum level. Correlation analysis showed that Prevotella had the highest proportion, while Rikenellaceae_RC9_gut_group correlated most closely with others genus. The microbial communities isovaleric acid molar concentration and proportion were strongly correlated. In addition, there were significant differences in correlations between microbial communities and isobutyric acid, butyric acid and valeric acid content, and their molar proportion, but they were not significantly correlated with digestive enzymes. From the functional enrichment analysis, it was found that hybrid progeny were mainly enriched in the pyruvate metabolism, microbial metabolism in diverse environments, carbon metabolism, and quorum sensing pathways. In contrast, the Hu sheep were primarily enriched in the cysteine and methionine, amino sugar and nucleotide sugar, and biosynthesis of secondary metabolite pathways. These results suggest that hybridization can play a role in regulating organismal metabolism and improve animal production performance by influencing the structure and characteristics of microbial communities. [ABSTRACT FROM AUTHOR]

Rumen microbial urease inhibitors have been proposed for regulating nitrogen emission and improving nitrogen utilization efficiency in ruminant livestock industry. However, studies on plant-derived natural inhibitors of rumen microbial urease are limited. Urease accessory protein UreG, plays a crucial role in facilitating urease maturation, is a new target for design of urease inhibitor. The objective of this study was to select the potential effective inhibitor of rumen microbial urease from major protoberberine alkaloids in Rhizoma Coptidis by targeting UreG. Our results showed that berberine chloride and epiberberine exerted superior inhibition potential than other alkaloids based on GTPase activity study of UreG. Berberine chloride inhibition of UreG was mixed type, while inhibition kinetics type of epiberberine was uncompetitive. Furthermore, epiberberine was found to be more effective than berberine chloride in inhibiting the combination of nickel towards UreG and inducing changes in the second structure of UreG. Molecular modeling provided the rational structural basis for the higher inhibition potential of epiberberine, amino acid residues in G1 motif and G3 motif of UreG formed interactions with D ring of berberine chloride, while interacted with A ring and D ring of epiberberine. We further demonstrated the efficacy of epiberberine in the ruminal microbial fermentation with low ammonia release and urea degradation. In conclusion, our study clearly indicates that epiberberine is a promising candidate as a safe and effective inhibitor of rumen microbial urease and provides an optimal strategy and suitable feed additive for regulating nitrogen excretion in ruminants in the future. Key points: • Epiberberine is the most effective inhibitor of rumen urease from Rhizoma Coptidis. • Urease accessory protein UreG is an effective target for design of urease inhibitor. • Epiberberine may be used as natural feed additive to reducing NH3 release in ruminants. [ABSTRACT FROM AUTHOR]

Simple Summary: In the context of large-scale production, it is necessary to improve ewes health status and reproductive performance to promote newborns survival rate and later fattening performance. Previous studies have indicated that phenolic acids could change the host rumen microflora and inhibit pathogenic bacteria to ensure rumen health and host body health. However, there are few studies on isochlorogenic acid (ICGA) in ruminants. Therefore, based on regulating the rumen environment of breeding ewes during the whole physiological period, the experiment was conducted to study the effects of ICGA on rumen fermentation, microbial diversity and immunity of ewes at estrus, pregnancy and lactation stages. The experimental data obtained showed that adding ICGA could regulate ewes rumen fermentation mode, optimize microbial flora of different physiological stages by increasing Bacteroidota relative abundance while reducing Firmicutes relative abundance, maintain rumen microbial homeostasis at the pregnancy stage, and increase ewes blood immuneglobulin content, thereby improving ewes health. The effects of isochlorogenic acid (ICGA) on ewes rumen environment, microbial diversity, and immunity at different physiological stages (estrus, pregnancy and lactation) were studied in this experiment. Twenty healthy female Hu lambs of 1.5 months with similar body weight (17.82 ± 0.98 kg) and body condition were selected and randomly divided into two groups: the control group (CON) and the ICGA group (ICGA). The lambs of CON were fed a basal diet, while the lambs of ICGA were supplemented with 0.1% ICGA based on the basal diet. Lambs rumen fermentation characteristics, microbial diversity and immunity at estrus, pregnancy, and lactation stages were determined and analyzed, respectively. The results showed that the rumen pH in CON increased first and then decreased as lambs grew (p < 0.05). However, it showed the opposite change in ICGA. The content of ammonia nitrogen (NH3-N) showed the highest at estrus stage in both groups, but it was significantly higher in ICGA than that in CON (p < 0.05). The Acetic acid/propionic acid (A/P) ratio at estrus stage and the volatile fatty acids (VFAs) at pregnancy stage in ICGA were significantly higher than those of the CON (p < 0.05). The 16S rDNA sequencing analysis showed that the Shannon, Chao 1 and ACE indexes of the ICGA were significantly higher than those of the CON both at estrus and lactation stages (p < 0.05), while they showed higher at the pregnancy stage in CON (p > 0.05). Principal component analysis (PCA) showed that there were significant differences in rumen microorganism structure between CON and ICGA at all physiological stages (p < 0.01). At the phylum level, compared with the CON, Firmicutes relative abundance of three physiological stages decreased (p > 0.05) while Bacteroidota increased (p > 0.05). The relative abundance of Synergistota at estrus stage and Patescibacteria at the lactation stage increased significantly too (p < 0.05). At the genus level, compared with the CON, the relative abundance of Prevotella at three stages showed the highest (p > 0.05), while the relative abundance of Succiniclasticum, unclassified_Selenomonadaceae and Rikenellaceae_RC9_gut_group showed different abundances at different physiological stages in ICGA. Compared with the CON, the lambs of the ICGA showed higher blood IgG, IgM, and TNF- α contents at three physiological stages and higher IL-6 contents at pregnancy stage (p < 0.05). Conclusion: Adding ICGA could regulate ewes rumen fermentation mode at different physiological stages by increasing rumen NH3-N at estrus, VFAs at pregnancy, and the ratio of A/P at lactation. It optimizes rumen microbial flora of different physiological stages by increasing Bacteroidota relative abundance while reducing Firmicutes relative abundance, maintaining rumen microbial homeostasis at pregnant stage, increasing the number of beneficial bacteria in later lactating and ewes blood immunoglobulins content at three physiological stages. [ABSTRACT FROM AUTHOR]

Rumen microbial urease inhibitors have been proposed for regulating nitrogen emission and improving nitrogen utilization efficiency in ruminant livestock industry. However, studies on plant-derived natural inhibitors of rumen microbial urease are limited. Urease accessory protein UreG, plays a crucial role in facilitating urease maturation, is a new target for design of urease inhibitor. The objective of this study was to select the potential effective inhibitor of rumen microbial urease from major protoberberine alkaloids in Rhizoma Coptidis by targeting UreG. Our results showed that berberine chloride and epiberberine exerted superior inhibition potential than other alkaloids based on GTPase activity study of UreG. Berberine chloride inhibition of UreG was mixed type, while inhibition kinetics type of epiberberine was uncompetitive. Furthermore, epiberberine was found to be more effective than berberine chloride in inhibiting the combination of nickel towards UreG and inducing changes in the second structure of UreG. Molecular modeling provided the rational structural basis for the higher inhibition potential of epiberberine, amino acid residues in G1 motif and G3 motif of UreG formed interactions with D ring of berberine chloride, while interacted with A ring and D ring of epiberberine. We further demonstrated the efficacy of epiberberine in the ruminal microbial fermentation with low ammonia release and urea degradation. In conclusion, our study clearly indicates that epiberberine is a promising candidate as a safe and effective inhibitor of rumen microbial urease and provides an optimal strategy and suitable feed additive for regulating nitrogen excretion in ruminants in the future. Key points: • Epiberberine is the most effective inhibitor of rumen urease from Rhizoma Coptidis. • Urease accessory protein UreG is an effective target for design of urease inhibitor. • Epiberberine may be used as natural feed additive to reducing NH3 release in ruminants. [ABSTRACT FROM AUTHOR]

Background: Specific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures. Results: We obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively. Conclusions: In conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources. [ABSTRACT FROM AUTHOR]

Plateau adaptation in animals involves genetic mechanisms as well as coevolutionary mechanisms of the microbiota and metabolome of the animal. Therefore, the characteristics of the rumen microbiome and metabolome, transcriptome, and serum metabolome of Tibetan sheep at different altitudes (4500 m, 3500 m, and 2500 m) were analyzed. The results showed that the rumen differential metabolites at 3500 m and 4500 m were mainly enriched in amino acid metabolism, lipid metabolism, and carbohydrate metabolism, and there was a significant correlation with microbiota. The differentially expressed genes and metabolites at middle and high altitudes were coenriched in asthma, arachidonic acid metabolism, and butanoate and propanoate metabolism. In addition, the serum differential metabolites at 3500 m and 4500 m were mainly enriched in amino acid metabolism, lipid metabolism, and metabolism of xenobiotics by cytochrome P450, and they were also related to microbiota. Further analysis revealed that rumen metabolites accounted for 7.65% of serum metabolites. These common metabolites were mainly enriched in metabolic pathways and were significantly correlated with host genes (p < 0.05). This study found that microbiota, metabolites, and epithelial genes were coenriched in pathways related to lipid metabolism, energy metabolism, and immune metabolism, which may be involved in the regulation of Tibetan sheep adaptation to plateau environmental changes. [ABSTRACT FROM AUTHOR]

Energy is a key factor regulated by the neuroendocrine system. The objective of this study was to compare growth performance, serum biochemical indices, carcass traits, meat quality, and nutrient composition of lambs fed restricted metabolizable energy (ME) intakes to mimic the seasonal changes of the natural grasslands of northwest China. Nineteen male Dorper × Small Tailed Han lambs were assigned to treatments, control (CON) fed at 1.0 MJ/W0.75 × d−1 throughout the 180 d study, and restricted ME (RES) fed by sequentially restricting ME every 30 d (0.56, 0.84, 1.0, 0.84, 0.56, and 0.28 MJ/W0.75 × d−1). Lambs were harvested at the end of the study. Lambs fed the CON diet demonstrated higher (P < 0.05) average daily gain (ADG) compared with RES-fed lambs (158.79 and 57.01 g/d, for CON and RES, respectively), although ADG were lower in each period with the last period being a negative ADG for RES-fed lambs resulting in a loss of body weight. Both treatments demonstrated lower ADG in the last 3 study periods compared with the first 2 periods, which may be explained by cold stress (<−3 °C) increasing the lamb’s energy requirement. Feeding lambs a restricted ME diet resulted in lower (P < 0.05) blood serum glucose, triglycerides, total protein, calcium, phosphorus, immunoglobulin G, immunoglobulin M, and immunoglobulin A concentrations compared with CON-fed lambs, but both treatments were similar (P > 0.05) for cholesterol and high-density lipoprotein-cholesterol. Feeding lambs a restricted ME diet increased (P < 0.05) meat pH, while reducing the cooked meat rate compared with CON-fed lambs. Thus, the carcass yield, rib eye muscle area, and shear force were lower (P < 0.05) for RES-fed lambs compared with CON-fed lambs. The meat water concentration was higher (P < 0.05), whereas the concentrations of dry matter, crude fat, crude protein, and carbohydrate were lower (P < 0.05) for lambs fed a RES ME diet compared to CON-fed lambs. These results demonstrate that sequentially restricting ME intake, as natural grasslands might experience during seasonal forage quality and quantity changes, resulted in a reduction of body weight because lambs were mobilizing body reserves as a source of ME. The reduction in concentrations of key serum nutrients, as well as carcass traits and meat composition, demonstrate the body is responding to the meet the lambs ME requirements, which has implications for both meat quality and the animal’s physiological functions. [ABSTRACT FROM AUTHOR]

Due to overgrazing, grasslands in northern China have been severely degraded since 1980s. Grassland biomass and plant populations decreased dramatically. Application of fertilizer is a common technique for pasture management in many countries, however, it has not been widely used on China grasslands. Nitrogen (N) is an important productivity driver in grassland ecosystems, but its transportation, allocation and utilization in temperate desert steppe remained unclear. In this study, a sequential nitrogen addition experiment was conducted on a farm in southwestern Jingtai County, Gansu Province, in the transition zone between Loess Plateau and Tengger Desert. Two different grassland plots with moderate grazing (MG) and heavy grazing (HG) were fenced in 2008. N (NH 4 NO 3 ) was applied at the rate of: 12.25 g N·m −2 , 24.5 g N·m −2 , 36.75 g N·m −2 and 49 g N·m −2 , respectively. To determine the amount and distribution of nitrogen applied to the grassland, the 15 N tracer technique was adopted. The results demonstrated that the recovery rates of 15 N ranged from 3.8% to 11.7% in the plants. The nitrogen recovery amount from both shoots and roots increased significantly ( P < 0.05), while the recovery rate decreased gradually with increasing nitrogen application. The 15 N recovery from shoots under HG was much less than from MG. In one growing season, only 18.2%–8.0% of labeled 15 N was derived from fertilizer, so soil nitrogen is still the main source absorbed and utilized by plants. As much as 50.4%–84.4% labeled 15 N remained in soil, which was evenly distributed throughout 0–20 cm soil layer, and significantly increased with nitrogen application rates. The nitrogen remained in the top soil (0–10 cm) pool was much less than that of 10–20 cm layer ( P < 0.05). The nitrogen loss amounts and rates were significantly different among N treatments, which indicated that there was an increasing trend in N loss with increasing N application rates. Loss/recovery analysis showed that 12.25 g N·m −2 was the recommended application rate. This work is expected to provide the lowest risk/return ratio and produce both economic and environmental benefits for the degraded grassland in Gansu and analogus regions in China. [ABSTRACT FROM AUTHOR]

The rumen is an important hallmark organ of ruminants and plays an important role in the metabolism and immune barrier of Tibetan sheep on the Plateau. However, there are few studies on rumen development and metabolism regulation in Tibetan sheep at different ages. Here, we comprehensively analyzed the immune function, fermentation function, rumen epithelial micromorphology and transcriptome profile of Tibetan sheep at different ages. The results showed that the concentration of IgG decreased and the concentration of IgM increased with age (p < 0.05), and the highest concentration of IgA was observed at 1.5 and 3.5 years of age. In terms of rumen fermentation characteristics, VFAs of 4-month-old lambs were the highest, followed by VFAs and NH3-N of Tibetan sheep at 3.5 years of age. Hematoxylin-eosin staining and transmission electron microscopy section examination of rumen epithelial tissue showed that the rumen papilla width increased with age (p < 0.001), the thickness of the stratum corneum decreased, the cells in the stratum corneum showed accelerated migration and the thickness of the rumen muscle layer increased (p < 0.001). Desmosomal junctions between the layers of rumen epithelium increased at 1.5 and 3.5 years old, forming a compact barrier structure, and the basal layer had more mitochondria involved in the regulation of energy metabolism. RNA-seq analysis revealed that a total of 1006 differentially expressed genes (DEGs) were identified at four ages. The DEGs of Tibetan sheep aged 4 months and 6 years were mainly enriched in the oxidation–reduction process and ISG15-protein conjugation pathway. The 1.5 and 3.5-year-olds were mainly enriched in skeletal muscle thin filament assembly, mesenchyme migration and the tight junction pathway. WGCNA showed that DEGs related to rumen microbiota metabolite VFAs and epithelial morphology were enriched in "Metabolism of xenobiotics by cytochrome P450, PPAR signaling pathway, Butanoate metabolism pathways" and participated in the regulation of rumen epithelial immune and fermentation metabolism functions of Tibetan sheep at different ages. This study systematically revealed the regulatory mechanism of rumen epithelial development and metabolism in the plateau adaptation of Tibetan sheep, providing a new approach for the study of plateau adaptation. [ABSTRACT FROM AUTHOR]

Simple Summary: Providing high-quality feed for animals to improve the quality of animal products and, therefore, meet the needs of the public is a focus of animal husbandry. As a high-altitude crop, quinoa has high and abundant nutritional value. In recent years, with the planting area increasing year by year in our country, feed development and utilization of quinoa seeds and by-products have increased. At present, few studies gave examined the optimal addition of quinoa seeds in livestock and poultry diets and, in particular, the effects of the dietary addition of quinoa seeds on the intestinal microorganisms and muscle fatty acids of Luhua chickens. Therefore, in this study, different proportions of quinoa seeds (raw grain) were added in the diets of Luhua chickens to analyze their effects on intestinal microbiota and muscle fatty acids. The results showed that the content of muscle docosahexaenoic acids (C22:6n3, DHA), unsaturated fatty acids (UFAs) and n-3 polyunsaturated fatty acids (n-3 PUFAs) was significantly increased by adding a certain proportion of quinoa seeds to the diet. The content of saturated fatty acids (SAFs) and the ratio of n-6/n-3 significantly decreased. The increase can effectively improve the cecal microbiota structure, regulate the intestinal environment and promote the body health of Luhua chickens. These data provide a theoretical basis for the scientific application of quinoa seeds in female Luhua chickens' feeding and fodder development. To study the effects of adding quinoa seed (raw grain) to the diet of the Luhua chicken on the cecal microorganism abundance and fatty acid composition of muscle, 120 49-day-old healthy female dewormed Luhua chickens (body weight 1476.21 ± 101.39 g) were randomly divided into 4 groups, with 3 replicates in each group and 10 chickens in each repetition. The control group (CK group) was fed a basal diet and the experimental groups were fed with 4% (Q4), 8% (Q8), and 12% (Q12) quinoa seed (raw grain) added to the basal diet for 75 days. After 121 days of age, the animals were slaughtered and the 16S rRNA characteristics of cecal flora, as well as composition and content of fatty acids in muscle, were determined and analyzed. The content of unsaturated fatty acids (UFAs), docosahexaenoic acid (C22:6n3; DHA) and n-3 polyunsaturated fatty acids (n-3 PUFAs) in the breast and leg muscles significantly increased in the experimental groups supplemented with quinoa seeds (p < 0.05). However, the content of saturated fatty acids (SAFs) and ratio of n-6/n-3 in breast muscle and leg muscle significantly decreased (p < 0.05). In addition, adding a certain percentage of quinoa seeds in the diet can also affect the community composition and content of microorganisms in the ceca of Luhua chickens. At the phylum level, the Proteobacteria, Actinobacteria, Synergistetes and Melainabacteria in experimental groups (Q4, Q8 and Q12) were significantly lower than those in the CK group (p < 0.05). At the genus level, Desulfovibrio, Synergistes, Olsenella, Parabacteroides, Mailhella, Sutterella and Ruminiclostridiu in group Q4 were significantly lower than those in group CK (p < 0.05) while Faecalibacterium in Q8 group, and Lawsonia and Faecalibacterium in Q12 group were significantly higher than those in the CK group (p < 0.05). Enrichment analysis of the microbial function showed that compared with the CK group, Metabolism and Enzyme Families were significantly enriched in the Q4 group (p < 0.05). Cellular Processes and Signaling were significantly enriched in the Q8 group (p < 0.05). The association analysis of fatty acids with microorganisms showed that the abundance of Faecalibacterium, Lawsonia and Meagmonas was significantly correlated with partial SFAs and UFAs (p < 0.05). In conclusion, adding quinoa seeds to diets significantly increased the content of muscle DHA, UFAs and n-3 PUFAs. The content of SAFs and the n-6/n-3 ratio were significantly reduced. Taken together, quinoa can effectively improve the cecal microbiota structure, inhibit the number of harmful bacteria and increase the number of beneficial bacteria, regulating the intestinal environment and promoting the body health of female Luhua chickens. [ABSTRACT FROM AUTHOR]

This study used oregano essential oil (EO), cobalt (Co) and synergistic of both of them additives instead of antibiotics to explore the effects of different additives on the corn silage fibre structure degradation, nutrient degradation rate and rumen fermentation characteristics of sheep. The additives used in the study as a product were provided by Ralco, Inc., USA. The Latin square experimental design was adopted with 5 treatments. The following treatments were fed through the rumen fistula: carrier (Car), carrier + EO, carrier + Co, carrier + EO + cobalt (EOC) and no additives as the control (CON). These treatments were fed to five sheep for five rounds at a dose of 80 mg/kg. At 48 h of degradation, the area of degraded corn leaf and husk reached 100%, SEM results showed that except for Car and CON treatment, there were obvious destroyed fibre structure differences under EO, Co and EOC treatment, showing total disappearance of leaf epidermal cells, palisade tissue and spongy tissue, especially under EOC. Under EOC treatment, DMD48 h, CPD48 h, NDFD48 h and ADFD48 h increased by 3.33%, 3.89%, 7.64% and 5.67%, respectively, compared with CON, while NDFD48 h and ADFD48 h increased by 4.70% and 6.05% under Co (p > 0.05). The NH3-N concentration in rumen fluid decreased by 19.36%, 27.20% and 19.48%, while the microbial protein (MCP) content increased by 6.32%, 4.29% and 5.97% (p > 0.05) under EO, Co and EOC treatments compared with CON at 48 h (p < 0.05). The total VFA concentration under EO, Co and EOC treatment was lower than CON at 6 and 48 h (p = 0.016, p = 0.022) and the propionate and acetate concentrations were higher under EOC treatment than CON at 48 h (p > 0.05). Feeding EOC increased the fibre structure degradation and nutrient degradation rate of corn silage and improved rumen fermentation in sheep, resulting in better effects than feeding EO or Co alone. This article revealed the significance of oregano essential oil synergistic with cobalt (EOC) on rumen fermentation characteristics and nutrient degradation rate of sheep. In this study, the degradation of leaves in the rumen was observed by scanning electron microscopy, and the degradation area was calculated by electron microscopy for the first time. The results of this study will provide the theoretical basis for EOC as a substitute for antibiotics. [ABSTRACT FROM AUTHOR]

The Tibetan pig is an endemic economic animal in the plateau region of China, and has a unique adaptation mechanism to the plateau hypoxic environment. Research into microRNAs (miRNAs) involved in the mechanism underlying hypoxia adaptation of Tibetan pig is very limited. Therefore, we isolated alveolar type II epithelial (ATII) cells from the lungs of the Tibetan pig, cultured them in normoxia/hypoxia (21% O2; 2% O2) for 48 h, and performed high-throughput sequencing analysis. We identified a hypoxic stress-related ssc-miR-141 and predicted its target genes. The target genes of ssc-miR-141 were mainly enriched in mitogen-activated protein kinase (MAPK), autophagy-animal, and Ras signaling pathways. Further, we confirmed that PDCD4 may serve as the target gene of ssc-miR-141. Real-time quantitative polymerase chain reaction (RT-qPCR) analysis was performed to confirm the expression levels of ssc-miR-141 and PDCD4, and a dual-luciferase gene reporter system was used to verify the targeted linkage of ssc-miR-141 to PDCD4. The results showed that the expression level of ssc-miR-141 in the hypoxia group was higher than that in the normoxia group, while the expression level of PDCD4 tended to show the opposite trend and significantly decreased under hypoxia. These findings suggest that ssc-miR-141 is associated with hypoxia adaptation and provide a new insight into the role of miRNAs from ATII cells of Tibetan pig in hypoxia adaptation. [ABSTRACT FROM AUTHOR]

Simple Summary: As a natural substitute for antibiotics, oregano essential oil is a feed additive drug approved by the Ministry of Agriculture, which can improve animal production and health. There are few reports on the combination of quinoa and oregano essential oil used in animal production for feed development and utilization. Therefore, the aim of this study was to analyze the effects of different proportions of oregano essential oil in a corn–quinoa–soybean meal diet on the intestinal microbiota and muscle fatty acids of Luhua chickens. The results showed that the addition of oregano essential oil to the corn–quinoa–soybean meal diet effectively improved the microbial community composition in the caecum of Luhua chickens, enriching the related pathways, so as to promote the digestion and absorption of nutrients and enhance intestinal barrier functioning. It significantly improved the content of some fatty acids in the muscles of Luhua chickens, and there was a certain correlation between cecal microorganisms and fatty acid deposition in muscles. These data provide a theoretical basis for the scientific application of oregano essential oil and quinoa in the feeding and fodder development of Luhua chickens. This experiment was conducted to investigate the effects of oregano essential oil on the cecal microorganisms and muscle fatty acids of Luhua chickens. One hundred and twenty 49-day-old healthy dewormed Luhua chickens were randomly divided into four groups with three replicates per group and ten chickens per replicate. The corn–quinoa and soybean meal diets were supplemented with 0 (Q8 group), 50 (QO50 group), 100 (QO100 group) and 150 mg·kg−1 (QO150 group) of oregano essential oil, respectively, and the experiment lasted for 75 days. The composition of intestinal flora was detected by Illumina sequencing of the 16S rRNA V4 region, and the composition and content of fatty acids in the muscles were analyzed by gas chromatography. The results showed that dietary oregano essential oil can effectively increase the contents of elaidic acid (C18:ln9t), polyunsaturated fatty acids (PUFAs) and n-3 polyunsaturated fatty acids (n-3 PUFAs) in breast muscle tissues. However, the fatty acid composition and PUFA content in leg muscle tissues were not significantly improved. According to a 16S rRNA high-throughput sequencing analysis, dietary oregano essential oil supplementation with a certain concentration can change the cecal microbial community composition of broilers. At the phylum level, Elusimicrobia in the QO150 group was significantly lower than that in Q8 group (p < 0.05). At the genus level, Phascolarctobacterium, Parasutterella and Bilophila in the experimental groups (QO50, QO100 and QO150) were significantly lower than those in the Q8 group (p < 0.05). An enrichment analysis of the microbial function found that the amino acid metabolism, energy metabolism, metabolism, signal transduction and genetic information processing were mainly enriched in the experimental groups, which promoted the digestion and absorption of nutrients and enhanced intestinal barrier functioning. An analysis of the association between fatty acids and microbes found that the abundance of microbiota was significantly correlated with partially saturated fatty acids (SFAs) and unsaturated fatty acids (UFAs) (p < 0.05). In conclusion, the dietary addition of oregano essential oil can effectively improve cecal microbial community composition, promote the digestion and absorption of nutrients, and enhance intestinal barrier functioning. It can significantly improve the content of some fatty acids, and there was a certain correlation between caecum microorganisms and fatty acid deposition in muscles. [ABSTRACT FROM AUTHOR]

Heat stress (HS) has an enormous economic impact on the dairy industry. In recent years, many researchers have investigated changes in the gene expression and metabolomics profiles in dairy cows caused by HS. However, the proteomics profiles of heat-stressed dairy cows have not yet been completely elucidated. We compared plasma proteomics from HS-free and heat-stressed dairy cows using an iTRAQ labeling approach. After the depletion of high abundant proteins in the plasma, 1472 proteins were identified. Of these, 85 proteins were differentially abundant in cows exposed to HS relative to HS-free. Database searches combined with GO and KEGG pathway enrichment analyses revealed that many components of the complement and coagulation cascades were altered in heat-stressed cows compared with HS-free cows. Of these, many factors in the complement system (including complement components C1, C3, C5, C6, C7, C8, and C9, complement factor B, and factor H) were down-regulated by HS, while components of the coagulation system (including coagulation factors, vitamin K-dependent proteins, and fibrinogens) were up-regulated by HS. In conclusion, our results indicate that HS decreases plasma levels of complement system proteins, suggesting that immune function is impaired in dairy cows exposed to HS. Biological significance Though many aspects of heat stress (HS) have been extensively researched, relatively little is known about the proteomics profile changes that occur during heat exposure. In this work, we employed a proteomics approach to investigate differential abundance of plasma proteins in HS-free and heat-stressed dairy cows. Database searches combined with GO and KEGG pathway enrichment analyses revealed that HS resulted in a decrease in complement components, suggesting that heat-stressed dairy cows have impaired immune function. In addition, through integrative analyses of proteomics and previous metabolomics, we showed enhanced glycolysis, lipid metabolic pathway shifts, and nitrogen repartitioning in dairy cows exposed to HS. Our findings expand our current knowledge on the effects of HS on plasma proteomics in dairy cows and offer a new perspective for future research. [ABSTRACT FROM AUTHOR]

Increased global use of highly productive commercial breeds has reduced genetic diversity in indigenous breeds. It is necessary to protect local porcine breeds. We therefore assessed the level of genetic diversity in global swine populations. In this study, the mitochondrial DNA D-loop region was examined in 1010 sequences from indigenous pigs and commercial swine as well as 3424 publicly available sequences We identified 334 haplotypes and 136 polymorphic sites. Genetic diversity was analyzed based on basic parameters, including haplotype diversity, nucleotide diversity and the average number of nucleotide differences, and also assessed by principal component analysis. A comparison of nucleotide diversity and the average number of nucleotide differences between indigenous breeds and commercial breeds showed that indigenous pigs had a lower level of diversity than commercial breeds. The principle component analysis result also showed the genetic diversity of the indigenous breeds was lower than that of commercial breeds. Collectively, our results reveal the Southeast Asian porcine population exhibited the higher nucleotide diversity, whereas Chinese population appeared consistently lower level in Asia. European, American and Oceanian pigs had a relatively higher degree of genetic diversity compared with that of Asian pigs. In conclusion, our findings indicated that the introgression of commercial into indigenous breeds decreased indigenous breeds' genetic diversity. [ABSTRACT FROM AUTHOR]

In this work we employed a comparative proteomic approach to evaluate seasonal heat stress and investigate proteomic alterations in plasma of dairy cows. Twelve lactating Holstein dairy cows were used and the treatments were: heat stress (n = 6) in hot summer (at the beginning of the moderate heat stress) and no heat stress (n = 6) in spring natural ambient environment, respectively. Subsequently, heat stress treatment lasted 23 days (at the end of the moderate heat stress) to investigate the alterations of plasma proteins, which might be employed as long-term moderate heat stress response in dairy cows. Changes in plasma proteins were analyzed by two-dimensional electrophoresis (2-DE) combined with mass spectrometry. Analysis of the properties of the identified proteins revealed that the alterations of plasma proteins were related to inflammation in long-term moderate heat stress. Furthermore, the increase in plasma tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) directly demonstrated that long-term moderate heat stress caused an inflammatory response in dairy cows. [ABSTRACT FROM AUTHOR]

• Dietary supplementation of isoflavone in cows enhances milk antioxidant capacity. • Milk from cows feeding red clover isoflavone improves antioxidant capacity of mice. • Changing animal diets is a natural and effective strategy for developing functional foods. Red clover (Trifolium pratense) isoflavone was supplemented to dairy cows, and antioxidant capacity of milk was assessed. Treated cows increased the activities of antioxidant enzymes, reduced production of oxidation products, and enhanced the concentrations of vitamin E and vitamin C. Moreover, milk fatty acid profile was positive influenced by 8 g/kg red clover isoflavone, with changes in the lower saturated and higher unsaturated fatty acids. We further demonstrated the efficacy of antioxidant capacity of milk in mice, found that milk from cows feeding red clover isoflavone increased the expressions of antioxidant enzymes, and alleviated lipopolysaccharide (LPS)-stimulated tissue damage of duodenum and jejunum, which was related to upregulated metabolism pathways of carbohydrate, lipid, and amino acid, as well as downregulated inflammatory related pathways. Together, dietary supplementation of red clover isoflavone is an effective way to improve milk antioxidant capacity, providing a natural strategy for developing functional foods. [ABSTRACT FROM AUTHOR]

Simple Summary: Few articles have reported the influence of whole and ground flaxseed intake on milk longer chain n-3 polyunsaturated fatty acid (PUFA) and the efficiency of diet α-linolenic acid (ALA) to convert to milk (milk ALA/ALA intake ratio). The objective of this experiment was to explore the effect of whole and ground flaxseed supplementation on the composition of n-3 polyunsaturated fatty acid (PUFA) in milk from dairy cows. This result indicated that whole and ground flaxseed supplementation can increase total n-3 PUFA. Compared with whole flaxseed, ground flaxseed supplementation showed higher content and yield of ALA in milk and milk ALA/ALA intake. The objective of this study was to determine the effect of whole flaxseed and ground flaxseed supplementation on the composition of fatty acids in plasma and milk, particularly the content of omega-3 polyunsaturated fatty acids (n-3 PUFAs). Thirty Holstein dairy cows were randomly assigned to three treatment groups. Cows were fed a total mixed ration without flaxseed (CK), 1500 g of whole flaxseed (WF), and 1500 g of ground flaxseed (GF) supplementation. There were no differences observed in dry matter intake, milk yield, energy-corrected milk, and 4% fat-corrected milk (p > 0.05). Compared with the CK group, the contents of α-linolenic acid (ALA), eicosatrienoic acid, and eicosapentaenoic acid increased in the plasma and milk WF and GF groups, and the content of docosahexaenoic acid and total n-3 PUFA was higher in GF than the other groups (p < 0.001). The ALA yield increased to 232% and 360% in WF and GF, respectively, compared to the CK group. Compared with the WF group, GF supplementation resulted in an increased milk ALA/ALA intake ratio (p < 0.001). Flaxseed supplementation increased the activity of GSH-Px and decreased the concentration of MDA in milk (p < 0.001). Plasma parameters did not differ among the treatments (p > 0.05). This result indicated that compared with the WF group, GF supplementation in the diet showed higher efficiency in increasing the total n-3 PUFA levels and the milk ALA/ALA intake ratio, and decreased the ratio of n-6 PUFAs to n-3 PUFAs in milk. [ABSTRACT FROM AUTHOR]

We compared the differences in testicular morphology and vascular anatomy between plateau‐type Tibetan sheep and low‐altitude Small‐tailed Han sheep to explore any adaptations of Tibetan sheep to high altitudes and hypoxia factors. Testicular artery architecture specimens of plateau‐type Tibetan sheep and lowland Small‐tailed Han sheep were used to compare the physical parameters of the testis, testicular artery architecture, arterial diameter, testicular leaflets and the characteristics of epididymal head arterioles. The results showed that the weight, major axis, minor axis, overall length, caput major axis and caput minor axis in Tibetan sheep were larger than those of Small‐tailed Han sheep; however, the caput major axis of epididymal head in Tibetan sheep was smaller than that of Small‐tailed Han sheep. Compared with Small‐tailed Han sheep, the testicular knot‐like arteries of Tibetan sheep had denser spiral distribution and more small arteries, and the diameters of centripetal arteries, knot‐like arteries, centrifugal arteries and epididymal microarterioles were also thicker. The 'spindle' indentation on the surface of the microarteriole of the head of the testicular leaflets and the epididymis in plateau Tibetan sheep was relatively shallow. The results showed that the physical testicular characteristics, testicular artery construction and arteriole surface structure of Tibetan sheep were adapted for the plateau environment. [ABSTRACT FROM AUTHOR]

Protein macroarray is a new, simple and multiple biochemistry detection system, in which the test spots are more than 1 mm diameter and results directly visible and instrumentation is not necessary. This technology, however, possesses recognized problems with spot quality and uniformity, issues that can limit its application. Previous methods have been developed for spot quality control, but they are complicated or require specific instrumentation. Therefore, we have developed a spot quality control buffer supplement with Ponceau S (SQCB-PS) as a direct and visible means of monitoring spot quality on nitrocellulose membrane prior to hybridization. In this report, 1% (w/v) Ponceau S and 10% (v/v) glycerol in spotting buffer were found to be optimal for spot quality control and food-borne pathogens multiple detection. Furthermore, the sensitivity and specificity of the protein macroarray were not compromised by spotting buffer with Ponceau S. Under optimal conditions, this visible spot quality control method makes the detection more reliable, and should enhance the wider use of the technique. [ABSTRACT FROM AUTHOR]

BACKGROUND Milk microRNA (miRNA) with bioactivity is beneficial for human health. However, the effect of heat treatment on miRNA in milk is still not clear. In this study, the miRNAs in raw (RM), pasteurized (PM) and ultra‐high‐temperature (UHT) milk (UM) from the same batch were extracted, sequenced and analyzed. RESULTS: The results showed that there was a significant difference in miRNAs between RM and UM, but not between RM and PM. The total read counts of milk miRNAs were significantly decreased by heat treatment, with the least counts in UM (P < 0.05). The average length and GC percentage of miRNAs were significantly reduced by heat treatment (P < 0.05), while there was no significant difference in these terms between RM and PM. The content of miRNAs was verified by qPCR, finding that miR‐17‐5p, miR‐25, miR‐27b and miR‐9‐5p were significantly reduced in UM (P < 0.05) but not significantly affected in PM (except miR‐27b). In addition, the targeting gene ontology enrichment functions of the different presented miRNAs were mostly enriched in biological process, cellular component and molecular function. The top 20 enriched miRNAs with different levels in heat‐treated milk were identified by the Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Interestingly, most of the functions of these miRNA targeting genes are involved in cancer or inflammation activity. CONCLUSION: This study revealed that the bioactive miRNA in RM was lost after UHT treatment but not in pasteurized treatment. © 2021 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Highlights: [•] HAP powders were synthesized by solid-state reaction at room temperature. [•] The morphology of HAP crystals was strongly dependant on the calcining temperature. [•] The obtained powders calcining at 600°C exhibit the morphology of platelets. [ABSTRACT FROM AUTHOR]

[Display omitted] • A ratiometric fluorescent probe for TBHQ detection based on NCPDs and AuNCs was first established. • The ratio of fluorescence intensity at 480 nm to 630 nm was monitored as analytical signal response. • The fluorescent color changed from red to orange red to green with the TBHQ concentration. • The method had high selectivity, sensitivity, wide linear range towards TBHQ assay. • The method had great application potential in the field of food safety monitoring and inspection. A novel ratiometric fluorescent probe based on non-conjugated polymer dots (NCPDs) and gold nanocluster (AuNCs) was constructed to determine tert -butylhydroquinone (TBHQ). The probe exhibited dual emission peaks at 480 nm and 630 nm under 370 nm excitation. The fluorescence of AuNCs was quenched by TBHQ due to strong electrostatic interactions, whereas the emission of NCPDs increased. The ratio of fluorescence intensity at 480 nm to 630 nm (F 480 / F 630) was monitored as analytical signal response. The probe have been utilized for the detection of TBHQ with good linear relationship in the range of 0.2 to 60 μg/mL. The limit of detection (LOD) and the limit of quantitation (LOQ) were 0.048 μg/mL and 0.159 μg/L, respectively. Three levels of spiked-in TBHQ concentrations were obtained with recovery rates from 80 % to 102 %. The present study provided an effective ratiometric fluorescence method for selective screening of TBHQ in food samples. [ABSTRACT FROM AUTHOR]

Background: Tibetan pigs have exhibited unique characteristics from low‐altitudes pigs and adapted well to the Qinghai‐Tibet Plateau. Objectives: The current study was undertaken to investigate the hypoxic adaptation of heart in Tibetan pigs. Methods: The hearts of Tibetan pigs and Landrace pigs raised at high or low altitudes were compared using 3D casting technology, scanning electron microscopy and real‐time quantitative PCR (qRT‐PCR). Results: We found that the ratio of the major axis to the minor axis and the density of the heart were significantly higher in Tibetan pigs than in Landrace pigs (p < 0.05). Tibetan pigs had larger diameters and higher densities of arterioles than Landrace pigs (p < 0.05), and these features have a similar variation with the expression of vascular endothelial growth factor (VEGF). The cardiac expression levels of hypoxia‐inducible factor‐1α (HIF‐1α) and endothelial nitric oxide synthase (eNOS) were significantly higher in pigs reared at high altitudes than in those reared at low altitudes (p < 0.05). In contrast, Egl nine homolog 1 (EGLN1) had the opposite trend with respect to HIF‐1α and eNOS and was related to red blood cell (RBC) counts. Notably, the expressions of erythropoietin (EPO) and endothelial PAS domain‐containing protein 1 (EPAS1) were significantly higher in Landrace pigs kept at high altitudes than in the others (p < 0.05) and were associated with haemoglobin. Conclusions: These findings show that the regulation of the heart function of Tibetan pigs in a hypoxic environment is manifested at various levels to ensure the circulation of blood under extreme environmental conditions. [ABSTRACT FROM AUTHOR]

Abstract: Bifunctional Fe3O4@MgSiO3 sub-microspheres with superparamagnetic property and high affinity toward metal ions were successfully synthesized via a solvothermal method using Fe3O4@SiO2 as a self-template, and well characterized by means of TEM, XRD, FT-IR, VSM and N2 adsorption isotherms. The as-prepared Fe3O4@MgSiO3 sub-microspheres were then assessed as the adsorbent for Pb2+ removal in water, and various factors influencing the adsorption of Pb2+ were investigated including pH, equilibrium time and initial metal ion concentration. The results indicated that Fe3O4@MgSiO3 sub-microspheres had a mean diameter of 220nm and high superparamagnetic cores, which endowed them with useful magnetic responsivity. Moreover, the large specific surface was beneficial for their strong affinity toward toxic metal ions. The pseudo-second-order equation could describe well the adsorption kinetics with correlation coefficients greater than 0.999. The maximum adsorption capacity for Pb2+ was calculated to be 242.1mg/g based on Langmuir model. Furthermore, the as-prepared Fe3O4@MgSiO3 showed an acceptable reusability using NaOH or Mg2+ solution as the desorbing agent. All information gives an indication that the as-prepared sub-microspheres show their potential as the adsorbent for highly efficient removal of heavy metal ions in wastewater. [Copyright &y& Elsevier]

Background: Yaks that inhabit the Tibetan Plateau exhibit striking phenotypic and physiological differences from cattle and have adapted well to the extreme conditions on the plateau. However, the mechanisms used by these animals for the regulation of gene expression at high altitude are not fully understood. Results: Here, we sequenced nine lung transcriptomes of yaks at altitudes of 3400, 4200 and 5000 m, and low-altitude Zaosheng cattle, which is a closely related species, served as controls. The analysis identified 21,764 mRNAs, 1377 circRNAs and 1209 miRNAs. By comparing yaks and cattle, 4975 mRNAs, 252 circRNAs and 75 miRNAs were identified differentially expressed. By comparing yaks at different altitudes, we identified 756 mRNAs, 64 circRNAs and 83 miRNAs that were differentially expressed (fold change ≥2 and P-value < 0.05). The pathways enriched in the mRNAs, circRNAs and miRNAs identified from the comparison of yaks and cattle were mainly associated with metabolism, including 'glycosaminoglycan degradation', 'pentose and glucuronate interconversions' and 'flavone and flavonol biosynthesis', and the mRNAs, circRNAs and miRNAs identified from the comparison of yaks at different altitude gradients were significantly enriched in metabolic pathways and immune and genetic information processing pathways. The core RNAs were identified from the mRNA-miRNA-circRNA networks constructed using the predominant differentially expressed RNAs. The core genes specific to the difference between yaks and cattle were associated with the endoplasmic reticulum and fat deposition, but those identified from the comparison among yaks at different altitude gradients were associated with maintenance of the normal biological functions of cells. Conclusions: This study enhances our understanding of the molecular mechanisms involved in hypoxic adaptation in yaks and might contribute to improvements in the understanding and prevention of hypoxia-related diseases. [ABSTRACT FROM AUTHOR]

Simple Summary: Natural flavor compounds can stimulate people's senses of smell and taste; as indicators of food sensory quality, such compounds influence the acceptance by consumers. In addition, natural antioxidants are becoming popular among consumers because they are safe and have no adverse side effects. Purple corn anthocyanins are polyphenolic compounds with natural antioxidant properties that exist widely in nature. Research has shown that anthocyanins can provide extra electrons to the free radicals, preventing lipid oxidation and improving muscle volatile components. However, no information is available concerning the effect of feeding anthocyanin on goat meat volatile compounds. This was the first study to investigate the effects of dietary anthocyanins from purple corn supplementation on lipid mechanism, body composition, volatile compound profiles, and related gene expression in the longissimus thoracis et lumborum muscle of goats. The current study indicates that the consumption of purple corn anthocyanin by growing goats improves mutton flavor by decreasing plasma lipid metabolism parameters and by modulating the abundance of several flavor-related genes in the longissimus thoracis et lumborum muscle. The results will help to understand the mechanism of action of anthocyanins on the flavor compounds, providing the rationale for anthocyanins regulating mutton flavor through related signaling pathways of ruminants in future studies. The current study aimed to investigate the effect of anthocyanins on muscle flavor compound profiles in goats. Goats in three groups were fed a basic diet or a diet supplemented with 0.5 g/d or 1 g/d anthocyanin-rich purple corn pigment (PCP). Compared to the control group, plasma total cholesterol was significantly decreased (p < 0.05) in the anthocyanin groups. The feeding of anthocyanin increased (p < 0.05) flavor compound types and total alcohol level, whereas it decreased (p < 0.05) total hydrocarbons, aromatics, esters, and miscellaneous compounds in the longissimusthoracis et lumborum muscle (LTL). Adding PCP to the diet enriched (p < 0.05) vegetal, herbaceous, grease, and fruity flavors compared to the control group. The 0.5 g/d PCP group had increased (p < 0.05) abundance of peroxisome proliferator-activated receptor gamma, but there was a decreased (p < 0.05) level of lipoprotein lipase in LTL. Collectively, this study indicated that anthocyanin can improve mutton flavor by decreasing plasma lipid parameters and by modulating the abundance of several flavor-related genes of goats. [ABSTRACT FROM AUTHOR]

Due to their long-term colonization of and widespread distribution in plateau environments, yaks can serve as an ideal natural animal model for the adaptive evolution of other plateau species, including humans. Some studies reported that the lung and heart are two key organs that show adaptive transcriptional changes in response to high altitudes, and most of the genes that show differential expression in lung tissue across different altitudes display nonlinear regulation. To explore the molecular mechanisms that are activated in yak lung tissue in response to hypoxia, the mRNAs, lncRNAs and miRNAs of lung tissue from 9 yaks living at three different altitudes (3400 m, 4200 m and 5000 m), with three repetitions per altitude, were sequenced. Two Zaosheng cattle from 1500 m were selected as low-altitude control. A total of 21,764 mRNAs, 14,168 lncRNAs and 1209 miRNAs (305 known and 904 novel miRNAs) were identified. In a comparison of yaks and cattle, 4975 mRNAs, 3326 lncRNAs and 75 miRNAs were differentially expressed. A total of 756 mRNAs, 346 lncRNAs and 83 miRNAs were found to be differentially expressed among yaks living at three different altitudes (fold change ≥ 2 and P-value < 0.05). The differentially expressed genes between yaks and cattle were functionally enriched in long-chain fatty acid metabolic process and protein processing, while the differentially expressed genes among yaks living at three different altitudes were enriched in immune response and the cell cycle. Furthermore, competing endogenous RNA (ceRNA) networks were investigated to illustrate the roles of ceRNAs in this process, the result was also support the GO and KEGG analysis. The present research provides important genomic insights for discovering the mechanisms that are activated in response to hypoxia in yak lung tissue. [ABSTRACT FROM AUTHOR]

The identification of genome-wide selection signatures can provide insights on the mechanisms of natural and/or artificial selection and uncover genes related to biological functions and/or phenotypes. Tibetan sheep are an important livestock in Tibet, providing meat and wool for Tibetans who are renown for breeding livestock that adapt well to high altitudes. Using whole-genome sequences with an effective sequencing depth of 5×, we investigated the genomic diversity and structure and, identified selection signatures of White Tibetan, Oula and Poll Dorset sheep. We obtained 30,163,679 Single Nucleotide Polymorphisms (SNPs) and 5,388,372 indels benchmarked against the ovine Oar_v4.0 genome assembly. Next, using FST, ZHp and XP-EHH approaches, we identified selection signatures spanning a set of candidate genes, including HIF1A, CAPN3, PRKAA1, RXFP2, TRHR and HOXA10 that are associated with pathways and GO categories putatively related to hypoxia responses, meat traits and disease resistance. Candidate genes and GO terms associated with coat color were also identified. Finally, quantification of blood physiological parameters, revealed higher levels of mean corpuscular hemoglobin measurement and mean corpuscular hemoglobin concentration in Tibetan sheep compared with Poll Dorset, suggesting a greater oxygen-carrying capacity in the Tibetan sheep and thus better adaptation to high-altitude hypoxia. In conclusion, this study provides a greater understanding of genome diversity and variations associated with adaptive and production traits in sheep. [ABSTRACT FROM AUTHOR]

To adapt to the plateau environment, Tibetan pigs' lungs have developed a unique physiological mechanism during evolution. The vascular corrosion casting technique and scanning electron microscopy were used to understand arterial architecture. Blood physiological index and quantitative real-time PCR (qRT-PCR) were used for assessing whether the lung can regulate the body through anatomical, physiological and molecular mechanisms to adapt to hypoxic environments. Our study showed that the lungs of Tibetan pigs were heavier and wider and that the pulmonary arteries were thicker and branched and had a denser vascular network than those of Landrace pigs. The hemoglobin (HGB), mean corpuscular hemoglobin concentration (MCHC) values of high-altitude pigs were significantly higher than those of low-altitude pigs. The expression levels of HIF - 1 α , EPAS1 , EPO and VEGF , but not those of eNOS and EGLN1 , were significantly higher in the lungs of high-altitude pigs than in those from pigs at a lower altitude (P<0.05). These findings and a comprehensive analysis help elucidate the pulmonary mechanism of hypoxic adaptation in pigs. [ABSTRACT FROM AUTHOR]

Simple Summary: Ureolytic bacteria produce urease that hydrolyzes dietary or recycled urea to ammonia, which can then be converted into microbial proteins. The diversity of ruminal ureolytic bacteria benefits N utilization efficiency in ruminants. However, there is no information at the complementary DNA (cDNA) level to reflect the active status of ureolytic bacteria. To reveal the diversity of active ureolytic bacteria in the rumen, we compared ureC amplicons between genomic DNA (gDNA) and cDNA. These results revealed distinct ureolytic bacterial community profiles based on gDNA and cDNA. The dominant ureolytic bacterial had high transcriptional activity, and the differential were mainly distributed in the genus of low abundance. In this study we revealed the diversity of active ureolytic bacteria in the rumen by compared ureC amplicons between gDNA and cDNA. Rumen fluid was collected from four Holstein dairy cows with rumen fistulas at 0, 2, and 6 h after morning feeding. Total microbial gDNA and RNA were isolated, and the RNA was reverse-transcribed into cDNA. The ureC gene amplicons of gDNA and cDNA were produced and sequenced by MiSeq. These results revealed that the sampling time had no significant difference on the alphssa and beta diversity indices of the ureolytic bacteria. The Shannon diversity of the ureC gene for cDNA was greater than that for gDNA (p < 0.05). There were significant difference in the beta diversity of ureolytic bacteria between gDNA and cDNA (p < 0.01), which indicates a shift in the community of active ureolytic bacteria. Approximately 67% of ureC sequences from cDNA could not be confidently classified at the genus level. The active ureolytic bacteria were mainly from Helicobacter, Herbaspirillum, Clostridium, Paenibacillus, Synechococcus, and Sphingobacterium sp. Changes in the operational taxonomic units revealed that the top abundant ureC genes were mostly consistent between gDNA and cDNA, and most differences occurred in the ureC genes with lower abundances. These results revealed distinct ureolytic bacteria community profiles based on gDNA and cDNA. The dominant ureolytic bacteria had high transcriptional activity, and the differential were mainly distributed in the genus of low abundance. [ABSTRACT FROM AUTHOR]

Background: Starch is an important substance that supplies energy to ruminants. To provide sufficient energy for high-yielding dairy ruminants, they are typically fed starch-enriched diets. However, starch-enriched diets have been proven to increase the risk of milk fat depression (MFD) in dairy cows. The starch present in ruminant diets could be divided into rumen-degradable starch (RDS) and rumen escaped starch (RES) according to their different degradation sites (rumen or intestine). Goats and cows have different sensitivities to MFD. Data regarding the potential roles of RDS in milk fat synthesis in the mammary tissue of dairy goats and in regulating the occurrence of MFD are limited. Results: Eighteen Guanzhong dairy goats (day in milk = 185 ± 12 d) with similar parity, weight, and milk yield were selected and randomly assigned to one of three groups (n = 6), which were fed an LRDS diet (Low RDS = 20.52%), MRDS diet (Medium RDS = 22.15%), or HRDS diet (High RDS = 24.88%) for 5 weeks. Compared with that of the LRDS group, the milk fat contents in the MRDS and HRDS groups significantly decreased. The yields of short-, medium- and long-chain fatty acids decreased in the HRDS group. Furthermore, increased RDS significantly decreased ruminal B. fibrisolvens and Pseudobutyrivibrio abundances and increased the trans-10, cis-12 conjugated linoleic acid (CLA) and trans-10 C18:1 contents in the rumen fluid. A multiomics study revealed that the HRDS diet affected mammary lipid metabolism down-regulation of ACSS2, MVD, AGPS, SCD5, FADS2, CERCAM, SC5D, HSD17B7, HSD17B12, ATM, TP53RK, GDF1 and LOC102177400. Remarkably, the significant decrease of INSIG1, whose expression was depressed by trans-10, cis-12 CLA, could reduce the activity of SREBP and, consequently, downregulate the downstream gene expression of SREBF1. Conclusions: HRDS-induced goat MFD resulted from the downregulation of genes involved in lipogenesis, particularly, INSIG1. Specifically, even though the total starch content and the concentrate-to-fiber ratio were the same as those of the high-RDS diet, the low and medium RDS diets did not cause MFD in lactating goats. [ABSTRACT FROM AUTHOR]

Yak is one of the largest native mammalian species at the Himalayas, the highest plateau area in the world with an average elevation of >4,000 m above the sea level. Yak is well adapted to high altitude environment with a set of physiological features for a more efficient blood flow for oxygen delivery under hypobaric hypoxia. Yet, the genetic mechanism underlying its adaptation remains elusive. We conducted a cross-tissue, cross-altitude, and cross-species study to characterize the transcriptomic landscape of domestic yaks. The generated multi-tissue transcriptomic data greatly improved the current yak genome annotation by identifying tens of thousands novel transcripts. We found that among the eight tested tissues (lung, heart, kidney, liver, spleen, muscle, testis, and brain), lung and heart are two key organs showing adaptive transcriptional changes and >90% of the cross-altitude differentially expressed genes in lung display a nonlinear regulation. Pathways related to cell survival and proliferation are enriched, including PI3K-Akt, HIF-1, focal adhesion, and ECM–receptor interaction. These findings, in combination with the comprehensive transcriptome data set, are valuable to understanding the genetic mechanism of hypoxic adaptation in yak. [ABSTRACT FROM AUTHOR]

Northwestern China, an important part of the Silk Road, was the birthplace of the Zhouzu farming culture. The domestication of cattle as an important aspect of farming culture has had a long history in northwestern China. In this study, we assessed the maternal structure and phylogeny of cattle by analyzing the mitochondrial DNA hypervariable segment I (HVS-I) in 698 native cattle from eight areas of northwestern China. The phylogenetic analyses revealed two highly divergent mtDNA clades: clade T, which had four sub-clades (Ta—Td), and clade I. The cattle domesticated from Bos taurus showed a clear dominant distribution pattern in northwestern China. The nucleotide diversity of the Bos indicus clade was lower than that of clades from Bos taurus. In summary, our results suggest that the native cattle of northwestern China were domesticated from two different maternal ancestors, Bos taurus and Bos indicus, which migrated to the central plains of China from the north and south, respectively, with Bos taurus remaining at the edges of the region. The population expansion of the cattle domesticated from Bos taurus occurred in the Longdong region of Gansu Province, and these cattle formed four relatively independent evolutionary branches. Subsequent to this expansion event, Bos indicus migrated from southern to northern China. [ABSTRACT FROM AUTHOR]

Abstract The milk fat globule membrane (MFGM) plays an important role in stabilizing fat in the aqueous phase, and the components of this membrane are involved in multiple biological functions. Here, we investigated changes in the protein composition of the MFGM fraction between raw and heated whole milk using a label free proteomic approach. In total, 612 MFGM-related proteins were identified in all groups. Compared with raw milk, the number of proteins that were not identified in the MFGM fraction was increased from pasteurized milk to ultra-high-temperature milk, whereas the number of milk proteins incorporated into the MFGM fraction was similar among heated groups. The abundances of several milk proteins (β-lactoglobulin and β-casein) were increased in the heated milk groups in a temperature-dependent manner. From our functional analysis, proteins that were not identified in the MFGM fraction of heated milk were mainly associated with multiple biological functions. These findings provided novel insights into the effects of heat procedures on MFGM protein components and their potential physiological functions, thereby yielding data on the appropriate heating procedures to use for raw milk. Graphical abstract Unlabelled Image Highlights • Distinct protein properties were identified in different types of heated whole milk. • Heat caused downregulation of proteins of milk fat globule membranes. • Milk proteins were incorporated into milk fat globule membranes following heating. [ABSTRACT FROM AUTHOR]

Specific pathogen-free ducks are important high-grade laboratory animals, with a key role in research related to poultry biosecurity, production, and breeding. However, the genetic characteristics of experimental duck varieties remain poorly explored. Herein we performed whole-genome resequencing to construct a single nucleotide polymorphism genetic map of the genomes of 3 experimental duck varieties [Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)] to determine their genetic characteristics and identify selection signatures. Subsequent analyses of population structure and genetic diversity revealed that each duck variety formed a monophyletic group, with SM showing richer genetic diversity than JD and SX. Further, on exploring shared selection signatures, we found 2 overlapping genomic regions on chromosome Z of all experimental ducks, which comprised immune response-related genes (IL7R and IL6ST). Moreover, growth and skeletal development (IGF1R and GDF5), meat quality (FoxO1), and stress resistance (HSP90B1 and Gpx8-b) candidate gene loci were identified in strongly selected signatures specific to JD, SM, and SX, respectively. Our results identified the population genetic basis of experimental ducks at the whole-genome level, providing a framework for future molecular investigations of genetic variations and phenotypic changes. We believe that such studies will eventually contribute to the management of experimental animal resources. [ABSTRACT FROM AUTHOR]

Commercial milk products worldwide come not only from cows, but also from goats, buffaloes, camels, and yaks. Milk from non-bovine animals is important culturally and economically. Pseudomonas spp. are frequently linked to milk spoilage under storage temperatures. The objectives of this study were to identify Pseudomonas spp. isolated from goat, buffalo, camel, and yak milks, and to measure proteolytic activity of Pseudomonas spp. under different storage temperatures. Raw milk samples of goat (n = 50), buffalo (n = 25), camel (n = 25), and yak (n = 25) were collected from 5 provinces in China. Pseudomonas spp. were analyzed by Pseudomonas-specific 16S, universal 16S rRNA, and rpoB gene sequence analyses. Proteolytic activity on milk agar, quantification via the trinitrobenzenesulfonic acid assay at 2°C, 4°C, 7°C, 10°C and 25°C, as well as alkaline peptidase gene (aprX) identification were performed to ascertain the proteolytic activity of these isolates. Pseudomonas spp. were found in 46 samples out of total 125 samples. A total of 67 Pseudomonas spp. were identified. Of Pseudomonas isolates, we obtained extracellular peptidase activity in 7 (10.4%) at 2°C, 17 (25.4%) at 4°C, 24 (35.8%) at 7°C, 39 (58.2%) at 10°C, and 41 (61.2%) at 25°C. The results revealed that a wide diversity of Pseudomonas spp. were present in different non-bovine raw milks, with the ability to produce peptidases at storage temperatures. However, proteolytic activity varied widely among the peptidase-positive isolates. A majority of isolates from yak milk had high proteolytic activity. [ABSTRACT FROM AUTHOR]