Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved metagenomics. In general terms, it ...refers to the recovery of draft or high-quality microbial genomes and their taxonomic classification and functional annotation. In recent years, several studies have utilized the genome-resolved metagenome analysis approach and identified previously unknown microbial species from human and environmental metagenomes. In this review, we describe genome-resolved metagenome analysis as a series of four necessary steps: (i) preprocessing of the sequencing reads, (ii) de novo metagenome assembly, (iii) genome binning and (iv) taxonomic and functional analysis of the recovered genomes. For each of these four steps, we discuss the most commonly used tools and the currently available pipelines to guide the scientific community in the recovery and subsequent analyses of genomes from any metagenome sample. Furthermore, we also discuss the tools required for validation of assembly quality as well as for improving quality of the recovered genomes. We also highlight the currently available pipelines that can be used to automate the whole analysis without having advanced bioinformatics knowledge. Finally, we will highlight the most widely adapted and actively maintained tools and pipelines that can be helpful to the scientific community in decision making before they commence the analysis.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Les neuropathies anti-MAG sont associées à une gammapathie monoclonale de signification indéterminée (MGUS) ou à une hémopathie maligne. Les symptômes de la maladie sont directement en lien ...l’activité pathogène de l’IgM produite.
Notre objectif est de déterminer si la présence d’une hémopathie maligne ou d’une mutation des gènes MYD88 et CXCR4 influence la présentation de la maladie et la réponse au rituximab (RTX) en monothérapie ou en combinaison avec une chimiothérapie.
Nous avons inclus 79 patients atteints de neuropathies anti-MAG. Les mutations MYD88L265P et CXCR4 ont été recherchées dans le sang des patients. Les données cliniques, biologiques et électrophysiologiques ont été collectées à l’inclusion. L’efficacité du traitement par RTX a été mesurée à 12 mois son administration.
Une hémopathie maligne a été diagnostiquée chez 17 patients (22 %). La mutation MYD88L265P et une mutation du gène CXCR4 ont été détectées chez respectivement 29/60 patients (48 %) et un patient. La présence d’une hémopathie ou d’une mutation MYD88L265P n’avaient aucune influence sur la présentation de la maladie ou la réponse au RTX. Les patients ayant répondu favorablement au RTX avaient des scores ISS plus faibles et des valeurs de MUSIX plus élevées que les patients non répondeurs (p=0,02).
Les caractéristiques phénotypiques de notre cohorte sont similaires à celles précédemment rapportées dans la littérature. Les mutations du gène MYD88 sont fréquemment retrouvées. Les mutations du gène CXCR4, sont rares. La recherche de ces mutations manque toutefois de sensibilité lorsqu’elle est faite dans le sang.
Le profil mutationnel MYD88L265P ou la présence d’une hémopathie maligne sous-jacente n’influent pas sur la neuropathie. La prévalence élevée de cette mutation constitue un argument pour l’utilisation d’inhibiteurs de la tyrosine kinase.
•Cost-effective TiO2/Mag composites were synthesized via facile ball milling method.•TiO2/Mag composites could be rapidly separated from solutions by a magnetic field.•Cefotaxime removal rate by ...10%TiO2/Mag was 8.2 times higher than ball-milled Mag.•Even at only 1 mmol/L H2O2, 10%TiO2/Mag showed high photo-Fenton catalytic activity.•The synergistic mechanism of TiO2/Mag-catalyzed photo-Fenton system was explored.
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Heterogeneous Fenton reaction is a usable technique to remove organic contaminants in water, while developing highly efficient and cost-effective catalysts with simple preparation method is critical for its practical application. In this work, novel TiO2/Mag composites were prepared from commercial TiO2 and natural magnetite (Mag) via a facile ball milling process. We expect the obtained composites to be efficient photo-Fenton catalysts, as photo-generated electrons from TiO2 can be transferred to Mag to accelerate the reduction of Fe(III) to Fe(II), promoting the decomposition of H2O2 and production of ·OH. Structural characterization results exhibited ball milling could not change mineral phases of both TiO2 and Mag. TiO2/Mag composites remained good magnetic saturation and could be rapidly separated from reaction medium. In degrading cefotaxime, TiO2/Mag composites showed high photo-Fenton catalytic activities, with the degradation rate by 10%TiO2/Mag at near neutral pH of 5.6 being about 11.6 and 8.2 times higher than that of natural and ball-milled Mag, respectively. Moreover, even at low H2O2 concentration of 1 mmol/L, 10%TiO2/Mag remained relatively high photo-Fenton catalytic activity when compared to natural and ball-milled Mag. The better production of ·OH in the photo-Fenton system catalyzed by 10%TiO2/Mag (0.244 mmol/L) than that by natural and ball-milled Mag (0.049 and 0.064 mmol/L) also illustrated efficient utilization of H2O2 by 10%TiO2/Mag. Above results well support our hypothesis that photo-generated electrons from TiO2 were transferred to Mag, which then benefited the Fenton reactivity of Mag and degradation of cefotaxime. In all, TiO2/Mag composites prepared by ball milling have promising practical application in water treatment, thanks to their merits such as high photo-Fenton catalytic activity, facile preparation, cost-effective, easy magnetic separation, good stability, suitable for near neutral pH, and efficient utilization of H2O2.
Bisphenol-A (BPA) is a conventional plasticizer and is considered a chemical of concern due to its potential for endocrine disruption. Therefore, bentonite (Bnt) clay-based silicon dioxide magnetic ...composite (Bnt/SiO2/Mag) was synthesized and used as an effective adsorbent for BPA removal from aqueous solutions. The factorial design study was applied for screening the experimental design of parameters. The isotherm modeling results indicated that the equilibrium data fitted to the non-linear Langmuir isotherm model with adoption capacity 276.5 mg g−1. The kinetic findings exhibited good suitability of pseudo-second-order (PSO) model with rate-limiting step involved in the chemical adsorption. The ΔG data between − 16.46 and − 18.02 kJ/mol for a temperature range of 293–323 K confirmed that the BPA adsorption process was taken place spontaneously. The ΔH parameter (−32.3 kJ/mol) characterized the exothermic nature of the adsorption process as the ΔS parameter (−53.44 J/mol.K) showed the reduced randomness at the solution-adsorbent interface after the adsorption process. The BPA adsorption can occur with a combination of different mechanisms including the filling of interlayer holes, electrostatic attraction, hydrogen bonds and π-π interaction. The cycling performance test demonstrated that Bnt/SiO2/Mag composite adsorbent still showed reasonable performance (70/75%) until five time-adsorption/desorption cycling. The results also designated that Bnt/SiO2/Mag composite can be valued as an alternative sorbent for the adsorption of BPA from water.
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•Btn/SiO2/Mag composite was designed for removal of BPA.•Factorial design study was applied to evaluate the optimized parameters.•Equilibrium adsorption capacity of Btn/SiO2/Mag for removal of BPA was 276.5 mg g−1.•Adsorption mechanism consisted of pores filling, electrostatic attraction, weak interactions.•Btn/SiO2/Mag composite exhibited excellent reuse performance.
Summary
Monoclonal immunoglobulin M (IgM) anti‐myelin‐associated glycoprotein (MAG) neuropathy is a rare disabling condition, most commonly treated with rituximab monotherapy (R), which leads to ...neurological improvement in only 30%–50% of patients. The combination of rituximab plus chemotherapy has been proven to improve the level of responses. We studied the outcomes of anti‐MAG neuropathy patients treated either by R, or by immunochemotherapy (ICT) in our centre, focusing on the incidence of the first neurological response evaluated by the modified Rankin scale (mRS). From 2011 to 2018, 64 patients were studied: 34 were treated with R and 30 with ICT. According to our treatment decision‐making process, the median mRS was higher in the ICT group (mRS 2) than in the R group (mRS 1). At one year, improvements of the mRS rates were 46% and 18% in the ICT and R groups of patients respectively, with median times to response of eight and 13 months (p = 0.023). Adverse effects were higher in the ICT group: 62% vs 15% (p ˂ 0.01), all grades included. One secondary acute leukaemia occurred five years after treatment with ICT. In conclusion, ICT may be used as a valid option for patients with rapidly progressive and/or severe anti‐MAG neuropathy symptoms.
The novel quaternary ammonium modified magnetic carboxyl-carbon nanotubes (QA-Mag-CCNTs) have been synthesised and characterized. QA-Mag-CCNTs were applied in magnetic dispersive solid phase ...extraction (Mag-dSPE) for preconcentration of perchlorate from tea leaves prior to liquid chromatography-tandem quadrupole mass spectrometry (LC-MS/MS) analysis. The Mag-dSPE procedure for preconcentration of perchlorate succeed in overcoming the flaw (containing target analyte randomly) of commercially available SPE cartridge. Under optimal conditions, the results showed higher extraction efficiency of QA-Mag-CCNTs, with recoveries between 85.2% and 107%. And the satisfactory precision with inter-day and intra-day RSD values were lower than 8.0%. Furthermore, QA-Mag-CCNTs were evaluated for reuse up to 20 times. The limit of quantification (LOQ) for perchlorate was 8.21 ng kg−1. The developed method was successfully applied in tea leaves for food-safety risk monitoring in Zhejiang province, China. The results showed the concentrations of perchlorate in 229 out of 240 collected samples were in the range of 0.082–988 μg kg−1. It was confirmed that QA-Mag-CCNTs were highly effective materials used for preconcentration of perchlorate.
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•QA-Mag-CCNTs have been synthesised and characterized by SEM, VSM and XPS.•QA-Mag-CCNTs are evaluated in Mag-dSPE for preconcentration of perchlorate from tea leaves.•It succeeds in overcoming the flaw (containing perchlorate randomly) of SPE cartridge.•The Mag-dSPE procedure is environmental friendly and effective to remove matrix.•Mag-dSPE LC-MS/MS method is efficient and promising for food-safety risk monitoring.
Porous materials have received extensive attention due to their superior adsorption properties, but there are few studies on oil adsorption. In this paper, a new self-design high-temperature reactor ...carried out MCC adsorption experiments, and a complete test system was used to study the adsorption characteristics, pyrolysis kinetics and pyrolysis products. The results of SEM and XRD showed that G3H gradually wetted the surface of MCC and the crystallinity increased. In addition, the pyrolysis parameters of MCC-adsorption-G3H (MAG) were measured by DSC and STA. The results showed that MCC was pyrolyzed in one step while MAG was in two. Meanwhile, thermodynamic model fitting indicated that the first stage was Fn and the second was Cnm autocatalytic. Notably, the variation of pyrolysis activation energy in the first stage was similar to that of adsorption capacity. Pyrolysis products of G3H were measured by Py-GC-MS, and pyrolysis residues of MAG were tested by FTIR. Combined with the volatiles determined by TG-IR, the influence of G3H on the pyrolysis characteristics was obtained, and the pyrolysis path of MAG was summarized. The results showed that porous materials can recycle oil and provided a guideline for industrial production.
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•G3H increases pyrolysis rate to 97.13%.•MAG’s main pyrolysis kinetic model is Cnm.•G3H advance synthesis of pyrolysis products.
Epidemiologic and preclinical studieshave shown that marine n‐3 polyunsaturated fatty acids (n‐3 PUFAs) elicit promising chemoprevention against breast cancer. Docosahexaenoic acid monoglyceride ...(MAG‐DHA), a docosahexaenoic acid sn‐1‐monoacylglycerol does not required pancreatic lipase to be absorbed, eliciting a better bioavailability when compared with other formulations such as DHA‐free fatty acid, DHA‐triglycerol, or DHA‐ethyl ester. However, the anticancer actions and underlying mechanisms of MAG‐DHA on breast cancer remain to be assessed. In this study, MAG‐DHA induced significant growth inhibition in MCF‐7 and MDA‐MB‐231 breast cancer cells in a dose‐dependent manner. MAG‐DHA treatment (80 µM) led to 83.8 and 94.3% growth inhibition between MCF‐7 and MDA‐MB‐231 cells, respectively. MAG‐DHA‐induced growth inhibition was tightly associated with apoptosis, as evidenced by increased active forms of caspase‐3, poly (ADP‐ribose) polymerase (PARP) and caspase‐12. In particular, MAG‐DHA‐induced apoptosis was triggered by oxidative stress‐mediated endoplasmic reticulum (ER) stress, as evidenced by activation of the PERK‐eIF2α pathway in ER. MAG‐DHA treatment also strongly suppressed the growth of E0771 murine breast cancer xenografts, significant differences of tumor volume were found between MAG‐DHA group (0.271 cm3) and control group (0.875 cm3) after 15 daily MAG‐DHA treatments. The in vitro antibreast cancer mechanism of MAG‐DHA was supported by the in vivo xenograft model. In addition, MAG‐DHA‐induced ER stress concomitantly triggered autophagy in these cancer cells, and the induction of autophagy suppressed its ability to induce apoptotic cell death. Our data suggested that MAG‐DHA as dietary supplement, in combination with autophagy inhibitors may be a useful therapeutic strategy in treating breast cancer.
The present work reports results obtained using computer-based system techniques to investigate the metal transfer in laser–MAG hybrid welding. This arc characteristic information can be recorded by ...combining the sensing of the welding current and arc voltage with high speed imaging of the droplet transfer. An LD pumped green laser was used to overcome the strong interference from the welding arc. The arc energy determined mode of droplet transfer. When the arc energy is less than 4kW, the transfer mode is short circuit transfer, or globular transfer or transfer mode between short circuit and globular. When the arc energy exceeds the 4.68kW, the transfer mode is spray type. The laser energy has an important influence on the arc length, droplet size and the droplet velocity. When the arc energy is less than 4kW, the attraction and compression of laser on arc play an important role, which caused the average arc length increases with increasing laser power. When the arc power is beyond 4.68kW, the average arc length is decreasing with increasing laser power, which is attributed to expansion of the arc plasma, and enhancement of jet force of metal vapor on droplet. The droplet velocity decreases with increasing laser power, which is attributed to the attraction force of laser plasma to arc and the jet force of metal vapor produced by laser keyhole on droplet.
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