Integrated Metabolomic and transcriptomic analyses reveal deoxycholic acid promotes transmissible gastroenteritis virus infection by inhibiting phosphorylation of NF-κB and STAT3.

BACKGROUND: Acute diarrhea, dehydration and death in piglets are all symptoms of transmissible gastroenteritis virus (TGEV), which results in significant financial losses in the pig industry. It is important to understand the pathogenesis and identify new antiviral targets by revealing the metabolic interactions between TGEV and host cells. RESULTS: We performed metabolomic and transcriptomic analyses of swine testicular cells infected with TGEV. A total of 1339 differential metabolites and 206 differentially expressed genes were detected post TEGV infection. The differentially expressed genes were significantly enriched in the HIF-1 signaling pathway and PI3K-Akt signaling. Integrated analysis of differentially expressed genes and differential metabolites indicated that they were significantly enriched in the metabolic processes such as nucleotide metabolism, biosynthesis of cofactors and purine metabolism. In addition, the results showed that most of the detected metabolites involved in the bile secretion was downregulated during TGEV infection. Furthermore, exogenous addition of key metabolite deoxycholic acid (DCA) significantly enhanced TGEV replication by NF-κB and STAT3 signal pathways. CONCLUSIONS: We identified a significant metabolite, DCA, related to TGEV replication. It added TGEV replication in host cells by inhibiting phosphorylation of NF-κB and STAT3. This study provided novel insights into the metabolomic and transcriptomic alterations related to TGEV infection and revealed potential molecular and metabolic targets for the regulation of TGEV infection.

LncRNA446 Regulates Tight Junctions by Inhibiting the Ubiquitinated Degradation of Alix after Porcine Epidemic Diarrhea Virus Infection.

Porcine epidemic diarrhea (PED) is a highly contagious disease, caused by porcine epidemic diarrhea virus (PEDV), which causes huge economic losses. Tight junction-associated proteins play an important role during virus infection; therefore, maintaining their integrity may be a new strategy for the prevention and treatment of PEDV. Long noncoding RNAs (lncRNAs) participate in numerous cellular functional activities, yet whether and how they regulate the intestinal barrier against viral infection remains to be elucidated. Here, we established a standard system for evaluating intestinal barrier integrity and then determined the differentially expressed lncRNAs between PEDV-infected and healthy piglets by lncRNA-seq. A total of 111 differentially expressed lncRNAs were screened, and lncRNA446 was identified due to significantly higher expression after PEDV infection. Using IPEC-J2 cells and intestinal organoids as in vitro models, we demonstrated that knockdown of lncRNA446 resulted in increased replication of PEDV, with further damage to intestinal permeability and tight junctions. Mechanistically, RNA pulldown and an RNA immunoprecipitation (RIP) assay showed that lncRNA446 directly binds to ALG-2-interacting protein X (Alix), and lncRNA446 inhibits ubiquitinated degradation of Alix mediated by TRIM25. Furthermore, Alix could bind to ZO1 and occludin and restore the expression level of the PEDV M gene and TJ proteins after lncRNA446 knockdown. Additionally, Alix knockdown and overexpression affects PEDV infection in IPEC-J2 cells. Collectively, our findings indicate that lncRNA446, by inhibiting the ubiquitinated degradation of Alix after PEDV infection, is involved in tight junction regulation. This study provides new insights into the mechanisms of intestinal barrier resistance and damage repair triggered by coronavirus. IMPORTANCE Porcine epidemic diarrhea is an acute, highly contagious enteric viral disease severely affecting the pig industry, for which current vaccines are inefficient due to the high variability of PEDV. Because PEDV infection can lead to severe injury of the intestinal epithelial barrier, which is the first line of defense, a better understanding of the related mechanisms may facilitate the development of new strategies for the prevention and treatment of PED. Here, we demonstrate that the lncRNA446 directly binds one core component of the actomyosin-tight junction complex named Alix and inhibits its ubiquitinated degradation. Functionally, the lncRNA446/Alix axis can regulate the integrity of tight junctions and potentially repair intestinal barrier injury after PEDV infection.

A Systematic Review and Meta-Analysis of Efficacy and Safety of Cilostazol Prescription in Patients With Femoropopliteal Peripheral Artery Disease After Endovascular Therapy.

PURPOSE: The purpose of this study is to assess the efficacy and safety of cilostazol prescription in patients with femoropopliteal peripheral artery disease (PAD) after endovascular therapy (EVT). MATERIALS AND METHODS: We conducted a systematic review and meta-analysis of all studies reporting the outcomes of cilostazol after femoropopliteal EVT of PAD up to September 2022. Clinical outcomes of interest included primary patency, in-stent restenosis (ISR), vessel re-occlusion, freedom from target lesion revascularization (TLR), repeat revascularization, all-cause mortality, amputation, major adverse cardiovascular events (MACEs) and major adverse limb events (MALEs), and bleeding complication. RESULTS: A total of 4 randomized controlled trials (RCTs) and 8 observational studies containing a total of 4898 patients met the inclusion criteria and were included in this systematic review and meta-analysis. We found that the use of cilostazol was associated with higher primary patency after femoropopliteal artery EVT (odds ratio [OR]=1.67, 95% confidence interval [CI]=1.50-1.87, p<0.001, I2=33.2%), a lower risk of ISR (OR=0.43, 95% CI=0.29-0.63, p<0.001, I2=37.6%), repeat revascularization (OR=0.43, 95% CI=0.24-0.76, p<0.005, I2=27.4%), and vessel re-occlusion (OR=0.59, 95% CI=0.38-0.93, p<0.05, I2=0%). There was an increase in freedom from TLR rate (OR=2.19, 95% CI=1.58-3.05, p<0.001, I2=0%), as well as a reduction in the occurrence of MALEs (OR=0.50, 95% CI=0.29-0.85, p<0.05, I2=0%). However, there was no significant difference in amputation, MACEs, all-cause mortality, and major bleeding complications. Subgroup analysis showed that cilostazol treatment in patients with femoropopliteal drug-eluting stents (DES) implantation remained associated with higher primary patency and a lower risk of ISR. CONCLUSIONS: After EVT of femoropopliteal artery lesions, additional oral cilostazol enhances primary patency, reduces the occurrences of ISR and vessel re-occlusion, diminishes the risks associated with MALEs, lowers the need for repeat revascularization, and increases freedom from TLR rates. However, it does not impact amputation, MACEs, all-cause mortality, or major bleeding complications. These findings suggest cilostazol as a potentially safe and effective adjunct therapy in patients with femoropopliteal PAD after EVT. CLINICAL IMPACT: After undergoing endovascular therapy (EVT) for femoropopliteal artery lesions, the addition of cilostazol to antiplatelet therapy can significantly improve primary patency, reducing the incidence of in-stent restenosis, repeat revascularization, vessel re-occlusion, and major adverse limb events while increasing freedom from target lesion revascularization rate. The simultaneous use of drug-eluting stents in the femoropopliteal artery lesions, combined with cilostazol, potentially results in a synergistic anti-stenotic effect. This therapeutic approach does not appear to be associated with an increased risk of major bleeding events or all-cause mortality. These findings provide additional evidence supporting the treatment of anti-stenosis in patients with femoropopliteal artery lesions after EVT.

Genetic aspects of immunoglobulins and cyclophilin A in milk as potential indicators of mastitis resistance in Holstein cows.

Mastitis is one of the most frequent and costly diseases affecting dairy cattle. Natural antibodies (immunoglobulins) and cyclophilin A (CyPA), the most abundant member of the family of peptidyl prolyl cis/trans isomerases, in milk may serve as indicators of mastitis resistance in dairy cattle. However, genetic information for CyPA is not available, and knowledge on the genetic and nongenetic relationships between these immune-related traits and somatic cell score (SCS) and milk yield in dairy cattle is sparse. Therefore, we aimed to comprehensively evaluate whether immune-related traits consisting of 5 Ig classes (IgG, IgG1, IgG2, IgA, and IgM) and CyPA in the test-day milk of Holstein cows can be used as genetic indicators of mastitis resistance by evaluating the genetic and nongenetic relationships with SCS in milk. The nongenetic factors affecting immune-related traits and the effects of these traits on SCS were evaluated. Furthermore, the genetic parameters of immune-related traits according to health status and genetic relationships under different SCS environments were estimated. All immune-related traits were significantly associated with SCS and directly proportional. Additionally, evaluation using a classification tree revealed that IgA, IgG2, and IgG were associated with SCS levels. Genetic factor analyses indicated that heritability estimates were low for CyPA (0.08) but moderate for IgG (0.37), IgA (0.44), and IgM (0.44), with positive genetic correlations among Ig (0.25-0.96). We also evaluated the differences in milk yield and SCS of cows between the low and high groups according to their sires' estimated breeding value for immune-related traits. In the high group, IgA had a significantly lower SCS in milk at 7 to 30 d compared with that in the low group. Furthermore, the Ig in milk had high positive genetic correlations between healthy and infected conditions (0.82-0.99), suggesting that Ig in milk under healthy conditions could interact with those under infected conditions, owing to the genetic ability based on the level of Ig in milk. Thus, Ig in milk are potential indicators for the genetic selection of mastitis resistance. However, because only the relationship between immune-related traits and SCS was investigated in this study, further study on the relationship between clinical mastitis and Ig in milk is needed before Ig can be used as an indicator of mastitis resistance.

Research on Magnetic Field-Based Damage Detection Technology for Ferromagnetic Microwires.

Composite materials are frequently exposed to external factors during their operational service, resulting in internal structural damage which subsequently impacts their structural performance. This paper employs ferromagnetic materials for their sensitivity to magnetic field strength. By detecting variations in the magnetic field within the embedded ferromagnetic microwires of composite materials, the aim is to indirectly assess the health status of the composite materials. Firstly, a theoretical numerical model for magnetic field intensity at the crack site was established. Subsequently, a finite element model was employed to analyze the variations in the magnetic characteristics of ferromagnetic microwires at the crack site. Under different parameter conditions, the patterns of magnetic signals at the crack site were determined. The results indicate that with an increase in the angle between the external magnetic field and the crack, the fitted curve of the magnetic signal shows a linear increase. The distance between the peak and valley of the radial magnetic signal in the axial direction decreases, and the axial magnetic signal transitions from double-peak to single-peak. With the increase in crack depth, the fitted curve of the magnetic signal shows a linear increase, and the magnetic signal at the crack tip also exhibits a linear increase. An increase in crack width leads to a non-linear decrease in the fitted curve of the magnetic signal, and after reaching a certain width, the magnetic signal stabilizes. For two identical cracks at different distances, the magnetic signal exhibits a transition from a complete pattern to two complete patterns. With the increase in the external magnetic field, the magnetic signal shows a completely regular linear increase. By analyzing and calculating the variations in magnetic signals, the patterns of magnetic characteristics under the damaged state of ferromagnetic microwires were obtained. This serves as a basis for assessing whether they can continue in service and for evaluating the overall health status of composite materials.

Silencing METTL3 Stabilizes Atherosclerotic Plaques by Regulating the Phenotypic Transformation of Vascular Smooth Muscle Cells via the miR-375-3p/PDK1 Axis.

PURPOSE: Atherosclerosis (AS) is a primary cause of cardiovascular diseases. This study investigated the mechanism of methyltransferase-like 3 (METTL3) in AS plaques via modulating the phenotypic transformation of vascular smooth muscle cells (VSMCs). METHODS: AS mouse models and MOVAS cell models were established through high-fat diet and the treatment of ox-LDL, respectively. METTL3 expression in AS models was detected via RT-qPCR and Western blot. The AS plaques, lipid deposition, and collagen fibers were examined via histological staining. The levels of Ly-6c, α-SMA, and OPN were examined via Western blot. The blood lipid indexes in mouse aortic tissues were determined using kits. The proliferation and migration of MOVAS cells were detected via CCK-8 and Transwell assays. The m6A modification level of mRNA was quantified. The binding relationship between pri-miR-375 and DGCR8, and the enrichment of m6A on pri-miR-375 were detected via RIP. The binding relationship between miR-375-3p and 3-phosphoinositide-dependent protein kinase-1 (PDK1) was verified via dual-luciferase assay. Joint experiments were designed to investigate the role of miR-375-3P/PDK1 in the phenotypic transformation of VSMCs. RESULTS: METTL3 was highly expressed in AS. Silencing METTL3 alleviated AS progression and stabilized AS plaques in mice, and limited the phenotypic transformation of VSMCs induced by ox-LDL. Silencing METTL3 inhibited m6A level and decreased the binding of DGCR8 to pri-miR-375 and further limited miR-375-3p expression. miR-375-3p targeted PDK1 transcription. miR-375-3p upregulation or PDK1 downregulation facilitated the phenotypic transformation of VSMCs. CONCLUSION: METTL3-mediated m6A modification promoted VSMC phenotype transformation and made AS plaques more vulnerable via the miR-375-3p/PDK1 axis.

Metabolomic and Proteomic Profiling of Porcine Intestinal Epithelial Cells Infected with Porcine Epidemic Diarrhea Virus.

Porcine epidemic diarrhea virus (PEDV) infection results in severe epidemic diarrhea and the death of suckling pigs. Although new knowledge about the pathogenesis of PEDV has been improved, alterations in metabolic processes and the functional regulators involved in PEDV infection with host cells remain largely unknow. To identify cellular metabolites and proteins related to PEDV pathogenesis, we synergistically investigated the metabolome and proteome profiles of PEDV-infected porcine intestinal epithelial cells by liquid chromatography tandem mass spectrometry and isobaric tags for relative and absolute quantification techniques. We identified 522 differential metabolites in positive and negative ion modes and 295 differentially expressed proteins after PEDV infection. Pathways of cysteine and methionine metabolism, glycine, serine and threonine metabolism, and mineral absorption were significantly enriched by differential metabolites and differentially expressed proteins. The betaine-homocysteine S-methyltransferase (BHMT) was indicated as a potential regulator involved in these metabolic processes. We then knocked down the BHMT gene and observed that down-expression of BHMT obviously decreased copy numbers of PEDV and virus titers (p < 0.01). Our findings provide new insights into the metabolic and proteomic profiles in PEDV-infected host cells and contribute to our further understanding of PEDV pathogenesis.

A High-Fat Diet Increases the Characteristics of Gut Microbial Composition and the Intestinal Damage Associated with Non-Alcoholic Fatty Liver Disease.

The prevalence of non-alcoholic fatty liver disease (NAFLD) is increasing annually, and emerging evidence suggests that the gut microbiota plays a causative role in the development of NAFLD. However, the role of gut microbiota in the development of NAFLD remains unclear and warrants further investigation. Thus, C57BL/6J mice were fed a high-fat diet (HFD), and we found that the HFD significantly induced obesity and increased the accumulation of intrahepatic lipids, along with alterations in serum biochemical parameters. Moreover, it was observed that the HFD also impaired gut barrier integrity. It was revealed via 16S rRNA gene sequencing that the HFD increased gut microbial diversity, which enriched Colidextribacter, Lachnospiraceae-NK4A136-group, Acetatifactor, and Erysipelatoclostridium. Meanwhile, it reduced the abundance of Faecalibaculum, Muribaculaceae, and Coriobacteriaceae-UCG-002. The predicted metabolic pathways suggest that HFD enhances the chemotaxis and functional activity of gut microbiota pathways associated with flagellar assembly, while also increasing the risk of intestinal pathogen colonization and inflammation. And the phosphotransferase system, streptomycin biosynthesis, and starch/sucrose metabolism exhibited decreases. These findings reveal the composition and predictive functions of the intestinal microbiome in NAFLD, further corroborating the association between gut microbiota and NAFLD while providing novel insights into its potential application in gut microbiome research for NAFLD patients.

Metabolomics and Transcriptomics Analyses of Curcumin Alleviation of Ochratoxin A-Induced Hepatotoxicity.

Ochratoxin A (OTA) is one of the mycotoxins that poses a serious threat to human and animal health. Curcumin (CUR) is a major bioactive component of turmeric that provides multiple health benefits. CUR can reduce the toxicities induced by mycotoxins, but the underlying molecular mechanisms remain largely unknown. To explore the effects of CUR on OTA toxicity and identify the key regulators and metabolites involved in the biological processes, we performed metabolomic and transcriptomic analyses of livers from OTA-exposed mice. We found that CUR can alleviate the toxic effects of OTA on body growth and liver functions. In addition, CUR supplementation significantly affects the expressions of 1584 genes and 97 metabolites. Integrated analyses of transcriptomic and metabolomic data showed that the pathways including Arachidonic acid metabolism, Purine metabolism, and Cholesterol metabolism were significantly enriched. Pantothenic acid (PA) was identified as a key metabolite, the exogenous supplementation of which was observed to significantly alleviate the OTA-induced accumulation of reactive oxygen species and cell apoptosis. Further mechanistical analyses revealed that PA can downregulate the expression level of proapoptotic protein BAX, enhance the expression level of apoptosis inhibitory protein BCL2, and decrease the level of phosphorylated extracellular signal-regulated kinase 1/2 (pERK1/2). This study demonstrated that CUR can alleviate the adverse effects of OTA by influencing the transcriptomic and metabolomic profiles of livers, which may contribute to the application of CUR in food and feed products for the prevention of OTA toxicity.

Surface Termination on Unstable Methylammonium-based Perovskite Using a Steric Barrier for Improved Perovskite Solar Cells.

Compared to widely adopted low-dimensional/three-dimensional (LD/3D) heterostructure, functional organic cation based surface termination on perovskite can not only realize advantage of defect passivation but also prevent potential disadvantage of the heterostructure induced intercalation into 3D perovskite. However, it is still very challenging to controllably construct surface termination on organic-inorganic hybrid perovskite because the functional organic cations' substitution reaction is easy to form LD/3D heterostructure. Here, we report using a novel benzyltrimethylammonium (BTA) functional cation with rational designed steric hindrance to effectively surface terminate onto methylammonium lead triiodide (MAPbI3 ) perovskite, which is composed of the most unstable MA cations. The BTA cation is difficult to form a specific 1.5-dimensional perovskite of BTA4 Pb3 I10 by cation substitution with MA cation, which then provides a wide processing window (around 10 minutes) for surface terminating on MAPbI3 films. Moreover, the BTAI surface terminated BTAI-MAPbI3 shows better passivation effect than BTA4 Pb3 I10 -MAPbI3 heterojunction. Finally, BTAI surface terminated solar cell (0.085 cm2 ) and mini-module (11.52 cm2 ) obtained the efficiencies of 22.03 % and 18.57 %, which are among the highest efficiencies for MAPbI3 based ones.

Analysis of the roles of the Notch1 signalling pathway in modulating deoxynivalenol cytotoxicity.

Deoxynivalenol (DON) is a trichothecenes produced by fungi that is widespread and poses a threat to human and animal health. The Notch1 signalling pathway is tightly involved in cell fate determination. The aim of this study was to investigate the role of the Notch1 signalling pathway in DON exposure. Herein, we found that the Notch1 signalling pathway was significantly activated after DON exposure, while Notch1 expression was negatively regulated by DON-induced ROS. Then, the Notch1 signalling pathway was blocked by the γ-secretase inhibitor DAPT in DON exposure. Flow cytometry analysis and antioxidant parameter measurements revealed that DAPT treatment significantly aggravated the oxidative stress induced by DON. The detection of apoptosis showed that DAPT treatment increased the cell apoptotic rate. Further analysis revealed that inhibiting the Notch1 signalling pathway reduced autophagy upon DON exposure. RT-qPCR and Western blot analysis showed that inhibiting the Notch1 signalling pathway aggravated cellular inflammation and activated the MAPK pathway, indicating that the MAPK pathway may be the downstream signalling pathway. Taken together, our research revealed that the Notch1 signalling pathway is essential for protection against DON. Inhibition of Notch1 signalling increases oxidative stress, causes cell apoptosis, reduces autophagy and aggravates cell inflammation after DON exposure. This study investigated the role of the Notch1 signalling pathway in DON exposure and provided a basis for exploring the mechanism of DON.

Analysis of RIOK2 Functions in Mediating the Toxic Effects of Deoxynivalenol in Porcine Intestinal Epithelial Cells.

Deoxynivalenol (DON) is a type of mycotoxin that threatens human and livestock health. Right open reading frame kinase 2 (RIOK2) is a kinase that has a pivotal function in ribosome maturation and cell cycle progression. This study aims to clarify the role of the RIOK2 gene in DON-induced cytotoxicity regulation in porcine intestinal epithelial cells (IPEC-J2). Cell viability assay and flow cytometry showed that the knockdown of RIOK2 inhibited proliferation and induced apoptosis, cell cycle arrest, and oxidative stress in DON-induced IPEC-J2. Then, transcriptome profiling identified candidate genes and pathways that closely interacted with both DON cytotoxicity regulation and RIOK2 expression. Furthermore, RIOK2 interference promoted the activation of the MAPK signaling pathway by increasing the phosphorylation of ERK and JNK. Additionally, we performed the dual-luciferase reporter and ChIP assays to elucidate that the expression of RIOK2 was influenced by the binding of transcription factor Sp1 with the promoter region. Briefly, the reduced expression of the RIOK2 gene exacerbates the cytotoxic effects induced by DON in IPEC-J2. Our findings provide insights into the control strategies for DON contamination by identifying functional genes and effective molecular markers.

Tough hybrid microgel-reinforced hydrogels dependent on the size and modulus of the microgels.

Microgel-reinforced (MR) hydrogels are tough hydrogels with dispersed rigid microgels embedded in a continuous soft matrix. MR gels have the great potential to provide not only mechanical toughness but also the desired functional matrix by incorporation of various functional microgels. Understanding the toughening mechanism of the MR hydrogels is critical for the rational design of the desired functionally tough MR gels. However, our current knowledge of the toughening mechanism of MR gels mainly comes from the MR hydrogels with both chemically crosslinked dispersed microgels and a continuous matrix. Little is known about the hybrid MR gels with physically crosslinked microgels embedded in a chemically crosslinked matrix. Herein, we synthesize such hybrid MR hydrogels with the ionic crosslinked calcium alginate microgels incorporated into the chemically crosslinked polyacrylamide (PAAm) matrix. The alginate microgels show strong size and modulus effects on the toughening enhancement: the larger microgels could toughen the MR gels more than the small ones, and the microgels with medium modulus could maximize the toughness of the MR gels. By comparison of the mechanical performances of the MR and the corresponding double network (DN) hydrogels, we have proposed that the hybrid MR gels may have the same toughening mechanism as the bulk DN gel. This work tries to better understand the structure-property relationships of both MR and DN gels and help in the design of more functionally tough MR gels with the desired properties.

Functional analysis of DNA methylation of the PACSIN1 promoter in pig peripheral blood mononuclear cells.

DNA methylation plays essential roles in regulating the activity of genes and may contribute to understanding the potential epigenetic biomarkers response to viruses. To explore the function of DNA methylation of protein kinase C and casein kinase substrate in neurons 1 (PACSNI1) promoter, herein we performed the bisulfite sequencing polymerase chain reaction and Western blot analysis to verify hypermethylation and downregulation of PACSIN1 expression in peripheral blood mononuclear cells of pig as the vitro model. Promoter methylation could reduce the transcriptional activity of the PACSIN1 gene potentially by affecting the binding of transcription factor Sp1. In addition, downregulation of the PACSIN1 gene expression could facilitate the production of interleukin-6 (IL-6), IL-8, tumor necrosis factor α, and NECAP2. The comprehensive analysis of PACSIN1 methylation and its function will help us to understand the gene to be served as an important candidate gene in pig for disease resistance breeding and aid in the identification of potential epigenetic biomarkers associated with responsiveness to viruses.

Ionic Gels and Their Applications in Stretchable Electronics.

Ionic gels represent a novel class of stretchable materials where ionic conducting liquid is immobilized in a polymer matrix. This review focuses on the design of ionic gel materials and device fabrication of ionic-gel-based stretchable electronics. In particular, recent progress in ionic-gel-based electronic skin (pressure/strain sensors, electric double-layer transistors, etc.), flexible displays, energy storage devices, and soft actuators are summarized, followed by a discussion of challenges in developing ionic-gel-based electronics and suggestions for future research directions that might overcome those challenges.

A genomic variant in IRF9 is associated with serum cytokine levels in pig.

The interferon regulatory factor 9 (IRF9) gene is a member of the IRF family and has been shown to play functionally diverse roles in the regulation of the immune system. Previous study revealed the IRF9 gene resides within the reported quantitative trait locus (QTLs) for cytokine levels. The aims of this study were to identify genomic variants in IRF9 and to test the association between the variants and cytokine levels in pig. A synonymous single-nucleotide polymorphism (c.459A>G) was identified in exon 4 of the IRF9 gene. Association analysis in 300 piglets (Landrace, n=68; large white, n=158; and Songliao black, n=74) showed that this variant was significantly associated with the level of interferon (IFN)-γ and the ratio of IFN-γ to IL-10 in serum (P<0.05). Relative quantification of messenger RNA (mRNA) revealed that spleen had the highest expression level and individuals with genotype AA had higher expression than those with genotype AG. Transfection-based mRNA stability assay analysis further showed that the mutant allele G could reduce the RNA stability of IRF9. These findings suggest that the SNP (c.459A>G) could be a causative mutation for the association between IRF9 and the serum cytokine levels in swine.

Preparation of Silica/Reduced Graphene Oxide Nanosheet Composites for Removal of Organic Contaminants from Water.

Graphene-based composites open up new opportunities as effective adsorbents for the removal of organic contaminants from water. In this article, we report a novel and facile process to synthesize well-dispersed silica/reduced graphene oxide (SiO2/RGO) nanosheet composites. The SiO2/RGO nanosheet composites are prepared through a modified sol-gel process with in situ hydrolysis of tetraethoxysilane (TEOS) on graphene oxide (GO) nanosheet, followed by reduction of GO to graphene. In comparison with the RGO nanosheets, the as-prepared SiO2/RGO nanosheet composites have a larger surface area and good aqueous disperse ability. In addition, the application of SiO2/RGO nanosheet composites was demonstrated on removing organic dyes from water. The SiO2/RGO nanosheet composites show rapid and stable adsorption performance on removal of Methylene Blue (MB) and thionine (TH) from water. It is indicated that the resulting SiO2/RGO composites can be utilized as efficient adsorbents for the removal of organic contaminants from water.

Differential expression of genes in milk of dairy cattle during lactation.

The milk fat globule (MFG) is one of the most representative of mammary gland tissues and can be utilized to study gene expression of lactating cows during lactation. In this study, RNA-seq technology was employed to detect differential expression of genes in MFGs at day 10 and day 70 after calving between two groups of cows with extremely high (H group) and low (L group) 305-day milk yield, milk fat yield and milk protein yield. In total, 1232, 81, 429 and 178 significantly differentially expressed genes (false discovery rate q < 0.05) were detected between H10 and L10, H70 and L70, H10 and H70, and L10 and L70 respectively. Gene Ontology enrichment and pathway analysis revealed that these differentially expressed genes were enriched in biological processes involved in mammary gland development, protein and lipid metabolism process, signal transduction, cellular process, differentiation and immune function. Among these differentially expressed genes, 178 (H10 vs. L10), 4 (H70 vs. L70), 68 (H10 vs. H70) and 22 (L10 vs. L70) were found to be located within previously reported QTL regions for milk production traits. Based on these results, some promising candidate genes for milk production traits in dairy cattle were suggested.

Resequencing diverse Chinese indigenous breeds to enrich the map of genomic variations in swine.

To enrich the map of genomic variations in swine, we randomly sequenced 13 domestic and wild individuals from China and Europe. We detected approximately 28.1 million single nucleotide variants (SNVs) and 3.6 million short insertions and deletions (INDELs), of which 2,530,248 SNVs and 3,456,626 INDELs were firstly identified compared with dbSNP 143. Moreover, 208,687 SNVs and 24,161 INDELs were uniquely observed in Chinese pigs, potentially accounting for phenotypic differences between Chinese and European pigs. Furthermore, significantly high correlation between SNV and INDEL was witnessed, which indicated that these two distinct variants may share similar etiologies. We also predicted loss of function genes and found that they were under weaker evolutionary constraints. This study gives interesting insights into the genomic features of the Chinese pig breeds. These data would be useful in the establishment of high-density SNP map and would lay a foundation for facilitating pig functional genomics study.

MicroRNA Transcriptome of Poly I:C-Stimulated Peripheral Blood Mononuclear Cells Reveals Evidence for MicroRNAs in Regulating Host Response to RNA Viruses in Pigs.

MicroRNAs (miRNAs) are one family of small noncoding RNAs that function to modulate the activity of specific mRNA targets in animals. To understand the role of miRNAs in regulating genes involved in the host immune response to RNA viruses, we profiled and characterized the miRNAs of swine peripheral blood mononuclear cells (PBMC) stimulated with poly I:C, a synthetic dsRNA analog, by miRNA-sequencing (miRNA-seq). We identified a total of 905 miRNAs, of which 503 miRNAs were firstly exploited herein with no annotation in the latest miRBase 21.0. Expression analysis demonstrated that poly I:C stimulation can elicit significantly differentially expressed (DE) miRNAs in Dapulian (n = 20), one Chinese indigenous breed, as well as Landrace (n = 23). By integrating the mRNA expression profiles of the same sample with miRNA profiles, we carried out function analyses of the target genes of these DE miRNAs, with the results indicating that target genes were most enriched in some immune-related pathways and gene ontology (GO) terms, suggesting that DE miRNAs play an important role in the regulation of host to poly I:C stimulation. Furthermore, we also detected 43 and 61 significantly DE miRNAs between the two breeds in the control sample groups and poly I:C stimulation groups, respectively, which may be involved in regulation of the different characteristics of the two breeds. This study describes for the first time the PBMC miRNA transcriptomic response to poly I:C stimulation in pigs, which not only contributes to a broad view of the pig miRNAome but improves our understanding of miRNA function in regulating host immune response to RNA viruses.