Identification and modeling of a novel chloramphenicol resistance protein detected by functional metagenomics in a wetland of Lerma, Mexico

The exploration of novel antibiotic resistance determinants in a particular environment may be limited because of the presence of uncultured microorganisms. In this work, a culture independent approach based on functional metagenomics was applied to search for chloramphenicol resistance genes in agro-industrial wastewater in Lerma de Villada, Mexico. To this end, a metagenomic library was generated in Escherichia coli DH10B containing DNA isolated from environmental samples of the residual arsenic-enriched (10 mg/ml) effl uent. One resistant clone was detected in this library and further analyzed. An open reading frame similar to a multidrug resistance protein from Aeromonas salmonicida and responsible for chloramphenicol resistance was identifi ed, sequenced, and found to encode a member of the major facilitator superfamily (MFS). Our results also showed that the expression of this gene restored streptomycin sensitivity in E. coli DH10B cells. To gain further insight into the phenotype of this MFS family member, we developed a model of the membrane protein multiporter that, in addition, may serve as a template for developing new antibiotics. [Int Microbiol 2013; 16(2):103-111]Keywords: Escherichia coli; chloramphenicol; functional metagenomics; major facilitator superfamily; homology models; membrane proteins; arseni

ARAMIS: From systematic errors of NGS long reads to accurate assemblies

NGS long-reads sequencing technologies (or third generation) such as Pacific BioSciences (PacBio) have revolutionized the sequencing field over the last decade improving multiple genomic applications like de novo genome assemblies. However, their error rate, mostly involving insertions and deletions (indels), is currently an important concern that requires special attention to be solved. Multiple algorithms are available to fix these sequencing errors using short reads (such as Illumina), although they require long processing times and some errors may persist. Here, we present Accurate long-Reads Assembly correction Method for Indel errorS (ARAMIS), the first NGS long-reads indels correction pipeline that combines several correction software in just one step using accurate short reads. As a proof OF concept, six organisms were selected based on their different GC content, size and genome complexity, and their PacBio-assembled genomes were corrected thoroughly by this pipeline. We found that the presence of systematic sequencing errors in long-reads PacBio sequences affecting homopolymeric regions, and that the type of indel error introduced during PacBio sequencing are related to the GC content of the organism. The lack of knowledge of this fact leads to the existence of numerous published studies where such errors have been found and should be resolved since they may contain incorrect biological information. ARAMIS yields better results with less computational resources needed than other correction tools and gives the possibility of detecting the nature of the found indel errors found and its distribution along the genome. The source code of ARAMIS is available at https://github.com/genomics-ngsCBMSO/ARAMIS.gi

The Sport Concussion Assessment Tool (SCAT2) for evaluating civilian mild traumatic brain injury

Post-concussion symptoms; SCAT2; Head injurySíntomas posteriores a la conmoción cerebral; SCAT2; Lesión cranealSímptomes posteriors a la commoció cerebral; SCAT2; Lesió cranialSelf-report measures, particularly symptom inventories, are critical tools for identifying patients with persistent post-concussion symptoms and their follow-up. Unlike in military or sports-related assessment, in general civilian settings pre-injury levels of concussion-like symptoms are lacking. Normative data are available in adolescent and college populations, but no reference data exist to guide clinical adult explorations. The purpose of this study was to use the second edition of the Sport Concussion Assessment Tool (SCAT2) to profile a cohort of 60 healthy community volunteers who had not sustained a head injury. Participating volunteers underwent MRI scanning and were evaluated with the Hospital Anxiety and Depression Scale (HADS). Participants reported a median of 3 concussion-like symptoms and the 97.5 percentile score was found at 10.5 symptoms, out of a total of 22. The median severity score was 4.9 points, and 28.9 was the upper limit of the reference interval. Only 10 participants (16.7%) did not endorse any symptom. The most frequently endorsed symptom was feeling difficulty in concentrating, with 41.7% of the sample reporting it. Age, sex and general distress, anxiety and depressive symptoms were not associated with concussion-like symptoms. Our data yielded elevated cut-offs scores for both the number of symptoms and the symptom severity. In conclusion, postconcussive-like symptoms are frequent in the general non-concussed adult population and it should be taken into account in any future models developed for screening patients at risk of developing physical, cognitive, and psychological complaints following mild traumatic injury.UNINN is supported by a Grant from the Generalitat de Catalunya (SGR 2014-844, http://agaur.gencat.cat). This work has been supported in part by the Fondo de Investigacion Sanitaria (Instituto de Salud Carlos III, https://portalfis.isciii.es) with grants FIS PI11/00700 (J.S.) and grant FIS PI13/02397 (M.A.P.), which were co-financed by the European Regional Development Fund (ERDF). A.R. was a recipient of a pre-doctoral grant from the Fundacio Institut de Recerca VHIR (PRED-VHIR-2012-26, http://en.vhir.org)

Selenium and impaired physical function in US and Spanish older adults

Background: Selenium (Se) is a trace element with a narrow safety margin. Objectives: To evaluate the cross-sectional and longitudinal dose-response association between Se exposure and measures of impaired physical function and disability in older adults. Design: NHANES 2011–2014 cross-sectional (US, n = 1733, age ≥60 years) and Seniors-ENRICA-2 2017–2019 cross-sectional and longitudinal (Spain, n = 2548 and 1741, respectively, age ≥65 years) data were analyzed. Whole blood and serum Se levels were measured using inductively coupled plasma-mass spectrometry. Lowerextremity performance was assessed with the Short Physical Performance Battery, and muscle weakness with a dynamometer. Incident mobility and agility limitations, and disability in instrumental activities of daily living (IADL) were ascertained with standardized questionnaires. Analyses were adjusted for relevant confounders, including physical activity. Results across studies were pooled using random-effects meta-analysis. Results: Meta-analyzed odds ratios (95% confidence interval) per log2 increase in whole blood Se were 0.54 (0.32; 0.76) for weakness, 0.59 (0.34; 0.83) for impaired lower-extremity performance, 0.48 (0.31; 0.68) for mobility limitations, 0.71 (0.45; 0.97) for agility limitations, and 0.34 (0.12; 0.56) for disability in at least one IADL. Analyses for serum Se in NHANES showed similar results. Findings suggest the inverse association with grip strength is progressive below 140 μg/L (p-value for non-linear trend in the Seniors-ENRICA-2 study = 0.13), and above 140 μg/L (p-value for non-linear trend in NHANES = 0.11). In the Seniors-ENRICA-2 cohort, with a 2.2 year follow-up period, a doubling in baseline Se levels were associated with a lower incidence of weakness [odds ratio (95% confidence interval): 0.45 (0.22; 0.91)], impaired lower-extremity performance [0.63 (0.32; 1.23)], mobility [0.43 (0.21; 0.91)] and agility [0.38 (0.18; 0.78)] limitations. Discussion: In US and Spanish older adults, Se concentrations were inversely associated with physical function limitations. Further studies are needed to elucidate underlying mechanisms.Instituto de Salud Carlos III European Commission PI18/287 16/609State Secretary of R + D + I PID2019-108973RB-C21/C22European Social Fund (ESF) European Commissio

Predominance of deterministic microbial community dynamics in salterns exposed to different light intensities

While the dynamics of microbial community assembly driven by environmental perturbations have been extensively studied, our understanding is far from complete, particularly for light‐induced perturbations. Extremely halophilic communities thriving in coastal solar salterns are mainly influenced by two environmental factors—salt concentrations and high sunlight irradiation. By experimentally manipulating light intensity through the application of shading, we showed that light acts as a deterministic factor that ultimately drives the establishment of recurrent microbial communities under near‐saturation salt concentrations. In particular, the stable and highly change‐resistant communities that established under high‐light intensities were dominated (>90% of metagenomic reads) by Haloquadratum spp. and Salinibacter spp. On the other hand, under 37‐fold lower light intensity, different, less stable and change‐resistant communities were established, mainly dominated by yet unclassified haloarchaea and relatively diverse photosynthetic microorganisms. These communities harboured, in general, much lower carotenoid pigment content than their high‐irradiation counterparts. Both assemblage types appeared to be highly resilient, re‐establishing when favourable conditions returned after perturbation (i.e. high‐irradiation for the former communities and low‐irradiation for the latter ones). Overall, our results revealed that stochastic processes were of limited significance to explain these patterns.This study was funded by the Spanish Ministry of Economy projects CGL2012-39627-C03-03 CLG2015_66686-C3-1-P and PGC2018-096956-B-C41 (to R.R.M.), CGL2015_66686-C3-3-P (to J.A.) and CGL2015_66686-C3-2-P (to J.E.G.P.), which were also supported with European Regional Development Fund (FEDER) funds. R.A. was funded by the Max Planck Society. KTK’s research was supported, in part, by the U.S. National Science Foundation (Award No. 1831582). T.V.P. received a pre-doctoral fellowship (No. BES-2013-064420) from the Spanish Government Ministry for Finance and Competition. R.R.M. acknowledges the financial support of the sabbatical stay at Georgia Tech supported by the Grant PRX18/00048 of the Ministry of Sciences, Innovation and Universities

Search for WZ resonances in the fully leptonic channel using pp collisions at s=8 TeV with the ATLAS detector

A search for resonant WZ production in the ℓνℓ'ℓ' (ℓ,ℓ'=e,μ) decay channel using 20.3 fb-1 of s=8TeV pp collision data collected by the ATLAS experiment at LHC is presented. No significant deviation from the Standard Model prediction is observed and upper limits on the production cross sections of WZ resonances from an extended gauge model W' and from a simplified model of heavy vector triplets are derived. A corresponding observed (expected) lower mass limit of 1.52 (1.49) TeV is derived for the W' at the 95% confidence level.Peer Reviewe

ATLAS search for a heavy gauge boson decaying to a charged lepton and a neutrino in pp collisions at root s=7 TeV

The ATLAS detector at the LHC is used to search for high-mass states, such as heavy charged gauge bosons (W'), decaying to a charged lepton (electron or muon) and a neutrino. Results are presented based on the analysis of pp collisions at a center-of-mass energy of 7 TeV corresponding to an integrated luminosity of 4.7 fb(-1). No excess beyond Standard Model expectations is observed. A W' with Sequential Standard Model couplings is excluded at the 95 % credibility level for masses up to 2.55 TeV. Excited chiral bosons (W*) with equivalent coupling strength are excluded for masses up to 2.42 TeV

Dynamics of isolated-photon plus jet production in pp collisions at root s=7 TeV with the ATLAS detector

The dynamics of isolated-photon plus jet production in pp collisions at a centre-of-mass energy of 7 TeV has been studied with the ATLAS detector at the LHC using an integrated luminosity of 37 pb(-1). Measurements of isolated-photon plus jet bin-averaged cross sections are presented as functions of photon transverse energy, jet transverse momentum and jet rapidity. In addition, the bin-averaged cross sections as functions of the difference between the azimuthal angles of the photon and the jet, the photon jet invariant mass and the scattering angle in the photon jet centre-of-mass frame have been measured. Next-to-leading-order QCD calculations are compared to the measurements and provide a good description of the data, except for the case of the azimuthal opening angle

Measurement of the cross-section for W boson production in association with b-jets in pp collisions at root s=7 TeV with the ATLAS detector

This paper reports a measurement of the W+b-jets (W+b+X and W+b (b) over bar +X) production cross-section in proton-proton collisions at a centre-of-mass energy of 7 TeV at the LHC. These results are based on data corresponding to an integrated luminosity of 4.6 fb(-1), collected with the ATLAS detector. Cross-sections are presented as a function of jet multiplicity and of the transverse momentum of the leading b-jet for both the muon and electron decay modes of the W boson. The W+b-jets cross-section, corrected for all known detector effects, is quoted in a limited kinematic range. Combining the muon and electron channels, the fiducial cross-section for W+b-jets is measured to be 7.1 +/- 0.5 (stat) +/- 1.4 (syst) pb, consistent with the next-to-leading order QCD prediction, corrected for non-perturbative and double-parton interactions (DPI) contributions, of 4.70 +/- 0.09 (stat) (+0.60)(-0.49) (scale) +/- 0.06 (PDF) +/- 0.16 (non-pert) (+0.52)(-0.38) (DPI) pb

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 8 TeV pp collisions with the ATLAS detector

Aad, G. et al.A search for the direct production of charginos and neutralinos in final states with three leptons and missing transverse momentum is presented. The analysis is based on 20.3 fb−1 of s√ = 8 TeV proton-proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with the Standard Model expectations and limits are set in R-parity-conserving phenomenological Minimal Supersymmetric Standard Models and in simplified supersymmetric models, significantly extending previous results. For simplified supersymmetric models of direct chargino (χ˜±1) and next-to-lightest neutralino (χ˜02) production with decays to lightest neutralino (χ˜01) via either all three generations of sleptons, staus only, gauge bosons, or Higgs bosons, (χ˜±1) and (χ˜02) masses are excluded up to 700 GeV, 380 GeV, 345 GeV, or 148 GeV respectively, for a massless (χ˜01).We acknowledge the support of ANPCyT, Argentina; YerPhI, Armenia; ARC, Australia; BMWF and FWF, Austria; ANAS, Azerbaijan; SSTC, Belarus; CNPq and FAPESP, Brazil; NSERC, NRC and CFI, Canada; CERN; CONICYT, Chile; CAS, MOST and NSFC, China; COLCIENCIAS, Colombia; MSMT CR, MPO CR and VSC CR, Czech Republic; DNRF, DNSRC and Lundbeck Foundation, Denmark; EPLANET, ERC and NSRF, European Union; IN2P3-CNRS, CEA-DSM/IRFU, France; GNSF, Georgia; BMBF, DFG, HGF, MPG and AvH Foundation, Germany; GSRT and NSRF, Greece; ISF, MINERVA, GIF, I-CORE and Benoziyo Center, Israel; INFN, Italy; MEXT and JSPS, Japan; CNRST, Morocco; FOM and NWO, Netherlands; BRF and RCN, Norway; MNiSW and NCN, Poland; GRICES and FCT, Portugal; MNE/IFA, Romania; MES of Russia and ROSATOM, Russian Federation; JINR; MSTD, Serbia; MSSR, Slovakia; ARRS and MIZˇS, Slovenia; DST/NRF, South Africa; MINECO, Spain; SRC and Wallenberg Foundation, Sweden; SER, SNSF and Cantons of Bern and Geneva, Switzerland; NSC, Taiwan; TAEK, Turkey.Peer reviewe