Proteomic and metabolomic analysis of the serum of patients with tick-borne encephalitis.

Tick-borne encephalitis virus (TBEV) is a common virus in Europe and Asia, causing around 10,000 to 10,500 infections annually. It affects the central nervous system and poses threats to public health. However, the exact molecular mechanisms of TBE pathogenesis are not yet fully understood due to the complex interactions between the virus and its host. In this study, a comprehensive analysis was conducted to characterize the serum metabolome and proteome of adult patients infected with TBEV, in comparison to a control group of healthy individuals. Liquid chromatography tandem mass spectrometry (LC-MS) was employed to monitor metabolic and proteomic alternations throughout the progression of the disease, significant physiological changes associated with different stages of the disease were identified. A total of 44 proteins and 115 metabolites exhibited significantly alternations in the sera of patients diagnosed with TBE. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of these metabolites and proteins revealed differential enrichment of genes associated with the extracellular matrix, complement binding, hemostasis, lipid metabolism, and amino acid metabolism between TBE patients and healthy controls. We gained valuable understanding of the specific metabolites implicated in the host's responses to TBE, establishing a basis for further research on TBE disease. SIGNIFICANCE: The current investigation revealed a comprehensive and systematic differences on TBE using LC-MS platform from human serum samples of TBE patients and healthy individuals providing the immune response to the invasion of TBE.

Identification of potential diagnostic and prognostic biomarkers for breast cancer based on gene expression omnibus.

BACKGROUND: Breast cancer is regarded as a highly malignant neoplasm in the female population, posing a significant risk to women's overall well-being. The prevalence of breast cancer has been observed to rise in China, accompanied by an earlier age of onset when compared to Western countries. Breast cancer continues to be a prominent contributor to cancer-related mortality and morbidity among women, primarily due to its limited responsiveness to conventional treatment modalities. The diagnostic process is challenging due to the presence of non-specific clinical manifestations and the suboptimal precision of conventional diagnostic tests. There is a prevailing uncertainty regarding the most effective screening method and target populations, as well as the specificities and execution of screening programs. AIM: To identify diagnostic and prognostic biomarkers for breast cancer. METHODS: Overlapping differentially expressed genes were screened based on Gene Expression Omnibus (GSE36765, GSE10810, and GSE20086) and The Cancer Genome Atlas datasets. A protein-protein interaction network was applied to excavate the hub genes among these differentially expressed genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, as well as gene set enrichment analyses, were conducted to examine the functions of these genes and their potential mechanisms in the development of breast cancer. For clarification of the diagnostic and prognostic roles of these genes, Kaplan-Meier and Cox proportional hazards analyses were conducted. RESULTS: This study demonstrated that calreticulin, heat shock protein family B member 1, insulin-like growth Factor 1, interleukin-1 receptor 1, Krüppel-like factor 4, suppressor of cytokine signaling 3, and triosephosphate isomerase 1 are potential diagnostic biomarkers of breast cancer as well as potential treatment targets with clinical implications. CONCLUSION: The screening of biomarkers is of guiding significance for the diagnosis and prognosis of the diseases.

Insights into the molecular basis of tick-borne encephalitis from multiplatform metabolomics.

BACKGROUND: Tick-borne encephalitis virus (TBEV) is the most prevalent arbovirus, with a tentative estimate of 10,000 to 10,500 infections occurring in Europe and Asia every year. Endemic in Northeast China, tick-borne encephalitis (TBE) is emerging as a major threat to public health, local economies and tourism. The complicated array of host physiological changes has hampered elucidation of the molecular mechanisms underlying the pathogenesis of this disease. METHODOLOGY/PRINCIPLE FINDINGS: System-level characterization of the serum metabolome and lipidome of adult TBEV patients and a healthy control group was performed using liquid chromatography tandem mass spectrometry. By tracking metabolic and lipid changes during disease progression, crucial physiological changes that coincided with disease stages could be identified. Twenty-eight metabolites were significantly altered in the sera of TBE patients in our metabolomic analysis, and 14 lipids were significantly altered in our lipidomics study. Among these metabolites, alpha-linolenic acid, azelaic acid, D-glutamine, glucose-1-phosphate, L-glutamic acid, and mannose-6-phosphate were altered compared to the control group, and PC(38:7), PC(28:3;1), TAG(52:6), etc. were altered based on lipidomics. Major perturbed metabolic pathways included amino acid metabolism, lipid and oxidative stress metabolism (lipoprotein biosynthesis, arachidonic acid biosynthesis, leukotriene biosynthesis and sphingolipid metabolism), phospholipid metabolism and triglyceride metabolism. These metabolites were significantly perturbed during disease progression, implying their latent utility as prognostic markers. CONCLUSIONS/SIGNIFICANCE: TBEV infection causes distinct temporal changes in the serum metabolome and lipidome, and many metabolites are potentially involved in the acute inflammatory response and immune regulation. Our global analysis revealed anti- and pro-inflammatory processes in the host and changes to the entire metabolic profile. Relationships between metabolites and pathologies were established. This study provides important insight into the pathology of TBE, including its pathology, and lays the foundation for further research into putative markers of TBE disease.

Effects of applying Lactobacillus helveticus H9 as adjunct starter culture in yogurt fermentation and storage.

Lactobacillus helveticus H9 is a probiotic bacterium originating from traditional Tibetan kurut. It has high angiotensin-converting enzyme-inhibitory (ACEI) and antihypertensive activities. We aimed to evaluate the effects of L. helveticus H9 supplementation in yogurt fermentation and storage. We monitored changes of multiple parameters over 28 d of storage at 4°C; namely, pH, titratable acidity, free amino groups, ACEI activity, physical properties, volatile flavor compounds, and sensory quality. Supplementation of L. helveticus H9 enhanced fermented milk acidification and proteolysis, resulting in a shorter fermentation time. The H9 treatment significantly increased the ACEI activity of the fermented milks. Fifteen key volatile flavors were detected by solid-phase microextraction-gas chromatography-mass spectrometry across all samples. More alcohols, aldehydes, and nitrogenous compounds, especially acetoin and benzaldehyde, were detected in the H9-supplemented fermented milks. The human sensory scores for flavor and texture, but not appearance, were lower for the H9-supplemented fermented milks, particularly beyond 2 wk of cold storage. Our results will be of interest to the dairy industry for developing novel functional dairy products.

Screening for Lactobacillus plantarum Strains That Possess Organophosphorus Pesticide-Degrading Activity and Metabolomic Analysis of Phorate Degradation.

This work performed a large scale assessment for organophosphorus pesticides (OPPs) degradation activity of 121 Lactobacillus (L.) plantarum strains. Six L. plantarum strains (P9, IMAU80110, IMAU40100, IMAU10585, IMAU10209, and IMAU80070) were found to possess high capacity of degrading three commonly used OPPs, namely dimethoate, phorate, and omethoate; and they were selected for more detailed characterization. Moreover, the three OPPs were mainly detected in the culture supernatants but not in the cell extracts, further confirming that the OPPs were degraded rather than absorbed by the cells. Among the six selected strains, P9 was most tolerant to gastrointestinal juices and bile. We thus used ultra-high performance liquid chromatography electron spray ionization coupled with time-of-flight mass spectrometry (UPLC/ESI-Q-TOF/MS) to generate the metabolomic profiles of the strain P9 growing in MRS medium with and without containing phorate. By using orthogonal partial least squares discriminant analysis, we identified some potential phorate-derived degradative products. This work has identified novel lactic acid bacteria resources for application in pesticide degradation. Our results also shed light on the phorate degradation mechanism by L. plantarum P9.

A Metabolomics Approach Uncovers Differences between Traditional and Commercial Dairy Products in Buryatia (Russian Federation).

Commercially available and traditional dairy products differ in terms of their manufacturing processes. In this study, commercially available and traditionally fermented cheese, yogurt, and milk beverages were analyzed and compared. The metabolomic technique of ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry (UPLC-Q-TOF) in the MSE mode was used in combination with statistical methods, including univariate analysis and chemometric analysis, to determine the differences in metabolite profiles between commercially and traditionally fermented dairy products. The experimental results were analyzed statistically and showed that traditional and commercial dairy products were well differentiated in both positive and negative ion modes, with significant differences observed between the samples. After screening for metabolite differences, we detected differences between traditional milk beverages and yogurt and their commercial counterparts in terms of the levels of compounds such as l-lysine, l-methionine, l-citrulline, l-proline, l-serine, l-valine and l-homocysteine, and of short peptides such as Asp-Arg, Gly-Arg, His-Pro, Pro-Asn. The greatest difference between commercially available and traditional cheese was in the short peptide composition, as commercially available and traditional cheese is rich in short peptides.

Characterization of the angiotensin-converting enzyme inhibitory activity of fermented milks produced with Lactobacillus casei.

Our study assayed angiotensin-converting enzyme (ACE) inhibitory activity and fermentation characteristics of 41 food-originated Lactobacillus casei strains in fermented milk production. Twenty-two of the tested strains produced fermented milks with a high ACE inhibitory activity of over 60%. Two strains (IMAU10408 and IMAU20411) expressing the highest ACE inhibitory activity were selected for further characterization. The heat stability (pasteurization at 63°C for 30 min, 75°C for 25 s, and 85°C for 20 s) and resistance to gastrointestinal proteases (pepsin, trypsinase, and sequential pepsin/trypsinase treatments) of the ACE inhibitory activity in the fermented milks produced with IMAU10408 and IMAU20411 were determined. Interestingly, such activity increased significantly after the heat or protease treatment. Because of the shorter milk coagulation time of L. casei IMAU20411 (vs. IMAU10408), it was selected for optimization experiments for ACE inhibitory activity production. Our results show that fermentation temperature of 37°C, inoculum density of 1 × 106 cfu/g, and fermentation time of 12 h were optimal for maximizing ACE inhibitory activity. Finally, the metabolite profiles of L. casei IMAU20411 after 2 and 42 h of milk fermentation were analyzed by ultra-HPLC electron spray ionization coupled with time-of-flight mass spectrometry. Nine differential abundant metabolites were identified, and 2 of them showed a strong and positive correlation with fermented milk ACE inhibitory activity. To conclude, we have identified a novel ACE inhibitory L. casei strain, which has potential for use as a probiotic in fermented milk production.

Ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry MSE-based untargeted milk metabolomics in dairy cows with subclinical or clinical mastitis.

In this study, a novel metabolomics technique based on ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry in the MSE mode was used to investigate the milk metabolomics of healthy, subclinical, and clinical mastitis cows, which were classified based on somatic cell count and presentation of clinical symptoms. Meanwhile, univariate and multivariate statistical analyses were performed to identify the significant differences across the 3 groups. Compared with healthy milk samples, less glucose, d-glycerol-1-phosphate, 4-hydroxyphenyllactate, l-carnitine, sn-glycero-3-phosphocholine, citrate, and hippurate were detected in the clinical mastitic milk samples, whereas less d-glycerol-1-phosphate, benzoic acid, l-carnitine, and cis-aconitate were found in the subclinical mastitic milk samples. Meanwhile, the milk concentration of arginine and Leu-Leu increased in both the clinical and subclinical mastitis groups. Besides, less 4-hydroxyphenyllactate, cis-aconitate, lactose, and oxoglutarate were detected in the clinical than the subclinical mastitic milk samples, whereas the abundance of some oligopeptides (Leu-Ala, Phe-Pro-Ile, Asn-Arg-Ala-Ile, and Val-Phe-Val-Tyr) increased by over 7.95-fold. Our results suggest that significant variations exist across healthy and mastitis cows. The current metabolomics approach will help in better understanding the pathobiology of mastitis, although clinical validation will be required before field application.

Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters.

The present study applied the PacBio single molecule, real-time sequencing technology (SMRT) in evaluating the quality of silage production. Specifically, we produced four types of Medicago sativa silages by using four different lactic acid bacteria-based additives (AD-I, AD-II, AD-III and AD-IV). We monitored the changes in pH, organic acids (including butyric acid, the ratio of acetic acid/lactic acid, γ-aminobutyric acid, 4-hyroxy benzoic acid and phenyl lactic acid), mycotoxins, and bacterial microbiota during silage fermentation. Our results showed that the use of the additives was beneficial to the silage fermentation by enhancing a general pH and mycotoxin reduction, while increasing the organic acids content. By SMRT analysis of the microbial composition in eight silage samples, we found that the bacterial species number and relative abundances shifted apparently after fermentation. Such changes were specific to the LAB species in the additives. Particularly, Bacillus megaterium was the initial dominant species in the raw materials; and after the fermentation process, Pediococcus acidilactici and Lactobacillus plantarum became the most prevalent species, both of which were intrinsically present in the LAB additives. Our data have demonstrated that the SMRT sequencing platform is applicable in assessing the quality of silage.