A genome walking strategy for the identification of eukaryotic nucleotide sequences adjacent to known regions

Determination of nucleotide sequences adjacent to a known region is a recurring need in many genome scale studies. Various methods have been developed based on PCR techniques in order to fulfill th..

Plant Health and Rhizosphere Microbiome: Effects of the Bionematicide Aphanocladium album in Tomato Plants Infested by Meloidogyne javanica

The artificial introduction in the soil of antagonistic microorganisms can be a successful strategy, alternative to agrochemicals, for the control of the root-knot nematodes (Meloidogyne spp.) and for preserving plant health. On the other hand, plant roots and the associated rhizosphere constitute a complex system in which the contribution of microbial community is fundamental to plant health and development, since microbes may convert organic and inorganic substances into available plant nutrients. In the present study, the potential nematicidal activity of the biopesticide Aphanocladium album (A. album strain MX-95) against the root-knot nematode Meloidogyne javanica in infected tomato plants was investigated. Specifically, the effect of the A. album treatment on plant fitness was evaluated observing the plant morphological traits and also considering the nematode propagation parameters, the A. album MX-95 vitality and population density. In addition, the treatment effects on the rhizosphere microbiome were analysed by a metabarcoding procedure. Treatments with A. album isolate MX-95 significantly decreased root gall severity index and soil nematode population. The treatment also resulted in increased rhizosphere microbial populations. A. album MX-95 can be favourably considered as a new bionematicide to control M. javanica infestation

Identification of an Amylomaltase from the Halophilic Archaeon Haloquadratum walsbyi by Functional Metagenomics: Structural and Functional Insights

Amylomaltases are prokaryotic 4-α-glucanotransferases of the GH77 family. Thanks to the ability to modify starch, they constitute a group of enzymes of great interest for biotechnological applications. In this work we report the identification, by means of a functional metagenomics screening of the crystallization waters of the saltern of Margherita di Savoia (Italy), of an amylomaltase gene from the halophilic archaeon Haloquadratum walsbyi, and its expression in Escherichia coli cells. Sequence analysis indicated that the gene has specific insertions yet unknown in homologous genes in prokaryotes, and present only in amylomaltase genes identified in the genomes of other H. walsbyi strains. The gene is not part of any operon involved in the metabolism of maltooligosaccharides or glycogen, as it has been found in bacteria, making it impossible currently to assign a precise role to the encoded enzyme. Sequence analysis of the H. walsbyi amylomaltase and 3D modelling showed a common structure with homologous enzymes characterized in mesophilic and thermophilic bacteria. The recombinant H. walsbyi enzyme showed starch transglycosylation activity over a wide range of NaCl concentrations, with maltotriose as the best acceptor substrate compared to other maltooligosaccharides. This is the first study of an amylomaltase from a halophilic microorganism

Polybrominated dibenzo-p-dioxins and furans (PBDD/Fs) in Italian food: Occurrence and dietary exposure

Human exposure to polychlorinated dioxins and furans (PCDD/Fs) through the dietary pathway is widely recognised and regulations in some regions of the world help to limit food contamination. Similar information on the analogous polybrominated dioxins and furans (PBDD/Fs) is scarce, partly due to the higher threshold to analytical access and unavailability of some standard materials. The analytical methodology developed here determined twelve planar PBDD/F congeners using 13Carbon labelled PBDD/F surrogates and high resolution mass spectrometric detection, and was extensively validated prior to the analysis of a range of commonly consumed Italian foods. The methodology also allowed simultaneous determination of PCDD/Fs and polychlorinated biphenyls (PCBs). The results show that PBDD/Fs occurred in different foods over a range of concentrations from <0.001 pg/g to 4.58 pg/g in fish. The dietary exposure (upper bound) of different Italian population groups, resulting from these occurrence levels was estimated using the toxic equivalency (TEQ) approach that is commonly used for dioxin-like contaminants and ranged from 0.17 to 0.42 pg TEQ/kg bodyweight/day (lower bound – 0.01 pg TEQ/kg bodyweight/day) depending on the population subgroup. Although precautionary, upper bound values may provide a more realistic estimate of toxicity as not all congeners and foods were measured. As expected, children were more highly exposed than adults due to lower body weight. These exposure levels were between a quarter and a third of that arising from the sum of PCDD/Fs and PCBs (0.61 to 1.38 pg WHO-TEQ/kg bodyweight/day), but they contribute to the dioxin-like toxicity. If this data is considered in view of the revised tolerable dioxin-like dietary intake published by EFSA in 2018, it is evident that the tolerable weekly intake of 2 pg/kg bodyweight/week would be exceeded by some of the assessed population sub-groups, or all sub-groups if the cumulative intake is considered

Search for Physics beyond the Standard Model in Events with Overlapping Photons and Jets

Results are reported from a search for new particles that decay into a photon and two gluons, in events with jets. Novel jet substructure techniques are developed that allow photons to be identified in an environment densely populated with hadrons. The analyzed proton-proton collision data were collected by the CMS experiment at the LHC, in 2016 at root s = 13 TeV, and correspond to an integrated luminosity of 35.9 fb(-1). The spectra of total transverse hadronic energy of candidate events are examined for deviations from the standard model predictions. No statistically significant excess is observed over the expected background. The first cross section limits on new physics processes resulting in such events are set. The results are interpreted as upper limits on the rate of gluino pair production, utilizing a simplified stealth supersymmetry model. The excluded gluino masses extend up to 1.7 TeV, for a neutralino mass of 200 GeV and exceed previous mass constraints set by analyses targeting events with isolated photons.Peer reviewe

Calibration of the CMS hadron calorimeters using proton-proton collision data at root s=13 TeV

Methods are presented for calibrating the hadron calorimeter system of theCMSetector at the LHC. The hadron calorimeters of the CMS experiment are sampling calorimeters of brass and scintillator, and are in the form of one central detector and two endcaps. These calorimeters cover pseudorapidities vertical bar eta vertical bar ee data. The energy scale of the outer calorimeters has been determined with test beam data and is confirmed through data with high transverse momentum jets. In this paper, we present the details of the calibration methods and accuracy.Peer reviewe

Search for top squark pair production in a final state with two tau leptons in proton-proton collisions at root s=13 TeV

A search for pair production of the supersymmetric partner of the top quark, the top squark, in proton-proton collision events at s = 13 TeV is presented in a final state containing hadronically decaying tau leptons and large missing transverse momentum. This final state is highly sensitive to high-tan beta or higgsino-like scenarios in which decays of electroweak gauginos to tau leptons are dominant. The search uses a data set corresponding to an integrated luminosity of 77.2 fb(-1), which was recorded with the CMS detector during 2016 and 2017. No significant excess is observed with respect to the background prediction. Exclusion limits at 95% confidence level are presented in the top squark and lightest neutralino mass plane within the framework of simplified models, in which top squark masses up to 1100 GeV are excluded for a nearly massless neutralino.Peer reviewe

Measurement of the t(t)over-barb(b)over-bar production cross section in the all-jet final state in pp collisions at root s=13 TeV

A measurement of the production cross section of top quark pairs in association with two b jets (t (t) over barb (b) over bar) is presented using data collected in proton-proton collisions at root s=13 TeV by the CMS detector at the LHC corresponding to an integrated luminosity of 35.9 fb(-1). The cross section is measured in the all-jet decay channel of the top quark pair by selecting events containing at least eight jets, of which at least two are identified as originating from the hadronization of b quarks. A combination of multivariate analysis techniques is used to reduce the large background from multijet events not containing a top quark pair, and to help discriminate between jets originating from top quark decays and other additional jets. The cross section is determined for the total phase space to be 5.5 +/- 0.3 (stat)(-1.3)(+)(1.6) (syst)pb and also measured for two fiducial t (t) over barb (b) over bar, definitions. The measured cross sections are found to be larger than theoretical predictions by a factor of 1.5-2.4, corresponding to 1-2 standard deviations. (C) 2020 The Author. Published by Elsevier B.V.Peer reviewe

Search for a Light Charged Higgs Boson Decaying to a W Boson and a CP-Odd Higgs Boson in Final States with eμμ or μμμ in Proton-Proton Collisions at √s=13 TeV

A search for a light charged Higgs boson (H+) decaying to a W boson and a CP-odd Higgs boson (A) in final states with eμμ or μμμ is performed using data from pp collisions at √s=13  TeV, recorded by the CMS detector at the LHC and corresponding to an integrated luminosity of 35.9  fb−1. In this search, it is assumed that the H+ boson is produced in decays of top quarks, and the A boson decays to two oppositely charged muons. The presence of signals for H+ boson masses between 100 and 160 GeV and A boson masses between 15 and 75 GeV is investigated. No evidence for the production of the H+ boson is found. Upper limits at 95% confidence level are obtained on the combined branching fraction for the decay chain, t→bH+→bW+A→bW+μ+μ−, of 1.9×10−6 to 8.6×10−6, depending on the masses of the H+ and A bosons. These are the first limits for these decay modes of the H+ and A bosons.Peer reviewe