IMGT/V-QUEST: the highly customized and integrated system for IG and TR standardized V-J and V-D-J sequence analysis

IMGT/V-QUEST is the highly customized and integrated system for the standardized analysis of the immunoglobulin (IG) and T cell receptor (TR) rearranged nucleotide sequences. IMGT/V-QUEST identifies the variable (V), diversity (D) and joining (J) genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. New functionalities were added through a complete rewrite in Java. IMGT/V-QUEST analyses batches of sequences (up to 50) in a single run. IMGT/V-QUEST describes the V-REGION mutations and identifies the hot spot positions in the closest germline V gene. IMGT/V-QUEST can detect insertions and deletions in the submitted sequences by reference to the IMGT unique numbering. IMGT/V-QUEST integrates IMGT/JunctionAnalysis for a detailed analysis of the V-J and V-D-J junctions, and IMGT/Automat for a full V-J- and V-D-J-REGION annotation. IMGT/V-QUEST displays, in ‘Detailed view’, the results and alignments for each submitted sequence individually and, in ‘Synthesis view’, the alignments of the sequences that, in a given run, express the same V gene and allele. The ‘Advanced parameters’ allow to modify default parameters used by IMGT/V-QUEST and IMGT/JunctionAnalysis according to the users’ interest. IMGT/V-QUEST is freely available for academic research at http://imgt.cines.f

Listeria monocytogenes in Milk Products

peer-reviewedMilk and milk products are frequently identified as vectors for transmission of Listeria monocytogenes. Milk can be contaminated at farm level either by indirect external contamination from the farm environment or less frequently by direct contamination of the milk from infection in the animal. Pasteurisation of milk will kill L. monocytogenes, but post-pasteurisation contamination, consumption of unpasteurised milk and manufacture of unpasteurised milk products can lead to milk being the cause of outbreaks of listeriosis. Therefore, there is a concern that L. monocytogenes in milk could lead to a public health risk. To protect against this risk, there is a need for awareness surrounding the issues, hygienic practices to reduce the risk and adequate sampling and analysis to verify that the risk is controlled. This review will highlight the issues surrounding L. monocytogenes in milk and milk products, including possible control measures. It will therefore create awareness about L. monocytogenes, contributing to protection of public health

Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia

NF-κB is constitutively activated in chronic lymphocytic leukemia (CLL); however, the implicated molecular mechanisms remain largely unknown. Thus, we performed targeted deep sequencing of 18 core complex genes within the NF-κB pathway in a discovery and validation CLL cohort totaling 315 cases. The most frequently mutated gene was NFKBIE (21/315 cases; 7%), which encodes IκBε, a negative regulator of NF-κB in normal B cells. Strikingly, 13 of these cases carried an identical 4-bp frameshift deletion, resulting in a truncated protein. Screening of an additional 377 CLL cases revealed that NFKBIE aberrations predominated in poor-prognostic patients and were associated with inferior outcome. Minor subclones and/or clonal evolution were also observed, thus potentially linking this recurrent event to disease progression. Compared with wild-type patients, NFKBIE-deleted cases showed reduced IκBε protein levels and decreased p65 inhibition, along with increased phosphorylation and nuclear translocation of p65. Considering the central role of B cell receptor (BcR) signaling in CLL pathobiology, it is notable that IκBε loss was enriched in aggressive cases with distinctive stereotyped BcR, likely contributing to their poor prognosis, and leading to an altered response to BcR inhibitors. Because NFKBIE deletions were observed in several other B cell lymphomas, our findings suggest a novel common mechanism of NF-κB deregulation during lymphomagenesis

Multi-Residue Determination of 7 β-Agonists in Liver and Meat Using Gas Chromatography-Mass Spectrometry

A robust and sensitive methodology, utilizing GC-MS, for the identification and quantitation of seven β-agonist residues (mabuterol, clenbuterol, brombuterol, mapenterol, clenpenterol, clenproperol, and clencyclohexerol), in liver and meat samples, is described. Different extraction procedures, followed by GC/MS measurement, were tested and compared in order to achieve optimum extraction conditions and eliminate matrix effects. The optimized method consisted of consecutive extractions with hydrochloric tris(hydroxymethyl)aminomethane (TRIS-HCl) and tert-butyl-methyl ether (TBME), defatting with hexane and solid-phase extraction (SPE) with C18 cartridges. Ν,O-bis(trimethylsilyl) trifluoroacetamide (BSTFA) with 1% trimethylchlorosilane (TMCS) was used as a derivatization agent and the GC-EI-MS determination was performed using a MDN-5S capillary column in single-ion monitoring (SIM) acquisition mode. The method was validated according to the Commission Decision 2002/657/EC, fulfilling all the EU criteria. Quantification was performed via internal standard calibration using deuterated analogs of the compounds. Recoveries ranged from 83 to 118% (mabuterol at concentration levels of 2.0 and 1.5 μg kg−1, respectively) and precision, expressed as %relative standard deviation (% RSD), was in every case lower than the % RSDs obtained from Horwitz equation. The obtained decision limit (CCα) and detection capability (CCβ) values varied from 0.21 ng g−1 (clenbuterol) to 0.49 ng g−1 (clenproperol, clencyclohexerol) and from 0.60 (mapenterol) to 0.69 ng g−1 (clenpenterol), respectively. © 2018, Springer Science+Business Media, LLC, part of Springer Nature

An investigation of the NO/H2/O2 (Lean-deNOx) reaction on a highly active and selective Pt/La0.5Ce0.5MnO3 catalyst

The NO/H2/O2 reaction has been studied under lean-burn conditions in the 100-400°C range over 0.1 wt% Pt supported on La0.5Ce0.5MnO3 (mixed oxide containing LaMnO3, CeO2, and MnO2 phases). For a critical comparison, 0.1 wt% Pt was supported on γ-Al2O3 and tested under the same reaction conditions. The maximum in the NO conversion has been observed at 140°C (74% conversion) for the Pt/La0.5Ce0.5MnO3 and at 125°C (66% conversion) for the Pt/γ3-Al2O3 catalyst using a GHSV of 80, 000 h−1. Addition of 5% H2O in the feed stream influenced the performance of the catalyst in a positive way. In particular, it widened the operating temperature window of the catalyst above 200°C with appreciable NO conversion and had no negative effect on the stability of the catalyst for a 20-h run on reaction stream. Remarkable N2 selectivity values in the 80-90% range have been observed on the Pt/La0.5Ce0.5MnO3 catalyst in the 100-200°C range either in the absence or in the presence of water in the feed stream. This result is reported for the first time for the NO/H2/O2 lean-deNOx reaction at least on Pt-based catalysts. A maximum specific integral reaction rate of 397 μmol of N2/s.g of Pt metal was measured at 140°C during reaction with 0.25% NO/1% H2/5% O2/5% H2O/He gas mixture on the 0.1 wt% Pt/La0.5Ce0.5MnO3 catalyst. This value was found to be higher by 40% than that observed on the 0.1 wt% Pt/γ-Al2O3 catalyst at 125°C, and it is the highest value ever reported in the 100-200°C range. A TOF value of 0.49 s−1 was calculated at 140°C for the Pt/La0.5Ce0.5MnO3 catalyst. Temperature-programmed desorption (TPD) of NO and transient titration experiments of the catalyst surface following reaction have revealed important information concerning several mechanistic steps of the present catalytic system. A hydrogen-assisted NO dissociation step and a nitrogen-assisted mechanism for N2 and N2O formation are proposed to explain all the transient experiments performed in a satisfactory manner

Synergistic effects of crystal phases and mixed valences in La-Sr-Ce-Fe-O mixed oxidic/perovskitic solids on their catalytic activity for the NO+CO reaction

Mixed oxidic and perovskite-type materials based on the La, Sr, Ce and Fe elements were prepared using a mixture of nitrates salts and heating at 1000°C. Three groups of solids were synthesized: (i) La1−yCeyFeO3 (y=0.2, 0.3, 0.5), (ii) La1−xSrxFeO3 (x=0.2, 0.3, 0.5) and (iii) La1−x−ySrxCeyFeO3 (x/y=0.05/0.15, 0.15/0.05, 0.1/0.2, 0.2/0.1, 0.2/0.3 and 0.3/0.2). The structure of the solids was examined by XRD and the main crystal phases determined were LaFeO3, α-Fe2O3 and CeO2 in group (i), LaFeO3 and SrFeO3−x in group (ii), and LaFeO3, α-Fe2O3, SrFeO3−x and CeO2 in group (iii), while traces of La(OH)3 and SrFe12O19 were also detected. The precise determination of the percentage amount of the iron-containing crystal phases in each solid composition was determined by Mössbauer spectroscopy at 20 K. The ceramic materials had low surface areas and were tested for their catalytic activity for the NO+CO reaction in a flow reactor in the range of 280–560°C. Conversions as high as 90% were achieved at 550°C at a GHSV=54 000 h−1. The reaction rate of NO conversion is favored by the increased amount of CeO2 in groups (i) and (iii) of solids that contain cerium. In the case of solids without CeO2 (group ii), the NO conversion is favored by the existence of SrFeO3−x phase at low temperatures (280–440°C), while it decreases at high temperatures (440–560°C). The double substituted solids La1−x−ySrxCeyFeO3 with x+y>0.3 and y>x were found to be the best catalysts for the NO+CO reaction as compared to the single substituted mixed oxides. Temperature programmed desorption (TPD) studies of NO and CO2 support the view that a synergistic effect takes place between the two phases of CeO2 and SrFeO3−x, whose co-existence results in the maximum enhancement of activity, via alternative oxidation–reduction cycles in the two phases

Catalytic behavior of La–Sr–Ce–Fe–O mixed oxidic/perovskitic systems for the NO+CO and NO+CH4+O2 (lean-NOx) reactions

Mixed oxides of the general formula La0.5SrxCeyFeOz were prepared by using the nitrate method and characterized by XRD and Mössbauer techniques. The crystal phases detected were perovskites LaFeO3 and SrFeO3−x and oxides α-Fe2O3 and CeO2 depending on x and y values. The low surface area ceramic materials have been tested for the NO+CO and NO+CH4+O2 (“lean-NOx”) reactions in the temperature range 250–550°C. A noticeable enhancement in NO conversion was achieved by the substitution of La3+ cation at A-site with divalent Sr+2 and tetravalent Ce+4 cations. Comparison of the activity of the present and other perovskite-type materials has pointed out that the ability of the La0.5SrxCeyFeOz materials to reduce NO by CO or by CH4 under “lean-NOx” conditions is very satisfying. In particular, for the NO+CO reaction estimation of turnover frequencies (TOFs, s−1) at 300°C (based on NO chemisorption) revealed values comparable to Rh/α-Al2O3 catalyst. This is an important result considering the current tendency for replacing the very active but expensive Rh and Pt metals. It was found that there is a direct correlation between the percentage of crystal phases containing iron in La0.5SrxCeyFeOz solids and their catalytic activity. O2 TPD (temperature-programmed desorption) and NO TPD studies confirmed that the catalytic activity for both tested reactions is related to the defect positions in the lattice of the catalysts (e.g., oxygen vacancies, cationic defects). Additionally, a remarkable oscillatory behavior during O2 TPD studies was observed for the La0.5Sr0.2Ce0.3FeOz and La0.5Sr0.5FeOz solids