Protein Metabolism Research Articles

Time-series transcriptome analysis reveals the cascade mechanism of biological processes following the perturbation of the MVA pathway in Salvia miltiorrhiza

Various biological processes are interconnected in plants. Transcription factors (TFs) often act as regulatory hubs to regulate plant growth and responses to stress by integrating various biological pathways. Despite extensive studies on TFs functions in various plant species, our understanding of the details of TFs regulation remains limited. In this study, clonal seedlings of Salvia miltiorrhiza were exposed to specific inhibitors for 12 h. Time-series transcriptome data, sampled hourly, were used to construct co-expression networks and gene regulatory networks (GRNs). Transcriptome dynamic analysis was utilized to capture the gene expression dynamics of various biological processes and decipher the potential molecular mechanisms that regulate these processes. The perturbation results showed the growth and development processes of S.miltiorrhiza were primarily affected at the early stage, whereas stress response-related biological processes were mainly influenced at the later stage. And there was a correlation between the series of key differentially expressed genes in terpenoid biosynthesis pathways and the topological distribution of these pathways. Furthermore, the GRNs based on TFs indicate that TFs play a crucial role in connecting various biological processes. In the cytoplasmic lysate gene regulatory module, SmWRKY48-SmTCP4-SmWRKY28 constituted a regulation hub regulating S.miltiorrhiza responses to perturbation of the MVA pathway. The regulation hub mediated various pathways, including pyruvate metabolism, glycolysis/gluconeogenesis, amino acid metabolism, and ubiquinone and other terpenoid-quinone biosynthesis.Our findings suggest that perturbation of a key biological pathway in S.miltiorrhiza has time-dependent effects on other biological processes. And SmWRKY48-SmTCP4-SmWRKY28 constitutes the regulatory hub in S.miltiorrhiza responses to perturbation of MVA pathway.

Alterations in newborn metabolite patterns with preterm birth and diabetes in pregnancy.

This study examines the influence of prematurity and diabetes (DM) in pregnancy on metabolite patterns at birth, and associations with adiposity development in a prospective cohort. Term and preterm (30-36 weeks gestational age [GA]) infants were enrolled and body composition assessments completed through discharge. Targeted metabolomics was used to assess metabolites in cord or infant blood in the first 2 days. Among 91 infants, 62 were preterm and 27 were exposed to DM. In factor analysis, variation in acylcarnitines' and non-essential amino acids differed by GA and DM exposure and were associated with adiposity at term age. DM-group had 1.95-fold increase in t4-OH-pro (p = 0.003) and 2.14-fold increase in taurine (p = 0.004) compared with non-DM group. Preterm infants had 1.77-fold increase in glycerophospholipid PC aa C32:2 versus term group (p < 0.001). Pathway analysis revealed differences across DM and GA groups in pathways associated with citrulline metabolism, amino acid transport/ synthesis, and fatty acid quantity/transport. In this cohort of infants, there are unique metabolite signatures associated with DM exposure, prematurity, and adiposity development after birth. These markers may reflect early metabolism changes in the developing infant which relate to known risks of adverse growth and cardiometabolic outcomes in this group. In this study of term and preterm infants, diabetes in pregnancy was associated with unique metabolic signatures at birth, including increased expression of metabolites related to protein synthesis and lipid metabolism. Metabolites related to lipid and protein metabolism were associated with adiposity development at term age, including estimated body fat percent, skin fold thickness measures, and arm circumference measures. Unique signatures of metabolites associated with prematurity and exposure to diabetes in pregnancy may reflect early metabolism changes in the developing infant which relate to known risks of adverse growth and cardiometabolic outcomes in this group.

Emergence of antibiotic-specific Mycobacterium tuberculosis phenotypes during prolonged treatment of mice.

A major challenge in tuberculosis (TB) therapeutics is that antibiotic exposure leads to changes in the physiology of M. tuberculosis (Mtb), which may enable the pathogen to withstand treatment. While antibiotic-treated Mtb has been evaluated in in vitro experiments, it is unclear if and how long-term in vivo treatment with diverse antibiotics with varying treatment-shortening activity (sterilizing activity) affects Mtb physiologic processes differently. Here, we used SEARCH-TB, a pathogen-targeted RNA-sequencing platform, to characterize the Mtb transcriptome in the BALB/c high-dose aerosol infection mouse model following 4 weeks of treatment with three sterilizing and three non-sterilizing antibiotics. Certain transcriptional changes were shared among most antibiotics, including decreased expression of genes associated with protein synthesis and metabolism and the induction of certain genes associated with stress responses. However, the magnitude of this shared response differed between antibiotics. Sterilizing antibiotics rifampin, pyrazinamide, and bedaquiline generated a more quiescent Mtb state than did non-sterilizing antibiotics isoniazid, ethambutol, and streptomycin, as indicated by the decreased expression of genes associated with translation, transcription, secretion of immunogenic proteins, metabolism, and cell wall synthesis. Additionally, we identified distinguishing transcriptional effects specific to each antibiotic, indicating that different mechanisms of action induce distinct patterns in response to cellular injury. In addition to elucidating the Mtb physiologic changes associated with antibiotic stress, this study demonstrates the value of SEARCH-TB as a highly granular pharmacodynamic assay that reveals antibiotic effects that are not apparent based on culture alone.

A murine model of acute and prolonged abdominal sepsis, supported by intensive care, reveals time-dependent metabolic alterations in the heart

BackgroundSepsis-induced cardiomyopathy (SICM) often occurs in the acute phase of sepsis and is associated with increased mortality due to cardiac dysfunction. The pathogenesis remains poorly understood, and no specific treatments are available. Although SICM is considered reversible, emerging evidence suggests potential long-term sequelae. We hypothesized that metabolic and inflammatory cardiac changes, previously observed in acute sepsis as potential drivers of SICM, partially persist in prolonged sepsis.MethodsIn 24-week-old C57BL/6J mice, sepsis was induced by cecal ligation and puncture, followed by intravenous fluid resuscitation, subcutaneous analgesics and antibiotics, and, in the prolonged phase, by parenteral nutrition. Mice were killed after 5 days of sepsis (prolonged sepsis, n = 15). For comparison, we included acutely septic mice killed at 30 h (acute sepsis, n = 15) and healthy controls animals (HC, n = 15). Cardiac tissue was collected for assessment of inflammatory and metabolic markers through gene expression, metabolomic analysis and histological assessment.ResultsIn prolonged sepsis, cardiac expression of IL-1β and IL-6 and macrophage infiltration remained upregulated (p ≤ 0.05). In contrast, tissue levels of Krebs cycle intermediates and adenosine phosphates were normal, whereas NADPH levels were low in prolonged sepsis (p ≤ 0.05). Gene expression of fatty acid transporters and of the glucose transporter Slc2a1 was upregulated in prolonged sepsis (p ≤ 0.01). Lipid staining and glycogen content were elevated in prolonged sepsis together with increased gene expression of enzymes responsible for lipogenesis and glycogen synthesis (p ≤ 0.05). Intermediate glycolytic metabolites (hexose-phosphates, GADP, DHAP) were elevated (p ≤ 0.05), but gene expression of several enzymes for glycolysis and mitochondrial oxidation of pyruvate, fatty-acyl-CoA and ketone bodies to acetyl-CoA were suppressed in prolonged sepsis (p ≤ 0.05). Key metabolic transcription factors PPARα and PGC-1α were downregulated in acute, but upregulated in prolonged, sepsis (p ≤ 0.05 for both). Ketone body concentrations were normal but ketolytic enzymes remained suppressed (p ≤ 0.05). Amino acid metabolism showed mild, mixed changes.ConclusionsOur results suggest myocardial lipid and glycogen accumulation and suppressed mitochondrial oxidation, with a functionally intact Krebs cycle, in the prolonged phase of sepsis, together with ongoing myocardial inflammation. Whether these alterations have functional consequences and predispose to long-term sequelae of SICM needs further research.

Amino acids and CART distinguish A-β+ Ketosis-Prone Diabetes from type 1 and type 2 diabetes during hyperglycemic crises.

When clinically stable, patients with A-β+ Ketosis-Prone Diabetes (KPD) manifest unique markers of amino acid metabolism. Biomarkers differentiating KPD from type 1 (T1D) and type 2 diabetes (T2D) during hyperglycemic crises would accelerate diagnosis and management. Compare serum metabolomics of KPD, T1D and T2D patients during hyperglycemic crises, and utilize Classification and Regression Tree (CART) modeling to distinguish these forms of diabetes. Urban hospital emergency center. Adults with KPD, T1D and T2D during hyperglycemic crises (with or without diabetic ketoacidosis (DKA), and healthy controls. Comparisons of serum metabolite and hormonal profiles, and CART analysis. Group differences in concentrations of amino acids, their metabolites and relationship to glucose counterregulatory hormones; C-peptide cutoffs and analytes to distinguish KPD, T1D and T2D. Concentrations of most amino acids were similar in KPD and T1D and lower compared to T2D (P<0.05). Glucagon and cortisol concentrations were correlated with 3-methylhistidine and blood urea nitrogen in KPD but not in T1D. A C-peptide cutoff of 0.496 ng/mL differentiated T1D from KPD during DKA. CART revealed that a regression model based on the concentrations of β-hydroxybutyrate, C-peptide, glucagon, alpha-keto-β-methylvalerate, cystine and myristoyl-L-carnitine distinguished KPD from T1D and T2D. During DKA, KPD and T1D patients have similarly altered amino acid profiles that differentiate them from T2D patients. Elevated protein catabolic hormones drive altered amino acid metabolism in KPD, rather than insulin deficiency as with T1D. A combination of 6 analytes differentiates KPD from T1D and T2D during hyperglycemic crises.

Integrated omics profiling of individual variations in intestinal damage to the soybean allergen in piglets

IntroductionA small number of soybean allergens [including Glycinin (11S) and β-Conglycinin (7S)] in the commercially available corn-soybean meal diet can still cause allergy in some weaned piglets, which may be the result of the interaction of genetic, and nutrition, but the specific mechanism is still unclear.MethodsIn this study, 20 allergic piglets and 20 non-allergic piglets were selected from 92 weaned piglets by skin sensitization tests, which were used to examine the whole sequence genome. The indicators related to humoral and cellular immunity, transcriptomics, and metabolomics analysis were determined by randomly selecting 5 boars in the allergic group and non-allergic group and then performing a validation in vitro.ResultsThe sensitization rate of soybean antigen in the corn-soybean meal diet was 21.74% and there was a gender difference with the sensitization rate of female pigs (31.34%) being higher than that of male pigs (13.23%). Moreover, the levels of inflammatory factors (IL-1β, IL-4, TNF-α) and antibodies (IgG, IgE, and specific IgG) in allergic piglets were significantly higher than those in non-allergic piglets (P &amp;lt; 0.05). Whole genome re-sequencing analysis revealed specific mutations in the exons and URT5 of TRAPPC2, PIR, CFP, and SOWAHD genes and showed significantly higher expression levels of related genes in the spleen of allergic piglets (P &amp;lt; 0.05). Transcriptome analysis identified IL17REL, CCL19, CD1E, CD1.1, etc. immune differential genes, metabolomics results showed that soybean antigen affected the utilization and metabolism of intestinal nutrients in piglets, mainly the digestion and absorption of protein and the synthesis and metabolism of amino acids. Transfection of CFP/TRAPPC2/CCL19 siRNA could partially alleviate the injury of RAW264.7 cells or IPEC-J2 cells induced by β-Conglycinin.ConclusionTherefore, the individual differences in intestinal damage induced by soybean antigen protein in the corn-soybean meal diet are closely related to PIR, CFP, TRAPPC2, SOWAHD, and CCL19 genes. Soybean antigens affect the intestinal nutrient utilization and metabolism of piglets, which provides a scientific reference for the study of soybean antigen sensitization mechanisms, precision nutrition, disease prevention, and control of piglets, and also lays a foundation for human foodborne diseases.

Undernutrition affects metabolism and immune response in subcutaneous adipose tissue of pregnant ewes.

Pregnant ewes mobilize body fat to increase energy supply for fetal growth and development upon undernutrition, which disrupts the metabolic homeostasis of the body. However, the comprehensive metabolic changes in subcutaneous adipose tissue upon undernutrition are poorly understood. In this study, an undernutrition sheep model was established to investigate the effects of undernutrition on metabolic changes, immune response, and inflammation in subcutaneous fat through transcriptome, RT-qPCR, and metabolome analysis. Results showed that undernutrition changed the total transcriptional and metabolic profiles of adipose tissue. Compared to the controls, differentially expressed genes (DEGs) involved in fatty acid synthesis, triglyceride genesis, and lipid transport were downregulated in undernourished ewes, while DEGs related to fatty acid and triglyceride degradation were upregulated. Almost all lipid-related differential metabolites (DMs) were downregulated. DEGs and DMs involved in glucose metabolism and glycogen degradation were downregulated, while glycogen synthesis and carbohydrate transport were upregulated. DEGs linked to amino acid degradation were upregulated and some amino acids and derivatives were downregulated. KEGG pathway analysis showed complement and coagulation cascades were enriched significantly by DEGs, and DEGs related to coagulation, macrophage, and inflammation were upregulated while DEGs associated with the complement system were downregulated. Undernutrition during late gestation disrupted the metabolism of lipids, carbohydrates, and amino acids in adipose tissue, which weakened the complement system and immune response and may have ultimately led to inflammation.

Genetic Background of Macular Telangiectasia Type 2

Macular telangiectasia type 2 (MacTel) is a slowly progressive macular disorder that is often diagnosed late due to the gradual onset of vision loss. Recent advances in diagnostic techniques have facilitated earlier detection and have shown that MacTel is more common than initially thought. The disease is genetically complex, and multiple variants contribute incrementally to the overall risk. The familial occurrence of the disease prompted the investigation of the genetic background of MacTel. To better understand the molecular milieu of the disease, a literature review of the clinical reports and publications investigating the genetic factors of MacTel was performed. To date, disease-associated variants have been found in genes involved in amino acid (glycine/serine) metabolism and transport, urea cycle, lipid metabolism, and retinal vasculature and thickness. Variants in genes implicated in sphingolipid metabolism and fatty acid/steroid/retinol metabolism have been found in patients with neurological disorders who also have MacTel. Retinal metabolism involves complex biochemical processes that are essential for maintaining the high energy requirements of the retina. Genetic alterations can disrupt key metabolic pathways, leading to retinal cell degradation and the subsequent vision loss that characterizes several retinal disorders, including MacTel. This review article summarizes genetic findings that may allow MacTel to be further investigated as an inherited retinal disorder.

Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development

The precise role of lncRNAs in skeletal muscle development and atrophy remain elusive. We conducted a bioinformatic analysis of 26 GEO datasets from mouse studies, encompassing embryonic development, postnatal growth, regeneration, cell proliferation, and differentiation, using R and relevant packages (limma et al.). LncRNA-miRNA relationships were predicted using miRcode and lncBaseV2, with miRNA-mRNA pairs identified via miRcode, miRDB, and Targetscan7. Based on the ceRNA theory, we constructed and visualized the lncRNA-miRNA-mRNA regulatory network using ggalluvial among other R packages. GO, Reactome, KEGG, and GSEA explored interactions in muscle development and regeneration. We identified five candidate lncRNAs (Xist, Gas5, Pvt1, Airn, and Meg3) as potential mediators in these processes and microgravity-induced muscle wasting. Additionally, we created a detailed lncRNA-miRNA-mRNA regulatory network, including interactions such as lncRNA Xist/miR-126/IRS1, lncRNA Xist/miR-486-5p/GAB2, lncRNA Pvt1/miR-148/RAB34, and lncRNA Gas5/miR-455-5p/SOCS3. Significant signaling pathway changes (PI3K/Akt, MAPK, NF-κB, cell cycle, AMPK, Hippo, and cAMP) were observed during muscle development, regeneration, and atrophy. Despite bioinformatics challenges, our research underscores the significant roles of lncRNAs in muscle protein synthesis, degradation, cell proliferation, differentiation, function, and metabolism under both normal and microgravity conditions. This study offers new insights into the molecular mechanisms governing skeletal muscle development and regeneration.

Can the supplementation of autolyzed yeast (Saccharomyces cerevisiae) affect the diet digestibility, feeding behavior, levels of blood metabolites, and performance of Dorper × Santa Ines lambs finished in feedlot?

This study aimed to evaluate the effect of autolyzed yeast (obtained from culture of Saccharomyces cerevisiae in sugarcane derivatives) supplementation on diet digestibility, feeding behavior, levels of blood metabolites associated with protein and energy metabolism, and performance of Dorper × Santa Ines lambs finished in feedlot. Twenty-four non-castrated male lambs with an average age of 4months and a body weight (BW) of 19.49 ± 3.08kg were allocated to individual pens within a covered and elevated shed. The pens had a slatted floor without bedding suspended 1.8m above the ground, and an area of 1.5 m2. The trial was set out in a completely randomized design with two treatments and twelve replicates each. The treatments consisted of a basal diet without yeast products (Control) or with yeast culture (Yeast, RumenYeast® at 5g/animal/day). Lambs were fed ad libitum with a total mixed ration (TMR) composed of 400g/kg of dry matter (DM) of Tifton 85 hay (Cynodon spp.) and 600g/kg DM of concentrate feed, and contained 146g/kg DM of crude protein and 2.30 Mcal/kg DM of metabolizable energy. The experiment was conducted over 84days, with the first 14days serving as an adaptation period. The subsequent experimental period was divided into two phases to evaluate animal performance (Days 1-63) and DM digestibility (Days 64-70). The supplementation with autolyzed yeast did not affect rumen or fecal pH, the DM digestibility, as well as the feeding behavior of lambs (the time spent on feeding, rumination, water intake, and idleness activities). In addition, yeast supplementation did not alter the serum levels of albumin, creatinine, urea, or level of plasma glucose, resulting in similar animal performance compared to the Control group. The mean values for final BW, DM intake, average daily gain, and feed conversion ratio were 37.52kg, 1.051kg/day, 0.286kg/day, and 3.74kg DM/kg gain, respectively. In the conditions of this study, the supplementation of autolyzed yeast in TMR (5g/animal/day) does not affect diet digestibility, feeding behavior, blood metabolites, or performance of lambs finished in feedlot. Regarding that metabolic and performance lamb responses were not improved, the supplementation of autolyzed yeast at the tested dose is not recommended. However, it is important to note that markers related to immunity and inflammation were not evaluated in our work, and these should be considered in future studies.

Inhibitory and Curative Effects and Mode of Action of Hydroxychloroquine on Botrytis cinerea of Tomato.

Gray mold is an important disease of crops and is widespread, harmful, difficult to control, and prone to developing fungicide resistance. Screening new fungicides is an important step in controlling this disease. Hydroxychloroquine is an anti-inflammatory and anti-malarial agent, which has shown marked inhibitory activity against many fungi in medicine. This study evaluated the inhibitory activity of hydroxychloroquine against several phytopathogenic fungi, finding a half-maximal effective concentration of 113.82 μg/ml against the hyphal growth of Botrytis cinerea, with significant in-vivo curative effects of 92.37% or 78.37% for gray mold on detached tomato leaves or fruits at 10.0 or 200.0 mg/ml, respectively. Ultrastructural studies indicated that hydroxychloroquine induced collapse of hyphae, with a wrinkled surface, unclear organelle boundaries, and organelle disintegration. Transcriptomic assays revealed that hydroxychloroquine could affect the expression of metabolism-related genes. Molecular docking and molecular dynamics analyses indicated that hydroxychloroquine bound to glucose-methanol-choline oxidoreductase, with low free energy value of -11.4 kcal/mol. Cell membrane permeability assays and hyphal staining confirmed that hydroxychloroquine damaged the cell membrane, causing leakage of hyphal contents and disturbing cell function. Biochemical assays indicated that hydroxychloroquine reduced the concentration of soluble proteins and reducing sugars in the hyphae. In total, hydroxychloroquine disturbed amino acid metabolism, therefore inhibiting the production of biomacromolecules, damaging the cell membrane, and restraining the growth of hyphae, and hence inhibiting gray mold on tomato. This study will explore the use of medicine in the development of agricultural fungicides and their application in managing crop diseases, providing valuable background information.

Gut microbiota modulation in cardiac cell therapy with immunosuppression in a nonhuman primate ischemia/reperfusion model

Gut microbiota affect transplantation outcomes; however, the influence of immunosuppression and cell therapy on the gut microbiota in cardiovascular care remains unexplored. We investigated gut microbiota dynamics in a nonhuman primate (NHP) cardiac ischemia/reperfusion model while under immunosuppression and receiving cell therapy with human induced pluripotent stem cell (hiPSC)-derived endothelial cells (EC) and cardiomyocytes (CM). Both immunosuppression and EC/CM co-treatment increased gut microbiota alpha diversity. Immunosuppression promoted anaerobes, such as Faecalibacterium, Streptococcus, Anaerovibrio and Dialister, and altered amino acid metabolism and nucleosides/nucleotides biosynthesis in host plasma. EC + CM cotreatment favors Phascolarctobacterium, Fusicatenibacter, Erysipelotrichaceae UCG-006, Veillonella and Mailhella. Remarkably, gut microbiota of the EC/CM co-treatment group resembled that of the pre-injury group, and the NHPs exhibited a metabolic shift towards amino acid and fatty acid/lipid biosynthesis in plasma following cell therapy. The interplay between shift in microbial community and host homeostasis during treatment suggests gut microbiome modulation could improve cell therapy outcomes.

Effects of Dietary Tea Polyphenols on the Growth, Antioxidant Status, Immune Function, and Intestinal Microbiota of Largemouth Bass (Micropterus salmoides)

This research aimed to explore the impact of tea polyphenol (TP) supplementation on the development, antioxidant properties, immune responses, and gut wellness in largemouth bass (Micropterus salmoides, LMB). Four diets with varying levels of TPs (0.00%, 0.02%, 0.04%, and 0.08%) were devised to feed LMB with an initial weight of 4.3 ± 0.02 g for 56 days, among which the intermittent feeding (IF) group was fed a diet supplemented with TP8 for 7 days, followed by a basal diet for another 7 days, and this was repeated until the end (56th day). The results demonstrated that supplementation with 0.04% or 0.08% TPs in the diet could reduce the crude lipid content and increase the crude protein content of LMB (p &lt; 0.05). The levels of total cholesterol (CHO) and low-density lipoprotein (LDL) in the serum significantly decreased with the addition of 0.08% dietary TPs to the diet (p &lt; 0.05). Dietary TPs can stimulate the activities of antioxidant enzymes such as superoxide dismutase (SOD) and catalase (CAT) and enhance the antioxidant capacity of LMB (p &lt; 0.05). The activities of immune enzymes such as acid phosphatase (ACP) were increased to improve the immune response via the addition of TPs (p &lt; 0.05). Supplementation with 0.02% and 0.04% TPs reduced liver fatty infiltration and alleviated hepatocyte damage. Compared with the control diet, dietary TPs significantly increased villus height (VH), villus width (VW), and lipase (LPS) activity in the intestine (p &lt; 0.05), and supplementation with 0.04% TPs significantly increased muscular layer thickness (MT) (p &lt; 0.05). With the increase in dietary TPs, distinct differences were observed in the intestinal microbial composition and the relative abundance of potential pathogens, especially Clostridiaceae, which decreased, along with the enrichment of pathways related to metabolism, including amino acid metabolism, carbohydrate metabolism, and lipid metabolism. Additionally, intermittent feeding could alleviate the adverse effects caused by a high dosage. In conclusion, dietary TPs of LMB could enhance antioxidant capacity and immunity and improve intestinal health, and intermittent feeding could mitigate the adverse effects caused by a high dosage.

Network pharmacology and multi-omics validation of the Jianpi-Yishen formula in the treatment of chronic kidney disease

ObjectiveChronic kidney disease (CKD) is a major global health problem. In clinical practice, the Chinese patent herbal medicine Jianpi-Yishen (JPYS) formula is commonly used to treat CKD. However, the molecular mechanisms by which JPYS targets and modulates the host immune response remain unclear.MethodsThis study utilized network pharmacology, RNA sequencing (RNA-seq), and metabolic analyses using in vivo and in vitro models to investigate the impact of the JPYS formula on inflammation and the immune system. Specifically, the study focused on macrophage polarization and metabolic changes that may slow down the progression of CKD.ResultsA total of 14,946 CKD-related targets were identified from the GeneCards and Online Mendelian Inheritance in Man (OMIM) databases through network pharmacology analyses. 227 potential targets of the JPYS formula were predicted using the TCMSP database. Additionally, network diagram demonstrated that 11 targets were associated with macrophage activity. In vivo studies indicated that the JPYS formula could reduce blood urea nitrogen and serum creatinine in adenine-induced CKD rats. Furthermore, the formula inhibited inflammatory damage and abnormal macrophage infiltration in this CKD model. RNA-seq, proteomic and metabolic analyses identified the regulation of amino acid metabolism by betaine, specifically referring to glycine, serine, and threonine metabolism, as a key target of the JPYS formula in slowing the progression of CKD. In addition, in vitro studies suggested that JPYS may enhance tryptophan metabolism in M1 macrophage polarization and betaine metabolism in M2 macrophage polarization.ConclusionsThe JPYS formula has been shown to have beneficial impact on CKD; a key mechanism is the mitigation of inflammatory damage through the interaction between amino acid metabolism and macrophage polarization. Of specific importance in this context are the roles of tryptophan in M1 polarization and betaine in M2 polarization.

Insights of cellular and molecular changes in sugarcane response to oxidative signaling

Main conclusionSignificant changes in the proteome highlight essential metabolic adaptations for development and oxidative signaling induced by the treatment of young sugarcane plants with hydrogen peroxide. These adaptations suggest that hydrogen peroxide acts not only as a stressor but primarily as a signaling molecule, triggering specific metabolic pathways that regulate growth and plant resilience.Sugarcane is a crucial crop for sugar and ethanol production, often influenced by environmental signals. Hydrogen peroxide (H2O2) is increasingly recognized as an important signaling molecule that regulates plant development and adaptation. In this study, two-month-old sugarcane plants were treated with varying concentrations of H2O2 to investigate how this molecule acts as a signal at the cellular, biochemical, and proteomic levels. Antioxidant enzyme activity exhibited fluctuations, suggesting a dynamic response to oxidative signaling. Lipid peroxidation, observed through TBARs and scanning electron microscopy, highlighted early membrane modifications. Proteomic analysis (ProteomeXchange PXD048142) identified 2,699 proteins, with 155 showing significant expression changes in response to H2O2 signaling. Bioinformatics, including Principal Component Analysis, revealed distinct proteomic profiles in roots and leaves, indicating tissue-specific metabolic reprogramming. Functional annotation through Gene Ontology and KEGG pathway enrichment showed that oxidative signaling led to the repression of photosynthesis-related pathways in leaves, while promoting pathways related to protein processing, glycolysis, and carbon metabolism in roots. Additionally, bioinformatic tools identified proteins involved in amino acid metabolism, the TCA cycle, and carbohydrate metabolism as critical components of sugarcane's adaptive signaling response. The data suggest that sugarcane plants responded to oxidative signals by adjusting their metabolic networks, promoting sustained development and potential pathways for targeted plant breeding.

ApWD40a, a Member of the WD40-Repeat Protein Family, Is Crucial for Fungal Development, Toxin Synthesis, and Pathogenicity in the Ginseng Alternaria Leaf Blight Fungus Alternaria panax

Alternaria panax, the primary pathogen that causes ginseng Alternaria leaf blight disease, can lead to a 20–30% reduction in ginseng yield. WD40 repeat-containing proteins are evolutionarily conserved proteins with diverse functions between different organisms. In this study, we characterized the roles of a WD40 repeat-containing protein in A. panax. The deletion of ApWD40a impaired the mycelial growth, reduced the sporulation, and significantly decreased the efficiency in utilizing various carbon sources. The ΔApwd40a mutant showed increased sensitivity to osmotic stress and metal ion stress induced by sorbitol, NaCl, and KCl, but decreased the sensitivity to a cell wall stress factor (SDS) and oxidative stress factors (paraquat and H2O2). Pathogenicity assays performed on detached ginseng leaves and roots revealed that the disruption of ApWD40a significantly decreased the fungal virulence through attenuating melanin and mycotoxin production by A. panax. A comparative transcriptome analysis revealed that ApWD40a was involved in many metabolic and biosynthetic processes, including amino acid metabolism, carbon metabolism, sulfate metabolic pathways, and secondary metabolite pathways. In particular, a significantly upregulated gene that encoded a sulfate permease 2 protein in ΔApwd40a, named ApSulP2, was deleted in the wild-type strain of A. panax. The deletion of ApSulP2 resulted in reduced biomass under sulfate-free conditions, demonstrating that the sulfate transport was impaired. Taken together, our findings highlight that ApWD40a played crucial roles in different biological processes and the pathogenicity of A. panax through modulating the expressions of genes involved in various primary and secondary metabolic processes.

Effects of feeding different proportions of steam-flaked corn-based starter on growth performance, immunity and serum metabolism of pre-weaned Simmental calves

IntroductionThis study examines the effects of steam-flaked corn starter on pre-weaned Simmental calves' growth, immunity, and metabolism. Despite benefits shown in adult cattle, research on calves is limited. The goal is to optimize calf feeding for better growth, health, and nutrient use.MethodsThirty-two Simmental bull calves (avg. wt: 50.50 ± 4.50 kg, avg. age: 21 ± 7 days) were divided into four groups of eight. The 127-day study included a 7-day pretest and a 120-day trial. Calves had unlimited access to starter feed, alfalfa hay, and water. Groups received starter diets with 0% (CK, control), 33% (SFC33, low), 66% (SFC66, medium), or 100% (SFC100, high) steam-flaked corn replacing regular corn. Other conditions were consistent.ResultsFeeding 33% steam-flaked corn to pre-weaned Simmental calves led to highest daily weight gain (0.80 kg/d), significantly boosting serum globulin, cholesterol, urea nitrogen, glucose, immunoglobulins, GH, INS, and IGF-1 (P &amp;lt; 0.05). Compared to control, 31 metabolites differed in SFC33 group, mostly up-regulated, including glycerophospholipids, linoleic/arachidonic acid metabolism, cholesterol pathway molecules, L-glutamine in multiple pathways, and mannose in fructose/mannose metabolism.DiscussionIn summary, feeding 33% steam-flaked corn-based starter can improve the growth performance, enhance immunity, and improve sugars, lipids, and proteins metabolism of pre-weaned Simmental calves.

Plasma metabolome reveals altered oxidative stress, inflammation, and amino acid metabolism in dogs with idiopathic epilepsy.

Idiopathic epilepsy (IE) is the most common chronic neurological disease in dogs and an established natural animal model for human epilepsy types with genetic and unknown etiology. However, the metabolic pathways underlying IE remain largely unknown. Plasma samples of healthy dogs (n = 39) and dogs with IE (n = 49) were metabolically profiled (n = 121 known target metabolites) and fingerprinted (n = 1825 untargeted features) using liquid chromatography coupled to mass spectrometry. Dogs with IE were classified as mild phenotype (MP; n = 22) or drug-resistant (DR; n = 27). All dogs received the same standard adult maintenance diet for a minimum of 20 days (35 ± 11 days) before sampling. Data were analyzed using a combination of univariate (one-way analysis of variance or Kruskal-Wallis rank sum test), multivariate (limma, orthogonal partial least squares-discriminant analysis), and pathway enrichment statistical analysis. In dogs with both DR and MP IE, a distinct plasma metabolic profile and fingerprint compared to healthy dogs was observed. Metabolic pathways involved in these alterations included oxidative stress, inflammation, and amino acid metabolism. Moreover, significantly lower plasma concentrations of vitamin B6 were found in MP (p = .001) and DR (p = .005) compared to healthy dogs. Our data provide new insights into the metabolic pathways underlying IE in dogs, further substantiating its potential as a natural animal model for humans with epilepsy, reflected by related metabolic changes in oxidative stress metabolites and vitamin B6. Even more, several metabolites within the uncovered pathways offer promising therapeutic targets for the management of IE, primarily for dogs, and ultimately for humans.

LC-MS/MS-based proteomics and metabolomics of HCT-116 colorectal cancer cells: A potential anticancer activity of atorvastatin

Colorectal cancer (CRC) is the third most prevalent tumor in men, the second most common in women, and the fourth leading cause of mortality worldwide. Statins reduce cholesterol levels by hampering the function of 3-hydroxy-3-methyl-glutaryl-CoA reductase enzymes in cholesterol synthesis. Strains have shown anticancer effects against CRC. However, statins’ anticancer mechanism is yet unknown. Liquid chromatography–mass spectrometry (LC–MS)-based untargeted metabolomics and proteomics were employed to study statins’ effects on CRC using the CRC cell line HCT-116. These approaches were utilized to identify potential underlying metabolic pathways and proteins altered in atorvastatin (a statin)-treated HCT-116 cells. Compared to the control, atorvastatin significantly altered numerous metabolites in HCT-116 cells, including a reduction in the levels of decanoylcarnitine and octanoyl-L-carnitine and in the biosynthesis and metabolism of amino acids like alanine and citrate cycle. Proteomic study showed that atorvastatin-treated HCT-116 cells expressed 127 proteins differently from controls. Novel findings were among them, such as centromere-associated protein E, cytochrome c oxidase subunit 6A1 mitochondrial, and hyaluronan synthase 1. The findings indicate that atorvastatin may have potential anticancer characteristics and highlight the essential role metabolomics and proteomics to understand complex metabolic pathways and proteins relevant to cancer and develop novel treatment targets.

Root Development of Tomato Plants Infected by the Cacao Pathogen Moniliophthora perniciosa Is Affected by Limited Sugar Availability.

Moniliophthora perniciosa is the causal agent of the witches' broom disease of cacao (Theobroma cacao), and it can infect the tomato (Solanum lycopersicum) 'Micro-Tom' (MT) cultivar. Typical symptoms of infection are stem swelling and axillary shoot outgrowth, whereas reduction in root biomass is another side effect. Using infected MT, we investigated whether impaired root growth derives from hormonal imbalance or sink competition. Intense stem swelling coincided with a reduction in root biomass, predominantly affecting lateral roots. RNA-seq analyses of root samples identified only a few differentially expressed genes involved in hormone metabolism, and root hormone levels were not expressively altered. Inoculation of the auxin highly-sensitive entire mutant genotype maintained the impaired root phenotype; in contrast, the low-cytokinin MT transgenic line overexpressing CYTOKININ OXIDASE-2 (35S::AtCKX2) with fewer symptoms did not exhibit root growth impairment. Genes involved in cell wall, carbohydrate, and amino acid metabolism were downregulated, accompanied by lower levels of carbohydrate and amino acid in roots, suggesting a reduction in metabolite availability. 13CO2 was supplied to MT plants, and less 13C was detected in the roots of infected MT but not in those of 35S::AtCKX2 line plants, suggesting that cytokinin-mediated sugar sink establishment at the infection site may contribute to impaired root growth. Exogenous sucrose application to roots of infected MT plants partially restored root growth. We propose that the impairment of lateral root development is likely attributed to disrupted sugar signalling and photoassimilate supply by establishing a strong sugar sink at the infected stem.