Metabolism-related Genes Research Articles

Adaptability and growth of Hippocampus kuda and Oryzias melastigma under rapid temperature changes.

Temperature changes had a huge impact on the growth of aquaculture organisms, which mainly involved two parameters: the changing amplitude and the changing speed. Wide-adaptability and narrow-adaptability were divided by the amplitude, while fast-adaptability and slow-adaptability proposed in this article were divided based on the speed. Investigating the impact of the changing speed on artificial farming was vital. In this study, two fish species of wide-adaptability, Hippocampus kuda and Oryzias melatigma, were selected as research objects, explored the effects of temperature changing speeds on them under 2 changing amplitudes of 2°C and 4°C. The similarities and differences in their responses to temperature changes were analyzed and compared from the aspects of feeding, metabolism, physiology, immunity, and growth. The results showed that all 3 changing speeds (0.5°C/h, 1°C/h, and direct input) had no effect on the growth of O. melatigma under the 2°C amplitude, while there were significant differences in various aspects of H. kuda in the treatments with the speeds between 0.5°C/h and direct input, such as a significant difference in growth, in food intake, and in response speeds and response levels of several enzymes and related genes. Under 4°C amplitude, the impact of all 4 changing speeds (0.5°C/h, 1°C/h, 2°C/h and direct input) on both fish was more pronounced. H. kuda showed a significant difference of growth among 3 groups, and the critical safe speed was about 0.5°C/h in its heating treatments. And the growth decrease only occured the heating treatment of direct input in O. melatigma. Furthermore, some genes responded quickly and efficiently to the low-speed changes of temperature in H. kuda, but were inhibited in the treatments with high-speed changes. However, they can still express rapidly and efficiently in the high-speed treatments of O. melatigma, included several stress-related genes, lipid metabolic-related genes, and immune-related genes. Seen from these differences, the energy source used in H. kuda to resist stress was single and short-lived. So, under a long-term stress, H. kuda gradually transformed from normal physiological stress into pathological stress, leading to the outbreak of diseases. Therefore, for precise aquaculture of H. kuda, stricter and more precise control of environmental temperature is necessary to prevent rapid and big temperature changes from affecting the growth and survival of the seahorse.

Identification of novel targets associated with cholesterol metabolism in nonalcoholic fatty liver disease: a comprehensive study using Mendelian randomization combined with transcriptome analysis.

There is limited research on cholesterol metabolism-related genes (CM-RGs) in non-alcoholic fatty liver disease (NAFLD), despite hypercholesterolemia being a recognized risk factor. The role of CM-RGs in NAFLD remains unclear. The differentially expressed genes (DEGs) between NAFLD and control were acquired by differential expression analysis. The differentially expressed genes associated with cholesterol metabolism (DE-CM-RGs) were identified and functional enrichment analyses were performed. Protein-protein interaction network analysis and a two-sample Mendelian randomization study were utilized for identifying hub genes. Nomogram model, competing endogenous RNA and messenger RNA-drug networks were established. In addition, immunoinfiltration analysis was performed. We identified four hub genes (MVK, HMGCS1, TM7SF2, and FDPS) linked to NAFLD risk. MVK and TM7SF2 were protective factors, HMGCS1 and FDPS were risk factors for NAFLD. The area under the curve values of nomograms in GSE135251 and GSE126848 were 0.79 and 0.848, respectively. The gene set enrichment analysis indicated that hub genes participated in calcium signaling pathways and biosynthesis of unsaturated fatty acids. NAFLD patients showed increased CD56dim NK cells and Th17. Tretinoin, alendronate, zoledronic acid, and quercetin are potential target agents in NAFLD. Our study has linked cholesterol metabolism genes (MVK, HMGCS1, TM7SF2, and FDPS) to NAFLD, providing a promising diagnostic framework, identifying treatment targets, and offering novel perspectives into its mechanisms.

Arbuscular mycorrhizal fungi enhance nitrogen assimilation and drought adaptability in tea plants by promoting amino acid accumulation.

The development and quality of tea plants (Camellia sinensis (L.) O. Ktze.) are greatly hampered by drought stress (DS), which affects them in a number of ways, including by interfering with their metabolism of nitrogen (N). Arbuscular mycorrhizal fungi (AMF) are known to enhance water and nutrient absorption in plants, but their specific effects on tea plant N metabolism under DS and the associated regulatory mechanisms remain unclear. This study aimed to evaluate the impact of Claroideoglomus etunicatum inoculation on N assimilation in tea plants (C. sinensis cv. Fuding Dabaicha) under well-watered (WW) and DS conditions, and to explore potential molecular mechanisms. After 8 weeks of DS treatment, root mycorrhizal colonization was significantly inhibited, and the biomass of tea shoots and roots, as well as the contents of various amino acids (AAs) were reduced. However, AMF inoculation significantly increased the contents of tea polyphenols and catechins in leaves by 13.74%-36.90% under both WW and DS conditions. Additionally, mycorrhizal colonization notably increased N content by 12.65%-35.70%, various AAs by 11.88%-325.42%, and enzymatic activities associated with N metabolism by 3.80%-147.62% in both leaves and roots. Gene expression analysis revealed a universal upregulation of N assimilation-related genes (CsAMT1;2, CsAMT3;1, CsGS1, CsNADH-GOGAT, CsTS2, CsGGT1, and CsADC) in AMF-colonized tea roots, regardless of water status. Under DS condition, AMF inoculation significantly upregulated the expressions of CsNRT1;2, CsNRT1;5, CsNRT2;5, CsNR, CsGS1, CsGDH1, CsGDH2, CsTS2, CsGGT1, CsGGT3, and CsSAMDC in tea leaves. These findings suggest that AMF improved tea plant adaptability to DS by enhancing N absorption and assimilation, accompanied by the synthesis and accumulation of various AAs, such as Glu, Gln, Asp, Lys, Arg, GABA and Pro. This is achieved through the upregulation of N metabolism-related genes and the activation of related enzymes in tea plants under DS condition. These findings provide valuable insights into the role of AMF in regulating tea plant N metabolism and enhancing stress tolerance.

Lipoprotein metabolism mediates hematopoietic stem cell responses under acute anemic conditions

Hematopoietic stem cells (HSCs) react to various stress conditions. However, it is unclear whether and how HSCs respond to severe anemia. Here, we demonstrate that upon induction of acute anemia, HSCs rapidly proliferate and enhance their erythroid differentiation potential. In severe anemia, lipoprotein profiles largely change and the concentration of ApoE increases. In HSCs, transcription levels of lipid metabolism-related genes, such as very low-density lipoprotein receptor (Vldlr), are upregulated. Stimulation of HSCs with ApoE enhances their erythroid potential, whereas HSCs in Apoe knockout mice do not respond to anemia induction. VldlrhighHSCs show higher erythroid potential, which is enhanced after acute anemia induction. VldlrhighHSCs are epigenetically distinct because of their low chromatin accessibility, and more chromatin regions are closed upon acute anemia induction. Chromatin regions closed upon acute anemia induction are mainly binding sites of Erg. Inhibition of Erg enhanced the erythroid differentiation potential of HSCs. Our findings indicate that lipoprotein metabolism plays an important role in HSC regulation under severe anemic conditions.

Phosphorus Metabolism-Related Genes Serve as Novel Biomarkers for Predicting Prognosis in Bladder Cancer: A Bioinformatics Analysis.

Phosphorus metabolism might be associated with tumor initiation and progression. We aimed to screen out the phosphorus metabolism genes related to bladder cancer and construct a clinical prognosis model. The dataset used for the analysis was obtained from TCGA database. GO and KEGG enrichment analyses were subsequently applied to differentially expressed genes. Consensus clustering was utilized, and different clusters of the tumor immune microenvironment and other features were compared. The phosphorus metabolism-related genes involved in prognosis were screened out by univariate Cox regression, LASSO regression and multivariate Cox regression analysis, and a nomogram was constructed. The performance of the nomogram was validated using TCGA dataset and the GEO dataset, respectively. Overall, 405 phosphorus metabolism-related differentially expressed genes from TCGA database were identified, which were associated with phosphorylation, cell proliferation, leukocyte activation, and signaling pathways. Two clusters were obtained by consistent clustering. After tumor immune microenvironment analysis, significant differences in immune cell infiltration between cluster 1 and cluster 2 were found. Four phosphorus metabolism-related genes (LIME1, LRP8, SPDYA, and MST1R) were associated with the prognosis of bladder cancer (BLCA) patients. We built a prognostic model and visualized the model as a nomogram. Calibration curves demonstrated the performance of this nomogram, in agreement with that shown by the ROC curves. We successfully identified four phosphorus metabolism-related genes associated with prognosis, providing potential targets for biomarkers and therapeutics. A nomogram based on these genes was developed. Nevertheless, this study is based on bioinformatics, and experimental validation remains essential.

Lipid profiling of RON and DEK-dependent signaling in breast cancer guides discovery of gene networks predictive of poor outcomes.

Recurrent and metastatic breast cancer is frequently treatment resistant. A wealth of evidence suggests that reprogrammed lipid metabolism supports cancer recurrence. Overexpression of the RON and DEK oncoproteins in breast cancer is associated with poor outcome. Both proteins promote cancer metastasis in laboratory models, but their influence on lipid metabolite levels remain unknown. To measure RON- and DEK-dependent steady-state lipid metabolite levels, a nuclear magnetic resonance (NMR)-based approach was utilized. The observed differences identified a lipid metabolism-related gene expression signature that is prognostic of overall survival (OS), distant metastasis-free survival (DMFS), post-progression survival (PPS), and recurrence-free survival (RFS) in patients with breast cancer. RON loss led to decreased cholesterol and sphingomyelin levels, whereas DEK loss increased total fatty acid levels and decreased free glycerol levels. Lipid-related genes were then queried to define a signature that predicts poor outcomes for patients with breast cancer patients. Taken together, RON and DEK differentially regulate lipid metabolism in a manner that predicts and may promote breast cancer metastasis and recurrence.

Genome-Wide Mapping of Main Histone Modifications and Coordination Regulation of Metabolic Genes under Salt Stress in Pea (Pisum sativum L)

Abstract Pea occupy a key position in modern biogenetics, playing a multifaceted roles as food, vegetable, fodder, and green manure. However, due to the complex nature of its genome and the prolonged unveiling of high-quality genetic maps, research into the molecular mechanisms underlying pea development and stress responses has been significantly delayed. Furthermore, the exploration of its epigenetic modification profiles and associated regulatory mechanisms remains uncharted. This research conducted a comprehensive investigation of four specific histone marks, namely H3K4me3, H3K27me3, H3K9ac, and H3K9me2 and the transcriptome in pea under normal condition, and established a global map of genome-wide regulatory elements, chromatin states, and dynamics based on these major modifications. Our analysis identified epigenomic signals across approximately 82.6% of the genome. Each modification exhibits distinct enrichment patterns: H3K4me3 is predominantly associated with the gibberellin response pathway, H3K27me3 is primarily associated with auxin and ethylene responses, and H3K9ac is primarily associated with negative regulatory stimulus responses. We also identified a novel bivalent chromatin state (H3K9ac-H3K27me3) in pea, which is related to their development and stress response. Additionally, we unveil that these histone modifications synergistically regulate metabolic-related genes, influencing metabolite production under salt stress conditions. Our findings offer a panoramic view of the major histone modifications in pea, elucidate their interplay, and highlight their transcriptional regulatory roles during salt stress.

An abnormal metabolism-related gene, ALG3, is a potential diagnostic and prognostic biomarker for lung adenocarcinoma.

To explore the abnormal metabolism-related genes that affect the prognosis of patients with lung adenocarcinoma (LUAD), and analyze the relationship with immune infiltration and competing endogenous RNA (ceRNA) network. Transcriptome data of LUAD were downloaded from the Cancer Genome Atlas database. Abnormal metabolism-related differentially expressed genes in LUAD were screened by the R language. Cox analysis was used to construct LUAD prognostic risk model. Kaplan-Meier test, ROC curve and nomograms were used to evaluate the predictive ability of metabolic related gene prognostic model. CIBERSORT algorithm was used to analyze the relationship between risk score and immune infiltration. The starBase database constructed a regulatory network consistent with the ceRNA hypothesis. IHC experiments were performed to verify the differential expression of ALG3 in LUAD and paracancerous samples. In this study, 42 abnormal metabolism-related differential genes were screened. After survival analysis, the final 5 metabolism-related genes were used as the construction of prognosis model, including ALG3, COL7A1, KL, MST1, and SLC52A1. In the model, the survival rate of LUAD patients in the high-risk subgroup was lower than that in the low-risk group. In addition, the risk score of the constructed LUAD prognostic model can be used as an independent prognostic factor for patients. According to the analysis of CIBERSORT algorithm, the risk score is related to the infiltration of multiple immune cells. The potential ceRNA network of model genes in LUAD was constructed through the starBase database. IHC experiments revealed that ALG3 expression was upregulated in LUAD. The prognostic model of LUAD reveals the relationship between metabolism and prognosis of LUAD, and provides a novel perspective for diagnosis and research of LUAD.

Energy metabolism-related GLUD1 contributes to favorable clinical outcomes of IDH-mutant glioma

BackgroundGlioma is the most common brain tumor. IDH mutations occur frequently in glioma, indicating a more favorable prognosis. We aimed to explore energy metabolism-related genes in glioma to promote the research and treatment.MethodsDatasets were obtained from TCGA and GEO databases. Candidate genes were screened by differential gene expression analysis, then functional enrichment analysis was conducted on the candidate genes. PPI was also carried out to help determine the target gene. GSEA and DO analysis were conducted in the different expression level groups of the target gene. Survival analysis and immune cell infiltrating analysis were performed as well.ResultsWe screened 34 candidate genes and selected GLUD1 as the target gene. All candidate genes were significantly enriched in 10 KEGG pathways and 330 GO terms. GLUD1 expression was higher in IDH-mutant samples than IDH-wildtype samples, and higher in normal samples than tumor samples. Low GLUD1 expression was related to poor prognosis according to survival analysis. Most types of immune cells were negatively related to GLUD1 expression, but monocytes and activated mast cells exhibited significantly positive correlation with GLUD1 expression. GLUD1 expression was significantly related to 119 drugs and 6 immune checkpoint genes. GLUD1 was able to serve as an independent prognostic indicator of IDH-mutant glioma.ConclusionIn this study, we identified an energy metabolism-related gene GLUD1 potentially contributing to favorable clinical outcomes of IDH-mutant glioma. In glioma, GLUD1 related clinical outcomes and immune landscape were clearer, and more valuable information was provided for immunotherapy.

Screening of potential targets and small-molecule drugs related to lipid metabolism in ovarian cancer based on bioinformatics

Backgroundabout 70 % of ovarian cancer (OC) patients with postoperative chemotherapy relapse within 2–3 years due to drug resistance and metastasis, and the 5-year survival rate is only about 30 %. Lipid metabolism plays an important role in OC. We try to explore the potential targets and drugs related to lipid metabolism to provide clues for the treatment of OC. Methodsthe gene expression profiles of OC and normal ovarian tissue samples were obtained from the cancer genome atlas (TCGA) and genotype-tissue expression databases (GTEx). The differentially expressed genes (DEGs) were analyzed. Lipid metabolism related genes (LMRGs) were downloaded from MSigDB database. The DEGs related to lipid metabolism in OC was obtained by intersection. And gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses were performed. The protein-protein interaction (PPI) network of lipid metabolism related DEGs was constructed, and seven algorithms were used to screen core potential target genes. Its expression in OC and prognostic ability were analyzed by Univariate Cox. Cmap database mining OC lipid metabolism related potential small-molecular drugs and docking. CCK8, scratch assay, transwell test and free fatty acid (FFA) assay, fluorescence detection of cellular fatty acid uptake, and the reactivity assay of CPT1A were used to detect the biological effects of drugs on OC cell.Rreverse transcription PCR(RT-qPCR) and WesternBlot were performed to measure the expression of core targets. Results437 DEGs related to lipid metabolism of OC were screened. GO and KEGG analysis showed that these DEGs were lipid metabolism, fatty acid metabolism, sphingolipid metabolism, PPAR signal pathway and so on. The PPI network based on lipid metabolism DEGs consists of 301 nodes and 1107 interaction pairs, and 6 core target genes were screened. ROC curve analysis showed that all of the 6 genes could predict the prognosis of OC. Three small molecular drugs Cephaeline, AZD8055 and GSK-1059615 were found by cmap and molecular docking showed that they all had good binding ability to target gene. Cephaeline has the strongest inhibitory effect on SKOV3 cells of OC, and could significantly inhibit cell migration and invasion regulate the mRNA and protein expression of some targets, and inhibit lipid metabolism process in ovarian cancer cells. Conclusionsix OC potential genes related to lipid metabolism were identified and verified, which can be used as potential biomarkers and therapeutic targets to evaluate the prognostic risk of OC patients. In addition, three small-molecular drugs that may be effective in the treatment of OC were unearthed, among which Cephaeline has the most potential. We speculate that Cephaeline may target six genes to inhibit progression of OC by affecting lipid metabolism.

Temporal analysis of water chemistry and smallmouth bass (Micropterus dolomieu) health at two sites with divergent land use in the Susquehanna River watershed, Pennsylvania, USA

Monitoring wild fish health and exposure effects in impacted rivers and streams with differing land use has become a valuable research tool. Smallmouth bass (Micropterus dolomieu) are a sensitive, indicator species that exhibit signs of immunosuppression and endocrine disruption in response to water quality changes and contaminant exposure. To determine the impact of agriculture and development on smallmouth bass health, two sites (a developed/agriculture site and a forested site) in the Susquehanna River watershed, Pennsylvania were selected where bass and water chemistry were sampled from 2015 to 2019. Smallmouth bass were sampled for histopathology to assess parasite and macrophage aggregate density in the liver and spleen, condition factor (Ktl), hepatic gene transcript abundance, hepatosomatic index (HSI), and a health assessment index (HAI). Land use at the developed/agriculture site included greater pesticide application rates and phytoestrogen crop cover and more detections and higher concentrations of pesticides, wastewater-associated contaminants, hormones, phytoestrogens, and mycotoxins than at the forested site. Additionally, at the developed/agriculture site, indicators of molecular changes, including oxidative stress, immune/inflammation, and lipid metabolism-related hepatic gene transcripts, were associated with more contaminants and land use variables. At both sites, there were multiple associations of contaminants with liver and/or spleen macrophage aggregate density, indicating that changes at the molecular level seemed to be a better indicator of exposures unique to each site. The findings illustrate the importance of timing for land management practices, the complex mixtures aquatic animals are exposed to, and the temporal changes in contaminant concentration. Agricultural practices that affect hepatic gene transcripts associated with immune function and disease resistance were demonstrated which could negatively affect smallmouth bass populations.

Brassinolide and gibberellin promote grape fruit development and quality

Brassinosteroid (BR) and Gibberellins (GA) are important hormones that significantly influences grapeberry development and ripening. In the present study, grape clusters were soaked separately with EBR (Epi brassinolide), GA3, and EBR+GA3 during fruit development. Results showed that anthocyanin content, soluble solids, and titratable acid content were all enhanced by EBR treatment, however fruit weight, transverse and longitudinal longitude, and hardness were not significantly changed, furthermore, GA3 treatment increased the fruit weight, longitudinal and transverse longitude, and hardness, decreased titratable acid, and increased the solid acid ratio; The EBR+GA3 significantly improved grape fruit quality, increased fruit anthocyanin content, reduced titratable acid content, improved sugar-acid ratio, and significantly improved fruit weight, transverse and longitudinal longitude, and hardness. EBR and GA3 treatment increased the contents of alcohols, esters, ketones, terpenes, and phenols in aroma substances, and glucose and fructose. They also increased the sugar, aroma, and anthocyanin metabolism-related genes, while down-regulated the expression of acid-related genes. EBR also increased the GA metabolism associated genes, but GA3 decereaed BR metabolism assocated genes. BR and GA had a crosstalk of that VvGAI could interact with VvBZR1, VvGAI could inhibit the VvBZR1 binding to the VvGA20ox2 promoter that decreased the VvGA20ox2 gene expression, but EBR and GA3 could alleviate the inhibition. In conclusion, both BR and GA alone could improve fruit quality to some extent, and the combination of them can better integrate the advantages of single-use to improve the fruit quality and enhance the commerciality of the grape fruit.

Zinc/Iron-Regulated Transporter-like Protein CsZIP4 Enhances Zinc and Nitrogen Uptake and Alleviates Zinc Stresses with Nitrogen Supply in Camellia sinensis.

Zinc (Zn) and nitrogen (N) are the two crucial nutrients for tea plant growth and development and contribute to the quality formation of tea fresh leaves. In this study, a zinc/iron-regulated transporter-like protein 4 gene (i.e., CsZIP4) was functionally characterized. Expression profiling showed that CsZIP4 could be induced by Zn stresses and a N deficiency. Heterologous expression of CsZIP4 in yeast revealed that CsZIP4 possessed the capacity for Zn transport but not ammonium. Moreover, CsZIP4 overexpression in Arabidopsis thaliana promoted Zn and N uptake and transport and contributed to alleviate Zn stresses by collaborating with N supply, which might be interrelated to the expression of N or Zn metabolism-related genes, such as AtNRT1.1 and AtZIP4. Additionally, CsZIP4 was localized in the plasma membrane and chloroplast, which was helpful in maintaining cellular homeostasis under a Zn excess. Furthermore, silencing of CsZIP4 in tea plants by virus-induced gene silencing increased the chlorophyll content but decreased the Zn content. Finally, the yeast one-hybrid assay demonstrated that CsbZIP2 bound to the CsZIP4 promoter. These results will shed light on the functions of CsZIP4 in the N and Zn interaction in tea plants.

Dynamic Brain Lipid Profiles Modulate Microglial Lipid Droplet Accumulation and Inflammation Under Ischemic Conditions in Mice.

Microglia are critically involved in post-stroke inflammation affecting neurological outcomes. Lipid droplet (LD) accumulation in microglia results in a dysfunctional and pro-inflammatory state in the aged brain and worsens the outcome of neuroinflammatory and neurodegenerative diseases. However, the role of LD-rich microglia (LDRM) under stroke conditions is unknown. Using in vitro and in vivo stroke models, herein accumulation patterns of microglial LD and their corresponding microglial inflammatory signaling cascades are studied. Interactions between temporal and spatial dynamics of lipid profiles and microglial phenotypes in different post-stroke brain regions are found. Hence, microglia display enhanced levels of LD accumulation and elevated perilipin 2 (PLIN2) expression patterns when exposed to hypoxia or stroke. Such LDRM exhibit high levels of TNF-α, IL-6, and IL-1β as well as a pro-inflammatory phenotype and differentially expressed lipid metabolism-related genes. These post-ischemic alterations result in distinct lipid profiles with spatial and temporal dynamics, especially with regard to cholesteryl ester and triacylglycerol levels, further exacerbating post-ischemic inflammation. The present study sheds new light on the dynamic changes of brain lipid profiles and aggregation patterns of LD in microglia exposed to ischemia, demonstrating a mutual mechanism between microglial phenotype and function, which contributes to progression of brain injury.

Molecular cross-talk among human intestinal bifidobacteria as explored by a human gut model.

Bifidobacteria are well known as common and abundant colonizers of the human gut and are able to exert multiple beneficial effects on their host, although the cooperative and competitive relationships that may occur among bifidobacterial strains are still poorly investigated. Therefore, to dissect possible molecular interactions among bifidobacterial species that typically colonize the human gut, three previously identified bifidobacterial prototypes, i.e., B. bifidum PRL2010, B. breve PRL2012, and B. longum PRL2022 were cultivated individually as well as in bi- and tri-association in a human gut-simulating medium. Transcriptomic analyses of these co-associations revealed up-regulation of genes predicted to be involved in the production of extracellular structures including pili (i.e., flp pilus assembly TadE protein gene), exopolysaccharides (i.e., GtrA family protein gene) and teichoic acids (i.e., ABC transporter permease), along with carbohydrate, amino acid and vitamin metabolism-related genes (i.e., exo-alpha-sialidase; beta-galactosidase and pyridoxamine kinase), suggesting that co-cultivation of bifidobacteria induces a response, in individual bifidobacterial strains, aimed at enhancing their proliferation and survival, as well as their ability to cooperate with their host to promote their persistence. Furthermore, exposure of the selected prototypes to human cell line monolayers unveiled the ability of the bifidobacterial tri-association to communicate with their host by increasing the expression of genes involved in adherence to/interaction with intestinal human cells. Lastly, bifidobacterial tri-association promoted the transcriptional upregulation of genes responsible for maintaining the integrity and homeostasis of the intestinal epithelial barrier.

Hydrogen sulfide alleviates pericarp browning in lichi fruit by modulating energy and sugar metabolisms.

Postharvest litchi is susceptible to browning that limits the development of litchi industry. Hydrogen sulfide (H2S) is an important bioactive molecule that can regulate many physiological processes. This study examined the effects of exogenous H2S on pericarp browning and related physiological mechanisms in postharvest litchi. The results exhibited that exogenous H2S treatment delayed the browning of litchi pericarp and reduced the damage to cell membrane integrity during storage. This treatment inhibited the energy losses of litchi fruit by increasing the activities of H+-ATPase, Ca2+- ATPase, cytochrome C oxidase (CCO) and succinate dehydrogenase (SDH) and regulating the expression of energy metabolism-related genes, including LcAtpB, LcSnRK2, LcAAC1, LcAOX1 and LcUCP1. In addition, H2S treatment increased the levels of fructose, glucose, sucrose, inositol, galactose and sorbose in litchi fruit, and promoted sucrose synthesis by regulating the activities of sucrose phosphate synthase (SPS), sucrose synthase (SS), acid invertase (AI) and neutral invertase (NI). Based on the current findings, we suggest that exogenous H2S enhances the energy supply and antioxidant activity of litchi by modulating energy and sugar metabolism, thereby inhibiting fruit browning and senescence. These results indicated that H2S treatment is an effective approach to maintaining the quality of litchi fruit and extending its shelf life.

Dynamic changes in pigmentation-related gene expression during morphogenesis in Plectropomus leopardus revealed by comparative transcriptome analysis

Plectropomus leopardus is a valuable marine aquaculture fish, prized by consumers for its high nutritional value and gorgeous appearance. The economic significance of this species is largely influenced by its body color, prompting researchers to become increasingly interested in understanding the mechanisms behind its color formation. However, previous studies have mainly focused on the molecular mechanisms of body color formation during the adult stage of this species. In this study, it was observed that the body color of P. leopardus undergoes four distinct stages during early morphogenesis: transparent (PT), red (PR), red with spots (PRS), and brown with spots (PBS). The L*a*b* values of skin at each stage differ significantly. The number and distribution of erythrophores and melanophores play a crucial role in determining the body colors of P. leopardus. Transcriptome analysis of the skin at these stages revealed multiple differentially expressed genes (DEGs) and signaling pathways related to pigmentation. These pigmentation-related DEGs can be categorized into carotenoid metabolism-related genes (e.g., scarb1, ldlr, plin2, apod, ttc39b, etc), melanin synthesis-related genes (e.g., tyr, tyrp1, dct, pmel, slc7a11, etc), and genes related to pigment cell development (pnp, ednrb, csf1r1, sox10, bnc2). GO and KEGG enrichment analysis indicated that processes like melanin synthesis (e.g., wnt signal pathway, melanogenesis, tyrosine metabolism, etc.), lipid metabolism (e.g., cholesterol metabolism, linoleic acid metabolism, arachidonic metabolism, fatty acid biosynthesis, etc.), and pigment cell development (e.g., pigment cell differentiation, cell development, etc.) are likely involved in the body color formation in P. leopardus. Finally, we proposed a hypothesis regarding carotenoid metabolism in erythrophores and melanin synthesis in melanophores of P. leopardus skin, drawing from existing research reports and transcriptome data. Overall, this study provides a new perspective on the molecular regulatory mechanisms of body color formation in P. leopardus, laying a theoretical foundation for molecular-assisted breeding of body color traits in this species.

Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation

Dinoflagellates, a class of unicellular eukaryotic phytoplankton, exhibit minimal transcriptional regulation, representing a unique model for exploring gene expression. The biosynthesis, distribution, regulation, and function of mRNA N1-methyladenosine (m1A) remain controversial due to its limited presence in typical eukaryotic mRNA. This study provides a comprehensive map of m1A in dinoflagellate mRNA and shows that m1A, rather than N6-methyladenosine (m6A), is the most prevalent internal mRNA modification in various dinoflagellate species, with an asymmetric distribution along mature transcripts. In Amphidinium carterae, we identify 6549 m1A sites characterized by a non-tRNA T-loop-like sequence motif within the transcripts of 3196 genes, many of which are involved in regulating carbon and nitrogen metabolism. Enriched within 3′UTRs, dinoflagellate mRNA m1A levels negatively correlate with translation efficiency. Nitrogen depletion further decreases mRNA m1A levels. Our data suggest that distinctive patterns of m1A modification might influence the expression of metabolism-related genes through translational control.

Influence of gut microbiome composition on effect variations of anti-cholesterol treatment among individual mice

This study investigated if the variation in the effect of anti-cholesterol (AC) treatment on individual mice are related to gut microbiome composition. The bile salt hydrolase (BSH) activity of 23 commercial fermented milk products was examined to select a fermented milk product for AC treatment. Mice were fed to different diets for 6 weeks: high-fat (660 % of total calories from fat; D1), high-dietary fibre (20 % cellulose; D2), and low-fat (17.2 % of total calories from fat; D3) diets to change their gut microbiomes. Subsequently, faecal microbiome was transplanted (FMT) into mice treated with high cholesterol diet contained 2 % cholesterol, followed by AC or non-AC (sterile tap water, STW) treatments. Control groups with normal (NC) and high-cholesterol diets (PC) were prepared for both AC and STW treatment. All experimental groups were subjected to serum and liver cholesterol, cholesterol metabolism-related (CMR) gene expression, and intestinal microbiome analyses. D3-FMT mice showed the most significant enhancements in cholesterol ratio and decreased hepatic cholesterol levels with AC treatment. Moreover, upregulation of the Cyp7a1 gene expression was observed in this group. Furthermore, the intestinal microbiome analysis indicated higher abundances of BSH-producing Eubacterium, Bifidobacterium, and Parabacteroides in the D3-FMT + AC group compare to others, potentially contributing to increased bile acid synthesis.

Integrated analysis reveals an aspartate metabolism-related gene signature for predicting the overall survival in patients with hepatocellular carcinoma.

Deregulating cellular metabolism is one of the prominent hallmarks of malignancy, with a critical role in tumor survival and growth. However, the role of reprogramming aspartate metabolism in hepatocellular carcinoma (HCC) are largely unknown. The multi-omics data of HCC patients were downloaded from public databases. Univariate and multivariate stepwise Cox regression were used to establish an aspartate metabolism-related gene signature (AMGS) in HCC. The Kaplan-Meier and receiver operating characteristic curve analyses were performed to evaluate the predictive ability for overall survival (OS) in HCC patients. Gene set enrichment analysis and immune infiltration analysis were operated to determine the potential mechanisms underlying the AMGS. Single-cell RNA sequencing (scRNA-seq) data of liver cancer stem cells were visualized by t-SNE algorithm. In vivo and in vitro experiments were implemented to investigate the biological function of CAD in HCC. In addition, a nomogram based on the AMGS and clinicopathologic characteristics was constructed by univariate and multivariate Cox regression analyses. Patients in the high-AMGS subgroup exerted advanced tumor status and poor prognosis. Mechanistically, the high-AMGS subgroup patients had significantly enhanced proliferation and stemness-related pathways, increased infiltration of regulatory T cells and upregulated expression levels of suppressive immune checkpoints in the tumor immune microenvironment. Notably, scRNA-seq data revealed CAD, one of the aspartate metabolism-related gene, is significantly upregulated in liver cancer stem cells. Silencing CAD inhibited proliferative capacity and stemness properties of HCC cells in vitro and in vivo. Finally, a novel nomogram based on the AMGS showed an accurate prediction in HCC patients. The AMGS represents a promising prognostic value for HCC patients, providing a perspective for finding novel biomarkers and therapeutic targets for HCC.