Developing neural network diagnostic models and potential drugs based on novel identified immune-related biomarkers for celiac disease.

BACKGROUND: As one of the most common intestinal inflammatory diseases, celiac disease (CD) is typically characterized by an autoimmune disorder resulting from ingesting gluten proteins. Although the incidence and prevalence of CD have increased over time, the diagnostic methods and treatment options are still limited. Therefore, it is urgent to investigate the potential biomarkers and targeted drugs for CD. METHODS: Gene expression data was downloaded from GEO datasets. Differential gene expression analysis was performed to identify the dysregulated immune-related genes. Multiple machine algorithms, including randomForest, SVM-RFE, and LASSO, were used to select the hub immune-related genes (HIGs). The immune-related genes score (IG score) and artificial neural network (ANN) were constructed based on HIGs. Potential drugs targeting HIGs were identified by using the Enrichr platform and molecular docking method. RESULTS: We identified the dysregulated immune-related genes at a genome-wide level and demonstrated their roles in CD-related immune pathways. The hub genes (MR1, CCL25, and TNFSF13B) were further screened by integrating several machine algorithms. Meanwhile, the CD patients were divided into distinct subtypes with either high- or low-immunoactivity using single-sample gene set enrichment analysis (ssGSEA) and consensus clustering. By constructing IG score based on HIGs, we found that patients with high IG score were mainly attributed to high-immunoactivity subgroups, which suggested a strong link between HIGs and immunoactivity of CD patients. In addition, the novel constructed ANN model showed the sound diagnostic ability of HIGs. Mechanistically, we validated that the HIGs play pivotal roles in regulating CD's immune and inflammatory state. Through targeting the HIGs, we also found potential drugs for anti-CD treatment by using the Enrichr platform and molecular docking method. CONCLUSIONS: This study unveils the HIGs and elucidates the networks regulated by these genes in the context of CD. It underscores the pivotal significance of HIGs in accurately predicting the presence or absence of CD in patients. Consequently, this research offers promising prospects for the development of diagnostic biomarkers and therapeutic targets for CD.

Acyl Chain Specificity of Marine Streptomyces klenkii PhosPholipase D and Its Application in Enzymatic Preparation of Phosphatidylserine.

Mining of phospholipase D (PLD) with altered acyl group recognition except its head group specificity is also useful in terms of specific acyl size phospholipid production and as diagnostic reagents for quantifying specific phospholipid species. Microbial PLDs from Actinomycetes, especially Streptomyces, best fit this process requirements. In the present studies, a new PLD from marine Streptomyces klenkii (SkPLD) was purified and biochemically characterized. The optimal reaction temperature and pH of SkPLD were determined to be 60 °C and 8.0, respectively. Kinetic analysis showed that SkPLD had the relatively high catalytic efficiency toward phosphatidylcholines (PCs) with medium acyl chain length, especially 12:0/12:0-PC (67.13 S-1 mM-1), but lower catalytic efficiency toward PCs with long acyl chain (>16 fatty acids). Molecular docking results indicated that the different catalytic efficiency was related to the increased steric hindrance of long acyl-chains in the substrate-binding pockets and differences in hydrogen-bond interactions between the acyl chains and substrate-binding pockets. The enzyme displayed suitable transphosphatidylation activity and the reaction process showed 26.18% yield with L-serine and soybean PC as substrates. Present study not only enriched the PLD enzyme library but also provide guidance for the further mining of PLDs with special phospholipids recognition properties.

Controlling Specific Growth Rate for Recombinant Protein Production by Pichia pastoris Under Oxidation Stress in Fed-batch Fermentation.

Methanol can be used by Pichia pastoris as the carbon source and inducer to produce recombinant proteins in high-cell-density fermentations. However, methanol oxidation at high specific growth rates can lead to the reactive oxygen species (ROS) accumulation, resulting in cell damage. Here, we study the relationship between methanol feeding and ROS accumulation by controlling specific growth rate during the induction phase. A higher specific growth rate increased the level of ROS accumulation caused by methanol oxidation. While the cell growth rate was proportional to specific growth rate, maximum total protein production and highest enzyme activity were achieved at a specific growth rate of 0.05 1/h as compared to that of 0.065 1/h. Moreover, oxidative damage induced by over-accumulation of ROS in P. pastoris during the methanol induction phase caused cell death and reduced protein expression ability. ROS scavenging system analysis revealed that the higher specific growth rate, especially 0.065 1/h, resulted in increased intracellular catalase activity and decreased glutathione content significantly. Finally, Spearman's correlation analysis further revealed that the reduced glutathione might be beneficial for maintaining cell viability and increasing protein production under oxidative stress caused by ROS toxic accumulation. Our findings suggest an integrated strategy to control the feeding of the essential substrate based on analyzing its response to oxidative stress caused by ROS toxic accumulation, as well as develop a strategy to optimize fed-batch fermentation.

Prebiotic Agrocybe cylindracea crude polysaccharides combined with Lactobacillus rhamnosus GG postpone aging-related oxidative stress in mice.

This study aimed to investigate the potential anti-aging mechanisms of Agrocybe cylindracea crude polysaccharides (APS), when used synergistically with Lactobacillus rhamnosus GG (APS + LGG) in a D-galactose-induced aging mouse model. In the Morris water maze test, APS + LGG showed a significantly higher memory and learning capacity compared to untreated, APS only treated and LGG treated mice. This was thought to be mediated by increased levels of brain-derived neurotrophic factor, which decreased escape latency. In addition to this, in the aging mouse model, APS + LGG co-treatment markedly alleviated liver oxidation and metabolism by enhancing the antioxidant activity of enzymes; this decreased the lipid metabolism and peroxidation levels. Furthermore, high throughput sequencing analysis revealed that an APS + LGG supplemented feed increased the relative abundance of positive bacteria in the gut microbiota such as Alloprevotella and Parvibacter. Importantly, Alloprevotella and Parvibacter showed a negative relationship with low density lipoprotein-cholesterol in the Spearman correlation analysis. These results illustrate that APS, in combination with LGG, postponed aging related oxidative stress when used as a prebiotic. The proposed mechanism for this is the reduction in liver oxidation and lipid metabolism, as well as the regulation of gut microbiota.

Enhancement of Phospholipid Binding and Catalytic Efficiency of Streptomyces klenkii Phospholipase D by Increasing Hydrophobicity of the Active Site Loop.

The mechanism of active site loops of Streptomyces phospholipase D (PLD) binding to the lipid-water interface for catalytic reactions still remains elusive. A flexible loop (residues 376-382) in the active site of Streptomyces klenkii PLD (SkPLD) is conserved within PLDs in most of the Streptomyces species. The residue Ser380 was found to be essential for the enzyme's adsorption to the interface and its substrate recognition. The S380V mutant showed a 4.8 times higher catalytic efficiency and nearly seven times higher adsorption equilibrium coefficient compared to the wild-type SkPLD. The monolayer film technique has confirmed that the substitution of Ser380 with valine in the loop exhibited positive interaction between the enzyme and PCs with different acyl chain lengths. The results of the interfacial binding properties indicated that the S380V mutant might display suitable phosphatidylserine synthesis activity. The present study will be helpful to explain the role of residue 380 in the active site loops of Streptomyces PLD.

Ganoderma polysaccharide and chitosan synergistically ameliorate lipid metabolic disorders and modulate gut microbiota composition in high fat diet-fed golden hamsters.

High-fat diet (HFD) and sucrose intake can lead to hyperlipidemia, hypercholesterolemia, and nonalcoholic fatty liver disease (NAFLD) as well as disturbed gastrointestinal microbiota and dysfunctional intestinal barrier. In the present study, we showed that Ganoderma lucidum polysaccharide and chitosan (PC) significantly mitigated the hyperlipidemia in HFD-fed hamsters via lowering the contents of serum total triglyceride (TG), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and aspartate aminotransferase (AST). Furthermore, PC changed the composition of gastrointestinal microbiota and elevated the relative abundances of beneficial bacteria, such as Prevotella, Oscillibacter, and SCFA-producers. Interestingly, we also found that the abundances of Prevotella, Alloprevotella, Bifidobacterium, and Alistipes were negatively associated with serum lipid profiles. Collectively, the above-mentioned findings indicated that PC could improve lipid metabolic disorders, at least in part, by modulating gastrointestinal microbiota, suggesting that PC could be used as a potential lipid-lowering ingredient in functional foods. PRACTICAL APPLICATIONS: PC could ameliorate lipid metabolism disorder, at least in part, by regulating specific gut microbiota, suggesting its potential as a novel lipid-lowering ingredient in functional foods. We believed that our findings could be of interest to the readers because they help others further understand the gut microbiota alterations that occurred after PC supplementation in the context of metabolic syndrome (MetS).

Fermented carrot juice attenuates type 2 diabetes by mediating gut microbiota in rats.

In the present study, we aimed to investigate the therapeutic mechanisms of carrot juice fermented with Lactobacillus rhamnosus GG (LGG) on type 2 diabetic mellitus (T2DM) based on the regulation of gut microbiota. Carrot juice fermented with LGG was enriched with free phenols, organic acids and short-chain fatty acids (SCFAs). Supplementation of carrot juice fermented with LGG (DFCL) could favorably regulate blood glucose, insulin, antioxidant capacity and morphology of the pancreas and kidney in the diabetic rats, accompanied by an increase of SCFAs in the cecum. Furthermore, high-throughput sequencing (HTS) analysis revealed that DFCL supplementation altered the composition of gut microbiota, showing increased relative abundances of functionally relevant enterotypes, such as Christensenellaceae_R-7_group, Oscillibacter, Ruminococcaceae_UCG-013, Lachnospiraceae_NK4A136_group and Akkermansia. In addition, Spearman's correlation analysis revealed that Desulfovibrio, Ruminococcaceae and Alloprevotella were closely correlated with biochemical biomarkers. Meanwhile, DFCL treatment regulated the expressions of genes involved in glucose metabolism at the mRNA and protein levels.