Leveraging a disulfidptosis-related signature to predict the prognosis and immunotherapy effectiveness of cutaneous melanoma based on machine learning.

BACKGROUND: Disulfidptosis is a recently discovered programmed cell death pathway. However, the exact molecular mechanism of disulfidptosis in cutaneous melanoma remains unclear. METHODS: In this study, clustering analysis was performed using data from public databases to construct a prognostic model, which was subsequently externally validated. The biological functions of the model genes were then investigated through various experimental techniques, including qRT-PCR, Western blotting, CCK-8 assay, wound healing assay, and Transwell assay. RESULTS: We constructed a signature using cutaneous melanoma (CM) data, which accurately predicts the overall survival (OS) of patients. The predictive value of this signature for prognosis and immune therapy response was validated using multiple external datasets. High-risk CM subgroups may exhibit decreased survival rates, alterations in the tumor microenvironment (TME), and increased tumor mutation burden. We initially verified the expression levels of five optimum disulfidptosis-related genes (ODRGs) in normal tissues and CM. The expression levels of these genes were further confirmed in HaCaT cells and three melanoma cell lines using qPCR and protein blotting analysis. HLA-DQA1 emerged as the gene with the highest regression coefficient in our risk model, highlighting its role in CM. Mechanistically, HLA-DQA1 demonstrated the ability to suppress CM cell growth, proliferation, and migration. CONCLUSION: In this study, a novel signature related to disulfidptosis was constructed, which accurately predicts the survival rate and treatment sensitivity of CM patients. Additionally, HLA-DQA1 is expected to be a feasible therapeutic target for effective clinical treatment of CM.

Effects of polyethylene microplastics on properties, enzyme activities, and the succession of microbial community in Mollisol: At the aggregate level.

Soil, as a heterogeneous body, is composed of different-sized aggregates. There is limited data available on the potential role of microplastics (MPs) in microbial properties at the soil aggregate level. In this study, changes in microbial construction and diversity in farmland bulk soil and aggregates induced by polyethylene MPs (PE-MPs) were investigated at a dose of 0.5% (w/w) through 16s rDNA sequencing and enzyme activity measurements of different particle size aggregates in incubated soil. The presence of low-dose PE-MPs increased the proportion of >1 mm soil aggregates fraction, and decreased soil available nitrogen and available phosphorus in bulk soils. Furthermore, low-dose PE-MPs increased bacterial richness and diversity in 1-0.5 and < 0.25 mm fractions and decreased operational taxonomic unit, abundance-based coverage estimator, and Chao1 indices in bulk soil and >1 mm fractions. The levels of predicted functional genes taking part in the biodegradation and metabolism of exogenous substances also increased. At the phylum level, PE-MPs changed the proportion of Proteobacteria and Actinobacteria. The variations in soil aggregate properties were significantly correlated with the bacterial communities' composition and diversity. This study deepens our perception of the soil microenvironment, microbial community composition, and diversity in response to PE-MPs.

An unexpected discovery of 1,4-benzoquinone as a lipophilic mediator for toxicity detection in water.

Since most toxicological risk assessments are based on individual single-species tests, there is uncertainty in extrapolating these results to ecosystem assessments. Herein, we successfully developed a mediated microbial electrochemical biosensor with mixed microorganisms for toxicity detection by microelectrode array (MEA). In order to fully mobilize all the mixed microorganisms to participate in electron transfer to amplify the current signal, 1,4-benzoquinone (BQ) was used as the lipophilic mediator to mediate the intracellular metabolic activities. Hydrophilic K3[Fe(CN)6] was employed as an extracellular electron acceptor to transport electrons from hydroquinone (HQ) to the working electrode. Under the optimal conditions of 50 mM phosphate buffer solution (PBS), 0.4 mM BQ, 10 mM K3[Fe(CN)6] and OD600 = 0.5 bacteria concentration, the half-maximal inhibitory concentration (IC50) values measured with the composite-mediated respiration (CM-RES) of BQ-K3[Fe(CN)6] for Cu2+, Cd2+ and Zn2+ were 5.95, 7.12 and 8.86 mg L-1, respectively. IC50 values obtained with the single mediator K3[Fe(CN)6] were 2.34, 5.88 and 2.42 mg L-1 for the same samples. The results indicate that the biosensor with the single mediator K3[Fe(CN)6] had higher sensitivity to heavy metal ions than the biosensor with composite mediators. After verification, we found that the addition of BQ cannot amplify the current. The IC50 value of 0.89 mg L-1 for BQ was obtained using K3[Fe(CN)6] as the single mediator. This suggests that BQ is highly toxic, which explained why the sensitivity of the biosensor with the combined mediator BQ-K3[Fe(CN)6] was lower than that of the biosensor with the single mediator K3[Fe(CN)6]. At the same time, this also implies that toxicity itself cannot be ignored when it is used as an electronic mediator in a mediated microbial electrochemical biosensor.

Simultaneous achievement of removing bensulfuron-methyl and reducing CO2 emission in paddy soil by Acinetobacter YH0317 immobilized boron-doping biochar.

Herbicide residue and greenhouse gas (GHG) emission are two main problems in the paddy rice field, which have barely been considered simultaneously. Herein, a bensulfuron-methyl (BSM)-degrading bacterium named Acinetobacter YH0317 was successfully immobilized on two kinds of biochars and subsequently applied in the paddy soil. The BSM removal rate of Acinetobacter YH0317 immobilized boron-doping biochar (BBC) was 80.42% after 30 d, which was significantly higher than that of BBC (39.05%) and Acinetobacter YH0317 (49.10%) applied alone. BBC acting as an immobilized carrier could enable Acinetobacter YH0317 to work in harsh and complex environment and thus improve the BSM removal efficiency. The addition of Acinetobacter YH0317 immobilized BBC (TP5) significantly improved the soil physicochemical properties (pH, SOC, and NH4+-N) and increased the diversity of soil microbial community compared to control group (CG). Meanwhile, Acinetobacter YH0317 immobilized BBC reduced the CO2-equivalent emission by 41.0%. Metagenomic sequencing results revealed that the decreasing CO2 emission in TP5 was correlated with carbon fixation gene (fhs), indicating that fhs gene may play an important role in reducing CO2 emission. The work presents a practical and supportive technique for the simultaneous achievement on the soil purification and GHG emission reduction in paddy soil.

Whole genome sequencing revealed the capability of Paenarthrobacter sp. KN0901 to simultaneously remove atrazine and corn straw at low temperatures: From gene identification to empirical validation.

Corn planting is often associated with serious atrazine pollution and excessive corn straw amounts, causing severe threats to environmental and ecological security, as well as to green agricultural development. In this context, a Paenarthrobacter sp. KN0901 strain was applied to simultaneously remove atrazine and straw at low temperatures. The results of whole genome sequencing indicated that KN0901 encoded over nine straw biodegradation-related enzymes. In addition, 100 % and 27.3 % of atrazine and straw were simultaneously degraded by KN0901 following an incubation period of seven days at 15 ºC and 180 rpm in darkness. The KN0901 strain maintained high atrazine and straw biodegradation rates under temperature and pH ranges of 4-25 ºC and 5-9, respectively. The simultaneous atrazine and corn straw additions improved the microbial growth and biodegradation rates by increasing the functional gene expression level, cell viability, inner membrane permeability, and extracellular polymeric substance contents of KN0901. The hydroponic experiment results demonstrated the capability of the KN0901 strain to mitigate the toxicity of atrazine to soybeans in four days under the presence of corn straw. The present study provides a new perspective on the development of bioremediation approaches and their application to restore atrazine-polluted cornfields with large straw quantities, particularly in cold areas.

One-step synthesis of ferrous disulfide and iron nitride modified hydrochar for enhanced adsorption and reduction of hexavalent chromium in Bacillus LD513 by promoting electron transfer and microbial metabolism.

Microbial immobilization technology is effective in improving bioremediation efficiency and heavy metal pollution. Herein, Bacillus LD513 with hexavalent chromium (Cr(VI)) tolerance was isolated and immobilized on a novel ferrous disulfide (FeS2)/iron nitride (FeN) modified hydrochar (Fe3-SNHC) prepared from waste straws. The prepared Fe3-SNHC-based LD513 (FeLD) significantly improves Cr(VI) adsorption and reduction by 31.4 % and 15.7 %, respectively, compared to LD513 alone. Furthermore, the FeLD composite system demonstrates efficient Cr(VI) removal efficiency and good environmental adaptability under different culture conditions. Microbial metabolism and electrochemical analysis indicate that Fe3-SNHC is an ideal carrier for protecting LD513 activity, promoting extracellular polymer secretion, and reducing oxidative stress. Additionally, the carrier serves as an electron shuttle that accelerates electron transfer and promotes Cr(VI) reduction. Overall, FeLD is an environmentally friendly biocomposite that shows good promise for reducing Cr(VI) contamination in wastewater treatment.

Enhanced adsorption performance of bensulfuron methyl with B doping biochar: Mechanism and density functional theory calculations.

It is an urgent task to develop suitable adsorbents for the control of herbicide-bensulfuron methyl (BSM) in the paddy rice fields at cold regions. Herein, B doping biochar was synthesized via one-step method. Results showed that the adsorption capacity for BSM on 1.0BBC was significantly superior to BC at 15 °C. Besides, low temperature resistance, wide pH adaptability, stable adsorption performance and reusability test suggested that 1.0BBC have potential practical application. The mechanisms of BSM removal by 1.0BBC were mainly attributed to pore filling and π-π electron donor-acceptor (EDA) interaction. Theoretical calculations revealed that BCO2 could enhance the adsorption capacity by π-π EDA between BSM and adsorbent. Meanwhile, hydroponic experiment demonstrated that the toxicity to soybean after adsorption of BSM by 1.0BBC was within the safe range. This study proves that 1.0BBC is an easy-to-prepare adsorbent with promising application in BSM removal in the rice paddy fields at lower temperature.

Enhanced removal efficiency of bensulfuron-methyl by a novel boron doping biochar-based Acinetobacter YH0317 at a lower temperature.

Biochar-based bacteria are regarded as an efficient strategy for remediating organic pollutants in aquatic environments. Herein, a strain named Acinetobacter YH0317 that could degrade bensulfuron-methyl (BSM) at a lower temperature (15 °C) was isolated from a paddy rice field with long-term BSM application. Then Acinetobacter YH0317 was loaded on unmodified biochar (BC) and boron doping biochar (BBC). Results showed that BBC-based YH0317 significantly enhanced the removal efficiency of BSM (71.8-99.1%) compared with BC-based YH0317 (41.9-44.0%) and YH0317 alone (18.1-20.7%) in 24 h. BBC promoted the growth of YH0317 and secretion of extracellular secretions by providing a carrier and shelter for YH0317. The electrochemical analysis suggested BBC improved the electron transfer rate, which ultimately facilitated the removal of BSM. Hydroponic experiments indicated that BBC-based YH0317 effectively improved the growth of soybean. This work reports a novel BBC-based Acinetobacter YH0317 that could effectively remediate BSM contamination in the water environment.

Atrazine decontamination by a newly screened psychrotroph Paenarthrobacter sp. KN0901 in an aquatic system: Metabolic pathway, kinetics, and hydroponics experiment.

Atrazine residues running off the fields and entering water resources are a major threat to food security and the ecosystem. In this study, a psychrotrophic functional strain named KN0901 to remove atrazine residues was screened. KN0901 could degrade 30 mg·L-1 atrazine in 4 days at 15ºC with 105 CFU·mL-1 incubation. The phylogenetic results showed KN0901 belonged to Paenarthrobacter sp. PCR results showed that the functional genes consist of trzN, atzB, and atzC, suggesting atrazine was transformed to cyanuric acid by KN0901. KN0901 could degrade atrazine without adding exogenous carbon and nitrogen sources. What's more, KN0901 could tolerate extreme low temperature (5ºC) and high atrazine concentration (100 mg·L-1). When growth and degradation curves were compared, the results indicated the length of lag time showed significant correlation to atrazine degradation rate. The hydroponic experiments showed that the toxicity of atrazine was significantly reduced with KN0901 treatment. The study provided an effective, economic, and eco-friendly bioremediation measure to address atrazine contamination.

The COVID-19 pandemic and the potential treatment of the novel coronavirus SARS-CoV-2.

Coronavirus SARS-CoV-2 is a novel coronavirus and the seventh that can infect human beings and result in severe and acute respiratory syndrome and deaths. Currently, the world is undergoing a global health emergency due to the SARS-CoV-2 pandemic. As of May 18, SARS-CoV-2 has spread to over two hundred countries and infected more than 4.8 million people, resulting in over 300,000 deaths since the first case of a novel pneumonia (COVID-19) patient was discovered in Wuhan, China at the end of December 2019. Currently, there are no effective and/or approved targeting drugs for it though various supportive therapy drugs such as small molecule drugs, vaccines, antibodies and even Chinese herb medicines have been used in the treatment of the first-line patients. However, certain drugs such as remdesivir and S416 are under clinical investigation and may become therapeutic drugs. In this article, we review and discuss SARS-CoV-2, its person-to-person transmission, genomics and proteomics, and the potential for drug development.

Study on simplified strategies for procedure of rapid detection of water toxicity.

In this work, a simplified procedure of detection of water toxicity based on Pt ultramicroelectrode (UME) and mixed microorganism cultured without sterilization was the first proposed. A stable Pt UME was successfully prepared with a special glass tube as insulation and support material, which was used as working electrode in the biosensor. The Pt UME exhibits the typical cyclic voltammogram (CV) of Pt UME with sigmoid shape and possesses good stability, enlarged current response and tunable dimension. In addition, it was an effective and simple method for toxicity biosensor using mixed microorganisms cultured in unsterilized lysogeny broth (LB) as the bioreceptor. K3[Fe(CN)6] was used as an electron mediator. Under the optimal conditions of 30 mM K3[Fe(CN)6], OD600 = 1 cell concentration, and 50 mM phosphate-buffered solution (PBS), the half-maximal inhibitory concentration (IC50) values measured for Cd2+, Cu2+ and Ni2+ were 3.99 mg/L, 1.16 mg/L and 2.37 mg/L, respectively. The results indicated that the biosensor with large diameter Pt UME and mixed microorganisms cultured in unsterilized LB realized rapid and simple detection of water toxicity.

Comparative studies on Pb(II) biosorption with three spongy microbe-based biosorbents: High performance, selectivity and application.

Lead pollution in industrial-derived water has become an increasingly serious concern. The development of adsorbents with excellent efficiency, selectivity and separability using diverse microorganisms is ideal for treating lead pollution. In this study, gram-negative bacteria Pseudomonas putida I3, gram-positive bacteria Microbacterium sp. OLJ1 and mycelial fungus Talaromyces amestolkiae Pb served as raw materials to facilely synthesize sponge-like biosorbents via a one-step method at room temperature. SEM, EDS, FTIR, 13C NMR, XRD and XPS were used for investigating the morphology and surface properties of these three biosorbents. The obtained biosorbents possessed the same three-dimensional porous structure but different productivities and mechanical strengths due to the similar chemical compositions and different cell structures of their microorganisms. Pb(II) adsorption on X-PI3, X-OLJ1 and X-TPb was fast and pH dependent, with maximal adsorption capacities of 345.02, 237.02 and 199.02 mg/g, respectively. The biosorbents had a high selectivity for Pb(II), while Pb(II) remarkably suppressed the adsorption of co-existing heavy metal ions. The analyses indicated that Pb(II) removal was mainly achieved by ion exchange reactions, surface complexation with heteroatom-containing functional groups and microprecipitation. The treatment effects of synthetic and real wastewater revealed that the as-prepared biosorbents are promising for Pb(II) removal.