Multi-omic characterization of allele-specific regulatory variation in hybrid pigs.

Hybrid mapping is a powerful approach to efficiently identify and characterize genes regulated through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we perform a comprehensive multi-omic characterization of regulatory variation across the brain, liver, muscle, and placenta through four developmental stages. We produce one of the largest multi-omic datasets in pigs to date, including 16 whole genome sequenced individuals, as well as 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We develop a read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We show that tissue specificity was much stronger than developmental stage specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identify 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. We integrate methylation, chromatin accessibility, and gene expression data to show that allele specific expression can be explained in great part by allele specific methylation and/or chromatin accessibility. This study provides a comprehensive characterization of regulatory variation across multiple tissues and developmental stages in pigs.

Discriminating the Active Ru Species Towards the Selective Generation of Singlet Oxygen from Peroxymonosulfate: Nanoparticles Surpass Single-Atom Catalysts.

Singlet oxygen (1O2) is an exceptional reactive oxygen species in advanced oxidation processes for environmental remediation. Despite single-atom catalysts (SACs) representing the promising candidate for the selective generation of 1O2 from peroxymonosulfate (PMS), the necessity to meticulously regulate the coordination environment of metal centers poses a significant challenge in the precisely-controlled synthetic method. Another dilemma to SACs is their high surface free energy, which results in an inherent tendency for the surface migration and aggregation of metal atoms. We here for the first time reported that Ru nanoparticles (NPs) synthesized by the facile pyrolysis method behave as robust Fenton-like catalysts, outperforming Ru SACs, towards efficient activation of PMS to produce 1O2 with nearly 100 % selectivity, remarkably improving the degradation efficiency for target pollutants. Density functional theory calculations have unveiled that the boosted PMS activation can be attributed to two aspects: (i) enhanced adsorption of PMS molecules onto Ru NPs, and (ii) decreased energy barriers by offering adjacent sites for promoted dimerization of *O intermediates into adsorbed 1O2. This study deepens the current understanding of PMS chemistry, and sheds light on the design and optimization of Fenton-like catalysts.

Identification of Candidate Genes for Economically Important Carcass Cutting in Commercial Pigs through GWAS.

During the process of pork production, the carcasses of pigs are divided and sold, which provides better economic benefits and market competitiveness for pork production than selling the carcass as a whole. Due to the significant cost of post-slaughter phenotypic measurement, the genetic architecture of tenderloin weight (TLNW) and rib weight (RIBW)-important components of pig carcass economic value-remain unknown. In this study, we conducted genome-wide association studies (GWAS) for TLNW and RIBW traits in a population of 431 Duroc × Landrace × Yorkshire (DLY) pigs. In our study, the most significant single nucleotide polymorphism (SNP) associated with TLNW was identified as ASGA0085853 (3.28 Mb) on Sus scrofa chromosome 12 (SSC12), while for RIBW, it was Affx-1115046258 (172.45 Mb) on SSC13. Through haplotype block analysis, we discovered a novel quantitative trait locus (QTL) associated with TLNW, spanning a 5 kb region on SSC12, and a novel RIBW-associated QTL spanning 1.42 Mb on SSC13. Furthermore, we hypothesized that three candidate genes, TIMP2 and EML1, and SMN1, are associated with TLNW and RIBW, respectively. Our research not only addresses the knowledge gap regarding TLNW, but also serves as a valuable reference for studying RIBW. The identified SNP loci strongly associated with TLNW and RIBW may prove useful for marker-assisted selection in pig breeding programs.

Ferrous ion enhanced Fenton-like degradation of emerging contaminants by sulfidated nanosized zero-valent iron with pH insensitivity.

In this study, the performance and mechanism of the integrated sulfidated nanosized zero-valent iron and ferrous ions (S-nZVI/Fe2+) system for oxygen activation to remove emerging contaminants (ECs) were comprehensively explored. The S-nZVI/Fe2+ system exhibited a 2.4-8.2 times of increase in the pseudo-first order kinetic rate constant for the oxidative degradation of various ECs compared to the S-nZVI system under aerobic conditions, whereas negligible removal was observed in both nZVI and nZVI/Fe2+ systems. Moreover, remarkable EC mineralization efficiency and benign detoxification capacity were also demonstrated in the S-nZVI/Fe2+ system. We revealed that dosing Fe2+ promoted the corrosion of S-nZVI by maintaining an acidic solution pH, which was conducive to O2 activation by dissolved Fe2+ and surface-absorbed Fe(II) to produce •OH. Furthermore, the generation of H* was enhanced for the further reduction of Fe(III) and H2O2 to Fe(II) and •O2-, resulting in the improvement of consecutive single-electron O2 activation for •OH production. Additionally, bisphenol A (BPA) degradation by S-nZVI/Fe2+ was positively correlated with the S-nZVI dosage, with an optimum S/Fe molar ratio of 0.15. The Fenton-like degradation process by S-nZVI/Fe2+ was pH-insensitive, indicating its robust performance over a wide pH range. This study provides valuable insights for the practical implementation of nZVI-based technology in achieving high-efficiency removal of ECs from water.

A pan-cancer analysis identifies SOAT1 as an immunological and prognostic biomarker.

Sterol o-acyltransferase1 (SOAT1) is an enzyme that regulates lipid metabolism. Nevertheless, the predictive value of SOAT1 regarding immune responses in cancer is not fully understood. Herein, we aimed to expound the predictive value and the potential biological functions of SOAT1 in pan-cancer. Raw data related to SOAT1 expression in 33 different types of cancer were acquired from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. SOAT1 expression was significantly increased in most cancers and showed a distinct correlation with prognosis. This enhanced expression of the SOAT1 gene was confirmed by evaluating SOAT1 protein expression using tissue microarrays. In addition, we found significant positive associations between SOAT1 expression levels and infiltrating immune cells, including T cells, neutrophils, and macrophages. Moreover, the co-expression analysis between SOAT1 and immune genes showed that many immune-related genes were increased with enhanced SOAT1 expression. A gene set enrichment analysis (GSEA) revealed that the expression of SOAT1 correlated with the tumor microenvironment, adaptive immune response, interferon signaling, and cytokine signaling. These findings indicate that SOAT1 is a potential candidate marker for predicting prognosis and a promising target for tumor immunotherapy in cancers.

The SWine IMputation (SWIM) haplotype reference panel enables nucleotide resolution genetic mapping in pigs.

Genetic mapping to identify genes and alleles associated with or causing economically important quantitative trait variation in livestock animals such as pigs is a major goal in animal genetic improvement. Despite recent advances in high-throughput genotyping technologies, the resolution of genetic mapping in pigs remains poor due in part to the low density of genotyped variant sites. In this study, we overcame this limitation by developing a reference haplotype panel for pigs based on 2259 whole genome-sequenced animals representing 44 pig breeds. We evaluated software combinations and breed composition to optimize the imputation procedure and achieved an average concordance rate in excess of 96%, a non-reference concordance rate of 88%, and an r2 of 0.85. We demonstrated in two case studies that genotype imputation using this resource can dramatically improve the resolution of genetic mapping. A public web server has been developed to allow the pig genetics community to fully utilize this resource. We expect this resource to facilitate genetic mapping and accelerate genetic improvement in pigs.

Improving the accuracy of genomic prediction for meat quality traits using whole genome sequence data in pigs.

BACKGROUND: Pork quality can directly affect customer purchase tendency and meat quality traits have become valuable in modern pork production. However, genetic improvement has been slow due to high phenotyping costs. In this study, whole genome sequence (WGS) data was used to evaluate the prediction accuracy of genomic best linear unbiased prediction (GBLUP) for meat quality in large-scale crossbred commercial pigs. RESULTS: We produced WGS data (18,695,907 SNPs and 2,106,902 INDELs exceed quality control) from 1,469 sequenced Duroc × (Landrace × Yorkshire) pigs and developed a reference panel for meat quality including meat color score, marbling score, L* (lightness), a* (redness), and b* (yellowness) of genomic prediction. The prediction accuracy was defined as the Pearson correlation coefficient between adjusted phenotypes and genomic estimated breeding values in the validation population. Using different marker density panels derived from WGS data, accuracy differed substantially among meat quality traits, varied from 0.08 to 0.47. Results showed that MultiBLUP outperform GBLUP and yielded accuracy increases ranging from 17.39% to 75%. We optimized the marker density and found medium- and high-density marker panels are beneficial for the estimation of heritability for meat quality. Moreover, we conducted genotype imputation from 50K chip to WGS level in the same population and found average concordance rate to exceed 95% and r2 = 0.81. CONCLUSIONS: Overall, estimation of heritability for meat quality traits can benefit from the use of WGS data. This study showed the superiority of using WGS data to genetically improve pork quality in genomic prediction.

Identification of candidate genes associated with carcass component weights in commercial crossbred pigs through a combined GWAS approach.

In the pork industry chain, carcass cutting is crucial for enhancing the commercial value of pork carcasses. However, the genetic mechanisms underlying carcass component weights remain poorly understood. Here, we used a combined genome-wide association study (GWAS) approach that integrated single- and multi-locus models to map genetic markers and genes associated with the weights of seven carcass components in Duroc × Landrace × Yorkshire (DLY) pigs. As multi-locus GWAS captures more single nucleotide polymorphisms (SNPs) with large effects than single-locus GWAS, the combined GWAS approach detected more SNPs than using the single-locus model alone. We identified 177 nonredundant SNPs associated with these traits in 526 DLY pigs, including boneless butt shoulder (BBS), boneless picnic shoulder (BPS), boneless leg (BL), belly (BELLY), front fat (FF), rear fat (RF), and skin-on whole loin (SLOIN). Using single-locus GWAS, we identified a quantitative trait locus (QTL) for SLOIN on Sus scrofa chromosome 15 (SSC15). Notably, a single SNP (ASGA0069883) in the proximity of this QTL was consistently detected by all GWAS models (one single-locus and four multi-locus models) and explained more than 4% of the phenotypic variance. Our findings suggest that the involved gene, MYO3B, is proposed to be a strong candidate for SLOIN. Further analysis also identified several candidate genes related to BBS (PPP3CA and CPEB4), BPS (ECH1), FF (CACNB2 and ZNF217), BELLY (FGFRL1), BL (CHST11), and RF (LRRK2). The identified SNPs can be used as molecular markers for the genetic improvement of pork carcasses in the molecular-guided breeding of modern commercial pigs.

Carcass cutting is the most effective method for enhancing the commercial value of pork carcasses in the industry chain. However, the genetic mechanisms underlying carcass component weights remain elusive. In this study, we used a combination of single- and multi-locus models to increase the power of genome-wide association analysis. We identified 177 important genetic variants that are potentially promising candidate markers for marker-assisted selection in breeding. Further investigation revealed one quantitative trait locus region and several candidate genes (PPP3CA, CPEB4, ECH1, CACNB2, ZNF217, FGFRL1, CHST11, LRRK2) associated with the weights of seven carcass components in Duroc × Landrace × Yorkshire pigs.

Asymmetrically Coordinated CoB1 N3 Moieties for Selective Generation of High-Valence Co-Oxo Species via Coupled Electron-Proton Transfer in Fenton-like Reactions.

High-valence metal species generated in peroxymonosulfate (PMS)-based Fenton-like processes are promising candidates for selective degradation of contaminants in water, the formation of which necessitates the cleavage of OH and OO bonds as well as efficient electron transfer. However, the high dissociation energy of OH bond makes its cleavage quite challenging, largely hampering the selective generation of reactive oxygen species. Herein, an asymmetrical configuration characterized by a single cobalt atom coordinated with boron and nitrogen (CoB1 N3 ) is established to offer a strong local electric field, upon which the cleavage of OH bond is thermodynamically favored via a promoted coupled electron-proton transfer process, which serves an essential step to further allow OO bond cleavage and efficient electron transfer. Accordingly, the selective formation of Co(IV)O in a single-atom Co/PMS system enables highly efficient removal performance toward various organic pollutants. The proposed strategy also holds true in other heteroatom doping systems to configure asymmetric coordination, thus paving alternative pathways for specific reactive species conversion by rationalized design of catalysts at atomic level toward environmental applications and more.

Tuning Fe3O4 for sustainable cathodic heterogeneous electro-Fenton catalysis by acetylated chitosan.

Peroxidase-like catalysts are safe and low-cost candidates to tackle the dilemma in constructing sustainable cathodic heterogeneous electro-Fenton (CHEF) catalysts for water purification, but the elusive structure-property relationship of enzyme-like catalysts constitutes a pressing challenge for the advancement of CHEF processes in practically relevant water and wastewater treatment. Herein, we probe the origins of catalytic efficiency in the CHEF process by artificially tailoring the peroxidase-like activity of Fe3O4 through a series of acetylated chitosan-based hydrogels, which serve as ecofriendly alternatives to traditional carbon shells. The optimized acetylated chitosan wrapping Fe3O4 hydrogel on the cathode shows an impressive activity and stability in CHEF process, overcoming the complicated and environmentally unfavored procedures in the electro-Fenton-related processes. Structural characterizations and theoretical calculations reveal that the amide group in chitosan can modulate the intrinsic redox capacity of surficial Fe sites on Fe3O4 toward CHEF catalysis via the neutral hydrogen bond. This work provides a sustainable path and molecule-level insight for the rational design of high-efficiency CHEF catalysts and beyond.

The Genetic Architecture of Meat Quality Traits in a Crossbred Commercial Pig Population.

Meat quality is of importance in consumer acceptance and purchasing tendency of pork. However, the genetic architecture of pork meat quality traits remains elusive. Herein, we conducted genome-wide association studies to detect single nucleotide polymorphisms (SNPs) and genes affecting meat pH and meat color (L*, lightness; a*, redness; b*, yellowness) in 1518 three-way crossbred pigs. All individuals were genotyped using the GeneSeek Porcine 50K BeadChip. In sum, 30 SNPs and 20 genes are found to be associated with eight meat quality traits. Notably, we detect one significant quantitative trait locus (QTL) on SSC15 with a 143 kb interval for meat pH (pH_12h), together with the most promising candidate TNS1. Interestingly, two newly identified SNPs located in the TTLL4 gene demonstrate the highest phenotypic variance of pH_12h in this QTL, at 2.67%. The identified SNPs are useful for the genetic improvement of meat quality traits in pigs by assigning higher weights to associated SNPs in genomic selection.

Capabilities of hepatitis B surface antigen are divergent from hepatitis B virus DNA in delimiting natural history phases of chronic hepatitis B virus infection.

Objective: Quantitative hepatitis B surface antigen (HBsAg) and hepatitis B virus (HBV) DNA in the natural history of chronic HBV infection have not been rationally evaluated. This study aimed to re-characterize quantitative HBsAg and HBV DNA in the natural history phases. Methods: A total of 595 and 651 hepatitis B e antigen (HBeAg)-positive patients and 485 and 705 HBeAg-negative patients were assigned to the early and late cohorts, respectively. Based on the 'S-shape' receiver operating characteristic (ROC) curves, the HBeAg-positive sub-cohorts with possibly high HBV replication (PHVR) and possibly low HBV replication (PLVR) and the HBeAg-negative sub-cohorts with possibly high HBsAg expression (PHSE) and possibly low HBsAg expression (PLSE) were designated. Results: The areas under the ROC curve (AUCs) of HBsAg and HBV DNA in predicting HBeAg-positive significant hepatitis activity (SHA) in the early cohort, sub-cohort with PHVR, and sub-cohort with PLVR were 0.655 and 0.541, 0.720 and 0.606, and 0.553 and 0.725, respectively; those in the late cohort, sub-cohort with PHVR, and sub-cohort with PLVR were 0.646 and 0.501, 0.798 and 0.622, and 0.603 and 0.674, respectively. The AUCs of HBsAg and HBV DNA in predicting HBeAg-negative SHA in the early cohort, sub-cohort with PHSE, and sub-cohort with PLSE were 0.508 and 0.745, 0.573 and 0.780, and 0.577 and 0.729, respectively; those in the late cohort, sub-cohort with PHSE, and sub-cohort with PLSE were 0.503 and 0.761, 0.560 and 0.814, and 0.544 and 0.722, respectively. The sensitivity and specificity of HBsAg ≤4.602 log10 IU/ml in predicting HBeAg-positive SHA in the early cohort were 82.6% and 45.8%, respectively; those in the late cohort were 87.0% and 44.1%, respectively. The sensitivity and specificity of HBV DNA >3.301 log10 IU/ml in predicting HBeAg-negative SHA in the early cohort were 73.4% and 60.8%, respectively; those in the late cohort were 73.6% and 64.1%, respectively. Conclusion: Quantitative HBsAg and HBV DNA are valuable, but their capabilities are divergent in delimiting the natural history phases.

A composite strategy of genome-wide association study and copy number variation analysis for carcass traits in a Duroc pig population.

BACKGROUND: Carcass traits are important in pig breeding programs for improving pork production. Understanding the genetic variants underlies complex phenotypes can help explain trait variation in pigs. In this study, we integrated a weighted single-step genome-wide association study (wssGWAS) and copy number variation (CNV) analyses to map genetic variations and genes associated with loin muscle area (LMA), loin muscle depth (LMD) and lean meat percentage (LMP) in Duroc pigs. RESULTS: Firstly, we performed a genome-wide analysis for CNV detection using GeneSeek Porcine SNP50 Bead chip data of 3770 pigs. A total of 11,100 CNVs were detected, which were aggregated by overlapping 695 CNV regions (CNVRs). Next, we investigated CNVs of pigs from the same population by whole-genome resequencing. A genome-wide analysis of 21 pigs revealed 23,856 CNVRs that were further divided into three categories (851 gain, 22,279 loss, and 726 mixed), which covered 190.8 Mb (~ 8.42%) of the pig autosomal genome. Further, the identified CNVRs were used to determine an overall validation rate of 68.5% for the CNV detection accuracy of chip data. CNVR association analyses identified one CNVR associated with LMA, one with LMD and eight with LMP after applying stringent Bonferroni correction. The wssGWAS identified eight, six and five regions explaining more than 1% of the additive genetic variance for LMA, LMD and LMP, respectively. The CNVR analyses and wssGWAS identified five common regions, of which three regions were associated with LMA and two with LMP. Four genes (DOK7, ARAP1, ELMO2 and SLC13A3) were highlighted as promising candidates according to their function. CONCLUSIONS: We determined an overall validation rate for the CNV detection accuracy of low-density chip data and constructed a genomic CNV map for Duroc pigs using resequencing, thereby proving a value genetic variation resource for pig genome research. Furthermore, our study utilized a composite genetic strategy for complex traits in pigs, which will contribute to the study for elucidating the genetic architecture that may be influenced and regulated by multiple forms of variations.

Identification of Homozygous Regions With Adverse Effects on the Five Economic Traits of Duroc Pigs.

Runs of homozygosity (ROH) are widely used to estimate genomic inbreeding, which is linked to inbreeding depression on phenotypes. However, the adverse effects of specific homozygous regions on phenotypic characteristics are rarely studied in livestock. In this study, the 50 K SNP data of 3,770 S21 Duroc (American origin) and 2,096 S22 Duroc (Canadian origin) pigs were used to investigate the harmful ROH regions on five economic traits. The results showed that the two Duroc lines had different numbers and distributions of unfavorable ROHs, which may be related to the different selection directions and intensities between the two lines. A total of 114 and 58 ROH segments were found with significant adverse effects on the economic traits of S21 and S22 pigs, respectively. Serval pleiotropic ROHs were detected to reduce two or multiple phenotypic performances in two Duroc populations. Candidate genes in these shared regions were mainly related to growth, fertility, immunity, and fat deposition. We also observed that some ROH genotypes may cause opposite effects on different traits. This study not only enhances our understanding of the adverse effects of ROH on phenotypes, but also indicates that ROH information could be incorporated into breeding programs to estimate and control the detrimental effects of homozygous regions.

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines.

Runs of homozygosity (ROH) are widely used to investigate genetic diversity, demographic history, and positive selection signatures of livestock. Commercial breeds provide excellent materials to reveal the landscape of ROH shaped during the intense selection process. Here, we used the GeneSeek Porcine 50K single-nucleotide polymorphism (SNP) Chip data of 3,770 American Duroc (AD) and 2,096 Canadian Duroc (CD) pigs to analyze the genome-wide ROH. First, we showed that AD had a moderate genetic differentiation with CD pigs, and AD had more abundant genetic diversity and significantly lower level of inbreeding than CD pigs. In addition, sows had larger levels of homozygosity than boars in AD pigs. These differences may be caused by differences in the selective intensity. Next, ROH hotspots revealed that many candidate genes are putatively under selection for growth, sperm, and muscle development in two lines. Population-specific ROHs inferred that AD pigs may have a special selection for female reproduction, while CD pigs may have a special selection for immunity. Moreover, in the overlapping ROH hotspots of two Duroc populations, we observed a missense mutation (rs81216249) located in the growth and fat deposition-related supergene (ARSB-DMGDH-BHMT) region. The derived allele of this variant originated from European pigs and was nearly fixed in Duroc pigs. Further selective sweep and association analyses indicated that this supergene was subjected to strong selection and probably contributed to the improvement of body weight and length in Duroc pigs. These findings will enhance our understanding of ROH patterns in different Duroc lines and provide promising trait-related genes and a functional-altering marker that can be used for genetic improvement of pigs.

Identify known and novel candidate genes associated with backfat thickness in Duroc pigs by large-scale genome-wide association analysis.

Backfat thickness (BFT) is complex and economically important traits in the pig industry, since it reflects fat deposition and can be used to measure the carcass lean meat percentage in pigs. In this study, all 6,550 pigs were genotyped using the Geneseek Porcine 50K SNP Chip to identify SNPs related to BFT and to search for candidate genes through genome-wide association analysis in two Duroc populations. In total, 80 SNPs, including 39 significant and 41 suggestive SNPs, and 6 QTLs were identified significantly associated with the BFT. In addition, 9 candidate genes, including a proven major gene MC4R, 3 important candidate genes (RYR1, HMGA1, and NUDT3) which were previously described as related to BFT, and 5 novel candidate genes (SIRT2, NKAIN2, AMH, SORCS1, and SORCS3) were found based on their potential functional roles in BFT. The functions of candidate genes and gene set enrichment analysis indicate that most important pathways are related to energy homeostasis and adipogenesis. Finally, our data suggest that most of the candidate genes can be directly used for genetic improvement through molecular markers, except that the MC4R gene has an antagonistic effect on growth rate and carcass lean meat percentage in breeding. Our results will advance our understanding of the complex genetic architecture of BFT traits and laid the foundation for additional genetic studies to increase carcass lean meat percentage of pig through marker-assisted selection and/or genomic selection.

Backfat thickness (BFT) is a complex and economically important trait in the pig industry because it reflects fat deposition and can be used to measure the carcass lean meat percentage in pigs. In this study, two Duroc populations were genotyped using SNP chips, and genome-wide association analysis was used to identify SNPs and candidate genes related to BFT. A number of genetic markers and candidate genes including MC4R, RYR1, HMGA1, NUDT3, SIRT2, NKAIN2, AMH, SORCS1, and SORCS3 were identified to be significantly related to BFT. Our data suggest that many of the candidate genes can be directly used for genetic improvement through molecular markers.

Enhanced reductive reactivity of zero-valent iron (ZVI) for pollutant removal by natural organic matters (NOMs) under aerobic conditions: Correlation between NOM properties and ZVI activity.

While ubiquitous natural organic matters (NOMs) are capable of enhancing zero-valent iron (ZVI) performance under aerobic conditions, there is limited understanding of how the properties of NOMs affect the reactivity of ZVI towards contaminants removal. Here, the corresponding activity of ZVI under aerobic conditions was investigated in the presence of humic acid (HA), fulvic acid (FA), bovine serum albumin (BSA). It was found that three models of NOMs were all effective in promoting diatrizoate (DTA) reduction via depassivating ZVI. Interestingly, fast adsorption of NOM onto ZVI surface initially caused inconspicuous impact or visible inhibition on hydrophilic DTA reduction depending on their hydrophobicity. However, subsequent exposure of more reactive sites with high hydrophilicity arising from the detachment of surfaced NOM-associated iron oxide finally contributed to the enhanced consumption of Fe0 with the ability: HA > FA ≈ BSA, and 1-2 times increase in DTA removal kinetic rate following the order: HA > FA > BSA. It further revealed that there were two key factors in determining DTA removal under aerobic conditions, including the ability of NOMs to boost Fe0 consumption as contributed by their aromaticity degree and amino groups, and the hydrophobicity of NOMs to initially affect the property of ZVI surfaces.

Firmicutes and Blautia in gut microbiota lessened in chronic liver diseases and hepatocellular carcinoma patients: a pilot study.

The gut microbiota system plays a vital role in liver diseases. This study aimed to address the diversity of gut microbiota and its correlations with clinical parameters in healthy individuals, chronic liver disease (CLD), and hepatocellular carcinoma (HCC) patients. Fecal specimens of nine healthy individuals, 11 CLD, and 21 HCC were collected. The diversity of gut microbiota was examined by PCR and Illumina MiSeq sequencing and analyzed using 16S rRNA gene sequencing database. The correlations between gut microbiota and the clinical parameters of participants were also addressed. Compared to healthy individuals, Firmicutes at a phylum level decreased in CLD and HCC patients and Proteobacteria increased (p < 0.05). The composition of Blautia on a genus level in CLD and HCC patients significantly decreased compared to healthy controls (p < 0.05). Firmicutes composition was negatively associated with age and number of males (p < 0.05) and was positively associated with monocytes, high-density lipoprotein cholesterol (HDL-C), and estimated glomerular filtration rate (eGFR) levels (p < 0.05). At a genus level, Blautia composition was negatively associated with cirrhosis, age, and number of males (p < 0.01), while it was positively associated with red blood cells (RBCs), triglycerides, HDL-C, and lymphocyte levels (p < 0.05). Conclusively, there was a significant compositional difference in gut microbiota in CLD and HCC patients compared with healthy subjects. Firmicutes and Blautia in gut microbiota system lessened in CLD and HCC patients. Clinical biochemical parameters have an impact on the diversity of gut microbiota in liver diseases.

A Novel Non-invasive Model Based on GPR for the Prediction of Liver Fibrosis in Patients With Chronic Hepatitis B.

Background: Some controversy remains regarding conventional serum indices for the evaluation of liver fibrosis. Therefore, we aimed to combine the existing index with other serum parameters to discriminate liver fibrosis stages in patients with chronic hepatitis B (CHB). Methods: A total of 1,622 treatment-naïve CHB patients were divided into training (n = 1,211) and validation (n = 451) cohorts. Liver histology was assessed according to the Scheuer scoring scheme. All common demographic and clinical parameters were analyzed. Results: By utilizing the results of the logistic regression analysis, we developed a novel index, the product of GPR, international normalized ratio (INR), and type IV collagen (GIVPR), to discriminate liver fibrosis. In the training group, the areas under the ROCs (AUROCs) of GIVPR, APRI, FIB-4, and GPR for significant fibrosis were 0.81, 0.75, 0.72, and 0.77, respectively; the AUROCs of GIVPR, APRI, FIB-4, and GPR for advanced fibrosis were 0.82, 0.74, 0.74, and 0.78, respectively; and the AUROCs of GIVPR, APRI, FIB-4, and GPR for cirrhosis were 0.87, 0.78, 0.78, and 0.83, respectively. Similar results were also obtained in the validation group. Furthermore, the decision curve analysis suggested that GIVPR represented superior clinical benefits in both independent cohorts. Conclusion: The GIVPR constructed on GPR represents a superior predictive model for discriminating liver fibrosis in CHB patients.

Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs.

The Duroc × (Landrace × Yorkshire) hybrid pigs (DLY) are the most popular commercial pigs, providing consumers with the largest source of pork. In order to gain more insights into the genetic architecture of economically important traits in pigs, we performed a genome-wide association study (GWAS) using the GeneSeek Porcine 50 K SNP Chip to map the genetic markers and genes associated with body conformation traits (BCT) in 311 DLY pigs. The quantitative traits analyzed included body weight (BW), carcass length (CL), body length (BL), body height (BH), and body mass index (BMI). BMI was defined as BMICL, BMIBL, and BMIBH, respectively, based on CL, BL, and BH phenotypic data. We identified 82 SNPs for the seven traits by GEMMA-based and FarmCPU-based GWASs. Both methods detected two quantitative trait loci (QTL) on SSC8 and SSC17 for body conformation traits. Several candidate genes (such as TNFAIP3, KDM4C, HSPG2, BMP2, PLCB4, and GRM5) were found to be associated with body weight and body conformation traits in pigs. Notably, the BMP2 gene had pleiotropic effects on CL, BL, BH, BMICL, and BMIBL and is proposed as a strong candidate gene for body size due to its involvement in growth and bone development. Furthermore, gene set enrichment analysis indicated that most of the pathway terms are associated with regulation of cell growth, negative regulation of cell population proliferation, and chondrocyte differentiation. We anticipate that these results further advance our understanding of the genetic architecture of body conformation traits in the popular commercial DLY pigs and provide new insights into the genetic architecture of BMI in pigs.