Antibiotic resistance at environmental multi-media interfaces through integrated genotype and phenotype analysis.

Antibiotic resistance is currently an unfolding global crisis threatening human health worldwide. While antibiotic resistance genes (ARGs) are known to be pervasive in environmental media, the occurrence of antibiotic resistance at interfaces between two or more adjacent media is largely unknown. Here, we designed a microcosm study to simulate plastic pollution in paddy soil and used a novel method, stimulated Raman scattering coupled with deuterium oxide (D2O) labelling, to compare the antibiotic resistance in a single medium with that at the interface of multiple environmental media (plastic, soil, water). Results revealed that the involvement of more types of environmental media at interfaces led to a higher proportion of active resistant bacteria. Genotypic analysis showed that ARGs (especially high-risk ARGs) and mobile genetic elements (MGEs) were all highly enriched at the interfaces. This enrichment was further enhanced by the co-stress of heavy metal (arsenic) and antibiotic (ciprofloxacin). Our study is the first to apply stimulated Raman scattering to elucidate antibiotic resistance at environmental interfaces and reveals novel pathway of antibiotic resistance dissemination in the environment and overlooked risks to human health.

Antioxidant Defenses Against Air Humidity Stress in Fruit Bodies of Auricularia heimuer (Agaricomycetes).

Air humidity is an important environmental factor restricting the fruit body growth of Auricularia heimuer. Low air humidity causes the fruit body to desiccate and enter dormancy. However, the survival mechanisms to low air humidity for fruit bodies before dormancy remain poorly understood. In the present study, we cultivated A. heimuer in a greenhouse and collected the fruit bodies at different air humidities (90%, 80%, 70%, 60%, and 50%) to determine the contents of malondialdehyde (MDA) and non-enzymatic antioxidants such as ascorbic acid (AsA) and glutathione (GSH); and the activities of enzymatic antioxidants including superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX), glutathione peroxidase (GPX) and glutathione reductase (GR). Results showed that the MDA contents tended to increase with decreasing relative air humidity. Relative air humidity below 90% caused membrane lipid peroxidation and oxidative stress (based on MDA contents) to the fruit body, which we named air humidity stress. In contrast to the control and with the degree of stress, the GSH contents and activities of SOD, CAT, GR, GPX, and APX tended to ascend, whereas AsA showed a declining trend; the POD activity only rose at 50%. The antioxidants favored the fruit body to alleviate oxidative damage and strengthened its tolerance to air humidity stress. The antioxidant defense system could be an important mechanism for the fruit body of A. heimuer in air humidity stress.

Selective enrichment of virulence factor genes in the plastisphere under antibiotic and heavy metal pressures.

The growing accumulation of plastic waste in the environment has created novel habitats known as the "plastisphere", where microorganisms can thrive. Concerns are rising about the potential for pathogenic microorganisms to proliferate in the plastisphere, posing risks to human health. However, our knowledge regarding the virulence and pathogenic potential of these microorganisms in the plastisphere remains limited. This study quantified the abundance of virulence factor genes (VFGs) in the plastisphere and its surrounding environments (water and soil) to better assess pathogenic risks. Our findings revealed a selective enrichment of VFGs in the plastisphere, which were attributed to the specific microbial community assembled. The presence of arsenic and ciprofloxacin in the plastisphere exerted additional co-selective pressures, intensifying the enrichment of VFGs. Notably, VFGs that encoded multiple functions or enhanced the survival of host microorganisms (e.g., encoding adherence functions) tended to accumulate in the plastisphere. These versatile and environmentally adaptable VFGs are more likely to be favored by bacteria in the environment, warranting increased attention in future investigations due to their potential for widespread dissemination. In terms of virulence and pathogenicity, this research offers new insights into evaluating pathogen-related risks in the plastisphere.

Flooding drives the temporal turnover of antibiotic resistance gene in manure-amended soil-water continuum.

Rice paddy soil is a hotspot of antibiotic resistance genes (ARGs) due to the application of organic fertilizers. However, the temporal dynamics of ARGs in rice paddy soil and its flooded water during the growing season remain underexplored. In this study, a microcosm experiment was conducted to explore the ARG profiles in a long term (130 days) flooded two-phase manure-amended soil-water system. By using high-throughput quantitative PCR array, a total of 23-98 and 34-85 ARGs were detected in the soil and overlying water, respectively. Regression analysis exhibited significant negative correlations between ARG profile similarities and flooding duration, indicating that flooding significantly altered the resistome (P < 0.001). This finding was validated by the increased ARG abundance in the soil and the overlying water, for example, after 130 days flooding, the abundance of ARGs in CK soil was increased from 0.03 to 1.20 copies per 16S rRNA. The PCoA analysis further suggested pig manure application resulted in distinct ARG profiles in the soil-water continuum compared with those of the non-amended control (Adonis, P < 0.05). The Venn diagram showed that all ARGs detected in the pig manure were present in the treated soil. Twelve ARGs (e.g., sul1) were shared among the pig manure, manure-amended soil, and overlying water, indicating that certain manure- or soil-borne ARGs were readily dispersed from the soil to the overlying water. Moreover, the enhanced relationships between the ARGs and mobile genetic elements in pig manure applied soil-water continuum indicate that the application of organic matter could accelerate the emergence and dissemination of ARGs. These findings suggested that flooding represents a crucial pathway for dispersal of ARGs from the soil to the overlying water. Identification of highly mobile ARGs in the soil-water continuum is essential for assessing their potential risk to human health and promoting the development of sustainable agricultural practices to mitigate their spread.

Application and planning of an energy-oriented stochastic disassembly line balancing problem.

End-of-life (EOL) products are getting more and more attention as a result of the rapid decline in environmental resources and the dramatic rise in population at the moment. Disassembly is a crucial step in the reuse of EOL products. However, the disassembly process for EOL products is highly uncertain, and the disassembly planning method may not produce the anticipated outcomes in actual implementation. Based on the physical nature of the product disassembly process with multiple uncertain variables, certainty disassembly cannot adequately characterize the uncertain variables effectively. Uncertainty disassembly takes into account the changes in parts caused by product use, such as wear and corrosion, which can better coordinate the arrangement of disassembly tasks and better match the actual remanufacturing process. After analysis, it was found that most of studies on uncertain disassembly focus on the economic efficiency perspective and lack of energy consumption considerations. For the gaps in the current study, this paper proposes a stochastic energy consumption disassembly line balance problem (SEDLBP) and constructs a mathematical model of SEDLBP based on the disassembly of spatial interference matrix, In this model, the energy consumption generated by the disassembly operation and workstation standby is not a constant value but is generated stochastically in a uniformly distributed interval. In addition, an improved social engineering optimization algorithm that incorporates stochastic simulation (SSEO) is proposed in this paper to effectively address the issue. The incorporation of swap operators and swap sequences in SSEO makes it possible to solve discrete optimization problems efficiently. A comparison of a case study with some well-tested intelligent algorithms demonstrates the efficacy of the solutions produced by the proposed SSEO.

pH drives the spatial variation of antibiotic resistance gene profiles in riparian soils at a watershed scale.

Owing to convenient water access, riparian areas are often sites for intensive livestock breeding industries and agriculture, which can increase the spread of antibiotic resistance genes (ARGs). However, studies on ARG profiles in riparian soils are limited and there is little information regarding the factors influencing ARGs at a watershed scale. Here, we analyzed ARG profiles, bacterial communities, and soil properties in riparian soils under different land-use types. A total of 124 ARGs and 25 mobile genetic elements (MGEs) were detected in the riparian soils, which covered almost all major classes of antibiotics. Non-metric multidimensional scaling analysis showed that both the distance to the water reservoir and land-use types played important roles in shaping ARG profiles in riparian soils at a watershed scale. Downstream soils harbored three times the abundance of ARGs compared with upstream and midstream soils. Distance-decay analysis indicated that the similarity of ARG profiles and bacterial community composition decreased significantly with the increase of geographical distance (p < 0.001). When taking the land-use type into consideration, the relative abundance and diversity of ARGs and MGEs in orchard and farmland soils were significantly higher than those in wasteland soils. This indicated that anthropogenic activities can also affect ARG patterns in riparian soils. MGE abundance was identified as major driving factors of ARG profiles. In addition, among all the examined soil properties, soil pH was found to be more important than nutrients and organic carbon in shaping ARG profiles. Our findings provide valuable data on ARG distribution in riparian soils in a reservoir catchment and highlight downstream soils is crucial for ensuring water source security.

Environment-oriented disassembly planning for end-of-life vehicle batteries based on an improved northern goshawk optimisation algorithm.

Due to environmental pollution and resource shortages, the electric vehicle industry has been developing swiftly, and the market demand for batteries, as an essential part of electric vehicles, has also surged. Proper disassembly of end-of-life vehicle batteries (ELV batteries) is necessary to achieve the integrity and closure of their life cycle, promote the development of green remanufacturing, effectively reduce the pollution of the environment caused by metal ion leakage, and reduce people's dependence on natural resources to a certain extent. To schedule the disassembly operations of ELV batteries more rationally and further promote their disassembly quality and efficiency, this paper proposes a dual-objective disassembly sequence planning (DSP) optimisation model, which aims to minimise the hazard index and energy cost during ELV battery disassembly operations. Since the proposed model is a complex NP-hard optimisation problem, this study develops an efficient metaheuristic algorithm for solving this model based on the northern goshawk optimisation algorithm. The main algorithm adds two types of discrete recombination operators and a local search operator. At the same time, the predatory behaviour of the goshawk is optimised by combining the characteristics of the disassembly sequence planning problem to improve its performance. Finally, the disassembly of the battery of a Tesla Model 1 is used as a case study to demonstrate the effectiveness and feasibility of the proposed method.

New insights into change of lens proteins' stability with ageing under physiological conditions.

BACKGROUND: Age-related cataract, which presents as a cloudy lens, is the primary cause of vision impairment worldwide and can cause more than 80% senile blindness. Previous studies mainly explored the profile of lens proteins at a low concentration because of technical limitations, which could not reflect physiological status. This study focuses on protein stability changes with ageing under physiological conditions using a novel equipment, Unchained Labs (Uncle), to evaluate protein thermal stability. METHODS: Samples were assessed through Unchained Labs, size-exclusion chromatography, western blot and biophysics approaches including the Thioflavin T, ultraviolet and internal fluorescence. RESULTS: With age, the melting temperature value shifted from 67.8°C in the young group to 64.2°C in the aged group. Meanwhile, crystallin may form more isomeric oligomers and easy to be degraded in aged lenses. The spectroscopic and size-exclusion chromatography results show a higher solubility after administrated with lanosterol under the environmental stress. CONCLUSION: We are the first to explore rabbit lens protein stability changes with ageing using biophysical methods under physiological conditions, and this study can conclude that the structural stability and solubility of lens proteins decrease with ageing. Additionally, lanosterol could aid in resolving protein aggregation, making it a potential therapeutic option for cataracts. So, this study provides cataract models for anti-cataract drug developments.

Heterozygous variants c.781G>A and c.1066dup of serine protease 56 cause familial nanophthalmos by impairing serine-type endopeptidase activity.

BACKGROUND/AIMS: Nanophthalmos is a rare developmental, bilateral, sporadic or hereditary form of microphthalmos. In this study, the heterozygous variants c.781G>A and c.1066dup of the PRSS56 gene were identified in two patients with nanophthalmos. This study reports the clinical manifestation and the underlying pathogenic mechanism. METHODS: Whole-exome sequencing was performed to identify the pathogenic genes in a Chinese family with nanophthalmos. The molecular simulation was used to predict the structures of wild-type or mutant PRSS56. The PRSS56 wild-type or mutation overexpression cellular models have been constructed accordingly. The subcellular localisation was then observed using immunofluorescence and Western-blot techniques. The Folin-Ciocalteu assay was carried out to evaluate serine-type endopeptidase activity, and a wound-healing assay was used to examine the cellular migratory ability. RESULTS: The whole-exome sequencing revealed that heterozygous variants c.781G>A and c.1066dup of the PRSS56 gene might contribute to nanophthalmos. Both variants were not identified in the dbSNP, 1000 Genome project or ESP6500 databases. Furthermore, the variants were highly conserved and were involved in biological functions. The mutations result in destructive protein structure and impede serine-type endopeptidase activity, thereby impairing subcellular localisation and cellular migration. CONCLUSION: The c.781G>A and c.1066dup variants of the PRSS56 gene might negatively affect protein structures, subcellular localisation, serine-type endopeptidase activity and cellular migratory ability. Together, these changes could lead to the development of nanophthalmos. This study identifies the PRSS56 gene as a potential target for nanophthalmos diagnosis and treatment.

Comparative analysis of antibiotic resistance genes on a pig farm and its neighboring fish ponds in a lakeside district.

Antibiotics usage in animal production is considered a primary driver of the occurrence, supply and spread of antibiotic resistance genes (ARGs) in the environment. Pig farms and fish ponds are important breeding systems in food animal production. In this study, we compared and analyzed broad ARGs profiles, mobile genetic elements (MGEs) and bacterial communities in a representative pig farm and neighboring fish ponds around Poyang Lake, the largest freshwater lake in China. The factors influencing the distribution of ARGs were also explored. The results showed widespread detection of ARGs (from 57 to 110) among 283 targeted ARGs in the collected water samples. The differences in the number and relative abundance of ARGs observed from the pig farm and neighboring fish ponds revealed that ARG contamination was more serious on the pig farm than in the fish ponds and that the water treatment plant on the pig farm was not very effective. Based on the variance partition analysis (VPA), MGEs, bacterial communities and water quality indicators (WIs) codrive the relative abundance of ARGs. Based on network analysis, we found that total phosphorus and Tp614 were the most important WIs and MGEs affecting ARG abundance, respectively. Our findings provide fundamental data on farms in lakeside districts and provide insights into establishing standards for the discharge of aquaculture wastewater.

Cataract-causing allele in CRYAA (Y118D) proceeds through endoplasmic reticulum stress in mouse model.

As small heat shock proteins, α-crystallins function as molecular chaperones and inhibit the misfolding and aggregation of ß/γ-crystallins. Genetic mutations of CRYAA are associated with protein aggregation and cataract occurrence. One possible process underlying cataract formation is that endoplasmic reticulum stress (ERS) induces the unfolded protein response (UPR), leading to apoptosis. However, the pathogenic mechanism related to this remains unexplored. Here, we successfully constructed a cataract-causing CRYAA (Y118D) mutant mouse model, in which the lenses of the CRYAA-Y118D mutant mice showed severe posterior rupture, abnormal morphological changes, and aberrant arrangement of crystallin fibers. Histological analysis was consistent with the clinical pathological characteristics. We also explored the pathogenic factors involved in cataract development through transcriptome analysis. In addition, based on key pathway analysis, up-regulated genes in CRYAA-Y118D mutant mice were implicated in the ERS-UPR pathway. This study showed that prolonged activation of the UPR pathway and severe stress response can cause proteotoxic and ERS-induced cell death in CRYAA-Y118D mutant mice.

Cataract-causing mutations L45P and Y46D impair the thermal stability of γC-crystallin.

Crystallin gene mutations are responsible for about half of the congenital cataract caused by genetic disorders. L45P and Y46D mutations of γC-crystallin have been reported in patients with nuclear congenital cataract. In this study, we explored the thermal stability of wild type (WT), L45P, and Y46D mutants of γC-crystallin at low and high concentrations, as well as the effect of αA-crystallin on the thermal stability of mutants. Spectroscopic experiments were used to monitor the structural changes on temperature-gradient and time-course heating process. Intermediate morphologies were determined through cryo-electron microscopy. The thermal stability of WT and mutants at concentrations ranging up to hundreds of milligrams were assessed via the UNcle multifunctional protein stability analysis system. The results showed that L45P and Y46D mutations impaired the thermal stability of γC-crystallin at low (0.2 mg/mL) and high concentrations (up to 200 mg/mL). Notably, with increase in protein concentration, the thermal stability of L45P and Y46D mutants of γC-crystallin simultaneously decreased. Thermal stability of L45P and Y46D mutants could be rescued by αA-crystallin in a concentration-dependent manner. The dramatic decrease in thermal stability of γC-crystallin caused by L45P and Y46D mutations contributed to congenital cataract in the mature human lens.

Timing Performance Simulation for 3D 4H-SiC Detector.

To meet the high radiation challenge for detectors in future high-energy physics, a novel 3D 4H-SiC detector was investigated. Three-dimensional 4H-SiC detectors could potentially operate in a harsh radiation and room-temperature environment because of its high thermal conductivity and high atomic displacement threshold energy. Its 3D structure, which decouples the thickness and the distance between electrodes, further improves the timing performance and the radiation hardness of the detector. We developed a simulation software-RASER (RAdiation SEmiconductoR)-to simulate the time resolution of planar and 3D 4H-SiC detectors with different parameters and structures, and the reliability of the software was verified by comparing the simulated and measured time-resolution results of the same detector. The rough time resolution of the 3D 4H-SiC detector was estimated, and the simulation parameters could be used as guideline to 3D 4H-SiC detector design and optimization.

Cataract-causing mutations L45P and Y46D promote γC-crystallin aggregation by disturbing hydrogen bonds network in the second Greek key motif.

Congenital cataracts caused by genetic disorders are the primary cause of child blindness across the globe. In this work, we investigated the underlying molecular mechanism of two mutations, L45P and Y46D of γC-crystallin in two Chinese families causing nuclear congenital cataracts. Spectroscopic experiments were performed to determine structural differences between the wild-type (WT) and the L45P or Y46D mutant of γC-crystallin, and the structural stabilities of the WT and mutant proteins were measured under environmental stress (ultraviolet irradiation, pH disorders, oxidative stress, or chemical denaturation). The L45P and Y46D mutants had lower protein solubility and more hydrophobic residues exposed, making them prone to aggregation under environmental stress. The dynamic molecular simulation revealed that the L45P and Y46D mutations destabilized γC-crystallin by altering the hydrogen bonds network around the Trp residues in the second Greek key motif. In summary, L45P and Y46D mutants of γC-crystallin caused more hydrophobic residues to be solvent-exposed, lowered the solubility of γC-crystallin, and increased aggregation propensity under environmental stress. These might be the pathogenesis of γC-crystallin L45P and Y46D mutants related to congenital cataract.

ßB2 W151R mutant is prone to degradation, aggregation and exposes the hydrophobic side chains in the fourth Greek Key motif.

Studies have established that congenital cataract is the major cause of blindness in children across the globe. The ß-crystallin protein family is the richest and most soluble structural protein in the lens. Their solubility and stability are essential in maintaining lens transparency. In this study, we identified a novel ßB2 mutation W151R in a rare progressive cortical congenital cataract family and explored its pathogenesis using purified protein and mutant related cataract-cell models. Due to its low solubility and poor structural stability, the ßB2 W151R mutation was prone to aggregation. Moreover, the W151R mutation enhanced the exposure of the hydrophobic side chains in the fourth Greek Key motif, which were readily degraded by trypsin. However, upon the administration of lanosterol, the negative effect of the W151R mutation was reversed. Therefore, lanosterol is a potential therapeutic option for cataracts.

The cataract-related S39C variant increases γS-crystallin sensitivity to environmental stress by destroying the intermolecular disulfide cross-links.

γS-crystallin, a crucial structural lens protein, plays an important role in maintaining lens transparency through its solubility and stability. The S39C mutation, a proven pathogenic mutation involved in congenital cataract, resulted in progressive cataract in adolescents. In this study, using biophysical methods, we thoroughly investigated the effects of the S39C mutation on the γS-crystallin structure, stability and propensity for aggregations. The data from spectroscopy analyses did not reveal an effect of the S39C mutation on the native structure of monomeric γS-crystallin. However, when faced with oxidative conditions, the S39C mutation prevented γS-crystallin from forming stable disulfide-linked dimers and remarkably increased hydrophobicity and the propensity to aggregate and precipitate. Under UV irradiation, heat shock, and GdnHCl-induced denaturation, the S39C mutant tended to aggregate and was prone to form more deleterious aggregates than the wild type protein. Therefore, the S39C mutation significantly increased the sensitivity of γS-crystallin to environmental stress. However, the addition of αA-crystallin and lanosterol did not change the tendency of the mutant to aggregate. According to molecular dynamic (MD) simulations, the S39C mutation had little effect on the secondary or tertiary structures of monomeric γS-crystallin but disrupted the disulfide-linked structure of the γS-crystallin dimer. The cleavage of this bond might largely reduce the structural stability of γS-crystallin. The significant decrease in the structural stability along with the increasing aggregation tendency under environmental stress might be the major causes of progressive juvenile onset cataracts induced by the S39C mutation.

Bimanual Microincision Cataract Surgery versus Coaxial Microincision Cataract Surgery: A Meta-Analysis of Randomized Controlled Trials and Cohort Studies.

PURPOSE: This meta-analysis was conducted to compare the intraoperative and postoperative outcomes of bimanual microincision cataract surgery (B-MICS) and coaxial microincision cataract surgery (C-MICS). METHODS: Three databases were searched for papers that compared B-MICS and C-MICS from inception to June 2016. The following intraoperative and postoperative outcomes were included in the final meta-analysis: ultrasound time (UST), effective phacoemulsification time (EPT), balanced salt solution use (BSS use), mean surgery time, best-corrected visual acuity (BCVA), central corneal thickness (CCT), and increased CCT. RESULTS: There were no statistically significant differences in mean surgery time, UST, BSS use, BCVA, CCT, or increased CCT (one subgroup at postoperative day 7-8 and another subgroup at postoperative day 30). However, there was less EPT needed during surgery (p < 0.01) and lower levels of increased CCT at postoperative day 1 (p = 0.02) in the B-MICS group compared with the C-MICS group. CONCLUSIONS: The EPT was shorter and increased CCT was less at postoperative day 1 in the B-MICS group. There were no statistically significant differences in other intraoperative and postoperative outcomes between the B-MICS group and the C-MICS group. B-MICS is an efficient and safe cataract surgery procedure.

Identification of drought-responsive microRNAs and their targets in Ammopiptanthus mongolicus by using high-throughput sequencing.

MicroRNAs (miRNAs) regulate target gene expression to modulate plant growth, development, and biotic and abiotic stress response at the post-transcriptional level. Ammopiptanthus mongolicus, an ecologically important desert plant, is increasingly used as a model for studying stress tolerance in plants. The miRNA-mediated gene regulatory network might remarkably contribute to the high stress tolerance of A. mongolicus. However, a genome-wide identification of miRNAs and their targets is still lacking in A. mongolicus. In this study, 170 conserved and 156 non-conserved miRNAs were identified in A. mongolicus. We experimentally identified 298 miRNA-target pairs from the degradome data. Quantitative real-time polymerase chain reaction analyses identified 28 drought-responsive miRNAs in leaves and 15 in roots. Some characteristics of the miRNA-mediated regulatory network were found in A. mongolicus. Multiple miRNAs, including 2 newly identified non-conserved miRNAs, miR-P11 and miR-P14, generated from the precursors of miR169, were found to be involved in drought stress response. Further, miR2118 and miR858 participated in drought stress response by up-regulating OZF1 gene and certain MYB genes that were involved in the regulation of flavonol biosynthesis in A. mongolicus. The findings of this study might provide new insights for understanding the functions of miRNA in stress response in plants.

Fabrication of Boron Nitride Nanosheets by Exfoliation.

Nanomaterials with layered structures, with their intriguing properties, are of great research interest nowadays. As one of the primary two-dimensional nanomaterials, the hexagonal boron nitride nanosheet (BNNS, also called white graphene), which is an analogue of graphene, possesses various attractive properties, such as high intrinsic thermal conductivity, excellent chemical and thermal stability, and electrical insulation properties. After being discovered, it has been one of the most intensively studied two-dimensional non-carbon nanomaterials and has been applied in a wide range of applications. To support the exploration of applications of BNNSs, exfoliation, as one of the most promising approaches to realize large-scale production of BNNSs, has been intensively investigated. In this review, methods to yield BNNSs by exfoliation will be summarized and compared with other potential fabrication methods of BNNSs. In addition, the future prospects of the exfoliation of h-BN will also be discussed.