A Combined Metabolomic and Proteomic Study Revealed the Difference in Metabolite and Protein Expression Profiles in Ruminal Tissue From Goats Fed Hay or High-Grain Diets

Identification of genomic regions and pathways associated with traits related to rumen acidosis in feedlot Nellore cattle

There may be an increased risk of metabolic disorders, such as rumen acidosis, in cattle fed high-concentrate diets, particularly those from Bos taurus indicus genotypes, which have shown to be more sensitive to ruminal acidification. Therefore, this study aimed to estimate (co)variance components and identify genomic regions and pathways associated with ruminal acidosis in feedlot Nellore cattle fed high-concentrate diets. It was utilized a dataset containing a total of 642 Nellore bulls that were genotyped from seven feedlot nutrition studies. The GGP Indicus 35k panel was used with the single step genome-wide association study methodology in which the effects of the markers were obtained from the genomic values estimated by the GBLUP model. A bivariate model to estimate genetic correlations between the economically important traits and indicator traits for acidosis was used. The traits evaluated in this study that were nutritionally related to rumen acidosis included average daily gain (ADG), final body weight, time spent eating (TSE), time spent ruminating, rumenitis score (RUM), rumen absorptive surface area (ASA), rumen keratinized layer thickness (KER) and hot carcass weight (HCW). The identified candidate genes were mainly involved in the negative or non-regulation of the apoptotic process, salivary secretion, and transmembrane transport. The genetic correlation between HCW and ASA was low positive (0.27 ± 0.23), and between ADG and ASA was high moderate (0.58 ± 0.59). A positive genetic correlation between RUM and all performance traits was observed, and TSE correlated negatively with HCW (-0.33 ± 0.21), ASA (-0.75 ± 0.48), and KER (-0.40 ± 0.27). The genetic association between economically important traits and indicator traits for acidosis suggested that Nellore cattle may be more sensitive to acidosis in feedlot systems.

Multi-omics analysis of functional substances and expression verification in cashmere fineness

BACKGROUND

Numerous factors influence the growth and development of cashmere. Existing research on cashmere has predominantly emphasized a single omics level. Integrating multi-omics analyses can offer a more comprehensive understanding by encompassing the entire spectrum. This study more accurately and comprehensively identified the key factors influencing cashmere fineness using multi-omics analysis.

METHODS

This study used skin tissues of coarse cashmere type (CT_LCG) and fine cashmere type Liaoning cashmere goats (FT_LCG) for the analysis. This study employed an integrated approach involving transcriptomics, translatomics, proteomics, and metabolomics to identify substances associated with cashmere fineness. The findings were validated using parallel reaction monitoring (PRM) and multiple reaction monitoring (MRM) techniques.

RESULTS

The GO functional enrichment analysis identified three common terms: multicellular organismal process, immune system process, and extracellular region. Furthermore, the KEGG enrichment analysis uncovered the involvement of the arachidonic acid metabolic pathway. Protein expression trends were verified using PRM technology. The expression trends of KRT79, as confirmed by PRM, were consistent with those observed in TMT proteomics and exhibited a positive regulatory effect on cashmere fineness. Metabolite expression trends were confirmed using MRM technology. The expression trends of 9 out of 15 validated metabolites were in agreement with those identified in the non-targeted metabolomics analysis.

CONCLUSIONS

This study employed multi-omics analysis to identify key regulators of cashmere fineness, including PLA2G12A, KRT79, and prostaglandin B2. The findings of this study offer valuable data and establish a theoretical foundation for conducting comprehensive investigations into the molecular regulatory mechanisms and functional aspects of cashmere fineness.

Rumen ciliates (Alveolata, Ciliophora) associated with goats: checklist, geographic distribution, host specificity, phylogeny and molecular dating

Although the diversity (~35 species) and worldwide distribution of goats (Ruminantia, Bovidae, Caprinae) are significant, studies on the diversity of symbiont ciliates in these mammals are scarce in comparison to other ruminants. The present work is a review and checklist of species based on taxonomic, morphologic, and ecologic studies of rumen ciliate protozoa in goats, presenting geographic distribution and hosts, as well as estimating the macroevolutionary relationships of the species observed in the studies. To that end, all of the available literature on databases was reviewed, the schematic drawings were made based on information present in the original description of the taxa, and the phylogenetic relationships were inferred based on Maximum Likelihood and Bayesian Inference analyses. According to our review, 72 species and 14 genera of ciliates have been associated with goats. Through the analysis of the association between ciliate genera and caprine hosts, it was shown that ciliates are more associated with domestic animals (Capra hircus—14 genera) than wild ones (Rupicapra rupicapra—six genera, Capra ibex—one genus, Capra pyrenaica—one genus). Thirteen countries were identified in the distribution map as having had reports of ciliate species associated with goats. The interaction networks of ciliates and their hosts showed that the species of ciliates associated with goats also occur in other herbivore mammal species. The recovered phylogenetic hypotheses show that the ciliate species in goats form a non-monophyletic group with maximum and minimum ages of ~8.2My and ~2.4My. We have also found that a large portion of the studies on the diversity of ciliates in goats does not employ all necessary techniques in an integrative way, despite it being essential for detailed descriptions and better knowledge of this fraction of biodiversity.  

Proteomic identification of ruminal epithelial protein expression profiles in response to starter feed supplementation in pre-weaned lambs

The present study aimed to comparatively characterize the ruminal epithelial protein expression profiles in lambs fed ewe milk or milk plus starter diet using proteome analysis. Twenty new-born lambs were randomly divided into a group receiving ewe milk (M, n = 10) and a group receiving milk plus starter diet (M + S, n = 10). From 10 d old, M group lambs remained with the ewe and suckled ewe milk without receiving the starter diet. The lambs in the M + S group were separated from the ewe and received starter feed. All lambs were slaughtered at 56 d old. Eight rumen epithelia samples (4 per group) were collected to characterize their protein expression profiles using proteomic technology. Proteome analysis showed that 31 upregulated proteins and 40 downregulated proteins were identified in the rumen epithelium of lambs in response to starter diet supplementation. The results showed that starter feeding regulates a variety of biological processes in the epithelium, especially blood vessel development and extracellular matrix protein expression. Meanwhile, the expression of proteins associated with synthesis and degradation of ketone bodies, butanoate metabolism, and citrate cycle signaling transduction pathway were upregulated in the group with starter diet supplementation, including 3-hydroxy-3-methylglutaryl coenzyme A synthase (HMGCS2, fold change [FC] = 1.93), 3-hydroxybutyrate dehydrogenase 1 (BDH1, FC = 1.91), and isocitrate dehydrogenase 1 (IDH1, FC = 8.12). The metabolic processes associated with ammonia detoxification and antioxidant stress were also affected by starter diet supplementation, with proteins, microsomal glutathione S-transferase 3 (MGST3, FC = 2.37) and IDH1, linked to the biosynthesis of glutamate and glutathione metabolism pathway being upregulated in the group with starter diet supplementation. In addition, starter feeding decreased the expression of Ras-related protein rap-1A (RAP1A, FC = 0.48) enriched in Rap1 signaling pathway, Ras signaling pathway, cyclic adenosine monophosphate (cAMP) signaling pathway, and mitogen-activated protein kinase (MAPK) signaling pathway. In summary, starter feed supplementation changed the expression of proteins related to energy production, ammonia detoxification, antioxidant stress, and signaling pathways related to proliferation and apoptosis, which facilitates the rumen epithelia development in lambs. The results provide new insights into the molecular adaptation of rumen epithelia in response to starter diet supplementation at the protein level in lambs.

Understanding the early ontogenetic stages of Mugil liza (Mugilidae): Morphological traits and digestive/metabolic profile of pre-juveniles after recruitment

The family Mugilidae consists mainly of diadromous species, whose reproduction occurs in offshore waters. Pre-juveniles shift their diet in the surf zone (zooplanktophagous to iliophagous). Later, during their recruitment into estuaries, huge changes take place in their digestive system. However, digestive and metabolic characteristics and some morphological traits at recruitment are unknown for Mugilidae. We performed comparative studies on early and late pre-juveniles of Mugil liza recruited in Mar Chiquita Coastal Lagoon (37°32'-37°45'S, 57°19'-57°26'W, Argentina). We determined digestive enzyme activities (intestine), energy reserves (liver/muscle), total/standard length, total weight, intestinal coefficient, hepatosomatic index and retroperitoneal fat. Pre-juveniles exhibited amylase, maltase, sucrase, lipase, trypsin and aminopeptidase-N (APN) activities, which were maintained over a wide range of pH and temperature, and exhibited Michaelis-Menten kinetics. In late pre-juveniles, amylase (422 ± 131 μmol maltose min^-1 mgprot^-1 ), sucrase (86 ± 14 mg glucose min^-1 mgprot^-1 ), trypsin (84 ± 9 μmoles min^-1 mgprot^-1 ) and APN (0.58 ± 0.08 μmoles min^-1 mgprot^-1 ) activities were higher (42%, 28%, 35% and 28%, respectively) than in the early stage. Also, the intestinal coefficient was higher in late (3.04) compared to early (2.06) pre-juveniles. Moreover, the liver appeared to be a main site of glycogen and triglyceride storage in late pre-juveniles, muscle being the site of storage in early pre-juveniles, exhibiting higher glycogen, free glucose and protein concentrations (92%, 82%, 32%, respectively). The results suggest that pre-juveniles of M. liza exhibit an adequate digestive battery to perform complete hydrolysis of various dietary substrates, availability of energy reserves and morphological characteristics to support their feeding habit and growth after recruitment. Our results represent an important contribution to knowledge of the ecology and digestive physiology of pre-juveniles of Mugilidae in the wild.

Circulating microRNAs May Serve as Biomarkers for Hypertensive Emergency End-Organ Injuries and Address Underlying Pathways in an Animal Model

There is an incomplete understanding of the underlying pathophysiology in hypertensive emergencies, where severely elevated blood pressure causes acute end-organ injuries, as opposed to the long-term manifestations of chronic hypertension. Furthermore, current biomarkers are unable to detect early end-organ injuries like hypertensive encephalopathy and renal thrombotic microangiopathy. We hypothesized that circulating microRNAs (c-miRs) could identify acute and chronic complications of severe hypertension, and that combinations of c-miRs could elucidate important pathways involved. We studied the diagnostic accuracy of 145 c-miRs in Dahl salt-sensitive rats fed either a low-salt (N = 20: 0.3% NaCl) or a high-salt (N = 60: 8% NaCl) diet. Subclinical hypertensive encephalopathy and thrombotic microangiopathy were diagnosed by histopathology. In addition, heart failure with preserved ejection fraction was evaluated with echocardiography and N-terminal pro-brain natriuretic peptide; and endothelial dysfunction was studied using acetylcholine-induced aorta ring relaxation. Systolic blood pressure increased severely in animals on a high-salt diet (high-salt 205 ± 20 mm Hg vs. low-salt 152 ± 18 mm Hg, p < 0.001). Partial least squares discriminant analysis revealed 68 c-miRs discriminating between animals with and without hypertensive emergency complications. Twenty-nine c-miRs were strongly associated with hypertensive encephalopathy, 24 c-miRs with thrombotic microangiopathy, 30 c-miRs with heart failure with preserved ejection fraction, and 28 c-miRs with endothelial dysfunction. Hypertensive encephalopathy, thrombotic microangiopathy and heart failure with preserved ejection fraction were associated with deviations in many of the same c-miRs, whereas endothelial dysfunction was associated with a different set of c-miRs. Several of these c-miRs demonstrated fair to good diagnostic accuracy for a composite outcome of hypertensive encephalopathy, thrombotic microangiopathy and heart failure with preserved ejection fraction in receiver-operating-curve analyses (area-under-curve 0.75–0.88). Target prediction revealed an enrichment of genes related to several pathways relevant for cardiovascular disease (e.g., mucin type O-glycan biosynthesis, MAPK, Wnt, Hippo, and TGF-beta signaling). C-miRs could potentially serve as biomarkers of severe hypertensive end-organ injuries and elucidate important pathways involved.

Metabolomic and Proteomic Profiles Associated With Ketosis in Dairy Cows

Ketosis is a common metabolic disease in dairy cows during early lactation. However, information about the metabolomic and proteomic profiles associated with the incidence and progression of ketosis is still limited. In this study, an integrated metabolomics and proteomics approach was performed on blood serum sampled from cows diagnosed with clinical ketosis (case, ≥ 2.60 mmol/L plasma β-hydroxybutyrate; BHBA) and healthy controls (control, < 1.0 mmol/L BHBA). Samples were taken 2 weeks before parturition and 2 weeks after parturition from 19 animals (nine cases, 10 controls). All serum samples (n = 38) were subjected to Liquid Chromatography-Mass Spectrometry (LC-MS) based metabolomic analysis, and 20 samples underwent Data-Independent Acquisition (DIA) LC-MS based proteomic analysis. A total of 97 metabolites and 540 proteins were successfully identified, and multivariate analysis revealed significant differences in both metabolomic and proteomic profiles between cases and controls. We investigated clinical ketosis-associated metabolomic and proteomic changes using statistical analyses. Correlation analysis of statistically significant metabolites and proteins showed 78 strong correlations (correlation coefficient, R ≥ 0.7) between 38 metabolites and 25 proteins, which were then mapped to pathways using IMPaLA. Results showed that ketosis altered a wide range of metabolic pathways, such as metabolism, metabolism of proteins, gene expression and post-translational protein modification, vitamin metabolism, signaling, and disease related pathways. Findings presented here are relevant for identifying molecular targets for ketosis and biomarkers for ketosis detection during the transition period.

Examining the Impacts of CO2 Concentration and Genetic Compatibility on Perennial Ryegrass-Epichloë festucae var lolii Interactions

Perennial ryegrass (Lolium perenne) is the most cultivated cool-season grass worldwide with crucial roles in carbon fixation, turfgrass applications, and fodder for livestock. Lolium perenne forms a mutualism with the strictly vertically transmitted fungal endophyte, Epichloë festucae var lolii. The fungus produces alkaloids that protect the grass from herbivory, as well as conferring protection from drought and nutrient stress. The rising concentration of atmospheric CO₂, a proximate cause of climatic change, is known to have many direct and indirect effects on plant growth. There is keen interest in how the nature of this plant-fungal interaction will change with climate change. Lolium perenne is an obligately outcrossing species, meaning that the genetic profile of the host is constantly being reshuffled. Meanwhile, the fungus is asexual implying both a relatively constant genetic profile and the potential for incompatible grass-fungus pairings. In this study, we used a single cultivar, "Alto", of L. perenne. Each plant was infected with one of four strains of the endophyte: AR1, AR37, NEA2, and Lp19 (the "common strain"). We outcrossed the Alto mothers with pollen from a number of individuals from different ryegrass cultivars to create more genetic diversity in the hosts. We collected seed such that we had replicate maternal half-sib families. Seed from each family was randomly allocated into the two levels of the CO₂ treatment, 400 and 800 ppm. Elevated CO₂ resulted in an c. 18% increase in plant biomass. AR37 produced higher fungal concentrations than other strains; NEA2 produced the lowest fungal concentrations. We did not find evidence of genetic incompatibility between the host plants and the fungal strains. We conducted untargeted metabolomics and quantitative proteomics to investigate the grass-fungus interactions between and within family and treatment groups. We identified a number of changes in both the proteome and metabalome. Taken together, our data set provides new understanding into the intricacy of the interaction between endophyte and host from multiple molecular levels and suggests opportunity to promote plant robustness and survivability in rising CO₂ environmental conditions through application of bioprotective epichloid strains.

Rumen function in goats, an example of adaptive capacity

The aim of this Research Reflection is to describe the basic rumen function of goats and its modification in response to environmental factors, as well as to discuss similarities and differences when compared to other ruminants. In so doing we shall reveal the adaptive capacity of goats to harsh environments. The basic rumen function in goats is similar to other species of ruminants, as stressed by the opportunity to apply the updates of feeding systems for ruminants to goats. The rumen epithelium acts as a protective barrier between the rumen and the host, but it can be damaged by toxic compounds or acidosis. The rumen also plays an important role in water balance, both for dehydration and rehydration. Recent studies show that the microbiota exhibits a high fractional stability due to functional redundancy and resilience, but this needs more investigation. The microbial community structure differs between goats and cows, which explains the difference in sensitivity to milk fat depression following intake of high lipid diets. Goats also differ from other ruminants by their enhanced ability to feed-sort, but as with cows they can suffer from acidosis. Nevertheless, goats can be considered to be very resistant to environmental factors such as water stress, salt stress or heat stress, and this is especially so in some endogenous breeds. They also are able to detoxify tannins, polyphenols and other secondary metabolites. Some new trials involving feeding behaviour, microbiota and omics or approaches by meta-analyses or modelling will improve our knowledge of rumen function in goats.