Driving factors for distribution and transformation of heavy metals speciation in a zinc smelting site.

Heavy metal pollution at an abandoned smelter pose a significant risk to environmental health. However, remediation strategies are constrained by inadequate knowledge of the polymetallic distribution, speciation patterns, and transformation factors at these sites. This study investigates the influence of soil minerals, heavy metal occurrence forms, and environmental factors on heavy metal migration behaviors and speciation transformations. X-ray diffraction analysis revealed that the minerals associated with heavy metals are mainly hematite, franklinite, sphalerite, and galena. Sequential extraction results suggest that lead and zinc are primarily present in the organic-sulfide fractions (F4) and residual form (F5) in the soil, accounting for over 70% of the total heavy metal content. Zinc displayed greater instability in carbonate-bound (16%) and exchangeable (2%) forms. The migration and diffusion patterns of heavy metals in the subsurface environment were visualized through the simulation of labile state heavy metals, demonstrating high congruence with groundwater pollution distribution patterns. The key environmental factors influencing heavy metal stable states (F4 and F5) were assessed by integrating random forest models and redundancy analysis. Primary factors facilitating Pb transformation into stable states were available phosphorus, clay content, depth, and soil organic matter. For Zn, the principal drivers were Mn oxides, soil organic matter, clay content, and inorganic sulfur ions. These findings enhance understanding of the distribution and transformation of heavy metal speciation and can provide valuable insights into controlling heavy metal pollution at non-ferrous smelting sites.

Quinoline-based compounds can inhibit diverse enzymes that act on DNA.

DNA methylation, as exemplified by cytosine-C5 methylation in mammals and adenine-N6 methylation in bacteria, is a crucial epigenetic mechanism driving numerous vital biological processes. Developing non-nucleoside inhibitors to cause DNA hypomethylation is a high priority, in order to treat a variety of significant medical conditions without the toxicities associated with existing cytidine-based hypomethylating agents. In this study, we have characterized fifteen quinoline-based analogs. Notably, compounds with additions like a methylamine ( 9 ) or methylpiperazine ( 11 ) demonstrate similar low micromolar inhibitory potency against both human DNMT1 (which generates C5-methylcytosine) and Clostridioides difficile CamA (which generates N6-methyladenine). Structurally, compounds 9 and 11 specifically intercalate into CamA-bound DNA via the minor groove, adjacent to the target adenine, leading to a substantial conformational shift that moves the catalytic domain away from the DNA. This study adds to the limited examples of DNA methyltransferases being inhibited by non-nucleotide compounds through DNA intercalation, following the discovery of dicyanopyridine-based inhibitors for DNMT1. Furthermore, our study shows that some of these quinoline-based analogs inhibit other enzymes that act on DNA, such as polymerases and base excision repair glycosylases. Finally, in cancer cells compound 11 elicits DNA damage response via p53 activation. Highlights: Six of fifteen quinoline-based derivatives demonstrated comparable low micromolar inhibitory effects on human cytosine methyltransferase DNMT1, and the bacterial adenine methyltransferases Clostridioides difficile CamA and Caulobacter crescentus CcrM. Compounds 9 and 11 were found to intercalate into a DNA substrate bound by CamA. These quinoline-based derivatives also showed inhibitory activity against various base excision repair DNA glycosylases, and DNA and RNA polymerases. Compound 11 provokes DNA damage response via p53 activation in cancer cells.

Activity, substrate preference and structure of the HsMCM8/9 helicase.

The minichromosomal maintenance proteins, MCM8 and MCM9, are more recent evolutionary additions to the MCM family, only cooccurring in selected higher eukaryotes. Mutations in these genes are directly linked to ovarian insufficiency, infertility, and several cancers. MCM8/9 appears to have ancillary roles in fork progression and recombination of broken replication forks. However, the biochemical activity, specificities and structures have not been adequately illustrated, making mechanistic determination difficult. Here, we show that human MCM8/9 (HsMCM8/9) is an ATP dependent DNA helicase that unwinds fork DNA substrates with a 3'-5' polarity. High affinity ssDNA binding occurs in the presence of nucleoside triphosphates, while ATP hydrolysis weakens the interaction with DNA. The cryo-EM structure of the HsMCM8/9 heterohexamer was solved at 4.3 Å revealing a trimer of heterodimer configuration with two types of interfacial AAA+ nucleotide binding sites that become more organized upon binding ADP. Local refinements of the N or C-terminal domains (NTD or CTD) improved the resolution to 3.9 or 4.1 Å, respectively, and shows a large displacement in the CTD. Changes in AAA+ CTD upon nucleotide binding and a large swing between the NTD and CTD likely implies that MCM8/9 utilizes a sequential subunit translocation mechanism for DNA unwinding.

The assembly process and co-occurrence patterns of soil microbial communities at a lead smelting site.

The potential toxic elements of the site are diverse and complex, seriously threatening the land utilization potential and soil ecological function. Microbial community is critical to maintaining ecosystem function, their assembly processes and diversity play an essential role in predicting changes in soil ecological function. However, our understanding of the mechanisms that shape community composition and successional direction in complex polluted environments is very limited. In this study, to explore the mechanisms driving community assembly and symbiosis in different contaminated regional environments, the biological characteristics of bacterial and fungal communities in four different polluted areas of a typical lead smelting site were studied. Contamination by PTEs appears to increase microbial networks, as well as altering microbial community composition, with relative abundance of dominant phyla such as Actinomycetes and Acidobacteria decreasing, whilst Proteobacteria and Ascomycota increased, this indicated that communities may shift from K-strategy to r-strategy and become opportunistic. Dispersal limitation (DL, 42 %-86 %), drift (Dr, 8 %-37 %) and homogeneous selection (HoS, 1 %-31 %) proved to be the important community assembly process. The top ten bins controlling the contribution of different biological processes were identified, and the relative abundance of these bacterial and fungal taxa varied with CPI. Collectively, our results suggest that CPI and nutrient availability regulate soil bacterial and fungal community assembly processes. The results of this study provide potential guidance for community regulation in the process of ecological restoration and mitigating degraded soils at smelting sites.

Effect of potentially toxic elements on soil multifunctionality at a lead smelting site.

Contaminated soil at smelting sites affects land utilization and environmental regulation, resulting in soil degradation. However, the extent to which potentially toxic elements (PTEs) contribute to site soil degradation and the relationship between soil multifunctionality and microbial diversity in the process remains poorly understood. In this study, we investigated changes in soil multifunctionality and the correlation between soil multifunctionality and microbial diversity under the influence of PTEs. The change in microbial community diversity was closely related to changes in soil multifunctionality caused by PTEs. Microbial diversity, not richness, drives the delivery of ecosystem services in smelting site PTEs-stressed environments. Structural equation modeling identified that soil contamination, microbial taxonomic profile and microbial functional profile could explain 70% of the variance in soil multifunctionality. Furthermore, our findings demonstrate that PTEs limit soil multifunctionality by affecting soil microbial communities and functionality, whilst the positive effect of microorganisms on soil multifunctionality was mainly driven by the fungal diversity and biomass. Finally, specific fungal genera closely related to soil multifunctionality were identified, with saprophytic fungi being particularly important for maintaining multiple soil functions. The results of the study provide potential guidance for the remediation, pollution control practices and mitigation of degraded soils at smelting sites.

Anthropogenic processes drive heterogeneous distributions of toxic elements in shallow groundwater around a smelting site.

Smelting activities have a far-reaching influence on the quality of soil and groundwater, while most studies have neglected the information on the pollution characteristics of groundwater. The hydrochemical parameters of shallow groundwater and the spatial distributions of toxic elements were investigated in this study. Correlations analysis and groundwater evolution revealed that the major ions were primarily determined by silicate weathering and calcite dissolution process, and anthropogenic processes had a significant effect on groundwater hydrochemistry. Almost 79%, 71%, 57%, 89%, 100%, and 78.6% of samples exceeded the standards of Cd, Zn, Pb, As, SO42-, and NO3-, and their distribution is closely related to the production process. Analysis of soil geochemistry indicated that the relatively mobile forms of toxic elements strongly influence the origin and concentration in shallow groundwater. Besides, rainfall with high magnitude would lead to a decrease of toxic elements in shallow groundwater, whereas the area once stacked waste residue was the opposite. It is recommended to strengthen risk management of the limited mobility fraction while devising a plan for waste residue treatment in accordance with the local pollution conditions. The research on controlling the mechanism of toxic elements in shallow groundwater, along with sustainable development in the study area and other smelting zones may benefit from this study.

A practical method for identifying key factors in the distribution and formation of heavy metal pollution at a smelting site.

Smelting activities are the main pathway for the anthropogenic release of heavy metals (HMs) into the soil-groundwater environment. It is vital to identify the factors affecting HMs pollution to better prevent and manage soil pollution. The present study conducted a comprehensive investigation of HMs in soil from a large abandoned Zn smelting site. An integrated approach was proposed to classify and quantify the factors affecting HMs pollution in the site. Besides, the quantitative relationship between hydrogeological characteristics, pollution transmission pathways, smelting activities and HMs pollution was established. Results showed that the soils were highly contaminated by HMs with a pollution index trend of As > Zn > Cd > Pb > Hg. In identifying the pollution hotspots, we conclude that the pollution hotspots of Pb, As, Cd, and Hg present a concentrated distribution pattern. Geo-detector method results showed that the dominant driving factors for HMs distribution and accumulation were the potential pollution source and soil permeability. Additionally, the main drivers are variable for different HMs, and the interaction among factors also enhanced soil HMs contamination. Our analysis illustrates how the confounding influences from complex environmental factors can be distilled to identify key factors in pollution formation to guide future remediation strategies.

Structural basis of DNA polymerase θ mediated DNA end joining.

DNA polymerase θ (Pol θ) plays an essential role in the microhomology-mediated end joining (MMEJ) pathway for repairing DNA double-strand breaks. However, the mechanisms by which Pol θ recognizes microhomologous DNA ends and performs low-fidelity DNA synthesis remain unclear. Here, we present cryo-electron microscope structures of the polymerase domain of Lates calcarifer Pol θ with long and short duplex DNA at up to 2.4 Šresolution. Interestingly, Pol θ binds to long and short DNA substrates similarly, with extensive interactions around the active site. Moreover, Pol θ shares a similar active site as high-fidelity A-family polymerases with its finger domain well-closed but differs in having hydrophilic residues surrounding the nascent base pair. Computational simulations and mutagenesis studies suggest that the unique insertion loops of Pol θ help to stabilize short DNA binding and assemble the active site for MMEJ repair. Taken together, our results illustrate the structural basis of Pol θ-mediated MMEJ.

Histone variants H3.3 and H2A.Z/H3.3 facilitate excision of uracil from nucleosome core particles.

At the most fundamental level of chromatin organization, DNA is packaged as nucleosome core particles (NCPs) where DNA is wound around a core of histone proteins. This ubiquitous sequestration of DNA within NCPs presents a significant barrier to many biological processes, including DNA repair. We previously demonstrated that histone variants from the H2A family facilitate excision of uracil (U) lesions by DNA base excision repair (BER) glycosylases. Here, we consider how the histone variant H3.3 and double-variant H2A.Z/H3.3 modulate the BER enzymes uracil DNA glycosylase (UDG) and single-strand selective monofunctional uracil DNA glycosylase (SMUG1). Using an NCP model system with U:G base pairs at a wide variety of geometric positions we generate the global repair profile for both glycosylases. Enhanced excision of U by UDG and SMUG1 is observed with the H3.3 variant. We demonstrate that these H3.3-containing NCPs form two species: (1) octasomes, which contain the full complement of eight histone proteins and (2) hexasomes which are sub-nucleosomal particles that contain six histones. Both the octasome and hexasome species facilitate excision activity of UDG and SMUG1, with the largest impacts observed at sterically-occluded lesion sites and in terminal regions of DNA of the hexasome that do not closely interact with histones. For the double-variant H2A.Z/H3.3 NCPs, which exist as octasomes, the global repair profile reveals that UDG but not SMUG1 has increased U excision activity. The enhanced glycosylase activity reveals potential functions for these histone variants to facilitate BER in packaged DNA and contributes to our understanding of DNA repair in chromatin and its significance regarding mutagenesis and genomic integrity.

Pollution simulation and remediation strategy of a zinc smelting site based on multi-source information.

Contaminated sites pose a significant risk to human health and the regional environment. A comprehensive study was dedicated to improving the understanding of the contamination condition of a smelting site by integrating multi-source information through 3D visualization techniques. The results showed that 3D visualization reveals excellent potential for application in the environmental studies to finely depict contamination in soils and establish relationships with geological features, hydrological conditions, and sources of contamination. The contamination plume model revealed that the soil environment at the site was seriously threatened by toxic metals, and dominated by multi-metal contamination, with contamination soil volume ranked as Cd > As > Pb> Zn > Hg. The stratigraphic model revealed the heterogeneous geological conditions of the site and identified the mixed fill layer as the primary remediation soil layer. The permeability model revealed that soil permeability significantly influenced contamination dispersion and contributed to delineate the contamination boundary accurately. The ecological hazard model targeted the high ecological hazard area and determined the high hazard contribution of Cd and Hg in the site soil. The outcomes can be directly applied to actual site remediation and provide a reference for the contaminated sites evaluation and restoration in the future.

Magnetization of Bauxite Residue to Enhance the Removal Efficiency Towards Heavy Metals.

Bauxite residues are a mass of industrial wastes derived from aluminum metallurgy. This work provided a simple pyrolysis method to magnetize the bauxite residue to serve as a magnetic adsorbent towards heavy metals removal. The X-ray diffraction patterns and Mossbauer spectrum results confirmed the partial reduction of iron species with an obvious enhancement in magnetization. The magnetized bauxite residue exhibited excellent removal efficiencies for Cu2+, Cd2+ and Pb2+ with maximum adsorption capacities of 219.0 mg g-1, 275.4 mg g-1, and 100.4 mg g-1, which could be quickly separated through a magnet. The adsorption equilibrium data were fitted to the Langmuir isotherm model, while the adsorption kinetics followed a pseudo-first-order model. According to the characterization results, chemical precipitation and sorption was the major mechanism for the removal of Cu2+, Pb2+, and Cd2+. Thus, the magnetized bauxite residue exhibited promising applications for heavy metals removal in wastewater.

Spatial distribution of toxic metal(loid)s at an abandoned zinc smelting site, Southern China.

Toxic metal(loid) (TM) soil pollution at large-scale non-ferrous metal smelting contaminated sites is of great concern in China, but there are no detailed reports relating to them. A comprehensive study was conducted to determine contamination characteristics and horizontal and vertical spatial distribution patterns of soils at an abandoned zinc smelting site in Southern China. The spatial distribution of TMs revealed that soil environmental quality was seriously threatened, with Cd, Zn, As, Pb and Hg being the main contaminants present. The distribution of all TMs showed strong spatial heterogeneity and were expressed as a "patchy aggregation" pattern due to strong anthropogenic and production activities. Vertical migration of TMs indicated that the pollutants were mainly concentrated in the fill layers. Different contaminants had various migration depths, with migration occurring as: Cd > Hg > As > Zn > Pb> Cu> Mn> Sb. Analysis of their spatial variability showed that As, Pb, Cd and Hg had strong regional spatial variability. This research provides a new approach to comprehensively analyze TM pollution characteristics of non-ferrous smelting sites. It provides valuable information for guiding post-remediation strategies at abandoned non-ferrous metal smelting sites.

Accelerated alkalinity regulation and long-term dry-wet aging durability for bauxite residue remediated with biomass pyrolysis.

Biomass fermentation provides a potential route toward the ecological disposal for the bauxite residue (BR) with high alkalinity issues. However, how to accelerate the remediation of the alkaline problem with a long-term durability is still a big challenge. Herein, we investigated the acceleration of the decomposition of straw toward organic acid species via a pyrolysis strategy as well as the pH stability during long-term dry-wet aging for the treated BR. The pH of pyrolytic BR at 300 °C is stabilized at around 8.90 after 70 days' dry-wet aging. During the aging, the main Ca-contained alkaline minerals of calcite and cancrinite are dissolved and the content of exchangeable Na+ is reduced. This pyrolysis process can decompose straw quickly and produce more organic matters that are easily degraded to fulvic and humic acid as evidenced by 3D fluorescence spectrum analysis. Compared to the fermentation with straw under natural conditions, the alkalinity regulation of BR after pyrolysis is featured with shorter period and lower pH as well as long-term pH stability. Therefore, the synergistic pyrolysis of BR with straw provides an alternative method to address the alkaline issues, which is conducive to promoting the soil formation of BR.

Alkalinity neutralization and structure upgrade of bauxite residue waste via synergistic pyrolysis with biomass.

Bauxite residues, a large volume solid waste, are in urgent need of effective disposal and management. Especially, strategies to alleviate the high alkalinity of bauxite residue remain a big challenge. Here, we developed a synergistic pyrolysis to neutralize the alkalinity of bauxite residue and upgrade the structure of biomass simultaneously. By cooperating the catalytic feature from bauxite residue, rice straw, a cellulose-enriched biomass, could prefer to produce acidic components under a hypothermal pyrolysis temperature (below 250 °C) and partial oxygen-contained atmosphere as evidenced by the synchronous TGA-FTIR analysis. In return, these in-situ produced acidic components neutralized the bauxite residue profoundly (pH decreased from 11.5 to 7.2) to obtain a neutral product with long-term water leaching stability. Also, a higher pyrolysis temperature led to neutral biochar-based products with well-defined carbonization characteristics. Thus, the biomass-driven pyrolysis strategy provides a potential to dispose the alkalinity issue of bauxite residue and further opportunities for the sustainable reuse and continuing management of bauxite residue.

Selective Electrocatalytic Water Oxidation to Produce H2O2 Using a C,N Codoped TiO2 Electrode in an Acidic Electrolyte.

Production of hydrogen peroxide (H2O2) via in situ electrochemical water oxidation possesses great potential applications in the energy and environment fields. In this work, for the first time, we reported a C,N codoped TiO2 electrode for selective electrocatalytic water oxidation to produce H2O2 in an acidic electrolyte. An electrochemical anodic oxidation method combined with postcalcination in the presence of urea was applied to fabricate such a C,N codoped TiO2 electrode, which was evidenced by detail structural characterizations. The calcination temperature and urea atmosphere were found to play key roles in its catalytic performances; the optimized 600N sample exhibited an onset potential of 2.66 V (vs Ag/AgCl) and a Tafel slope of 51 mV dec-1 at pH 3. Under the optimal applied potential, the cumulative H2O2 concentration for this sample reached 0.29 µmol L-1 cm-2 h-1. More importantly, a simple recalcination strategy was developed to recover the deactivation electrode. This study proposed an efficient C,N codoped TiO2 electrode toward water oxidation to selectively produce H2O2 in the acidic electrolyte, which could be further used to in situ generate H2O2 for the energy- and environment-related fields with water as the precursor.

Challenges for base excision repair enzymes: Acquiring access to damaged DNA in chromatin.

Repair of damaged DNA plays a crucial role in maintaining genomic integrity and normal cell function. The base excision repair (BER) pathway is primarily responsible for removing modified nucleobases that would otherwise cause deleterious and mutagenic consequences and lead to disease. The BER process is initiated by a DNA glycosylase, which recognizes and excises the target nucleobase lesion, and is completed via downstream enzymes acting in a well-coordinated manner. A majority of our current understanding about how BER enzymes function comes from in vitro studies using free duplex DNA as a simplified model. In eukaryotes, however, BER is challenged by the packaging of genomic DNA into chromatin. The fundamental structural repeating unit of chromatin is the nucleosome, which presents a more complex substrate context than free duplex DNA for repair. In this chapter, we discuss how BER enzymes, particularly glycosylases, engage in the context of packaged DNA with insights obtained from both in vivo and in vitro studies. Furthermore, we review factors and mechanisms that can modify chromatin architecture and/or influence DNA accessibility to BER machinery, such as the geometric location of the damage site, nucleosomal DNA unwrapping, histone post-translational modifications, histone variant incorporation, and chromatin remodeling.

Global Repair Profile of Human Alkyladenine DNA Glycosylase on Nucleosomes Reveals DNA Packaging Effects.

Alkyladenine DNA glycosylase (AAG) is the only known human glycosylase capable of excising alkylated purines from DNA, including the highly mutagenic 1,N6-ethenoadenine (εA) lesion. Here, we examine the ability of AAG to excise εA from a nucleosome core particle (NCP), which is the primary repeating unit of DNA packaging in eukaryotes. Using chemical synthesis techniques, we assembled a global population of NCPs in which A is replaced with εA. While each NCP contains no more than one εA lesion, the total population contains εA in 49 distinct geometric positions. Using this global εA-containing NCP system, we obtained kinetic parameters of AAG throughout the NCP architecture. We observed monophasic reaction kinetics across the NCP, but varying amounts of AAG excision. AAG activity is correlated with solution accessibility and local histone architecture. Notably, we identified some highly solution-accessible lesions that are not repaired well, and an increase in repair within the region of asymmetric unwrapping of the nucleosomal DNA end. These observations support in vivo work and provide molecular-level insight into the relationship between repair and NCP architecture.

Histone H2A Variants Enhance the Initiation of Base Excision Repair in Nucleosomes.

Substituting histone variants for their canonical counterparts can profoundly alter chromatin structure, thereby impacting multiple biological processes. Here, we investigate the influence of histone variants from the H2A family on the excision of uracil (U) by the base excision repair (BER) enzymes uracil DNA glycosylase (UDG) and single-strand selective monofunctional uracil DNA glycosylase. Using a DNA population with globally distributed U:G base pairs, enhanced excision is observed in H2A.Z and macroH2A-containing nucleosome core particles (NCPs). The U with reduced solution accessibility exhibit limited UDG activity in canonical NCPs but are more readily excised in variant NCPs, reflecting the ability of these variants to facilitate excision at sites that are otherwise poorly repaired. We also find that U with the largest increase in the level of excision in variant NCPs are clustered in regions with differential structural features between the variants and canonical H2A. Within 35-40 bp of the DNA terminus in macroH2A NCPs, the activities of both glycosylases are comparable to that on the free duplex. We show that this high level of activity results from two distinct species within the macroH2A NCP ensemble: octasomes and hexasomes. These observations reveal potential functions for H2A variants in promoting BER and preventing mutagenesis within the context of chromatin.

Phosphogypsum stabilization of bauxite residue: Conversion of its alkaline characteristics.

Reduction of the high alkalinity of bauxite residue is a key problem to solve to make it suitable for plant growth and comprehensive utilization. In this study, phosphogypsum, a waste product from the phosphate fertilizer industry, was used to drive the alkaline transformation of the bauxite residue. Under optimal water washing conditions (liquid/solid ratio of 2 mL/g, 30°C, 24 hr), the impact of quantity added, reaction time and reaction mechanism during phosphogypsum application were investigated. Phosphogypsum addition effectively lowered pH levels and reduced the soluble alkalinity by 92.2%. It was found that the concentration of soluble Na and Ca ions in the supernatant increased gradually, whilst the exchangeable Na+ and Ca2+ in solid phase changed 112 mg/kg and 259 mg/kg, respectively. Ca2+ became the dominant element in the solid phase (phosphogypsum addition of 2%, liquid/solid ratio of 2 mL/g, 30°C, 12 hr). X-ray diffraction data indicated that cancrinite and hydrogarnet were the primary alkaline minerals. SEM images suggested that phosphogypsum could promote the formation of stable macro-aggregates, whilst the content of Ca2+ increased from 5.6% to 18.2% and Na reduced from 6.8% to 2.4%. Treatment with phosphogypsum could significantly promote the transformation of alkalinity cations by neutralization, precipitation and replacement reactions. This research provided a feasible method to promote soil formation of bauxite residue by phosphogypsum amendment.