Gene Expression In Metabolic Pathways Research Articles

Molecular disruptions in microalgae caused by Acidithiobacillus ferrooxidans: Photosynthesis, oxidative stress, and energy metabolism in acid mine drainage.

Microalgae are recognized for their potential in the bioremediation of acid mine drainage (AMD), despite the challenges posed by AMD's low pH, high heavy metal content, and oligotrophic conditions. However, the impact of AMD chemoautotrophic microorganisms on microalgal growth and remediation efforts within AMD has been largely overlooked. This study aims to elucidate the effects the chemoautotrophic microorganism, Acidithiobacillus ferrooxidans, on the growth activity and metabolism of acid-tolerant microalgae, and to explore the molecular mechanisms of microalgal response. Our findings reveal that the presence of A. ferrooxidans inhibits the growth and alkaline production of Parachlorella sp. MP1, resulting in a 90.86 % reduction in biomass. Physiological, biochemical, and transcriptomic studies, indicate that oxidative stress, photosynthesis, and energy metabolism are the metabolic processes most affected by A. ferrooxidans. Specifically, A. ferrooxidans introduces an increased production of reactive oxygen species (ROS) in Parachlorella sp. MP1, leading to an upregulation of genes and enzymes associated with peroxisome activity and intensifying oxidative stress within the cells. Downregulation of photosynthesis-related genes disrupts the electron transport chain, inhibiting photosynthesis. Furthermore, alterations in the gene expression of pyruvate and acetyl-CoA metabolic pathways result in energetic pathway disruption. These insights contribute to a better understanding of how A. ferrooxidans influence the growth metabolism of acid-tolerant microalgae in AMD environments and inform the optimization of microalgal application strategies in AMD bioremediation engineering.

7885 Thyroid Hormone Stimulates Heaptic Lipid Metabolism in the Resolution of Liver Fibrosis

Abstract Disclosure: A. Mendoza: None. C. Wang: None. A. Lugo: None. V. Rodrigues: None. S. Houghton: None. D. Redmond: None. A. Hollenberg: None. Metabolic dysfunction-associated steatotic liver disease (MASLD) progression to steatohepatitis and fibrosis is a global health burden, leading to liver failure and death. While the pathogenesis is complex, dysregulated lipid metabolism plays a crucial role. Thyroid hormones (THs) are key metabolic regulators in the liver, promoting lipogenesis and fatty acid oxidation. Previously, we demonstrated that the carbohydrate-responsive element binding protein (ChREBP) is a critical mediator of both these processes in hepatocytes, acting downstream of the thyroid hormone receptor beta1 (TRβ1). Interestingly, while ChREBP ablation abolished TH-induced lipogenesis through downregulation of lipogenic gene expression, its role in TH-mediated fatty acid oxidation remained unclear, suggesting a multifaceted role for ChREBP in TH-regulated hepatic metabolism. Given the critical role of lipid metabolism in the progression of MASLD to metabolic dysfunction-associated steatohepatitis (MASH) and fibrosis, we aim to delineate the mechanisms by which TH promotes the regression of fibrosis. Here, we used a carbon tetrachloride (CCL4) model of liver fibrosis in TRβ1KO and ChREBPKO mice (0.4 ul/g biweekly, 9 injections). All mice in the experiments were also on a PTU-Low Iodine diet to induce hypothyroidism. In the last week of the protocol, all mice were sorted into two groups which received either water or T3 (1ug/ml). 24 hours after the last CCL4 injection all mice were sacrificed and the livers were harvested and prepared for analysis. Herein we show that T3 promotes the resolution of liver fibrosis in wild-type mice. Importantly, this resolution was abolished in both TRβ1 and ChREBP KO mice demonstrating this pathways essential role in TH-induced resolution of fibrosis. RNA-Seq analysis of TRβ1KO mice demonstrated a dual mechanism of TH action: 1. TH upregulates gene expression in multiple metabolic pathways, suggesting a rescue of hepatic metabolism towards normal liver function and 2., TH has antifibrotic action via downregulation of pathways controlling extracellular matrix synthesis and inflammation, key drivers of fibrosis. Strikingly, ChREBP was dispensable for the antifibrotic action of TH suggesting that the ChREBP-dependent regulation of hepatic metabolism is critical for the resolution of fibrosis mediated by TH. To identify novel metabolic pathways regulated by TH via ChREBP, we intersected liver mRNA-seq from TRβ1KO mice with liver-specific ChREBP Chip-Seq and identifed multiple targets regulating autophagy that require ChREBP for their activation after TH treatment. These data suggest that the ability of ChREBP to regulate TH-induced fatty-acid oxidation is mediated by the upregulation of autophagy. This supports the notion that the ability of T3 to promote the resolution of liver fibrosis is primarily dependent of it’s ability to stimulate hepatic fatty acid metabolism. Presentation: 6/1/2024

Effects of Foliar Ca and Mg Nutrients on the Respiration of ‘Feizixiao’ Litchi Pulp and Identification of Differential Expression Genes Associated with Respiration

The ‘Feizixiao’ litchi cultivar, predominantly grown in Hainan Province, faces the issue of “sugar receding” during fruit ripening. The application of mixed foliar nutrients containing calcium and magnesium (Ca+Mg) during the fruit pericarp’s full coloring stage was investigated to overcome this issue. Experimental trials unveiled significant alterations in litchi pulp physiochemical properties, including the main nutrient and flavor quality, the total respiration rates of the main respiratory pathways, and the activities of some important enzymes associated with Embden–Meyerhof–Parnas (EMP), the tricarboxylic acid cycle (TCA) and the pentose phosphate pathway (PPP). The Ca+Mg treatment showed higher sugar levels than the control (CK) during ripening. Notably, the application of Ca+Mg in litchi pulp inhibited respiration rates through the EMP, TCA, and PPP pathways, resulting in a strong effect. RNA sequencing analysis revealed the impact of Ca+Mg treatment on respiratory pathways, revealing differentially expressed genes (DEGs) such as pyruvate PK1, PK2 (pyruvate kinase), and PDC (pyruvate dehydrogenase complex), validated through qRT-PCR with a significant correlation to RNA-seq results. In general, Ca+Mg treatment during litchi fruit ripening overcame “sugar receding” by inhibiting the expression of respiration key metabolic pathway genes. These findings provide insights for enhancing cultivation management strategies.

Rab4A-directed endosome traffic shapes pro-inflammatory mitochondrial metabolism in T cells via mitophagy, CD98 expression, and kynurenine-sensitive mTOR activation

Activation of the mechanistic target of rapamycin (mTOR) is a key metabolic checkpoint of pro-inflammatory T-cell development that contributes to the pathogenesis of autoimmune diseases, such as systemic lupus erythematosus (SLE), however, the underlying mechanisms remain poorly understood. Here, we identify a functional role for Rab4A-directed endosome traffic in CD98 receptor recycling, mTOR activation, and accumulation of mitochondria that connect metabolic pathways with immune cell lineage development and lupus pathogenesis. Based on integrated analyses of gene expression, receptor traffic, and stable isotope tracing of metabolic pathways, constitutively active Rab4AQ72L exerts cell type-specific control over metabolic networks, dominantly impacting CD98-dependent kynurenine production, mTOR activation, mitochondrial electron transport and flux through the tricarboxylic acid cycle and thus expands CD4+ and CD3+CD4−CD8− double-negative T cells over CD8+ T cells, enhancing B cell activation, plasma cell development, antinuclear and antiphospholipid autoantibody production, and glomerulonephritis in lupus-prone mice. Rab4A deletion in T cells and pharmacological mTOR blockade restrain CD98 expression, mitochondrial metabolism and lineage skewing and attenuate glomerulonephritis. This study identifies Rab4A-directed endosome traffic as a multilevel regulator of T cell lineage specification during lupus pathogenesis.

The flame retardant triphenyl phosphate alters the epigenome of embryonic cells in an aquatic in vitro model.

Triphenyl phosphate (TPhP) is an organophosphate flame retardant and plasticizer that is added to a wide variety of consumer and industrial products. It is also a ubiquitous environmental pollutant. Exposure to TPhP has been shown to alter gene expression in metabolic and estrogenic signaling pathways in in vitro and in vivo models of a variety of species, and as such, is considered to be an endocrine disrupting chemical. Exposure to endocrine disrupting chemicals is increasingly being associated with changes to the epigenome, especially during embryonic development. The aim of this study was to evaluate whether TPhP exposure in aquatic ecosystems has the ability to alter the epigenome in two immortal cell lines derived from trout (Oncorhynchus mykiss). This study assessed whether 24 h exposure to TPhP resulted in changes to histone modification and DNA methylation profiles in steelhead trout embryonic cells and rainbow trout gill epithelial cells. Results show that several epigenetic modifications on histone H3 and DNA methylation are altered in the embryonic cells following TPhP exposure, but not in the gill epithelial cells. Specifically, histone H3 acetylation, histone H3 mono-methylation and global DNA methylation were found to be reduced. The alterations of these epigenetic modification profiles in the embryonic cells suggest that exposure to TPhP during fetal development may alter gene expression in the developing embryo, likely in metabolic and estrogenic pathways. The impacts to the epigenome determined in this study may even carry multigenerational detrimental effects on human and ecosystem health, which requires further investigation.

Synergistic interplay of selenium (Se) and antimony (Sb)-oxidizing bacteria Bacillus sp. S3 alleviates the Sb toxicity in pak choi (Brassica chinensis L.) by limiting Sb uptake, enhancing antioxidant systems and regulating key metabolic pathways

Antimony (Sb) contamination is a serious environmental concern. To detoxify Sb(III) toxicity in crops, two common strategies used are application of exogenous selenium (Se) and inoculation of antimony oxidizing bacteria. However, the potential synergistic effects of these strategies in alleviating Sb(III) stress in plants have not been fully explored. In this study, we proposed a new strategy of co-applying Se with an Sb(III)-oxidizing bacteria, Bacillus sp. S3 to reduce the growth inhibition in pak choi in Sb(III)-contaminated soil. Our findings demonstrated that Se and Bacillus sp. S3 co-application significantly increased plant growth, reduced oxidative and osmotic stress, and enhanced the antioxidant contents of pak choi, compared to either Se or Bacillus sp. S3 alone under Sb(III) exposure. Furthermore, this co-application effectively limited Sb uptake (up to 81.03%) in pak choi roots and enhanced the subcellular distribution of Sb (up to 79.58%) in shoot cell walls. Fourier-transform infrared spectroscopy (FTIR) spectra confirmed that synergistic interplay of Se and Bacillus sp. S3 could facilitate the fixation of more Sb on the cell wall by increasing the number of functional groups present in the cell walls. Transcriptome analysis revealed that the synergistic interplay of Se and Bacillus sp. S3 also triggered gene expression in key metabolic pathways involved in the defense and detoxification response to Sb(III), including the cytochrome P450 metabolism and phenylpropanoid biosynthesis pathways. These findings provide valuable insight for reducing the hazardous effects of Sb on crop growth and yield, ultimately improving the food safety of vegetable crops.

An examination of the carbon metabolic pathways in Acinetobacter sp. TAC-1 in the context of poly (3-hydroxybutyrate-co-3-hydroxyvalerate) utilization

The present study aimed to unravel the carbon metabolism pathway of Acinetobacter sp. TAC-1, a heterotrophic nitrification-aerobic denitrification (HN-AD) strain that utilizes poly (3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) as a carbon source. Sodium acetate was employed as a control to assess the gene expression of carbon metabolic pathways in the TAC-1 strain. The results of genome sequencing demonstrated that the TAC-1 strain possessed various genes encoding carbon metabolic enzymes, such as gltA, icd, sucAB, acs, and pckA. KEGG pathway database analysis further verified the presence of carbon metabolism pathways, including the glycolytic pathway (EMP), pentose phosphate pathway (PPP), glyoxylate cycle (GAC), and tricarboxylic acid (TCA) cycle in the TAC-1 strain. The differential expression of metabolites derived from distinct carbon sources provided further evidence that the carbon metabolism pathway of TAC-1 utilizing PHBV follows the sequential process of PHBV (via the PPP pathway)→gluconate (via the EMP pathway)→acetyl-CoA (entering the TCA cycle)→CO2+H2O (generating electron donors and releasing energy). This study is expected to furnish a theoretical foundation for the advancement and implementation of novel denitrification processes based on HN-AD and solid carbon sources.

Transcriptomic analysis of the effect of shaking and tumbling degree on quality formation of Wuyi rock tea.

Shaking and tumbling are extremely important for the formation of the special flavor of Wuyi rock tea. In this study, we analyzed the effects of different shaking and tumbling degrees on the quality index content of tea leaves and determined changes in gene expression in tea leaves using RNA sequencing technology. On this basis, the correlation between gene expression intensities in tea leaves and tea quality index content was analyzed. The results showed that heavy shaking and tumbling (MW3) increased gene expression of metabolic pathways, biosynthesis of secondary metabolites, starch and sucrose metabolism, biosynthesis of amino acids, glycine, serine, and threonine metabolism, alpha-linolenic acid metabolism pathways and decreased gene expression of flavonoid biosynthesis, carbon fixation in photosynthetic organisms, phenylpropanoid biosynthesis, and plant hormone signal transduction pathways in tea leaves, which in turn increased the content of caffeine, soluble sugar, amino acid and decreased the content of flavone, tea polyphenol, catechin component in tea leaves; the opposite was true for light shaking and tumbling. Second, this study found that MW3 was more beneficial in improving the mellowness, sweetness, and fresh and brisk taste of tea leaves and reducing the bitterness of tea leaves. This study provides some references to guide the processing of Wuyi rock tea with different flavors. PRACTICAL APPLICATION: Heavy shaking and tumbling was more beneficial in improving the mellowness, sweetness, and fresh and brisk taste of tea leaves and reducing the bitterness of tea leaves. Therefore, the degree of shaking and tumbling in Wuyi production can be appropriately improved to produce high-quality tea and improve the economic benefits of tea.

Antibiotics, Sedatives, and Catecholamines Further Compromise Sepsis-Induced Immune Suppression in Peripheral Blood Mononuclear Cells.

We hypothesized that the immunosuppressive effects associated with antibiotics, sedatives, and catecholamines amplify sepsis-associated immune suppression through mitochondrial dysfunction, and there is a cumulative effect when used in combination. We thus sought to determine the impact of the exemplar drugs ciprofloxacin, propofol, and norepinephrine, used alone and in combination, at clinically relevant concentrations, on the ex vivo functionality of peripheral blood mononuclear cells (PBMCs) drawn from healthy, infected, and septic individuals. In vitro/ex vivo investigation. University laboratory. Healthy volunteers, infected (nonseptic) patients in the emergency department, and septic ICU patients. PBMCs were isolated from these subjects and treated with ciprofloxacin (100 µg/mL), propofol (50 µg/mL), norepinephrine (10 µg/mL), or all three drugs combined, with and without lipopolysaccharide (100 ng/mL) for 6 or 24 hours. Comparison was made between study groups and against untreated cells. Measurements were made of cell viability, cytokine production, phagocytosis, human leukocyte antigen-DR (HLA-DR) status, mitochondrial membrane potential, mitochondrial reactive oxygen species production, and oxygen consumption. Gene expression in immune and metabolic pathways was investigated in PBMCs sampled from healthy volunteers coincubated with septic serum. Coincubation with each of the drugs reduced cytokine production and phagocytosis in PBMCs isolated from septic patients, and healthy volunteers coincubated with septic serum. No effect was seen on HLA-DR surface expression. No cumulative effects were seen with the drug combination. Sepsis-induced changes in gene expression and mitochondrial functionality were not further affected by addition of any of the drugs. Drugs commonly used in critical care lead to significant immune dysfunction ex vivo and enhance sepsis-associated immunosuppression. Further studies are required to identify underlying mechanisms and potential impact on patient outcomes.

Combined analysis of metagenome and transcriptome revealed the adaptive mechanism of different golden Camellia species in karst regions

Camellia sect. Chrysantha is an important rare and protected plant species. Some golden Camellia species grow in karst soil while others grow in acidic soil. In order to study the adaptation mechanism of golden Camellia to the karst environment, four species of golden Camellia growing in the karst soil (Camellia pubipetala, Camellia perpetua, Camellia grandis, and Camellia limonia) and four species growing in the acidic soil (Camellia nitidissima, Camellia euphlebia, Camellia tunghinensis, and Camellia parvipetala) were selected for this study. Combining the metagenome and transcriptome, the structure and function of the rhizosphere microbial communities and the gene expression in roots of golden Camellia were analyzed. The results showed that the rhizosphere microbial communities in different golden Camellia were significantly different in abundance of Acidobacteria, Actinobacteria, Candidatus_Rokubacteria, Nitrospirae, Planctomycetes, and Candidatus_Tectomicrobia. The proportion of Candidatus_Rokubacteria was significantly higher in the rhizosphere soil of four species of golden Camellia grown in karst areas, compared to C. nitidissima, C. euphlebia, and C. tunghinensis. The linear discriminant analysis Effect Size showed that C. parvipetala was similar to karst species in the enrichment of ABC transporters and quorum sensing. During the transcriptome analysis, numerous upregulated genes in four karst species, including CYP81E, CHS, F3H, C12RT1, NAS, and CAD, were found to be enriched in the secondary metabolite synthesis pathway in the KEGG library, when compared to C. tunghinensis. This study provides information for plant adaptation mechanisms on the rhizosphere soil microbial composition and gene expression in secondary metabolic pathways to karst habitats and its distribution in karst areas.

Response of exogenous melatonin on transcription and metabolism of soybean under drought stress.

Amino acid metabolism is an important factor in regulating nitrogen source assimilation and source/sink transport in soybean. Melatonin can improve plant stress resistance, but whether it affects amino acid metabolism is not known. Therefore, this study investigated whether exogenous melatonin had an effect on amino acid metabolism of soybean under drought conditions and explored its relationship with yield. The treatments were normal water supply treatment (WW), drought stress treatment (D), drought stress and melatonin treatment group (D + M), sprayed with 100 μmol/L melatonin. The effects of melatonin on amino acid metabolism and grain filling were studied by physiological and omics experiments using Kangxian 9 (drought-sensitive variety) and Suinong 26 (drought-resistant variety) soybean cultivars. The results showed that drought stress decreased the activity of carbon and nitrogen metabolizing enzymes, which inhibited the accumulation of dry matter and protein, and decreased the yield. In the drought-sensitive soybean variety, glycoenzymes and amino acid synthetases synthetic genes were upregulated in melatonin-treated soybeans, hence carbon and nitrogen metabolism enzyme activity increased, increasing the carbohydrate and amino acid contents simultaneously. This resulted in higher dry matter and yield than drought-stressed soybean not treated with melatonin. In the drought-resistant variety, the grain weight per plant increased by 7.98% and 6.57% in 2020 and 2021, respectively, while it increased by 23.20% and 14.07% in the drought-sensitive variety during the respective years. In conclusion, melatonin treatment can enhance the activity of nitrogen and carbon metabolism and amino acid content by upregulating the expression of soybean metabolic pathway and related genes, thus increasing the yield of soybean under drought stress.

Integration of transcriptomics and proteomics to elucidate inhibitory effect and mechanism of rosmarinic acid from Perilla frutescens (L.) Britt. in treating Trichophyton mentagrophytes

BackgroundDermatophyte caused by Trichophyton mentagrophytes is a global disease with a growing prevalence that is difficult to cure. Perilla frutescens (L.) Britt. is an edible and medicinal plant. Ancient books of Traditional Chinese Medicine and modern pharmacological studies have shown that it has potential anti-fungi activity. This is the first study to explore the inhibitory effects of compounds from P. frutescens on Trichophyton mentagrophytes and its mechanism of action coupled with the antifungal activity in vitro from network pharmacology, transcriptomics and proteomics.MethodsFive most potential inhibitory compounds against fungi in P. frutescens was screened with network pharmacology. The antifungal activity of the candidates was detected by a broth microdilution method. Through in vitro antifungal assays screening the compound with efficacy, transcriptomics and proteomics were performed to investigate the pharmacological mechanisms of the effective compound against Trichophyton mentagrophytes. Furthermore, the real-time polymerase chain reaction (PCR) was applied to verify the expression of genes.ResultsThe top five potential antifungal compounds in P. frutescens screened by network pharmacology are: progesterone, luteolin, apigenin, ursolic acid and rosmarinic acid. In vitro antifungal assays showed that rosmarinic acid had a favorable inhibitory effect on fungi. The transcriptomic findings exhibited that the differentially expressed genes of fungus after rosmarinic acid intervention were mainly enriched in the carbon metabolism pathway, while the proteomic findings suggested that rosmarinic acid could inhibit the average growth of Trichophyton mentagrophytes by interfering with the expression of enolase in the glycolysis pathway. Comparison of real-time PCR and transcriptomics results showed that the trends of gene expression in glycolytic, carbon metabolism and glutathione metabolic pathways were identical. The binding modes and interactions between rosmarinic acid and enolase were preliminary explored by molecular docking analysis.ConclusionThe key findings of the present study manifested that rosmarinic acid, a medicinal compound extracted from P. frutescens, had pharmacological activity in inhibiting the growth of Trichophyton mentagrophytes by affecting its enolase expression to reduce metabolism. Rosmarinic acid is expected to be an efficacious product for prevention and treatment of dermatophytes.

Electromagnetic fields disrupt the pollination service by honeybees.

We assessed the effect that electromagnetic field (EMF) exerts on honeybees' pollination efficiency using field and laboratory experiments. First, we measured levels of gene and protein expression in metabolic pathways involved in stress and behavioral responses elicited by EMF. Second, we assessed the effect of EMF on honeybee behavior and seed production by the honeybee-pollinated California poppy and, lastly, by measuring the consequences of pollination failure on plants' community richness and abundance. EMF exposure exerted strong physiological stress on honeybees as shown by the enhanced expression of heat-shock proteins and genes involved in antioxidant activity and affected the expression levels of behavior-related genes. Moreover, California poppy individuals growing near EMF received fewer honeybee visits and produced fewer seeds than plants growing far from EMF. Last, we found a hump-shaped relationship between EMF and plant species richness and plant abundance. Our study provides conclusive evidence of detrimental impacts of EMF on honeybee's pollination behavior, leading to negative effects on plant community.

Pulmonary immune response regulation, genotoxicity, and metabolic reprogramming by menthol- and tobacco-flavored e-cigarette exposures in mice.

Menthol and tobacco flavors are available for almost all tobacco products, including electronic cigarettes (e-cigs). These flavors are a mixture of chemicals with overlapping constituents. There are no comparative toxicity studies of these flavors produced by different manufacturers. We hypothesized that acute exposure to menthol and tobacco-flavored e-cig aerosols induces inflammatory, genotoxicity, and metabolic responses in mouse lungs. We compared two brands, A and B, of e-cig flavors (PG/VG, menthol, and tobacco) with and without nicotine for their inflammatory response, genotoxic markers, and altered genes and proteins in the context of metabolism by exposing mouse strains, C57BL/6J (Th1-mediated) and BALB/cJ (Th2-mediated). Brand A nicotine-free menthol exposure caused increased neutrophils and differential T-lymphocyte influx in bronchoalveolar lavage fluid and induced significant immunosuppression, while brand A tobacco with nicotine elicited an allergic inflammatory response with increased Eotaxin, IL-6, and RANTES levels. Brand B elicited a similar inflammatory response in menthol flavor exposure. Upon e-cig exposure, genotoxicity markers significantly increased in lung tissue. These inflammatory and genotoxicity responses were associated with altered NLRP3 inflammasome and TRPA1 induction by menthol flavor. Nicotine decreased surfactant protein D and increased PAI-1 by menthol and tobacco flavors, respectively. Integration of inflammatory and metabolic pathway gene expression analysis showed immunometabolic regulation in T cells via PI3K/Akt/p70S6k-mTOR axis associated with suppressed immunity/allergic immune response. Overall, this study showed the comparative toxicity of flavored e-cig aerosols, unraveling potential signaling pathways of nicotine and flavor-mediated pulmonary toxicological responses, and emphasized the need for standardized toxicity testing for appropriate premarket authorization of e-cigarette products.

Transcriptome analysis of the biofilm formation mechanism of Vibrio parahaemolyticus under the sub-inhibitory concentrations of copper and carbenicillin

Biofilm formation of Vibrio parahaemolyticus enhanced its tolerance to the environment, but caused many serious problems to food safety and human health. In this paper, the effects of copper and carbenicillin (CARB) stress on the formation of the biofilms of V. parahaemolyticus organisms were studied, and RNA sequencing technology was used to compare the differences in transcriptome profiles of the biofilm-related genes of V. parahaemolyticus organisms under different sub-inhibitory stresses. The results proved that V. parahaemolyticus had a large growth difference under the two stresses, copper and CARB at 1/2 minimal inhibitory concentration (MIC), and it could form a stable biofilm under both stress conditions. The amount of biofilm formed under CARB stress was significantly higher than that of copper stress (p < 0.05). Based on the analysis of transcriptome sequencing results 323, 1,550, and 1,296 significantly differential expressed genes were identified in the three treatment groups namely 1/2 MIC CARB, Cu2+, and Cu2++CARB. Through COG annotation, KEGG metabolic pathway analysis and gene expression analysis related to biofilm formation, the functional pathways of transcriptome changes affecting V. parahaemolyticus were different in the three treatment groups, and the CARB treatment group was significantly different from the other two groups. These differences indicated that the ABC transport system, two-component system and quorum sensing were all involved in the biofilm formation of the V. parahaemolytic by regulating flagellar motility, extracellular polysaccharides and extracellular polymer synthesis. Exploring the effects of different stress conditions on the transcriptome of V. parahaemolyticus could provide a basis for future research on the complex network system that regulates the formation of bacterial biofilms.

The "Superoncogene" Myc at the Crossroad between Metabolism and Gene Expression in Glioblastoma Multiforme.

The concept of the Myc (c-myc, n-myc, l-myc) oncogene as a canonical, DNA-bound transcription factor has consistently changed over the past few years. Indeed, Myc controls gene expression programs at multiple levels: directly binding chromatin and recruiting transcriptional coregulators; modulating the activity of RNA polymerases (RNAPs); and drawing chromatin topology. Therefore, it is evident that Myc deregulation in cancer is a dramatic event. Glioblastoma multiforme (GBM) is the most lethal, still incurable, brain cancer in adults, and it is characterized in most cases by Myc deregulation. Metabolic rewiring typically occurs in cancer cells, and GBM undergoes profound metabolic changes to supply increased energy demand. In nontransformed cells, Myc tightly controls metabolic pathways to maintain cellular homeostasis. Consistently, in Myc-overexpressing cancer cells, including GBM cells, these highly controlled metabolic routes are affected by enhanced Myc activity and show substantial alterations. On the other hand, deregulated cancer metabolism impacts Myc expression and function, placing Myc at the intersection between metabolic pathway activation and gene expression. In this review paper, we summarize the available information on GBM metabolism with a specific focus on the control of the Myc oncogene that, in turn, rules the activation of metabolic signals, ensuring GBM growth.

Specificity of the innate immune responses to different classes of non-tuberculous mycobacteria.

Mycobacterium avium is the most common nontuberculous mycobacterium (NTM) species causing infectious disease. Here, we characterized a M. avium infection model in zebrafish larvae, and compared it to M. marinum infection, a model of tuberculosis. M. avium bacteria are efficiently phagocytosed and frequently induce granuloma-like structures in zebrafish larvae. Although macrophages can respond to both mycobacterial infections, their migration speed is faster in infections caused by M. marinum. Tlr2 is conservatively involved in most aspects of the defense against both mycobacterial infections. However, Tlr2 has a function in the migration speed of macrophages and neutrophils to infection sites with M. marinum that is not observed with M. avium. Using RNAseq analysis, we found a distinct transcriptome response in cytokine-cytokine receptor interaction for M. avium and M. marinum infection. In addition, we found differences in gene expression in metabolic pathways, phagosome formation, matrix remodeling, and apoptosis in response to these mycobacterial infections. In conclusion, we characterized a new M. avium infection model in zebrafish that can be further used in studying pathological mechanisms for NTM-caused diseases.

Nutritional geometry framework of sleep

AimsSleep is a fundamental physiological function and is essential for all animals. Sleep is affected by diet compositions including protein (P) and carbohydrates (C), but there has not been a systematic investigation on the effect of dietary macronutrient balance on sleep. Main methodsWe used the nutritional geometry framework (NGF) to explore the interactive effects on sleep of protein (P) and carbohydrates (C) in the model organism Drosophila. Both female and male flies were fed various diets containing seven ratios of protein-to-carbohydrates at different energetic levels for 5 days and sleep was monitored by the Drosophila Activity Monitor (DAM) system. Key findingsOur results showed that the combination of low protein and high carbohydrates (LPHC) prolonged sleep time and sleep quality, with fewer sleep episodes and longer sleep duration. We further found that the effects of macronutrients on sleep mirrored levels of hemolymph glucose and whole-body glycogen. Moreover, transcriptomic analyses revealed that a high-protein, low-carbohydrate (HPLC) diet significantly elevated the gene expression of metabolic pathways when compared to the LPHC diet, with the glycine, serine, and threonine metabolism pathway being most strongly elevated. Further studies confirmed that the contents of glycine, serine, and threonine affected sleep. SignificanceOur results demonstrate that sleep is affected by the dietary balance of protein and carbohydrates possibly mediated by the change in glucose, glycogen, glycine, serine, and threonine.

Proanthocyanidins Alleviate Cadmium Stress in Industrial Hemp (Cannabis sativa L.).

Industrial hemp (Cannabis sativa L.), an annual herbaceous cash crop, is widely used for the remediation of heavy metal-contaminated soils due to its short growth cycle, high tolerance, high biomass, and lack of susceptibility to transfer heavy metals into the human food chain. In this study, a significant increase in proanthocyanidins was found in Yunnan hemp no. 1 after cadmium stress. Proanthocyanidins are presumed to be a key secondary metabolite for cadmium stress mitigation. Therefore, to investigate the effect of proanthocyanidins on industrial hemp under cadmium stress, four experimental treatments were set up: normal environment, cadmium stress, proanthocyanidin treatment, and cadmium stress after pretreatment with proanthocyanidins. The phenotypes from the different treatments were compared. The experimental results showed that pretreatment with proanthocyanidins significantly alleviated cadmium toxicity in industrial hemp. The transcriptome and metabolome of industrial hemp were evaluated in the different treatments. Proanthocyanidin treatment and cadmium stress in industrial hemp mainly affected gene expression in metabolic pathways associated with glutathione metabolism, phenylpropanoids, and photosynthesis, which in turn altered the metabolite content in metabolic pathways of phenylalanine, vitamin metabolism, and carotenoid synthesis. The combined transcriptomic and metabolomic analysis revealed that proanthocyanidins mitigated cadmium toxicity by enhancing photosynthesis, secondary metabolite synthesis, and antioxidant synthesis. In addition, exogenous proanthocyanidins and cadmium ions acted simultaneously on EDS1 to induce the production of large amounts of salicylic acid in the plant. Finally, overexpression of CsANR and CsLAR, key genes for proanthocyanidins synthesis in industrial hemp, was established in Arabidopsis plants. The corresponding plants were subjected to cadmium stress, and the results showed that CsLAR transgenic plants were more tolerant to cadmium than the CsANR transgenic and wild-type Arabidopsis plants. The results showed that salicylic acid and jasmonic acid were increased in Arabidopsis overexpressing CsLAR compared to AT wild-type Arabidopsis, and levels of secondary metabolites were significantly higher in Arabidopsis overexpressing CsLAR than in AT wild-type Arabidopsis. These results revealed how proanthocyanidins alleviated cadmium stress and laid the foundation for breeding industrial hemp varieties with higher levels of proanthocyanidins and greater tolerance.

Loss of Serpina1 in Mice Leads to Altered Gene Expression in Inflammatory and Metabolic Pathways.

The SERPINA1 gene encodes alpha1-antitrypsin (AAT), an acute phase glycoprotein and serine protease inhibitor that is mainly (80–90%) produced in the liver. Point mutations in the SERPINA1 gene can lead to the misfolding, intracellular accumulation, and deficiency of circulating AAT protein, increasing the risk of developing chronic liver diseases or chronic obstructive pulmonary disease. Currently, siRNA technology can knock down the SERPINA1 gene and limit defective AAT production. How this latter affects other liver genes is unknown. Livers were taken from age- and sex-matched C57BL/6 wild-type (WT) and Serpina1 knockout mice (KO) aged from 8 to 14 weeks, all lacking the five serpin A1a-e paralogues. Total RNA was isolated and RNA sequencing, and transcriptome analysis was performed. The knockout of the Serpina1 gene in mice changed inflammatory, lipid metabolism, and cholesterol metabolism-related gene expression in the liver. Independent single-cell sequencing data of WT mice verified the involvement of Serpina1 in cholesterol metabolism. Our results from mice livers suggested that designing therapeutic strategies for the knockout of the SERPINA1 gene in humans must account for potential perturbations of key metabolic pathways and consequent mitigation of side effects.