Abstract Background The refractory acute severe UC patients are often complicated by C. difficile infection (CDI), resulting in higher surgery and mortality rates. However, few studies have observed C. difficile’s pathogenicity in real UC patients’ gastrointestinal microenvironments, and the actual role of C. difficile in UC development remains unknown. We found zinc concentrations among UC patients’ feces were significantly higher than those among Crohn’s disease patients and healthy subjects. Additionally, we previously reported that excessive zinc would promote the growth and virulence of C. difficile. Therefore, we hypothesized that the increased UC patients’ luminal zinc may up-regulate C. difficile virulence and promote intestinal inflammatory responses, leading to an exacerbated UC progression. Methods UC patients’ stool samples (n=40) were collected and analyzed by qPCR and ICP-MS to determine the presence of C. difficile and the fecal zinc concentrations. C. difficile was cultured in BHIs with or without zinc (ZnSO4) in an anaerobic chamber. Expression of virulence genes was analyzed using RT-qPCR, transcriptome sequencing, and western blot. Human colonic organoids and Caco-2 cells were co-cultured with C. difficile or zinc-treated C. difficile, and cytotoxicity, permeability, and inflammatory cytokine release were assessed. TLR5 knock-out Caco-2 cells were constructed using sgRNA-guided Cas9 nuclease and co-cultured with C. difficile or zinc-treated C. difficile to verify whether zinc-induced C. difficile’s pathogenicity was mainly through flagellar formation. Results C. difficile was detected in ~35% of UC patients’ fecal samples. Luminal zinc concentrations (~915μM, p<0.01) were significantly higher among UC patients than CD patients or healthy subjects. The UC patients’ luminal concentration of zinc promoted C. difficile growth, suppressed its exotoxins release, and induced higher expression of its flagella-related genes, resulting in higher cytotoxicity and inflammatory responses in human colonic organoids and Caco-2 cells. However, zinc-treated C. difficile did not induce higher inflammation and pathogenicity in TLR5 knock-out Caco-2 cells. Conclusion The association between C. difficile and UC aggravation may partially stem from UC patients’ excess luminal zinc promoting C. difficile flagellin expression, inducing inflammatory responses, and worsening UC progression.

Abstract Background IBD has become a common chronic intestinal disease in China. Considering the important role of amino acid metabolism in inflammatory diseases, inhibition amino acid metabolism of inflammatory sites may be effective in alleviating UC (ulcerative colitis). SLC7A5 is involved in the progression of UC, but the mechanism of its functional regulation still needs to be investigated. In this study, we aimed to clarify the link among SLC7A5 expression in UC, mTOR pathway activation and immunoregulation. Methods We previously discovered through high-throughput screening that SLC7A5, as a cellular amino acid transport carrier, is significantly elevated in the colonic tissues of UC patients; in vivo experiments have demonstrated for the first time that JPH203, a specific inhibitor of SLC7A5, alleviates DSS-induced intestinal inflammation and inhibits mTOR pathway activation to promote intestinal autophagy. This study utilized model animals, transcriptomics, amino acid-targeted metabolomics assays, and macro-genome sequencing to elucidate the mechanism of SLC7A5-regulated amino acids in mTOR pathway activation and intestinal autophagy dysfunction. Results SLC7A5 expression is increased in the colon of UC patients and DSS-induced mice lesions. SLC7A5 inhibitor (JPH203) restrained the inflammatory responses induced by DSS. SLC7A5 deletion or inhibition dampens the release of IL-1β, IL-18, and IL-23 and the production of ROS in the LPS-induced FHC and RAW264.7 cells. Moreover, upregulating SLC7A5 expression induces mTOR signaling pathway activation in FHC cells. Deletion or inhibition of SLC7A5 efficiently blocks the SLC7A5-dependent amino acid transport, inhibits the mTOR activation, and results in the activation of autophagy. Conclusion Targeting SLC7A5-mediated amino acid uptake is a potentially useful immunosuppressive strategy to regulate colonic inflammation through mTOR pathway and autophagy. This study is expected to reveal the intrinsic factors of metabolic disorders promoting the UC progression from the perspective of amino acid metabolism, and to lay a new theoretical and experimental foundation for potential UC treatment.

Neoadjuvant therapy can improve outcome by increasing the resection rate, down staging the primary tumor and improving postoperative survival. PD-1/PD-L1 inhibitors have been approved in the treatment of advanced lung cancer, breast cancer, melanoma and other common cancers, and its success has moved immunotherapy forward to the early stage setting. In this study, we summarized the ongoing clinical trials which focus on neoadjuvant immunotherapy in solid cancers, and discussed their treatment strategy, efficacy and adverse events.

Haplotype prediction models open many possibilities to improve the accuracy of genomic selection but require more data processing and computing time than single-SNP prediction models. To facilitate haplotype analysis for genomic prediction and estimation using structural and functional genomic information, we developed a computing pipeline to implement haplotype analysis with capabilities for preparation of input data for haplotype analysis, genomic prediction and estimation using GVCHAP, and analysis of GVCHAP results. Data preparation includes utility programs for haplotype imputing; defining haplotype blocks by a fixed number of SNPs, a fixed distance in base pairs per block, or user defined block lengths based on structural or functional genomic information or a mixture of both types of information; and defining haplotype genotypes within each haplotype block. GVCHAP is the main program for genomic prediction and estimation, calculates GREML (genomic restricted maximum likelihood) estimates of variance components and heritabilities, and calculates GBLUP (genomic best linear unbiased prediction) for additive and dominance values of single SNPs as well as additive values of haplotypes with reliability estimates for training and validation populations. A two-step strategy and a method of multi-node processing are implemented to remove the computing bottleneck due to the creation of genomic relationship matrices for large samples. The analysis of GVCHAP results includes calculation of observed prediction accuracies from validation studies and preparation of input files for graphical visualization of heritability estimates of haplotype blocks as well as estimates of SNP effects and heritabilities. The entire pipeline provides an efficient and versatile computing tool for identifying the most accurate haplotype model among many candidate haplotype models utilizing structural and functional genomic information for genomic selection.

Before fertility traits were incorporated into selection, dairy cattle breeding primarily focused on production traits, which resulted in an unfavorable decline in the reproductive performance of dairy cattle. This reduced fertility is constantly challenging the dairy industry on the efficiency and sustainability of dairy production. Recent development of genomic selection on fertility traits has stabilized and even reversed the decreasing trend, showing the effectiveness of genomic selection. Meanwhile, genome-wide association studies (GWAS) have been performed to identify quantitative trait loci (QTL) and candidate genes associated with dairy fertility, providing a better understanding of the genetic architecture of fertility traits. In this review, we provide an overview of the genetics of fertility traits, summarize the findings from existing GWAS of female fertility in dairy cattle, and update the recent research progress in US dairy cattle. Because of the polygenic nature of fertility traits, many GWAS of dairy fertility tended to be underpowered. Only 1 major QTL, on BTA18, was identified across multiple studies. This QTL was associated with a range of fertility traits from conception to calving, but the candidate gene or mutation is still missing. Collectively, with the promising success from genomic selection but low power of GWAS on dairy fertility traits, this review calls for continuous data collection of fertility traits to enable more powerful studies of dairy fertility in the future.

Haplotype analysis of SNP markers in genomic prediction and estimation may utilize haplotype effects unaccounted for by single-SNP analysis, whereas haplotype analysis alone may not account for all single-SNP effects. The objective of this study was to establish a theoretical model by mathematical derivation and validation studies to show why haplotype analysis and the joint SNP-haplotype analysis may improve the accuracy of genomic prediction. We first modeled the genotypic value of a two-haplotype genotype as the summation of the single-SNP effects and the haplotype effects unaccounted for by the single SNPs within the haplotype block plus a potential loss of single-SNP effects of the haplotypes. Then we established an invariance property to duplicate SNPs. Assume that a set of SNP markers is duplicated r times in the mixed model. Genomic best linear unbiased prediction (GBLUP) of genetic values (additive, dominance and genotypic values) of individuals and SNP genetic variance components as well as the associated heritability estimates by genomic restricted maximum likelihood estimation (GREML) are invariant to the duplication of SNPs, and GBLUP of SNP additive, dominance and genotypic effects differ from those without duplicate SNPs by the square root of r. Based on this invariance property, adding single SNPs to the haplotype analysis would recover any loss of single-SNP effects of haplotype-only analysis and maintain the haplotype effects not utilized by single-SNP analysis without overestimating single-SNP effects. Validation studies using 6000 individuals with 423,131 SNPs from the Framingham Heart Study showed that heritability estimates under the joint SNP-haplotype model were lower than those from the haplotype-only model, confirming that adding SNPs to the haplotype model did not result in overestimation of the total genetic contribution. In most validation samples, haplotype analysis was at least as accurate as single-SNP analysis, and the joint SNP-haplotype analysis had further improvement in prediction accuracy over the SNP-only or haplotype-only models. These validation results provided a confirmation of the benefit predicted by our theoretical model for the joint SNP-haplotype analysis of genomic prediction based on the invariance property of duplicate SNPs.

Some studies report that ammonia is an important factor of disease development in tobacco plants and various post-harvest fruits. Four tobacco (Nicotiana tabacum L.) varieties resistant or susceptible to Alternaria alternata (Fries) Keissler, a tobacco pathogenic fungus, were used to investigate whether there are differences in ammonia accumulation and the related metabolism of senescing leaves. The results showed that: (a) the leaves of susceptible varieties had significantly higher apoplastic [NH 4 + ], pH, and ammonia emission potential (Γ-values) than resistant varieties during the period from 40 to 60 days of leaf age; (b) leaf tissue [NH 4 + ] and total N concentrations in the tobacco varieties were not in line with their susceptibility or resistance to disease; (c) the increases in the apoplastic pH, Γ-values, and leaf [NH 4 + ] occurred in parallel with a significant decline in glutamine synthetase activity. Compared with the resistant varieties, apoplastic pH values and Γ values were increased more rapidly in the susceptible varieties due to a steeper decline in glutamine synthetase activity and a slower increase in glutamate dehydrogenase activity. In conclusion, NH3 accumulation or NH3-dependent alkalinization rather than [NH 4 + ] and total N appears to be mainly attributed to the enhanced susceptibility of tobacco plants to A. alternata.

Shank length affects chicken leg health and longer shanks are a source of leg problems in heavy-bodied chickens. Identification of quantitative trait loci (QTL) affecting shank length traits may be of value to genetic improvement of these traits in chickens. A genome scan was conducted on 238 F(2) chickens from a reciprocal cross between the Silky Fowl and the White Plymouth Rock breeds using 125 microsatellite markers to detect static and developmental QTL affecting weekly shank length and growth (from 1 to 12 weeks) in chickens. Static QTL affected shank length from birth to time t, while developmental QTL affected shank growth from time t-1 to time t. Seven static QTL on six chromosomes (GGA2, GGA3, GGA4, GGA7, GGA9 and GGA23) were detected at ages of 2, 3, 4, 5, 6, 7, 9 and 12 weeks, and six developmental QTL on five chromosomes (GGA1, GGA2, GGA4, GGA5 and GGA23) were detected for five shank growth periods, weeks 2-3, 4-5, 5-6, 10-11 and 11-12. A static QTL and a developmental QTL (SQSL1 and DQSL2) were identified at GGA2 (between ADL0190 and ADL0152). SQSL1 explained 2.87-5.30% of the phenotypic variation in shank length from 3 to 7 weeks. DQSL2 explained 2.70% of the phenotypic variance of shank growth between 2 and 3 weeks. Two static and two developmental QTL were involved chromosome 4 and chromosome 23. Two chromosomes (GGA7 and GGA9) had static QTL but no developmental QTL and another two chromosomes (GGA1 and GGA5) had developmental QTL but no static QTL. The results of this study show that shank length and shank growth at different developmental stages involve different QTL.

This paper reports the quantitative analysis of the historical database of a herd of Sinclair swine affected by cutaneous malignant melanoma. The herd was under partial and non-systematic selection for melanoma susceptibility (animals having at least one tumour during the first 6 weeks of life). Weighted selection differentials for the number of tumours at birth and the number of tumours at 6 weeks were generally positive and between -0.43 and 4.76 tumours for the number of tumours at 6 weeks. Estimates of the heritability for number of tumours at birth and at 6 weeks using 1934 animals were 0.27 (+/- 0.03) and 0.25 (+/- 0.03), respectively. The estimate of the genetic correlation between these two traits was 0.95 (+/- 0.03). Genetic trends were positive for the number of tumours at birth and at 6 weeks. In spite of positive selection differentials and a moderate heritability, there was a negative phenotypic trend in the number of tumours. Natural selection might be acting in a direction opposite to artificial selection in the Sinclair herd. The slopes of the regression of the number of tumours at birth, at 6 weeks, and melanoma susceptibility on individual inbreeding coefficients were non-significant, indicating no evidence of dominance. The number of live-born pigs was lower in litters from parents susceptible to the disease (p < 0.01).