Clarification of the molecular mechanisms underlying glyphosate-induced major depressive disorder: a network toxicology approach.

Major depressive disorder (MDD) is predicted to become the second most common cause of disability in the near future. Exposure to glyphosate (Gly)-based herbicides has been linked to the onset of MDD. However, the underlying mechanisms remain unclear. The aim of this study was to investigate the potential molecular mechanisms of MDD induced by Gly using network toxicology approach. The MDD dataset GSE76826 from the Gene Expression Omnibus database was referenced to identify differentially expressed genes (DEGs) in peripheral blood leukocytes of MDD patients and controls. The potential intersection targets of Gly-induced MDD were screened by network toxicology. The intersection targets were used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and to construct protein-protein interaction networks. The binding potentials of hub targets with Gly were validated by molecular docking. In total, 1216 DEGs associated with Gly-induced MDD were identified. Subsequent network pharmacology further refined the search to 43 targets. GO and KEGG enrichment analyses revealed multiple signaling pathways involved in GLY-induced MDD. Six potential core targets (CD40, FOXO3, FOS, IL6, TP53, and VEGFA) were identified. Finally, molecular docking demonstrated that Gly exhibited strong binding affinity to the core targets. The results of this study identified potential molecular mechanisms underlying Gly induced MDD and provided new insights for prevention and treatment.

Identification and validation of DNA methylation-driven gene PCDHB4 as a novel tumor suppressor for glioblastoma diagnosis and prognosis.

Aberrant DNA methylation is a critical regulator of gene expression in the development and progression of glioblastoma (GBM). However, the impact of methylation-driven gene PCDHB4 changes on GBM occurrence and progression remains unclear. Therefore, this study aimed to identify the PCDHB4 gene for early diagnosis and prognostic evaluation and clarify its functional role in GBM. Methylation-driven gene PCDHB4 was selected for GBM using the multi-omics integration method based on publicly available data sets. The diagnostic capabilities of PCDHB4 methylation and 5-hydroxymethylcytosines were validated in tissue and blood cell-free DNA (cfDNA) samples, respectively. Combined survival analysis of PCDHB4 methylation and immune infiltration cells evaluated the prognostic predictive performance of GBM patients. We identified that the PCDHB4 gene achieved high discriminative capabilities for GBM and normal tissues with an area under the curve value of 0.941. PCDHB4 hypermethylation was observed in cfDNA blood samples from GBM patients. Compared with GBM patients with PCDHB4 hypermethylation level, patients with PCDHB4 hypomethylation level had significantly poorer overall survival (p = 0.035). In addition, GBM patients with PCDHB4 hypermethylation and high infiltration of CD4+ T cell activation level had a favorable survival (p = 0.026). Moreover, we demonstrated that mRNA expression of PCDHB4 was downregulated in GBM tissues and upregulated in GBM cell lines with PCDHB4 demethylation, and PCDHB4 overexpression inhibited GBM cell proliferation and migration. In summary, we discovered a novel methylation-driven gene PCDHB4 for the diagnosis and prognosis of GBM and demonstrated that PCDHB4 is a tumor suppressor in vitro experiments.

Molecular mechanisms of atrazine toxicity on H19-7 hippocampal neurons revealed by integrated miRNA and mRNA "omics".

Atrazine (ATR) is a widely applied herbicide in Asia and South America with slow natural degradation and documented deleterious effects on human and animal health, including hippocampal toxicity. However, relatively little is known about the molecular mechanisms responsible for ATR-induced hippocampal damage. Screening for differentially expressed mRNAs and microRNAs (miRNAs), and construction of potential miRNA-mRNA regulatory networks can reveal such mechanisms, so we analyzed the mRNA and miRNA expression profiles of rat hippocampus-derived H19-7 cells in response to ATR (500 µM) and conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes enrichment (KEGG) analyses. Integration of miRNA sequencing (miRNA-seq) and mRNA sequencing (mRNA-seq) results identified 114 differentially expressed miRNAs (DEMIs, 40 upregulated and 74 downregulated), and 510 differentially expressed mRNAs (DEMs, 177 upregulated and 333 downregulated) targeted by these DEMIs. The top 10 hub mRNAs (Fos, Prkcb, Ncf1, Vcam1, Atf3, Pak3, Pak1, Cacna1s, Junb, and Ccl2) and 19 related miRNAs (rno-miR-194-5p, rno-miR-24-3p, rno-miR-3074, rno-miR-1949, rno-miR-218a-1-3p, rno-miR-1843a-5p, rno-miR-1843b-5p, rno-miR-296-3p, rno-miR-320-3p, rno-miR-219a-1-3p, rno-miR-122-5p, rno-miR-1839-5p, rno-miR-1843a-3p, rno-miR-215, rno-miR-3583-3p, rno-miR-194-3p, rno-miR-128-1-5p, rno-miR-1956-5p, and rno-miR-466b-2-3p) were validated by quantitative real-time PCR. GO analysis indicated that these DEMs were enriched in genes associated with synaptic plasticity and antioxidant capacity, while KEGG analysis suggested that enriched DEMs were involved in calcium signaling, axon guidance, MAPK signaling, and glial carcinogenesis. The miRNA-mRNA regulatory network identified here may provide potential biomarkers and novel strategies for the treatment of hippocampal neurotoxicity induced by ATR.

Bioinformatics analysis of the potential mechanisms of Alzheimer's disease induced by exposure to combined triazine herbicides.

BACKGROUND: The development of Alzheimer's disease (AD) is promoted by a combination of genetic and environmental factors. Notably, combined exposure to triazine herbicides atrazine (ATR), simazine (SIM), and propazine (PRO) may promote the development of AD, but the mechanism is unknown. AIM: To study the molecular mechanism of AD induced by triazine herbicides. METHODS: Differentially expressed genes (DEGs) of AD patients and controls were identified. The intersectional targets of ATR, SIM, and PRO for possible associations with AD were screened through network pharmacology and used for gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analysis. The binding potentials between the core targets and herbicides were validated by molecular docking and molecular dynamics. RESULTS: A total of 1,062 DEGs were screened between the AD patients and controls, which identified 148 intersectional targets of herbicides causing AD that were screened by network pharmacology analysis. GO and KEGG enrichment analysis revealed that cell cycling and cellular senescence were important signalling pathways. Finally, the core targets EGFR, FN1, and TYMS were screened and validated by molecular docking and molecular dynamics. CONCLUSION: Our results suggest that combined exposure to triazine herbicides might promote the development of AD, thereby providing new insights for the prevention of AD.

Revealing the Mechanisms of Enhanced ß-Farnesene Production in Yarrowia lipolytica through Metabolomics Analysis.

ß-Farnesene is an advanced molecule with promising applications in agriculture, the cosmetics industry, pharmaceuticals, and bioenergy. To supplement the shortcomings of rational design in the development of high-producing ß-farnesene strains, a Metabolic Pathway Design-Fermentation Test-Metabolomic Analysis-Target Mining experimental cycle was designed. In this study, by over-adding 20 different amino acids/nucleobases to induce fluctuations in the production of ß-farnesene, the changes in intracellular metabolites in the ß-farnesene titer-increased group were analyzed using non-targeted metabolomics. Differential metabolites that were detected in each experimental group were selected, and their metabolic pathways were located. Based on these differential metabolites, targeted strain gene editing and culture medium optimization were performed. The overexpression of the coenzyme A synthesis-related gene pantothenate kinase (PanK) and the addition of four mixed water-soluble vitamins in the culture medium increased the ß-farnesene titer in the shake flask to 1054.8 mg/L, a 48.5% increase from the initial strain. In the subsequent fed-batch fermentation, the ß-farnesene titer further reached 24.6 g/L. This work demonstrates the tremendous application value of metabolomics analysis for the development of industrial recombinant strains and the optimization of fermentation conditions.

Integrating network pharmacology and in vitro model to investigate hippocampal neurotoxicity induced by atrazine.

Atrazine (ATR), a commonly applied herbicide in agriculture, has been found to cause hippocampal injury in rodents. However, the underlying toxicological targets and mechanisms are unclear. In this study, network pharmacology analysis and in vitro model were integrated to investigate the effect and mechanism of ATR-induced hippocampal neurotoxicity. In total, 71 targets of hippocampal neurotoxicity induced by ATR were predicted. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes enrichment (KEGG) enrichment analysis suggested that these targets were related to multiple GO terms and signaling pathways. To further investigate the underlying mechanisms, the top 10 hub targets were screened and included tumor protein p53 (Tp53), caspase 3 (Casp3), prostaglandin-endoperoxide synthase 2 (Ptgs2), cAMP-responsive element-binding protein 1 (Creb1), estrogen receptor 1 (Esr1), Jun proto-oncogene (Jun), brain-derived neurotrophic factor (Bdnf), catalase (Cat), sirtuin 1 (Sirt1) and Fos proto-oncogene (Fos). Moreover, the cell counting kit-8 (CCK8) and lactate dehydrogenase (LDH) assay showed that ATR had time and dose-dependent cytotoxicity on H19-7 cells. TUNEL staining revealed that ATR increased the apoptotic ratio. In addition, Real-time quantitative polymerase chain reaction (RT-qPCR) results indicated that the mRNA expression levels of all hub targets showed significant changes, except Esr1 and Jun. Our study demonstrated that ATR mainly acted on multiple targets and signaling pathways to exert its hippocampal neurotoxicity. These results provided initial evidence for the further exploration of the toxicological mechanism of ATR.

Nicotine-derived NNK induces the stemness enrichment of CRC cells through regulating the balance of DUSP4-ERK1/2 feedback loop.

Cigarette smoking has been considered as an independent risk factor for colorectal cancer (CRC) initiation and progression. In this study, we found that cigarette smoking was significantly associated with poor CRC differentiation (P = 0.040). Since studies have indicated that poorly differentiated tumors are more aggressive and metastasize earlier, leading to poorer prognosis; and cancer stem cells (CSCs) are largely responsible for tumor differentiation state, here we observed that the exposure of nicotine-derived 4-(methylnitrosamino)- 1-(3-pyridyl)- 1-butanone (NNK) promoted cell sphere formation and the expression of the stem cell markers, CD44, OCT4, C-MYC and NANOG in HCT8 and DLD-1 cells. Further colony formation assay, CCK-8 assay and tumor-bearing experiment showed that NNK exposure significantly increased the proliferative and growth ability of CRC cells. In mechanism, we found that NNK-activated ERK1/2 played an important role in enrichment of CRC stem cells and the up-regulation of DUSP4, a major negative regulator of ERK1/2. Moreover, DUSP4 up-regulation was essential for maintaining NNK-activated ERK1/2 in an appropriate level, which was an required event for NNK-induced stemness enrichment of CRC cells. Taken together, our findings provided a possible mechanistic insight into cigarette smoking-induced CRC progression.

DNA methylation of SFRP1, SFRP2, and WIF1 and prognosis of postoperative colorectal cancer patients.

BACKGROUND: As biomarkers, DNA methylation is used to detect colorectal cancer (CRC) and make assessment of CRC prognosis. The published findings showed the association between the methylation of SFRP1, SFRP2, and WIF1, located in the Wnt signaling pathway, and the prognosis of CRC were not consistent. Our study aimed to explore the potential possibility of SFRP1, SFRP2, and WIF1 concomitant promoter methylation as prognostic biomarkers of postoperative CRC patients. METHODS: As a total of 307 sporadic postoperative CRC patients were followed up, we detected SFRP1, SFRP2, and WIF1 methylation obtained from tumor tissues and adjacent non-tumor tissues respectively on the basis of methylation-sensitive high resolution melting analysis. Univariate and multivariate Cox regressions were carried out so as to assess the potential possibility of SFRP1, SFRP2, and WIF1 promoter methylation as predictors of prognosis. Confounders in our study were controlled by Propensity Score (PS) analysis. RESULTS: The SFRP1, SFRP2, and WIF1 methylation levels in tumor tissues were significantly higher than that in adjacent non-tumor tissues (P < 0.001). SFRP2 hypermethylation was significantly associated with a favorable clinical outcome at the hazard ratio (HR) of 0.343 [95% confidence intervals (CI): 0.164-0.718, P = 0.005] and 0.410 (95% CI: 0.200-0.842, P = 0.015) in multivariate Cox regression and PS analysis, respectively. Co-hypermethylation of SFRP1 and SFRP2 was significantly associated with a favorable clinical outcome at the HR of 0.333 (95% CI: 0.159-0.694, P = 0.003) and 0.398 (95% CI: 0.192-0.821, P = 0.013) in multivariate Cox regression and PS analysis, respectively. Co-hypermethylation of SFRP1, SFRP2 and WIF1 was significantly associated with a favorable clinical outcome at the HR of 0.326 (95% CI: 0.117-0.908, P = 0.032) and 0.401 (95% CI: 0.146-1.106, P = 0.077) in multivariate Cox regression and PS analysis, respectively. CONCLUSIONS: SFRP1, SFRP2, and WIF1 were frequently hypermethylated in CRC tumor tissues. It was apparent that the promoter hypermethylation of SFRP2 and co-hypermethylation of SFRP1 and SFRP2 might be considered as independent prognostic predictors for survival advantage of postoperative CRC patients.

CHST7 Gene Methylation and Sex-Specific Effects on Colorectal Cancer Risk.

BACKGROUND: X chromosome aberrations are involved in carcinogenesis and are associated with gender differences in cancer development. Abnormal DNA methylation also contributes to cancer. Carbohydrate Sulfotransferase 7 (CHST7), encoded by the X chromosome, is abnormally expressed during tumor development. However, its impact on colorectal cancer (CRC) and the effect of CHST7 methylation on sex-specific CRC risk remain unclear. AIMS: To investigate the effect of CHST7 methylation in white blood cells on CRC risk and to evaluate its impact on gender-specific differences. METHODS: CHST7 methylation in white blood cells was determined using methylation-sensitive high-resolution melting. A propensity score analysis was performed to control potential confounders. Furthermore, extensive sensitivity analyses were applied to assess the robustness of our findings. In addition, we validated the initial findings with a GEO dataset (GSE51032). RESULTS: CHST7 hypermethylation in white blood cells was associated with an increased CRC risk [odds ratio (OR)adj = 4.447, 95% confidence interval (CI) 2.662-7.430; p < 0.001]. The association was validated with the GEO dataset (ORadj = 2.802, 95% CI 1.235-6.360; p = 0.014). In particular, CHST7 hypermethylation significantly increased the CRC risk in females (ORadj = 7.704, 95% CI 4.222-14.058; p < 0.001) and younger patients (≤ 60 years) (ORadj = 5.755, 95% CI 2.540-13.038; p < 0.001). Subgroup analyses by tumor location and Duke's stage also observed these associations. CONCLUSION: CHST7 methylation in white blood cells is positively associated with CRC risk, especially in females, and may potentially serve as a blood-based predictive biomarker for CRC risk.

Engineering and manipulation of a mevalonate pathway in Escherichia coli for isoprene production.

Isoprene is a useful phytochemical with high commercial values in many industrial applications including synthetic rubber, elastomers, isoprenoid medicines, and fossil fuel. Currently, isoprene is on large scale produced from petrochemical sources. An efficient biological process for isoprene production utilizing renewable feedstocks would be an important direction of research due to the fossil raw material depletion and air pollution. In this study, we introduced the mevalonate (MVA) pathway genes/acetoacetyl-coenzyme A thiolase (mvaE) and MVA synthase (mvaS) from Enterococcus faecalis (E. faecalis); MVA kinase (mvk) derived from Methanosarcina mazei (M. mazei); and phosphomevalonate kinase (pmk), diphosphomevalonate decarboxylase (mvaD), and isopentenyl diphosphate isomerase (idi) from Streptococcus pneumoniae (S. pneumoniae) to accelerate dimethylallyl diphosphate (DMAPP) accumulation in Escherichia coli (E. coli). Together with a codon-optimized isoprene synthase (ispS) from Populus alba (P. alba), E. coli strain succeeded in formation of isoprene. We then manipulated the heterologous MVA pathway for high-level production of isoprene, by controlling the gene expression levels of the MVA pathway genes. We engineered four E. coli strains which showed different gene expression levels and different isoprene productivities, and we also characterized them with quantitative real-time PCR and metabolite analysis. To further improve the isoprene titers and release the toxicity to cells, we developed the extraction fermentation by adding dodecane in cultures. Finally, strain BL2T7P1TrcP harboring balanced gene expression system produced 587 ± 47 mg/L isoprene, with a 5.2-fold titer improvement in comparison with strain BL7CT7P. This work indicated that a balanced metabolic flux played a significant role to improve the isoprene production via MVA pathway.

The MEK/ERK/CREB signaling pathway is involved in atrazine induced hippocampal neurotoxicity in Sprague Dawley rats.

Atrazine (ATR) is a commonly used artificial synthetic herbicide world-wide, which has been implicated as a potential threat to human health. Previous studies have demonstrated that exposure to ATR affects hippocampus-dependent learning and memory in rodents, but the exact molecular mechanism remains to be elucidated. In this study, we investigated the effect of ATR on the hippocampus of postnatal day 35 male Sprague Dawley (SD) rats administered doses of either 10 or 100 mg/kg body weight (BW)/day of ATR for a period of 30 days. A Morris water maze (MWM) test revealed that ATR treatment impaired memory performance in the spatial probe test, especially amongst the high-dose group. Moreover, analysis by electron microscopy showed that hippocampal neuron ultrastructure in the dentate gyrus (DG) and cornu ammonis 1 (CA1) sub-regions was impaired in the ATR-treated groups. Finally, a downregulation in the mRNA and protein expression levels of members of the MEK/ERK/CREB pathway and downstream factors brain-derived neurotrophic factor (BDNF) and Zif268 was observed in hippocampal tissue following ATR treatment. Taken together, these results suggest that developmental exposure to ATR is able to induce functional and morphological lesions in the hippocampus of SD rats, and that the MEK/ERK/CREB signaling pathway may be involved in this process.

A novel DMAPP-responding genetic circuit sensor for high-throughput screening and evolving isoprene synthase.

High-throughput screening is a popular tool for collating biological data which would otherwise require the use of excessive resources. In this study, an artificial genetic circuit sensor responding to dimethylallyl diphosphate (DMAPP) was constructed based on a modified L-arabinose operon for high-throughput screening and isoprene synthase (ispS) evolution in Escherichia coli (E. coli). As a first step, the DNA sequence of the L-arabinose ligand-binding domain (LBD) was replaced with an ispS gene to enable the AraC operon responding to DMAPP, which is the substrate of the IspS enzyme. Then, an enhanced GFP (eGFP) was also introduced as a reporter for pBAD promoter. The expression level of the reporter was monitored using either of the two tools: flow cytometer (FCM) and microplate reader. Sequentially, we observed that a high DMAPP concentration led to low eGFP fluorescence, and the overexpression of ispS gene, which consumes DMAPP, resulted in a high eGFP expression. These results demonstrated that the artificial genetic circuit sensor responded directly to the intracellular concentration of DMAPP, and the expression of IspS enzyme could be positively correlated to the expression level of eGFP. Finally, we identified two IspS mutants with different activities from an ispS gene library and further validated the screening method.

Developmental Exposure to Atrazine Impairs Spatial Memory and Downregulates the Hippocampal D1 Dopamine Receptor and cAMP-Dependent Signaling Pathway in Rats.

Atrazine (ATR) is a widely used herbicide that has been implicated as a neurotoxicant. Recent experimental evidence has implicated that ATR exposure also appears to have adverse effects on the hippocampus, which is a critical region for learning and memory. The aim of the present study was to investigate the effects of ATR toxicity on the hippocampus of developing rats. Postnatal day (PND) 28 male Sprague⁻Dawley (SD) rats received ATR by oral gavage at 10 or 100 mg/kg bodyweight (BW) for 30 consecutive days and were sacrificed at PND 90. Behavioral test results indicated that spatial learning and memory were affected by ATR treatment. Electron microscopy analysis showed that the ultrastructures of the hippocampus were altered in the ATR-treated groups, as compared to the control group. Additionally, ATR treatment impacted dopamine and D1 dopamine receptor (D1DR) contents through different mechanisms. Reduced mRNA and protein expression levels of factors involved in the cAMP-dependent signaling pathway were also detected. These results indicate that the developmental exposure of rats to ATR can damage the hippocampus and spatial memory, which might be related to the downregulation of expression levels of the D1DR and its downstream signaling pathway.

Surfactant-assisted dilute ethylenediamine fractionation of corn stover for technical lignin valorization and biobutanol production.

In this study, a surfactant-assisted diluted ethylenediamine (EDA) fractionation process was investigated for co-generation of technical lignin and biobutanol from corn stover. The results showed that the addition of PEG 8000 significantly enhanced cellulose recovery (88.9 %) and lignin removal (68.9 %) in the solid fraction. Moreover, the pulp achieved 86.5 % glucose yield and 82.6 % xylose yield in enzymatic hydrolysis. Structural characterization confirmed that the fractionation process promoted the preservation of active ß-O-4 bonds (35.8/100R) in isolated lignin and functionalized the lignin through structural modification using EDA and surfactant grafting. The enzymatic hydrolysate of the pulps yielded a sugar solution for acetone-butanol-ethanol (ABE) fermentation, resulting in an ABE concentration of 15.4 g/L and an overall yield of 137.2 g/Kg of dried corn stalk. Thus, the surfactant-assisted diluted EDA fractionation has the potential to enhance the overall economic feasibility of second-generation biofuels production within the framework of biorefinery.

Identification of the mechanisms underlying per- and polyfluoroalkyl substance-induced hippocampal neurotoxicity as determined by network pharmacology and molecular docking analyses.

Background: Per- and polyfluoroalkyl substances (PFASs) are a class of environmental contaminants that pose significant health risks to both animals and humans. Although the hippocampal neurotoxic effects of numerous PFASs have been reported, the underlying mechanisms of combined exposure to PFASs-induced hippocampal neurotoxicity remain unclear. Methods: In this study, network pharmacology analysis was performed to identify the intersectional targets of PFASs for possible associations with hippocampal neurotoxicity. The evaluation of the influence of PFASs on intersectional targets was assessed using a weighted method. Additionally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the screened targets were performed, the intersected hub targets calculated by various algorithms were screened in the network and molecular docking was also used to analyze binding activities. Results: Our results indicated that eight PFASs, which acted on key targets (MYC, ESR1, STAT3, RELA, MAPK3) impacted the NF-κB signaling pathway, STAT3 signaling pathway, and MAPK signaling pathways to exert neurotoxicity in the hippocampus. The molecular docking results revealed that PFASs have strong binding potential to the hub targets. Conclusions: Our findings provided a basis for future studies to investigate the detailed mechanisms of PFASs-induced hippocampal neurotoxicity and to develop preventative and control strategies.

Metabolic Engineering for Effective Synthesis of 2-Hydroxyadipate.

Adipic acid is an important monomer in the synthesis of nylon-6,6. In recent years, the biosynthesis of adipic acid has received more and more attention. The pathway with l-lysine as a precursor has potential for adipic acid synthesis, and 2-hydroxyadipate is a key intermediate metabolite in this pathway. In this Letter, the biosynthesis pathway of 2-hydroxyadipate was constructed in Escherichia coli. Through enhancement of precursor synthesis and cofactors regulation, 7.11 g/L of 2-hydroxyadipate was produced in the 5 L bioreactor, which verified the scale-up potential of 2-hydroxyadipate production. Furthermore, 11.1 g/L of 2-hydroxyadipate was produced in the 5 L bioreactor on the basis of potential optimization strategies via transcriptome analysis. This is the first time for the biosynthesis of 2-hydroxyadipate. The results lay a solid foundation for the biosynthesis of adipic acid and the production of bionylon.

Fermentative Production of Diacylglycerol by Endophytic Fungi Screened from Taxus chinensis var. mairei.

Diacylglycerol (DAG) production by microbial fermentation has broad development prospects. In the present study, five endophytic fungi which could accumulate DAG were screened from Taxus chinensis var. mairei by using potato dextrose agar plate and flask cultivation in potato dextrose broth culture medium. The strains were biologically identified based on morphological features and semi-quantitative PCR. The identification results indicated that the five strains belonged to different genera: Fusarium annulatum (F. annulatum, coded as MLP41), Trichoderma dorotheae (T. dorotheae, coded as MLG23), Colletotrichum aeschynomenes (C. aeschynomenes, coded as MLY23), Pestalotiopsis scoparia (P. scoparia, coded as MLY31W), and Penicillium cataractarum (P. cataractarum, coded as MLGP11). The crude lipids from the strains and their corresponding triacylglycerol, 1,2-DAG, and 1,3-DAG fractions separated via thin-layer chromatography were mainly composed of palmitic acid, stearic acid, oleic acid, and linoleic acid, which in total accounted for higher than 94% of the content. The effects of fermentation conditions on the DAG productivity were discussed, and the yields of DAG were determined based on the 1H NMR spectra of crude lipids. The highest total DAG yields of F. annulatum, T. dorotheae, C. aeschynomenes, P. scoparia, and P. cataractarum were 112.28, 126.42, 189.87, 105.61, and 135.56 mg/L, respectively. C. aeschynomenes had the strongest potential to produce DAG. The results showed that this may be a new promising route for the production of DAG via fermentation by specific endophytic fungi, such as C. aeschynomenes.

Development and validation of cuproptosis molecular subtype-related signature for predicting immune prognostic characterization in gliomas.

PURPOSE: Cuproptosis, a novel programmed cell death, plays an important role in glioma growth, angiogenesis, and immune response. Nonetheless, the role of cuproptosis-related genes (CRGs) in the prognosis and tumor microenvironment (TME) of gliomas remains unknown. METHODS: By non-negative matrix factorization consensus clustering, 1286 glioma patients were classified based on the mRNA expression levels of 27 CRGs and investigated the association of immune infiltration and clinical characteristics with cuproptosis subtypes. A CRG-score system was constructed using LASSO and multivariate Cox regression methods and validated in independent cohorts to predict the prognosis of glioma patients. RESULTS: Glioma patients were divided into two cuproptosis subtypes. Cluster C2 was enriched in immune-related pathways, had higher macrophage M2, neutrophils, and CD8 + T cells, and poorer prognosis compared with cluster C1 which was enriched in metabolism-related pathways. We further constructed and validated the ten-gene CRG risk scores. Glioma patients in the high CRG-score group had higher tumor mutation burden, higher TME scores, and poorer prognoses compared with the low CRG-score group. Additionally, the AUC value of the CRG-score was 0.778 in predicting the prognosis of gliomas. WHO grading, IDH mutation, 1p/19q codeletion, and MGMT methylation were significant differences between high and low CRG-score groups. CONCLUSION: This study demonstrated that CRG-score was related to immune cell infiltration and could accurately predict gliomas' prognosis. Our findings may provide a novel understanding of the potential role of cuproptosis molecular pattern and TME in the immune response and prognosis of glioma patients.

Enhancing precursor supply and modulating metabolism to achieve high-level production of ß-farnesene in Yarrowia lipolytica.

ß-Farnesene is a sesquiterpene commonly found in essential oils of plants, with applications spanning from agricultural pest control and biofuels to industrial chemicals. The use of renewable substrates in microbial cell factories offers a sustainable approach to ß-farnesene biosynthesis. In this study, malic enzyme from Mucor circinelloides was examined for NADPH regeneration, concomitant with the augmentation of cytosolic acetyl-CoA supply by expressing ATP-citrate lyase from Mus musculus and manipulating the citrate pathway via AMP deaminase and isocitrate dehydrogenase. Carbon flux was modulated through the elimination of native 6-phosphofructokinase, while the incorporation of an exogenous non-oxidative glycolysis pathway served to bridge the pentose phosphate pathway with the mevalonate pathway. The resulting orthogonal precursor supply pathway facilitated ß-farnesene production, reaching 810 mg/L in shake-flask fermentation. Employing optimal fermentation conditions and feeding strategy, a titer of 28.9 g/L of ß-farnesene was attained in a 2 L bioreactor.

Association between the methylation of CpG islands in JAK-STAT pathway-related genes and colorectal cancer.

BACKGROUND: Aberrant promoter methylation of CpG islands plays an important role in carcinogenesis. However, the association between the DNA methylation of JAK-STAT pathway-related genes in peripheral blood leukocytes and colorectal cancer (CRC) susceptibility remains unclear. METHODS: We conducted a case-control study of 403 patients with CRC and 419 cancer free controls, and the DNA methylation levels of JAK2, STAT1, STAT3, and SOCS3 in peripheral blood samples from all subjects were assessed using a methylation-sensitive high-resolution melting (MS-HRM) analysis. RESULTS: Compared with controls, the methylation of the JAK2, STAT1 and SOCS3 genes increased the CRC risk (ORadjusted=1.96, 95% CI, 1.12-3.41, P=0.01; ORadjusted=5.37, 95% CI, 3.74-7.71, P<0.01; ORadjusted=3.30, 95% CI, 1.58-6.87, P<0.01). In the multiple CpG site methylation (MCSM) analysis, a high MCSM value denoted an increased CRC risk (ORadjusted=4.97, 95% CI, 3.34-7.37, P<0.01). CONCLUSION: In peripheral blood, the methylation of JAK2, STAT1, and high levels of MCSM are promising biomarkers for CRC risk.