Effects of different assembly strategies on gene annotation in activated sludge.

Activated sludge comprises diverse bacteria, fungi, and other microorganisms, featuring a rich repertoire of genes involved in antibiotic resistance, pollutant degradation, and elemental cycling. In this regard, hybrid assembly technology can revolutionize metagenomics by detecting greater gene diversity in environmental samples. Nonetheless, the optimal utilization and comparability of genomic information between hybrid assembly and short- or long-read technology remain unclear. To address this gap, we compared the performance of the hybrid assembly, short- and long-read technologies, abundance and diversity of annotated genes, and taxonomic diversity by analysing 46, 161, and 45 activated sludge metagenomic datasets, respectively. The results revealed that hybrid assembly technology exhibited the best performance, generating the most contiguous and longest contigs but with a lower proportion of high-quality metagenome-assembled genomes than short-read technology. Compared with short- or long-read technologies, hybrid assembly technology can detect a greater diversity of microbiota and antibiotic resistance genes, as well as a wider range of potential hosts. However, this approach may yield lower gene abundance and pathogen detection. Our study revealed the specific advantages and disadvantages of hybrid assembly and short- and long-read applications in wastewater treatment plants, and our approach could serve as a blueprint to be extended to terrestrial environments.

Development of a Five-Chemical-Probe Method to Determine Multiple Radicals Simultaneously in Hydroxyl and Sulfate Radical-Mediated Advanced Oxidation Processes.

Advanced oxidation processes (AOPs), such as hydroxyl radical (HO•)- and sulfate radical (SO4•-)-mediated oxidation, are attractive technologies used in water and wastewater treatments. To evaluate the treatment efficiencies of AOPs, monitoring the primary radicals (HO• and SO4•-) as well as the secondary radicals generated from the reaction of HO•/SO4•- with water matrices is necessary. Therefore, we developed a novel chemical probe method to examine five key radicals simultaneously, including HO•, SO4•-, Cl•, Cl2•-, and CO3•-. Five probes, including nitrobenzene, para-chlorobenzoic acid, benzoic acid, 2,4,6-trimethylbenzoic acid, and 2,4,6-trimethylphenol, were selected in this study. Their bimolecular reaction rate constants with diverse radicals were first calibrated under the same conditions to minimize systematic errors. Three typical AOPs (UV/H2O2, UV/S2O82-, and UV/HSO5-) were tested to obtain the radical steady-state concentrations. The effects of dissolved organic matter, Br-, and the probe concentration were inspected. Our results suggest that the five-probe method can accurately measure radicals in the HO•- and SO4•--mediated AOPs when the concentration of Br- and DOM are less than 4.0 µM and 15 mgC L-1, respectively. Overall, the five-probe method is a practical and easily accessible method to determine multiple radicals simultaneously.

Phages in different habitats and their ability to carry antibiotic resistance genes.

As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95-7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.

Mechanistic and Kinetic Consideration of the Photochemically Generated Oxidative Organic Radicals in Dissolved Black Carbon Solutions under Simulated Solar Irradiation.

The photochemically generated oxidative organic radicals (POORs) in dissolved black carbon (DBC) was investigated and compared with that in dissolved organic matter (DOM). POORs generated in DBC solutions exhibited higher one-electron reduction potential values (1.38-1.56 V) than those in DOM solutions (1.22-1.38 V). We found that the photogeneration of POORs from DBC is enhanced with dissolved oxygen (DO) increasing, while the inhibition of POORs is observed in reference to DOM solution. The behavior of the one-electron reducing species (DBC•-/DOM•-) was employed to explain this phenomenon. The experimental results revealed that the DO concentration had a greater effect on DBC•- than on DOM•-. Low DO levels led to a substantial increase in the steady-state concentration of DBC•-, which quenched the POORs via back-electron reactions. Moreover, the contribution of POORs to the degradation of 19 emerging organic contaminants (EOCs) in sunlight-exposed DBC and DOM solutions was estimated. The findings indicate that POORs play an important role in the photodegradation of EOCs previously known to react with triplets, especially in DBC solutions. Compared to DOM solutions, POOR exhibits a lower but considerable contribution to EOC attenuation. This study enhances the understanding of pollutant fate in aquatic environments by highlighting the role of DBC in photochemical pollutant degradation and providing insights into pollutant transformation mechanisms involving POORs.

Stromal score is a promising index in tumor patients' outcome determination.

Background: Immune status is widely acknowledged as a valuable marker for predicting cancer prognosis and therapy response. However, there has been a limited understanding of the stromal landscape in cancer. Methods: By employing ESTIMATE, stromal- and immune-scores were inferred for 6193 tumor samples spanning 12 cancer types sourced from The Cancer Genome Atlas (TCGA). Subsequently, the samples were categorized into seven groups based on their stromal and immune scores. A comparison of prognosis, lymphocyte and stromal cell infiltration, and the response to programmed death ligand 1 (PD-L1) therapy was conducted among these subtypes. Results: It was unveiled by the analysis that, in the majority of cancer types, stromal score exhibited a more potent predictive capability for outcomes compared to the immune score. Furthermore, it was observed that in four cancer types, intermediate immune infiltration coupled with low stromal infiltration correlated with the most favorable overall survival, whereas an unfavorable outcome was predicted in colorectal cancer (CRC) and stomach adenocarcinoma (STAD) when high immune infiltration coexisted with intermediate or high stromal infiltration. Conclusion: In summary, while high immune scores frequently correlate with a positive prognosis, such correlation is not universal. A potential strategy to address the current limitations of the immune score in specific circumstances could involve a focus on stromal scores or a subtle integration of stromal and immune status.

A global atlas of marine antibiotic resistance genes and their expression.

Oceans serve as global reservoirs of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). However, little is known about the traits and expression of ARGs in response to environmental factors. We analyzed 347 metagenomes and 182 metatranscriptomes to determine the distribution, hosts, and expression of ARGs in oceans. Our study found that the diversity and abundance of ARGs varied with latitude and depth. The core marine resistome mainly conferred glycopeptide and multidrug resistance. The hosts of this resistome were mainly limited to the core marine microbiome, with phylogenetic barriers to the horizontal transfer of ARGs, transfers being more frequent within species than between species. Sixty-five percent of the marine ARGs identified were expressed. More than 90% of high-risk ARGs were more likely to be expressed. Anthropogenic activity might affect the expression of ARGs by altering nitrate and phosphate concentrations and ocean temperature. Machine-learning models predict >97% of marine ARGs will change expression by 2100. High-risk ARGs will shift to low latitudes and regions with high anthropogenic activity, such as the Pacific and Atlantic Oceans. Certain ARGs serve a dual role in antibiotic resistance and potentially participate in element cycling, along with other unknown functions. Determining whether changes in ARG expression are beneficial to ecosystems and human health is challenging without comprehensive understanding of their functions. Our study identified a core resistome in the oceans and quantified the expression of ARGs for the development of future control strategies under global change.

Photobleaching-induced changes in the optical and photochemical properties of algal organic matter.

Algal organic matter (AOM), a significant source of endogenous dissolved organic matter (DOM) is released in high concentrations during cyanobacterial blooms, along with cyanotoxins. Subsequent photobleaching of AOM is an important phenomenon to investigate. In this study, intracellular organic matter (IOM) and extracellular organic matter (EOM) were extracted from cultured cyanobacteria taken from Taihu Lake in China. The formation of photochemically produced reactive intermediates in different stages of IOM and EOM photobleaching was compared to Suwannee River DOM (SRDOM, reference standard DOM). Results revealed notable differences influenced by the pigment component among IOM, EOM, and SRDOM. The pigment in IOM contributed to a triplet state pool with strong energy-transfer but limited electron-transfer capabilities. Notably, IOM exhibited the highest triplets state quantum yield value in the visible region, suggesting its potential significance in pollutant degradation in deeper water layers. For EOM, one of the pools exhibits photolability and remarkable electron-transfer capability, indicating it as a high-energy triplet state component. Moreover, three cyanotoxins (MC-LR, ACA, and ATX-a) were detected in the extracted AOM, and their photodegradation was monitored during the AOM photobleaching process. This highlights the potential role of AOM as a photosensitizer in the natural self-cleaning mechanisms of water bodies, facilitating the degradation of organic pollutants through photochemical reactions. The findings of this study contribute to understanding the dynamic nature of AOM and its implications in environmental processes.

Antimicrobial Peptides in the Global Microbiome: Biosynthetic Genes and Resistance Determinants.

Antimicrobial peptides are a promising new class of antimicrobials that could address the antibiotic resistance crisis, which poses a major threat to human health. These peptides are present in all kingdoms of life, but especially in microorganisms, having multiple origins in diverse taxa. To date, there has been no global study on the diversity of antimicrobial peptides, the hosts in which these occur, and the potential for resistance to these agents. Here, we investigated the diversity and number of antimicrobial peptides in four main habitats (aquatic, terrestrial, human, and engineered) by analyzing 52,515 metagenome-assembled genomes. The number of antimicrobial peptides was higher in the human gut microbiome than in other habitats, and most hosts of antimicrobial peptides were habitat-specific. The relative abundance of genes that confer resistance to antimicrobial peptides varied between habitats and was generally low, except for the built environment and on human skin. The horizontal transfer of potential resistance genes among these habitats was probably constrained by ecological barriers. We systematically quantified the risk of each resistance determinant to human health and found that nearly half of them pose a threat, especially those that confer resistance to multiple AMPs and polymyxin B. Our results help identify the biosynthetic potential of antimicrobial peptides in the global microbiome, further identifying peptides with a low risk of developing resistance.

Global distribution of marine microplastics and potential for biodegradation.

Microplastics are a growing marine environmental concern globally due to their high abundance and persistent degradation. We created a global map for predicting marine microplastic pollution using a machine-learning model based on 9445 samples and found that microplastics converged in zones of accumulation in subtropical gyres and near polar seas. The predicted global potential for the biodegradation of microplastics in 1112 metagenome-assembled genomes from 485 marine metagenomes indicated high potential in areas of high microplastic pollution, such as the northern Atlantic Ocean and the Mediterranean Sea. However, the limited number of samples hindered our prediction, a priority issue that needs to be addressed in the future. We further identified hosts with microplastic degradation genes (MDGs) and found that Proteobacteria accounted for a high proportion of MDG hosts, mainly Alphaproteobacteria and Gammaproteobacteria, with host-specific patterns. Our study is essential for raising awareness, identifying areas with microplastic pollution, providing a prediction method of machine learning to prioritize surveillance, and identifying the global potential of marine microbiomes to degrade microplastics, providing a reference for selecting bacteria that have the potential to degrade microplastics for further applied research.

Assessment of global health risk of antibiotic resistance genes.

Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health in the last decade. Many genes can confer resistance, but evaluating the relative health risks of ARGs is complex. Factors such as the abundance, propensity for lateral transmission and ability of ARGs to be expressed in pathogens are all important. Here, an analysis at the metagenomic level from various habitats (6 types of habitats, 4572 samples) detects 2561 ARGs that collectively conferred resistance to 24 classes of antibiotics. We quantitatively evaluate the health risk to humans, defined as the risk that ARGs will confound the clinical treatment for pathogens, of these 2561 ARGs by integrating human accessibility, mobility, pathogenicity and clinical availability. Our results demonstrate that 23.78% of the ARGs pose a health risk, especially those which confer multidrug resistance. We also calculate the antibiotic resistance risks of all samples in four main habitats, and with machine learning, successfully map the antibiotic resistance threats in global marine habitats with over 75% accuracy. Our novel method for quantitatively surveilling the health risk of ARGs will help to manage one of the most important threats to human and animal health.

BacAnt: A Combination Annotation Server for Bacterial DNA Sequences to Identify Antibiotic Resistance Genes, Integrons, and Transposable Elements.

Whole genome sequencing (WGS) of bacteria has become a routine method in diagnostic laboratories. One of the clinically most useful advantages of WGS is the ability to predict antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in bacterial sequences. This allows comprehensive investigations of such genetic features but can also be used for epidemiological studies. A plethora of software programs have been developed for the detailed annotation of bacterial DNA sequences, such as rapid annotation using subsystem technology (RAST), Resfinder, ISfinder, INTEGRALL and The Transposon Registry. Unfortunately, to this day, a reliable annotation tool of the combination of ARGs and MGEs is not available, and the generation of genbank files requires much manual input. Here, we present a new webserver which allows the annotation of ARGs, integrons and transposable elements at the same time. The pipeline generates genbank files automatically, which are compatible with Easyfig for comparative genomic analysis. Our BacAnt code and standalone software package are available at https://github.com/xthua/bacant with an accompanying web application at http://bacant.net.

Rapid gelation of oxidized hyaluronic acid and succinyl chitosan for integration with insulin-loaded micelles and epidermal growth factor on diabetic wound healing.

In this work, poly(ethylene glycol)-b-poly[3-acrylamidophenylboronic acid-co-styrene] (PEG-b-P(PBA-co-St) has been firstly synthesized for loading of insulin to form insulin-loaded micelles. Insulin-loaded micelles (ILM) and epidermal growth factor (EGF) are further embedded into the composite hydrogels that can be rapidly gelled by mixing of oxidized hyaluronic acid (OHA) and succinyl chitosan (SCS). Then, the morphology, rheology, degradation, swelling and cytotoxicity properties of the as-prepared composite hydrogels are further investigated to evaluate their physical properties and biocompatibility of as the wound dressing. The as-prepared composite hydrogels show the excellent cell compatibility and low toxicity. To evaluate the wound healing ability of as-prepared composite hydrogels, the tests of wound healing in vivo are conducted on streptozotocin-induced rat models. And the as-prepared composite hydrogels with ILM and EGF show an excellent wound healing performance for promotion of fibroblast proliferation and tissue internal structure integrity, as well as the deposition of collagen and myofibrils. These results suggest that the as-prepared composite hydrogels with loading of ILM and EGF could be a promising candidate for wound healing applications.

A modified thermal radiation model with multiple factors for investigating temperature rise around pool fire.

Hazardous chemical tanks are widely distributed in China, while tank fires occur frequently. Thermal radiation of pool fire plays a critical role in multi-points combustion and accident expansion, resulting in severe thermal damage to the surrounding targets. There are kinds of classical models used to predict the temperature rise of the target, but inaccuracies still exist in the application. In this work, we had conducted a series of pool fire tests in a full-size tunnel and open space for three petroleum products, and observed the temperature variations around the pool fire. A basic thermal radiation model with multiple factors was established first to predict the surrounding temperature rise, but its accuracy was still low. Subsequently, a correction approach of view factor and other aspects was proposed to accord with the experimental data, and the basic prediction model of temperature rise was then modified accordingly. Calculative results of the modified model agreed well with the experimental measuring temperatures, which verified the accuracy and reliability of the modified model. This modified model has a functional applicability to estimate the thermal radiation of pool fire on the surrounding objects.

Incorporation of ZnO/Bioactive Glass Nanoparticles into Alginate/Chitosan Composite Hydrogels for Wound Closure.

Development of proper skin wound dressing is a vital step for wound repair, especially for those patients with serious skin injuries. Herein, zinc-doped bioactive glass (ZBG)/succinyl chitosan (SCS)/oxidized alginate (OAL) composite hydrogels (Gel-ZBG) have been developed as wound dressings to accelerate wound closure. Schiff-based linkages have been introduced into the composite hydrogels, which provide a humid microenvironment for the proliferation of cells on wound sites. The amino groups from SCS and Zn2+ released from ZBG exhibited excellent antibacterial properties to composite hydrogels, confirmed by the antibacterial tests in vitro. Si4+ and Ca2+ ions are essential factors that stimulate fibroblasts to secrete beneficial factors for angiogenesis and wound closure. The epidermal growth factor (EGF) was further embedded into the hydrogels to improve cell proliferation and tissue remodeling in the wound bed. Finally, the formation of granulation tissue, deposition of collagen and myofibril, the release of anti-inflammatory factors, and angiogenesis have been investigated to determine the healing mechanism of the composite hydrogels as the wound dressings.

Polymeric Microneedles Integrated with Metformin-Loaded and PDA/LA-Coated Hollow Mesoporous SiO2 for NIR-Triggered Transdermal Delivery on Diabetic Rats.

Herein, an NIR-responsive polymeric microneedle (MN) system incorporated with metformin-loaded and polydopamine/lauric-acid-coated (PDA/LA-coated) hollow mesoporous SiO2 has been developed for transdermal delivery of antidiabetic drug (metformin). First, an antidiabetic drug was loaded within hollow mesoporous SiO2 nanoparticles (HMSNs) by a diffusion method. Then, PDA as photothermal conversion agent and lauric acid (LA) as phase change material (PCM) were coated onto the HMSN to form NIR-responsive drug nanocarriers. Finally, these metformin-loaded and PDA/LA-coated HMSNs were encapsulated into poly(vinylpyrrolidone) (PVP) MNs. After insertion into skin tissue, LA could melt with the photothermal conversion of PDA under NIR light, thus enabling release of encapsulated metformin from MNs. The in vivo release behavior of metformin from MNs into skin was further studied to investigate its hypoglycemic effect on diabetic rats. Compared with the subcutaneous injection of metformin, the bioavailability of MN-NIR groups was 95.8 ± 2.7%. The antidiabetic drug can be precisely released by adjustment of exposure time and power densities of NIR light.

Dual effects of daidzein on chicken hepatic vitellogenin II expression and estrogen receptor-mediated transactivation in vitro.

Two in vitro systems were employed to delineate the estrogenic activity of daidzein (Da), alone or in combination with high or low concentrations of estrogen in two cell types possessing different estrogen-receptor (ER) isoforms, ERalpha and/or ERbeta: (1) vitellogenin II (VTG), the egg yolk precursor protein and the endpoint biomarker for estrogenicity, in chicken primary hepatocytes, and (2) CHO-K1 cells transiently co-transfected with ERalpha or ERbeta and estrogen-response elements (ERE) linked to a luciferase reporter gene. Da (100 microM) alone induced VTG mRNA expression in chicken hepatocytes, albeit with much less potency compared to estradiol (E(2)). Da exhibited different effects in the presence of 1 microM and 10 microM E(2). At a concentration of 100 microM, Da enhanced 1 microM E(2)-induced VTG transcription by 2.4-fold, but significantly inhibited 10 microM E(2)-induced VTG mRNA expression in a dose-dependent fashion from 1 to 100 microM. Tamoxifen completely blocked the estrogenic effect of daidzein, alone or in combination with 1 microM of E(2), but did not influence its anti-estrogenic effect on 10 microM E(2)-induced VTG mRNA expression. Furthermore, neither E(2) nor daidzein, alone or in combination, affected ERalpha mRNA expression, yet all the treatments significantly up-regulated ERbeta mRNA expression in chicken hepatocytes. E(2) effectively triggered estrogen-response elements (ERE)-driven reporter gene transactivation in CHO-K1 cells expressing ERalpha or ERbeta and showed much greater potency with ERalpha than with ERbeta. In contrast, daidzein was 1000 times more powerful in stimulating ERbeta- over ERalpha-mediated transactivation. Daidzein, in concentrations ranging from 5 nM to 50 microM, did not affect ERbeta-mediated transactivation induced by 1 nM E(2), but it significantly inhibited ERbeta-mediated transactivation induced by 10 nM E(2) at 500 nM. Despite the tremendous difference in sensitivity between the two in vitro systems, daidzein exhibited greater potency as an estrogen-antagonist for ERbeta-mediated activity.