PubMed

Animals (Basel). 2025 Jan 30;15(3):393. doi: 10.3390/ani15030393.ABSTRACTDuring pregnancy and lactation, maternal nutrition is linked to the full development of offspring and may have long-term or lifelong effects. However, the influence of the doe's diet on the gastrointestinal (GI) tract of young kids remains largely unexplored. Therefore, we investigated the effects of doe roughage sources (alfalfa hay, AH, or corn straw, CS) during pregnancy and lactation on kid growth, GI morphology, barrier function, metabolism, immunity, and microbiome composition. The results indicate that, compared with the CS group, does fed an AH diet had significantly higher feed intake (p < 0.01). However, CS-fed does exhibited higher neutral detergent fiber (NDF) digestibility (p < 0.05). There were no significant differences in animal (doe or kid) weight among the groups (p > 0.05). In the rumen of goat kids, the AH group exhibited a higher papillae width and increased levels of interleukin-10 (IL-10) compared with the CS group (p < 0.05). In the jejunum of goat kids, the AH group showed a higher villus-height-to-crypt-depth (VH/CD) ratio, as well as elevated levels of secretory immunoglobulin A (SIgA), immunoglobulin G (IgG), IL-10, acetate, and total volatile fatty acids (TVFAs), when compared with the CS group (p < 0.05). Transcriptome analysis revealed that the source of roughage in does was associated with changes in the GI transcriptome of the kids. Differentially expressed genes (DEGs) in the rumen were mainly associated with tissue development and immune regulation, while the DEGs in the jejunum were mainly associated with the regulation of transferase activity. Spearman correlation analyses indicated significant associations between GI DEGs and phenotypic indicators related to GI development, immunity, and metabolism. LEfSe analysis identified 14 rumen microbial biomarkers and 6 jejunum microbial biomarkers. Notably, these microorganisms were also enriched in the rumen or day 28 milk of the does. Further microbial composition analysis revealed significant correlations between the rumen and milk microbiomes of does and the rumen or jejunum microbiomes of kids. Association analyses indicated that microbial biomarkers interact with host genes, thereby affecting the development and function of the GI system. Additionally, correlation analyses revealed significant association between milk metabolites and the rumen and jejunum microbiomes of kids. This study demonstrated that maternal diet significantly influences the development of microbial ecosystems in offspring by modulating microbial communities and metabolite composition. The early colonization of GI microorganisms is crucial for the structural development, barrier function, immune capacity, and microbial metabolic activity of the GI system.PMID:39943163 | DOI:10.3390/ani15030393

Plants (Basel). 2025 Jan 24;14(3):359. doi: 10.3390/plants14030359.ABSTRACTSoilborne diseases are important problems in modern agricultural production. Fusarium oxysporum f. sp. cucumerinum (FOC) is one of the predominant soilborne pathogens threatening cucumber cultivation, especially in Hainan, China. This study assessed FOC-resistant rootstocks using incidence rate, disease severity index (DSI), and area under the disease severity index curve (AUDRC), revealing "JinJiaZhen (Mc-4)" as resistant and "JinGangZhuan 1901 (Mc-18)" as susceptible. Comprehensive transcriptome and metabolome analyses were conducted to investigate the defense mechanisms of these rootstocks, revealing key pathways, such as the mitogen-activated protein kinase (MAPK) signaling pathway, starch and sucrose metabolism, and phenylpropanoid biosynthesis, which are crucial for plant disease resistance. Additionally, the study compared the resistance mechanisms of two other rootstocks, Mc-4 and Mc-18, against FOC infection through transcriptomic and metabolomic analyses. Mc-4 exhibited a higher number of differentially expressed genes (DEGs) related to phenylpropanoid biosynthesis compared to Mc-18. Untargeted metabolomics identified 4093 metabolites, with phenylpropanoid biosynthesis, isoquinoline alkaloid biosynthesis, and porphyrin metabolism as primary annotated pathways. On the sixth day post-inoculation, when the number of DEGs and differentially accumulated metabolites (DAMs) was highest, phenylpropanoid biosynthesis emerged as a key pathway in Mc-4, with 37 DEGs and 8 DAMs identified. Notably, Mc-4 showed upregulated expression of genes encoding enzymes involved in phenylpropanoid biosynthesis and increased accumulation of related metabolites, such as coniferyl-aldehyde, coniferyl alcohol, and coniferyl acetate. These findings highlight the differential defense mechanisms between resistant and sensitive rootstocks and provide insights into plant-pathogen interactions. This study's results will contribute to the development of better and disease-free cucumber varieties, promoting sustainable agriculture.PMID:39942921 | DOI:10.3390/plants14030359

Molecules. 2025 Feb 6;30(3):734. doi: 10.3390/molecules30030734.ABSTRACTArnebia euchroma (Royle) Johnst. has high medicinal and economic value, but in recent years, wild resources of this species have been depleted and the quality of artificially cultivated A. euchroma has been poor. The endophyte community of medicinal plants is rich, serving as an internal resource that promotes the growth of medicinal plants and the accumulation of secondary metabolites, and has important potential application value in improving the quality of medicinal materials. A. euchroma cultivars and wild varieties contain abundant endophyte communities and metabolites in different tissues. However, the relationships between A. euchroma endophytes and metabolites with different growth patterns and different tissue sites remain unclear. In this study, microbiome analysis and metabolomics were used to analyze the diversity of endophytes in the root and leaf tissues of cultivated and wild A. euchroma and their correlations with metabolites. The results revealed that the diversity of endophytes in A. euchroma was different from that in wild A. euchroma and that there was tissue specificity among different tissues. A species composition analysis revealed that the dominant endophytic fungi belonged to Ascomycota and Basidiomycota, and the dominant endophytic bacteria belonged to Proteobacteria and Cyanobacteria. A total of 248 metabolites, including quinones, flavonoids, alkaloids, organic acids, sugars, amino acids, coumarins, sterols, terpenoids, polyphenols, fatty ketones, and their derivatives, were identified in positive ion mode via LC-MS/MS. According to their different growth patterns and associated tissue parts, 9 differentially abundant metabolites were screened between AEZ-L (cultivated leaf tissue of A. euchroma) and AEY-L (wild leaf tissue of A. euchroma), 6 differentially abundant metabolites were screened between AEZ-R (cultivated root tissue of A. euchroma) and AEY-R (wild root tissue of A. euchroma), and 104 differentially abundant metabolites were screened between AEZ-R and AEZ-L. Eighty-two differentially abundant metabolites were screened between AEY-R and AEY-L. The contents of eight naphthoquinones in AEZ-R and AEY-R were determined via HPLC. The contents of β,β'-dimethylacrylylakanin in wild A. euchroma were greater than those in cultivated A. euchroma. A correlation analysis revealed that the dominant endophytes in the four groups were significantly correlated with a variety of metabolites, and the eight naphthoquinones in the root tissue were also significantly correlated with the dominant endophytes. The diversity of the A. euchroma endophyte community differed across different growth patterns and different tissue parts. There were significant differences in the relative contents of A. euchroma metabolites in different tissues. A correlation analysis verified the correlation between A. euchroma endophytes and metabolites.PMID:39942836 | DOI:10.3390/molecules30030734

Molecules. 2025 Feb 6;30(3):726. doi: 10.3390/molecules30030726.ABSTRACTSebum lipids, accessible via groomed latent fingerprints, may be a valuable, underappreciated sample source for future biomarker research. Sampling sebum lipids from the skin is painless for patients, efficient for researchers, and has already demonstrated the potential to contain disease biomarkers. However, before sebum sampling can be implemented in routine studies, more information is needed regarding sampling reproducibility and variability. This information will enable researchers to choose the best practices for sebum-based studies. Herein, we use our recently established workflow for the collection and analysis of groomed fingerprints to assess the reproducibility of lipid profiles obtained via mass spectrometry. Using 180 fingerprint samples collected from 30 participants, we also assess lipid changes according to biological sex and anatomical grooming region (cheek, neck, and forehead) via supervised and unsupervised classification. The results demonstrate that this sampling protocol achieves satisfactory reproducibility, and negligible differences exist between male and female groomed fingerprint lipids. Moreover, the anatomical grooming region can impact the fingerprint lipid profile: cheek- and forehead-groomed fingerprints are more similar to one another than either collection site is to neck-groomed fingerprints. This information will inform future sebum-based biomarker investigations, enabling researchers to collect meaningful lipidomic datasets from groomed fingerprint samples.PMID:39942829 | DOI:10.3390/molecules30030726

Molecules. 2025 Feb 3;30(3):670. doi: 10.3390/molecules30030670.ABSTRACTPolysaccharides are the major bioactive components of Polygonatum cyrtonema Hua, and their biosynthesis and accumulation are influenced by many agronomic practices. In this study, we applied integrative metabolome and transcriptome analyses to investigate the accumulation of bioactive components in one-year-old (1Y) and six-year-old (6Y) rhizomes of P. cyrtonema Hua treated with a plucking flower. The compound content analysis suggested that six-year-old treated rhizomes (T6) accumulated the highest polysaccharide content compared to that of one-year-old treated rhizomes (T1), one-year-old untreated rhizomes (C1), and six-year-old untreated rhizomes (C6). Metabolomics analysis showed that 4-O-galactopyranosylxylose, 6-O-α-l-arabinopyranosyl-d-glucopyranose, d-arabinose and dl-xylose significantly accumulated in T6 rhizomes. Carbohydrate metabolic pathways, including "glycolysis/gluconeogenesis", "pentose and glucoronate interconversions" and "amino sugar and nucleotide sugar metabolism" were highly correlated with polysaccharide biosynthesis and accumulation. The transcriptome data indicated that UPG2, GPI, and GALE were positively upregulated in T6_vs_C6. In parallel, RHM and PEI were down-regulated in T6_vs_C6. Taken together, this study not only indicates that the candidate metabolites/metabolic pathways and genes affected by plucking flowers may influence the accumulation of polysaccharides in the rhizomes but also provides an easy and feasible agronomic practice to facilitate the accumulation of polysaccharides in the rhizomes of P. cyrtonema Hua.PMID:39942775 | DOI:10.3390/molecules30030670

Molecules. 2025 Jan 22;30(3):468. doi: 10.3390/molecules30030468.ABSTRACTThe dried rhizome of Notopterygium incisum (NI) from the Umbelliferae family, genuinely produced in Sichuan, China, is a classic traditional Chinese medicinal herb for treating wind-dampness arthralgia. Due to scarce natural resources, wild NI is gradually being replaced by cultivated types. However, knowledge is limited regarding the differences in chemical composition and pharmacological effects between wild and cultivated NI and between Sichuan-grown and other-region-grown NI. In this study, a plant metabolomics strategy, based on GC-MS and UHPLC-Orbitrap MS, was employed to compare metabolic profiles between wild and cultivated NI and between cultivated NI from Sichuan and cultivated NI from Gansu and Qinghai. In total, 195 metabolites were identified, and the biosynthetic pathways of coumarins and phenolic acids, which were the most abundant secondary metabolites in NI, were summarized. Additionally, seven key metabolic intermediates were uncovered, revealing the reasons for the differences in metabolic profiles between wild and cultivated NI. The anti-inflammatory effect of wild and cultivated NI was verified by inflammatory gene expression and neutrophil count using a zebrafish yolk sac inflammation model. Overall, this study presents information on the types and synthesis of pharmacodynamic substances in NI and provides a basis for its cultivation and applications.PMID:39942574 | DOI:10.3390/molecules30030468

Foods. 2025 Feb 6;14(3):530. doi: 10.3390/foods14030530.ABSTRACTFermented milk has a long history. It is fermented by lactic acid bacteria and is rich in protein, minerals, vitamins, and other nutrients. As people's pursuit of quality of life improves, consumers are paying increasing attention to fermented milk. Streptococcus salivarius ssp. thermophilus is commonly used to make fermented milk. This study investigated the fermentation characteristics and physicochemical properties of Streptococcus salivarius ssp. thermophilus Snew-fermented milk, as well as transcriptomic and metabolomic analyses of different fermentation stages. Streptococcus salivarius ssp. thermophilus Snew can be used as a fermenter strain, as evaluated from the point of view of fermentation time, titratable acidity, post-acidification, viable bacteria count, water holding capacity, and viscosity. The flavor and odor of Snew-fermented milk varied across fermentation stages. The analysis of the detected volatiles revealed that ketones and esters were the main substances responsible for the flavor of Snew-fermented milk. The differentially expressed genes and differential metabolites screened from several categories, such as carbohydrates, proteins, amino acids, fats, and fatty acids, varied at different fermentation stages, while differentially expressed genes and differential metabolites were also threaded together for joint analysis in this study. This study provides theoretical guidance for the practical production application of Streptococcus salivarius ssp. thermophilus in cow's milk fermentation.PMID:39942123 | DOI:10.3390/foods14030530

Foods. 2025 Jan 28;14(3):431. doi: 10.3390/foods14030431.ABSTRACTTo compare the impact of different post-harvest handling methods on volatile and non-volatile compounds, a total of 54 live large yellow croakers were subjected to commercial slaughter (CS), spinal cord cutting (SCC), or spinal cord cutting and bleeding (SCCB). The fish samples were ice-stored for 72 h, followed by the analysis of volatile compounds using gas chromatography-ion mobility spectrometry and non-volatile compounds using LC-MS-based untargeted metabolomics. The results revealed the detection of a total of 28 volatile organic compounds, with 23 being successfully identified, predominantly including alcohols, aldehydes, esters, ketones, and heterocyclic compounds. Substances such as (E)-2-nonenal and 2-butanone are highly sensitive to post-harvest handling methods during ice storage. Furthermore, 943 non-volatile metabolites were identified, showing significant differences in 180, 100, 117, and 186 metabolites across comparisons of SCC 0 h/CS 0 h, SCCB 0 h/CS 0 h, SCC 72 h/CS 72 h, and SCCB 72 h/CS 72 h, respectively. Notably, the altered metabolic pathways mainly involved fatty acid and amino acid metabolism, including pathways like glycerophospholipid metabolism and arginine biosynthesis. This study revealed the potential mechanisms underlying the enhancement of fish quality through spinal cord cutting and bleeding.PMID:39942024 | DOI:10.3390/foods14030431

Foods. 2025 Jan 24;14(3):387. doi: 10.3390/foods14030387.ABSTRACTImmune checkpoint inhibitors (ICIs) have revolutionized cancer treatment and significantly improved outcomes for patients with certain malignancies. However, immunotherapy with ICIs is only effective in a subset of patients and the gut microbiota have been identified as an important factor associated with response to ICI therapy. Polysaccharides from sea cucumber (Stichopus japonicus) (SCP) have been shown to modulate the gut microbiota and exhibit beneficial health functions, but whether SCP could synergize with anti-PD1 immunotherapy remains unexplored. In this study, mice with ICI-sensitive MC38 tumors were treated with anti-PD1 antibody after supplementation with or without SCP to examine the potential impact of SCP on the efficacy of immunotherapy. SCP strongly amplified the anti-tumor activity of anti-PD1 in MC38 tumor-bearing mice. Flow cytometry and immunohistological staining demonstrated that SCP treatment increased cytotoxic CD8+ T lymphocytes while decreasing regulatory Foxp3+ CD4+ T lymphocytes. Gut microbiota and metabolomic analysis revealed that SCP modulated the microbiota and increased the abundance of certain metabolites such as indole-3-carboxylic acid. Furthermore, fecal microbiota transplantation experiments justified that the synergistic effect of SCP with anti-PD1 was partially mediated through the gut microbiota. Mice receiving microbiota from SCP-treated mice showed a boosted response to anti-PD1, along with enhanced anti-tumor immunity. These findings indicate that SCP could be utilized as a dietary strategy combined with anti-PD1 therapy to achieve improved outcomes in patients.PMID:39941980 | DOI:10.3390/foods14030387

Cancers (Basel). 2025 Feb 5;17(3):532. doi: 10.3390/cancers17030532.ABSTRACTBackground: Patients with relapsed or refractory (R/R) diffuse large B-cell lymphoma (DLBCL) who are ineligible for high-dose chemotherapy have limited treatment options and poor life expectancy. The purpose of this study is to identify a serum metabolomic profile that may be predictive of outcome in patients with R/R-DLBCL. Methods: This study included 69 R/R DLBCL patients from the R2-GDP-GOTEL trial (EudraCT 2014-001620-299). Serum samples were collected at baseline, and the mean length of follow-up was 41 months. Serum metabolites were analyzed by nuclear magnetic resonance (NMR). Metabolites were correlated with treatment response, progression-free survival (PFS), and overall survival (OS). Results: Serum levels of 3-hydroxybutyrate (3OHB) and acetone were significantly (p < 0.001) associated with PFS (3OHB: hazard ratio [HR] 7.7, 95% confidence interval [CI] 2.5-24.1; acetone: HR 9.32, 95% CI 2.75-31.6) and OS (3OHB: HR 9.32, 95% CI 2.75-31.6; acetone: HR 1.92, 95% CI 1.36-2.69). Serum values of 141 µM for 3OHB and 40 µM for acetone were the optimal cutoffs associated with the survival outcomes. Elevated 3OHB levels (>141 μM) were specific to the ABC subtype of DLBCL, while acetone levels were elevated in both types of DLCBL but more pronounced in ABC cases. In a multivariate survival analysis, including the International Prognostic Index (IPI) score and refractoriness status (R/R), 3OHB and acetone remained significant. To aid oncologists employing the R2-GDP regime, we constructed PFS and OS nomograms for R/R-DLBCL risk stratification, incorporating 3OHB levels or acetone levels, IPI score, and refractoriness status. The nomogram with 3OHB and refractoriness status showed a time-dependent AUC of 0.86 for 6-month PFS and 0.84 for 12-month OS. These nomograms provide a comprehensive tool for individualized risk assessment and treatment optimization. Conclusions: The ketone bodies 3OHB and acetone are potential prognostic biomarkers of poor outcome in R/R DLBCL patients treated with the R2-GDP regimen, independently of IPI score and chemorefractoriness status.PMID:39941898 | DOI:10.3390/cancers17030532

Diagnostics (Basel). 2025 Jan 22;15(3):252. doi: 10.3390/diagnostics15030252.ABSTRACTIn recent years, novel findings have progressively and promisingly supported the potential role of Artificial intelligence (AI) in transforming the management of various neoplasms, including hepatocellular carcinoma (HCC). HCC represents the most common primary liver cancer. Alarmingly, the HCC incidence is dramatically increasing worldwide due to the simultaneous "pandemic" spreading of metabolic dysfunction-associated steatotic liver disease (MASLD). MASLD currently constitutes the leading cause of chronic hepatic damage (steatosis and steatohepatitis), fibrosis, and liver cirrhosis, configuring a scenario where an HCC onset has been reported even in the early disease stage. On the other hand, HCC represents a serious plague, significantly burdening the outcomes of chronic hepatitis B (HBV) and hepatitis C (HCV) virus-infected patients. Despite the recent progress in the management of this cancer, the overall prognosis for advanced-stage HCC patients continues to be poor, suggesting the absolute need to develop personalized healthcare strategies further. In this "cold war", machine learning techniques and neural networks are emerging as weapons, able to identify the patterns and biomarkers that would have normally escaped human observation. Using advanced algorithms, AI can analyze large volumes of clinical data and medical images (including routinely obtained ultrasound data) with an elevated accuracy, facilitating early diagnosis, improving the performance of predictive models, and supporting the multidisciplinary (oncologist, gastroenterologist, surgeon, radiologist) team in opting for the best "tailored" individual treatment. Additionally, AI can significantly contribute to enhancing the effectiveness of metabolomics-radiomics-based models, promoting the identification of specific HCC-pathogenetic molecules as new targets for realizing novel therapeutic regimens. In the era of precision medicine, integrating AI into routine clinical practice appears as a promising frontier, opening new avenues for liver cancer research and treatment.PMID:39941182 | DOI:10.3390/diagnostics15030252

Int J Mol Sci. 2025 Feb 2;26(3):1284. doi: 10.3390/ijms26031284.ABSTRACTTelocytes (TCs) are distinctive cells widely localized in the stromal compartment of several human organs, including the skin. By means of their peculiar prolongations named telopodes, skin TCs are organized in networks interconnected with a variety of adjacent cells, being thus supposed to take part in skin homeostasis through both cell-to-cell contacts and the release of extracellular vesicles. A disarrangement/loss of the TC network was shown in human fibrotic skin as well as in the murine model of bleomycin-induced cutaneous fibrosis, but whether such TC alterations may represent just a consequence or a trigger of the fibrotic process still remains to be clarified. Thus, we investigated the effects of skin TC secretome as conditioned medium (TC-CM) on the transition of skin fibroblasts into myofibroblasts promoted by the master profibrotic cytokine transforming growth factor β1 (TGFβ1). Primary cultures of both adult human skin TCs and fibroblasts were obtained by means of immunomagnetic cell separation. Nanoparticle tracking analysis was carried out to measure extracellular vesicles in TC-CM. The combination of multiple morphological, gene/protein expression, and functional assessments demonstrated that TC-CM was able to significantly prevent TGFβ1-induced fibroblast-to-myofibroblast transition. TC-CM did not influence cell viability, while it effectively inhibited TGFβ1-induced fibroblast proliferation, migration, and morphological changes. Indeed, TC-CM was able to reduce TGFβ1-mediated skin fibroblast phenotypic and functional differentiation into myofibroblasts, as shown by a significant decrease in FAP, ACTA2, COL1A1, COL1A2, FN1, and CTGF gene expression, α-smooth muscle actin, N-cadherin, COL1A1, and FN-EDA protein levels, and collagen gel matrix contraction. Furthermore, TC-CM significantly lowered TGFβ1-mediated ERK1/2 signaling pathway activation. This in vitro study proves for the first time that TCs may play an important role in skin homeostasis through the prevention of fibroblast-to-myofibroblast transition via paracrine mechanisms and affords the necessary basis to investigate in the future the feasibility of TC secretome as an innovative antifibrotic therapeutic tool.PMID:39941052 | DOI:10.3390/ijms26031284

Plant Cell Rep. 2025 Feb 13;44(3):54. doi: 10.1007/s00299-025-03443-8.ABSTRACTProteomics has revealed complex immune responses in fruits, leading to the identification of potential disease biomarkers and resistance mechanisms. Fruit diseases caused by fungal and bacterial pathogens present critical challenges to global food security by reducing fruit shelf life and quality. This review explores the molecular dynamics of fruit-pathogen interactions using advanced proteomic techniques. These approaches include mass spectrometry-based identification, gel-based, and gel-free strategies, tailored to the unique compositions of fruit tissues for accurate protein extraction and identification. Proteomic studies reveal pathogen-induced changes in fruit proteomes, including the upregulation of defence-related proteins and suppression of metabolic pathways crucial for pathogen survival. Case studies on tomatoes, apples, and bananas highlight specific pathogen-responsive proteins, such as PR proteins and enzymes involved in ROS scavenging, which play roles in disease resistance mechanisms. The review further demonstrates the utility of proteomic data in identifying early disease biomarkers, guiding genetic improvements for disease resistance, and optimizing pathogen control measures. Integrating proteomic insights with transcriptomics and metabolomics provides a multidimensional understanding of fruit-pathogen interactions, paving the way for innovative solutions in agriculture. Future research should prioritize multi-omics approaches and field-level validations to translate laboratory findings into practical applications. The advancements discussed underscore the transformative role of proteomics in improving food security and sustainability amid challenges posed by climate change and increasing global food demand.PMID:39945834 | DOI:10.1007/s00299-025-03443-8

Environ Sci Technol. 2025 Feb 13. doi: 10.1021/acs.est.4c12852. Online ahead of print.ABSTRACTBiofilm formation, which is facilitated by quorum sensing (QS), significantly impairs the performance of pressure-driven membrane systems in water treatment. Herein, we present a quorum quenching (QQ)-phage phoresy system to control biofouling by disrupting QS-mediated interactions. This system, which is composed of the QQ bacterium Paenarthrobacter nicotinovorans as carriers and hitchhiking lytic phages infecting Pseudomonas aeruginosa with active QS systems, significantly decreased QS signal levels, inhibited the extracellular polymeric substance (EPS), and reduced bacterial abundance in mature biofilms. Transcriptomic analysis revealed that phage treatment upregulated QS and EPS synthesis genes in P. aeruginosa, but the QQ bacteria downregulated QS-related genes, weakening the bacterial EPS secretion and antiviral systems and facilitating phages to infect and lyse the target bacteria. Metabolomic profiling corroborated that the phoresy system disrupted pathways critical to biofilm stability, including the tricarboxylic acid cycle, carbohydrate metabolism, and amino acid metabolism. In off-site membrane cleaning experiments, the phoresy system promoted P. nicotinovorans colonization and replaced the niche of P. aeruginosa on the membrane surface, which restored membrane flux (i.e., 90% recovery in severely biofouling systems). Operation studies showed that the phoresy system reduced fouling rates, extended the membrane lifespan, and maintained salt rejection performance for reverse osmosis (RO) membrane systems. These findings highlight the potential of the QQ bacterium-phage system as a sustainable alternative to conventional chemical treatments that damage polymeric membranes.PMID:39945492 | DOI:10.1021/acs.est.4c12852

Vavilovskii Zhurnal Genet Selektsii. 2024 Dec;28(8):882-896. doi: 10.18699/vjgb-24-96.ABSTRACTThe metabolomic profiles of glioblastoma and surrounding brain tissue, comprising 17 glioblastoma samples and 15 peritumoral tissue samples, were thoroughly analyzed in this investigation. The LC-MS/MS method was used to analyze over 400 metabolites, revealing significant variations in metabolite content between tumor and peritumoral tissues. Statistical analyses, including the Mann-Whitney and Cucconi tests, identified several metabolites, particularly ceramides, that showed significant differences between glioblastoma and peritumoral tissues. Pathway analysis using the KEGG database, conducted with MetaboAnalyst 6.0, revealed a statistically significant overrepresentation of sphingolipid metabolism, suggesting a critical role of these lipid molecules in glioblastoma pathogenesis. Using computational systems biology and artificial intelligence methods implemented in a cognitive platform, ANDSystem, molecular genetic regulatory pathways were reconstructed to describe potential mechanisms underlying the dysfunction of sphingolipid metabolism enzymes. These reconstructed pathways were integrated into a regulatory gene network comprising 15 genes, 329 proteins, and 389 interactions. Notably, 119 out of the 294 proteins regulating the key enzymes of sphingolipid metabolism were associated with glioblastoma. Analysis of the overrepresentation of Gene Ontology biological processes revealed the statistical significance of 184 processes, including apoptosis, the NF-kB signaling pathway, proliferation, migration, angiogenesis, and pyroptosis, many of which play an important role in oncogenesis. The findings of this study emphasize the pivotal role of sphingolipid metabolism in glioblastoma development and open new prospects for therapeutic approaches modulating this metabolism.PMID:39944803 | PMC:PMC11811506 | DOI:10.18699/vjgb-24-96

Vavilovskii Zhurnal Genet Selektsii. 2024 Dec;28(8):927-939. doi: 10.18699/vjgb-24-100.ABSTRACTParkinson's disease (PD) and vascular parkinsonism (VP) are characterized by similar neurological syndromes but differ in pathogenesis, morphology, and therapeutic approaches. The molecular genetic mechanisms of these pathologies are multifactorial and involve multiple biological processes. To comprehensively analyze the pathophysiology of PD and VP, the methods of systems biology and gene network reconstruction are essential. In the current study, we performed metabolomic screening of amino acids and acylcarnitines in blood plasma of three groups of subjects: PD patients, VP patients and the control group. Comparative statistical analysis of the metabolic profiles identified significantly altered metabolites in the PD and the VP group. To identify potential mechanisms of amino acid and acylcarnitine metabolism disorders in PD and VP, regulatory gene networks were reconstructed using ANDSystem, a cognitive system. Regulatory pathways to the enzymes converting significant metabolites were found from PD-specific genetic markers, VP-specific genetic markers, and the group of genetic markers common to the two diseases. Comparative analysis of molecular genetic pathways in gene networks allowed us to identify both specific and non-specific molecular mechanisms associated with changes in the metabolomic profile in PD and VP. Regulatory pathways with potentially impaired function in these pathologies were discovered. The regulatory pathways to the enzymes ALDH2, BCAT1, AL1B1, and UD11 were found to be specific for PD, while the pathways regulating OCTC, FURIN, and S22A6 were specific for VP. The pathways regulating BCAT2, ODPB and P4HA1 were associated with genetic markers common to both diseases. The results obtained deepen the understanding of pathological processes in PD and VP and can be used for application of diagnostic systems based on the evaluation of the amino acids and acylcarnitines profile in blood plasma of patients with PD and VP.PMID:39944797 | PMC:PMC11811507 | DOI:10.18699/vjgb-24-100

Front Microbiol. 2025 Jan 29;16:1452423. doi: 10.3389/fmicb.2025.1452423. eCollection 2025.ABSTRACTAttention Deficit Hyperactivity Disorder (ADHD) is a clinically common neurodevelopmental disorder of the brain. In addition to genetic factors, an imbalance in gut flora may also play a role in the development of ADHD. Currently, it is critical to investigate the function of gut flora and related metabolites, which may form the fundamental basis of bidirectional cross-linking between the brain and the gut, in addition to focusing on the changed gut flora in ADHD. This study aimed to investigate the possible relationship between changes in gut flora and metabolites and ADHD by analyzing metagenome and untargeted metabolomics of fecal samples from ADHD patients. Specifically, we attempted to identify key metabolites and the metabolic pathways they are involved in, as well as analyze in detail the structure and composition of the gut flora of ADHD patients. In order to further investigate the relationship between gut flora and ADHD symptoms, some behavioral studies were conducted following the transplantation of gut flora from ADHD patients into rats. The results of the metagenome analysis revealed several distinct strains, including Bacteroides cellulosilyticus, which could be important for diagnosing ADHD. Additionally, the ADHD group showed modifications in several metabolic pathways and metabolites, including the nicotinamide and nicotinic acid metabolic pathways and the metabolite nicotinamide in this pathway. The behavioral results demonstrated that rats with ADHD gut flora transplants displayed increased locomotor activity and interest, indicating that the onset of behaviors such as ADHD could be facilitated by the flora associated with ADHD. This research verified the alterations in gut flora and metabolism observed in ADHD patients and provided a list of metabolites and flora that were significantly altered in ADHD. Simultaneously, our findings revealed that modifications to the microbiome could potentially trigger behavioral changes in animals, providing an experimental basis for comprehending the function and influence of gut flora on ADHD. These results might provide new perspectives for the development of novel treatment strategies.PMID:39944648 | PMC:PMC11817268 | DOI:10.3389/fmicb.2025.1452423

Sensors (Basel). 2025 Jan 30;25(3):848. doi: 10.3390/s25030848.ABSTRACTExosomes carry diverse tumor-associated molecular information that can reflect real-time tumor progression, making them a promising tool for liquid biopsy. However, traditional methods for exosome isolation and detection often rely on large, expensive equipment and are time-consuming, limiting their practical applicability in clinical settings. Microfluidic technology offers a versatile platform for exosome analysis, with advantages such as seamless integration, portability and reduced sample volumes. Aptamers, which are single-stranded oligonucleotides with high affinity and specificity for target molecules, have been frequently employed in the development of aptamer-based microfluidics for the isolation, signal amplification, and quantitative detection of exosomes. This review summarizes recent advances in aptamer-based microfluidic strategies for exosome analysis, including (1) strategies for on-chip exosome capture mediated by aptamers combined with nanomaterials or nanointerfaces; (2) aptamer-based on-chip signal amplification techniques, such as enzyme-free hybridization chain reaction (HCR), rolling circle amplification (RCA), and DNA machine-assisted amplification; and (3) various aptamer-assisted detection methods, such as fluorescence, electrochemistry, surface-enhanced Raman scattering (SERS), and magnetism. The limitations and advantages of these methods are also summarized. Finally, future challenges and directions for the clinical analysis of exosomes based on aptamer-based microfluidics are discussed.PMID:39943486 | DOI:10.3390/s25030848

Animals (Basel). 2025 Jan 31;15(3):403. doi: 10.3390/ani15030403.ABSTRACTHibernation is a crucial adaptive strategy for amphibians, facilitating survival in harsh environmental conditions by lowering metabolic rates and reducing energy use. This study employed GC-MS and LC-MS metabolomics to systematically analyze the serum metabolome of Bufo gargarizans during hibernation, aiming to uncover its metabolic adaptation mechanisms. A total of 136 differentially expressed metabolites (DEMs) were identified, of which 115 were downregulated and 21 upregulated, mainly involved in amino acid, carbohydrate, and lipid metabolism. KEGG pathway analysis showed that most metabolic pathways were inhibited in the hibernating group, underscoring a significant reduction in overall metabolic activity. Notably, while amino acid and carbohydrate metabolism were significantly reduced, lipid metabolism exhibited a distinctive adaptive response. Enhanced β-oxidation of fatty acids, including palmitoleic acid, arachidonic acid, and sodium caprylate, suggests a metabolic shift toward lipid-based energy utilization. The reduction in key metabolites like fumaric acid and succinic acid in the TCA cycle further supports the hypothesis of reduced energy requirements. These results enhance our current understanding of amphibian hibernation metabolisms and provide a targeted approach for future mechanistic investigations.PMID:39943173 | DOI:10.3390/ani15030403

Plants (Basel). 2025 Feb 6;14(3):494. doi: 10.3390/plants14030494.ABSTRACTIn this study, we investigated the mechanism of conversion of active components as well as the color change of forest ginseng (FG) during the drying process with the self-developed negative-pressure circulating airflow-assisted desiccator (PCAD) drying method, using a widely targeted metabolomics analytical method based on ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). During the drying process, a total of 1862 metabolites were identified in FG, along with 748 differential abundant metabolites (DAMs). Further analysis of the types and metabolic pathways of the DAMs revealed that both primary and secondary metabolites changed by 50-70% moisture content (MC); secondary metabolites dominated with a 30-50% MC, and primary metabolites dominated with a 10-30% MC, which revealed the differences in the transformation of the active ingredients in the drying process. In addition, the results showed the browning characteristics during the drying process. MC-50 and MC-10 showed the smallest and largest color changes, as well as enzyme activities, compared to the other MCs, respectively. As drying proceeded, browning reactions were mainly related to lipid and nucleotide metabolism and phenylpropane and flavonoid biosynthesis. In conclusion, the present study provides theoretical support for the mechanisms of active ingredient transformation as well as the color change of FG during PCAD drying.PMID:39943056 | DOI:10.3390/plants14030494