Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks.

Accurate identification of genetic variants from family child-mother-father trio sequencing data is important in genomics. However, state-of-the-art approaches treat variant calling from trios as three independent tasks, which limits their calling accuracy for Nanopore long-read sequencing data. For better trio variant calling, we introduce Clair3-Trio, the first variant caller tailored for family trio data from Nanopore long-reads. Clair3-Trio employs a Trio-to-Trio deep neural network model, which allows it to input the trio sequencing information and output all of the trio's predicted variants within a single model to improve variant calling. We also present MCVLoss, a novel loss function tailor-made for variant calling in trios, leveraging the explicit encoding of the Mendelian inheritance. Clair3-Trio showed comprehensive improvement in experiments. It predicted far fewer Mendelian inheritance violation variations than current state-of-the-art methods. We also demonstrated that our Trio-to-Trio model is more accurate than competing architectures. Clair3-Trio is accessible as a free, open-source project at https://github.com/HKU-BAL/Clair3-Trio.

Deciphering the influence of salinity stress on the biological aniline degradation system: Pollutants degradation performance and microbial response.

In order to evaluate the impact of salinity gradients on the aniline biodegradation system, six reactors at salinity concentrations (0%-5%) were established. The results presented the salinity except for 5% imposed negligible effects on aniline degradation performance. Nitrification had prominent resistance to salinity (0%-1.5%) while were significantly restrained when salinity increased. The total nitrogen (TN) removal efficiency of Z4 (1.5%) was 20.5% higher than Z1 (0%) during the stable operation phase. Moreover, high throughput sequencing analysis showed that halophilic bacterium, such as Halomonas, Rhodococcus, remained greater survival advantages in high salinity system. The substantial enrichment of Flavobacterium, Dokdonella, Paracoccus observed in Z4 ensured its excellent nitrogen removal performance. The close cooperation among dominant functional bacteria was strengthened when salt content was below 1.5% while exceeding 1.5% led to the collapse of metabolic capacity through integrating the toxicity of aniline and high osmotic pressure.

Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP.

BACKGROUND: With the continuous advances in third-generation sequencing technology and the increasing affordability of next-generation sequencing technology, sequencing data from different sequencing technology platforms is becoming more common. While numerous benchmarking studies have been conducted to compare variant-calling performance across different platforms and approaches, little attention has been paid to the potential of leveraging the strengths of different platforms to optimize overall performance, especially integrating Oxford Nanopore and Illumina sequencing data. RESULTS: We investigated the impact of multi-platform data on the performance of variant calling through carefully designed experiments with a deep learning-based variant caller named Clair3-MP (Multi-Platform). Through our research, we not only demonstrated the capability of ONT-Illumina data for improved variant calling, but also identified the optimal scenarios for utilizing ONT-Illumina data. In addition, we revealed that the improvement in variant calling using ONT-Illumina data comes from an improvement in difficult genomic regions, such as the large low-complexity regions and segmental and collapse duplication regions. Moreover, Clair3-MP can incorporate reference genome stratification information to achieve a small but measurable improvement in variant calling. Clair3-MP is accessible as an open-source project at: https://github.com/HKU-BAL/Clair3-MP . CONCLUSIONS: These insights have important implications for researchers and practitioners alike, providing valuable guidance for improving the reliability and efficiency of genomic analysis in diverse applications.

Long-Read Sequencing with Hierarchical Clustering for Antiretroviral Resistance Profiling of Mixed Human Immunodeficiency Virus Quasispecies.

BACKGROUND: HIV infections often develop drug resistance mutations (DRMs), which can increase the risk of virological failure. However, it has been difficult to determine if minor mutations occur in the same genome or in different virions using Sanger sequencing and short-read sequencing methods. Oxford Nanopore Technologies (ONT) sequencing may improve antiretroviral resistance profiling by allowing for long-read clustering. METHODS: A new ONT sequencing-based method for profiling DRMs in HIV quasispecies was developed and validated. The method used hierarchical clustering of long amplicons that cover regions associated with different types of antiretroviral drugs. A gradient series of an HIV plasmid and 2 plasma samples was prepared to validate the clustering performance. The ONT results were compared to those obtained with Sanger sequencing and Illumina sequencing in 77 HIV-positive plasma samples to evaluate the diagnostic performance. RESULTS: In the validation study, the abundance of detected quasispecies was concordant with the predicted result with the R2 of > 0.99. During the diagnostic evaluation, 59/77 samples were successfully sequenced for DRMs. Among 18 failed samples, 17 were below the limit of detection of 303.9 copies/µL. Based on the receiver operating characteristic analysis, the ONT workflow achieved an F1 score of 0.96 with a cutoff of 0.4 variant allele frequency. Four cases were found to have quasispecies with DRMs, in which 2 harbored quasispecies with more than one class of DRMs. Treatment modifications were recommended for these cases. CONCLUSIONS: Long-read sequencing coupled with hierarchical clustering could differentiate the quasispecies resistance profiles in HIV-infected samples, providing a clearer picture for medical care.

Understanding the impacts of intermittent electro field on the bioelectrochemical aniline degradation system: Performance, microbial community and functional enzyme.

On account of the lack of a sustainable electron donor source and the inhibitory effect of aniline on denitrogenation make it tough to achieve simultaneous removal of aniline and nitrogen. Herein, the strategy of adjusting electric field mode was applied to the electro-enhanced sequential batch reactors (E-SBRs: R1 (continuous ON), R2 (2 h-ON/2 h-OFF), R3 (12 h-ON/12 h-OFF), R4 (in the aerobic phase ON), R5 (in the anoxic phase ON)) to treat aniline wastewater. Aniline removal rate reached approximately 99% in the five systems. Decreasing electrical stimulation interval from 12 to 2 h significantly improved the electron utilization efficiency for aniline degradation and nitrogen metabolism. The total nitrogen removal was achieved from 70.31% to 75.63%. Meanwhile, the hydrogenotrophic denitrifiers of Hydrogenophaga, Thauera, and Rhodospirillales, enriched in reactors of minor electrical stimulation interval. Accordingly, the expression of functional enzyme related to electron transport was incremental with the proper electrical stimulation frequency.

SKSV: ultrafast structural variation detection from circular consensus sequencing reads.

SUMMARY: Circular consensus sequencing reads are promising for the comprehensive detection of structural variants (SVs). However, alignment-based SV calling pipelines are computationally intensive due to the generation of complete read-alignments and its post-processing. Herein, we propose a SKeleton-based analysis toolkit for Structural Variation detection (SKSV). Benchmarks on real and simulated datasets demonstrate that SKSV has an order of magnitude of faster speed than state-of-the-art SV calling approaches; moreover, it achieves higher F1 scores for various types of SVs. AVAILABILITY AND IMPLEMENTATION: SKSV is available from https://github.com/ydLiu-HIT/SKSV. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Understanding the effect of residual aluminum salt coagulant on activated sludge in sequencing batch reactor: Performance response, activity restoration and microbial community evolution.

To investigate the effect of residual coagulant after coagulation pretreatment on activated sludge system of wastewater treatment plants (WWTPs), comparative evaluation of lab-scale sequencing batch reactors under different poly-aluminum chloride (PAC) concentrations (20 and 55 mg/L), presenting the performance differences of reactors. Results showed that the PAC concentration of 20 mg/L slightly enhanced the average removal efficiencies of chemical oxygen demand (COD) and total nitrogen (TN), up to 93.43% and 72.52%. Whereas, an inhibition effect was exerted at the PAC concentration of 55 mg/L, the average removal efficiencies decreased to 88.56% and 57.80% respectively. Similarly, the residual aluminum salts showed a concentration effect of low promotion and high inhibition on sludge activity index. The content of specific oxygen utilization rate (SOUR) and dehydrogenase (DHA) sharply decreased by 30.17% and 53.56% under the high PAC concentration of 55 mg/L. Activity recovery phase showed that the suppression of aluminum salt coagulant on biological system was reversible. High-throughput sequencing presented that the relative abundance of microbes showed obvious variations at different PAC concentrations, and certain bacteria in Chloroflexi and Bacteroidota exhibited better adaptability to the high PAC concentration environment. Nevertheless, the antagonism action between denitrifying genera and other genera as well as the downregulation of functional enzymes regarding nitrogen metabolism gave rise to the deterioration of denitrification under the high PAC concentration of 55 mg/L. This study revealed the influence mechanism of residual aluminum salt coagulant on activated sludge system, providing strategies for efficient decontamination and long-term stable operation of biological system in wastewater treatment plant under the condition of adding PAC.

Adaptive Multi-ROI Agricultural Robot Navigation Line Extraction Based on Image Semantic Segmentation.

Automated robots are an important part of realizing sustainable food production in smart agriculture. Agricultural robots require a powerful and precise navigation system to be able to perform tasks in the field. Aiming at the problems of complex image background, as well as weed and light interference factors of the visual navigation system in field and greenhouse environments, a Faster-U-net model that retains the advantages of the U-net model feature jump connection is proposed. Based on the U-net model, pruning and optimization were carried out to predict crop ridges. Firstly, a corn dataset was trained to obtain the weight of the corn dataset. Then, the training weight of the obtained corn dataset was used as the pretraining weight for the cucumber, wheat, and tomato datasets, respectively. The three datasets were trained separately. Finally, the navigation line between ridges and the yaw angle of the robot were generated by B-spline curve fitting. The experimental results showed that the parameters of the improved path segmentation model were reduced by 65.86%, and the mPA was 97.39%. The recognition accuracy MIoU of the Faster-U-net model for maize, tomatoes, cucumbers, and wheat was 93.86%, 94.01%, 93.14%, and 89.10%, respectively. The processing speed of the single-core CPU was 22.32 fps/s. The proposed method had strong robustness in predicting rows of different crops. The average angle difference of the navigation line under a ridge environment such as that for corn, tomatoes, cucumbers, or wheat was 0.624°, 0.556°, 0.526°, and 0.999°, respectively. This research can provide technical support and reference for the research and development of intelligent agricultural robot navigation equipment in the field.

Pregnancy exposure of titanium dioxide nanoparticles causes intestinal dysbiosis and neurobehavioral impairments that are not significant postnatally but emerge in adulthood of offspring.

BACKGROUND: Pregnancy exposure to titanium dioxide nanoparticles (TiO2NPs) is a vital consideration due to their inadvertent ingestion from environmental contamination. The potential health effects of TiO2NPs on the neurodevelopmental process should be seriously concerned in health risk assessment, especially for the pregnant women who are susceptible to the neurodevelopmental toxicity of nano-sized particles. However, the available evidence of neurodevelopmental toxicity of TiO2NPs remains very limited. METHODS: In the present study, the pregnant mice were intragastric administered with 150 mg/kg TiO2NPs from gestational day (GD) 8 to 21, the maternal behaviors and neurodevelopment-related indicators in offspring were all assessed at different time points after delivery. The gut microbial community in both dams and their offspring were detected by using 16S ribosomal RNA (rRNA) gene sequencing. The gut-brain axis related indicators were also determined in the offspring. RESULTS: The results clearly demonstrated that exposure to TiO2NPs did not affect the maternal behaviors of pregnant mice, or cause the deficits on the developmental milestones and perturbations in the early postnatal development of offspring. Intriguingly, our data revealed that pregnancy exposure of TiO2NPs did not affect locomotor function, learning and memory ability and anxiety-like behavior in offspring at postnatal day (PD) 21, but resulted in obvious impairments on these neurobehaviors at PD49. Similar phenomena were obtained in the composition of gut microbial community, intestinal and brain pathological damage in offspring in adulthood. Moreover, the intestinal dysbiosis induced by TiO2NPs might be highly associated with the delayed appearance of neurobehavioral impairments in offspring, possibly occurring through disruption of gut-brain axis. CONCLUSIONS: This is the first report elucidated that pregnancy exposure to TiO2NPs caused delayed appearance of neurobehavioral impairments in offspring when they reached adulthood, although these perturbations did not happen at early life after delivery. These findings will provide valuable insights about neurodevelopmental toxicity of TiO2NPs, and call for comprehensive health risk assessment of TiO2NPs on the susceptible population, such as pregnant women.

Silicon dioxide nanoparticles induced neurobehavioral impairments by disrupting microbiota-gut-brain axis.

BACKGROUND: Silicon dioxide nanoparticles (SiO2NPs) are widely used as additive in the food industry with controversial health risk. Gut microbiota is a new and hot topic in the field of nanotoxicity. It also contributes a novel and insightful view to understand the potential health risk of food-grade SiO2NPs in children, who are susceptible to the toxic effects of nanoparticles. METHODS: In current study, the young mice were orally administrated with vehicle or SiO2NPs solution for 28 days. The effects of SiO2NPs on the gut microbiota were detected by 16S ribosomal RNA (rRNA) gene sequencing, and the neurobehavioral functions were evaluated by open field test and Morris water maze. The level of inflammation, tissue integrity of gut and the classical indicators involved in gut-brain, gut-liver and gut-lung axis were all assessed. RESULTS: Our results demonstrated that SiO2NPs significantly caused the spatial learning and memory impairments and locomotor inhibition. Although SiO2NPs did not trigger evident intestinal or neuronal inflammation, they remarkably damaged the tissue integrity. The microbial diversity within the gut was unexpectedly enhanced in SiO2NPs-treated mice, mainly manifested by the increased abundances of Firmicutes and Patescibacteria. Intriguingly, we demonstrated for the first time that the neurobehavioral impairments and brain damages induced by SiO2NPs might be distinctively associated with the disruption of gut-brain axis by specific chemical substances originated from gut, such as Vipr1 and Sstr2. Unapparent changes in liver or lung tissues further suggested the absence of gut-liver axis or gut-lung axis regulation upon oral SiO2NPs exposure. CONCLUSION: This study provides a novel idea that the SiO2NPs induced neurotoxic effects may occur through distinctive gut-brain axis, showing no significant impact on either gut-lung axis or gut-liver axis. These findings raise the exciting prospect that maintenance and coordination of gastrointestinal functions may be critical for protection against the neurotoxicity of infant foodborne SiO2NPs.

ClusterV-Web: a user-friendly tool for profiling HIV quasispecies and generating drug resistance reports from nanopore long-read data.

Summary: Third-generation long-read sequencing is an increasingly utilized technique for profiling human immunodeficiency virus (HIV) quasispecies and detecting drug resistance mutations due to its ability to cover the entire viral genome in individual reads. Recently, the ClusterV tool has demonstrated accurate detection of HIV quasispecies from Nanopore long-read sequencing data. However, the need for scripting skills and a computational environment may act as a barrier for many potential users. To address this issue, we have introduced ClusterV-Web, a user-friendly web-based application that enables easy configuration and execution of ClusterV, both remotely and locally. Our tool provides interactive tables and data visualizations to aid in the interpretation of results. This development is expected to democratize access to long-read sequencing data analysis, enabling a wider range of researchers and clinicians to efficiently profile HIV quasispecies and detect drug resistance mutations. Availability and implementation: ClusterV-Web is freely available and open source, with detailed documentation accessible at http://www.bio8.cs.hku.hk/ClusterVW/. The standalone Docker image and source code are also available at https://github.com/HKU-BAL/ClusterV-Web.

Unraveling the mechanisms and responses of aniline-degrading biosystem to salinity stress in high temperature condition: pollutants removal performance and microbial community.

To explore the intrinsic influence of different salinity content on aniline biodegradation system in high temperature condition of 35±1 °C, six groups at various salinity concentration (0.0%-5.0%) were applied. The results showed that the salinity exerted insignificant impact on aniline removal performance. The low-level salinity (0.5%-1.5%) stimulated the nitrogen metabolism performance. The G5-2.5% had excellent adaptability to salinity while the nitrogen removal capacity of G6-5.0% was almost lost. Moreover, high throughput sequencing analysis revealed that the g__norank_f__NS9_marine_group, g__Thauera and g__unclassified_f__Rhodobacteraceae proliferated wildly and established positive correlation each other in low salinity systems. The g__SM1A02 occupying the dominant position in G5 ensured the nitrification performance. In contrast, the Rhodococcus possessing great survival advantage in tremendous osmotic pressure competed with most functional genus, triggering the collapse of nitrogen metabolism capacity in G6. This work provided valuable guidance for the aniline wastewater treatment under salinity stress in high temperature condition.

Evolution of aniline degradation and nitrogen removal performance in electro-enhanced sequence batch reactor under salinity stress: Sludge characteristics and microbial diversity.

To explore the influence mechanism of different concentrations of salinity on the electro-enhanced aniline biodegradation system, a control group and experimental groups (0%-NaCl, 0.5%-NaCl, 1.5%-NaCl, 2.5%-NaCl, 3.5%-NaCl) were established. The experimental results showed that the electric field strengthened the denitrification performance, while salinity had little effect on the degradation efficiency of aniline and chemical oxygen demand (COD). The removal rate of TN reached 79.6% and 74.9% in 0.5%-NaCl and 1.5%-NaCl, respectively, which were superior than 0%-NaCl. As salinity increased, the nitrogen removal effect was negatively affected. Microbial diversity analysis indicated that the microbial community structure was uniform in the control group, 0%-NaCl, and 0.5%-NaCl, with the dominant genus OLB8 ensuring the nitrogen removal performance. In contrast, in the 2.5%-NaCl and 3.5%-NaCl experimental groups, the organic degrading bacteria were still active, while nitrifiers and denitrifiers were severely damaged. In conclusion, this study suggested that low concentrations of salinity can improve the decontamination performance of the electro-enhanced aniline biodegradation system, while high concentrations of salinity could lead to the collapse of the decontamination mechanism.

Integrated modeling framework reveals co-regulation of transcription factors, miRNAs and lncRNAs on cardiac developmental dynamics.

AIMS: Dissecting complex interactions among transcription factors (TFs), microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are central for understanding heart development and function. Although computational approaches and platforms have been described to infer relationships among regulatory factors and genes, current approaches do not adequately account for how highly diverse, interacting regulators that include noncoding RNAs (ncRNAs) control cardiac gene expression dynamics over time. METHODS: To overcome this limitation, we devised an integrated framework, cardiac gene regulatory modeling (CGRM) that integrates LogicTRN and regulatory component analysis bioinformatics modeling platforms to infer complex regulatory mechanisms. We then used CGRM to identify and compare the TF-ncRNA gene regulatory networks that govern early- and late-stage cardiomyocytes (CMs) generated by in vitro differentiation of human pluripotent stem cells (hPSC) and ventricular and atrial CMs isolated during in vivo human cardiac development. RESULTS: Comparisons of in vitro versus in vivo derived CMs revealed conserved regulatory networks among TFs and ncRNAs in early cells that significantly diverged in late staged cells. We report that cardiac genes ("heart targets") expressed in early-stage hPSC-CMs are primarily regulated by MESP1, miR-1, miR-23, lncRNAs NEAT1 and MALAT1, while GATA6, HAND2, miR-200c, NEAT1 and MALAT1 are critical for late hPSC-CMs. The inferred TF-miRNA-lncRNA networks regulating heart development and contraction were similar among early-stage CMs, among individual hPSC-CM datasets and between in vitro and in vivo samples. However, genes related to apoptosis, cell cycle and proliferation, and transmembrane transport showed a high degree of divergence between in vitro and in vivo derived late-stage CMs. Overall, late-, but not early-stage CMs diverged greatly in the expression of "heart target" transcripts and their regulatory mechanisms. CONCLUSIONS: In conclusion, we find that hPSC-CMs are regulated in a cell autonomous manner during early development that diverges significantly as a function of time when compared to in vivo derived CMs. These findings demonstrate the feasibility of using CGRM to reveal dynamic and complex transcriptional and posttranscriptional regulatory interactions that underlie cell directed versus environment-dependent CM development. These results with in vitro versus in vivo derived CMs thus establish this approach for detailed analyses of heart disease and for the analysis of cell regulatory systems in other biomedical fields.

Unraveling the nexus of Cr (VI), aniline, and microbial ecology on aniline-degrading biosystem: Removal efficiency, sludge type, microbial ecology.

In order to explore the stress principle of Cr (Ⅵ) on aniline biodegradation system, a control group and experimental groups with the concentration of Cr (Ⅵ) at 2, 5, 8 mg/L were set up. The results demonstrated that Cr (Ⅵ) had minimal effects on the degradation efficiency of aniline but significantly inhibited nitrogen removal function. When Cr (Ⅵ) concentration was below 5 mg/L, the nitrification performance recovered spontaneously, while denitrification performance was severely impaired. Furthermore, the secretion of extracellular polymeric substances (EPS) and its fluorescence substance concentration were strongly inhibited with increasing Cr (Ⅵ) concentration. High-throughput sequencing revealed that the experimental groups were enriched with Leucobacter and Cr (Ⅵ)-reducing bacteria, but the abundance of nitrifiers and denitrifiers was significantly decreased compared to the control group. Overall, the effects of Cr (Ⅵ) stress at different concentrations on nitrogen removal performance were more significant than those on aniline degradation.

Integrated fixed-film activated sludge systems in continuous-flow and batch mode acclimated from low to high aniline concentrations: Performance, mechanism and metabolic pathways.

Integrated fixed-film activated sludge (IFAS) system has considerable advantages in treating aniline wastewater economically and efficiently. However, the response mechanism of IFAS to aniline needs further study. Herein, IFAS in continuous-flow (CF-IFAS) and batch mode (B-IFAS) were set up to investigate it. The removal efficiency of aniline exceeded 99% under different stress intensities. At low stress intensity (aniline ≈ 200 mg/L), the total nitrogen removal efficiency of B-IFAS was approximately 37.76% higher than CF-IFAS. When the stress intensity increased (aniline ≥ 400 mg/L), both were over 82%. CF-IFAS was restrained by denitrification while nitrification in B-IFAS. The legacy effect of perturbation of B-IFAS made microflora quickly reach new stability. The closer interspecific relationship in B-IFAS and more key species: Leucobacter, Rhodococcus, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Ellin6067 and norank_f_NS9_marine_group. Metabolic and Cell growth and death were the most abundant metabolic pathways, resulting both systems the excellent pollutant removal and stability under high stress intensity.

Shape Dependence of Silver-Nanoparticle-Mediated Synthesis of Gold Nanoclusters with Small Molecules as Capping Ligands.

In this study, differently shaped silver nanoparticles used for the synthesis of gold nanoclusters with small capping ligands were demonstrated. Silver nanoparticles provide a reaction platform that plays dual roles in the formation of Au NCs. One is to reduce gold ions and the other is to attract capping ligands to the surface of nanoparticles. The binding of capping ligands to the AgNP surface creates a restricted space on the surface while gold ions are being reduced by the particles. Four different shapes of AgNPs were prepared and used to examine whether or not this approach is dependent on the morphology of AgNPs. Quasi-spherical AgNPs and silver nanoplates showed excellent results when they were used to synthesize Au NCs. Spherical AgNPs and triangular nanoplates exhibited limited synthesis of Au NCs. TEM images demonstrated that Au NCs were transiently assembled on the surface of silver nanoparticles in the method. The formation of Au NCs was observed on the whole surface of the QS-AgNPs if the synthesis of Au NCs was mediated by QS-AgNPs. In contrast, formation of Au NCs was only observed on the edges and corners of AgNPts if the synthesis of Au NCs was mediated by AgNPts. All of the synthesized Au NCs emitted bright red fluorescence under UV-box irradiation. The synthesized Au NCs displayed similar fluorescent properties, including quantum yields and excitation and emission wavelengths.

Evaluation of Mycobacterium tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling.

Sensitive detection of Mycobacterium tuberculosis (TB) in small percentages in metagenomic samples is essential for microbial classification and drug resistance prediction. However, traditional methods, such as bacterial culture and microscopy, are time-consuming and sometimes have limited TB detection sensitivity. Oxford nanopore technologies (ONT) MinION sequencing allows rapid and simple sample preparation for sequencing. Its recently developed adaptive sequencing selects reads from targets while allowing real-time base-calling to achieve sequence enrichment or depletion during sequencing. Another common enrichment method is PCR amplification of the target TB genes. In this study, we compared both methods using ONT MinION sequencing for TB detection and variant calling in metagenomic samples using both simulation runs and those with synthetic and patient samples. We found that both methods effectively enrich TB reads from a high percentage of human (95%) and other microbial DNA. Adaptive sequencing with readfish and UNCALLDE achieved a 3.9-fold and 2.2-fold enrichment compared to the control run. We provide a simple automatic analysis framework to support the detection of TB for clinical use, openly available at https://github.com/HKU-BAL/ONT-TB-NF . Depending on the patient's medical condition and sample type, we recommend users evaluate and optimize their workflow for different clinical specimens to improve the detection limit.

An attempt to stimulate aniline degrading bioreactor by exogenous auto-inducer: Decontamination performance, sludge characteristics, and microbial community structure response.

To break the contradiction between aniline and nitrogen metabolism in activated sludge reactor by influencing microbial interspecific communication, Auto-inducer C6-HSL and 3-oxo-C8-HSL were selected in this study to interfere with aniline degradation system. The two Auto-inducers enhanced the aniline degradation rate and ammonia removal efficiency of the systems, especially C6-HSL. Meanwhile, the main ammonia removal way was assimilation. Exogenous Auto-inducer effectively stabilized the sludge structure and activity from the destruction of aniline, and promoted EPS secretion. Microbial diversity analysis showed that most of functional microflora of seed sludge gradually deactivated with the operation of the reactor, while Rhodococcus, Leucobacter, g_norank_f_Saprospiraceae proliferated wildly under the action of Auto-inducer. Additionally, the interspecific relationship also demonstrated a different trend. Exogenous Auto-inducer was proved to exert positive effects on aniline degradation system to a certain extent, providing new insights in the field of aniline wastewater bio-degradation.

The changing C/N of aggressive aniline: Metagenomic analysis of pollutant removal, metabolic pathways and functional genes.

In order to optimize the degradation of high-concentration aniline wastewater, the operation of sequencing batch bioaugmentation reactors with different aniline concentrations (200 mg/L, 600 mg/L, 1000 mg/L) was studied. The results showed that the removal rates of aniline and COD in the three reactors could reach 100%. When the aniline increased to 600 mg/L, the nitrogen removal efficiency reached the peak (51.85%). The increase of aniline inhibited the nitrification, while denitrification was enhanced due to the increase of C/N ratio. But this change was reversed by the toxicity of high concentrations of aniline. The metagenomic analysis showed that when the aniline concentration was 600 mg/L, the abundance distribution of microbial samples was more uniform. The improved of aniline concentration had led to the increase of aromatic compounds degradation metabolic pathways. In addition, the abundance of aniline degradation and nitrogen metabolism genes (dmpB, xylE, norB) was also promoted.