VPTMdb: a viral posttranslational modification database.

In viruses, posttranslational modifications (PTMs) are essential for their life cycle. Recognizing viral PTMs is very important for a better understanding of the mechanism of viral infections and finding potential drug targets. However, few studies have investigated the roles of viral PTMs in virus-human interactions using comprehensive viral PTM datasets. To fill this gap, we developed the first comprehensive viral posttranslational modification database (VPTMdb) for collecting systematic information of PTMs in human viruses and infected host cells. The VPTMdb contains 1240 unique viral PTM sites with 8 modification types from 43 viruses (818 experimentally verified PTM sites manually extracted from 150 publications and 422 PTMs extracted from SwissProt) as well as 13 650 infected cells' PTMs extracted from seven global proteomics experiments in six human viruses. The investigation of viral PTM sequences motifs showed that most viral PTMs have the consensus motifs with human proteins in phosphorylation and five cellular kinase families phosphorylate more than 10 viral species. The analysis of protein disordered regions presented that more than 50% glycosylation sites of double-strand DNA viruses are in the disordered regions, whereas single-strand RNA and retroviruses prefer ordered regions. Domain-domain interaction analysis indicating potential roles of viral PTMs play in infections. The findings should make an important contribution to the field of virus-human interaction. Moreover, we created a novel sequence-based classifier named VPTMpre to help users predict viral protein phosphorylation sites. VPTMdb online web server (http://vptmdb.com:8787/VPTMdb/) was implemented for users to download viral PTM data and predict phosphorylation sites of interest.

Enhancing the extracellular electron transfer ability via Polydopamine@S. oneidensis MR-1 for Cr(VI) reduction.

Microbial reduction of hexavalent chromium (Cr (VI)) shows better efficiency and cost-effectiveness. However, immobilization of Cr (III) remains a challenge as there is a limited supply of electron donors. A greener and cleaner option for donating external electrons was using bioelectrochemical systems to perform the microbial reduction of Cr(VI). In this system, we constructed a polydopamine (PDA) decorated Shewanella oneidensis MR-1 (S. oneidensis MR-1) bioelectrode with bidirectional electron transport, abbreviated as PDA@S. oneidensis MR-1. The conjugated PDA distributed on the intracellular and extracellular of individual S. oneidensis MR-1 has been shown to accelerate electron transfer by outer membrane C-type cytochromes and flavin-bound MtrC/OmcA pathway by various electrochemical analyses. As expected, the PDA@S. oneidensis MR-1 biofilm achieved 88.1% Cr (VI) removal efficiency (RE) and 58.1% Cr (III) immobilization efficiency (IE) within 24 h under the autotrophic conditions at the optimal voltage (-150 mV) compared with the control potential (0 mV). The PDA@S. oneidensis MR-1 biofilm showed increased RE activity was attributed to the shortening of the distance between individual bacteria by PDA. This research provides a viable strategy for in situ bioremediation of Cr(VI) polluted aquatic environment.

Carbon-based materials as adsorbent for antibiotics removal: Mechanisms and influencing factors.

With the development of the removal of organic pollutants in the soil and water environment, antibiotics have been considered as emerging pollutants and received considerable attention among the scientific community. Thus, there is a need for an effective, economical, fast, operational feasible and environmental-friendly technology to remove antibiotics. Adsorption technology would be one of the most promising option on the basis that it best meets the criteria we set out above. From the most primitive activated carbon to the most innovative modified biochar, carbon-based materials have played a significant role in the adsorption process of antibiotics all the time. This paper reviews the adsorption behavior of some representative antibiotics (e.g., chloramphenicols, sulfonamides, tetracyclines, flouroquinolones) over various carbonaceous materials (i.e., activated carbon, carbon nanotubes, graphene, and biochar). Nevertheless, in addition to the structural characteristics and adsorption capacities of carbon-based materials, a special emphasis was placed on the underlying adsorption mechanisms and roles of different influencing factors in the adsorption process. Moreover, the knowledge gaps and research challenges have been highlighted, including design and optimization of the carbonaceous materials for antibiotics adsorption.

Selenium contamination, consequences and remediation techniques in water and soils: A review.

Selenium (Se) contamination in surface and ground water in numerous river basins has become a critical problem worldwide in recent years. The exposure to Se, either direct consumption of Se or indirectly may be fatal to the human health because of its toxicity. The review begins with an introduction of Se chemistry, distribution and health threats, which are essential to the remediation techniques. Then, the review provides the recent and common removal techniques for Se, including reduction techniques, phytoremediation, bioremediation, coagulation-flocculation, electrocoagulation (EC), electrochemical methods, adsorption, coprecipitation, electrokinetics, membrance technology, and chemical precipitation. Removal techniques concentrate on the advantages, drawbacks and the recent achievements of each technique. The review also takes an overall consideration of experimental conditions, comparison criteria and economic aspects.

Boosting bioelectricity generation in microbial fuel cells via biomimetic Fe-N-S-C nanozymes.

Anode performance has been regarded as a crucial factor determining long-term stability and electricity generation of microbial fuel cells (MFCs), which restricts by the difficult extracellular electron transfer (EET) on the microbe/anode interface. Herein, inspired by biological enzyme systems, this study synthesized the biomimetic nanozymes with Fe-N-S-C active sites as the anode materials of MFCs, which was similar to the hemes of c-type cytochromes (c-Cyts) for boosting EET process. As excepted, an obviously faster start-up and a much higher power density were achieved by the MFCs equipped with Fe-N-S-C nanozymes (startup time, 3.5 d; power density, 2366 ± 34 mW m-2) than that based on traditional carbon cloth (startup time, 5.6 d; power density, 1009 ± 26 mW m-2). Such unique features of Fe-N-S-C nanozymes anode not only greatly favored the bacterial adhesion and the electroactive bacteria enrichment on the anode surface, but also efficiently facilitated the EET process between the electroactive bacteria and anode surface. This study provided a feasible strategy for designing the novel MFC anode materials from the perspective of bionic enzyme.

Vinasse-based biochar magnetic composites: adsorptive removal of tetracycline in aqueous solutions.

Highly efficient and cost-effective adsorbents for antibiotic removal are the key to mitigate pollution by industrial wastewaters. Pyrolyzing low-cost winemaking waste into biochar is a promising means for waste biomass utilization. This study assembled vinasse-derived biochar with manganese ferrite into vinasse-manganese ferrite biochar-magnetic composites (V-MFB-MCs) through simultaneous pyrolysis of waste biomass and metal (Mn and Fe) hydroxide precipitates. Batch experiments were conducted to evaluate the kinetics and isotherms of tetracycline (TC) adsorption as well as the influence of pH value, humic acid, and ionic strength. Morphological characterization showed that crystalline MnFe2O4 nanoparticles were impregnated within the framework of fabricated V-MFB-MCs. Superior TC adsorption capacity and fast pseudo-second-order kinetics could be achieved by the V-MFB-MCs-800 at pH 3.0. The TC adsorption onto V-MFB-MCs-800 was highly pH-dependent and controlled by the positive influence of ionic strength and humic acid. V-MFB-MCs-800 showed excellent adsorption performance in different natural water. Multiple interaction mechanisms including pore filling effect, π-π stacking interaction, and hydrogen bonding contribute to TC removal by V-MFB-MCs-800, which can be an innovative biowaste-derived material for industrial wastewater treatment.

Microplastics and environmental pollutants: Key interaction and toxicology in aquatic and soil environments.

Nowadays, a growing number of microplastics are released into the environment due to the extensive use and inappropriate management of plastic products. With the increasing body of evidence about the pollution and hazards of microplastics, microplastics have drawn major attention from governments and the scientific community. As a kind of emerging and persistent environmental pollutants, microplastics have recently been detected on a variety of substrates in the world. Therefore, this paper reviews the recent progress in identifying the sources of microplastics in soil, water, and atmosphere and describing the transport and fate of microplastics in the terrestrial, aquatic and atmospheric ecosystems for revealing the circulation of microplastics in the ecosystem. In addition, considering the persistence of microplastics, this study elucidates the interactions of microplastics with other pollutants in the environment (i.e., organic pollutants, heavy metals) with emphasis on toxicity and accumulation, providing a novel insight into the ecological risks of microplastics in the environment. The negative impacts of microplastics on organisms and environmental health are also reviewed to reveal the environmental hazards of microplastics. The knowledge gaps and key research priorities of microplastics are identified to better understand and mitigate the environmental risks of microplastics.

Highly efficient adsorption of chromium on N, S-codoped porous carbon materials derived from paper sludge.

The synergistic effect of heteroatoms is a viable method to enhance the adsorption performance of heavy metal onto carbon-based materials. However, the high cost, complex operation and a lot of pollution from the synthesis process have limited its development. Herein, a facile two-step pyrolysis method is used to prepare in situ N and S doped porous biochar from paper mill sludge for the removal of Cr(VI) from aqueous environment. The NSC-450 sample prepared under the optimum conditions has a large specific surface area of 3336.7 m2 g-1, an average pore size of 2.56 nm and a total pore volume of 2.10 cm3 g-1, manifesting the excellent adsorption capacity of 356.25 mg g-1 for Cr(VI). The adsorption of Cr(VI) by NSC-450 is consistent with the Langmuir isotherm and pseudo-second-order model, suggesting a spontaneous and endothermic chemisorption process. The analysis results show that the NH, graphitic nitrogen and thiophene structures have a positive effect on converting a large amount of Cr(VI) to Cr(III) by synergistic reduction, indicating obviously facilitating Cr(VI) removal compared to other sites. Therefore, in this material, the strong adsorption mechanism is mainly reductive complexation. Moreover, the effects of real water quality, anions, cations and fulvic acid on the adsorption behavior of Cr(VI) onto the NSC-450 were further investigated. The results demonstrate that the chromium removal rate remains above 82% even in actual electroplating wastewater, suggesting NSC-450 has great practical application prospect. This work offered a feasible method for high-value utilization of sludge, but also provided a novel perspective for the future design of heteroatom-doped carbon materials for promoting to eliminate hexavalent chromium from water environment.

Pan-Cancer Analysis of Canonical and Modified miRNAs Enhances the Resolution of the Functional miRNAome in Cancer.

Epitranscriptomic studies of miRNAs have added a new layer of complexity to the cancer field. Although there is fast-growing interest in adenosine-to-inosine (A-to-I) miRNA editing and alternative cleavage that shifts miRNA isoforms, simultaneous evaluation of both modifications in cancer is still missing. Here, we concurrently profiled multiple miRNA modification types, including A-to-I miRNA editing and shifted miRNA isoforms, in >13,000 adult and pediatric tumor samples across 38 distinct cancer cohorts from The Cancer Genome Atlas and The Therapeutically Applicable Research to Generate Effective Treatments data sets. The differences between canonical miRNAs and the wider miRNAome in terms of expression, clustering, dysregulation, and prognostic standpoint were investigated. The combination of canonical miRNAs and modified miRNAs boosted the quality of clustering results, outlining unique clinicopathologic features among cohorts. Certain modified miRNAs showed opposite expression from their canonical counterparts in cancer, potentially impacting their targets and function. Finally, a shifted and edited miRNA isoform was experimentally validated to directly bind and suppress a unique target. These findings outline the importance of going beyond the well-established paradigm of one mature miRNA per miRNA arm to elucidate novel mechanisms related to cancer progression. SIGNIFICANCE: Modified miRNAs may act as cancer biomarkers and function as allies or antagonists of their canonical counterparts in gene regulation, suggesting the concurrent consideration of canonical and modified miRNAs can boost patient stratification.

Use of scREAD to explore and analyze single-cell and single-nucleus RNA-seq data for Alzheimer's disease.

Single-cell RNA-sequencing (scRNA-seq) and single-nucleus RNA-sequencing (snRNA-seq) studies have provided remarkable insights into understanding the molecular pathogenesis of Alzheimer's disease. We recently developed scREAD, a database to provide comprehensive analyses of all the existing AD scRNA-seq and snRNA-seq data from the public domain. Here, we report protocols for using the scREAD web interface and running the backend workflow locally. Our protocols enable custom analyses of AD single-cell and single-nucleus gene expression profiles. For complete details on the use and execution of this protocol, please refer to Jiang et al. (2020).

Manganese ferrite modified biochar from vinasse for enhanced adsorption of levofloxacin: Effects and mechanisms.

The primitive biochar (BC) and NiFe2O4/biochar composites (NFBC), biological adsorbents prepared from vinasse wastes, possess the environmental application in levofloxacin (LEV) removal. In this study, the efficient adsorption of LEV onto biochar synthesized by pyrolysis of vinasse wastes from aqueous environment was investigated. The influencing factors (i.e., pH, reaction time, and temperature) of adsorption process were also well studied. The results indicated that the maximum adsorption capacities of both BC and NFBC were occurred in mildly acidic condition (pH 6). In addition, the biochar adsorption capacities were obviously increased in higher temperature (25-45 °C). The chemistry adsorption and monolayer homogeneous dominated adsorption process of LEV onto BC and NFBC. The adsorption process was spontaneous and endothermic by thermodynamic analysis. The SEDA (site energy distribution analysis) explained that the adsorption effectivity increased by increasing site energy of biochar surface. The SEDA revealed the more energy heterogeneity in NFBC, fitting the characterization result of Fourier-transform infrared (FT-IR) spectroscopy and X-ray photoelectron spectroscopy (XPS). The electron-donor-acceptor (EDA) interactions and hydrogen bonds is suggested as the major adsorption mechanism. And as for the adsorption of the various biowaste recycled synthetic, this study can be referred in discussion of performance analysis and optimal condition.

A Reference Genome of Bursaphelenchus mucronatus Provides New Resources for Revealing Its Displacement by Pinewood Nematode.

The Bursaphelenchus mucronatus, which was highly similar with Bursaphelenchus xylophilus in terms of morphological characteristics and biological properties-but had weaker pathogenicity to forests-was a native species often displaced by B. xylophilus when occupying the same niche. Since the draft genome of the invasive B. xylophilus has been published, the absence of a reference genome of B. mucronatus still prevents us from understanding the molecular evidences behind competitive displacement. In this study, we employed Single Molecule, Real-Time (SMRT) sequencing and a Hi-C scaffolding approach to yield a near chromosome-level assembly of B. mucronatus, including six pseudo-chromosomes. The assembly size is 73 Mb, with scaffold N50 of 11.50 Mb and contig N50 of 1.48 Mb. Comparative genomics results showed high similarity between B. xylophilus and B. mucronatus. However, the losing of orphan genes and species-specific orthologous genes in B. mucronatus may indicate weaker adaptability to the environment. The gene family contractions of GPCRs (G Protein-Coupled Receptors) and cellulases in B. mucronatus may jointly contribute to its displacement by B. xylophilus. Overall, we introduced a valuable genomic resource for molecular and evolutionary studies of B. mucronatus, especially for studying the competitive displacement by the pinewood nematode, which could help us control the pathogenicity of pine wilt diseases.

Fabrication of sustainable manganese ferrite modified biochar from vinasse for enhanced adsorption of fluoroquinolone antibiotics: Effects and mechanisms.

An effective adsorbent towards fluoroquinolone antibiotics was synthesized via a facile two-step approach, the co-precipitation of Fe, Mn with vinasse wastes and then pyrolysis under controlled conditions which denoted as FMB. Its adsorption behavior was examined based on a batch adsorption experiment of fluoroquinolone antibiotics pefloxacin (PEF) and ciprofloxacin (CIP). Experimental factors, such as pH, adsorbent dose, ionic strength, contact time and temperature have done a great deal to influence the adsorption of PEF and CIP. The FMB demonstrated excellent performance in reusability tests towards to both PEF and CIP, which showed that the recycling efficiency of PEF and CIP could remain ~55% and ~80% after five recycle cycles, respectively. The dominated adsorption mechanisms included pore filling effect, π-π stacking interaction, π-π EDA, hydrogen bonding and hydrophobicity. Overall, this work presented FMB was recognized as an effective, environmental-friendly and magnetically separable adsorbent for alleviating fluoroquinolone antibiotics contamination from water.

A sustainable ferromanganese biochar adsorbent for effective levofloxacin removal from aqueous medium.

This present study reported the synthesis and characterization of a low-cost, environment friendly and high efficient biochar, ferromanganese modified biochar (Fe/Mn-BC) for the removal of levofloxacin (LEV) from aqueous medium. Fe/Mn-BC was synthesized through the facile co-precipitation of Fe, Mn with vinasse wastes and then pyrolysis under controlled conditions. The characterization of Fe/MnBC was analyzed by scanning electron microscope (SEM), transmission electron microscope (TEM), X-ray diffraction patterns (XPS), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and Raman. Some influencing factors (e.g., pH, Fe/Mn-BC dosage, initial LEV concentration, ionic strength, contact time and temperature) were comprehensively investigated. The results manifested that the adsorption process of LEV onto Fe/Mn-BC was high pH dependence and the maximum adsorption capacity was achieved at pH 5. Moreover, the adsorption capacity of LEV was increased with increasing ionic strength. To gain a clearer perspective on the adsorption behavior of LEV onto Fe/Mn-BC, the adsorption kinetics and isotherms were also performed, revealing pseudo-second-order and Freundlich model had a better fitting effect. Reusability experiments indicated that Fe/Mn-BC could maintain a certain adsorption capacity for LEV after 5 recycles. Overall, this work showed that Fe/Mn-BC was an effective and promising adsorbent for eliminating LEV from aqueous medium.

Single and simultaneous adsorption of pefloxacin and Cu(II) ions from aqueous solutions by oxidized multiwalled carbon nanotube.

In this study, the oxidized multiwalled carbon nanotube (O-MWCNTs) was obtained by a simple method, and investigated by various techniques (SEM, TEM, FT-IR, XPS and zeta potential) for the removal of pefloxacin and Cu(II). The mutual effects of their adsorption onto O-MWCNTs were comprehensively clarified with sole and binary systems with adsorption kinetics, sorption thermodynamic and sorption isotherm models. The results indicated that there are site enhancement and competition of pefloxacin and Cu(II) on O-MWCNTs. According to mechanism investigation on the adsorption of pefloxacin and Cu(II) by XPS analysis, pH impact study, electrostatic interaction and π-π interactions, the low concentration of Cu(II)/pefloxacin could act as a bridge between pefloxacin/Cu(II) and O-MWCNTs, which significantly enhances the adsorption of pefloxacin/Cu(II). This study provided effective method and valuable reference for the elimination of pefloxacin/Cu(II) from aquatic environments.

Applications and factors influencing of the persulfate-based advanced oxidation processes for the remediation of groundwater and soil contaminated with organic compounds.

Persulfate is the latest oxidant which is being used increasingly for the remediation of groundwater and soil contaminated with organic compounds. It is of great significant to offer readers a general summary about different methods of activating persulfate, mainly including heat-activated, metal ions-activated, UV-activated, and alkaline-activated. Meanwhile, in addition to persulfate concentration as an influencing factor for persulfate oxidation process, selected information like temperature, anions, cations, pH, and humic acid are presented and discussed. The last section focuses on the advantages of different activated persulfate processes, and the suggestions and research needs for persulfate-based advanced oxidation in the remediation of polluted groundwater and soil.

Modification of biochar derived from sawdust and its application in removal of tetracycline and copper from aqueous solution: Adsorption mechanism and modelling.

Highly efficient simultaneous removal of Cu(II) and tetracycline (TET) from aqueous solution was accomplished by iron and zinc doped sawdust biochar (Fe/Zn-biochar). The mutual effects and inner mechanisms of their adsorption onto Fe/Zn-biochar were systematically investigated via sole and binary systems, sorption isotherm and adsorption kinetics models. The liquid-film diffusion step might be the rate-limiting step for tetracycline, the interaction of Cu(II) was more likely controlled by both intra particle diffusion model and liquid film diffusion model. The fitting of experimental data with kinetic models, Temkin model indicates that the adsorption process of tetracycline and Cu(II) involve chemisorption, and physico-chemical adsorption, respectively. There exists site competition and enhancement of Cu(II) and tetracycline on the sorption to Fe/Zn-biochar. The results of this study indicate that modification of biochar derived from sawdust shows great potential for simultaneous removal of Cu(II) and tetracycline from co-contaminated water.