Search Results (88)

This study analyzed the heavy metal tolerance and chromium reduction and the potential of plant growth to promote Rhizobium sp. OS-1. By genetic makeup, the Rhizobium strain is nitrogen-fixing and phosphate-solubilizing in metal-contaminated agricultural soil. Among the Rhizobium group, bacterial strain OS-1 showed a significant tolerance to heavy metals, particularly chromium (900 µg/mL), zinc (700 µg/mL), and copper. In the initial investigation, the bacteria strains were morphologically short-rod, Gram-negative, appeared as light pink colonies on media plates, and were biochemically positive for catalase reaction and the ability to ferment glucose, sucrose, and mannitol. Further, bacterial genomic DNA was isolated and amplified with the 16SrRNA gene and sequencing; the obtained 16S rRNA sequence achieved accession no. HE663761.1 from the NCBI GenBank, and it was confirmed that the strain belongs to the Rhizobium genus by phylogenetic analysis. The strain’s performance was best for high hexavalent chromium [Cr(VI)] reduction at 7–8 pH and a temperature of 30 °C, resulting in a total decrease in 96 h. Additionally, the adsorption isotherm Freundlich and Langmuir models fit best for this study, revealing a large biosorption capacity, with Cr(VI) having the highest affinity. Further bacterial chromium reduction was confirmed by an enzymatic test of nitro reductase and chromate reductase activity in bacterial extract. Further, from the metal biosorption study, an Artificial Neural Network (ANN) model was built to assess the metal reduction capability, considering the variables of pH, temperature, incubation duration, and initial metal concentration. The model attained an excellent expected accuracy (R² > 0.90). With these features, this bacterial strain is excellent for bioremediation and use for industrial purposes and agricultural sustainability in metal-contaminated agricultural fields. Full article

The dramatic increase in urban construction waste poses severe environmental challenges. Utilizing waste concrete to produce recycled aggregates (RA) for manufacturing recycled concrete (RC) represents an effective strategy for resource utilization. However, inherent defects in RA, such as high porosity, microcracks, and adherent old mortar layers, lead to significant performance degradation of the resulting RC, limiting its widespread application. Traditional methods for enhancing RA often suffer from limitations, including high energy consumption, increased costs, or the introduction of new pollutants. MICP offers an innovative approach for enhancing RC performance. This technique employs the metabolic activity of specific microorganisms to induce the formation of a three-dimensionally interwoven calcium carbonate gel network within the pores and on the surface of RA. This gel network can improve the inherent defects of RA, thereby enhancing the performance of RC. Compared to conventional techniques, this approach demonstrates significant environmental benefits and enhances concrete compressive strength by 5–30%. Furthermore, embedding mineralizing microbial spores within the pores of RA enables the production of self-healing RC. This review systematically explores recent research advances in microbial mineral gel network for improving RC performance. It begins by delineating the fundamental mechanisms underlying microbial mineralization, detailing the key biochemical reactions driving the formation of calcium carbonate (CaCO₃) gel, and introducing the common types of microorganisms involved. Subsequently, it critically discusses the key environmental factors influencing the effectiveness of MICP treatment on RA and strategies for their optimization. The analysis focuses on the enhancement of critical mechanical properties of RC achieved through MICP treatment, elucidating the underlying strengthening mechanisms at the microscale. Furthermore, the review synthesizes findings on the self-healing efficiency of MICP-based RC, including such metrics as crack width healing ratio, permeability recovery, and restoration of mechanical properties. Key factors influencing self-healing effectiveness are also discussed. Finally, building upon the current research landscape, the review provides perspectives on future research directions for advancing microbial mineralization gel techniques to enhance RC performance, offering a theoretical reference for translating this technology into practical engineering applications. Full article

Epigenetic modifications act as crucial regulators of gene activity and are influenced by both internal and external environmental factors, with diet being the most impactful external factor. On the other hand, cellular metabolism encompasses a complex network of biochemical reactions essential for maintaining cellular function, and it impacts every cellular process. Many metabolic cofactors are critical for the activity of chromatin-modifying enzymes, influencing methylation and the global acetylation status of the epigenome. For instance, dietary nutrients, particularly those involved in one-carbon metabolism (e.g., folate, vitamins B12 and B6, riboflavin, methionine, choline, and betaine), take part in the generation of S-adenosylmethionine (SAM), which represents the main methyl donor for DNA and histone methylation; α-ketoglutarate and ascorbic acid (vitamin C) act, respectively, as a co-substrate and cofactor for Ten-eleven Translocation (TET), which is responsible for DNA demethylation; and metabolites such as Acetyl-CoA directly impact histone acetylation, linking metabolism of the TCA cycle to epigenetic regulation. Further, bioactive compounds, such as polyphenols, modulate epigenetic patterns by affecting methylation processes or targeting epigenetic enzymes. Since diet and nutrition play a critical role in shaping epigenome functions and supporting human health, this review offers a comprehensive update on recent advancements in metabolism, epigenetics, and nutrition, providing insights into how nutrients contribute to metabolic balance, epigenome integrity maintenance and, consequently, disease prevention. Full article

Markov chain perturbation theory is a rapidly developing subfield of the theory of stochastic processes. This review outlines emerging applications of this theory in the analysis of stochastic models of chemical reactions, with a particular focus on biochemistry and molecular biology. We begin by discussing the general problem of approximate modeling in stochastic chemical kinetics. We then briefly review some essential mathematical results pertaining to perturbation bounds for continuous-time Markov chains, emphasizing the relationship between robustness under perturbations and the rate of exponential convergence to the stationary distribution. We illustrate the use of these results to analyze stochastic models of biochemical reactions by providing concrete examples. Particular attention is given to fundamental problems related to approximation accuracy in model reduction. These include the partial thermodynamic limit, the irreversible-reaction limit, parametric uncertainty analysis, and model reduction for linear reaction networks. We conclude by discussing generalizations and future developments of these methodologies, such as the need for time-inhomogeneous Markov models. Full article

Accelerating healing is a clinical goal in both acute and chronic non-healing skin wounds. We leveraged the public Recon database, which seeks to aggregate all of the metabolic pathways in the human body, to uncover whether increasing the supply of specific metabolites can bolster cellular metabolism and, in turn, enhance wound healing. The database was reduced to a set of 357 reactions and 339 metabolites that were better suited for human cells in culture. Monte Carlo simulations were performed to identify the impact of 25 different inputs on the metabolic fluxes within the cellular biochemical network. Biomass and ATP production were used as surrogate markers for cell proliferation and cell migration (an energy-intensive process), respectively, both of which are critical to wound healing. The subset of simulations yielding the highest ATP production or biomass production were those where glycine and/or glutamine uptake was increased. Maximizing ATP and biomass also generally increased oxygen uptake. Due to its low availability in chronic wounds, another set of simulations was carried out in which oxygen uptake was held constant to mimic the effect of a limited oxygen supply. However, even with this constraint, glycine and glutamine remained the most promising interventions. The predictions were tested in vitro using immortalized human keratinocytes. Amino acid uptake was tentatively increased by supplementing the base culture media with additional glycine and/or glutamine, with valine supplementation with a similar nitrogen load as a control. Glycine supplementation significantly increased cellular proliferation above the base media and accelerated wound closure rate in wound scratch assay. However, glutamine and valine supplementation did not improve these parameters above base media, and glutamine even suppressed the benefit of glycine in cultures supplemented with both amino acids. In conclusion, glycine supplementation enhances cellular processes that are associated with wound healing. Full article

Background: During the germination of soybean seeds, many biochemical metabolic reactions become extremely active, resulting in a series of physiological and biochemical activities, and the seeds being rich in nutrients. Studying the network and key genes that regulate the nutritional content of bean sprouts is particularly important. Methods: In this study, the nutrient contents of Dongnong 254 and Heze small beans were measured when the bean sprouts were 1 cm, 3 cm, 5 cm and 7 cm long, and transcriptome sequencing was performed. Results: Clustering and principal component analysis (PCA) revealed that the samples could be divided into three groups. The differences between Dongnong 254 and Heze small bean samples with sprout lengths of 5 cm and 7 cm were greater than those between materials. Through differential expression analysis, 18,472 differentially expressed genes (DEGs) in the material included 1816 unique DEGs, and a total of six clusters with statistical significance were identified, which were enriched in pathways related to photosynthesis and sugar metabolism. The 6938 DEGs among the materials included 1044 unique DEGs, and a total of nine statistically significant clusters were identified, which were mainly annotated in pathways related to photosynthesis, hormones and flavonoids. Three specific modules that were significantly related to the nutritional content of bean sprouts were identified via WGCNA. The connectivity and functional annotation of genes within the modules were calculated, and nine candidate genes were found, nine of which encoded transcription factors (Glyma.16G071900 (WD40), Glyma.17G172400 (bHLH), Glyma.18G148000 (AP2) and Glyma.01G003000 (MYB)). Conclusions: These research results provide a theoretical basis for an in-depth understanding of the molecular mechanisms of soybean sprout development and nutritional components and provide new genetic resources for the study of nutritional components in soybean sprouts. Full article

Routing and application mapping are critical stages in the design of continuous-flow microfluidic biochips (CFMBs). The routing stage determines the channel network connecting components and ports, while application mapping schedules fluid transportation and wash operations based on the designed biochip architecture. Existing methods typically handle these stages separately: routing focuses solely on physical metrics without considering subsequent scheduling requirements, while application mapping adopts one-shot scheduling strategies that can lead to suboptimal solutions. This paper proposes an integrated path-driven methodology that jointly optimizes routing and application mapping. For routing, we develop a hybrid particle swarm optimization algorithm that incorporates conflict awareness and channel utilization strategies. For application mapping, we introduce an iterative approach that leverages historical scheduling information to progressively optimize fluidic-handling and wash operations. Experimental results on both real and synthetic benchmarks demonstrate significant improvements over state-of-the-art methods, achieving reductions of 22.05% in total channel length, 21.79% in intersections, 21.97% in total delay time, and 8.30% in biochemical reaction completion time. The proposed methodology provides an effective solution for the automated design of CFMBs with enhanced physical and operational efficiency. Full article

Ischemic stroke (IS) is a high-mortality, multi-complication cardiovascular disease. Reducing brain injury and promoting neuronal repair after IS onset remain important challenges for current treatments. Our team previously found that PAS840, an extract from Periplaneta americana (L.), protects nerve function; this study further uses LC-MS/MS and peptidomics to analyze PAS840’s components and network pharmacology to predict its ischemic stroke (IS) therapeutic targets. We then employed Transwell, a biochemical kit, real-time quantitative polymerase chain reaction (RT-qPCR), and transcriptomics to investigate PAS840’s effects on migration ability, oxidative stress levels, and cellular pathways in mouse microglial cells (BV-2) following oxygen–glucose deprivation/reoxygenation (OGD/R) injury. Finally, using Evans blue staining, immunohistochemical analysis, and RT-qPCR, we investigated PAS840’s effects on the blood–brain barrier, inflammation pathways, and neural function in a transient middle cerebral artery occlusion (tMCAO) rat model. PAS840 components target multiple IS pathways, effectively inhibit NF-κB/NLRP3/Caspase-1/IL-1β inflammasome pathway activation in BV-2 cells following OGD/R, reduce cellular oxidative stress, inflammation, and pyroptosis, and improve cell viability and migration ability. PAS840 decreases NF-κB/NLRP3/Caspase-1/IL-1β inflammasome pathway expression in tMCAO rat brains, reduces inflammation, activates BDNF/VGF/NGR1/Erbb4 neurotrophic factor and vascular endothelial growth factor pathways, enhances neuronal cell viability, and effectively protects and repairs the blood–brain barrier. Full article

Class III peroxidases are plant-specific enzymes that play indispensable roles in catalyzing oxidative–reductive reactions, which are integral to numerous biochemical processes in plants. In this study, we identified 69 members of the class III peroxidase (POD) gene family in the Populus simonii genome and classified them into four subfamilies based on phylogenetic analysis. Chromosomal localization revealed that these PsPOD genes are unevenly distributed across 19 chromosomes, with chromosomes 3 and 7 harboring the highest densities. Conserved domain and motif analyses demonstrated that all PsPOD proteins contain the characteristic peroxidase domain and share highly conserved motif structures. Cis-acting element analysis of promoter regions revealed the presence of numerous regulatory elements associated with light responsiveness, phytohormone signaling, stress responses, and plant growth and development. Transcriptome data showed that the expression of PsPOD genes varies significantly across different tissues and organs and under various stress conditions, suggesting their involvement in both developmental processes and abiotic stress responses. These findings were further validated by qRT-PCR analysis of selected PsPOD genes. Notably, PsPOD45, PsPOD69, PsPOD33, and PsPOD64 were identified as central hub genes in the protein–protein interaction network, making them promising candidates for further functional characterization. Overall, this study provides a comprehensive overview of the PsPOD gene family in P. simonii, laying a solid foundation for future functional studies and offering valuable insights for comparative research in other plant species. Full article

Metabolism, the network of biochemical reactions that powers life, arose under conditions radically different from those on Earth today. Investigating its origins reveals how initially simple chemical processes gradually integrated nucleic acid and then protein catalysts, becoming progressively more complex and regulated until they evolved into the enzyme-rich systems observed in modern organisms. Here, we integrate multiple perspectives on the origin of metabolism, focusing primarily on an evolutionary trajectory from an RNA-based world, where ribozymes, metal ions, coenzymes, small peptides, and other small organic molecules worked in concert, to enzyme-driven metabolic networks. We also address the longstanding debates on whether these early metabolic pathways were largely autotrophic or heterotrophic, and consider so-called “pre-metabolisms” (non-enzymatic networks) as an alternative conceptual framework. We discuss key examples such as the Wood–Ljungdahl (W–L) pathway and the reverse tricarboxylic acid (TCA) cycle, both posited to function under early Earth conditions. Finally, we examine how the environment (e.g., minerals, clays, hydrothermal vents) shaped early metabolism, describe unresolved questions about the Last Common Ancestor’s catalytic repertoire and propose future directions that link geochemical insights with molecular biology and synthetic approaches. Full article

The presence of paracetamol (PCT) in aquatic environments has raised environmental concerns due to its incomplete removal in conventional wastewater treatment plants. This study evaluates the degradation kinetics of PCT using an ozonation system enhanced with blast furnace slags (BFSs) as a heterogeneous catalyst under acidic (pH 3), neutral (pH 7), and basic (pH 10) conditions. Experimental results show that a simple ozonation process achieves up to 85% PCT removal within 30 min, with the highest rates being observed at pH 10. The addition of BFSs increases the reaction rate constants by 20–30% across all pH levels, attributed to the catalytic activity of metallic oxides in BFSs, which promote radical-based degradation pathways. Biochemical oxygen demand (BOD5) and HPLC analyses confirm a significant reduction in PCT and its byproducts, while ozone consumption is optimized in the catalytic system. A hybrid kinetic modeling approach, integrating pseudo-first-order kinetics and a long short-term memory (LSTM) neural network, was developed and validated, demonstrating superior predictive accuracy (R² > 0.98) for PCT degradation dynamics compared with traditional models. Full article

Nicotinamide mononucleotide (NMN) has emerged as a promising non-natural cofactor with significant potential to transform biocatalysis, synthetic biology, and therapeutic applications. By modulating NAD⁺ metabolism, NMN offers unique advantages in enzymatic reactions, metabolic engineering, and regenerative medicine. This review provides a comprehensive analysis of NMN’s biochemical properties, mechanisms of action, and diverse applications. Emphasis is placed on its role in addressing challenges in multi-enzyme cascades, biofuel production, and the synthesis of high-value chemicals. The paper also highlights critical research gaps, including the need for scalable NMN synthesis methods, improved integration into enzymatic systems, and comprehensive toxicity studies for therapeutic use. Emerging technologies such as AI-driven enzyme design and CRISPR-based genome engineering are discussed as transformative tools for optimizing NMN-dependent pathways. Furthermore, the synergistic potential of NMN with synthetic biology innovations, such as cell-free systems and dynamic regulatory networks, is explored, paving the way for precise and modular biotechnological solutions. Looking forward, NMN’s versatility as a cofactor positions it as a pivotal tool in advancing sustainable bioprocessing and precision medicine. Addressing current limitations through interdisciplinary approaches will enable NMN to redefine the boundaries of metabolic engineering and therapeutic innovation. This review serves as a roadmap for leveraging NMN’s potential across diverse scientific and industrial domains. Full article

The gut microbiota, a complex ecosystem, is vital to host health as it aids digestion, modulates the immune system, influences metabolism, and interacts with the brain-gut axis. Various factors influence the composition of this microbiota. Enzymes, as essential catalysts, actively participate in biochemical reactions that have an impact on the gut microbial community, affecting both the microorganisms and the gut environment. Enzymes play an important role in the regulation of the intestinal microbiota, but the interactions between enzymes and microbial communities, as well as the precise mechanisms of enzymes, remain a challenge in scientific research. Enzymes serve both traditional nutritional functions, such as the breakdown of complex substrates into absorbable small molecules, and non-nutritional roles, which encompass antibacterial function, immunomodulation, intestinal health maintenance, and stress reduction, among others. This study categorizes enzymes according to their source and explores the mechanistic principles by which enzymes drive gut microbial activity, including the promotion of microbial proliferation, the direct elimination of harmful microbes, the modulation of bacterial interaction networks, and the reduction in immune stress. A systematic understanding of enzymes in regulating the gut microbiota and the study of their associated molecular mechanisms will facilitate the application of enzymes to precisely regulate the gut microbiota in the future and suggest new therapeutic strategies and dietary recommendations. In conclusion, this review provides a comprehensive overview of the role of enzymes in modulating the gut microbiota. It explores the underlying molecular and cellular mechanisms and discusses the potential applications of enzyme-mediated microbiota regulation for host gut health. Full article

Water exists in the beginning and hydrates all matter. Life emerged in water, requiring three essential components in compartmentalized spaces: (1) universal energy sources driving biochemical reactions and processes, (2) molecules that store, encode, and transmit information, and (3) functional players carrying out biological activities and structural organization. Phosphorus has been selected to create adenosine triphosphate (ATP) as the universal energy currency, nucleic acids for genetic information storage and transmission, and phospholipids for cellular compartmentalization. Meanwhile, proteins composed of 20 α-amino acids have evolved into extremely diverse three-dimensional forms, including folded domains, intrinsically disordered regions (IDRs), and membrane-bound forms, to fulfill functional and structural roles. This review examines several unique findings: (1) insoluble proteins, including membrane proteins, can become solubilized in unsalted water, while folded cytosolic proteins can acquire membrane-inserting capacity; (2) Hofmeister salts affect protein stability by targeting hydration; (3) ATP biphasically modulates liquid–liquid phase separation (LLPS) of IDRs; (4) ATP antagonizes crowding-induced protein destabilization; and (5) ATP and triphosphates have the highest efficiency in inducing protein folding. These findings imply the following: (1) hydration might be encoded in protein sequences, central to manifestation and modulation of protein structures, dynamics, and functionalities; (2) phosphate anions have a unique capacity in enhancing μs-ms protein dynamics, likely through ionic state exchanges in the hydration shell, underpinning ATP, polyphosphate, and nucleic acids as molecular chaperones for protein folding; and (3) ATP, by linking triphosphate with adenosine, has acquired the capacity to spacetime-specifically release energy and modulate protein hydration, thus possessing myriad energy-dependent and -independent functions. In light of the success of AlphaFolds in accurately predicting protein structures by neural networks that store information as distributed patterns across nodes, a fundamental question arises: Could cellular networks also handle information similarly but with more intricate coding, diverse topological architectures, and spacetime-specific ATP energy supply in membrane-compartmentalized aqueous environments? Full article

The modulation of autophagy plays a dual role in tumor cells, with the potential to both promote and suppress tumor proliferation. In order to gain a deeper understanding of the nature of autophagy, we have developed a chemical reaction kinetic model of autophagy and apoptosis based on the mass action kinetic models that have been previously described in the literature. It is regrettable that the authors did not provide all of the information necessary to reconstruct their model, which made their simulation results irreproducible. In this study, based on an extensive literature review, we have identified concentrations for each species in the stress-free, homeostatic state. These ranges were randomly sampled to generate sets of initial concentrations, from which the simulations were run. In every case, abnormal behavior was observed, with apoptosis and autophagy being activated, even in the absence of stress. Consequently, the model failed to reproduce even the basal conditions. Detailed examination of the model revealed erroneous reactions, which were corrected. The influential kinetic parameters of the corrected model were identified and optimized using the Optima++ code. The model is now capable of simulating homeostatic states, and provides a suitable basis for further model development to describe cell response to various stresses. Full article