Search Results (1,930)

The NAD⁺-dependent alcohol dehydrogenase AdhB from Aromatoleum aromaticum EbN1 belongs to family III of Fe-dependent alcohol dehydrogenases. It was recombinantly produced in Escherichia coli and biochemically characterized, showing activity only with ethanol or n-propanol. The enzyme contained substoichiometric amounts of Fe, Zn, and Ni and a yet unidentified nucleotide-like cofactor, as indicated by mass spectrometric data. As suggested by its narrow substrate spectrum and complementation of a related species to growth on ethanol, the most probable physiological function of AdhB is the oxidation of short aliphatic alcohols such as ethanol or n-propanol. The enzyme also exhibits a very high tolerance to ethanol and n-propanol, showing moderately substrate-inhibited Michaelis–Menten kinetics up to concentrations of 20% (v/v). AdhB can also be applied biotechnologically to convert acetate to ethanol in coupled enzyme assays with the tungsten enzyme aldehyde oxidoreductase, showing activity with either another aldehyde or pre-reduced benzyl viologen as electron donors. Full article

Lactiplantibacillus plantarum is a widely studied probiotic species with significant strain-specific functional diversity, yet the molecular mechanisms underlying these variations remain largely unexplored. In this study, whole genome sequencing (WGS) and untargeted metabolomics were employed to comprehensively characterize the genetic architecture and extracellular metabolic profile of Lp. plantarum FRT4 (CGMCC 17955), a probiotic strain previously studied for its metabolic effects in animal models. WGS revealed a circular chromosome and five plasmids, encoding 3301 protein-coding genes enriched in amino acid biosynthesis, carbohydrate metabolism, and environmental response pathways. Carbohydrate-active enzymes (CAZy) annotation revealed 135 carbohydrate-active enzyme genes, dominated by glycoside hydrolases and glycosyl transferases. Untargeted metabolomic analysis comparing the fermentation supernatant of FRT4 with non-inoculated MRS medium revealed significant alterations in metabolite composition, including elevated levels of acetylcholine, nicotinamide adenine dinucleotide (NAD), and trans-3-coumarate, and reduced levels of uridine, inosine, and fructose-1-phosphate, indicating active modulation of neurotransmission, redox balance, and purine metabolism. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment showed significant regulation of pathways related to amino acid metabolism, carbon metabolism, and cofactor biosynthesis. These findings highlight the metabolic versatility and functional potential of FRT4, offering mechanistic insights into its probiotic effects and providing a basis for its potential application in fermentation-based formulations. Full article

Bacillus cereus AS_3 and Bacillus cereus AS_5 are bacterial endophytes isolated from sterilized leaves of the medical plant Alectra sessiliflora, which were previously identified using 16S rRNA sequencing. Here, we present the whole-genome sequencing and annotation of strains AS_3 and AS_5, the first genome report of Bacillus cereus strains from A. sessiliflora. The genome of strain AS_3 has 59 contigs, 5 503 542 bp draft circular chromosome, an N₅₀ of 211,274 bp, and an average G+C content of 35.2%; whereas strain AS_5 has 38 contigs, 5,510,121 bp draft circular chromosome, an N₅₀ of 536,033 bp, and an average G+C content of 35.2%. A total of 5679 protein-coding genes, 62 genes coding for RNAs, and 122 pseudogenes in the strain AS_3 genome were identified by the National Center for Biotechnology Information Prokaryotic Annotation pipeline, whereas a total of 5688 gene protein-coding genes were identified in AS_5, with 60 genes coding for RNAs and 120 pseudogenes. Phenotypic analysis and whole-genome sequencing analysis showed that AS_3 and AS_5 share similar characteristics, including Gram-positive, motile, rod-shaped, and endospore-forming have shown a high sequence similarity with Bacillus cereus, type strain ATCC 14579^T. Strains AS_3 and AS_5 had genomic digital DNA–DNA hybridization (dDDH) with the type strain Bacillus cereus ATCC 14579^T of 85.8% and 86%, respectively, and average nucleotide identities (ANIs) of 98% and 98.01%, respectively. Phylogenomic analysis confirmed that strains AS_3 and AS_5 share very similar genomic and phenotypic characteristics, and are closely related to the type strain Bacillus cereus type strain ATCC 14579^T, supporting their classification within the Bacillus cereus species. A total of 10 secondary metabolite gene clusters, including siderophore type petrobactin, terpene type molybdenum cofactor, non-ribosomal peptide synthetase (NRPS) type bacillibactin, and β-lactone type fengycin, were predicted using AntiSMASH software (version 5.0). Putative genes potentially involved in bioremediation and endophytic lifestyle were identified in the genome analysis. Genome sequencing of Bacillus cereus AS_3 and Bacillus cereus AS_5 has provided genomic information and demonstrated potential biotechnological applications. Full article

Currently, D-fructose (DF) is produced through enzymatic isomerization of beta-D-glucose (DG) under disadvantageous conditions (equilibrium conversion of 50%, costly separation, etc.). Alternatively, the two-step Cetus enzymatic process became a promising approach for producing high-purity DF. First, DG is oxidized to keto-glucose (kDG) using commercial pyranose 2-oxidase (P2Ox). To avoid the fast P2Ox inactivation by the in situ produced hydrogen peroxide, catalase is added to decompose this byproduct. The DG oxidation occurs with high conversion and selectivity, leading to kDG free of allergenic aldose compounds. Then, kDG is reduced to DF by using the NADPH cofactor and aldose reductase (ALR). This study aims to evaluate the continuous in situ regeneration of NADPH at the expense of formate decomposition in the presence of formate dehydrogenase (FDH). By adopting a kinetic model from literature, this in silico analysis determines the optimal operation of a batch reactor (BR) used in the Cetus second step to maximize the DF production and minimize the consumption of costly NADPH. Compared to its simple operation, the optimized BR with cofactor regeneration reported a 25% lower NADPH consumption, though the amount of the processed substrate is ca. 3× higher. Also, the costly enzymes (ALR, FDH) consumption is 2× smaller. Full article

The undifferentiated nasopharyngeal cancer (NPC) is a multifactorial disease mainly due to Epstein-Barr Virus (EBV) infection. The transmembrane tyrosine kinase ‘EphA2’ and the protease ‘Furin’ are implicated in the EBV entry into epithelial cells and other physiological processes. To gain insights into the association of single-nucleotide polymorphisms (SNPs) rs4702 and rs6603883 (FURIN and EPHA2 genes, respectively) with the risk and prognosis of the NPC, the genotypes of 471 individuals (228 cases and 243 controls) were assessed alongside risk cofactors (sex, tobacco, alcohol, occupation, and recurrent Ear, Nose and Throat infections) and prognosis cofactors (Tumor stage, local invasion, lymph node involvement, and metastasis) using multivariable logistic regression. We found that only the rs4702 AG/GG genotypes were statistically significantly associated with a reduced risk of cancer, both in the overall population and in men (approximately 50% reduction). The rs4702 GG genotype was also associated with a low frequency of local tumor invasion in the whole population (OR = 0.382, p = 0.017, co-dominant model, and OR = 0.409, p = 0.02, recessive model), but heterozygous women were associated with a higher lymph node involvement (OR = 3.53, p = 0.031, co-dominant model, and OR = 3.62, p = 0.02, overdominant model). The rs6603883 GG genotype was associated, in the dominant model, with distant metastasis in the whole population (OR = 2.5, p = 0.024), with advanced clinical stage in men (OR = 2.22, p = 0.034), and with advanced clinical stage and distant metastasis in patients under 49 years (OR = 3.13, p = 0.009, and OR = 5.15, p = 0.011, respectively). Additionally, men having the rs6603883 GA genotype were associated with lymph node invasion (OR = 2.22, p = 0.027, overdominant model). Our study is the first to demonstrate that FURIN and EPHA2 germline gene polymorphisms are associated with NPC risk (for rs4702) and prognosis (for both rs4702 and rs6603883), with sex-specific differences. These results need to be replicated and further investigated in other populations. Full article

Antheraea pernyi (Lepidoptera: Saturniidae) is an economically important silk-producing insect, whose gut microbiota play a crucial role in growth, development, and nutrient metabolism. This study focused on the entire larval developmental stages of A. pernyi. Using the Illumina MiSeq high-throughput sequencing platform, we performed 16S rRNA gene amplicon sequencing on the gut microbiota of laboratory-reared A. pernyi larvae, analyzing in detail the composition and diversity characteristics of the gut microbial communities across all five instars (1st to 5th instar). Additionally, functional predictions were conducted to explore the potential roles of these microbiota during larvae development. The study revealed that the core gut microbiota of A. pernyi larvae primarily consisted of Actinomycetota (39.78%), Cyanobacteriota (32.46%), Bacillota (18.08%), and Pseudomonadota (9.02%). Among these, Actinomycetota dominated in the 1st to 4th-instar larvae, while Cyanobacteriota became the predominant phylum in the 5th instar. Linear discriminant analysis effect size identified statistically significant biomarkers across different instar larvae of A. pernyi. Alpha diversity analysis showed that gut microbiota diversity initially increased and then decreased with larval development, peaking in the 3rd instar, and reaching its lowest level in the 5th instar. Principal coordinate analysis (PCoA) of beta diversity indicated that the gut microbiota structures of the 1st to 4th instars were similar but significantly differed from that of the 5th instar. Functional prediction analysis based on the KEGG database revealed that Carbohydrate metabolism and Amino acid metabolism-related genes were significantly lower in the 5th instar compared to other instars, while Energy metabolism and Cofactor and vitamin metabolism-related genes were significantly higher. This study offers valuable insights for the development of gut microbial resources in Lepidoptera insects. Full article

Cylindrospermopsis raciborskii is a toxin-producing cyanobacterium that is easy to overlook. It has strong environmental adaptability and is currently spreading around the world and gradually dominating to form a persistent bloom, causing ecological and environmental risks and drinking water safety issues. In this study, we systematically investigated the inhibitory effects of oleic acid on C. raciborskii and elucidated the underlying mechanisms through morphological observation, physiological assays, and bioinformatics analysis. Our results demonstrated that oleic acid strongly inhibits the growth of C. raciborskii, with a 72 h half-maximal effective concentration (EC₅₀) of 0.903 mg·L⁻¹. At 1.6 mg·L⁻¹, oleic acid achieved an inhibition rate of 99.5% within 48 h, indicating rapid suppression of cyanobacterial growth. Physiological analyses revealed that oleic acid severely impaired photosynthetic activity, as evidenced by significant reductions in key parameters (rETRmax, α, Fv/Fm, and Fv/Fo) and altered photosynthetic pigment composition, suggesting structural and functional damage to the photosynthetic apparatus. Morphological observations further showed that oleic acid disrupted filament integrity, inducing cell shrinkage, cytoplasmic vacuolation, cell wall detachment, membrane rupture, and eventual cellular disintegration. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that oleic acid interferes with multiple metabolic processes, including nutrient and cofactor synthesis, membrane transport, and signal transduction, ultimately triggering algal cell death. This study highlights oleic acid as a promising eco-friendly agent for mitigating C. raciborskii blooms, offering potential applications in ecological prevention and emergency bloom control. Full article

Sand mining activities can significantly impact the microecology of rivers. Scientific studies are needed for the effective protection and restoration of river ecosystems impacted by sand mining activities. In this study, we used high-throughput sequencing technology to analyse the structure and function of sediment bacterial communities in three river habitats of the Jialing River Basin, namely, a natural river channel (no sand mining activities), a channel with continuous large-scale sand mining activities, and a channel in which sand mining had been terminated one year prior, as well as to analyse the main constraints leading to changes in sediment bacterial communities. The results revealed that the dominant bacteria in the different sand mining environments of the Jialing River were Proteobacteria, Chloroflexi, and Acidobacteria, and that total organic carbon (TOC), moisture content (MC) and total nitrogen (TN) were the main limiting factors affecting the structure of the bacterial community. In addition, large-scale sand mining activities caused significant changes (p < 0.05) in major secondary functions, such as energy metabolism, cofactor and vitamin metabolism, and translation. In summary, the persistence of large-scale sand mining activities led to heterogeneous changes in sediment bacterial community structure and function, which had an important impact on the stability of the ecosystem in the Jialing River Basin. Full article

To investigate the impacts of dietary Bacillus-based probiotics and yeast-derived prebiotics on the hepatic transcriptome profile, 500 Hisex White laying hens were randomly allotted into five dietary treatments from 37 to 52 weeks of age: control; control + Bacillus subtilis; control + Bacillus subtilis and Bacillus licheniformis; control + Bacillus coagulans; and control + Saccharomyces cerevisiae yeast cell wall. Transcriptome analysis revealed a substantial number of differentially expressed genes exclusively between the control and prebiotic groups, identifying 2221 genes (FDR ≤ 0.05), with 980 genes upregulated (log₂ fold change 0.69 to 24.62) and 1241 downregulated (log₂ fold change −0.74 to −26.46). The top 10 upregulated KEGG pathways included protein export, glycerophospholipid metabolism, tryptophan metabolism, amino acid biosynthesis, alanine, aspartate, and glutamate metabolism, cofactor biosynthesis, propanoate metabolism, ABC transporters, 2-oxocarboxylic acid metabolism, and protein processing within the endoplasmic reticulum. In contrast, the most prominently downregulated pathways encompassed fructose and mannose metabolism, hedgehog signaling, PPAR signaling, Notch signaling, GnRH signaling, cell adhesion molecules, cytokine–cytokine receptor interactions, apelin signaling, glycosaminoglycan degradation, and RIG-I-like receptor signaling. These findings advance understanding of the hepatic transcriptomic response to yeast-derived prebiotics and identify key molecular pathways that could be targeted to enhance metabolic function in laying hens. Full article

Copper ions serve as essential cofactors for many enzymes but exhibit toxicity at elevated concentrations. In Gram-negative bacteria, the Cop system, typically encoded by copABCD, plays a crucial role in maintaining copper homeostasis and detoxification. The chromosome of Pseudomonas putida harbors two copAB clusters but lacks copCD, along with two copR-copS clusters that encode the cognate two-component system. Here, the roles of these Cop components in countering copper toxicity were studied. We found that copAB2 was essential for full resistance to Cu²⁺ in P. putida, while copAB1 made only a minor contribution, partially due to its low expression. The two-component systems CopRS1 and CopRS2 both played significant regulatory roles in copper resistance. Although they could compensate for the absence of each other to mediate copper resistance, they exhibited distinct regulatory effects. CopR1 bound to all four cop promoters and activated their transcription under copper stress. In contrast, though CopR2 bound to the same sites as CopR1 in each cop promoter, it significantly activated only copAB2 and copRS2 expression. Its competitive binding at the copAB1 and copRS1 promoters likely impeded CopR1-mediated activation of these genes. Overall, this study reveals the distinct contributions of the two Cop systems to copper resistance and their regulatory interplay in P. putida. Full article

Treatment-resistant mental health concerns significantly contribute to society in terms of financial costs and individually by creating emotional and functional costs. An important yet little-recognized cause of treatment-resistant mental health conditions is tetrahydrobiopterin (BH4) deficiency. BH4 is an essential cofactor for producing serotonin, dopamine, norepinephrine, and nitric oxide—molecules critical to mood and focus. The enzyme GTP Cyclohydrolase 1 (GCH1), produced by a gene of the same name, catalyzes the first step in synthesizing BH4. Variants in this gene have been associated with low BH4 levels, as well as depression and ADHD. The case reports presented in this article illustrate that a partial BH4 deficiency, as conveyed by the GCH1 rs841 variant, may contribute to wider issues in mental and neurological health including depression and ADHD but also severe treatment-resistant anxiety, Premenstrual Dysphoric Disorder, insomnia, complex behavioral issues, and autism. The effects of GCH1-mediated BH4 deficiency may be able to be rescued with a low-dose BH4 replacement, as illustrated by these cases, where substantial observational improvements in mental health concerns were reported in all five cases. This paper also demonstrates how a genomics clinical decision support tool can non-invasively flag “low producers” by identifying individuals with the AA genotype for GCH1 rs841, as well as other modifiable genomic contributing factors to mental health concerns. These cases broaden the understanding of BH4′s psychiatric relevance and also serve to further the medical literature by documenting positive responses to low-dose BH4 (ranging from 0.09 to 0.3 mg/kg/day) and other genotype-guided interventions across diverse mental and neurological health presentations, highlighting the potential benefits and importance of a genomically targeted, precision approach to psychiatry. Full article

Phosphine (PH₃) is a fumigant often used to control insect pests, but its metabolic effects on insect physiology remain unclear. In this study, a comparative metabolomics analysis was performed to elucidate the physiological metabolic pathways affected by PH₃ exposure in Planococcus citri, and significant changes in the metabolic profiles induced by PH₃ treatment were identified. Principal component analysis and correlation analysis revealed different metabolic changes, and a total of 45 metabolites were identified and mapped to metabolic pathways using the KEGG database. PH₃ exposure inhibited energy metabolism by down-regulating riboflavin and flavin adenine dinucleotide, which are important cofactors in oxidative phosphorylation and reactive oxygen species generation. In addition, purine and pyrimidine metabolism, essential for nucleotide synthesis and cellular energy homeostasis, were also suppressed. Notably, lipid metabolism was significantly altered, and the juvenile hormone biosynthesis pathway was down-regulated. These results suggest that PH₃ inhibits electron transport chain activity, induces oxidative stress, and disrupts lipid homeostasis. This study enhances our understanding of the potential biomarkers of PH₃ exposure, the metabolic processes involved, and the resistance mechanisms that pests may develop in response to such exposure. Full article

MicroRNAs (miRNAs) are key post-transcriptional regulators controlling gene expression across several cellular processes, including development, proliferation, and apoptosis. Their biogenesis involves a multi-step pathway, including the processing of primary transcripts and the assembly of the RNA-Induced Silencing Complex (RISC) with Argonaute (AGO) proteins at its core. This review provides a comprehensive overview of the molecular dynamics of miRNA-loaded RISC (miRISC), focusing on the post-translational modifications, the interactors of AGOs and the mechanisms that fine-tune and coordinate miRISC activity. The composition of miRISC influences AGO stability, localization, and silencing efficiency, thereby maintaining cellular homeostasis and development and mediating the response to various types of cellular stress. Uncommon regulatory mechanisms, including AGO modifications during, e.g., hypoxia or Type 2 T cell responses and miRISC functionality, with myriad RNA-binding proteins (RBPs), will be discussed. This review aims at highlighting the recent advances in the understanding of the intricate regulation of miRISC-driven gene silencing. Full article

Poly(lactic acid)/barium titanate (PLA/BT) composites exhibit piezoelectric properties desirable for bone tissue engineering, but their low biodegradability limits implant resorption. In this study, riboflavin (RF) is introduced as a dual-function additive that enhances biodegradation in PLA/BT composites. Its addition led to significantly increased microbial colonization and a five-fold higher mass loss compared to unmodified samples. These observations are consistent with the known polarity of RF and its role as a cofactor in microbial metabolism. The PLA/BT/RF composites are subjected to full characterization, including thermogravimetric analysis (TG), differential scanning calorimetry (DSC), tensile testing, dynamic mechanical analysis (DMA), dielectric permittivity measurements, and determination of piezoelectric coefficient d₃₃. Compared to PLA/BT, RF-containing composites exhibit significantly accelerated biodegradation, with mass loss reaching up to 16% after 28 days, while maintaining functional piezoelectricity (d₃₃ ≈ 3.9 pC/N). Scanning electron microscopy (SEM) performed after biodegradation reveals intensified microbial colonization and surface deterioration in the RF-modified samples. The data confirm that riboflavin serves as an effective modifier, enabling controlled biodegradation without compromising electromechanical performance. These results support the use of PLA-based piezoelectric composites for resorbable biomedical implants. Full article

According to a recent experimental phenomenology–information processing theory, the sensory strength, or vividness, of visual mental images self-reported by human observers reflects the intensive variation in subjective time duration during the process of generation of said mental imagery. The primary objective of this study was to test the hypothesis that a biologically plausible essential multilayer perceptron (MLP) architecture can validly map the phenomenological categories of subjective time duration onto levels of subjectively self-reported vividness. A secondary objective was to explore whether this type of neural network cognitive modeling approach can give insight into plausible underlying large-scale brain dynamics. To achieve these objectives, vividness self-reports and reaction times from a previously collected database were reanalyzed using multilayered perceptron network models. The input layer consisted of six levels representing vividness self-reports and a reaction time cofactor. A single hidden layer consisted of three nodes representing the salience, task positive, and default mode networks. The output layer consisted of five levels representing Vittorio Benussi’s subjective time categories. Across different models of networks, Benussi’s subjective time categories (Level 1 = very brief, 2 = brief, 3 = present, 4 = long, 5 = very long) were predicted by visual imagery vividness level 1 (=no image) to 5 (=very vivid) with over 90% success in classification accuracy, precision, recall, and F1-score. This accuracy level was maintained after 5-fold cross validation. Linear regressions, Welch’s t-test for independent coefficients, and Pearson’s correlation analysis were applied to the resulting hidden node weight vectors, obtaining evidence for strong correlation and anticorrelation between nodes. This study successfully mapped Benussi’s five levels of subjective time categories onto the activation patterns of a simple MLP, providing a novel computational framework for experimental phenomenology. Our results revealed structured, complex dynamics between the task positive network (TPN), the default mode network (DMN), and the salience network (SN), suggesting that the neural mechanisms underlying temporal consciousness involve flexible network interactions beyond the traditional triple network model. Full article