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Plant anatomy is patterned early during leaf development which suggests studying the spatial–temporal transcriptomes of primordia will help identify critical regulative and functional genes. We successfully isolated the leaf primordia tissues from the C3 grass rice and the C4 grass foxtail millet by laser capture microdissection (LCM) and studied the gene expression throughout leaf developmental stages. Our data analysis uncovered the conserved expression patterns of certain gene clusters both in rice and foxtail millet during leaf development. We revealed genes and transcription factors involved in vein formation, stomatal development, and suberin accumulation. We identified 79 candidate genes associated with functional regulation of C4 anatomy formation. Screening phenotype of the candidate genes revealed that knock-out of a putative polar auxin transport related gene NAL1 resulted significantly reduced veinal space in rice leaf. Our present work provides a foundation for future analyses of genes with novel functions in grasses and their role in leaf development, in particular the role in leaves with a contrasting C3 vs. C4 biosynthetic pathway.

Abstract Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) poses a major threat to the global swine industry, yet effective prevention and control measures remain elusive. This study unveils Nitazoxanide (NTZ) as a potent inhibitor of PRRSV both in vitro and in vivo. Through High-Throughput Screening techniques, 16 potential anti-PRRSV compounds are identified from a library comprising FDA-approved and pharmacopeial drugs. We show that NTZ displays strong efficacy in reducing PRRSV proliferation and transmission in a swine model, alleviating viremia and lung damage. Additionally, Tizoxanide (TIZ), the primary metabolite of NTZ, has been identified as a facilitator of NMRAL1 dimerization. This finding potentially sheds light on the underlying mechanism contributing to TIZ’s role in augmenting the sensitivity of the IFN-β pathway. These results indicate the promising potential of NTZ as a repurposed therapeutic agent for Porcine Reproductive and Respiratory Syndrome (PRRS). Additionally, they provide valuable insights into the antiviral mechanisms underlying NTZ’s effectiveness.

Porcine reproductive and respiratory syndrome virus (PRRSV) remains one of the major threats to swine industry, resulting in huge economic losses worldwide. Currently, PRRSV has diversified into multiple lineages with characteristics of extensive recombination in China. In this research, three virus strains were isolated and four virus whole genome sequences were generated and analyzed from clinical samples collected in Gansu province of China in 2023. The four virus strains were designated GSTS4-2023, GSLX2-2023, GSFEI2-2023 and GSBY4-2023. Phylogenetic analysis based on ORF5 sequences showed that GSTS4-2023, GSLX2-2023, GSFEI2-2023 and GSBY4-2023 shared 91.7, 91.2, 93.2 and 92.9% homology with NADC30 strain respectively, and belonged to lineage 1 of PRRSV-2. In addition, one amino acid deletion was observed at position 33 in ORF5 of GSTS4-2023, GSLX2-2023 and GSFEI2-2023. Moreover, amino acid alignment of the four strains showed a typical discontinuous 131-amino acid (aa) deletion in NSP2 for NADC30-like virus strains. Recombination analysis revealed that all four strains originated from NADC30 (lineage 1), with their minor parents coming from JXA1-like strains (lineage 8), VR-2332-like strains (lineage5) and QYYZ-like strains (lineage3). Finally, the three isolated virus strains, GSTS4-2023, GSLX2-2023 and GSFEI2-2023 showed relatively low levels of replication in cell culture. Our findings provide important implications for the field epidemiology of PRRSV.

Abstract Background Eurasian pigs have undergone lineage admixture throughout history. It has been confirmed that the genes of indigenous pig breeds in China have been introduced into Western commercial pigs, providing genetic materials for breeding Western pigs. Pigs in Taihu Lake region (TL), such as the Meishan pig and Erhualian pig, serve as typical representatives of indigenous pig breeds in China due to their high reproductive performances. These pigs have also been imported into European countries in 1970 and 1980 s. They have played a positive role in improving the reproductive performances in European commercial pigs such as French Large White pigs (FLW). However, it is currently unclear if the lineage of TL pigs have been introgressed into the Danish Large White pigs (DLW), which are also known for their high reproductive performances in European pigs. To systematically identify genomic regions in which TL pigs have introgressed into DLW pigs and their physiological functions, we collected the re-sequencing data from 304 Eurasian pigs, to identify shared haplotypes between DLW and TL pigs. Results The findings revealed the presence of introgressed genomic regions from TL pigs in the genome of DLW pigs indeed. The genes annotated within these regions were found to be mainly enriched in neurodevelopmental pathways. Furthermore, we found that the 115 kb region located in SSC16 exhibited highly shared haplotypes between TL and DLW pigs. The major haplotype of TL pigs in this region could significantly improve reproductive performances in various pig populations. Around this genomic region, NDUFS4 gene was highly expressed and showed differential expression in multiple reproductive tissues between extremely high and low farrowing Erhualian pigs. This suggested that NDUFS4 gene could be an important candidate causal gene responsible for affecting the reproductive performances of DLW pigs. Conclusions Our study has furthered our knowledge of the pattern of introgression from TL into DLW pigs and the potential effects on the fertility of DLW pigs.

This article proposes a low cross-axis sensitivity resonant MEMS(Micro-Electro-Mechanical Systems) accelerometer that is optimized based on the BP and NSGA-II algorithms. When resonant accelerometers are used in seismic monitoring, automotive safety systems, and navigation applications, high immunity and low cross-axis sensitivity are required. To improve the high immunity of the accelerometer, a coupling structure is introduced. This structure effectively separates the symmetric and antisymmetric mode frequencies of the DETF resonator and prevents mode coupling. To obtain higher detection accuracy and low cross-axis sensitivity, a decoupling structure is introduced. To find the optimal dimensional parameters of the decoupled structure, the BP and NSGA-II algorithms are used to optimize the dimensional parameters of the decoupled structure. The optimized decoupled structure has an axial stiffness of 6032.21 N/m and a transverse stiffness of 6.29 N/m. The finite element analysis results show that the sensitivity of the accelerometer is 59.1 Hz/g (Y-axis) and 59 Hz/g (X-axis). Cross-axis sensitivity is 0.508% (Y-axis) and 0.339% (X-axis), which is significantly lower than most resonant accelerometers. The coupling structure and optimization method proposed in this paper provide a new solution for designing resonant accelerometers with high interference immunity and low cross-axis sensitivity.

Muscle satellite cells (MuSCs) are crucial for muscle development and regeneration. The primary pig MuSCs (pMuSCs) is an ideal in vitro cell model for studying the pig’s muscle development and differentiation. However, the long-term in vitro culture of pMuSCs results in the gradual loss of their stemness, thereby limiting their application. To address this conundrum and maintain the normal function of pMuSCs during in vitro passaging, we generated an immortalized pMuSCs (SV40 T-pMuSCs) by stably expressing SV40 T-antigen (SV40 T) using a lentiviral-based vector system. The SV40 T-pMuSCs can be stably sub-cultured for over 40 generations in vitro. An evaluation of SV40 T-pMuSCs was conducted through immunofluorescence staining, quantitative real-time PCR, EdU assay, and SA-β-gal activity. Their proliferation capacity was similar to that of primary pMuSCs at passage 1, and while their differentiation potential was slightly decreased. SiRNA-mediated interference of SV40 T-antigen expression restored the differentiation capability of SV40 T-pMuSCs. Taken together, our results provide a valuable tool for studying pig skeletal muscle development and differentiation.

With the continuous progress of aerospace, military technology, and marine development, the MEMS resonance pressure sensor puts forward the requirements of not only a wide range but also high sensitivity. However, traditional resonators are hardly compatible with both. In response, we propose a new sensor structure. By arranging the resonant beam and the sensitive diaphragm vertically in space, the new structure improves the rigidity of the diaphragm without changing the thickness of the diaphragm and achieves the purpose of increasing the range without affecting the sensitivity. To find the optimal structural parameters for the sensor sensitivity and range, and to prevent the effects of modal disturbances, we propose a multi-objective optimization design scheme based on the BP and NSGA-II algorithms. The optimization of the structure parameters not only improved the sensitivity but also increased the interference frequency to solve the issue of mode interference. The optimized structure achieves a sensitivity and range of 4.23 Hz/kPa and 1–10 MPa, respectively. Its linear influence factor is 38.07, significantly higher than that of most resonant pressure sensors. The structural and algorithmic optimizations proposed in this paper provide a new method for designing resonant pressure sensors compatible with a wide range and high sensitivity.

Foot-and-mouth disease virus (FMDV) serotype A is antigenically most variable within serotypes. The structures of conserved and variable antigenic sites were not well resolved. Here, a historical A/AF72 strain from A22 lineage and a latest A/GDMM/2013 strain from G2 genotype of Sea97 lineage were respectively used as bait antigen to screen single B cell antibodies from bovine sequentially vaccinated with A/WH/CHA/09 (G1 genotype of Sea97 lineage), A/GDMM/2013 and A/AF72 antigens. Total of 39 strain-specific and 5 broad neutralizing antibodies (bnAbs) were isolated and characterized. Two conserved antigenic sites were revealed by the Cryo-EM structures of FMDV serotype A with two bnAbs W2 and W125. The contact sites with both VH and VL of W125 were closely around icosahedral threefold axis and covered the B-C, E-F, and H-I loops on VP2 and the B-B knob and H-I loop on VP3; while contact sites with only VH of W2 concentrated on B-B knob, B-C and E-F loops on VP3 scattering around the three-fold axis of viral particle. Additional highly conserved epitopes also involved key residues of VP158, VP1147 and both VP272 / VP1147 as determined respectively by bnAb W153, W145 and W151-resistant mutants. Furthermore, the epitopes recognized by 20 strain-specific neutralization antibodies involved the key residues located on VP3 68 for A/AF72 (11/20) and VP3 175 position for A/GDMM/2013 (9/19), respectively, which revealed antigenic variation between different strains of serotype A. Analysis of antibody-driven variations on capsid of two virus strains showed a relatively stable VP2 and more variable VP3 and VP1. This study provided important information on conserve and variable antigen structures to design broad-spectrum molecular vaccine against FMDV serotype A.

The introduction of single-cell RNA sequencing (scRNA-seq) technology has spurred additional advancements in analyzing the cellular composition of tissues. The longissimus dorsi (LD) in pigs serves as the primary skeletal muscle for studying meat quality in the pig industry. However, the single-cell profile of porcine LD is still in its infancy stage. In this study, we profiled the transcriptomes of 16,018 cells in the LD of a newborn Suhuai pig at single-cell resolution. Subsequently, we constructed a cellular atlas of the LD, identifying 11 distinct cell populations, including endothelial cells (24.39%), myotubes (18.82%), fibro-adipogenic progenitors (FAPs, 18.11%), satellite cells (16.74%), myoblasts (3.99%), myocytes (5.74%), Schwann cells (3.81%), smooth muscle cells (3.22%), dendritic cells (2.99%), pericytes (1.86%), and neutrophils (0.33%). CellChat was employed to deduce the cell–cell interactions by evaluating the gene expression of receptor–ligand pairs across different cell types. The results show that FAPs and pericytes are the primary signal contributors in LD. In addition, we delineated the developmental trajectory of myogenic cells and examined alterations in the expression of various marker genes and molecular events throughout various stages of differentiation. Moreover, we found that FAPs can be divided into three subclusters (NR2F2-FAPs, LPL-FAPs, and TNMD-FAPs) according to their biological functions, suggesting that the FAPs could be associated with the differentiation of tendon cell. Taken together, we constructed the cellular atlas and cell communication network in LD of a newborn Suhuai pig, and analyzed the developmental trajectory of myogenic cells and the heterogeneity of FAPs subpopulation cells. This enhances our comprehension of the molecular features involved in skeletal muscle development and the meat quality control in pigs.

Abstract Integrating the single‐nucleotide polymorphisms (SNPs) significantly affecting target traits from imputed whole‐genome sequencing (iWGS) data into the genomic prediction (GP) model is an economic, efficient, and feasible strategy to improve prediction accuracy. The objective was to dissect the genetic architecture of intramuscular fat content (IFC) by genome wide association studies (GWAS) and to investigate the accuracy of GP based on pedigree‐based BLUP (PBLUP) model, genomic best linear unbiased prediction (GBLUP) models and Bayesian mixture (BayesMix) models under different strategies. A total of 482 Suhuai pigs were genotyped using an 80 K SNP chip. Furthermore, 30 key samples were selected for resequencing and were used as a reference panel to impute the 80 K chip data to the WGS dataset. The 80 K data and iWGS data were used to perform GWAS and test GP accuracies under different scenarios. GWAS results revealed that there were four major regions affecting IFC. Two important functional candidate genes were found in the two most significant regions, including protein kinase C epsilon (PRKCE) and myosin light chain 2 (MYL2). The results of the predictions showed that the PBLUP model had the lowest reliability (0.096 ± 0.032). The reliability (0.229 ± 0.035) was improved by replacing pedigree information with 80 K chip data. Compared with using 80 K SNPs alone, pruning iWGS SNPs with the R‐squared cutoff of linkage disequilibrium (0.55) led to a slight improvement (0.006), adding significant iWGS SNPs led to an improvement of reliability by 0.050 when using a one‐component GBLUP, a further increase of 0.033 when using a two‐component GBLUP model. For BayesMix models, compared with using 80 K SNPs alone, adding additional significant iWGS SNPs into one‐ or two‐component BayesMix models led to improvements of reliabilities for IFC by 0.040 and 0.089, respectively. Our results may facilitate further identification of causal genes for IFC and may be beneficial for the improvement of IFC in pig breeding programs.

Unlike microbes and mammals, cistrome dynamics in plants remains unclear. Here, using GOLDEN2-LIKE (GLK) transcription factor as an example, the authors find that most GLK binding sites are species-specific and the binding divergence is caused by cis-variations through inter-species transformation experiment.

Dietary fiber plays an important role in porcine gut health and welfare. Fiber is degraded by microbial fermentation in the intestine, and most gut microbiota related to fiber digestibility in pigs are worth pursuing. The aim of this study was to identify gut microbiota associated with the apparent total tract digestibility (ATTD) of neutral detergent fiber (NDF) and of acid detergent fiber (ADF) in pigs. Large phenotypic variations in the ATTD of NDF and of ADF were separately found among 274 Suhuai pigs. Microbial community structures were significantly different between high and low fiber digestibility groups. Fourteen genera separately dominated the communities found in the high ATTD (H-AD) of NDF and ADF samples and were in very low abundance in the low ATTD (L-AD) of NDF and ADF samples. In conclusion, norank_f__Bacteroidales_S24-7_group (p < 0.05), Ruminococcaceae_UCG-005 (p < 0.05), unclassified_f__Lachnospiraceae (p < 0.05), Treponema_2 (p < 0.01), and Ruminococcaceae_NK4A214_group (p < 0.01) were the main genera of gut microbiota affecting the ATTD of NDF in pigs. Christensenellaceae_R-7_group (p < 0.01), Treponema_2 (p < 0.05), Ruminococcaceae_NK4A214_group (p < 0.05), Ruminococcaceae_UCG-002 (p < 0.05), and [Eubacterium]_coprostanoligenes_group (p < 0.05) were the main genera of gut microbiota affecting the ATTD of ADF in pigs. The most important functions of the above different potential biomarkers were: carbohydrate transport and metabolism, general function prediction only, amino acid transport and metabolism, cell wall/membrane/envelope biogenesis, translation, transcription, replication, energy production and conversion, signal transduction mechanisms, and inorganic ion transport and metabolism. The most important metabolic pathways of the above different potential biomarkers were: membrane transport, carbohydrate metabolism, amino acid metabolism, replication and repair, translation, cell motility, energy metabolism, poorly characterized, nucleotide metabolism, metabolism of cofactors and vitamins, and cellular processes and signaling.

Abstract Foot-and-mouth disease (FMD) remains a very serious barrier to agricultural development and the international trade of animals and animal products. Recently, serotype O has been the most prevalent FMDV serotype in China, and it has evolved into four different lineages: O/SEA/Mya-98, O/ME-SA/PanAsia, O/ME-SA/Ind-2001 and O/Cathay. PanAsia-2, belonging to the O/ME-SA topotype, is prevalent in neighbouring countries and poses the risk of cross-border spread in China. This study aimed to develop a promising vaccine candidate strain that can not only provide the best protection against all serotype O FMDVs circulating in China but also be used as an emergency vaccine for the prevention and control of transboundary incursion of PanAsia-2. Here, two chimeric FMDVs (rHN/TURVP1 and rHN/NXVP1) featuring substitution of VP1 genes of the O/TUR/5/2009 vaccine strain (PanAsia-2) and O/NXYCh/CHA/2018 epidemic strain (Mya98) were constructed and evaluated. The biological properties of the two chimeric FMDVs were similar to those of the wild-type (wt) virus despite slight differences in plaque sizes observed in BHK-21 cells. The structural protein-specific antibody titres induced by the rHN/TURVP1 and wt virus vaccines in pigs and cows were higher than those induced by the rHN/NXVP1 vaccine at 28–56 dpv. The vaccines prepared from the two chimeric viruses and wt virus all induced the production of protective cross-neutralizing antibodies against the viruses of the Mya-98, PanAsia and Ind-2001 lineages in pigs and cattle at 28 dpv; however, only the animals vaccinated with the rHN/TURVP1 vaccine produced a protective immune response to the field isolate of the Cathay lineage at 28 dpv, whereas the animals receiving the wt virus and the rHN/NXVP1 vaccines did not, although the wt virus and O/GXCX/CHA/2018 both belong to the Cathay topotype. This study will provide very useful information to help develop a potential vaccine candidate for the prevention and control of serotype O FMD in China.

ABSTRACT Senecavirus A (SVA) is an emerging viral pathogen related to vesicular disease and neonatal mortality in swine, which results in enormous economic losses to the global swine industry. The clinical signs of SVA are indistinguishable from those of other vesicular diseases, such as foot-and-mouth disease, which is an economically devastating animal disease. Therefore, development of a rapid, sensitive, and specific diagnostic method for the detection of SVA infection is critical for the prevention and control of SVA and would help to rule out other exotic diseases. In this study, two whole-porcine anti-SVA antibodies (1M5 and 1M25) were produced using single B cell antibody technology. 1M5 and 1M25 possessed neutralizing activity against SVA but recognized different conformational epitopes that depended on the intact virion. Using 1M5 as the capture antibody and biotinylated 1M25 as the detection antibody, a reliable and rapid competitive enzyme-linked immunosorbent assay for detecting neutralizing antibodies (NAC-ELISA) against SVA was developed. Receiver-operating characteristic curve analysis showed that the sensitivity and specificity of the assay were 98.11% and 100%, respectively, with a cutoff percent inhibition value of 45%. The NAC-ELISA was specific for detecting SVA-specific antibodies, without cross-reactivity to other virus-infected sera. The results of the NAC-ELISA showed a strong agreement with the results of the virus neutralization test. Therefore, the NAC-ELISA developed in this study represents a sensitive, specific, and reliable tool for the detection of SVA-specific antibodies, which is applicable for serodiagnosis and serological surveillance of SVA and is conducive to the prevention and control of SVA. IMPORTANCE Senecavirus A (SVA) is an emerging picornavirus related to vesicular disease and neonatal mortality in swine, which results in enormous economic losses worldwide. Additionally, the clinical characteristics of the disease are indistinguishable from those of other vesicular diseases, such as foot-and-mouth disease. Therefore, developing tools for rapidly and accurately detecting SVA infection is critical and urgent. In this study, two porcine-derived monoclonal antibodies against SVA were generated, and a competitive ELISA for the detection of neutralizing antibodies (NAC-ELISA) against SVA was successfully developed using these two porcine monoclonal antibodies. The NAC-ELISA was SVA specific with no cross-reactivity to other related pathogens and had high sensitivity, specificity, and reproducibility for detecting SVA-specific antibody. Therefore, the NAC-ELISA developed in this study may be of great value as a simple and reliable tool for serodiagnosis or surveillance of SVA and may facilitate the prevention and control of SVA.

To evaluate the tolerance of a high-fiber diet in Erhualian pigs (Er-HL), the present investigation systematically investigated the ramifications of varying wheat bran fiber levels, specified as total dietary fiber (TDF) values of 14.07%, 16.32%, 17.99%, and 18.85%, on growth performance, fiber digestibility and gut microbiota in Er-HL, large Large White pigs (L-LW, the same physiological stage as the Er-HL) and small Large White pigs (S-LW, the same body weight as the Er-HL). Our results revealed that fiber levels exerted no discernable impact on growth performance (average daily feed intake (ADFI), and average daily gain (ADG)) of Er-HL (p > 0.05). Conversely, L-LW exhibited a decrease in ADFI and ADG with increasing fiber levels (p < 0.05). Notably, the apparent total tract digestibility (ATTD) of various fiber components, including neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose, TDF and insoluble dietary fiber (IDF), in Er-HL were significantly higher than those in S-LW and L-LW irrespective of diets (p < 0.05). The ATTD of cellulose and hemicellulose in Er-HL significantly decreased with increasing fiber levels (p < 0.05), yet remained statistically indifferent when comparing the 7%-wheat-bran-replaced diet (7% WRB, TDF 16.32%) to the basal diet (TDF 14.07%) (p > 0.05). The cecal microbiota of Er-HL had higher richness estimators (Chao1 and ACE) than those of S-LW and L-LW irrespective of diets (p < 0.01). Breed serves as a pivotal determinant in shaping swine gut microbiota. Thirteen genera were selected as the key bacteria related to high fiber digestibility of Er-HL. Further functional examination of these key genera elucidated an enrichment of pathways pertinent to carbohydrate metabolism in Er-HL samples compared with S-LW and L-LW samples. In summary, Er-HL exhibited high-fiber tolerance both in terms of growth performance and fiber digestibility compared with Large White pigs. Specifically, the ATTD of NDF, ADF, hemicellulose, IDF and TDF were significantly higher in Er-HL compared with L-LW and S-LW, irrespective of diets. Fiber level exerted no discernable impact on growth performance (ADFI, ADG) and the ATTD of fiber (NDF, ADF, IDF and TDF) in Er-HL. The optimum fiber level of the Er-HL was identified as 7% WRB (TDF 16.32%). Thirteen genera were ascertained to significantly contribute to high fiber digestibility of Er-HL, correlating with an enhancement of carbohydrate metabolism pathways.

Abstract Background The primary determinant of crop yield is photosynthetic capacity, which is under the control of photosynthesis-related genes. Therefore, the mining of genes involved in photosynthesis is important for the study of photosynthesis. MapMan Mercator 4 is a powerful annotation tool for assigning genes into proper functional categories; however, in maize, the functions of approximately 22.15% (9520) of genes remain unclear and are labeled “not assigned”, which may include photosynthesis-related genes that have not yet been identified. The fast-increasing usage of the machine learning approach in solving biological problems provides us with a new chance to identify novel photosynthetic genes from functional “not assigned” genes in maize. Results In this study, we proved the ensemble learning model using a voting eliminates the preferences of single machine learning models. Based on this evaluation, we implemented an ensemble based ML(Machine Learning) methods using a majority voting scheme and observed that including RNA-seq data from multiple photosynthetic mutants rather than only a single mutant could increase prediction accuracy. And we call this approach “A Machine Learning-based Photosynthetic-related Gene Detection approach (PGD)”. Finally, we predicted 716 photosynthesis-related genes from the “not assigned” category of maize MapMan annotation. The protein localization prediction (TargetP) and expression trends of these genes from maize leaf sections indicated that the prediction was reliable and robust. And we put this approach online base on google colab. Conclusions This study reveals a new approach for mining novel genes related to a specific functional category and provides candidate genes for researchers to experimentally define their biological functions.

ABSTRACT Previous study found that appropriate high-fiber diet (containing 19.10% total dietary fiber [TDF], treatment II) did not reduce apparent fiber digestibility of Chinese Suhuai finishing pigs and increased the yield of short-chain fatty acids (SCFAs), but too high-fiber diet (containing 24.11% TDF, treatment IV) significantly reduced apparent fiber digestibility compared with normal diet (containing 16.70% TDF, control group). However, characteristics of microbiota at the species level and histological structure in pigs with the ability to digest appropriate high-fiber diets were still unknown. This study conducted comparative analysis of cecal physiology and microbial populations colonizing cecal mucosa. The results showed intestinal development indexes including cecum length, densities of cecal goblet cells, and renewal of cecal epithelial cells in treatment II and IV had better performance than those in the control. Paludibacter jiangxiensis, Coprobacter fastidiosus, Bacteroides coprocola CAG:162, Bacteroides barnesiae, and Parabacteroides merdae enriched in treatment II expressed large number of glycoside hydrolase (GH)-encoding genes and had the largest number of GH families. In addition, pathogenic bacteria (Shigella sonnei, Mannheimia haemolytica, and Helicobacter felis) were enriched in treatment IV. Correlation analysis revealed that the intestinal development index positively correlated with the relative abundance of cecal mucosal microbiota and the amount of digested fiber. These results indicated that increased proportions of fiber-degrading microbes and enhanced intestinal development jointly promote the host to digest an appropriate high-fiber diet. However, although too-high fiber levels in diet could maintain the adaptive development of cecal epithelium, the proportions of pathogenic bacteria increased, which might lead to a decrease of fiber digestion in pigs. IMPORTANCE Although studies about the effects of dietary fiber on fiber digestion and intestinal microbiota of pigs were widely in progress, few studies have been conducted on the dynamic response of intestinal microbiota to dietary fiber levels, and the characteristics of intestinal microbiota and intestinal epithelial development adapted to high-fiber diet s were still unclear. Appropriate high fiber promoted the thickness of large intestine wall, increased the density of cecal goblet cells, and promoted the renewal of cecal epithelial cells. In addition, appropriate high fiber improves the microbial abundance with fiber-digesting potential. However, excessive dietary fiber caused an increase in the abundance of pathogenic bacteria. These results indicated that an increased proportion of fiber-degrading microbes and enhanced intestinal development jointly promote host to digest appropriate high-fiber diets. However, although too-high fiber levels in diet could maintain the adaptive development of cecal epithelium, the proportions of pathogenic bacteria increased, which might lead to a decrease of fiber digestion in pigs. Our data provided a theoretical basis for rational and efficient utilization of unconventional feed resources in pig production.

Abstract Background Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most significant threats to the global swine industry. It is of great importance to understand viral-host interactions to develop novel antiviral strategies. Long non-coding RNAs (lncRNAs) have emerged as critical factors regulating host antiviral immune responses. However, lncRNAs participating in virus-host interactions during PRRSV infection remain largely unexplored. Method RNA transcripts of porcine alveolar macrophages (PAMs) infected with two different PRRSV strains, GSWW/2015 and VR2332, at 24 h post-infection were sequenced by high-throughput sequencing. Four programs namely, CNCI, CPC, PFAM, and phyloCSF, were utilized to predict the coding potential of transcripts. mRNAs co-localized or co-expressed with differentially expressed lncRNAs were considered as their targets. Fuction of lncRNAs was predicted by GO and KEGG analysis of their target mRNAs. The effect of LNC_000397 on PRRSV replication was validated by knockdown its expression using siRNA. Target genes of LNC_000397 were identified by RNA-Sequencing and validated by RT-qPCR. Result In this study, we analyzed lncRNA and mRNA expression profiles of PRRSV GSWW/2015 and VR2332 infected porcine alveolar macrophages. A total of 1,147 novel lncRNAs were characterized, and 293 lncRNAs were differentially expressed. mRNAs co-localized and co-expressed with lncRNAs were enriched in pathogen-infection-related biological processes such as Influenza A and Herpes simplex infection. Functional analysis revealed the lncRNA, LNC_000397, which was up-regulated by PRRSV infection, negatively regulated PRRSV replication. Knockdown of LNC_000397 significantly impaired expression of antiviral ISGs such as MX dynamin-like GTPase 1 (MX1), ISG15 Ubiquitin-like modifier (ISG15), and radical S-adenosyl methionine domain containing 2 (RSAD2). Conclusions LNC_000397 negatively regulated PRRSV replication by inducing interferon-stimulated genes (ISGs) expression. Our study is the first report unveiling the role of host lncRNA in regulating PRRSV replication, which might be beneficial for the development of novel antiviral therapeutics.

Abstract C4 photosynthesis in the maize leaf involves the exchange of organic acids between mesophyll (M) and the bundle sheath (BS) cells. The transport is mediated by plasmodesmata embedded in the suberized cell wall. We examined the maize Kranz anatomy with a focus on the plasmodesmata and cell wall suberization with microscopy methods. In the young leaf zone where M and BS cells had indistinguishable proplastids, plasmodesmata were simple and no suberin was detected. In leaf zones where dimorphic chloroplasts were evident, the plasmodesma acquired sphincter and cytoplasmic sleeves, and suberin was discerned. These modifications were accompanied by a drop in symplastic dye mobility at the M-BS boundary. We compared the kinetics of chloroplast differentiation and the modifications in M-BS connectivity in ppdk and dct2 mutants where C4 cycle is affected. The rate of chloroplast diversification did not alter, but plasmodesma remodeling, symplastic transport inhibition, and cell wall suberization were observed from younger leaf zone in the mutants than in wild type. Our results indicate that inactivation of the C4 genes accelerated the changes in the M-BS interface, and the reduced permeability suggests that symplastic transport between M and BS could be regulated for normal operation of C4 cycle.

ABSTRACT The maintenance of viral protein homeostasis depends on the machinery of the infected host cells, giving us an insight into the interplay between host and virus. Accumulating evidence suggests that heat shock protein 60 (HSP60), as one molecular chaperone, is involved in regulating virus infection. However, the role of HSP60 during foot-and-mouth disease virus (FMDV) replication and its specific mechanisms have not been reported. We demonstrate that HSP60 modulates the FMDV life cycle. HSP60 plays a role at the postentry stage of the viral life cycle, including RNA replication and mRNA translation; however, HSP60 does not affect viral replication of Seneca Valley virus (SVA) or encephalomyocarditis virus (EMCV). We found that HSP60 is involved in FMDV replication complex (RC) formation. Furthermore, our results indicate that HSP60 interacts with FMDV nonstructural proteins 3A and 2C, key elements of the viral replication complex. We also show that HSP60 regulates the stability of 3A and 2C via caspase-dependent and autophagy-lysosome-dependent degradation, thereby promoting FMDV RNA synthesis and mRNA translation mediated by the RC. Additionally, we determined that the apical domain of HSP60 is responsible for interacting with 3A and 2C. The N terminus of 3A and ATPase domain of 2C are involved in binding to HSP60. Importantly, HSP60 depletion potently reduced FMDV pathogenicity in infected mice. Altogether, this study demonstrates a specific role of HSP60 in promoting FMDV replication. Furthermore, targeting host HSP60 will help us design the FMDV-specific antiviral drugs. IMPORTANCE FMDV is the leading cause of the foot-and-mouth disease (FMD), affecting cloven-hoofed animals with high morbidity and mortality. We determined that HSP60 is required for efficient viral RNA replication and mRNA translation during FMDV infection. Furthermore, we demonstrate that HSP60 interacts with FMDV nonstructural proteins 3A and 2C, the elements of the RC; HSP60 contributes to the stability of 3A and 2C to affect the formation and function of the RC. We also validated the potential role of HSP60 as the antiviral target in vivo using small interfering RNA. These findings deepen the understanding of the host-virus interaction and provide information supporting the design of novel therapeutics for FMDV infection.

MicroRNAs (miRNAs) are posttranscriptional regulators that play key roles in meat color regulation. Changes in miRNA expression affect their target mRNAs, leading to multifunctional effects on biological processes and phenotypes. In this study, a G > A mutation site located upstream of the precursor miR-22 sequence in Suhuai pigs was significantly correlated with the meat color parameter a*(redness) of the porcine longissimus dorsi (LD) muscle. AA genotype individuals had the highest average meat color a* value and the lowest miR-22 level. When G > A mutation was performed in the miR-22 overexpression vector, miR-22 expression significantly decreased. Considering that Ca2+ homeostasis is closely related to pig meat color, our results further demonstrated that ELOVL6 is a direct target of miR-22 in pigs. The effects of miR-22 on skeletal muscle intracellular Ca2+ were partially caused by the suppression of ELOVL6 expression.

Finishing pigs can adapt to high-fiber diet smoothly according to the production performance and their intestinal microbiota through a 28-day trial or longer. However, it is unclear, at which stage during the experimental period, the adaptation occurred. Here we studied the dosage effects of dietary fiber (Total dietary fiber (TDF) from 16.70 to 24.11%) on growth performance, fiber digestibility, fecal microbiota, and microbial fermentation of finishing pigs during a 14-day feeding period. The results showed that the average daily feed intake (ADFI) and feed/gain (F/G) of pigs were not affected as the dietary fiber increased. Apparent total tract digestibility (ATTD) of cellulose, hemicellulose, insoluble dietary fiber (IDF), soluble dietary fiber (SDF), and TDF of pigs remained unchanged when TDF was between 16.70 and 17.75%, while strikingly decreased when TDF increased from 17.75 to 24.11%. It is worth noting that increasing fiber intake seemed to favor hemicellulose digestion. In addition, the increase in fiber intake increased fecal microbial diversity, especially improved the proportion of the members of the family Prevotellaceae, Ruminococcaceae, and Lachnospiraceae, and decreased the abundance of the genus Streptococcus. Moreover, the increase in fiber intake promoted the digestion of fiber, production of short chain fatty acids (SCFAs), and enhanced microbial pyruvate metabolism and butanoate metabolism. In conclusion, short-term high fiber feeding has no adverse effects on the growth performance of finishing pigs. ATTD of dietary fiber of finishing pigs was maintained when TDF was at 17.75%. And short-term high fiber feeding improved microbial diversity and fiber degradation functions of finishing pigs.

As an effective capacitance signal produced by a micro-hemisphere gyro is usually below the pF level, and the capacitance reading process is susceptible to parasitic capacitance and environmental noise, it is highly difficult to acquire an effective capacitance signal. Reducing and suppressing noise in the gyro capacitance detection circuit is a key means to improve the performance of detecting the weak capacitance generated by MEMS gyros. In this paper, we propose a novel capacitance detection circuit, where three different means are utilized to achieve noise reduction. Firstly, the input common-mode feedback is applied to the circuit to solve the input common-mode voltage drift caused by both parasitic capacitance and gain capacitance. Secondly, a low-noise, high-gain amplifier is used to reduce the equivalent input noise. Thirdly, the modulator–demodulator and filter are introduced to the proposed circuit to effectively mitigate the side effects of noise; thus, the accuracy of capacitance detection can be further improved. The experimental results show that with the input voltage of 6 V, the newly designed circuit produces an output dynamic range of 102 dB and the output voltage noise of 5.69 nV/√Hz, achieving a sensitivity of 12.53 V/pF.

Although one of the poster children of high-performance MEMS (Micro Electro Mechanical Systems) gyroscopes, the MEMS hemispherical resonator gyroscope (HRG) is faced with the barrier of technical and process limits, which makes it unable to form a resonator with the best structure. How to obtain the best resonator under specific technical and process limits is a significant topic for us. In this paper, the optimization of a MEMS polysilicon hemispherical resonator, designed by patterns based on PSO-BP and NSGA-II, was introduced. Firstly, the geometric parameters that significantly contribute to the performance of the resonator were determined via a thermoelastic model and process characteristics. Variety regulation between its performance parameters and geometric characteristics was discovered preliminarily using finite element simulation under a specified range. Then, the mapping between performance parameters and structure parameters was determined and stored in the BP neural network, which was optimized via PSO. Finally, the structure parameters in a specific numerical range corresponding to the best performance were obtained via the selection, heredity, and variation of NSGAII. Additionally, it was demonstrated using commercial finite element soft analysis that the output of the NSGAII, which corresponded to the Q factor of 42,454 and frequency difference of 8539, was a better structure for the resonator (generated by polysilicon under this process within a selected range) than the original. Instead of experimental processing, this study provides an effective and economical alternative for the design and optimization of high-performance HRGs under specific technical and process limits.

Porcine epidemic diarrhea virus (PEDV) causes a highly contagious intestinal disease in neonatal pigs. Aquaporin-3 (AQP3) plays important roles in maintenance of intestinal barrier function and regulation of immune responses. However, the roles of AQP3 in mediating PEDV infection to host cells and the regulatory mechanisms of AQP3 expression remain poorly understood. Here, we identified one 16 bp (GGGCGGGGTTGCGGGC) insertion mutation in the AQP3 gene promoter in Large White pigs, with the frequencies of 49.3% of heterozygotes and 31.3% of mutant homozygotes. Functional analysis by luciferase activity assay indicated that the insertion mutation results in significant enhancement in AQP3 transcriptional activity (P < 0.01). Mechanistic analysis showed that the inserted sequence adds binding sites for transcription factor CEBPA, which promotes the expression of AQP3. Downregulation of AQP3 by shRNA silencing in porcine intestinal epithelial cells revealed obvious increases in genome copies and viral titers of PEDV. Expression of proinflammatory cytokines (IL-6, IL-8, and IL-18) and interferons (IFN-α and IFN-β) were significantly reduced (P < 0.01) in AQP3 knockdown cells upon PEDV infection. Furthermore, decreased level of ZO-1 protein was also detected in AQP3 knockdown cells in response to PEDV infection. Our findings suggested a previously unknown mechanism linking the effects of promoter genetic variants on the expression of AQP3, revealed the roles of AQP3 in response to PEDV pathogenesis, and indicated the potential associations of the 16 bp insertion mutation with resistance to PEDV infection in porcine intestinal epithelial cells.

Meat color is the primary criterion by which consumers evaluate meat quality. However, there are a few candidate genes and molecular markers of meat color that were reported for pig molecular breeding. The purpose of the present study is to identify the candidate genes affecting meat color and provide the theoretical basis for meat color molecular breeding. A total of 306 Suhuai pigs were slaughtered, and meat color was evaluated at 45 min and 24 h after slaughter by CIELAB color space. All individuals were genotyped using GeneSeek GGP-Porcine 80K SNP BeadChip. The genomic estimated breeding values (GEBVs), heritability, and genetic correlation of meat color were calculated by DMU software. The genome-wide association studies (GWASs) and the fixation index (FST) tests were performed to identify SNPs related to meat color, and the candidate genes within 1 Mb upstream and downstream of significant SNPs were screened by functional enrichment analysis. The heritability of L* 45 min, L* 24 h, a* 45 min, a* 24 h, b* 45 min, and b* 24 h was 0.20, 0.16, 0.30, 0.13, 0.29, and 0.22, respectively. The genetic correlation between a* (a* 45 min and a* 24 h) and L* (L* 45 min and L* 24 h) is strong, whereas the genetic correlation between b* 45 min and b* 24 h is weak. Forty-nine significant SNPs associated with meat color were identified through GWAS and FST tests. Among these SNPs, 34 SNPs were associated with L* 45 min within a 5-Mb region on Sus scrofa chromosome 11 (SSC11); 22 SNPs were associated with a* 45 min within a 14.72-Mb region on SSC16; six SNPs were associated with b* 45 min within a 4.22-Mb region on SSC13; 11 SNPs were associated with b* 24 h within a 2.12-Mb region on SSC3. These regions did not overlap with meat color–associated QTLs reported previously. Moreover, six candidate genes (HOMER1, PIK3CG, PIK3CA, VCAN, FABP3, and FKBP1B), functionally related to muscle development, phosphatidylinositol phosphorylation, and lipid binding, were detected around these significant SNPs. Taken together, our results provide a set of potential molecular markers for the genetic improvement of meat color in pigs.

Salt stress is an important environmental factor limiting plant growth and crop production. Plant adaptation to salt stress can be improved by chemical pretreatment. This study aims to identify whether hydrogen peroxide (H2O2) pretreatment of seedlings affects the stress tolerance of Arabidopsis thaliana seedlings. The results show that pretreatment with H2O2 at appropriate concentrations enhances the salt tolerance ability of Arabidopsis seedlings, as revealed by lower Na+ levels, greater K+ levels, and improved K+/Na+ ratios in leaves. Furthermore, H2O2 pretreatment improves the membrane properties by reducing the relative membrane permeability (RMP) and malonaldehyde (MDA) content in addition to improving the activities of antioxidant enzymes, including superoxide dismutase, and glutathione peroxidase. Our transcription data show that exogenous H2O2 pretreatment leads to the induced expression of cell cycle, redox regulation, and cell wall organization-related genes in Arabidopsis, which may accelerate cell proliferation, enhance tolerance to osmotic stress, maintain the redox balance, and remodel the cell walls of plants in subsequent high-salt environments.

As a MEMS gyroscope is susceptible to environmental interference, its performance is degraded due to random noise. Accurate and rapid analysis of random noise of MEMS gyroscope is of great significance to improve the gyroscope’s performance. A PID-DAVAR adaptive algorithm is designed by combining the PID principle with DAVAR. It can adaptively adjust the length of the truncation window according to the dynamic characteristics of the gyroscope’s output signal. When the output signal fluctuates drastically, the length of the truncation window becomes smaller, and the mutation characteristics of the intercepted signal are analyzed detailed and thoroughly. When the output signal fluctuates steadily, the length of the truncation window becomes larger, and the intercepted signals are analyzed swiftly and roughly. The variable length of the truncation window ensures the confidence of the variance and shortens the data processing time without losing the signal characteristics. Experimental and simulation results show that the PID-DAVAR adaptive algorithm can shorten the data processing time by 50%. The tracking error of the noise coefficients of angular random walk, bias instability, and rate random walk is about 10% on average, and the minimum error is about 4%. It can accurately and promptly present the dynamic characteristics of the MEMS gyroscope’s random noise. The PID-DAVAR adaptive algorithm not only satisfies the requirement of variance confidence but also has a good signal-tracking ability.

Making full use of high fiber and low-cost crop coproducts is helpful to alleviate the situation of people and livestock competing for crops. Digestion of dietary fibers in pigs is mainly through microbial fermentation in the large intestine. To reveal microbiota related to fiber digestion in pigs, fecal samples have been collected from 274 healthy female Suhuai pigs at 160 days of age under the same feeding conditions and have measured apparent neutral detergent fiber (NDF) and acid detergent fiber (ADF) digestibility. Samples from Suhuai pigs with extreme high and low apparent NDF digestibility and extreme high and low apparent ADF digestibility were subjected to shotgun metagenomic sequencing. At the species level, 62 microbial species in H_NDF group and 54 microbial species in H_ADF group were related to high fiber digestibility. Among them, Lachnospiraceae bacterium 3-1 and Alistipes sp. CAG:514 may be new types of microorganisms associated with fiber digestion. In addition, we found that more abundant GH5 and GH48 family (contribute to cellulose degradation) genes, GH39 and GH53 family (contribute to hemicellulose degradation) genes in microorganisms may contribute to the higher apparent NDF digestibility of pigs, and more abundant GH3 and GH9 family (contribute to cellulose degradation) genes in microorganisms may contribute to the higher apparent ADF digestibility of pigs. The abundance of AA4 family (helps in lignin degradation) genes in H_NDF and H_ADF groups was significantly higher than that in L_NDF and L_ADF groups, respectively (P < 0.05). Three pathways in H_NDF group and four pathways in H_ADF group are important pathways associated with degradation of non-starch polysaccharides, and their relative abundance is significantly higher than that in L_NDF and L_ADF groups, respectively. Gut microbiota of Suhuai pigs with high apparent fiber digestibility had higher abundance of genes and microbiota related to fiber digestion and may have stronger fiber digestion potential compared with low apparent fiber digestibility group. This study revealed that the characteristics of gut microbiota and microbial gene functions of pigs with high fiber apparent digestibility, which provided a theoretical basis and reference for further understanding the impact of gut microbiota on fiber digestibility of pigs.

Vulvar size and angle are meaningful traits in pig production. Sows with abnormal vulva generally show reproductive disorders. In order to excavate candidate loci and genes associated with pig’s vulvar traits, 270 Suhuai pigs with vulvar phenotype were genotyped by a porcine single nucleotide polymorphisms (SNP) Chip. Then, Chip data were imputed using resequenced data of 30 Suhuai pigs as a reference panel. Next, we estimated the heritability and performed a genome-wide association study (GWAS) for vulvar traits. The heritabilities for the traits vulvar length (VL), vulvar width (VW) and vulvar angle (VA) in this pig population were 0.23, 0.32 and 0.22, respectively. GWAS based on Chip data identified nine significant SNPs on the Sus scrofa chromosomes (SSC) 2, 7, 9 and 13 for VL or VW. GWAS based on imputed data identified 11 new quantitative trait loci (QTL) on SSC1, 2, 7, 8, 9, 11, 13, 16 and 17 for VL or VW. The most significant QTL for VL on SSC2 were refined to a 3.48–3.97 Mb region using linkage disequilibrium and linkage analysis (LDLA). In this refined region, FGF19 and CCND1, involved in the development of the reproductive tract, cell growth and vulvar cancer, could be new candidate genes affecting VL. Our results provided potential genetic markers for the breeding of vulvar traits in pigs and deepened the understanding of the genetic mechanism of vulvar traits.

The x-SnO2/α-Fe2O3 (x = 0.04, 0.07, and 0.1) heterogeneous composites were successfully prepared via a two-step solvothermal method. These composites were systematically characterized by the X-ray diffraction technique, field emission scanning electron microscopy, an energy dispersive spectrometer, X-ray photoelectron spectroscopy and a UV–visible spectrometer. It was found that SnO2 nanoparticles were uniformly decorated on the surface of α-Fe2O3 particles in these heterogeneous composites. A comparative study of methylene blue (MB) photodegradation by α-Fe2O3 and x-SnO2/α-Fe2O3 composites was carried out. All x-SnO2/α-Fe2O3 composites showed higher MB photodegradation efficiency than α-Fe2O3. When x = 0.07, the MB photodegradation efficiency can reach 97% in 60 min. Meanwhile, the first-order kinetic studies demonstrated that the optimal rate constant of 0.07-SnO2/α-Fe2O3 composite was 0.0537 min−1, while that of pure α-Fe2O3 was only 0.0191 min−1. The catalytic mechanism of MB photodegradation by SnO2/α-Fe2O3 was examined. The SnO2 can act as a sink and help the effective transfer of photo-generated electrons for decomposing hydrogen peroxide (H2O2) into active radicals. This work can provide a new insight into the catalytic mechanism of the photo-Fenton process.

Abstract Objectives The proper procedure for inferior pulmonary ligament (IPL) during upper lobectomy remains a topic of debate. To address this matter, we carried out a trial comparing the clinical outcomes of IPL preservation versus IPL dissection during thoracoscopic upper lobectomy (TUL). Methods Patients undergoing thoracoscopic left/right upper lobectomy (TLUL/TRUL) were assigned to either the dissection group (Group D) or the preservation group (Group P). Our primary objective was to quantify and compare the alterations in postoperative residual bronchial angle and lung volume changes between the two groups. Our secondary objective encompassed the assessment of various other intraoperative and postoperative outcomes. Results Following adherence to the inclusion and exclusion criteria, we enrolled 100 patients (41 left and 59 right) in Group P and 108 patients (41 left and 67 right) in Group D for the study. Our findings revealed that in TLUL, Group P was able to reduce the degree of postoperative residual bronchial angle change (P 0.05) with regard to alterations in lung volume or the occurrence of postoperative complications—except for the duration of postoperative hospital stay (P

This paper explores the life and works of Su Shi, a prominent intellectual and statesman during China’s Song Dynasty, as a champion of interreligious harmony. We examine how Su Shi’s vast philosophical and literary output demonstrates his deep engagement with Confucian ethics, Buddhist compassion, and Daoist tranquility. By analyzing his poems, essays, and other writings, we explore how Su Shi navigated these diverse traditions, finding common ground and promoting mutual understanding. This analysis highlights Su Shi’s ability to bridge religious and philosophical divides, offering a valuable perspective for contemporary discussions on interfaith dialogue and peaceful coexistence.