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The COVID-19 pandemic is unceasingly spreading across the globe, and recently a highly transmissible Omicron SARS-CoV-2 variant (B.1.1.529) has been discovered in South Africa and Botswana. Rapid identification of this variant is essential for pandemic assessment and containment. However, variant identification is mainly being performed using expensive and time-consuming genomic sequencing. In this study we propose an alternative RT-qPCR approach for the detection of the Omicron BA.1 variant using a low-cost and rapid SYBR Green method. We have designed specific primers to confirm the deletion mutations in the spike (S Δ143-145) and the nucleocapsid (N Δ31-33) which are characteristics of this variant. For the evaluation, we used 120 clinical samples from patients with PCR-confirmed SARS-CoV-2 infections, and displaying an S-gene target failure (SGTF) when using TaqPath COVID-19 kit (Thermo Fisher Scientific, Waltham, USA) that included the ORF1ab, S, and N gene targets. Our results showed that all the 120 samples harbored S Δ143-145 and N Δ31-33, which was further confirmed by Whole genome sequencing (WGS) of 10 samples thereby validating our SYBR Green-based protocol. This protocol can be easily implemented to rapidly confirm the diagnosis of the Omicron BA.1 variant in COVID-19 patients and prevent its spread among populations, especially in countries with high prevalence of SGTF profile.

Background and Aims Multi-contamination of soils by various organic and inorganic pollutants is considered an obstacle for the development of hyperaccumulator plants and phytoextraction of metals. The aim of this study was to investigate the effect of polycyclic aromatic hydrocarbons (PAHs) in combination with trace elements on the antioxidant response and phytoextraction efficiency of the Ganges and Chavignée populations of the hyperaccumulator Noccaea caerulescens.Methods Plants were grown in soil containing some heavy metals at moderate concentrations under phenanthrene (PHE), a model PAH stress condition, for 17 days.Results In general, exposure to PHE resulted in a reduction of growth parameters, along with the upregulation of antioxidant enzymes and compounds and limitations in nutrient uptake and heavy metal extraction in N. caerulescens. Variations were observed in the magnitude of enzymatic activities and the amount of extracted metals between the two studied populations. Chavignée plants exhibited a slightly more tolerant response to stress than Ganges.Conclusion The presence of PHE in the soil proved to be highly toxic for N. caerulescens. Nevertheless, to some extent, growth, metals extraction, and antioxidant defense responses differed slightly between the studied populations, suggesting that the difference in defense capacity might ensue different tolerance. This distinction may be related to the adaptations acquired by each population depending on the soil type it originated from.

BackgroundThe new SARS-CoV-2 variant VUI (202012/01), identified recently in the United Kingdom (UK), exhibits a higher transmissibility rate compared to other variants, and a reproductive number 0.4 higher. In the UK, scientists were able to identify the increase of this new variant through the rise of false negative results for the spike (S) target using a three-target RT-PCR assay (TaqPath kit).MethodsTo control and study the current coronavirus pandemic, it is important to develop a rapid and low-cost molecular test to identify the aforementioned variant. In this work, we designed primer sets specific to SARS-CoV-2 variant VUI (202012/01) to be used by SYBR Green-based RT-PCR. These primers were specifically designed to confirm the deletion mutations Δ69/Δ70 in the spike and the Δ106/Δ107/Δ108 in the NSP6 gene. We studied 20 samples from positive patients, 16 samples displayed an S-negative profile (negative for S target and positive for N and ORF1ab targets) and four samples with S, N and ORF1ab positive profile.ResultsOur results emphasized that all S-negative samples harbored the mutations Δ69/Δ70 and Δ106/Δ107/Δ108. This protocol could be used as a second test to confirm the diagnosis in patients who were already positive to COVID-19 but showed false negative results for S-gene.ConclusionsThis technique may allow to identify patients carrying the VUI (202012/01) variant or a closely related variant, in case of shortage in sequencing.

Bacillus subtilis is a widely used bacterial model to decipher biofilm formation, genetic determinants and their regulation. For several years, studies were conducted on colonies or pellicles formed at the interface with air, but more recent works showed that non-domesticated strains were able to form thick and structured biofilms on submerged surfaces. Taking advantage of time-lapse confocal laser scanning microscopy, we monitored bacterial colonization on the surface and observed an unexpected biphasic submerged biofilm development. Cells adhering to the surface firstly form elongated chains before being suddenly fragmented and released as free motile cells in the medium. This switching coincided with an oxygen depletion in the well which preceded the formation of the pellicle at the liquid-air interface. Residual bacteria still associated with the solid surface at the bottom of the well started to express matrix genes under anaerobic metabolism to build the typical biofilm protruding structures.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to an outbreak of a pandemic worldwide. The spike (S) protein of SARS-CoV-2, which plays a key role in the receptor recognition and cell membrane fusion process, is composed of two subunits, S1 and S2. The S1 subunit contains a receptor-binding domain that recognizes and binds to the host receptor angiotensin-converting enzyme 2 (ACE2), while the S2 subunit mediates viral cell membrane fusion with the cell membrane and subsequent entry into cells. Mutations in the spike protein (S) are of particular interest due to their potential for reduced susceptibility to neutralizing antibodies or increasing the viral transmissibility and infectivity. Recently, many mutations in the spike protein released new variants, including the Delta and Kappa ones (known as the Indian variants). The variants Delta and Kappa are now of most recent concern because of their well-increased infectivity, both a spin-off of the B.1.617 lineage, which was first identified in India in October 2020. This study employed homology modeling to probe the potential structural effects of the mutations. It was found that the mutations, Leu452Arg, Thr478Lys, and Glu484Gln in the spike protein increase the affinity for the hACE2 receptor, which explains the greater infectivity of the SARS-Cov-2 B.1.617 (Indian Variant).

Recently, a new variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) designated VOC 202012/01 (or B.1.1.7 lineage) has become highly prevalent in several countries, after first being described in the United Kingdom (UK). Its rate of transmission has been estimated to be increased compared to other lineages. In the present study, we show the emergence, dominance and the rapid spread of the B.1.1.7 lineage in Lebanon.

Surface-associated multicellular assemblage is an important bacterial trait to withstand harsh environmental conditions. Bacillus subtilis is one of the most studied Gram-positive bacteria, serving as a model for the study of genetic pathways involved in the different steps of 3D biofilm formation. B. subtilis biofilm studies have mainly focused on pellicle formation at the air-liquid interface or complex macrocolonies formed on nutritive agar. However, only few studies focus on the genetic features of B. subtilis submerged biofilm formation and their link with other multicellular models at the air interface. NDmed, an undomesticated B. subtilis strain isolated from a hospital, has demonstrated the ability to produce highly structured immersed biofilms when compared to strains classically used for studying B. subtilis biofilms. In this contribution, we have conducted a multi-culturing comparison (between macrocolony, swarming, pellicle, and submerged biofilm) of B. subtilis multicellular communities using the NDmed strain and mutated derivatives for genes shown to be required for motility and biofilm formation in pellicle and macrocolony models. For the 15 mutated NDmed strains studied, all showed an altered phenotype for at least one of the different culture laboratory assays. Mutation of genes involved in matrix production (i.e., tasA, epsA-O, cap, ypqP) caused a negative impact on all biofilm phenotypes but favored swarming motility on semi-solid surfaces. Mutation of bslA, a gene coding for an amphiphilic protein, affected the stability of the pellicle at the air-liquid interface with no impact on the submerged biofilm model. Moreover, mutation of lytF, an autolysin gene required for cell separation, had a greater effect on the submerged biofilm model than that formed at aerial level, opposite to the observation for lytABC mutant. In addition, B. subtilis NDmed with sinR mutation formed wrinkled macrocolony, less than that formed by the wild type, but was unable to form neither thick pellicle nor structured submerged biofilm. The results are discussed in terms of the relevancy to determine whether genes involved in colony and pellicle formation also govern submerged biofilm formation, by regarding the specificities in each model.

Communications are directly related to human activity and are inherent in the mental characteristics of human associations. They directly affect the personal space of each individual because...

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains a rapid spread emerging disease. Recently, a new variant of this virus called SARS-CoV-2 VOC 202012/01 (or B.1.1.7 lineage), described in the United Kingdom (UK), has become highly prevalent in several countries. Its rate of transmission has been estimated to be greatly higher. B.1.1.7 lineage harbors 23 mutations co-existed for the first time in the same variant. Herein, we are interested only by the deletion mutation ΔH69/ΔV70 in the spike protein.In the UK they were able to identify the increase of this new variant through the increase in the false negative result for the spike target of a three-target RT-PCR assay from Thermo Fisher Scientific (TaqPath kit). Later, the manufacturer announced that this false negative result is because of the deletion ΔH69/ΔV70 in the area targeted by the TaqPath Kit. Furthermore, The European CDC recommended that the use of this kit help to track the new variant.Genome sequencing is the gold method to confirm the new variant, but observational studies provide also stronger evidence if similar models are observed in multiple countries, especially when randomized studies are not possible. In Lebanon, the highest number of confirmed cases were reported in first week of 2021. In the present study, we show the emergence and the fast spreading of the new variant in Lebanon and a relationship between SARS-CoV-2 transmission intensity and the frequency of the new variant during the first twelve days of January.

Recently the first genome sequences for 11 SARS-CoV-2 isolates from Lebanon became available. Here, we report the detection of variants within the genome of these strains. Pairwise alignment analysis using blastx was performed between these sequences and the UniProtKB data for the SARS-CoV-2 coronavirus to identify amino acid variations. Variants analysis was performed using multiple Bioinformatics tools. We noticed for the first time 18 mutations that have never been reported before. Among those, a frame shift (8651A>) in NSP4, a stop codon 6887A > T in NSP3 and two missense mutations in spike S2 were found. In addition, we found 28 variants in ORF1ab alone. A previously reported variant, 23403A > G, in the spike protein S2 was mostly seen. Two other known mutations 25563G > T in ORF3a and 14408C > T in ORF1ab were detected respectively in 6 and 8 out of the 11 isolates. Our results may help to prognose forthcoming infections in this region.

International audience; This paper shows the VNA calibration for a DUT with a differential input and a single output embedded into a measurement board. Simulations have validated the concept. © 2019 IEEE.

International audience; Semiconductor devices are tested within a complex environment including a loadboard and a socket. In this paper, we propose a calibration methodology and a RF de‐embedding technique that allows the extraction of the device parameters. This method is based on the utilization of several calibration elements inspired by the TRL method. This study has been applied on an active device and the results have been validated using a real test solution.

The variation of the linear inductance of a CPW with the frequency is used to extract the effective permeability that depends on the metallic losses. The result allows to separate the dielectric and metallic losses and to calculate some characteristics of the waveguide.

Swarming Experiments were carried on with Bacillus subtilis strains to identify the activity of certain genes in the swarming ability and surfactin production. We will examine the effect of comXP as well as pta mutations on the capability of swarming. In different experiments we showed that strain OMG 903 that carries mutation in comXP managed to produce surfactin but showed attenuated defective and random swarming pattern strain OMG 928 that carries mutation in pta gene managed to produce surfactin and showed normal swarming pattern meanwhile double mutation in comXP and pta in strain OMG 929 lead to the absence of surfactin production and didnt manage Thesetoswarmdatashowed. that a threshold of surfactin production is necessary for a normal swarming pattern.

International audience; A bended and straight coplanar waveguides are modeled by using HFSS 3D electromagnetic software. The behavior of bend CPW is described by matrix calculations in order to show the effect of the parasitic even mode on the propagation of a signal. A comparison is done in this article with several works done before to show that there is a significant error when using bended CPW standard instead of straight ones in calibration.

International audience; The purpose of this article is to describe the effect of the parasitic even mode on the propagation of a signal along a bended coplanar waveguide and to evaluate the errors when bended standards are used in a TRL calibration instead of straight ones.

The non-domesticated Bacillus subtilis strain 3610 displays, over a wide range of humidity, hyper-branched, dendritic, swarming-like migration on a minimal agar medium. At high (70 %) humidity, the laboratory strain 168 sfp + (producing surfactin) behaves very similarly, although this strain carries a frameshift mutation in swrA, which another group has shown under their conditions (which include low humidity) is essential for swarming. We reconcile these different results by demonstrating that, while swrA is essential for dendritic migration at low humidity (30–40 %), it is dispensable at high humidity. Dendritic migration (flagella- and surfactin-dependent) of strains 168 sfp + swrA and 3610 involves elongation of dendrites for several hours as a monolayer of cells in a thin fluid film. This enabled us to determine in situ the spatiotemporal pattern of expression of some key players in migration as dendrites develop, using gfp transcriptional fusions for hag (encoding flagellin), comA (regulation of surfactin synthesis) as well as eps (exopolysaccharide synthesis). Quantitative (single-cell) analysis of hag expression in situ revealed three spatially separated subpopulations or cell types: (i) networks of chains arising early in the mother colony (MC), expressing eps but not hag; (ii) largely immobile cells in dendrite stems expressing intermediate levels of hag; and (iii) a subpopulation of cells with several distinctive features, including very low comA expression but hyper-expression of hag (and flagella). These specialized cells emerge from the MC to spearhead the terminal 1 mm of dendrite tips as swirling and streaming packs, a major characteristic of swarming migration. We discuss a model for this swarming process, emphasizing the importance of population density and of the complementary roles of packs of swarmers driving dendrite extension, while non-mobile cells in the stems extend dendrites by multiplication.

Highly branched dendritic swarming ofB. subtilison synthetic B-medium involves a developmental-like process that is absolutely dependent on flagella and surfactin secretion. In order to identify new swarming genes, we targeted the two-component ComPA signalling pathway and associated global regulators. In liquid cultures, the histidine kinase ComP, and the response regulator ComA, respond to secreted pheromones ComX and CSF (encoded byphrC) in order to control production of surfactin synthases and ComS (competence regulator). In this study, for what is believed to be the first time, we established that distinct early stages of dendritic swarming can be clearly defined, and that they are amenable to genetic analysis. In a mutational analysis producing several mutants with distinctive phenotypes, we were able to assign the genessfp(activation of surfactin synthases),comA, abrBandcodY(global regulators),hag(flagellin),mecAandyvzB(hag-like),and swrB(motility), to the different swarming stages. Surprisingly, mutations in genescomPX, comQ, comS,rapCandoppD, which are normally indispensable for import of CSF, had only modest effects, if any, on swarming and surfactin production. Therefore, during dendritic swarming, surfactin synthesis is apparently subject to novel regulation that is largely independent of the ComXP pathway; we discuss possible alternative mechanisms for drivingsrfABCDtranscription. We showed that thephrCmutant, largely independent of any effect on surfactin production, was also, nevertheless, blocked early in swarming, forming stunted dendrites, with abnormal dendrite initiation morphology. In a mixed swarm co-inoculated withphrC sfp+andphrC+sfp(GFP), an apparently normal swarm was produced. In fact, while initiation of all dendrites was of the abnormalphrCtype, these were predominantly populated bysfpcells, which migrated faster than thephrCcells. This and other results indicated a specific migration defect in thephrCmutant that could not betrans-complemented by CSF in a mixed swarm. CSF is the C-terminal pentapeptide of the surface-exposed PhrC pre-peptide and we propose that the residual PhrC 35 aa residue peptide anchored in the exterior of the cytoplasmic membrane has an apparently novel extracellular role in swarming.

International audience; Surfactins are a family of heptacyclopeptides in which the C-terminal carbonyl is linked with the beta-hydroxy group of a fatty acid acylating the N-terminal function of a glutamic acid residue. The fatty acyl chain is 12-16 carbon atoms long. These compounds, which are secreted by the Gram-positive bacterium Bacillus subtilis in stationary phase in liquid cultures, play an important role in swarming communities on the surface of agar media in the formation of dendritic patterns. TOF secondary ion MS (TOF-SIMS) imaging was used to map surfactins within 16-17 h swarming patterns, with a 2 mum spatial resolution. Surfactins were mainly located in the central mother colony (the site of initial inoculation), in a 'ring' surrounding the pattern and along the edges of the dendrites. In the mother colony and the interior of the dendrites, surfactins with shorter chain lengths are present, whereas in the ring surrounding the swarm community and between dendrites, surfactins with longer fatty acyl chain lengths were found. A quantitative analysis by MALDI-TOF MS showed a concentration gradient of surfactin from the mother colony to the periphery. The concentration of surfactin was approximately 400 pmol/mL in the mother colony and approximately 10 pmol/mL at the base of the dendrites, decreasing to 2 pmol/mL at their tips.

Depletion of the Bacillus subtilis GTPase CpgA produces abnormal cell shapes, nonuniform deposition of cell wall, and five- to sixfold accumulation of peptidoglycan precursors. Nevertheless, the inherent structure of the cell wall appeared mostly unchanged. The results are consistent with CpgA being involved in coordinating normal peptidoglycan deposition.

YloQ, from Bacillus subtilis, was identified previously as an essential nucleotide-binding protein of unknown function. YloQ was successfully over-expressed in Escherichia coli in soluble form. The purified protein displayed a low GTPase activity similar to that of other small bacterial GTPases such as Bex/Era. Based on the demonstrated GTPase activity and the unusual order of the yloQ G motifs, we now designate this protein as CpgA (circularly permuted GTPase). An unexpected property of this low abundance GTPase was the demonstration, using gel filtration and ultracentrifugation analysis, that the protein formed stable dimers, dependent upon the concentration of YloQ(CpgA), but independent of GTP. In order to investigate function, cpgA was placed under the control of the pspac promotor in the B. subtilis chromosome. When grown in E or Spizizen medium in the absence of IPTG, the rate of growth was significantly reduced. A large proportion of the cells exhibited a markedly perturbed morphology, with the formation of swollen, bent or 'curly' shapes. To confirm that this was specifically due to depleted CpgA a plasmid-borne cpgA under pxyl control was introduced. This restored normal cell shape and growth rate, even in the absence of IPTG, provided xylose was present. The crystal structure of CpgA(YloQ) suggests a role as a translation initiation factor and we discuss the possibility that CpgA is involved in the translation of a subset of proteins, including some required for shape maintenance.

AimMicroleakage quantification of fluids and microorganisms through the connections of different implant parts seems to be sparse. Moreover, no data exist regarding the determination of the volumes of inner parts of dental implant systems.This study aims to determine the volumes of inner parts of three dental implant systems with the same interface and to evaluate the microleakage phenomenon.Materials and methodsThree implant system sets (Euroteknika ®, Astra Tech® and Implantium®) were used in this study. Implants were inoculated with safranin, brain heart infusion and distilled water. After inoculation and assembly of the different parts, different inner volumes (V1, V2, V3, V4, V5and V6) were measured and, the surfaces of the micro gaps were observed through a stereomicroscope. Implants containing safranin were immersed in vials containing distilled water. Samples then were taken to determine optical density using a spectrophotometer.ResultsRegardless the used substance, volumes of the 3-implant systems are different. Although volumes V1, V2, V3and V5appeared to be constant within the same system regardless the used substance, volumes V4and V6were not.ConclusionThe determination of the volumes and the evaluation of leaked substance using stereomicroscopic and spectrophotometric methods showed the accuracy of these methods and the importance of their use in the study of microleakage.Clinical significanceLeakage is an important factor for chronic inflammatory infiltration and marginal bone resorption. Studies have shown fluid and bacterial leakage into abutmentimplant (A-I) assemblies of certain implants with ‘closely locked’ abutments and the creation of a constant bacterial reservoir in the empty space found between the implant and the abutment.How to cite this articleBerberi A, Tehini G, Tabaja Z, Kobaissi A, Hamze K, Rifai K, Ezzedine M, Badran B, Chokr A. Determination of Inner Implant's Volumes: A Pilot Study for Microleakage Quantification by Stereomicroscopy and Spectrophotometry. J Contemp Dent Pract 2013;14(6):1122-1130.