Energy Metabolism Research Articles

Gene Expression Shifts in Emperor Penguin Adaptation to the Extreme Antarctic Environment.

Gene expression can accelerate ecological divergence by rapidly tweaking the response of an organism to novel environments, with more divergent environments exerting stronger selection and supposedly, requiring faster adaptive responses. Organisms adapted to extreme environments provide ideal systems to test this hypothesis, particularly when compared to related species with milder ecological niches. The Emperor penguin (Aptenodytes forsteri) is the only endothermic vertebrate breeding in the harsh Antarctic winter, in stark contrast with the less cold-adapted sister species, the King penguin (A. patagonicus). Assembling the first de novo transcriptomes and analysing multi-tissue (brain, kidney, liver, muscle, skin) RNA-Seq data from natural populations of both species, we quantified the shifts in tissue-enhanced genes, co-expression gene networks, and differentially expressed genes characterising Emperor penguin adaptation to the extreme Antarctic. Our analyses revealed the crucial role played by muscle and liver in temperature homeostasis, fasting, and whole-body energy metabolism (glucose/insulin regulation, lipid metabolism, fatty acid beta-oxidation, and blood coagulation). Repatterning at the regulatory level appears as more important in the brain of the Emperor penguin, showing the lowest signature of differential gene expression, but the largest co-expression gene network shift. Nevertheless, over-expressed genes related to mTOR signalling in the brain and the liver support their central role in cold and fasting responses. Besides contributing to understanding the genetics underlying complex traits, like body energy reservoir management, our results provide a first insight into the role of gene expression in adaptation to one of the most extreme environmental conditions endured by an endotherm.

Metal-Organic Nanomaterials for Tumor Metabolic Blockade and Image to Increase Tumor Therapy.

The abnormal energy metabolism level of a tumor reduces the efficiency of chemotherapy. Metal-organic nanomaterials (MONs) with high drug loading efficiency, easy processes of synthesis, and controlled drug release have shown great potential in metabolic blocking and enhancement of tumor therapy. These metal-organic nanomedicines have been reported to modulate glycolysis or oxidative phosphorylation to provide monotherapy or combined therapies in tumorous treatments. In addition, the encapsulation or coordination of fluorescent dyes into MONs endowed them with the imaging ability of tumor metabolism. Herein, this Perspective summarizes the progress of MONs as therapeutic agents or imaging probes for application during tumor metabolic blocking or imaging, providing solid inspiration for biomedical applications of effective biomaterials. In addition, the current drawbacks of MONs for further biological applications in the future were discussed, giving stimulation of innovation and development in biomedical applications of MONs.

Stress Response of Aphid Population Under Combined Stress of Cadmium and Lead and Its Effects on Development of Harmonia axyridis.

Heavy metal pollution is a serious global environmental issue. It threatens human and ecological health. Heavy metals can accumulate in the soil over extended periods and inevitably transfer through the food chain to herbivorous insects and their natural enemies, leading to various adverse effects. This study aimed to investigate the stress responses and biochemical metabolic changes of aphids and one of aphids' predators, ladybugs, under cadmium (Cd) and lead (Pb) stress by constructing a food chain of Vicia faba L., Megoura crassicauda, and Harmonia axyridis. The results showed that aphids and ladybugs had a notable accumulation of Cd2+ and Pb2+. Insects can adapt to heavy metal stress by regulating their energy metabolism pathways. Glycogen content in the first filial generation (F1) aphids decreased significantly, glucose content in the second filial generation (F2) to the fourth filial generation (F4) adult aphids significantly increased, and trehalose content in the F1 adult aphids increased significantly. Moreover, the relative expression levels of trehalase (TRE) and trehalose-6-phosphate synthase (TPS) in the F1 adult aphids were significantly higher than those in the control group, and the expression levels of TPS genes in the second filial generation to the fifth filial generation (F2 to F5) aphids decreased, suggesting that insects can resist heavy metal stress by regulating trehalose metabolism. The fertility of female aphids in all treatment groups was reduced compared to the control group. Additionally, the relative expression level of vitellogenin (Vg) was down-regulated in all aphid generations except the F1 aphids. There was interaction between heavy metal concentration and aphid generation, and it significantly affected the number of aphids' offspring and the expression of the aphid Vg gene. The developmental duration of the ladybugs from the second to fourth instars was prolonged, and the weight decreased significantly from the prepupa to the adult stages. These results contribute to understanding the effects of Cd2+-Pb2+ accumulation on phytophagous insects and higher trophic levels' natural enemies, laying the foundation for protecting natural enemies and maintaining ecosystem stability.

Unveiling the Metabolic Trajectory of Pig Feces Across Different Ages and Senescence.

Porcine models are increasingly recognized for their similarities to humans and have been utilized in disease modeling and organ grafting research. While extensive metabolomics studies have been conducted in swine, primarily focusing on conventional cohorts or specific animal models, the composition and functions of fecal metabolites in pigs across different age groups-particularly in the elderly-remain inadequately understood. In this study, an untargeted metabolomics approach was employed to analyze the fecal metabolomes of pigs at three distinct age stages: young (one year), middle-aged (four years), and elderly (eight years). The objective was to elucidate age-associated changes in metabolite composition and functionality under standardized rearing conditions. The untargeted metabolomic analysis revealed a diverse array of age-related metabolites. Notably, L-methionine sulfoxide levels were found to increase with age, whereas cytidine-5-monophosphate levels exhibited a gradual decline throughout the aging process. These metabolites demonstrated alterations across various biological pathways, including energy metabolism, pyrimidine metabolism, lipid metabolism, and amino acid metabolism. Collectively, the identified key metabolites, such as L-methionine sulfoxide and Cholecalciferol, may serve as potential biomarkers of senescence, providing valuable insights into the mechanistic understanding of aging in pigs.

Reconfiguring the Escherichia coli Electron Transport Chain to Enhance trans-2-Decenoic Acid Production.

trans-2-Decenoic acid is a pivotal α,β-medium-chain unsaturated fatty acid that serves as an essential intermediary in the synthesis of 10-hydroxy-2-decenoic acid and various pharmaceutical compounds. Biosynthesis yield of trans-2-decenoic acid by decanoic acid has significantly improved in recent years; however, the oxidative stress of Escherichia coli at high fatty acid concentrations restricts the conversion rate. Here, we introduced a combination of rational design and metabolic rewiring of the E. coli electron transport chain (ETC) to improve trans-2-decenoic acid production. Overexpressing ubiquinone (UbQ) biosynthesis genes enhanced the expression of ETC complex III: UbQ to reduce reactive oxygen species (ROS) accumulation. Furthermore, applying rotenone to inhibit ETC complex I improved the electron transfer efficiency of complex II. The integration of Vitamin B5 and B2 into the fermentation process increased the activities of fatty acyl-CoA synthetase (MaMACS) and fatty acyl-CoA dehydrogenase (PpfadE). Finally, the constructed E. coli BL21(DE3)(ΔfadBJR/pCDFDuet-1-PpfadE-MaMACS/pRSFDuet-1-sumo-CtydiI-ubiI) strain exhibited a 51.50% decrease in ROS and a 93.33% enhancement in trans-2-decenoic acid yield, reaching 1.45 g/L after 66 h, which is the highest yield reported for flask fermentation. This study reports the feasibility of rewiring the ETC regulation and energy metabolism to improve α,β-UCA biosynthesis efficiency.

Optimizing Energy and Protein Contents in A Leucaena (Leucaena leucocephala lam.) Leaf-Based Concentrate for Dairy Goats Fed Napier Grass (Pennisetum purpureum schumach) Basal Diet in Kenya

Dairy goats provide food and financial security through their milk and meat. The main basal diet for confined dairy goats in Kenya is Napier grass (Pennisetum purpureum Schumach). However, optimal milk production is hampered by the high cost of protein and energy supplements that are required while feeding the grass. The protein supplement affordability is of greater limitation among farmers, therefore use of protein-rich forages in a supplement can lower the concentrate cost. Information on the optimal protein and energy inclusion levels in a forage-based concentrate for dairy goats is hardly available in Kenya. A study was therefore conducted whereby Leucaena (Leucaena leucocephala Lam.) leaf hay was used as the main protein source in four concentrates formulated with crude protein (CP) content (gkg-1) and metabolizable energy (ME) levels (MJkg-1), respectively, of: 135, 12; 160, 10; 185, 8; and 210, 6; respectively. A fifth supplement was formulated, representing the commonly used cattle dairy meal (160 g CPkg-1 DM and 10 MJ MEkg-1 DM, respectively), using commercial sunflower seedcake as a protein source. The concentrates were fed at 300 gday-1 to lactating Toggenburg dairy goats on Napier grass basal diet, in a 5 x 5 Latin square design. The total dry matter intake by the goats was 1.059-1.128 kg DM/goat day-1, with a milk production of 221.3-285.5 mL/goat day-1. It was concluded that the appropriate CP and ME levels in the Leucaena-based concentrate are 135 gkg-1 DM and 12 MJkg-1 DM, respectively. It was recommended that other protein-rich forages be explored

The Effects of Concentrate Supplement Levels on Feed Utilization and Red Meat Production of Blackhead Somali Sheep Fed Natural Pasture Grass Hay as a Basal Diet.

In recent years, consumers have become aware of their health, and their preference has been rapidly changing to consume less fatty meat. Therefore, devising a strategy to produce lean meat is a concern in this study. One of the strategies, among others, for lean meat production is controlling the amount of supplements given to sheep. Hence, muscle (lean) and adipose tissue (fat) require different amounts of energy to lie down. This study was conducted to evaluate the effects of concentrate supplementation levels on feed utilization and red meat production in Blackhead Somali sheep (BHS) fed natural pasture grass hay as a basal diet. A total of 16 BHS sheep weighing 19.5±0.2kg (mean±SE) at the beginning of the experiment were kept for 90 days by feeding two levels (1% [T1] and 1.75% [T2] body weight [BW] of sheep) of supplement. The sheep were blocked according to their initial BW (IBW), and the supplements were randomly assigned within a block. At the end of the feeding period, all sheep were slaughtered, and carcass and non-carcass data were recorded. Data were analysed using the SAS software version 9.1 of PROC GLM programme. Sheep fed T1 and T2 consumed 6.1 and 8.2MJ/day metabolizable energy (ME), respectively, and 73.1 and 93.6g/day crude protein (CP), in that order. Consequently, sheep fed T2 produced 1.37kg extra BW by growing an average rate of 15g/day greater (p<0.0001) over their counterpart fed T1. They also produced 0.9kg, 0.8 cm2 and 2.64% heavier carcasses, a wider rib eye area and a higher intramuscular fat content (p<0.0001), respectively, over the sheep fed T1. On the other hand, the lean-to-fat ratio was significantly lower in sheep fed T2 than T1. In most parameters considered in this study, sheep fed T2 (1.75% BW) were superior, but its intramuscular fat (IMF) content was much higher than the limit that the consumers needed. Therefore, it can be concluded that 1% BW supplementation is enough for BHS to produce lean meat containing the optimal fat content in stall feeding condition.

Profiling of Key Hub Genes Using a Two-State Weighted Gene Co-Expression Network of 'Jao Khao' Rice under Soil Salinity Stress Based on Time-Series Transcriptome Data.

RNA-sequencing enables the comprehensive detection of gene expression levels at specific time points and facilitates the identification of stress-related genes through co-expression network analysis. Understanding the molecular mechanisms and identifying key genes associated with salt tolerance is crucial for developing rice varieties that can thrive in saline environments, particularly in regions affected by soil salinization. In this study, we conducted an RNA-sequencing-based time-course transcriptome analysis of 'Jao Khao', a salt-tolerant Thai rice variety, grown under normal or saline (160 mM NaCl) soil conditions. Leaf samples were collected at 0, 3, 6, 12, 24, and 48 h. In total, 36 RNA libraries were sequenced. 'Jao Khao' was found to be highly salt-tolerant, as indicated by the non-significant differences in relative water content, cell membrane stability, leaf greenness, and chlorophyll fluorescence over a 9-day period under saline conditions. Plant growth was slightly retarded during days 3-6 but recovered by day 9. Based on time-series transcriptome data, we conducted differential gene expression and weighted gene co-expression network analyses. Through centrality change from normal to salinity network, 111 key hub genes were identified among 1,950 highly variable genes. Enriched genes were involved in ATP-driven transport, light reactions and response to light, ATP synthesis and carbon fixation, disease resistance and proteinase inhibitor activity. These genes were upregulated early during salt stress and RT-qPCR showed that 'Jao Khao' exhibited an early upregulation trend of two important genes in energy metabolism: RuBisCo (LOC_Os10g21268) and ATP synthase (LOC_Os10g21264). Our findings highlight the importance of managing energy requirements in the initial phase of the plant salt-stress response. Therefore, manipulation of the energy metabolism should be the focus in plant resistance breeding and the genes identified in this work can serve as potentially effective candidates.

Characterization and Proteomic Analysis of Geobacter sulfurreducens PCA under Long-Term Electron-Donor Starvation

The natural environment of Geobacter sulfurreducens is oligotrophic and described as limiting in both electron donors and terminal electron acceptors (TEA). In previous studies we examined the effects of long-term TEA (fumarate) limitation, and in this study we examine long-term batch cultures under limiting electron donor. The microorganism survived under long-term electron donor (acetate) starvation, maintaining a stable population of ∼1–2 × 108 cells mL−1 for >650 days. Proteins that varied in abundance with a high level of statistical significance (p < 0.05) for stages between mid-log to survival phase (acetate starved) were identified using iTRAQ based mass spectroscopy. The most highly represented proteins that significantly increased in level in the survival phase cells are generally membrane-associated and are involved in energy metabolism and protein fate. These results document that changes in the outer and cytoplasmic membranes may help G. sulfurreducens survive during starvation through detection and transport of nutrients into the cell. A sizeable portion of the identified proteins with unknown or hypothetical function further suggest that much of the biological process involved in survival have yet to be fully understood. Geobacter sulfurreducens was also able to survive under long-term TEA-starvation conditions with ferric citrate as TEA and maintained a stable population of 1.5–3 × 107 cells mL−1 for >650 days. We also found that survival phase cells from fumarate-limiting conditions were able to quickly resuscitate and reduce metal such as ferric iron as compared to the mid-log phase cells.

Ketogenic β-hydroxybutyrate regulates β-hydroxybutyrylation of TCA cycle-associated enzymes and attenuates disease-associated pathologies in Alzheimer's mice.

Lysine β-hydroxybutyrylation (Kbhb) is a post-translational modification that has recently been found to regulate protein functions. However, whether and how protein Kbhb modification participates in Alzheimer's disease (AD) remains unknown. Herein, we carried out 4D label-free β-hydroxybutylation quantitative proteomics using brain samples of 8-month-old and 2-month-old APP/PS1 AD model mice and wild-type (WT) controls. We identified a series of tricarboxylic acid (TCA) cycle-associated enzymes including citrate synthase (CS) and succinate-CoA ligase subunit alpha (SUCLG1), whose Kbhb modifications were decreased in APP/PS1 mice at pathological stages. Sodium β-hydroxybutyrate (Na-β-OHB) treatment markedly increased Kbhb modifications of CS and SUCLG1 and their enzymatic activities, leading to elevated ATP production. We further found that Kbhb modifications at lysine 393 site in CS and at lysine 81 site in SUCLG1 were crucial for their enzymatic activities. Finally, we found that β-OHB levels were decreased in the brain of APP/PS1 mice at pathological stages. While ketogenic diet not only significantly increased β-OHB levels, Kbhb modifications and enzymatic activities of CS and SUCLG1, and ATP production, but also dramatically attenuated β-amyloid plaque pathologies and microgliosis in APP/PS1 mice. Together, our findings indicate the importance of protein Kbhb modification for maintaining normal TCA cycle and ATP production and provide a novel molecular mechanism underlying the beneficial effects of ketogenic diet on energy metabolism and AD intervention.

Exploring the potential role of microbiota and metabolites in acute exacerbation of chronic obstructive pulmonary disease

The acute exacerbation of chronic obstructive pulmonary disease seriously affects the respiratory system function and quality of life of patients. This study employed 16S rRNA sequencing and metabolomics techniques to analyze the respiratory microbiota and serum metabolites of COPD and AECOPD patients. The results showed that the microbial diversity in the respiratory tract of AECOPD patients was significantly lower than that of COPD patients, and the relative abundance of Bacteroidetes, Prevotella and Neisseria in the respiratory tract of AECOPD patients was significantly lower than that of COPD patients. However, the relative abundance of Haemophilus_D, Veillonella_A and Pseudomonas_E, in AECOPD patients was significantly higher than that of COPD patients, and the ability of respiratory microbiota in AECOPD patients to participate in alanine metabolism was significantly lower than that of COPD patients. Metabolome results further revealed that the serum alanine levels in AECOPD patients were significantly lower than those in COPD patients, and these differential metabolites were mainly involved in linoleic acid metabolism, protein digestion and absorption and regulation of lipolysis in adipocytes. In summary, the structural characteristics of respiratory microbiota in COPD and AECOPD patients are different from those in healthy populations, and their microbiota diversity decreases and microbial community structure and function will also undergo changes when acute exacerbations occur. In addition, the predicted microbial community function and metabolomics results indicate that the onset of AECOPD is mainly related to energy and amino acid metabolism disorders, especially alanine metabolism.

A lactate metabolism-related gene signature to diagnose osteoarthritis based on machine learning combined with experimental validation.

Lactate is gradually proved as the essential regulator in intercellular signal transduction, energy metabolism reprogramming, and histone modification. This study aims to clarify the diagnosis value of lactate metabolism-related genes in osteoarthritis (OA). Lactate metabolism-related genes were retrieved from the MSigDB. GSE51588 was downloaded from the Gene Expression Omnibus (GEO) as the training dataset. GSE114007, GSE117999, and GSE82107 datasets were adopted for external validation. Genomic difference detection, protein-protein interaction network analysis, LASSO, SVM-RFE, Boruta, and univariate logistic regression (LR) analyses were used for feature selection. Multivariate LR, Random Forest (RF), Support Vector Machine (SVM), and XGBoost (XGB) were used to develop the multiple-gene diagnosis models. 12 control and 12 OA samples were collected from the local hospital for re-verification. The transfection assays were conducted to explore the regulatory ability of the gene to the apoptosis and vitality of chondrocytes. Through the bioinformatical analyses and machine learning algorithms, SLC2A1 and NDUFB9 of the 273 lactate metabolism-related genes were identified as the significant diagnosis biomarkers. The LR, RF, SVM, and XGB models performed impressively in the cohorts (AUC > 0.7). The local clinical samples indicated that SLC2A1 and NDUFB9 were both down-regulated in the OA samples (both P < 0.05). The knockdown of NDUFB9 inhibited the viability and promoted the apoptosis of the CHON-001 cells treated with IL-1beta (both P < 0.05). A lactate metabolism-related gene signature was constructed to diagnose OA, which was validated in multiple independent cohorts, local clinical samples, and cellular functional experiments.

Energy Metabolic Profile in Oral Potentially Malignant Disorders and Oral Squamous Cell Carcinoma: A Preliminary Landscape of Warburg Effect in Oral Cancer.

We hypothesized that cell energy metabolic profiles correlate with normal, dysplastic, and tumor cell/tissue statuses and may be indicators of aggressiveness in oral squamous cell carcinoma (OSCC) cells. The energy-related proteins that were differentially expressed in human OSCC fragments (n = 3) and their adjacent epithelial tissue (TAE) were verified using mass spectrometry (MS). Immunohistochemistry for 4-hydroxynonenal (4-HNE) was performed to evaluate the oxidative stress patterns in OSCC (n = 10), epithelial dysplasia (n = 9), and normal epithelial (n = 4) biopsies. The metabolic energy profile of OSCC aggressiveness was investigated in human OSCC cell lines with different levels of epithelial-mesenchymal transition proteins. The genes associated with the proteins found by MS in this study were analyzed using survival analysis (OS), whereas the genes associated with a poorer prognosis were analyzed using context-specific expression, Gene Ontology (GO) and Cancer Hallmarks for function enrichment analysis. The rationale for all experimental approach was to investigate whether the variation in energy metabolism profile accompanies the different phenotypes (from epithelial to mesenchymal) during the epithelial-mesenchymal transition. All OSCC fragments exhibited an increase in glycolysis-related proteins and a decrease in mitochondrial activity compared to the TAE region (p < 0.05), probably due to the downregulation of pyruvate dehydrogenase and antioxidant proteins. Additionally, the OSCC cell lines with a mesenchymal profile (SCC4, SCC9, and SCC25) had a lower mitochondrial mass and membrane potential and generated lower levels of reactive oxygen and nitrogen species than the TAE region. When we analyzed 4-HNE, the reactive species levels were increased in the epithelial regions of OSCC and potentially malignant lesions. A decrease in the levels of 4-HNE/reactive species was observed in the connective tissue underlying the dysplastic regions and the OSCC invasion zone. Based on this scenario, aggressive OSCC is associated with high glycolytic and oxidative metabolism and low mitochondrial and antioxidant activities, which vary according to the differentiation level of the tumor cells and the stage of carcinogenesis.

Fecal microbiome analysis uncovers hidden stress effects of low stocking density on rainbow trout

BackgroundRecirculating aquaculture systems can cause chronic stress in fish when stocking density is too high. However, this study tested whether low stocking density can cause fish stress. Adult rainbow trout, with an average weight of 1.517 kg (± 0.39), were subjected to low (12 kg/m3 ± 0.94) and moderate (43 kg/m3 ± 2.03) stocking densities for 24 days in a recirculating system maintained at 15 °C. At the end of the experiment, fecal microbiome analysis was carried out using a 16S rRNA amplicon sequencing. Additionally, an untargeted plasma metabolomics analysis was conducted.ResultsThe moderate stocking density group harboured greater numbers of commensals, such as C. somerae, R. lituseburensis, and L. plantarum. In contrast, detrimental species such as S. putrifacens and P. putida were abundant in the low-stocking density fish. Functional microbiome profiling revealed vitamin B12 salvage and synthesis in moderate stocking densities, which may support intestinal tight junction function. Additionally, vitamin B1 biosynthesis pathways were more abundant in the moderate stocking density group, which may function towards oxidative energy metabolism and protect against oxidative stress. A complementary plasma metabolomics study, although done at slightly different stocking densities and duration, confirmed the presence of blood metabolic stress markers. Elevated levels of L-lactic acid and L-Norvaline, L-Valine, and L-glutamine, indicate low stocking density fish were under stress. Furthermore, a P4HA2 stress gene biomarker confirmed the occurrence of stress in low-density fish. This study suggests that low stocking density can induce stress in fish. Moreover, moderate stocking density leads to a distinct and beneficial fecal microbiome profile.ConclusionOur study highlights the potential benefits of optimizing the stocking density of fish in recirculating aquaculture systems. This can improve fish health and welfare, promoting a more resilient fecal microbiome.Graphical abstract

Development of Malate Biosensor-Containing Hydrogels and Living Cell-Based Sensors.

Malate is a key intermediate in the citric acid cycle, an enzymatic cascade that is central to cellular energy metabolism and that has been applied to make biofuel cells. To enable real-time sensing of malate levels, we have engineered a genetically encoded, protein-based fluorescent biosensor called Malon specifically responsive to malate by performing structure-based mutagenesis of the Cache-binding domain of the Citron GFP-based biosensor. Malon demonstrates high specificity and fluorescence activation in response to malate, and has been applied to monitor enzymatic reactions in vitro. Furthermore, we successfully incorporated Malon into redox polymer hydrogels and bacterial cells, enabling analysis of malate levels in these materials and living systems. These results show the potential for fluorescent biosensors in enzymatic cascade monitoring within biomaterials and present Malon as a novel tool for bioelectronic devices.

Activity of novel virus families infecting soil nitrifiers is concomitant with host niche differentiation.

Chemolithoautotrophic nitrifiers are model groups for linking phylogeny, evolution, and ecophysiology. Ammonia-oxidising bacteria (AOB) typically dominate the first step of ammonia oxidation at high ammonium supply rates, ammonia-oxidising archaea (AOA) and complete ammonia-oxidising Nitrospira (comammox) are often active at lower supply rates or during AOB inactivity, and nitrite-oxidising bacteria (NOB) complete canonical nitrification. Soil virus communities are dynamic but contributions to functional processes are largely undetermined. In addition, characterising viruses infecting hosts with low relative abundance, such as nitrifiers, may be constrained by vast viral diversity, partial genome recovery, and difficulties in host linkage. Here, we describe a targeted incubation study that aimed to determine whether growth of different nitrifier groups in soil is associated with active virus populations and if process-focussed analyses facilitate characterisation of high-quality virus genomes. dsDNA viruses infecting different nitrifier groups were enriched in situ via differential host inhibition. Growth of each nitrifier group was consistent with predicted inhibition profiles and concomitant with the abundance of their viruses. These included 61 high-quality/complete virus genomes 35-173kb in length with minimal similarity to validated families. AOA viruses lacked ammonia monooxygenase sub-unit C (amoC) genes found in marine AOA viruses but some encoded AOA-specific multicopper oxidase type 1 (MCO1), previously implicated in copper acquisition, and suggesting a role in supporting energy metabolism of soil AOA. Findings demonstrate focussed incubation studies facilitate characterisation of active host-virus interactions associated with specific processes and viruses of soil AOA, AOB and NOB are dynamic and potentially influence nitrogen cycling processes.

The Integrated Transcriptome Bioinformatics Analysis of Energy Metabolism-Related Profiles for Dorsal Root Ganglion of Neuropathic Pain.

Neuropathic pain (NP) is a debilitating disease and is associated with energy metabolism alterations. This study aimed to identify energy metabolism-related differentially expressed genes (EMRDEGs) in NP, construct a diagnostic model, and analyze immune cell infiltration and single-cell gene expression characteristics of NP. GSE89224, GSE123919, and GSE134003 were downloaded from the Gene Expression Omnibus. Differentially expressed genes (DEGs) analysis and an intersection with highly energy metabolism-related modules in weighted gene co-expression network analysis (WGCNA) was performed in GSE89224. Least absolute shrinkage and selection operator (LASSO), random forest, and logistic regression were used for model genes selection. NP samples were divided into high- and low-risk groups and different disease subtypes based on risk score of LASSO algorithm and consensus clustering analysis, respectively. Immune cell composition was estimated in different risk groups and NP subtypes. Datasets 134,003 were performed for identification of single-cell DEGs and functional enrichment. Cell-cell communications and pseudo-time analysis to reveal the expression profile of NP. A total of 38 EMRDEGs were obtained and are majorly enriched in metabolism about glioma and inflammation. LASSO, random forest, and logistic regression identified 6 model genes, which were Itpr1, Gng8, Socs3, Fscn1, Cckbr, and Camk1. The nomogram, based on six model genes, had a good predictive ability, concordance, and diagnostic value. The comparisons between different risk groups and NP subtypes identified important pathways and different immune cells component. The immune infiltration results majorly associated with inflammation and energy metabolism. Single-cell analysis revealed cell-cell communications and cells differentiation characteristics of NP. In conclusion, our results not only elucidate the involvement of energy metabolism in NP but also provides a robust diagnostic tool with six model genes. These findings might give insight into the pathogenesis of NP and provide effective therapeutic regimens for the treatment of NP.

Effects of Different Additives on the Chemical Composition, Fermentation Quality, Bacterial Community and Gene Function Prediction of Caragana korshinskii Kom. Silage

The aim of this study was to investigate the effects of Lentilactobacillus plantarum (LP), cellulase (CE), and xylanase (XE) supplementation on the fermentation quality, chemical composition, and bacterial community of Caragana korshinskii Kom. silage. Four groups were designed for the study. No additives were used in the control group (CK), and LP (1 × 106 cfu/g), CE (1 × 104 IU/g) and XE (2 × 105 IU/g) were added to the experimental groups on a fresh matter basis, with three replicates per group. To promote fermentation, 5% molasses was added to all of the groups. On days 15 and 60, fermentation quality, chemical composition and the bacterial community were analysed. The pH of groups CE and XE was lower than that of the CK group at 60 days. During ensiling, the lactic acid (LA) content in the experimental groups and the acetic acid (AA) content in the CK and LP groups increased. At 60 days, the dominant genera in the CK and LP groups was Weissella and the dominant genera in the CE and XE groups was Lentilactobacillus. At different times during silage, nucleotide metabolism was enhanced, whereas the metabolism of carbohydrate, amino acids, energy, cofactors and vitamins was inhibited in the LP group. However, the metabolism of amino acids, energy, cofactors and vitamins in the CE and XE groups was increased, whereas the metabolism of nucleotides was inhibited. In conclusion, LP, CE and XE could exert a positive effect on the fermentation quality of C. korshinskii Kom. silage by shifting the bacterial community composition.

Roles of Nitric Oxide and Brassinosteroid in Improving Fruit Quality during Postharvest: Potential Regulators?

Most postharvest fruits are highly perishable, which directly impairs fruit taste and causes an economic loss of fresh products. Thus, it is necessary to find effective techniques to alleviate this issue. Recently, nitric oxide (NO) and brassinosteroid (BR) have been developed as postharvest alternatives to improve fruit quality. This work mainly reviews the recent processes of NO and BR in improving fruit quality during postharvest. Exogenous NO or BR treatments delayed fruit senescence, enhanced disease resistance, and alleviated chilling injury in postharvest fruit, and potential physiological and biochemical mechanisms mainly include (1) enhancing antioxidant and defense ability, (2) affecting ethylene biosynthesis, (3) regulating sugar and energy metabolism, (4) mediating plant hormone signaling, and (5) regulating protein S-nitrosylation and DNA methylation. This review concludes the functions and mechanisms of NO and BR in improving postharvest fruit quality. Additionally, a specific finding is the possible crosstalk of applications of NO and BR during postharvest fruit storage, which provides new insights into the applicability of NO and BR for delaying fruit senescence, enhancing disease resistances of fruit, and alleviating chilling injury in postharvest fruit.

Role of blood metabolites in mediating the effect of gut microbiota on chronic gastritis.

Exploring the link between gut microbiota and chronic gastritis (CG), and assessing the potential mediating influence of blood metabolites. Using aggregated data from genome-wide association studies (GWAS), we performed a two-sample Mendelian randomization (MR) analysis to explore the genetic links between gut microbiota (412 types) and CG (623,822 cases). Furthermore, we utilized a two-step MR approach to measure the extent to which blood metabolites (1,400 types) mediate the impact of gut microbiota on CG. Through MR, we identified that three genetically predicted gut microbiota increased the risk of CG: the ubiquinol-8 biosynthesis pathway (OR 1.149, 95%CI 1.022-1.291), Odoribacter from the Porphyromonadaceae family (OR 1.260, 95%CI 1.044-1.523), and Coprococcus from the Lachnospiraceae family (OR 1.125, 95%CI 1.010-1.253). Currently, there is no evidence to suggest that genetically predicted CG affects the risk of gut microbiota. Four blood metabolites mediated the proportionate changes in genetically predicted gut microbiota: levels of 4-hydroxyphenylacetate levels by 14.9% (95% CI -0.559%, 30.3%), palmitoleate (16:1n7) levels, and the phosphate to alanine ratio together mediated the same microbiota by 6.97% (95% CI -1.61%, 15.6%) and 7.91% (95% CI -1.67%, 17.5%), while the phosphate to alanine ratio and X-12839 levels together mediated the same microbiota by 8.48% (95% CI -2.87%, 19.8%) and 10.7% (95% CI 0.353%, 21.1%). In conclusion, our research has confirmed a causal link between gut microbiota, blood metabolites, and CG. Metabolites such as 4-hydroxyphenylacetate levels, palmitoleate (16:1n7) levels, the phosphate to alanine ratio, and X-12839 levels have relatively significant mediating roles between gut microbiota and CG. These metabolites may influence the occurrence and development of CG by regulating inflammatory responses, energy metabolism, and gut barrier function. However, the majority of the influence of gut microbiota on CG remains unclear, necessitating further research into other potential mediating risk factors. Clinically, it is crucial to focus on patients suffering from CG who exhibit dysbiosis of gut microbiota.IMPORTANCEThe results indicate that interactions between particular gut microbiota and blood metabolites may significantly contribute to the onset and progression of CG. These findings offer new insights and potential targets for early diagnosis, personalized treatment, and prevention of CG.