Combined remediation of polychlorinated naphthalene-contaminated soil under multiple scenarios: An integrated method of genetic engineering and environmental remediation technology

Biodegradability analysis of Dioxins through in silico methods: Model construction and mechanism analysis

The biodegradation treatment of dioxins has long been of interest due to its good ecological and economic effects. In this study, the biodegradability of polychlorinated dibenzo-p-dioxins (PCDDs) were investigated by constructing machine learning and multiple linear regression models. The maximum chlorine atomic charge (qHirshfeldCl+), which characterizes the biodegradation ability of PCDDs, was used as the response value. The random forest model was used to rank the importance on the 1471 descriptors of PCDDs, and the BCUTp-1 h, QXZ, JGI4, ATSC8c, VE3_Dt, topoShape, and maxwHBa were screened as the important descriptors by Pearson's correlation coefficient method. A quantitative structure-activity relationship (QSAR) model was constructed to predict the biodegradability of PCDDs. In addition, the extreme gradient boosting (XGBoost) and random forest model were also constructed and proved the good predictability of QSAR model. The biodegradability of polychlorinated dibenzofurans (PCDFs) can also be predicted by the constructed three models from a certain level after adjusting some model parameters, which further proved the versatility of the models. Besides, the sensitivity analysis of the QSAR model and a 3D-QSAR model was developed to investigate the biodegradability mechanisms of PCDDs. Results showed that the descriptors BCUTp-1 h, JGI4, and maxwHBa were the key descriptors in the biodegradability effect by the sensitivity analysis of the QSAR model. Coupled with the results of PCDDs biodegradability 3D-QSAR model, BCUTp-1 h, JGI4, and maxwHBa were confirmed as the main descriptors that affect the biodegradability of dioxins. This study provides a novel theoretical perspective for the research of the biodegradation of both PCDDs and PCDFs dioxins.

Amide herbicides: Analysis of their environmental fate, combined plant-microorganism soil remediation scheme, and risk prevention and control strategies for sensitive populations

In this study, we predicted the environmental fate of amide herbicides (AHs) using the EQC (EQuilibrium Criterion) model. We found that the soil phase is the main reservoir of AHs in the environment. Second, a toxicokinetic prediction indicated that butachlor have a low human health risk, while the alachlor, acetochlor, metolachlor, napropamide, and propanil are all uncertain. To address the environmental and human-health-related threats posed by AHs, 27 new proteins/enzymes that easily absorb, degrade, and mineralize AHs were designed. Compared with the target protein/enzyme, the comprehensive evaluation value of the new proteins/enzymes increased significantly: the absorption protein increased by 20.29-113.49%; the degradation enzyme increased by 151.26-425.22%; and the mineralization enzyme increased by 23.70-52.16%. Further experiments revealed that the remediating effect of 13 new proteins/enzymes could be significantly enhanced to facilitate their applicability under real environmental conditions. The hydrophobic interactions, van der Waals forces, and polar solvation are the key factors influencing plant-microorganism remediation. Finally, the simulations revealed that appropriate consumption of kiwifruit or simultaneous consumption of ginseng, carrot, and spinach, and avoiding the simultaneous consumption of maize and carrot/spinach are the most effective means reduce the risk of exhibiting AH-linked toxicity.

Combined forage grass-microbial for remediation of strontium-contaminated soil

Enrichment plants were screened from six forage grasses in this study to establish a complete combined forage grass-microbial remediation system of strontium-contaminated soil, and microbial groups were added to the screened dominant forage grasses. The occurrence states of strontium in forage grasses were explored by the BCR sequential extraction method. The results showed that the annual removal rate of Sudan grass (Sorghum sudanense (Piper) Stapf.) reached 23.05% in soil with a strontium concentration of 500 mg·kg^-1. Three dominant microbial groups: E, G and H, have shown good facilitation effects in co-remediation with Sudan grass and Gaodan grass (Sorghum bicolor × sudanense), respectively. When compared to the control, the strontium accumulation of forage grasses in kg of soil with microbial groups was increased by 0.5-4 fold. The optimal forage grass-microbial combination can theoretically repair contaminated soil in three years. The microbial group E was found to promote the transfer of the exchangeable state and the reducible state of strontium to the overground part of the forage grass. Metagenomic sequencing results showed that the addition of microbial groups increased Bacillus spp. in rhizosphere soil, enhanced the disease resistance and tolerance of forage grasses, and improved the remediation ability of forage grass-microbial combinations.

Application of molecular dynamics simulation for exploring the roles of plant biomolecules in promoting environmental health

Understanding the dynamic changes of plant biomolecules is vital for exploring their mechanisms in the environment. Molecular dynamics (MD) simulation has been widely used to study structural evolution and corresponding properties of plant biomolecules at the microscopic scale. Here, this review (i) outlines structural properties of plant biomolecules, and the crucial role of MD simulation in advancing studies of the biomolecules; (ii) describes the development of MD simulation in plant biomolecules, determinants of simulation, and analysis parameters; (iii) introduces the applications of MD simulation in plant biomolecules, including the response of the biomolecules to multiple stresses, their roles in corrosive environments, and their contributions in improving environmental health; (iv) reviews techniques integrated with MD simulation, such as molecular biology, quantum mechanics, molecular docking, and machine learning modeling, which bridge gaps in MD simulation. Finally, we make suggestions on determination of force field types, investigation of plant biomolecule mechanisms, and use of MD simulation in combination with other techniques. This review provides comprehensive summaries of the mechanisms of plant biomolecules in the environment revealed by MD simulation and validates it as an applicable tool for bridging gaps between macroscopic and microscopic behavior, providing insights into the wide application of MD simulation in plant biomolecules.

Multi-Dimensional Elimination of β-Lactams in the Rural Wetland: Molecule Design and Screening for More Antibacterial and Degradable Substitutes

Restricted economic conditions and limited sewage treatment facilities in rural areas lead to the discharge of small-scale breeding wastewater containing higher values of residual beta-lactam antibiotics (β-lactams), which seriously threatens the aquatic environment. In this paper, molecular docking and a comprehensive method were performed to quantify and fit the source modification for the combined biodegradation of β-lactams. Using penicillin (PNC) as the target molecule, combined with contour maps for substitute modification, a three-dimensional quantitative structure-activity relationship (3D-QSAR) model was constructed for the high-performance combined biodegradation of β-lactams. The selected candidate with better environmental friendliness, functionality, and high performance was screened. By using the homology modeling algorithms, the mutant penicillin-binding proteins (PBPs) of Escherichia coli were constructed to have antibacterial resistance against β-lactams. The molecular docking was applied to obtain the target substitute by analyzing the degree of antibacterial resistance of β-lactam substitute. The combined biodegradation of β-lactams and substitute in the constructed wetland (CW) by different wetland plant root secretions was studied using molecular dynamics simulations. The result showed a 49.28% higher biodegradation of the substitutes than PNC when the combined wetland plant species of Eichhornia crassipes, Phragmites australis, and Canna indica L. were employed.

Phthalate's multiple hormonal effects and their supplementary dietary regulation scheme of health risks for children

Four common phthalic acid esters (PAEs), namely, butylbenzyl phthalate (BBzP), dibutyl phthalate (DBP), di(2-ethylhexyl) phthalate (DEHP), and di-n-octyl phthalate (DNOP) that are known to affect children upon exposure, were selected, and the hormone effects were explored during different supplementary food intakes by using methods such as factorial design experiment, molecular docking, and dynamics simulation techniques. A supplementary diet regulation scheme to prevent health risks of PAEs was constructed to avoid or mitigate the hormonal effects in children exposed to PAEs. Firstly, the MM/PBSA binding energy of PAEs with single hormone receptors and multiple hormone receptor complexes was calculated. In addition, 10 foods were selected as external interference conditions to carry out dynamic simulation, which showed that kiwi fruit and broccoli can effectively alleviate the PAEs' hormone effects. Furthermore, inference of the metabolic process of DEHP found that the supplementary diets could effectively promote the metabolism of PAEs. Finally, based on the mechanism analysis, it was confirmed that the selected supplementary diets could inhibit the binding process. This study aims to explore the role of supplementary diets in regulating various PAEs' hormone effects and thereby provide theoretical support for slowing down hormonal effects in children.

Theoretical design and process control of neonicotinoids insecticides suitable for synergistic degradation with the rubisco enzyme from rhizobia and carbon-fixing bacteria in soil

In this study, we studied and developed the modification schemes of environmentally friendly substitutes of neonicotinoid insecticides (NNIs) along with the regulatory measures that effectively enhanced the synergistic degradation of NNIs by soil rhizobia and carbon-fixing bacteria. Firstly, the binding ability of NNIs to the two key proteins was characterized by molecular docking; secondly, the mean square deviation decision method, which is a comprehensive evaluation method, was used to investigate the binding ability of NNI molecules with the two Rubisco rate-limiting enzymes. The three-dimensional quantitative structure-activity relationship (3D-QSAR) model was established for the synergistic degradation and single effect of rhizobia and carbon-fixing bacteria. Finally, after combining the 3D-QSAR model with a contour map analysis of the synergistic degradation effect of soil rhizobia and carbon-fixing bacteria, 102 NNI derivatives were designed. Flonicamid-36 and other four NNI derivatives passed the functional and environmentally friendly evaluation. Taguchi orthogonal experiment and factorial experiment-assisted molecular dynamics method were used to simulate the effects of 32 regulation schemes on the synergistic degradation of NNIS and its derivatives by rhizobia and carbon fixing bacteria. The synergistic degradation capacity of soil rhizobia and carbon-fixing bacteria was increased to 33.32% after right nitrogen supplementation. This indicated that supplementing the correct amount of nitrogen in the soil environment was beneficial to the microbial degradation of NNIs and their derivatives.

Inhalation and ingestion of Synthetic musks in pregnant women: In silico spontaneous abortion risk evaluation and control

Synthetic musks (SMs) are odor additives commonly used in the personal care products. Their wide existence in the environment and the recently reported adverse impact on the production and activity of progesterone and estrogen have raised pregnancy red flags and even lead to a pregnancy loss. Apart from the suggestion of limiting SM contact and exposure, effective abortion risk control measures for SMs remain to be blank. Facing the above challenges, this study tried to establish a new theoretical circumvention strategy to reduce the abortion risk of SMs to pregnant women by designing the supplementary diet plan and environmentally friendly SMs derivatives using molecular docking and three-dimensional quantitative structure-activity relationship (3D-QSAR) models. According to the supplementary diet plan, the diet combination of vitamin E, vitamin B₂, niacin, vitamin A, and vitamin B₆ were confirmed to not only provide essential nutrients for human health, but also reduce the abortion risk in pregnant women in daily life. The multi-activity (binding ability of SMs with progesterone-estrogen) 3D-QSAR model was constructed to screen SMs derivatives. The LibDock score, a parameter reflecting the binding ability between SMs' Derivative-24 with progesterone-estrogen, decreased as much as 137.67% compared with its precursor galaxolide (HHCB). The 3D-QSAR models assisted screening indicated that Derivative-24 had lower environmental impacts (i.e., bioconcentration and mobility) and improved functional properties (odor stability, musky scent, and odor intensity). The integration of the optimum candidate, Derivative-24, with optimum three supplementary diet plans exhibited a much lower abortion risk than HHCB, demonstrating the effectiveness of the proposed theoretical circumvention strategy as a comprehensive abortion risk control measure. It also shed light on the design of new pharmaceutical and personal care products using advanced computing tools.

Molecular Modifications and Control of Processes to Facilitate the Synergistic Degradation of Polybrominated Diphenyl Ethers in Soil by Plants and Microorganisms Based on Queuing Scoring Method

In this paper, a combination of modification of the source and regulation of the process was used to control the degradation of PBDEs by plants and microorganisms. First, the key proteins that can degrade PBDEs in plants and microorganisms were searched in the PDB (Protein Data Bank), and a molecular docking method was used to characterize the binding ability of PBDEs to two key proteins. Next, the synergistic binding ability of PBDEs to the two key proteins was evaluated based on the queuing integral method. Based on this, three groups of three-dimensional quantitative structure-activity relationship (3D-QSAR) models of plant-microbial synergistic degradation were constructed. A total of 30 PBDE derivatives were designed using BDE-3 as the template molecule. Among them, the effect on the synergistic degradation of six PBDE derivatives, including BDE-3-4, was significantly improved (increased by more than 20%) and the environment-friendly and functional evaluation parameters were improved. Subsequently, studies on the synergistic degradation of PBDEs and their derivatives by plants and microorganisms, based on the molecular docking method, found that the addition of lipophilic groups by modification is beneficial to enhance the efficiency of synergistic degradation of PBDEs by plants and microorganisms. Further, while docking PBDEs, the number of amino acids was increased and the binding bond length was decreased compared to the template molecules, i.e., PBDE derivatives could be naturally degraded more efficiently. Finally, molecular dynamics simulation by the Taguchi orthogonal experiment and a full factorial experimental design were used to simulate the effects of various regulatory schemes on the synergistic degradation of PBDEs by plants and microorganisms. It was found that optimal regulation occurred when the appropriate amount of carbon dioxide was supplied to the plant and microbial systems. This paper aims to provide theoretical support for enhancing the synergistic degradation of PBDEs by plants and microorganisms in e-waste dismantling sites and their surrounding polluted areas, as well as, realize the research and development of green alternatives to PBDE flame retardants.

A model for phthalic acid esters' biodegradability and biotoxicity multi-effect pharmacophore and its application in molecular modification

The objective of this study was to investigate 13 phthalic acid esters (PAEs) with medium or long straight-alkyl-chain, branching or unsaturated side chains, because their structural characteristics make them difficult to biodegrade or highly toxic. A biodegradability and biotoxicity multi-effect pharmacophore model was built using comprehensive evaluation method. The results suggested that introducing hydrophobic groups to the side chains of the PAEs could improve the molecules' biodegradability and biotoxicity effects simultaneously. Thus, 40 target PAE (HEHP, DNOP, DUP) derivatives were designed. Two environmentally friendly PAE derivatives (HEHP-Anthryl and HEHP-Naphthyl) were screened via the test of environmental friendliness and functionality. In addition, the biodegradation and biotoxicity of derivatives were found to have improved as a result of the change in van der Waals forces between molecules and their corresponding proteins. Moreover, the environmental safety of the screened PAE derivatives was confirmed by predicting the toxicity of their intermediates and calculating the energy barrier values for biodegradation and metabolic pathways. This study could provide theoretical guidance for the practical development of environmentally friendly plasticizer.