Sextuple knockouts of a highly conserved and coexpressed AUXIN/INDOLE-3-ACETIC ACID gene set confer shade avoidance-like responses in Arabidopsis.

AUXIN/INDOLE-3-ACETIC ACIDs are transcriptional repressors for auxin signalling. Aux/IAAs of Arabidopsis thaliana display some functional redundancy. The IAA3/SHY2 clade (IAA1, IAA2, IAA3 and IAA4) show strong sequence similarity, but no higher-order mutants have been reported. Here, through CRISPR/Cas9 genome editing, we generated loss-of-function iaa1/2/3/4 mutants. The quadruple mutants only exhibited a weak phenotype. Thus, we additionally knocked out IAA7/AXR2 and IAA16, which are coexpressed with IAA1/2/3/4. Remarkably, under white light control conditions, the iaa1/2/3/4/7/16 mutants exhibited a shade avoidance-like phenotype with over-elongated hypocotyls and petioles and hyponastic leaves. The sextuple mutants were highly sensitive to low light intensity, and the hypocotyl cells of the mutants were excessively elongated. Transcriptome profiling and qRT-PCR analyses revealed that the sextuple mutation upregulated IAA19/MSG2 and IAA29, two shared shade/auxin signalling targets. Besides, genes encoding cell wall-remodelling proteins and shade-responsive transcription regulators were upregulated. Using dual-luciferase reporter assays, we verified that IAA2/IAA7 targeted the promoters of cell wall-remodelling genes to inhibit their transcription. Our work indicates that the IAA1/2/3/4/7/16 gene set is required for the optimal integration of auxin and shade signalling. The mutants generated here should be valuable for exploring the complex interactions among signal sensors, transcription activators and transcription repressors during hormone/environmental responses.

Antibacterial Efficacy and Mechanisms of Curcumin-Based Photodynamic Treatment against Staphylococcus aureus and Its Application in Juices.

Antimicrobial Photodynamic Treatment (aPDT) is a non-thermal sterilization technology, which can inactivate common foodborne pathogens. In the present study, photodynamic inactivation on Staphylococcus aureus (S. aureus) with different concentrations of curcumin and light dose was evaluated and the mechanisms were also investigated. The results showed that curcumin-based aPDT could inactivate S. aureus cells by 6.9 log CFU/mL in phosphate buffered saline (PBS). Moreover, the modified Gompertz model presented a good fit at the inactivation data of S. aureus. Photodynamic treatment caused cell membrane damage as revealed by analyzing scanning electron microscopy (SEM) images. Leakage of intracellular constituents further indicated that cell membrane permeability was changed. Flow cytometry with double staining demonstrated that cell membrane integrity and the activity of nonspecific esterase were destroyed. Compared with the control group, intracellular reactive oxygen species (ROS) levels caused by photodynamic treatment significantly increased. Furthermore, curcumin-based aPDT reduced S. aureus by 5 log CFU/mL in juices. The color of the juices was also tested using a Chromatic meter, and it was found that b* values were the most markedly influenced by photodynamic treatment. Overall, curcumin-based aPDT had strong antibacterial activity against S. aureus. This approach has the potential to remove foodborne pathogens from liquid food.

Degrading Characterization of the Newly Isolated Nocardioides sp. N39 for 3-Amino-5-methyl-isoxazole and the Related Genomic Information.

3-amino-5-methyl-isoxazole (3A5MI) is a persistent and harmful intermediate in the degradation of antibiotic sulfamethoxazole. It was accumulated in the environments day by day and has caused great environmental risks due to its refractory characteristic. Microbial degradation is economic and environmentally friendly and a promising method to eliminate this pollutant. In this study, a bacterial strain, Nocardioides sp. N39, was isolated. N39 can grow on 3A5MI as the sole carbon, nitrogen and energy resource. The effect of different factors on 3A5MI degradation by N39 was explored, including initial 3A5MI concentration, temperature, pH value, dissolved oxygen and additional carbon or nitrogen source. The degradation ability of N39 to various 3A5MI analogs was also explored. Nevertheless, the degrading ability of N39 for 3A5MI is not permanent, and long-term storage would lead to the loss of this ability. This may result from the mobile genetic elements in the bacterium according to the genomic comparison of N39 and its degrading ability-lost strain, N40. Despite this, N39 could support a lot of useful information about the degradation of 3A5MI and highlight the importance of studies about the environmental effects and potential degradation mechanism.

Thermoresponsive dendritic oligoethylene glycols.

Monodispersed molecules of low molar masses showing thermoresponsiveness are appealing both for mechanism investigation of the thermally-modulated dehydration and aggregation on molecular levels and for designing functional intelligent materials. In the present report, thermoresponsive properties of a homologous series of monodispersed dendritic macromolecules carrying three-, four- or six-fold dendritic oligoethylene glycol (OEG) segments were investigated. These dendritic macromolecules carry either methoxyl or ethoxyl terminals, and have different cores (alcohol, methyl ester or methacryloyl) to exhibit different overall hydrophilicity. They show characteristic thermoresponsive properties with sharp phase transitions when suitable structural units are combined. Three structural factors determine their phase transition temperatures, including the cores, branching density and peripheral terminals. Thermally-induced collapse and aggregation are monitored with temperature-varied NMR spectroscopy at the microscale level and optical microscopy at the macroscale level. At elevated temperature, these dendritic macromolecules undergo fast exchange between the dehydrated and the hydrated states. These dendritic macromolecules afford structure-dependent confinement to guest dyes through their multi-valent interactions.

Bioelectrochemical catabolism of triclocarban through the cascade acclimation of triclocarban-hydrolyzing and chloroanilines-oxidizing microbial communities.

Chlorinated antimicrobial triclocarban (3,4,4'-trichlorocarbanilide, TCC) is an emerging refractory contaminant omnipresent in various environments. Preferential microbial hydrolysis of TCC to chloroanilines is essential for its efficient mineralization. However, the microbial mineralization of TCC in domestic wastewater is poorly understood. Here, the bioelectrochemical catabolism of TCC to chloroanilines (3,4-dichloroaniline and 4-chloroaniline) and then to CO2 was realized through the cascade acclimation of TCC-hydrolyzing and chloroanilines-oxidizing microbial communities. The biodegradation of chloroanilines was obviously enhanced in the bioelectrochemical reactors. Pseudomonas, Diaphorobacter, and Sphingomonas were the enriched TCC or chloroanilines degraders in the bioelectrochemical reactors. The addition of TCC enhanced the synergistic effect within functional microbial communities based on the feature of the phylogenetic ecological networks. This study provides a new idea for the targeted domestication and construction of functionally differentiated microbial communities to efficiently remove TCC from domestic wastewater through a green and low-carbon bioelectrochemical method.

Staphylococcus aureus biofilm inhibition by high voltage prick electrostatic field (HVPEF) and the mechanism investigation.

The study was to investigate the inhibitory effect and mechanism of high voltage prick electrostatic field (HVPEF) on Staphylococcus aureus biofilms. Results showed that HVPEF effectively inactivated 24-h and 48-h established S. aureus biofilms, and the effect was verified on different food-contact materials. Confocal laser scanning microscopy and scanning electron microscopy analysis suggested that HVPEF disintegrated the established biofilms by killing the embedded bacteria, but it hardly reduced the bacteria adhesion. HVPEF also effectively inhibit the formation of S. aureus biofilms, the effects varied with electric voltage, treatment time and biofilm culture conditions. The direct effect of HVPEF on planktonic S. aureus was a possible mode of biofilm formation inhibition. HVPEF also suppressed biofilm formation by reducing the release of key compositions of extracellular polymeric substance, including extracellular DNA (eDNA), protein and polysaccharide intercellular adhesion (PIA), and regulating the expression of biofilm formation related genes (icaA, ebh, cidA, sarA, icaR and sigB). We propose HVPEF as a novel method to inhibit bacteria biofilm, based on the results, HVPEF has positive effects to prevent biofilm-associated contamination of S. aureus.

Complete genome sequences of the antibiotic sulfamethoxazole-mineralizing bacteria Paenarthrobacter sp. P27 and Norcardiodes sp. N27.

Sulfonamide antibiotics (SAs) have been produced and consumed on a large scale over the last few decades. SAs are a typical class of refractory contaminants that are omnipresent in various environments. Although several [phenyl]-SA-degrading bacteria and their corresponding genomes have been documented, limited genetic information is available for the degraders of heterocyclic products (e.g., 3-amino-5-methylisoxazole [3A5MI] produced via sulfamethoxazole [SMX] catabolism). In this study, the previously isolated SMX-mineralizing bacterial partners, Paenarthrobacter sp. P27 (responsible for the initial cleavage of the -C-S-N- bond of SMX and further degradation of [phenyl]-SMX) and Norcardiodes sp. N27 (responsible for 3A5MI catabolism), were further studied and their complete genomes were sequenced. Complete degradation and bacterial growth were verified by pure-culture experiments with SMX or 3A5MI as the sole carbon, nitrogen, and energy source. By cross-feeding strains P27 and N27, complete catabolism of SMX could be achieved over a wide range of initial SMX concentrations. Moreover, strain P27 was capable of transforming the additional nine SA representatives into their corresponding nitrogen-containing heterocyclic products, strongly indicating the broad substrate spectrum and marked bioremediation potential of strain P27. The genome of strain P27 contained the highly homologous monooxygenase gene cluster, sadABC, which initially attacked the sulfonamide molecules. The complete genome sequences of the two important degraders will benefit future research centering on the molecular mechanism underlying advanced SMX mineralization and will aid in further understanding the interspecific interactions and metabolite exchanges for the optimization of artificially constructed synthetic functional microbiomes.

Microbial Interactions Drive the Complete Catabolism of the Antibiotic Sulfamethoxazole in Activated Sludge Microbiomes.

Microbial communities are believed to outperform monocultures in the complete catabolism of organic pollutants via reduced metabolic burden and increased robustness to environmental challenges; however, the interaction mechanism in functional microbiomes remains poorly understood. Here, three functionally differentiated activated sludge microbiomes (S1: complete catabolism of sulfamethoxazole (SMX); S2: complete catabolism of the phenyl part of SMX ([phenyl]-SMX) with stable accumulation of its heterocyclic product 3-amino-5-methylisoxazole (3A5MI); A: complete catabolism of 3A5MI rather than [phenyl]-SMX) were enriched. Combining time-series cultivation-independent microbial community analysis, DNA-stable isotope probing, molecular ecological network analysis, and cultivation-dependent function verification, we identified key players involved in the SMX degradation process. Paenarthrobacter and Nocardioides were primary degraders for the initial cleavage of the sulfonamide functional group (-C-S-N- bond) and 3A5MI degradation, respectively. Complete catabolism of SMX was achieved by their cross-feeding. The co-culture of Nocardioides, Acidovorax, and Sphingobium demonstrated that the nondegraders Acidovorax and Sphingobium were involved in the enhancement of 3A5MI degradation. Moreover, we unraveled the internal labor division patterns and connections among the active members centered on the two primary degraders. Overall, the proposed methodology is promisingly applicable and would help generate mechanistic, predictive, and operational understanding of the collaborative biodegradation of various contaminants. This study provides useful information for synthetic activated sludge microbiomes with optimized environmental functions.

Combined bioaugmentation with electro-biostimulation for improved bioremediation of antimicrobial triclocarban and PAHs complexly contaminated sediments.

Haloaromatic antimicrobial triclocarban (TCC) is an emerging refractory contaminant that commonly coexisted with conventional contaminants such as polycyclic aromatic hydrocarbons (PAHs). TCC may negatively affect the metabolic activity of sediment microorganisms and persist in environment; however, remediation methods that relieve the TCC inhibitory effect in sediments remain unknown. Here, a novel electro-biostimulation and bioaugmentation combined remediation system was proposed by the simultaneous introduction of a TCC-degrading Ochrobactrum sp. TCC-2 and electrode into the TCC and PAHs co-contaminated sediments. Results indicated the PAHs and TCC degradation efficiencies of the combined system were 2.9-3.0 and 4.6 times respectively higher than those of the control group (no electro-biostimulation and no bioaugmentation treatments). The introduced strain TCC-2 and the enriched electroactive bacteria and PAHs degraders (e.g. Desulfobulbus, Clostridium, and Paenarthrobacter) synergistically contributed to the accelerated degradation of PAHs and TCC. The preferential elimination of the TCC inhibitory effect through bioaugmentation treatment could restore microbial functions by increasing the functional gene abundances related to various metabolic processes. This study offers new insights into the response of sediment functional communities to TCC stress, electro-biostimulation and bioaugmentation operations and provides a promising system for the enhanced bioremediation of the PAHs and TCC co-contaminated sediments.

Novel Pathway for Chloramphenicol Catabolism in the Activated Sludge Bacterial Isolate Sphingobium sp. CAP-1.

The chlorinated nitroaromatic antibiotic chloramphenicol (CAP) is a refractory contaminant that is widely present in various environments. However, few CAP-mineralizing bacteria have been documented, and a complete CAP catabolism pathway has yet to be identified. In this study, the bacterial strain Sphingobium sp. CAP-1 was isolated from an activated sludge sample and was shown to be capable of aerobically subsisting on CAP as the sole carbon, nitrogen, and energy source while simultaneously and efficiently degrading CAP. p-Nitrobenzoic acid (PNBA), p-nitrobenzaldehyde (PNBD), protocatechuate (PCA), and the novel side chain C3-hydroxy-oxygenated product of CAP (O-CAP) were identified during CAP degradation. Strain CAP-1 was able to convert O-CAP to intermediate product PNBA. The putative functional genes associated with PNBA catabolism into the tricarboxylic acid cycle via PCA and floc formation were also identified by genome sequencing and comparative proteome analysis. A complete pathway for CAP catabolism was proposed. The discovery of a novel CAP oxidation/detoxification process and a complete pathway for CAP catabolism enriches the fundamental understanding of the bacterial catabolism of antibiotics, providing new insights into the microbial-mediated fate, transformation, and resistance risk of CAP in the environment. The molecular basis of CAP catabolism and floc formation in strain CAP-1 also offers theoretical guidance for the enhanced bioremediation of CAP-containing environments.

The SAUR41 subfamily of SMALL AUXIN UP RNA genes is abscisic acid inducible to modulate cell expansion and salt tolerance in Arabidopsis thaliana seedlings.

BACKGROUND AND AIMS: Most primary auxin response genes are classified into three families: AUX/IAA, GH3 and SAUR genes. Few studies have been conducted on Arabidopsis thaliana SAUR genes, possibly due to genetic redundancy among different subfamily members. Data mining on arabidopsis transcriptional profiles indicates that the SAUR41 subfamily members of SMALL AUXIN UP RNA genes are, strikingly, induced by an inhibitory phytohormone, abscisic acid (ABA). We aimed to reveal the physiological roles of arabidopsis SAUR41 subfamily genes containing SAUR40, SAUR41, SAUR71 and SAUR72. METHODS: Transcriptional responses of arabidopsis SAUR41 genes to phytohormones were determined by quantitative real-time PCR. Knock out of SAUR41 genes was carried out with the CRISPR/Cas9 (clustered regulatory interspaced short palindromic repeats/CRISPR-associated protein 9) genome editing technique. The saur41/40/71/72 quadruple mutants, SAUR41 overexpression lines and the wild type were subjected to ultrastructural observation, transcriptome analysis and physiological characterization. KEY RESULTS: Transcription of arabidopsis SAUR41 subfamily genes is activated by ABA but not by gibberellic acids and brassinosteroids. Quadruple mutations in saur41/40/71/72 led to reduced cell expansion/elongation in cotyledons and hypocotyls, opposite to the overexpression of SAUR41; however, an irregular arrangement of cell size and shape was observed in both cases. The quadruple mutants had increased transcription of calcium homeostasis/signalling genes in seedling shoots, and the SAUR41 overexpression lines had decreased transcription of iron homeostasis genes in roots and increased ABA biosynthesis in shoots. Notably, both the quadruple mutants and the SAUR41 overexpression lines were hypersensitive to salt stress during seedling establishment, whereas specific expression of SAUR41 under the ABA-responsive RD29A (Responsive to Desiccation 29A) promoter in the quadruple mutants rescued the inhibitory effect of salt stress. CONCLUSIONS: The SAUR41 subfamily genes of arabidopsis are ABA inducible to modulate cell expansion, ion homeostasis and salt tolerance. Our work may provide new candidate genes for improvement of plant abiotic stress tolerance.

QSAR modelling study of the bioconcentration factor and toxicity of organic compounds to aquatic organisms using machine learning and ensemble methods.

Bioconcentration factors and median lethal concentrations (LC50s) are important when assessing risks posed by organic pollutants to aquatic ecosystems. Various quantitative structure-activity relationship models have been developed to predict bioconcentration factors and classify acute toxicity. In the study, we developed a regression model using Recursive Feature Elimination (RFE) method combined with the Support Vector Machine (SVM) algorithm. We calculated 2D molecular descriptors from a dataset containing 450 diverse chemicals in our regression model. Then we built three ensemble models using three machine learning algorithms and calculated 12 molecular fingerprints from a dataset containing 400 diverse chemicals in our classification models. In the regression model, the R2 and Rpred2 for the regression model were 0.860 and 0.757, respectively. Other parameters indicated that the regression model made good predictions and could efficiently predict a new set of compounds following standards set by Golbraikh, Tropsha, and Roy. In the classification models, the ensemble-SVM classification model gave an overall accuracy, sensitivity, specificity, and area under the receiver operating characteristic curve of 92.2, 95.1, 86.0, and 0.965, respectively, in a five-fold cross-validation and of 87.3, 92.6, 76.0, and 0.940, respectively, in an external validation. These parameters indicated that our ensemble-SVM model was more stable and gave more accurate predictions than previous models. The model could therefore be used to effectively predict aquatic toxicity and assess risks posed to aquatic ecosystems. We identified several structures most relevant to acute aquatic toxicity through predictions made by the two types of models, and this information may be important to aquatic toxicology experiments and aquatic system management.

Characterization of an efficient chloramphenicol-mineralizing bacterial consortium.

Obtaining efficient antibiotic-mineralizing consortium or pure cultures is a central issue for the deep elimination of antibiotic-contaminated environments. However, the antibiotic chloramphenicol (CAP) mineralizing consortium has not yet been reported. In this study, an efficient CAP-mineralizing consortium was successfully obtained with municipal activated sludge as the initial inoculum. This consortium is capable of aerobically subsisting on CAP as the sole carbon, nitrogen and energy sources and completely degrading 50 mg L-1 CAP within 24 h. After 5 d, 71.50 ±â€¯2.63% of CAP was mineralized and Cl- recovery efficiency was 90.80 ±â€¯7.34%. Interestingly, the CAP degradation efficiency obviously decreased to 18.22 ±â€¯3.52% within 12 h with co-metabolic carbon source glucose. p-nitrobenzoic acid (p-NBA) was identified as an intermediate product during CAP biodegradation. The consortium is also able to utilize p-NBA as the sole carbon and nitrogen sources and almost completely degrade 25 mg L-1p-NBA within 24 h. Microbial community analysis indicated that the dominant genera in the CAP-mineralizing consortium all belong to Proteobacteria (especially Sphingobium with the relative abundance over 63%), and most bacteria could degrade aromatics including p-NBA, suggesting these genera involved in the upstream and downstream pathway of CAP degradation. Although the acclimated consortium has been successively passaged 152 times, the microbial community structure and core genera were not obviously changed, which was consistent with the stable CAP degradation efficiency observed under different generations. This is the first report that the acclimated consortium is able to mineralize CAP through an oxidative pathway with p-NBA as an intermediate product.

Bioremediation of contaminated urban river sediment with methanol stimulation: Metabolic processes accompanied with microbial community changes.

The intense pollution of urban river sediments with rapid urbanization has attracted considerable attention. Complex contaminated sediments urgently need to be remediated to conserve the ecological functions of impacted rivers. This study investigated the effect of using methanol as a co-substrate on the stimulation of the indigenous microbial consortium to enhance the bioremediation of petroleum hydrocarbons (PHs) and polycyclic aromatic hydrocarbons (PAHs) in an urban river sediment. After 65 days of treatment, the PAHs degradation efficiencies in the sediment adding methanol were 4.87%-40.3% higher than the control. The removal rate constant of C31 was 0.0749 d-1 with 100 mM of supplied methanol, while the corresponding rate was 0.0399 d-1 in the control. Four-ring PAHs were effectively removed at a degradation efficiency of 65%-69.8%, increased by 43.3% compared with the control. Sulfate reduction and methanogenesis activity were detected, and methane-producing archaea (such as Methanomethylovorans, with a relative abundance of 25.87%-58.53%) and the sulfate-reducing bacteria (SRB, such as Desulfobulbus and Desulfobacca) were enriched. In addition, the chemolithoautotrophic sulfur-oxidizing bacteria (SOB, such as Sulfuricurvum, with a relative abundance of 34%-39.2%) were predominant after the depletion of total organic carbon (TOC), and markedly positively correlated with the PHs and PAHs degradation efficiencies (P < 0.01). The SRB and SOB populations participated in the sulfur cycle, which was associated with PHs and PAHs degradation. Other potential functional bacteria (such as Dechloromonas) were also obviously enriched and significantly positively correlated with the TOC concentration after methanol injection (P < 0.001). This study provides a new insight into the succession of the indigenous microbial community with methanol as a co-substrate for the enhanced bioremediation of complexly contaminated urban river sediments.

Response of chloramphenicol-reducing biocathode resistome to continuous electrical stimulation.

Understanding the fate of overall antibiotic resistance genes (ARGs) during the biological treatment of antibiotic containing wastewater is a central issue for the water ecological safety assessment. Although the microbial electrode-respiration based biotransformation process could significantly detoxify some antibiotic contaminants, e.g. chloramphenicol (CAP), the response of CAP-reducing biocathode microbiome and resistome to continuous electrical stimulation, especially ARGs network interactions, are poorly understood. Here, using highthroughput functional gene array (GeoChip v4.6) and Illumina 16S rRNA gene MiSeq sequencing, the structure, composition, diversity and network interactions of CAP-reducing biocathode microbiome and resistome in response to continuous electrical stimulation were investigated. Our results indicate that the CAP bioelectroreduction process could significantly accelerate the elimination of antibacterial activity of CAP during CAP-containing wastewater treatment compared to the pure bioreduction process. Continuous electrical stimulation could obviously alter both the microbiome and resistome structures and consistently decrease the phylogenetic, functional and overall ARGs diversity and network complexity within the CAP-reducing biofilms. The relative abundances of overall ARGs and specific CAP resistance related major facilitator superfamily (MFS) transporter genes were significantly negatively correlated with the reduction efficiency of CAP to inactive antibacterial product AMCl (partially dechlorinated aromatic amine), which may reduce the ecological risk associated with the evolution of multidrug-resistant bacteria and ARGs during antibiotic-containing wastewater treatment process. This study offers new insights into the response of an antibiotic reducing biocathode resistome to continuous electrical stimulation and provides useful information on the assessment of overall ARGs risk for the bioelectrochemical treatment of antibiotic contaminants.

Effects of surface charge, hydrophilicity and hydrophobicity on functional biocathode catalytic efficiency and community structure.

The bioelectrotransformation efficiency of various organic matters and corresponding electrode biofilm community formation as well as electron transfer efficiency in bioelectrochemical systems (BESs) with different modified electrodes has been extensively studied on the anode side. However, the effects of cathode interface characteristics towards the BESs bioelectrotransformation performance remain poorly understood. In this study, the nitrobenzene-reducing biocathode catalytic efficiency and community structure in response to different modified electrodes (control: hydrophobic and no charge; -SH: hydrophobic and single negative charge; -NH2: hydrophilic and single positive charge -NH-NH2: hydrophilic and double positive charges) were investigated. The biocathode transformation efficiency of nitrobenzene (NB) to aniline (AN) (ENB-AN) was affected by the nature of electrode interface as well as the biocathode community formation and structure. Cathodes with hydrophilic surface and positive charges have performed well in the bioelectrotransformation experiments, and especially made an outstanding performance when inorganic NaHCO3 was supplied as carbon source and cathode as the sole electron donor. Importantly, the hydrophilic surfaces with positive charges were dominated by the electroactive nitroaromatic reducers (Enterococcus, Desulfovibrio and Klebsiella) with the relative abundance as high as 72.20 ±â€¯1.87% and 74.86 ±â€¯8.71% for -NH2 and -NH-NH2 groups respectively. This could explain the higher ENB-AN in the hydrophilic groups than that of the hydrophobic -SH modified group. This study provides new insights into the effects of electrode interface characteristics on the BESs biocathode performance and offers some suggestions for the future design for the improvement of bioelectroremediation performance.

Study on the Mechanisms of Active Compounds in Traditional Chinese Medicine for the Treatment of Influenza Virus by Virtual Screening.

In recent years, new strains of influenza virus such as H7N9, H10N8, H5N6 and H5N8 had continued to emerge. There was an urgent need for discovery of new anti-influenza virus drugs as well as accurate and efficient large-scale inhibitor screening methods. In this study, we focused on six influenza virus proteins that could be anti-influenza drug targets, including neuraminidase (NA), hemagglutinin (HA), matrix protein 1 (M1), M2 proton channel (M2), nucleoprotein (NP) and non-structural protein 1 (NS1). Structure-based molecular docking was utilized to identify potential inhibitors for these drug targets from 13144 compounds in the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. The results showed that 56 compounds could inhibit more than two drug targets simultaneously. Further, we utilized reverse docking to study the interaction of these compounds with host targets. Finally, the 22 compound inhibitors could stably bind to host targets with high binding free energy. The results showed that the Chinese herbal medicines had a multi-target effect, which could directly inhibit influenza virus by the target viral protein and indirectly inhibit virus by the human target protein. This method was of great value for large-scale virtual screening of new anti-influenza virus compounds.

Enhanced bioelectroremediation of a complexly contaminated river sediment through stimulating electroactive degraders with methanol supply.

Bioelectroremediation is an efficient, sustainable, and environment-friendly remediation technology for the complexly contaminated sediments. Although various recalcitrant pollutants could be degraded in the electrode district, the degradation efficiency was generally confined by the low total organic carbon (TOC) content in the sediment. How to enhance the electroactive degraders' activity and efficiency remain poorly understood. Here we investigated the bioeletroremediation of a complexly contaminated river sediment with low TOC in a cylindric sediment microbial fuel cell stimulated by methanol. After 200 days treatment, the degradation efficiencies of total petroleum hydrocarbons (TPH), polycyclic aromatic hydrocarbons (PAH), and cycloalkenes (CYE) in the electrode district with methanol stimulation were 1.45-4.38 times higher compared with those in the non-electrode district without methanol stimulation. The overall electrode district communities were significantly positively correlated with the variables of the enhanced TPH, PAH, CYE and TOC degradation efficiencies (p < .01). The joint electrical and exogenous methanol stimulation selectively enriched electroactive degraders (Geobacter and Desulfobulbus) in the anode biofilms, and their proportion was markedly positively correlated with the characteristic and total pollutants degradation efficiencies (p < .001). This study offers a new insight into the response of key electroactive degraders to the joint stimulation process.

Virtual screening approach to identifying influenza virus neuraminidase inhibitors using molecular docking combined with machine-learning-based scoring function.

In recent years, an epidemic of the highly pathogenic avian influenza H7N9 virus has persisted in China, with a high mortality rate. To develop novel anti-influenza therapies, we have constructed a machine-learning-based scoring function (RF-NA-Score) for the effective virtual screening of lead compounds targeting the viral neuraminidase (NA) protein. RF-NA-Score is more accurate than RF-Score, with a root-mean-square error of 1.46, Pearson's correlation coefficient of 0.707, and Spearman's rank correlation coefficient of 0.707 in a 5-fold cross-validation study. The performance of RF-NA-Score in a docking-based virtual screening of NA inhibitors was evaluated with a dataset containing 281 NA inhibitors and 322 noninhibitors. Compared with other docking-rescoring virtual screening strategies, rescoring with RF-NA-Score significantly improved the efficiency of virtual screening, and a strategy that averaged the scores given by RF-NA-Score, based on the binding conformations predicted with AutoDock, AutoDock Vina, and LeDock, was shown to be the best strategy. This strategy was then applied to the virtual screening of NA inhibitors in the SPECS database. The 100 selected compounds were tested in an in vitro H7N9 NA inhibition assay, and two compounds with novel scaffolds showed moderate inhibitory activities. These results indicate that RF-NA-Score improves the efficiency of virtual screening for NA inhibitors, and can be used successfully to identify new NA inhibitor scaffolds. Scoring functions specific for other drug targets could also be established with the same method.

Response of antimicrobial nitrofurazone-degrading biocathode communities to different cathode potentials.

Bioelectrodegradation of various organic pollutants has been extensively studied. However, whether different cathode potentials could alter the antimicrobial-degrading biocathode community structure and composition remain poorly understood. Here, the microbial community structure and composition of the nitrofurans nitrofurazone (NFZ) degrading biocathode in response to different cathode potentials (-0.45±0.01, -0.65±0.01 and -0.86±0.05V vs standard hydrogen electrode, with applied cell voltages of 0.2, 0.5 and 0.8V, respectively) were investigated. The bioelectrodegradation efficiency and degree of NFZ were highly related to different cathode potentials. The 0.2 and 0.5V performed biocathode communities were similar but significantly differed from those of the 0.8V and open circuit biofilms. The bacteria possessing functions of nitroaromatics reduction and electrons transfer (e.g. Klebsiella, Enterococcus, Citrobacter and Desulfovibrio) were selectively enriched in different biocathode communities. This study offers new insights into the ecological response of antimicrobial-degrading biocathode communities to different cathode potentials.