Development and validation of a pyroptosis-related prognostic signature associated with osteosarcoma metastasis and immune infiltration.

Pyroptosis is a programmed cell death, which has garnered increasing attention because it relates to the immune and therapy response. However, few studies focus on the application of pyroptosis-related genes (PRGs) in predicting osteosarcoma (OS) patients' prognoses. In this study, the gene expression and clinical information of OS patients were downloaded from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database. Based on these PRGs and unsupervised clustering analysis, all OS samples can be classified into 2 clusters. The 8 key differential expressions for PRGs (LAG3, ITGAM, CCL2, TLR4, IL2RA, PTPRC, FCGR2B, and CD5) were established through the univariate Cox regression and utilized to calculate the risk score of all samples. According to the 8-gene signature, OS samples can be divided into high and low-risk groups and correlation analysis can be performed using immune cell infiltration and immune checkpoints. Finally, we developed a nomogram to improve the PRG-predictive model in clinical application. We verified the predictive performance using receiver operating characteristic (ROC) and calibration curves. There were significant differences in survival, immune cell infiltration and immune checkpoints between the low and high-risk groups. A nomogram was developed with clinical indicators and the risk scores were effective in predicting the prognosis of patients with OS. In this study, a prognostic model was constructed based on 8 PRGs were proved to be independent prognostic factors of OS and associated with tumor immune microenvironment. These 8 prognostic genes were involved in OS development and may serve as new targets for developing therapeutic drugs.

Development and validation of two redox-related genes associated with prognosis and immune microenvironment in endometrial carcinoma.

In recent studies, the tumourigenesis and development of endometrial carcinoma (EC) have been correlated significantly with redox. We aimed to develop and validate a redox-related prognostic model of patients with EC to predict the prognosis and the efficacy of immunotherapy. We downloaded gene expression profiles and clinical information of patients with EC from the Cancer Genome Atlas (TCGA) and the Gene Ontology (GO) dataset. We identified two key differentially expressed redox genes (CYBA and SMPD3) by univariate Cox regression and utilised them to calculate the risk score of all samples. Based on the median of risk scores, we composed low-and high-risk groups and performed correlation analysis with immune cell infiltration and immune checkpoints. Finally, we constructed a nomogram of the prognostic model based on clinical factors and the risk score. We verified the predictive performance using receiver operating characteristic (ROC) and calibration curves. CYBA and SMPD3 were significantly related to the prognosis of patients with EC and used to construct a risk model. There were significant differences in survival, immune cell infiltration and immune checkpoints between the low-and high-risk groups. The nomogram developed with clinical indicators and the risk scores was effective in predicting the prognosis of patients with EC. In this study, a prognostic model constructed based on two redox-related genes (CYBA and SMPD3) were proved to be independent prognostic factors of EC and associated with tumour immune microenvironment. The redox signature genes have the potential to predict the prognosis and the immunotherapy efficacy of patients with EC.

Intergenerational toxic effects of parental exposure to [Cn mim]NO3 (n = 2,4,6) on nervous and skeletal development in zebrafish offspring.

Ionic liquids (ILs) are thought to have negative effects on human health. Researchers have explored the effects of ILs on zebrafish development during the early stages, but the intergenerational toxicity of ILs on zebrafish development has rarely been reported. Herein, parental zebrafish were exposed to different concentrations (0, 12.5, 25, and 50 mg/L) of [Cn mim]NO3 (n = 2, 4, 6) for 1 week. Subsequently, the F1 offspring were cultured in clean water for 96 h. [Cn mim]NO3 (n = 2, 4, 6) exposure inhibited spermatogenesis and oogenesis in F0 adults, even causing obvious lacunae in the testis and atretic follicle oocytes in ovary. After parental exposure to [Cn mim]NO3 (n = 2, 4, 6), the body length and locomotor behavior were measured in F1 larvae at 96 hours post-fertilization (hpf). The results showed that the higher the concentration of [Cn mim]NO3 (n = 2, 4, 6), the shorter the body length and swimming distance, and the longer the immobility time. Besides, a longer alkyl chain length of [Cn mim]NO3 had a more negative effect on body length and locomotor behavior. RNA-seq analysis revealed several downregulated differentially expressed genes (DEGs)-grin1b, prss1, gria3a, and gria4a-enriched in neurodevelopment-related pathways, particularly the pathway for neuroactive ligand-receptor interaction. Moreover, several upregulated DEGs, namely col1a1a, col1a1b, and acta2, were mainly associated with skeletal development. Expression of DEGs was tested by RT-qPCR, and the outcomes were consistent with those obtained from RNA-Seq. We provide evidence showing the effects of parental exposure to ILs on the regulation of nervous and skeletal development in F1 offspring, demonstrating intergenerational effects.

Intergenerational effects of parental [Cnmim]BF4 (n = 4, 6, 8) ionic liquids exposure on zebrafish development based on transcriptomic analysis.

Ionic liquids (ILs) have been developed as alternatives to traditional solvents, and their toxicity may be affected by alkyl chain length. Currently, there is limited evidence for whether parental exposure to different alkyl chain length ILs will induce intergenerational toxicity in zebrafish offspring. To address this knowledge gap, the parental zebrafish (F0) were exposed to 25 mg/L [Cnmim]BF4 (n = 4, 6, 8) for 7 days. Following this, fertilized F1 embryos from the exposed parents were reared in clean water for 120 h. Increased mortality, higher deformity rate, increased pericardial edema rate, and a shorter swimming distance and average speed were detected in the unexposed F1 embryonic larvae from the exposed F0 compared to the F1 generation from the unexposed F0. Parental exposure to [Cnmim]BF4 (n = 4, 6, 8) resulted in cardiac malformations and dysfunction in F1 larvae, including increased pericardial areas, increased yolk sac areas and decreased heart rate. Moreover, the intergenerational toxicity of [Cnmim]BF4 (n = 4, 6, 8) in F1 offspring appeared to be alkyl chain length-dependent. Parental [Cnmim]BF4 (n = 4, 6, 8) exposure led to global transcriptomic changes involved in developmental processes, nervous system process, cardiomyopathy, cardiac muscle contraction, and metabolic signalling pathways such as PI3K-Akt, PPAR and cAMP pathways in unexposed F1 offspring. Overall, the present study provides evidence that the neurotoxicity and cardiotoxicity of ILs in zebrafish can be markedly transmitted to offspring, and the intergenerational developmental toxicity is probably linked to transcriptomic alterations, highlighting the necessity of assessing ILs' environmental safety and human health risks.

Single-Cell Transcriptomics-Based Study of Transcriptional Regulatory Features in the Non-Obstructive Azoospermia Testis.

Non-obstructive azoospermia (NOA) is one of the most important causes of male infertility. Although many congenital factors have been identified, the aetiology in the majority of idiopathic NOA (iNOA) cases remains unknown. Herein, using single-cell RNA-Seq data sets (GSE149512) from the Gene Expression Omnibus (GEO) database, we constructed transcriptional regulatory networks (TRNs) to explain the mutual regulatory relationship and the causal relationship between transcription factors (TFs). We defined 10 testicular cell types by their marker genes and found that the proportion of Leydig cells (LCs) and macrophages (tMΦ) was significantly increased in iNOA testis. We identified specific TFs including LHX9, KLF8, KLF4, ARID5B and RXRG in iNOA LCs. In addition, we found specific TFs in iNOA tMΦ such as POU2F2, SPIB IRF5, CEBPA, ELK4 and KLF6. All these identified TFs are strongly engaged in cellular fate, function and homeostasis of the microenvironment. Changes in the activity of the above-mentioned TFs might affect the function of LCs and tMΦ and ultimately cause spermatogenesis failure. This study illustrate that these TFs play important regulatory roles in the occurrence and development of NOA.

The Activated AMPK/mTORC2 Signaling Pathway Associated with Oxidative Stress in Seminal Plasma Contributes to Idiopathic Asthenozoospermia.

Asthenozoospermia is a common form of abnormal sperm quality in idiopathic male infertility. While most sperm-mediated causes have been investigated in detail, the significance of seminal plasma has been neglected. Herein, we aimed to investigate the possible pathogenic factors leading to decreased sperm motility based on seminal plasma. Semen was collected from normo- (NOR, n = 70), idiopathic oligo- (OLI, n = 57), and idiopathic asthenozoospermic (AST, n = 53) patients. Using attenuated total reflection-Fourier transform infrared coupled with chemometrics, distinct differences in the biochemical compositions of nucleic acids, protein structure (amides I, II, and III), lipids, and carbohydrates in seminal plasma of AST were observed when compared to NOR and OLI. Compared with NOR and OLI, the levels of peptide aggregation, protein phosphorylation, unsaturated fatty acid, and lipid to protein ratio were significantly increased in AST; however, the level of lipid saturation was significantly decreased in seminal plasma of AST. Compared with NOR, the levels of ROS, MDA, 8-iso-prostaglandin F2α (8-isoPGF2α), and the ratio of phospho-AMPKα/AMPKα1 were significantly increased in AST; however, the levels of SOD, glutathione S-transferase (GSTs), protein carbonyl derivative (PC), and the ratio of phospho-Rictor/Rictor were significantly decreased in seminal plasma of AST. Changes of the AMPK/mTORC2 signaling in the seminal microenvironment possibly induce abnormal glucose and lipid metabolism, which impairs energy production. Oxidative stress potentially damages seminal plasma lipids and proteins, which in turn leads to impaired sperm structure and function. These findings provide evidence that the changes in seminal plasma compositions, oxidative stress, and activation of the AMPK/mTORC2 signaling contribute to the development of asthenozoospermia.

Polystyrene microplastics sunlight-induce oxidative dissolution, chemical transformation and toxicity enhancement of silver nanoparticles.

The coexistence of microplastics (MPs) and nanomaterials has been increasingly studied, but the influence of MPs on the chemical transformation of nanomaterials remains unclear. Herein, it was demonstrated that polystyrene (PS) MPs induce the oxidative dissolution, transformation and toxicity of silver nanoparticles (Ag NPs) under simulated sunlight irradiation. The PS MPs induced the oxidation dissolution of pristine Ag NPs by 1O2, OH and/or acid release and simultaneously reduced the released Ag+ to secondary Ag NPs by O2-. The sizes, functional groups and ageing status of the PS MPs and pH characterized secondary Ag NPs formation. Secondary formation of Ag NPs induced by PS MPs also occurred in realistic water and was governed by dissolved organic matter (DOM) and Cl-, rather than SO42- or CO32-. Moreover, PS MPs remarkably promoted Ag+ release, altered the Ag+:Ag0 ratio, and presented vehicle effects on Ag+ toxicity to Daphnia magna. The concentration addition model demonstrated that the ion-related toxicity of Ag NPs was significantly increased by PS MPs. Therefore, PS MPs induced the oxidative dissolution, transformation and toxicity enhancement of Ag NPs under sunlight irradiation, and accordingly, the coexistence of PS MPs and Ag NPs in freshwater environments should be seriously considered.

Multi- and transgenerational biochemical effects of low-dose exposure to bisphenol A and 4-nonylphenol on testicular interstitial (Leydig) cells.

Bisphenol A (BPA) and 4-nonylphenol (NP) are well-known endocrine-disrupting chemicals (EDCs) that have been proven to affect Leydig cell (LC) functions and testosterone production, but whether BPA and NP have multi- and transgenerational biochemical effects on Leydig cells (LCs) is unknown. Fourier transform infrared (FTIR) spectroscopy is a powerful analytical technique that enables label-free and non-destructive analysis of the tissue specimen. Herein we employed FTIR coupled with chemometrics analysis to identify biomolecular changes in testicular interstitial (Leydig) cells of rats after chronic exposure to low doses of BPA and NP. Cluster segregations between exposed and control groups were observed based on the fingerprint region of 1800-900 cm-1 in all generations. The main biochemical alterations for segregation were amide I, amide II and nucleic acids. BPA and NP single and co-exposure induced significant differences in the ratio of amide I to amide II compared to the corresponding control group in all generations. BPA exposure resulted in remarkable changes of cellular gene transcription and DNA oxidative damage across all generations. Direct exposure to BPA, NP, and BPA&NP of F0 and F1 generations could significantly decrease lipid accumulation in LCs in the F2 and F3 generations. The overall findings revealed that single or co-exposure to BPA and NP at environmental concentrations affects the biochemical structures and properties of LCs.

Influence of polystyrene microplastics on the volatilization, photodegradation and photoinduced toxicity of anthracene and pyrene in freshwater and artificial seawater.

In this study, the influences of polystyrene microplastics (PS MPs) on the volatilization, photodegradation and photoinduced toxicities of anthracene and pyrene were determined in freshwater and artificial seawater. The PS MPs reduced the volatilization of anthracene and pyrene, and the volatilization reduction was highly dependent on the PS MPs sizes and concentrations. The PS MPs increased the photodegradation kinetics (kp) of anthracene by promoting 1O2 generation and altered the photodegradation pathways through OH attack of the photodegradation byproducts. However, the kp of pyrene was decreased by PS MPs suppressing the transfer of electrons from excited pyrene to oxygen. The PS MPs modified the pathways of pyrene photodegradation via OH attack of the photodegradation byproducts. Due to light shielding by DOM and/or PS MPs aggregates in seawater, the modification of the photodegradation pathways of anthracene and pyrene by PS MPs was hardly happened in seawater compared with in freshwater. By changing the concentrations of anthracene or pyrene and their photodegradation byproducts, the PS MPs greatly affected the photoinduced toxicities of anthracene and pyrene to Selenastrum capricornutum and Phaeodactylum tricornutum. The influences of PS MPs on the volatilization, photodegradation and photoinduced toxicity of anthracene and pyrene are important and should be carefully considered during environmental risk assessments of anthracene and pyrene.

The contributions and mechanisms of iron-microbes-biochar in constructed wetlands for nitrate removal from low carbon/nitrogen ratio wastewater.

The removal efficiency of nitrate from low carbon/nitrogen ratio wastewater has been restricted by the lack of organics for several decades. Here, a system coupling chemical reduction, microbial denitrification and constructed wetlands (RDCWs) was developed to investigate the effect and possible mechanisms for nitrate degradation. The results showed that this coupling system could achieve a nitrate removal efficiency of 97.07 ± 1.76%, 85.91 ± 3.02% and 56.63 ± 2.88% at a hydraulic retention time of 24 h, 12 h and 6 h with feeding nitrate of 15 mg L-1, respectively. These removal efficiencies of nitrate were partly caused by microbes and biochar with a contribution rate of 31.08 ± 4.43% and 9.50 ± 3.30%. Besides, microbes were closely related to iron and biochar for the removal of nitrate. Simplicispira was able to utilize hydrogen produced by iron corrosion as an electron donor while nitrate accepted electrons to be reduced. Porous biochar could release dissolved organic matter, which provided a good living circumstance and carbon source for microbes. Therefore, the RDCW system is potential for large-scale application due to its low cost and simple operation.

Bacteria-supported iron scraps for the removal of nitrate from low carbon-to-nitrogen ratio wastewater.

A novel bacteria-supported iron scraps (BSIS) system was developed for nitrate removal from low carbon-to-nitrogen ratio (C/N) wastewater. The system consisted of low-cost iron scraps and the accumulated denitrifying-related bacteria enriched from an Fe-wastewater environment when the system was operating. After operating for 39 d, the nitrate removal rate of the system increased to 73.55% within 24 h. The extraction of bacteria from the system revealed that iron scraps and bacteria had a synergistic effect on nitrate removal and bacteria only took effect when cooperating with iron. Microbial analysis using high-throughput sequencing showed that Hydrogenophaga, which is closely related to hydrogenotrophic denitrification, became the dominant genus in the system. The system provides a promising approach to the treatment of nitrate in low C/N wastewater and it has the potential for large-scale application due to the low cost, simple operation and relatively high removal rate.

Dual impact of dissolved organic matter on cytotoxicity of PVP-Ag NPs to Escherichia coli: Mitigation and intensification.

Cytotoxicity of silver nanoparticles (Ag NPs) is attributed to silver internalization, which can be depressed by dissolved organic matter (DOM) to form Ag-DOM. Ag-DOM are bioavailable and then silver internalization could be increased. Herein, 3 and 48-h Escherichia coli viability bioassays were employed to evaluate effect of fulvic acid and humic acid (10 mg L-1) on cytotoxicity of 30 and 100 nm PVP-Ag NPs. Moreover, zebrafish embryos were used as reference model to understand silver internalization routes. Ag ions or Ag-DOM internalization varied in routes to Escherichia coli and zebrafish embryos. Cytotoxicity mechanisms of PVP-Ag NPs are dynamic. In 3-h bioassays, cytotoxicity of PVP-Ag NPs mainly involves Ag particle-related toxicity. DOM significantly mitigated cytotoxicity of PVP-Ag NPs (p < 0.05) through adhering on surface of PVP-Ag NPs. Ag ions or Ag-DOM were hardly internalized into Escherichia coli cells during 3-h exposures duration. In 48-h bioassays, cytotoxicity of PVP-Ag NPs is dependent on Ag ion-related and particle-related toxicity. Silver was internalized into Escherichia coli via Ag-DOM consumption as an indirect route. Thus, DOM promoted silver internalization into Escherichia coli but not into zebrafish embryos, significantly intensifying cytotoxicity (p < 0.05). The results suggested DOM has a dual impact on cytotoxicity of PVP-Ag NPs: mitigation and intensification. For risk assessment, it should be considered that cytotoxicity mechanisms of PVP-Ag NPs are dynamic and threats can be intensified by DOM during prolonged exposure.

Removal and fate of silver nanoparticles in lab-scale vertical flow constructed wetland.

Engineered nanomaterials (ENMs) are increasingly produced and consequently released into the environment. Therefore, there is a strong need to find a valid way to treat the ENMs pollution. In this study, the removal efficiencies of silver nanoparticles (AgNPs) from synthetic wastewater in lab-scale vertical flow constructed wetland (CW) systems with different operations (plant, hydraulic loading rates, bed depth) were investigated. Moreover, the environmental fate and impacts of AgNPs in CWs were also investigated. The results showed that CWs with plants were more effective in removing AgNPs than the unplanted CWs. Hydraulic loading had a significant effect on the performance of CWs in treating AgNPs, however, the influence of bed depth was negligible. AgNPs stopped in the CWs were mainly resided in the wetland substrate, indicating the main mechanism of AgNPs removal in CWs was through substrate adsorption. Although plant biomass, root activity, peroxidase activity of leaves and biofilm biomass were significantly altered following exposure to AgNPs (P < 0.05), CWs maintained constant high efficiency (63.2-93.8%) in removing AgNPs from wastewater during a continuous 2-month running. Overall, this paper suggests the feasibility and high-efficiency of using CWs to handle AgNPs contamination.

Tissue distribution of Ag and oxidative stress responses in the freshwater snail Bellamya aeruginosa exposed to sediment-associated Ag nanoparticles.

Silver nanoparticles (AgNPs) are among the most widely used engineered nanomaterials and may eventually accumulate in sediments. Limited information is currently available regarding the toxicity, bioaccumulation and distribution of sediment-associated AgNPs in aquatic organisms. In the present study, a freshwater snail Bellamya aeruginosa was exposed via sediment to commercial Ag particles of four nominal sizes: 20 nm (AgNPs-20), 40 nm (AgNPs-40), 80 nm (AgNPs-80), and < 10 µm (bulk Ag), and to silver nitrate at sub-lethal concentrations (1, 10 and 100 µg Ag/g sediment). Ag burden and biomarkers of oxidative stress were assessed in different tissues of B. aeruginosa: hepatopancreas, gonad, foot and digestive tracts. All five Ag types were available for uptake by B. aeruginosa when spiked into sediment, and Ag accumulation in different tissues presented the following pattern: hepatopancreas > gonad ≈ digestive tracts > foot. Snails accumulated higher levels of Ag from aqueous Ag than from particulate Ag. In contrast, AgNPs-40 and AgNPs-80 treatments occasionally induced higher oxidative stress than aqueous Ag, indicating the significant role of nanoparticle itself in exerting toxicity. Size-dependent toxicity of AgNPs in sediment was also found, with AgNPs-20 showing lower toxicity than other Ag particles. Overall, this study demonstrated that the toxicity of sediment-associated AgNPs to B. aeruginosa varies with size and differs from aqueous Ag.

Ground-based synchronous optical instrument for measuring atmospheric visibility and turbulence intensity: theories, design and experiments.

Atmospheric visibility and turbulence are important meteorological factors in light propagation and optical communication, air quality prediction, and climate environment model. They are often measured separately by the conventional instruments, but the interaction between aerosol (closely relate to visibility) and turbulence may potentially influence their measurement accuracy. In this paper, a novel instrument, the atmospheric visibility and turbulence optical meter (AVTOM), is developed to synchronously measure atmospheric visibility and turbulence intensity through a transmission method. The atmospheric visibility is measured by the extinction principle whereas the turbulence intensity is measured by the light intensity flicker principle. We validated the measurement results by comparing them to other two conventional instruments in July 2017, at Nanjing, in southeast China. They agree well with the relative differences of 4.7% for the visibility and 3.5% for the turbulence intensity, respectively. We further demonstrated their dynamic changes under the different weather or aerosol loadings through the synchronous measurements, which may be associated with the aerosol-turbulence-interaction. Finally, we proposed a calibration method and discussed the measurement errors.

A simple method to detect the heterogeneity of nucleotide substitution processes by measuring asymmetry in paired comparison.

A simple method is presented, which uses a chi2 statistic to measure asymmetry of the substitution matrix between two DNA sequences in order to test a homogeneity hypothesis of the substitution processes. In theory, this chi2 test holds irrespective of whether there is among-site (i) heterogeneity in substitution rates, (ii) correlation in evolutionary rates/models, and (iii) variation in substitution models. Computer simulations showed that the chi2 test is powerful under a variety of models of sequence evolution. Comparison of the eleven sequenced arthropod mtDNAs by using this test revealed that most of the observed evolutionary models were homogeneous between the two mosquitoes but not between Daphnia pulex or Artemia franciscan and the other arthropods, probably due to shifts to a high AT content. A comparison to Kumar and Gadagkar's test by computer simulation as well as empirical data analysis is also given.