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.
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•Mechanisms of magnetic and photo-induced hyperthermia for designing relevant nanomaterials.•Comprehensive comparison between both modalities and requirement for clinical ...translation.•Illustrations of different nanoparticles for both modalities of therapy.•Advocate the combining two modalities as a novel avenue for research.
Nanoscience provides several modalities to combat cancer disease effectively. Magnetic hyperthermia and photothermal therapy techniques are central research themes among various groups in the world by utilizing magnetic and optical characteristics of distinct or composite nanoentities. This review provides the current research on both the techniques and their successes towards clinical translation. This review discusses about the various heating mechanisms involved in magnetic and photo-induced hyperthermia. We have evaluated potential functional nanoparticles with excellent properties capable of providing innovative future solutions to current problems associated with these therapies. Several factors (extracellular and intracellular) have been covered and explained which may affect such thermal treatments. We have provided some instrumental and technical details of both the techniques that are important for consideration in using these modalities of treatments. A direct comparison of these two techniques and a further need of the combined therapy (magnetic hyperthermia plus photothermal therapy) was highlighted as a new pathway for cancer treatments.
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.
A large number of microbial genomes have already been identified from the human gut microbiome, but the understanding of the role of the low-abundance species at the individual level remains ...challenging, largely due to the relatively shallow sequencing depth used in most studies. To improve genome assembling performance, a HiSeq-PacBio hybrid, ultra-deep metagenomic sequencing approach was used to reconstruct metagenomic-assembled genomes (MAGs) from 12 fecal samples. Such approach combined third-generation sequencing with ultra-deep second-generation sequencing to improve the sequencing coverage of the low-abundance subpopulation in the gut microbiome. Our study generated a total of 44 megabase-scale scaffolds, achieving four single-scaffolds of complete (circularized, no gaps) MAGs (CMAGs) that were the first circular genomes of their species. Moreover, 475 high-quality MAGs were assembled across all samples. Among them, 234 MAGs were currently uncultured, including 24 MAGs that were not found in any public genome database. Additionally, 287 and 77 MAGs were classified as low-abundance (0.1-1%) and extra-low-abundance (<0.1%) gut species in each individual, respectively. Our results also revealed individual-specific genomic features in the MAG profiles, including microbial genome growth rate, selective pressure, and frequency of chromosomal mobile genetic elements. Finally, thousands of extrachromosomal mobile genetic elements were identified from the metagenomic data, including 5097 bacteriophages and 79 novel plasmid genomes. Overall, our strategy represents an important step toward comprehensive genomic and functional characterization of the human gut microbiome at an individual level.
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.
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