Protein Metabolism Research Articles

Metabolic Response to Small Molecule Therapy in Colorectal Cancer Tracked with Raman Spectroscopy and Metabolomics.

Despite numerous screening tools for colorectal cancer (CRC), 25% of patients are diagnosed with advanced disease. Novel diagnostic technologies that are early, accurate, and rapid are imperative to assess the therapeutic efficacy of clinical drugs and identify new biomarkers of treatment response. Here Raman spectroscopy (RS) was used to track metabolic reprogramming in KRAS-mutant HCT116 and SW837 cells, and KRAS wild-type CC cells. RS combined with multivariate analysis methods distinguished nonresponsive, partially responsive, and responsive cells treated with cetuximab, a monoclonal antibody for EGFR inhibition, sotorasib, a clinically approved KRAS inhibitor, and various doses of trametinib, an inhibitor of the MAPK pathway. Cells treated with a combination of subtoxic doses of trametinib and BKM120, an inhibitor of the PI3K pathway, showed a synergistic response between the two pathways. Using a supervised machine learning regression model, we established a scoring methodology trained to a priori predict therapeutic response to new treatment combinations. RS metabolites were verified with mass spectrometry, and enrichment pathways were identified, including amino acid, purine, and nicotinate and nicotinamide metabolism that differentiated monotherapy from combination therapy. Our approach may ultimately be applicable to patient-derived primary cells and cultures of patient tumors to predict effective drugs for individualized care.

Effect of Guanidinoacetic Acid on Production Performance, Serum Biochemistry, Meat Quality and Rumen Fermentation in Hu Sheep.

Guanidinoacetic acid (GAA) can effectively improve the metabolism of energy and proteins by stimulating creatine biosynthesis. We present a study exploring the impact of GAA on production performance, serum biochemistry, meat quality and rumen fermentation in Hu sheep. A total of 144 weaned male Hu sheep (body weight 16.91 ± 3.1 kg) were randomly assigned to four groups with three replicates of twelve sheep in each group. The diets were supplemented with 0 (CON), 500 (GAA-1), 750 (GAA-2) and 1000 mg/kg (GAA-3) of GAA (weight of feed), respectively. After a comprehensive 90-day experimental period, we discovered that the supplementation of GAA had a remarkable impact on various muscle parameters. Specifically, it significantly enhanced the average daily growth (ADG) of the animals and improved the shear force and fiber diameter of the muscle, while also reducing the drip loss and muscle fiber density. Furthermore, the addition of GAA to the feed notably elevated the serum concentrations of high-density lipoprotein cholesterol (HDL-C), total protein (TP) and globulin (GLB), as well as the enzyme activity of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px). Concurrently, there was a decrease in the levels of triglycerides (TG) and malondialdehyde (MDA) in the serum. In addition, GAA decreased the pH and the acetate-to-propionate ratio and increased the total volatile fatty acids (TVFA) and ammoniacal nitrogen (NH3-N) levels of rumen fluid. Additionally, GAA upregulated acetyl-CoA carboxylase (ACC) gene expression in the Hu sheep's muscles. In conclusion, our findings suggest that GAA supplementation not only enhances muscle quality but also positively affects serum biochemistry and ruminal metabolism, making it a potential candidate for improving the overall health and performance of Hu sheep.

Understanding the Conundrum of Pancreatic Cancer in the Omics Sciences Era.

Pancreatic cancer (PC) is an increasing cause of cancer-related death, with a dismal prognosis caused by its aggressive biology, the lack of clinical symptoms in the early phases of the disease, and the inefficacy of treatments. PC is characterized by a complex tumor microenvironment. The interaction of its cellular components plays a crucial role in tumor development and progression, contributing to the alteration of metabolism and cellular hyperproliferation, as well as to metastatic evolution and abnormal tumor-associated immunity. Furthermore, in response to intrinsic oncogenic alterations and the influence of the tumor microenvironment, cancer cells undergo a complex oncogene-directed metabolic reprogramming that includes changes in glucose utilization, lipid and amino acid metabolism, redox balance, and activation of recycling and scavenging pathways. The advent of omics sciences is revolutionizing the comprehension of the pathogenetic conundrum of pancreatic carcinogenesis. In particular, metabolomics and genomics has led to a more precise classification of PC into subtypes that show different biological behaviors and responses to treatments. The identification of molecular targets through the pharmacogenomic approach may help to personalize treatments. Novel specific biomarkers have been discovered using proteomics and metabolomics analyses. Radiomics allows for an earlier diagnosis through the computational analysis of imaging. However, the complexity, high expertise required, and costs of the omics approach are the main limitations for its use in clinical practice at present. In addition, the studies of extracellular vesicles (EVs), the use of organoids, the understanding of host-microbiota interactions, and more recently the advent of artificial intelligence are helping to make further steps towards precision and personalized medicine. This present review summarizes the main evidence for the application of omics sciences to the study of PC and the identification of future perspectives.

Metabolomic and Proteomic Analysis of ApoE4-Carrying H4 Neuroglioma Cells in Alzheimer's Disease Using OrbiSIMS and LC-MS/MS.

Growing clinical evidence reveals that systematic molecular alterations in the brain occur 20 years before the onset of AD pathological features. Apolipoprotein E4 (ApoE4) is one of the most significant genetic risk factors for Alzheimer's disease (AD), which is not only associated with the AD pathological features such as amyloid-β deposition, phosphorylation of tau proteins, and neuroinflammation but is also involved in metabolism, neuron growth, and synaptic plasticity. Multiomics, such as metabolomics and proteomics, are applied widely in identifying key disease-related molecular alterations and disease-progression-related changes. Despite recent advances in the development of analytical technologies, screening the entire profile of metabolites remains challenging due to the numerous classes of compounds with diverse chemical properties that require different extraction processes for mass spectrometry. In this study, we utilized Orbitrap Secondary Ion Mass Spectrometry (OrbiSIMS) as a chemical filtering screening tool to examine molecular alterations in ApoE4-carried neuroglioma cells compared to wild-type H4 cells. The findings were compared using liquid chromatography (LC)-MS/MS targeted metabolomics analysis for the confirmation of specific metabolite classes. Detected alterations in peptide fragments by OrbiSIMS provided preliminary indications of protein changes. These were extensively analyzed through proteomics to explore ApoE4's impact on proteins. Our metabolomics approach, combining OrbiSIMS and LC-MS/MS, revealed disruptions in lipid metabolism, including glycerophospholipids and sphingolipids, as well as amino acid metabolism, encompassing alanine, aspartate, and glutamate metabolism; aminoacyl-tRNA biosynthesis; glutamine metabolism; and taurine and hypotaurine metabolism. Further LC-MS/MS proteomics studies confirmed the dysfunction in amino acid and tRNA aminoacylation metabolic processes, and highlighted RNA splicing alterations influenced by ApoE4.

Genomic variation of 363 diverse tea accessions unveils the genetic diversity, domestication, and structural variations associated with tea adaptation.

Domestication has shaped the population structure and agronomic traits of tea plants, yet the complexity of tea population structure and genetic variation that determines these traits remains unclear. We here investigated the resequencing data of 363 diverse tea accessions collected extensively from almost all tea distributions and found that the population structure of tea plants was divided into eight subgroups, which were basically consistent with their geographical distributions. The genetic diversity of tea plants in China decreased from southwest to east as latitude increased. Results also indicated that Camellia sinensis var. assamica (CSA) illustrated divergent selection signatures with Camellia sinensis var. sinensis (CSS). The domesticated genes of CSA were mainly involved in leaf development, flavonoid and alkaloid biosynthesis, while the domesticated genes in CSS mainly participated in amino acid metabolism, aroma compounds biosynthesis, and cold stress. Comparative population genomics further identified ~730 Mb novel sequences, generating 6,058 full-length protein-encoding genes, significantly expanding the gene pool of tea plants. We also discovered 217,376 large-scale structural variations and 56,583 presence and absence variations (PAVs) across diverse tea accessions, some of which were associated with tea quality and stress resistance. Functional experiments demonstrated that two PAV genes (CSS0049975 and CSS0006599) were likely to drive trait diversification in cold tolerance between CSA and CSS tea plants. The overall findings not only revealed the genetic diversity and domestication of tea plants, but also underscored the vital role of structural variations in the diversification of tea plant traits.

Modulation of gene expression in immune-related organs by in ovo stimulation with probiotics and prophybiotics in broiler chickens.

In ovo stimulation has been studied intensively as an alternative to antibiotic use in poultry production. We investigated the potential use of a probiotic in combination with a phytobiotic as a prophybiotic for in ovo stimulation and reported its beneficial effects on the gut microbiome of broiler chickens. The current study further investigates the gene expression in the immune-related organs of these chickens to understand the tissue-specific immunomodulatory effects of the treatments. The selected prophybiotic (Leuconostoc mesenteroides with garlic aqueous extract) and its probiotic component alone were injected into ROSS308 chicken eggs on the 12th day of incubation, and gene expression in cecal tonsils, spleen, and liver at 35 days of age was determined using qPCR method. The relative expression of each treatment was compared to the positive control, chickens injected with physiological saline in ovo. The results displayed a downregulation of pro- and anti-inflammatory cytokines in the cecal tonsils of the probiotic group and the liver of the prophybiotic group. The spleen displayed upregulated AVBD1 in both groups and upregulated IL1-β in the probiotic group. The probiotic group displayed increased expression of genes related to metabolism of energy (COX16), protein (mTOR), and lipids (CYP46A1) whereas the prophybiotic group displayed reduced expression of genes related to cholesterol synthesis (SREBP1) and glucose transportation (SLC2A2) in the liver. In conclusion, Leuconostoc mesenteroides differentially modulated gene expression in chickens when administered in ovo in combination with garlic aqueous extract. Further in ovo studies with different prophybiotic combinations are required to optimize the benefits in broiler chickens.

The Role of Branched Chain Ketoacid Dehydrogenase Kinase (BCKDK) in Skeletal Muscle Biology and Pathogenesis.

Muscle wasting can be caused by nutrition deficiency and inefficient metabolism of amino acids, including Branched Chain Amino Acids (BCAAs). Branched Chain Amino Acids are a major contributor to the metabolic needs of healthy muscle and account for over a tenth of lean muscle mass. Branched chain alpha-ketoacid dehydrogenase (BCKD) is the rate limiting enzyme of BCAA metabolism. Inhibition of BCKD is achieved through a reversible phosphorylation event by Branched Chain a-ketoacid dehydrogenase kinase (BCKDK). Our study set out to determine the importance of BCKDK in the maintenance of skeletal muscle. We used the Gene Expression Omnibus Database to understand the role of BCKDK in skeletal muscle pathogenesis, including aging, muscular disease, and interrupted muscle metabolism. We found BCKDK expression levels were consistently decreased in pathologic conditions. These results were most consistent when exploring muscular disease followed by aging. Based on our findings, we hypothesize that decreased BCKDK expression alters BCAA catabolism and impacts loss of normal muscle integrity and function. Further research could offer valuable insights into potential therapeutic strategies for addressing muscle-related disorders.

Evidence for archaeal metabolism of D-amino acids in the deep marine sediments

The deep marine sediments represent a major repository of organic matter whilst hosting a great number of uncultivated microbes. Microbial metabolism plays a key role in the recycling of organic matter in the deep marine sediments. D-amino acids (DAAs) and DAA-containing muropeptides, an important group of organic matter in the deep marine sediments, are primarily derived from bacterial peptidoglycan decomposition. Archaea are abundant in the deep ocean microbiome, yet their role in DAA metabolism remains poorly studied. Here, we report bioinformatic investigation and enzymatic characterization of deep marine sedimentary archaea involved in DAA metabolism. Our analyses suggest that a variety of archaea, particularly the Candidatus Bathyarchaeota and the Candidatus Lokiarchaeaota, can metabolize DAAs. DAAs are converted into L-amino acids via amino acid racemases (Ala racemase, Asp racemase and broad substrate specificity amino acid racemase), and converted into α-keto acid via d-serine ammonia-lyase, whereas DAA-containing di−/tri-muropeptides can be hydrolyzed by peptidases (dipeptidase and D-aminopeptidase). Overall, this study reveals the identity and activity of deep marine sedimentary archaea involved in DAA metabolism, shedding light on the mineralization and biogeochemical cycling of DAAs in the deep marine sediments.

The Anabolic Response to Protein Ingestion During Recovery From Exercise Has No Upper Limit in Magnitude and Duration In Vivo in Humans: A Commentary.

A comprehensive recent study by Trommelen et al. demonstrated that muscle tissue exhibits a greater capacity to incorporate exogenous exogenous protein-derived amino acids into bound muscle protein than was previously appreciated, at least when measured in "anabolically sensitive," recreationally active (but not resistance-trained), young men following resistance exercise. Moreover, this study demonstrated that the duration of the postprandial period is modulated by the dose of ingested protein contained within a meal, that is, the postexercise muscle protein synthesis response to protein ingestion was more prolonged in 100PRO than 25PRO. Both observations represent important scientific advances in the field of protein metabolism. However, we respectfully caution that the practical implications of these findings may have been misinterpreted, at least in terms of dismissing the concept of protein meal distribution as an important factor in optimizing muscle tissue anabolism and/or metabolic health. Moreover, based on emerging evidence, this idea that the anabolic response to protein ingestion has no upper limit does not appear to translate to resistance-trained young women.

Metabolomics analysis of splenectomy of Nile tilapia (Oreochromis niloticus) reveals the spleen involved in regulating liver lipids and amino acids metabolism

The liver is essential for nutritional balance in fish, and liver damage in farmed fish often arises from factors like overfeeding, causing various health issues. Clinical observations indicate that liver diseases frequently involve spleen dysfunction, and there is evidence to suggest that the spleen has a significant impact on liver function. However, there has been no discussion on the role of the spleen in maintaining liver health in fish. To understand the role of fish spleen in liver metabolism, this study selected Nile tilapia (Oreochromis niloticus) as the experimental material and first established a tilapia splenectomy model. Various biochemical parameters of the liver and serum were measured, and the liver metabolism characteristics of the splenectomy group (SP group) and the sham operation group (SO group) were analyzed using metabolomics. After splenectomy, biochemical parameters of the liver and serum showed abnormalities, including significant increases in total cholesterol (T-CHO) and serum total bile acid (TBA) levels, alongside a significant decrease in liver TBA levels, suggesting impaired metabolic function and cholesterol deposition in the liver. Metabolomics analysis showed that metabolites such as lipids, lipid-like molecules, and organic acids and derivatives were differentially regulated between the SO and SP group. KEGG analysis showed that differential metabolites were enriched in lipid metabolism and amino acid metabolism. The metabolic pathway analysis of differential metabolites showed that after splenectomy, the low-activity urea cycle in the liver may accelerate lipid synthesis, while low concentrations of aromatic amino acids and taurine may inhibit lipid catabolism. These results indicate that after splenectomy, the liver metabolic capacity is impaired, which causes abnormal lipid metabolism by interfering with amino acid metabolism, making splenectomy tilapia liver at risk of liver disease, including cholesterol deposition, hepatic steatosis and nonalcoholic fatty liver disease (NAFLD). Our results show that the spleen is involved in regulating liver lipid and amino acid metabolism, and the spleen may interfere with lipid metabolism by regulating liver amino acid metabolism. Our data can provide support for further research on liver and spleen functions and the immune-nutrient metabolism mechanisms in fish, as well as new ideas for healthy fish farming.

Untargeted metabolomics reveals the mechanism of ultrasound combined with L-cysteine treatment inhibiting the browning of fresh-cut potatoes

Freshly cut potatoes tend to brown during processing and preservation, which is an important issue worldwide. Ultrasound (US) combined with L-cysteine (L-Cys) treatment (US-L-Cys) has been reported to inhibit the browning of fresh-cut potatoes in our laboratory. However, the underlying mechanism remains to be elucidated. Untargeted metabolomics, a popular high-throughput technique, has been used to investigate the biochemical changes that are closely associated with the browning of fresh-cut fruits and vegetables. The present study investigated the effect of US-L-Cys treatment on the browning index (BI), related enzyme activities, total phenolic content, antioxidant capacity, malondialdehyde (MDA) content, and relative electrical conductivity of fresh-cut potatoes during 6-d storage. Metabolomics was used to compare the metabolites of US-L-Cys-treated and control samples on days 0 and 6. The results showed that US-L-Cys treatment reduced BI; decreased polyphenol oxidase, peroxidase, and phenylalanine ammonia-lyase activities; maintained high total phenolic content; increased antioxidant capacity; and decreased MDA content and relative electrical conductivity in fresh-cut potatoes during storage. Metabolomic analysis revealed that tyrosine and amino acid metabolisms were enriched. Higher levels of alanine and lower levels of dopamine were observed in US-L-Cys-treated samples compared with control samples. Therefore, depressed tyrosine and activated alanine metabolisms may be involved in the mechanism through which US-L-Cys inhibits the enzymatic browning of fresh-cut potatoes during storage.

Coordinated responses of rice (Oryza sativa) to the stresses of benzotriazole ultraviolet stabilizers (BZT-UVs): Antioxidative system, photosynthetic activity, and metabolic regulation

Massive use of plastic products has caused their accumulation in soils, releasing large amounts of endogenous plastic additives (e.g., benzotriazole ultraviolet stabilizers, in short BZT-UVs) into terrestrial ecosystems. However, their plant toxicity is little known. Herein, we investigated the occurrence of BZT-UVs in contaminated farmland and selected three BZT-UV congeners to explore their toxic effects on the antioxidant, photosynthetic, and metabolic perturbation on rice (Oryza sativa). Results showed that the mean concentrations of ∑BZT-UVs in soil and plant samples were 180.7 ng/g dw and 156.4 ng/g dw, respectively. UV-P, UV-327 and UV-328 were the dominant BZT-UV congeners in both of soils and plants. Three BZT-UV congeners caused oxidative damages to rice in a dose-dependent manner, especially for UV-328. Functional genes involved in chlorophyll synthetases was inhibited by over 50 % under the stress of BZT-UVs, whereas those responsible for chlorophyll degradation were obviously promoted. The chlorophyll content was thus decreased, leading to a weakened photosynthesis system and an unbalanced carbon metabolism. The transcriptome and metabolome proved that the flux of carbohydrate metabolism and amino acid metabolism were obviously promoted in plants induced by BZT-UVs, which could inhibit the growth of rice. These findings offered insights into the coordinated responses of plants and advanced our understanding of potential ecological risks of BZT-UVs to terrestrial ecosystems.

The impact of oxygen content on Staphylococcus epidermidis pathogenesis in ocular infection based on clinical characteristics, transcriptome and metabolome analysis.

This study aims to delineate the etiology and prevalence of isolated pathogens, along with the clinical characteristics of endophthalmitis patients over a 9-year period at hospital in Southwest of China. Additionally, we investigating the metabolic and cellular processes related to environmental factors may offer novel insights into endophthalmitis. We analyzed data pertaining to endophthalmitis patients treated at the Affiliated Hospital of Yunnan University from 2015 to 2023. According to our clinical data, we conducted an experiment based on transcriptomics and metabolomics analysis to verify whether environmental factors affect behavior of S. epidermidis by culturating S. epidermidis under oxic and microoxic condition. In this study, 2,712 fungi or bacteria strains have been analyzed, gram-positive bacteria constituted 65.08%, with S. epidermidis being the most predominant species (25.55%). Ophthalmic trauma was the primary pathogenic factor for S. epidermidis ocular infections. Regarding fluoroquinolones, S. epidermidis exhibited the higher resistance rate to levofloxacin than moxifloxacin. Moreover, our investigation revealed that S. epidermidis in microoxic environment increase in energy metabolism, amino acid metabolism, and membrane transport. Our findings underscore the significance of S. epidermidis as a crucial pathogen responsible for infectious endophthalmitis. It is crucial to exercise vigilance when considering Levofloxacin as the first-line drug for empiric endophthalmitis treatment. The metabolites alteration observed during the commensal-to-pathogen conversion under microoxic condition serve as a pivotal environmental signal contributing to S. epidermidis metabolism remodeling, toward more pathogenic state.

Hepatic Transcriptomic Responsiveness of Polar Cod, Boreogadus saida, to Ocean Acidification and Warming

Background: This study was part of a larger comprehensive project (BIOACID) addressing the physiological resilience of Polar cod, Boreogadus saida, to ocean acidification and global warming and aimed to unravel underlying molecular mechanisms of the observed physiological responses. Methods: Fish were acclimated long-term to three CO2 concentrations comprising control conditions (390 ppm) and two projected climate scenarios (780 ppm and 1170 ppm). Each CO2 treatment was combined with four temperatures: 0, 3, 6, and 8 °C. Here, we focused on the hepatic transcriptomic profiles from these previously physiologically characterized fish. Results: Generally, we did not detect signs of a classical stress response. Consistent with functional observations, warming induced much stronger molecular responses compared to elevated PCO2, but an interaction between both factors existed to some extent. Gene ontology analysis revealed a strong response in lipid, amino acid, and protein metabolism. With increasing temperature, we observed a shift away from lipid metabolism, while carbohydrate metabolic pathways remained stable. Conclusions: Although we found Polar cod to be quite resilient to ocean acidification, temperature will remain a critical parameter for this valuable Arctic keystone species, and the question remains as to whether the observed acclimation strategies can be implemented in its natural habitat, especially when food supply is limited.

Impact of Varying Dietary Calcium Contents on the Gut Metabolomics of Yunnan Semi-Fine Wool Sheep (Ovis aries).

Yunnan semi-fine wool (YSFW) is a recently developed dual-purpose (meat and wool) sheep breed mainly found in Yunnan Province, China. Moreover, dietary calcium is essential for animal health and productivity. The current experiment aimed to investigate the impact of dietary calcium on sheep gut metabolite profile. For this, thirty YSFW rams (male, age = 10 months, and body weight = 40.37 ± 0.49 kg) were randomized into three groups (n = 10 rams/group), followed by a completely randomized design, and the groups were allotted to one of three dietary calcium levels (Q_1 = 0.50%, Q_3 = 0.73%, and Q_5 = 0.98% on a dry basis). The rams were fed ad libitum by feeding twice a day (at 08:00 and 17:00 h/day) throughout the experimental period (44 day). On the 21st day of the experiment, fecal samples were collected from 27 rams (9/group) and untargeted metabolite profiling was performed by using ultra-performance liquid chromatography. The PCA plot showed that the Q_5 group metabolites were clustered more tightly than for Q_1 and Q_3, respectively. The tightly clustering molecules were mainly alkaloids and their derivatives, benzenoids, lignans and related compounds, lipids, nucleotides, organic acids, and nitrogenous-based derivatives. According to the Kyoto Encyclopedia of Genes and Genomes pathway analysis, these molecules potentially contribute to metabolic pathways, biosynthesis of secondary metabolites, proteinaceous compounds, and the metabolism of the protein derivatives, particularly amino acids. The PLS-DA plots revealed a significant difference between the Q_1, Q_3, and Q_5 groups, suggesting that Q_5 had a clear separation across the groups. Based on the metabolomic analysis, feeding different levels of dietary calcium significantly changed the metabolomic profile of YSFW rams, which primarily entails metabolic pathways such as energy, protein, and lipid metabolism.

Intestinal flora analysis and serum metabolomics reveal the effectiveness of Bacillus coagulans BC66 in treating bacterial enteritis in bullfrogs

Bacterial enteritis is a major disease of bullfrogs that is characterized by rapid onset, high infectivity, and high mortality. This disease causes significant economic losses to the bullfrog farming industry and threatens food and environmental safety. Bacillus coagulans has gained more and more attention in the field of livestock and poultry replacement resistance due to its common advantages of acid-producing bacterial inhibition by Lactobacillus lactis and heat resistance of Bacillus subtilis suitable for feed pelleting. In this study, the therapeutic effect of B. coagulans BC66, administered as a feed supplement, on bacterial enteritis in bullfrogs was revealed based on intestinal flora analysis and serum metabolomics. Bullfrogs with bacterial enteritis were administered B. coagulans BC66 in feed for 20 days, where the concentration of the bacterial solution was 100 billion CFU/g, during which the number of treatments totaled 20, then studies were conducted to analyze intestinal histomorphology, the expression of intestinal proinflammatory factors, microbial diversity of the intestinal mucosa, immune indexes, and metabolite levels in serum. Compared with the untreated group, treatment of bullfrogs with B. coagulans BC66 resulted in repair of the intestinal tissue, a significant reduction in the expression of proinflammatory factors IL-1β, IL-8, IL-17, and TNF-α, increased diversity of microorganisms in the digestive tract, a decreased number of pathogenic bacteria, an increase in the number of probiotics, elevated levels of alkaline phosphatase, lysozyme, lactate dehydrogenase, glycolysin, and creatine kinase, upregulated levels of D-alkaline phosphatase, upregulated D-amino acid metabolism and aminoacyl-tRNA biosynthesis, and downregulated sphingolipid metabolic pathways. These results showed that B. coagulans could effectively treat bacterial enteritis in bullfrogs, increasing their survival rate, enhancing microbial homeostasis of the intestinal tract, reducing the occurrence of inflammation, and enhancing their immune ability. Taken together, the findings of this study provide insight that may aid the management of disease in the bullfrog farming industry, thereby ensuring improved food and environmental safety.

Metabolic Profiling Changes Induced by Fermented Blackberries in High-Fat-Diet-Fed Mice Utilizing Gas Chromatography-Mass Spectrometry Analysis.

The aim of this study was to investigate the metabolic changes associated with the anti-obesity effects of fermented blackberry extracts in the liver tissues of high-fat-diet-fed mice using mass spectrometry-based metabolomics analysis. C57BL/6J mice were divided into eight groups: normal-diet-fed mice, high-fat-diet-fed mice, high-fat diet treated with blackberry extract, high-fat-diet mice treated with blackberry fermented by L. plantarum, and high-fat diet with blackberry fermented by L. brevis. After 12 weeks, the high-fat-diet group exhibited a greater increase in liver weight compared to the control group, and among the groups, the group administered with blackberry fermented with L. plantarum showed the most pronounced reduction in liver weight. As the primary organ responsible for amino acid metabolism, the liver is crucial for maintaining amino acid homeostasis. In our study, we observed that the levels of several essential amino acids, including isoleucine and valine, were decreased by the high-fat diet, and were recovered by administration of blackberry extract fermented with L. plantarum. Our results demonstrated the potential of blackberry extract fermented with L. plantarum as a functional material for metabolic disorders by restoring some of the amino acid metabolism disturbances induced by a high-fat diet.

Transcriptomic analysis of the antibacterial mechanism of ε-polylysine-functionalized magnetic composites against Alicyclobacillus acidoterrestris and its application in apple juice.

Alicyclobacillus acidoterrestris is a common microorganism in fruit juice. It can produce off-odor metabolites and has been considered to be an important factor in juice contamination. Thus, the development of new strategy for the control of A. acidoterrestris has important practical significance. The primary objective of this work was to assess the antibacterial performance of ε-polylysine-functionalized magnetic composites (Fe3O4@MoS2@PAA-EPL) in apple juice and its effect on juice quality. Moreover, the molecular mechanism of Fe3O4@MoS2@PAA-EPL against A. acidoterrestris was explored by RNA sequencing (RNA-Seq). Experimental results indicated that the synthesized composites possessed the ability to inhibit the viability of A. acidoterrestris vegetative cells and spores. Besides, investigation on the quality of apple juice incubated with Fe3O4@MoS2@PAA-EPL implied that the fabricated composites displayed negligible adverse effects on juice quality. In addition, the results of RNA-Seq demonstrated that 833 differentially expressed genes (DEGs) were identified in Fe3O4@MoS2@PAA-EPL-treated A. acidoterrestris, which were associated with translation, energy metabolism, amino acid metabolism, membrane transport and cell integrity. These results suggested that the treatment of Fe3O4@MoS2@PAA-EPL disrupted energy metabolism, repressed cell wall synthesis and caused membrane transport disorder of bacterial cells. This work provides novel insights into the molecular antibacterial mechanism for ε-polylysine-functionalized magnetic composites against A. acidoterrestris. © 2024 Society of Chemical Industry.

High temperature aggravated hypoxia-induced intestine toxicity on juvenile Chinese mitten crab (Eriocheir sinensis)

High temperature and hypoxia in water due to global warming threaten the growth and development of aquatic animals. In natural or cultured environments, stress usually does not occur independently, whereas the synergistic effect of high temperature and hypoxia on Chinese mitten crab (Eriocheir sinensis) are rarely reported. In this study, 450 juvenile crabs were equally divided into control group (24 °C ± 0.5 °C, DO 6.8 ± 0.1 mg/L), hypoxia stress group (24 °C ± 0.5 °C, DO 1 ± 0.1 mg/L) and combined stress group (30 °C ± 0.5 °C, DO 1 ± 0.1 mg/L), and the intestinal health status, microbial diversity and metabolite profiles were evaluated for 24 h treatment. The results showed that hypoxia stress induced the expression level of pro-inflammatory related genes were significantly up-regulated in intestine of juvenile E. sinensis, and intestinal peritrophic membrane factor related genes were significantly down-regulated. High temperature further amplified the effects of hypoxia on pro-inflammatory and peritrophic membrane factor-related genes. Interesting, hypoxia stress induced a significant up-regulated of intestinal antioxidant-related genes, whereas high temperature reversed this trend. In addition, single stress or/and combined stress led to changes in intestinal microbiota diversity and abundance, and intestinal metabolite profiles. Compared with hypoxia stress, the synergistic effect of high temperature and hypoxia led to an increase in the abundance of pathogenic bacteria and a decrease in the abundance of probiotic bacteria. Moreover, intestinal metabolic pathways were significantly changed, especially amino acid metabolism and glycerophospholipid metabolism. Therefore, the results indicated that hypoxia stress could induce intestinal inflammatory response and oxidative stress, and lead to abnormal changes in intestinal microbiota and metabolic profiles, whereas high temperature further aggravate the toxic effects of hypoxia on the intestine. This study preliminarily revealed the synergistic toxic effects of high temperature and hypoxia on the intestine of juvenile E. sinensis.

Structural idiosyncrasies of glycyl T-box riboswitches among pathogenic bacteria.

T-box riboswitches are widespread bacterial regulatory noncoding RNAs that directly interact with tRNAs and switch conformations to regulate the transcription or translation of genes related to amino acid metabolism. Recent studies in Bacilli have revealed the core mechanisms of T-boxes that enable multivalent, specific recognition of both the identity and aminoacylation status of the tRNA substrates. However, in-depth knowledge of a vast number of T-boxes in other bacterial species remains scarce, although a remarkable structural diversity particularly among pathogens, is apparent. In the present study, analysis of T-boxes that control the transcription of glycyl-tRNA synthetases from four prominent human pathogens revealed significant structural idiosyncrasies. Nonetheless, these diverse T-boxes maintain functional T-box:tRNAGly interactions both in vitro and in vivo. Probing analysis not only validated recent structural observations but also expanded our knowledge on the substantial diversities among T-boxes and suggest interesting distinctions from the canonical Bacilli T-boxes. Surprisingly, some glycyl T-boxes seem to redirect the T-box trajectory in the absence of recognizable K-turns or contain Stem II modules that are generally absent in glycyl T-boxes. These results consolidate the notion of lineage-specific diversification and elaboration of the T-box mechanism and corroborate the potential of T-boxes as promising species-specific RNA targets for next-generation antibacterial compounds.