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Abstract Alternative polyadenylation (APA) is emerging as a post-transcriptional regulatory mechanism, similar as that of alternative splicing (AS), and plays a prominent role in regulating gene expression and increasing the complexity of the transcriptome and proteome. We use polyadenylation selected long-read isoform sequencing to obtain full-length transcript sequences in porcine muscles at five developmental stages. We identify numerous novel transcripts unannotated in the existing pig genome, including transcripts mapping to known and unknown gene loci, and widespread transcript diversity in porcine muscles. The top 100 most isoformic genes are mainly enriched in Gene Ontology terms related to muscle growth and development. It is revealed that intron retention/exon inclusion and the usage of distal polyadenylation site (PAS) are associated with ageing through analyzing changes of AS and PAS during muscle development. We also identify developmental changes in major transcripts and major PASs. Furthermore, genes/transcripts important for muscle development are identified. The results confirm the importance of AS and APA in pig muscles, substantially increasing transcriptional diversity and showing an important mechanism underlying gene regulation in muscles.

Dietary fiber is a key nutritional regulatory factor that has been studied intensively for its role in improving reproduction in sows during gestation. However, the metabolic mechanism underlying the effect of interactions between metabolites and gut microbes on coarse feeding tolerance in indigenous sows remains to be elucidated. Therefore, the present study aimed to investigate the effects of dietary supplementation with alfalfa at different content ratios on the reproductive performance of pregnant Songliao Black sows. In total, 40 Songliao Black sows at 30 days of gestation were allocated to four treatments, which received the following diets: (1) a corn–soybean meal basal diet with no alfalfa meal (CON group), (2) a corn–soybean meal basal diet +10% alfalfa meal (Treatment 1 group), (3) a corn–soybean meal basal diet +20% alfalfa meal (Treatment 2 group), and (4) a corn–soybean meal basal diet +30% alfalfa meal (Treatment 3 group). Untargeted metabolomics, 16S rDNA sequencing, and enzyme-linked immunosorbent assay (ELISA) were performed to determine the possible effects of metabolites, the microbial communities in fecal samples and their functional potential, and the effects of dietary fiber on serum biochemical parameters, oxidative stress, and reproductive hormones in Songliao Black sows during gestation. The results revealed that the meals with 10 and 20% alfalfa had a beneficial effect on sows in terms of improving the reproductive performance of these sows. Bacterial 16S rDNA sequencing of the fecal samples revealed that the 10% alfalfa meal group had a higher α-diversity and higher abundance of probiotics. Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria were revealed as the most abundant groups at the phylum level and Lactobacillus, Prevotella, Ruminococcus, Streptococcus, and Clostridium were the most abundant at the genus level in the sows fed with diets containing higher fiber levels. A total of 239 differential metabolites were identified in the sows fed with alfalfa meals. These metabolites were enriched mainly in the cAMP signaling pathway, biosynthesis of amino acids, and steroid biosynthesis. Pearson correlation analysis revealed significant positive correlations between Blautia and Daizein, Fibrobacter and 5-alpha-Cholestanone, Sphaerochaeta, Sutterella, and Metaraminol. Negative correlations were revealed between Sphaerochaeta and Erucic acid, Prevotellaceae and Harmaline, and Streptococcus and 5-alpha-Cholestanone. Collectively, these findings provide novel insights into the application of dietary fiber in sow diets.

Abstract Lacticaseibacillus is one of the predominant microorganisms in gut from human and animal, and the lacticaseibacillus have effective applications against the viral diarrhea of piglets in the farm. However, the function and the concrete cell single pathways of the active ingredient from lacticaseibacillus was not clear within anti-infection in the postbiotics research. Here, we compared the biological function of extracellular polysaccharides (EPS) purified from lacticaseibacillus casei (L. casei) and gene editing lacticaseibacillus casei with the CRISPER-Cas9 technology, which were with the ability of antioxidation and anti-inflammation, and the EPS could also inhibit the ROS production within the Porcine Small Intestinal Epithelial Cells-J2 (IPEC-J2). Interestingly, we found that both of EPS and genome editing lacticaseibacillus casei could specifically target the IFN-λ expression in the IPEC-J2, which was beneficial against the PEDV infection in the virus replication and production with the qRT-PCR and indirect immunofluorescence methods. Finally, the STAT3 cell single pathway was stimulated to transcribe IFN-λ with the EPS to elucidate the detailed mechanism of activating type III IFN signals receptor of IL-10R2, which play the function between anti-inflammation and anti-virus in the PEDV infection. Taken together, our research linked a postbiotics of EPS with the antiviral infection of PEDV, which suggest that the lacticaseibacillus itself still have displayed the potential immunomodulatory activities, and highlight the immunomodulatory potential of EPS-producing microbes. Graphical Abstract

Soil physicochemical properties affect crop growth and yield. The addition of fertilizers can improve the soil quality during crop cultivation, leading to increased agricultural production. Organic fertilizers may be produced by composting straw that would otherwise be discarded as agricultural waste, with potential implications for sustainable agricultural development. However, the mechanism underlying the effects of straw compost on crop growth is unknown. In this study, a microbial agent suitable for straw decomposition in cold regions was used for a large-scale biological fermentation. Organic compost was obtained after the decomposition of straw. The straw compost was mixed with soil in different proportions and then used to cultivate Songjing 2 rice plants. The addition of straw compost significantly increased the growth and yield of the rice plants and enhanced various physiological indices. Moreover, the straw compost treatment significantly improved soil physicochemical properties (e.g., pH, enzyme activity, nutrient composition, and microbial diversity) and optimized the soil conditions for crop growth. In addition, the application of straw compost influenced the expression of genes in rice metabolic pathways as well as pathways mediating secondary metabolite synthesis and plant hormone signal transduction. The study data reflect the potential applicability of low-temperature straw fermentation technology for maximizing crop production.

Abstract Objectives This study was conducted to investigate the effects of dietary supplementation of Perilla frutescens seed (PFS) on growth performance, blood profiles, meat quality and meat nutrient characteristics in finishing castrated male Songliao black pigs. Methods A total of 80 castrated male Songliao black pigs with an average initial body weight (BW) of 84.1 ± 2.1 kg were used in a 75 days feeding trial. All pigs were randomly assigned into four dietary treatments: CON, basal diet; PFS3.0, basal diet + 3.0% of PFS; PFS6.0, basal diet + 6.0% of PFS and PFS9.0, basal diet + 9.0% of PFS. Results As a result of this experiment, dietary supplementation of PFS improved the growth performance parameters, blood albumin and blood lipid parameters. Whereas, on FBW, average daily feed intake and average daily gain there showed a non‐dose‐dependent manner that pigs in PFS9.0 had lowest performance compared with other two PFS treatments. Furthermore, meat colour of yellowness, pH, cook meat rate, moisture, crude protein and crude fat were increased by PFS addition. However, lower growth performance was observed in PFS9.0 group. As well as, dietary inclusion of PFS also alters the meat amino acid composition and meat fatty acids composition. Particularly, umami amino acid contents and polyunsaturated fatty acid were all enhanced by PFS addition. Conclusions In summary, dietary supplementation of PFS have beneficial effects on the performance and meat quality and nutritional values in Songliao black pigs.

Lactobacillus casei (L. casei) has four possible mechanisms: antimicrobial antagonism, competitional adhesion, immunoregulation, and the inhibition of bacterial toxins. To delineate the metabolic reactions of nucleotides from L. casei that are associated with mechanisms of inhibiting pathogens and immunoregulation, we report that a PyrR-deficient L. casei strain was constructed using the CRISPR-Cas9D10A tool. Furthermore, there were some changes in its basic biological characterization, such as its growth curve, auxotroph, and morphological damage. The metabolic profiles of the supernatant between the PyrR-deficient and wild strains revealed the regulation of the synthesis of genetic material and of certain targeting pathways and metabolites. In addition, the characteristics of the PyrR-deficient strain were significantly altered as it lost the ability to inhibit the growth of pathogens. Moreover, we identified PyrR-regulating pyrimidine biosynthesis, which further improved its internalization and colocalization with macrophages. Evidence shows that the PyrR gene is a key active component in L. casei supernatants for the regulation of pyrimidine biosynthesis against a wide range of pathogens.

The Min pig is a famous native pig breed in northeast China, which has the special genetic character of villi hair growth in cold seasons. At present, little research has focused on the genetic mechanism of villi hair growth in Min pigs. Copy number variations (CNVs) are a type of variant that may influence many traits. In this study, we first investigated the phenotype of Large White × Min pigs’ F2 pig villi hair in detail and then performed a CNV-based genome-wide association study (GWAS) between CNVs and pig villi hair appearance. Finally, a total number of 15 significant CNVRs were found to be associated with Min pig villi hair. The most significant CNVR was located on chromosome 1. Nearest gene annotation analysis indicated that the pig villi hair traits may be associated with the biological process of the G-protein-coupled receptor signaling pathway. QTL overlapping analysis found that among the CNVRs, 14 CNVRs could be co-located with known QTLs. Some genes such as MCHR2, LTBP2, and GFRA2 may be candidate genes for pig villi traits and are worth further study. Our study may provide a basic reference for the selection and breeding of cold-resistant pigs and outdoor breeding.

In China, the national-level protected pig, the Min pig, is characterized by the development of secondary hairs and hair follicles in winter. Factors that dominate the genotype in the growth of secondary hairs are not clear through the concrete cell signaling pathways. This study compared hair phenotypes based on morphological structure, transcriptomics, and potential targeting molecules in the breeds of Min, Berkshire, and Yorkshire pigs. The results indicated that Min pigs have specific characteristics for the growth of secondary hairs compared with the Berkshire and Yorkshire pigs. The transcriptome analyses and quantitative reverse transcription-polymerase chain reaction results revealed that secondary hair growth was activated by follicle stem cells. The specific inhibitors of Wnt and BMP were studied using respective signals. The density of follicles, activity of follicle stem cells, and relative gene expression results have shown that Wnt and BMP stimulate the activity of follicle stem cells, and the Wnt signaling molecule has a significantly better effect than the BMP signaling molecule on stem cells. Wnt and BMP can promote the growth of local secondary hair and gene expression. Therefore, this study was conducted to verify the development mechanisms of secondary hairs, which have potential applications in laboratory animals and comparative medicine.

The processes involved in soil domestication have altered the soil microbial ecology. We examined the question of whether animal manure application affects the soil microbial ecology of farmlands. The effects of global animal manure application on soil microorganisms were subjected to a meta-analysis based on randomized controlled treatments. A total of 2303 studies conducted in the last 30 years were incorporated into the analysis, and an additional 45 soil samples were collected and sequenced to obtain 16S rRNA and 18S rRNA data. The results revealed that manure application increased soil microbial biomass. Manure application alone increased bacterial diversity (M-Z: 7.546 and M-I: 8.68) and inhibited and reduced fungal diversity (M-Z: −1.15 and M-I: −1.03). Inorganic fertilizer replaced cattle and swine manure and provided nutrients to soil microorganisms. The soil samples of the experimental base were analyzed, and the relative abundances of bacteria and fungi were altered compared with no manure application. Manure increased bacterial diversity and reduced fungal diversity. Mrakia frigida and Betaproteobacteriales, which inhibit other microorganisms, increased significantly in the domesticated soil. Moreover, farm sewage treatments resulted in a bottleneck in the manure recovery rate that should be the focus of future research. Our results suggest that the potential risks of restructuring the microbial ecology of cultivated land must be considered.

In the northeast plains of China, the intensive utilization of agricultural soils has been a persistent issue, and finding ways to utilize soil resources efficiently and sustainably through a scientifically-driven management system has become a crucial challenge for agricultural production. Conservation tillage is a crucial technology for sustainable agriculture. Currently, plow and rotary tillage are the dominant methods used in Mollisols, but there is limited information on the effects of different conservation tillage practices in this region. The objective of this study was to investigate the short-term impact of tillage and sowing methods on soil physical properties and corn plant growth and to examine the relationship between soil physical properties and plant characteristics during various stages of growth. This study consisted of four tillage and sowing methods: plow tillage and precision seeder sowing (PTS), rotary tillage and precision seeder sowing (RTS), no-tillage and no-tillage seeder sowing (NTS), and no-tillage and precise sowing in stubble field (STS) (all four treatments involved total straw return). The results indicated that the soil penetration resistance (SPR) in the 10–40 cm soil layer under the PTS treatment was significantly lower (by 11.9% to 18%) compared to the other treatments (p < 0.05). On average, the soil moisture content in the NTS treatment was 2.7% and 1.4% higher than that of the PTS and RTS treatments. Additionally, soil temperature was 5.6% to 8.6% lower under the STS treatment compared to the other treatments during late corn growth. The RTS treatment also significantly reduced the bulk density of surface soil. High SPR impeded early crop growth but did not impact mid-crop development, while low soil temperature was one of the main factors affecting late corn growth and development as temperatures decreased. Based on the comparisons, we found that the short-term implementation of conservation tillage did not result in a significant decrease in corn yield. We believe that the short-term implementation of NTS tillage sowing practices in Mollisol regions is a feasible option.

The porcine epidemic diarrhea virus, PEDV, which causes diarrhea, vomiting and death in piglets, causes huge economic losses. Therefore, understanding how to induce mucosal immune responses in piglets is essential in the mechanism and application against PEDV infection with mucosal immunity. A method of treatment in our research was used to make an oral vaccine that packaged the inactive PEDV with microencapsulation, which consisted of sodium alginate and chitosan, and adapted the condition of the gut in mice. The in vitro release experiment of microcapsules showed that inactive PEDV was not only easily released in saline and acid solutions but also had an excellent storage tolerance, and was suitable for use as an oral vaccine. Interestingly, both experimental groups with different doses of inactive virus enhanced the secretion of specific antibodies in the serum and intestinal mucus, which caused the effective neutralization against PEDV in the Vero cell by both IgG and IgA, respectively. Moreover, the microencapsulation could stimulate the differentiation of CD11b+ and CD11c+ dendritic cells, which means that the microencapsulation was also identified as an oral adjuvant to help phagocytosis of dendritic cells in mice. Flow cytometry revealed that the B220+ and CD23+ of the B cells could significantly increase antibody production with the stimulation from the antigens’ PEDV groups, and the microencapsulation could also increase the cell viability of B cells, stimulating the secretion of antibodies such as IgG and IgA in mice. In addition, the microencapsulation promoted the expression of anti-inflammatory cytokines, such as IL-10 and TGF-β. Moreover, proinflammatory cytokines, such as IL-1, TNF-α, and IL-17, were inhibited by alginate and chitosan in the microencapsulation groups compared with the inactivated PEDV group. Taken together, our results demonstrate that the microparticle could play the role of mucosal adjuvant, and release inactivated PEDV in the gut, which can effectively stimulate mucosal and systemic immune responses in mice.

The Min pig, a local pig breed in China, has a special trait which has intermittent villus and coat hair regeneration. However, the regulation and mechanism of villus in Min pigs have not yet been described. We observed and described the phenotype of Min pig dermal villi in detail and sequenced the mRNA transcriptome of Min pig hair follicles. A total of 1520 differentially expressed genes (DEG) were obtained.K-means hierarchical clustering showed that there was a significant expression pattern difference in winter compared with summer. Gene enrichment and network analysis results showed that the hair growth in Min pigs was closely related to the composition of desmosomes and regulated by an interaction network composed of eight core genes, namely DSP, DSC3, DSG4, PKP1, TGM1, KRT4, KRT15, and KRT84. Methylation analysis of promoters of target genes showed that the PKP1 gene was demethylated. Our study will help to supplement current knowledge of the growth mechanism of different types of hair.

Ferroptosis, a new type of non-apoptotic cell death modality, is different from other modes of cell death and has been primarily found in tumor cells. Previous studies have reported that ferroptosis can be triggered by specific modulators (e.g., drugs, nutrients, and iron chelators), leading to increased intracellular lipid reactive oxygen species (ROS) accumulation and iron overload. Recent reports have shown that ferroptosis at the cellular and organism levels can prevent an inflammatory storm and cancer development. Emerging evidence suggests potential mechanisms (e.g., system Xc-, glutathione peroxidase 4 (GPX4), lipid peroxidation, glutathione (GSH), and iron chelators) are involved in ferroptosis, which may mediate biological processes such as oxidative stress and iron overload to treat cancer. To date, there are at least three pathways that mediate ferroptosis in cancer cells: system Xc-/GSH/GPX4, FSP1/CoQ10/NAD(P)H, and ATG5/ATG7/NCOA4. Here, we summarize recent advances in the occurrence and development of ferroptosis in the context of cancer, the associations between ferroptosis and various modulators, and the potential mechanisms and therapeutic strategies targeting ferroptosis for the treatment of cancer.

BackgroundUlva prolifera extract contains a variety of functional active substances. Whether these substances had any beneficial effects on the small intestine of weaned piglets under oxidative stress remained unknown.MethodWe explored the effects of U. prolifera extract on oxidative stress and related mechanisms in weaned piglets and intestinal porcine epithelial cells (IPEC-J2) challenged with hydrogen peroxide.ResultsU. prolifera extract was found to mainly consist of polyphenols and unsaturated fatty acids. U. prolifera extract increased total antioxidant capacity and superoxide dismutase (SOD) activity, while it decreased malondialdehyde content, in the serum of weaned piglets challenged with hydrogen peroxide. Moreover, U. prolifera extract increased mRNA expression of SOD and catalase, as well as the intestinal expression of nuclear NF-E2-related factor 2 (Nrf2), both in vitro and in vivo. Furthermore, U. prolifera extract decreased reactive oxygen species and improved mitochondrial respiration in IPEC-J2 cells treated with hydrogen peroxide. However, AMPK inhibition did not affect nuclear Nrf2 expression and only partially affected the effects of U. prolifera extract on oxidative stress.ConclusionWe suggest that U. prolifera extract alleviates oxidative stress via Nrf2 signaling, but independent of AMPK pathway in weaned piglets challenged with hydrogen peroxide. These results shed new insight into the potential applications of U. prolifera extract as a therapeutic agent for the prevention and treatment of oxidative stress-induced intestinal diseases.

The demand for animal protein has increased considerably worldwide, especially in China, where large numbers of livestock and poultry are produced. Antibiotics have been widely applied to promote growth and prevent diseases. However, the overuse of antibiotics in animal feed has caused serious environmental and health risks, especially the wide spread of antimicrobial resistance (AMR), which seriously affects animal and human health, food safety, ecosystems, and the sustainable future development of animal protein production. Unfortunately, AMR has already become a worldwide challenge, so international cooperation is becoming more important for combatting it. China’s efforts and determination to restrict antibiotic usage through law enforcement and effective management are of significance. In this review, we address the pollution problems of antibiotics; in particular, the AMR in water, soil, and plants caused by livestock and poultry manure in China. The negative impact of widespread and intensive use of antibiotics in livestock production is discussed. To reduce and mitigate AMR problems, we emphasize in this review the development of antibiotic substitutes for the era of antibiotic prohibition.

Aims:Lactobacillus strains have protective effects against heavy metals while relieving oxidative stress and modulating the immune response. Mechanisms that ameliorate heavy metal toxicity and the relationship between probiotics and gut barrier protection in the process of heavy metal pathogenesis was poorly understood.Methods and Results: In this study, Lactobacillus brevis 23017 (LAB, L. brevis 23017), a selected probiotics strain with strong mercury binding capacities, was applied to evaluate the efficiency against mercury toxicity in a mouse model. Histopathological results along with HE stains show that L. brevis 23017 protects the integrity of the small intestinal villus, which slows weight loss in response to Hg exposure. The qRT-PCR results demonstrate that L. brevis 23017 maintains a normal mucosal barrier via modulation of tight junction proteins. Importantly, the present study demonstrates that L. brevis 23017 effectively ameliorates injury of the small intestine by reducing intestinal inflammation and alleviating oxidative stress in animal models. Moreover, L. brevis 23017 blocks oxidative stress and inflammation through MAPK and NF-κB pathways, as shown by western blot.Conclusions: Together, these results reveal that L. brevis 23017 may have applications in the prevention and treatment of oral Hg exposure with fermented functional foods by protecting gut health in daily life.

The complete mitochondrial genomes of Min pig (Hebao) are published in this paper. The full length of mtDNA is 16,719 bp and contained 13 PCGs, 2 rRNA and 22 tRNA, and 1D-loop(MN258706). A phylogenetic tree with the 13 protein-coding genes sequences of Min pig (Hebao) together with 45 other Chinese pig breeds and 7 foreign pig breeds was constructed. The results can be subsequently used to provide information for pig phylogenetic and insights into the evolution of genomes. The result of phylogenetic analysis showed that the genetic relationship of Min pig (Hebao) is closer to that of Dapulian pigs.

Streptococcus suis (S. suis) form biofilms and causes severe diseases in humans and pigs. Biofilms are communities of microbes embedded in a matrix of extracellular polymeric substances. Eradicating biofilms with the use of antibiotics or biocides is often ineffective and needs replacement with other potential agents. Compared to conventional agents, promising and potential alternatives are biofilm-inhibiting compounds without impairing growth. Here, we screened a S. suis adhesion inhibitor, rutin, derived from Syringa. Rutin, a kind of flavonoids, shows efficient biofilm inhibition of S. suis without impairing its growth. Capsular polysaccharides(CPS) are reported to be involved in its adherence to influence bacterial biofilm formation. We investigated the effect of rutin on S. suis CPS content and structure. The results showed that rutin was beneficial to improve the CPS content of S. suis without changing its structure. We further provided evidence that rutin specifically affected S. suis biofilm susceptibility by affecting CPS biosynthesis in vitro. The study explores the antibiofilm potential of rutin against S. suis which can be used as an adhesion inhibitor for the prevention of S. suis biofilm-related infections. Nevertheless, rutin could be used as a novel natural inhibitor of biolfilm and its molecular mechanism provide basis for its pharmacological and clinical applications.