HemoDL: Hemolytic peptides prediction by double ensemble engines from Rich sequence-derived and transformer-enhanced information.

Hemolytic peptides can trigger hemolysis by rupturing red blood cells' membranes and triggering cell disruption. Due to the labor-intensive and time-consuming in-lab identification process, accurate, high-throughput hemolytic peptide prediction is crucial for the growth of peptide sequence data in proteomics and peptidomics. In this study, we offer the HemoDL ensemble learning model, which learns the distinct distribution of sequence characteristics for predicting the hemolytic activity of peptides using a double LightGBM framework. To determine the most informative encoding features, we compare 17 widely used features across four benchmark datasets. Our investigation reveals that CTD, BPF, Charge, AAC, GDPC, ATC, QSO, and transformer-based features exhibit more positive contributions to detecting the hemolytic activity of peptides. Comparison with eight state-of-the-art methods demonstrates that HemoDL outperforms other models, attaining higher Matthews Correlation Coefficient values on four test datasets, ranging from 6.30% to 16.04%, 6.63%-11.26%, 4.76%-9.92%, and 7.41%-15.03%, respectively. Additionally, we provide the HemoDL with a user-friendly graphical interface available at https://github.com/abcair/HemoDL. In summary, the HemoDL model, leveraging CTD, BPF, Charge, AAC, GDPC, ATC, QSO and transformer-based encoding features within a double LightGBM learning framework, achieves high accuracy in predicting the hemolytic activity of peptides.

Tunable schiff-based networks with different bonding sites for enhanced photocatalytic activity under visible-light irradiation: The effects of steric hindrance.

Organic polymers hold great potential in photocatalysis considering their low cost, structural tailorability, and well-controlled degree of conjugation for efficient electron transfer. Among the polymers, Schiff base networks (SNWs) with high nitrogen content have been noticed. Herein, a series of SNWs is synthesized based on the melamine units and dialdehydes with different bonding sites. The chemical and structural variation caused by steric hindrance as well as the related photoelectric properties of the SNW samples are investigated, along with the application exploration on photocatalytic degradation and energy production. The results demonstrate that only SNW-o based on o-phthalaldehyde responds to visible light, which extends to over 550 nm. SNW-o shows the highest tetracycline degradation rate of 0.02516 min-1, under 60-min visible light irradiation. Moreover, the H2O2 production of SNW-o is 2.14 times higher than that of g-C3N4. The enhanced photocatalytic activity could be ascribed to the enlarged visible light adsorption and intramolecular electron transfer. This study indicates the possibility to regulate the optical and electrical properties of organic photocatalysts on a molecular level, providing an effective strategy for rational supramolecular engineering to the applications of organic materials in photocatalysis.

Sporosarcina jiandibaonis sp. nov., isolated from saline soil.

A Gram-stain-positive, aerobic, motile, rod-shaped bacterium, designated strain LAM9210T, was isolated from a saline soil sample collected from Lingxian County, Shandong Province, PR China. Analysis of the 16S rRNA gene sequence of the isolate revealed highest sequence similarities to the type strain of Sporosarcina pasteurii NCIMB 8841T (97.6 % sequence similarity). The genomic G+C content was 40.4 mol%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain LAM9210T and the type strain of the most closely related species S. pasteurii NCIMB 8841T were 73.6 and 20.6 %, respectively. Strain LAM9210T was found to grow at 10-40 °C (optimum, 30 °C), at pH 6.0-10.0 (optimum, pH 9.0) and with 0-6 % (w/v) NaCl (optimum, 0.5 %), respectively. The major fatty acids were anteiso-C15 : 0 and iso-C14 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unidentified phospholipid. Menaquinone-7 was detected as the predorminant respiratory quinone. Strain LAM9210T contained glycine, lysine, alanine and glutamic acid as the diagnostic amino acids in the cell-wall peptidoglycan. On the basis of phenotypic, phylogenetic and genotypic data, strain LAM9210T is considered to represent a novel species of the genus Sporosarcina, for which the name Sporosarcina jiandibaonis sp. nov. is proposed. The type strain is LAM9210T (=CGMCC 1.18607T=GDMCC 1.2002T=JCM 32514T).

Cobalt Single Atoms Anchored on Oxygen-Doped Tubular Carbon Nitride for Efficient Peroxymonosulfate Activation: Simultaneous Coordination Structure and Morphology Modulation.

Simultaneous regulation of the coordination environment of single-atom catalysts (SACs) and engineering architectures with efficient exposed active sites are efficient strategies for boosting peroxymonosulfate (PMS) activation. We isolated cobalt atoms with dual nitrogen and oxygen coordination (Co-N3 O1 ) on oxygen-doped tubular carbon nitride (TCN) by pyrolyzing a hydrogen-bonded cyanuric acid melamine-cobalt acetate precursor. The theoretically constructed Co-N3 O1 moiety on TCN exhibited an impressive mass activity of 7.61×105  min-1 mol-1 with high 1 O2 selectivity. Theoretical calculations revealed that the cobalt single atoms occupied a dual nitrogen and oxygen coordination environment, and that PMS adsorption was promoted and energy barriers reduced for the key *O intermediate that produced 1 O2 . The catalysts were attached to a widely used poly(vinylidene fluoride) microfiltration membrane to deliver an antibiotic wastewater treatment system with 97.5 % ciprofloxacin rejection over 10 hours, thereby revealing the suitability of the membrane for industrial applications.

How Do Enzymes 'Meet' Nanoparticles and Nanomaterials?

Enzymes are fundamental biological catalysts responsible for biological regulation and metabolism. The opportunity for enzymes to 'meet' nanoparticles and nanomaterials is rapidly increasing due to growing demands for applications in nanomaterial design, environmental monitoring, biochemical engineering, and biomedicine. Therefore, understanding the nature of nanomaterial-enzyme interactions is becoming important. Since 2014, enzymes have been used to modify, degrade, or make nanoparticles/nanomaterials, while numerous nanoparticles/nanomaterials have been used as materials for enzymatic immobilization and biosensors and as enzyme mimicry. Among the various nanoparticles and nanomaterials, metal nanoparticles and carbon nanomaterials have received extensive attention due to their fascinating properties. This review provides an overview about how enzymes meet nanoparticles and nanomaterials.

Covalent organic framework photocatalysts: structures and applications.

In the light of increasing energy demand and environmental pollution, it is urgently required to find a clean and renewable energy source. In these years, photocatalysis that uses solar energy for either fuel production, such as hydrogen evolution and hydrocarbon production, or environmental pollutant degradation, has shown great potential to achieve this goal. Among the various photocatalysts, covalent organic frameworks (COFs) are very attractive due to their excellent structural regularity, robust framework, inherent porosity and good activity. Thus, many studies have been carried out to investigate the photocatalytic performance of COFs and COF-based photocatalysts. In this critical review, the recent progress and advances of COF photocatalysts are thoroughly presented. Furthermore, diverse linkers between COF building blocks such as boron-containing connections and nitrogen-containing connections are summarised and compared. The morphologies of COFs and several commonly used strategies pertaining to photocatalytic activity are also discussed. Following this, the applications of COF-based photocatalysts are detailed including photocatalytic hydrogen evolution, CO2 conversion and degradation of environmental contaminants. Finally, a summary and perspective on the opportunities and challenges for the future development of COF and COF-based photocatalysts are given.

Recent progress in covalent organic framework thin films: fabrications, applications and perspectives.

As a newly emerging class of porous materials, covalent organic frameworks (COFs) have attracted much attention due to their intriguing structural merits (e.g., total organic backbone, tunable porosity and predictable structure). However, the insoluble and unprocessable features of bulk COF powder limit their applications. To overcome these limitations, considerable efforts have been devoted to exploring the fabrication of COF thin films with controllable architectures, which open the door for their novel applications. In this critical review, we aim to provide the recent advances in the fabrication of COF thin films not only supported on substrates but also as free-standing nanosheets via both bottom-up and top-down strategies. The bottom-up strategy involves solvothermal synthesis, interfacial polymerization, room temperature vapor-assisted conversion, and synthesis under continuous flow conditions; whereas, the top-down strategy involves solvent-assisted exfoliation, self-exfoliation, mechanical delamination, and chemical exfoliation. In addition, the applications of COF thin films including energy storage, semiconductor devices, membrane-separation, sensors, and drug delivery are summarized. Finally, to accelerate further research, a personal perspective covering their synthetic strategies, mechanisms and applications is presented.

Peroxidase-Like Activity of Smart Nanomaterials and Their Advanced Application in Colorimetric Glucose Biosensors.

Diabetes is a dominating health issue with 425 million people suffering from the disease worldwide and 4 million deaths each year. To avoid further complications, the diabetic patient blood glucose level should be strictly monitored despite there being no cure for diabetes. Colorimetric biosensing has attracted significant attention because of its low cost, simplicity, and practicality. Recently, some nanomaterials have been found that possess unexpected peroxidase-like activity, and great advances have been made in fabricating colorimetric glucose biosensors based on the peroxidase-like activity of these nanomaterials using glucose oxidase. Compared with natural horseradish peroxidase, the nanomaterials exhibit flexibility in structure design and composition, and have easy separation and storage, high stability, simple preparation, and tunable catalytic activity. To highlight the significant progress in the field of nanomaterial-based peroxidase-like activity, this work discusses the various smart nanomaterials that mimic horseradish peroxidase and its mechanism and development history, and the applications in colorimetric glucose biosensors. Different approaches for tunable peroxidase-like activity of nanomaterials are summarized, such as size, morphology, and shape; surface modification and coating; and metal doping and alloy. Finally, the conclusion and challenges facing peroxidase-like activity of nanomaterials and future directions are discussed.

Influence of surfactants on anaerobic digestion of waste activated sludge: acid and methane production and pollution removal.

The objective of this study is to summarize the effects of surfactants on anaerobic digestion (AD) of waste activated sludge (WAS). The increasing amount of WAS has caused serious environmental problems. Anaerobic digestion, as the main treatment for WAS containing three stages (i.e. hydrolysis, acidogenesis, and methanogenesis), has been widely investigated. Surfactant addition has been demonstrated to improve the efficiency of AD. Surfactant, as an amphipathic substance, can enhance the efficiency of hydrolysis by separating large sludge and releasing the encapsulated hydrolase, providing more substance for subsequent acidogenesis. Afterwards, the short chain fatty acids (SCFAs), as the major product, have been produced. Previous investigations revealed that surfactant could affect the transformation of SCFA. They changed the types of acidification products by promoting changes in microbial activity and in the ratio of carbon to nitrogen (C/N), especially the ratio of acetic and propionic acid, which were applied for either the removal of nutrient or the production of polyhydroxyalkanoate (PHA). In addition, the activity of microorganisms can be affected by surfactant, which mainly leads to the activity changes of methanogens. Besides, the solubilization of surfactant will promote the solubility of contaminants in sludge, such as organic contaminants and heavy metals, by increasing the bioavailability or desorbing of the sludge.

Effects of silver nanoparticles with different dosing regimens and exposure media on artificial ecosystem.

Due to the wide use of silver nanoparticles (AgNPs) in various fields, it is crucial to explore the potential negative impacts on the aquatic environment of AgNPs entering into the environment in different ways. In this study, comparative experiments were conducted to investigate the toxicological impacts of polyvinylpyrrolidone-coated silver nanoparticles (PVP-AgNPs) with two kinds of dosing regimens, continuous and one-time pulsed dosing, in different exposure media (deionized water and XiangJiang River water). There were a number of quite different experimental results (including 100% mortality of zebrafish, decline in the activity of enzymes, and lowest number and length of adventitious roots) in the one-time pulsed dosing regimen at high PVP-AgNP concentration exposure (HOE) compared to the three other treatments. Meanwhile, we determined that the concentration of leached silver ions from PVP-AgNPs was too low to play a role in zebrafish death. Those results showed that HOE led to a range of dramatic ecosystem impacts which were more destructive than those of other treatments. Moreover, compared with the continuous dosing regimen, despite the fact that higher toxicity was observed for HOE, there was little difference in the removal of total silver from the aquatic environment for the different dosing regimens. No obvious differences in ecological impacts were observed between different water columns under low concentration exposure. Overall, this work highlighted the fact that the toxicity of AgNPs was impacted by different dosing regimens in different exposure media, which may be helpful for assessments of ecological impacts on aquatic environments.

Advancement of Ag-Graphene Based Nanocomposites: An Overview of Synthesis and Its Applications.

Graphene has been employed as an excellent support for metal nanomaterials because of its unique structural and physicochemical properties. Silver nanoparticles (AgNPs) with exceptional properties have received considerable attention in various fields; however, particle aggregation limits its application. Therefore, the combination of AgNPs and graphene based nanocomposites (Ag-graphene based nanocomposites) has been widely explored to improve their properties and applications. Excitingly, enhanced antimicrobial, catalytic, and surface enhanced Raman scattering properties are obtained after their combination. In order to have a comprehensive knowledge of these nanocomposites, this Review highlights the chemical and biological synthesis of Ag-graphene nanocomposites. In particular, their applications as antimicrobial agents, catalysts, and sensors in biomedicine, agricultural protection, and environmental remediation and detection are covered. Meanwhile, the factors that influence the synthesis and applications are also briefly discussed. Furthermore, several important issues on the challenges and new directions are also provided for further development of these nanocomposites.

Remediation of contaminated soils by biotechnology with nanomaterials: bio-behavior, applications, and perspectives.

Soil contamination caused by heavy metals and organic pollutants has drawn world-wide concern. Biotechnology has been applied for many years to the decontamination of soils polluted with organic and inorganic contaminants, and novel nanomaterials (NMs) has attracted much concern due to their high capacity for the removal/stabilization/degradation of pollutants. Recently, developing advanced biotechnology with NMs for the remediation of contaminated soils has become a hot research topic. Some researchers found that bioremediation efficiency of contaminated soils was enhanced by the addition of NMs, while others demonstrated that the toxicity of NMs to the organism negatively influenced the repair capacity of polluted soils. This paper reviews the application of biotechnology and NMs in soil remediation, and further provides a critical view of the effects of NMs on the phytoremediation and micro-remediation of contaminated soils. This review also discusses the future research needs for the combined application of biotechnology and NMs in soil remediation.

White rot fungi and advanced combined biotechnology with nanomaterials: promising tools for endocrine-disrupting compounds biotransformation.

Endocrine-disrupting compounds (EDCs) can interfere with endocrine systems and bio-accumulate through the food chain and even decrease biodiversity in contaminated areas. This review discusses a critical overview of recent research progress in the biotransformation of EDCs (including polychlorinated biphenyl and nonylphenol, and suspected EDCs such as heavy metals and sulfonamide antibiotics) by white rot fungi (WRF) based on techniques with an emphasis on summarizing and analyzing fungal molecular, metabolic and genetic mechanisms. Not only intracellular metabolism which seems to perform essential roles in the ability of WRF to transform EDCs, but also advanced applications are deeply discussed. This review mainly reveals the removal pathway of heavy metal and antibiotic pollutants because the single pollution almost did not exist in a real environment while the combined pollution has become more serious and close to people's life. The trends in WRF technology and its related advanced applications which use the combined technology, including biocatalysis of WRF and adsorption of nanomaterials, to degrade EDCs have also been introduced. Furthermore, challenges and future research needs EDCs biotransformation by WRF are also discussed. This research, referring to metabolic mechanisms and the combined technology of WRF with nanomaterials, undoubtedly contributes to the applications of biotechnology. This review will be of great benefit to an understanding of the trends in biotechnology for the removal of EDCs.

Molecular docking simulation on the interactions of laccase from Trametes versicolor with nonylphenol and octylphenol isomers.

The biodegradation of nonylphenol (NP) and octylphenol (OP) isomers by laccase has attracted increasing concerns. However, the interaction mechanism between these isomers and laccase remains unclear, especially for fungal laccase. In this work, molecular docking was employed to study this issue. The results indicated that the structural characteristic of alkyl chain (position and branching degree) affected the interactions between Trametes versicolor (T. versicolor) laccase and isomers. The binding affinity between them was closely related to the position and branching degree of alkyl chain in isomers. The binding affinities between linear isomers and T. versicolor laccase were para-position < meta-position < ortho-position. For selected branched 4-NP, the isomers with bulky α-substituent in alkyl chain had higher binding affinities. In addition, hydrophobic contacts between T. versicolor laccase and NP or OP isomers were necessary, while H-bonds were optional. The isomers with similar structure may have more common residues involved in hydrophobic contacts. The H-bonds of selected NPs and OPs were all connected with phenolic hydroxyl. These findings provide an insight into detailed interaction mechanism between T. versicolor laccase and isomers of NP and OP. It is helpful to broaden the knowledge of degradation technology of NPs and OPs and provide theoretical basis on biological remediation of these contaminants.

Effects of calcium at toxic concentrations of cadmium in plants.

MAIN CONCLUSION: This review provides new insight that calcium plays important roles in plant growth, heavy metal accumulation and translocation, photosynthesis, oxidative damage and signal transduction under cadmium stress. Increasing heavy metal pollution problems have raised word-wide concerns. Cadmium (Cd), being a highly toxic metal, poses potential risks both to ecosystems and human health. Compared with conventional technologies, phytoremediation, being cost-efficient, highly stable and environment-friendly, is believed to be a promising green technology for Cd decontamination. However, Cd can be easily taken up by plants and may cause severe phytotoxicity to plants, thus limiting the efficiency of phytoremediation. Various researches are being done to investigate the effects of exogenous substances on the mitigation of Cd toxicity to plants. Calcium (Ca) is an essential plant macronutrient that involved in various plant physiological processes, such as plant growth and development, cell division, cytoplasmic streaming, photosynthesis and intracellular signaling transduction. Due to the chemical similarity between Ca and Cd, Ca may mediate Cd-induced physiological or metabolic changes in plants. Recent studies have shown that Ca could be used as an exogenous substance to protect plants against Cd stress by the alleviation of growth inhibition, regulation of metal uptake and translocation, improvement of photosynthesis, mitigation of oxidative damages and the control of signal transduction in the plants. The effects of Ca on toxic concentrations of Cd in plants are reviewed. This review also provides new insight that plants with enhanced Ca level have improved resistance to Cd stress.

Manganese-enhanced degradation of lignocellulosic waste by Phanerochaete chrysosporium: evidence of enzyme activity and gene transcription.

Lignolytic fungi initiate lignocellulose decay by producing extracellular oxidative enzymes. For better understanding the enzymatic degradation of lignocellulose by white-rot fungi, we investigated the effect of manganese on the organic matter loss, manganese peroxidase (MnP) activity, and manganese peroxidase gene (mnp) transcription levels during solid-state fermentation of rice straw with Phanerochaete chrysosporium. The results showed that the addition of manganese improved MnP activity and made it reach the peak earlier, promoted fungal growth at the early period (0-9 days), and enhanced the degradation of lignocellulosic waste. The total organic matter loss had a good correlation with fungal biomass during 30 days of cultivation, and manganese amendment promoted the ability of P. chrysosporium to degrade lignocellulose. Quantitative real-time RT-PCR revealed the differential expression of mnp1, mnp2, and mnp3: manganese amendment increased the transcription of mnp1 and mnp2 but not mnp3. The results indicated that manganese stimulated mnp transcription levels and played a post-transcriptional role in MnP production. These findings provide opportunity of development in enzymatic degradation of lignocellulosic waste by P. chrysosporium amended with manganese.

The rapid degradation of bisphenol A induced by the response of indigenous bacterial communities in sediment.

In the present study, sediment was spiked with bisphenol A (BPA) solution to explore the interaction between indigenous bacterial communities and BPA biodegradation in sediment. Results showed that BPA could be adsorbed to the sediment and then biodegraded rapidly. Biodegradation efficiency of BPA in treatments with 10 and 50 mg/L BPA reached 64.3 and 61.8% on the first day, respectively. Quantitative polymerase chain reaction and denaturing gradient gel electrophoresis analysis indicated that BPA affected the densities, species, and diversities of bacteria significantly. The response of bacterial community to BPA favored BPA biodegradation by promoting the growth of BPA-reducing bacteria and inhibiting other competitors. According to the results of sequencing, Pseudomonas and Sphingomonas played vital roles in the degradation of BPA. They presented over 73% of the original bacterial community, and both of them were promoted by BPA comparing with controls. Laccase and polyphenol oxidase contributed to the degradation of BPA and metabolic intermediates, respectively. This paper illustrates the rapid biodegradation of BPA induced by the response of indigenous bacterial communities to the BPA stress, which will improve the understandings of BPA degradation in sediment.

Responses of bacterial community and functional marker genes of nitrogen cycling to biochar, compost and combined amendments in soil.

Biochar and compost are seen as two attractive waste management options and are used for soil amendment and pollution remediation. The interaction between biochar and composting may improve the potential benefits of biochar and compost. We investigated soil physicochemical properties, bacterial community, bacterial 16S rRNA, and functional marker genes of nitrogen cycling of the soil remedied with nothing (S), compost (SC), biochar (SB), a mixture of compost and biochar (SBC), composted biochar (SBced), and a composted mixture of biochar and biomass (SBCing). The results were that all amendments (1) increased the bacterial community richness (except SB) and SBCing showed the greatest efficiency; (2) increased the bacterial community diversity (SBCing > SBC > SC > SBced > SB > S); and (3) changed the gene copy numbers of 16S rRNA, nirK, nirS, and nosZ genes of bacteria, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB). All amendments (except SB) could increase the gene copy number of 16S rRNA, and SBCing had the greatest efficiency. The changes of soil bacterial community richness and diversity and the gene copy numbers of 16S rRNA, nirK, nirS, nosZ, AOA, and AOB would affect carbon and nitrogen cycling of the ecosystem and also implied that BCing had the greatest efficiency on soil amendment.

Cadmium induced oxalic acid secretion and its role in metal uptake and detoxification mechanisms in Phanerochaete chrysosporium.

This study examines the role of oxalic acid in the uptake of Cd and participation in detoxification process in Phanerochaete chrysosporium. Cd-induced oxalic acid secretion was observed with growth inhibition and enzyme inactivation (LiP and MnP) of P. chrysosporium. The peak value of oxalic acid concentration was 16.6 mM at initial Cd concentration of 100 mg L(-1). During the short-term uptake experiments, the uptake of Cd was enhanced and accelerated in the presence of oxalic acid and resulted in alleviated growth and enzyme inhibition ratios. The formation of a metal-oxalate complex therefore may provide a detoxification mechanism via effect on metal bioavailability, whereby many fungi can survive and grow in environments containing high concentrations of toxic metals. The present findings will advance the understanding of fungal resistance to metal stress, which could show promise for a more useful application of microbial technology in the treatment of metal-polluted waste.