High Level Of Similarity Research Articles

Mapping Archaeal Diversity in Soda Lakes by Coupling 16S rRNA PCR-DGGE Analysis with Remote Sensing and GIS Technology

The haloarchaeal diversity of four hypersaline alkaline lakes from the Wadi El-Natrun depression (Northern Egypt) was investigated using culture-independent polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) of 16S rRNA gene phylotypes, which was combined with remote sensing and geographic information system (GIS) data to highlight the distribution pattern of the microbial diversity in water and sediment samples. The majority of archaeal sequences identified in all four lakes belonged to the phyla Euryarchaeota and Crenarchaeota. Sediment samples from Beida Lake and water samples from El-Hamra Lake showed the highest levels of archaeal diversity. Sequence similarities ≥ 95% were found between six of the acquired clones and uncultured Halorhabdus, Euryarchaeota, and archaeon clones. In addition, two clones shared a high level of sequence similarity (97%) with unclassified archaea, while other nine clones exhibited 96% to 99% sequence similarity with uncultured archaeon clones, and only one clone showed 97% identity with an uncultured Crenarchaeota. Likewise, 7 DGGE bands presented a sequence similarity of 90 to 98% to Halogranum sp., Halalkalicoccus tibetensis, Halalkalicoccus jeotgali, uncultured Halorubrum, Halobacteriaceae sp., or uncultured haloarchaeon. In conclusion, while the variety of alkaliphilic haloarchaea in the examined soda lakes was restricted, the possibility of uncovering novel species for biotechnological applications from these extreme habitats remains promising.

Substrate degradation pathways, conserved functions and community composition of the hindgut microbiota in the herbivorous marine fish Kyphosus sydneyanus

Symbiotic gut microbiota in the herbivorous marine fish Kyphosus sydneyanus play an important role in digestion by converting refractory algal carbohydrate into short-chain fatty acids. Here we characterised community composition using both 16S rRNA gene amplicon sequencing and shotgun-metagenome sequencing. Sequencing was carried out on lumen and mucosa samples (radial sections) from three axial sections taken from the hindgut of wild-caught fish. Both lumen and mucosa communities displayed distinct distributions along the hindgut, likely an effect of the differing selection pressures within these hindgut locations, as well as considerable variation among individual fish. In contrast, metagenomic sequences displayed a high level of functional similarity between individual fish and gut sections in the relative abundance of genes (based on sequencing depth) that encoded enzymes involved in algal-derived substrate degradation. These results suggest that the host gut environment selects for functional capacity in symbionts rather than taxonomic identity. Functional annotation of the enzymes encoded by the gut microbiota was carried out to infer the metabolic pathways used by the gut microbiota for the degradation of important dietary substrates: mannitol, alginate, laminarin, fucoidan and galactan (e.g. agar and carrageenan). This work provides the first evidence of the genomic potential of K. sydneyanus hindgut microbiota to convert highly refractory algal carbohydrates into metabolically useful short-chain fatty acids.

Consequences, Impact and Washback of CET Test Within Assessment for Use Argument to Validation

The high-stakes College English Test (CET), developed, administered, and reformed over the last 20 years, has received great attention in the aspect of washback on teaching and learning from previous research. Very few studies explored its consequences in the workplace domain—being used as a screening lever. This research aimed to 1) compare difference and similarities between skills measured in the test and performance required in the workplace, as well as the relevance between tasks in two domains, 2) investigate employers and employees’ interpretation on the use of the test in the working environment, 3) explore the impacts of the test per se on both stakeholders and consequences of the test use. To reach this goal, the researcher adopted Bachman and Palmer’s (2010) Assessment for Use Argument (AUA) framework and constructed three claims as research questions. This research employed qualitative method, carrying out in-depth interviews with eight participants consisted of employers and just-graduated students as employees. These participants’ responses to the interviewing questions were fully transcribed and analyzed. The study found that though some task methods in two domains are different; there is a high level of similarity between skills measured in two areas. The test is proved in this study to be impartial, generalizable, and sufficient for employment. Therefore, the CET can be used for selection decision in commercial domain and beneficial to both groups of stakeholders.

Combining segments 9 and 10 in DNA and recombinant protein vaccines conferred superior protection against tilapia lake virus in hybrid red tilapia (oreochromis sp.) compared to single segment vaccines.

Tilapia lake virus (TiLV) now affects Nile tilapia culture worldwide, with no available commercial vaccine for disease prevention. DNA and recombinant protein-based vaccines were developed and tested following viral isolation and characterization. The viral strain isolated from diseased hybrid red tilapia (Oreochromis sp.) shared high levels of morphological and genomic similarity (95.49-99.52%) with other TiLV isolates in the GenBank database. TiLV segment 9 (Tis9) and segment 10 (Tis10) DNA vaccines (pcDNA-Tis9 and pcDNA-Tis10) and recombinant protein vaccines (Tis9 and Tis10) were prepared and tested for their efficacy in juvenile hybrid red tilapia. Fish were immunized with either single vaccines (pcDNA-Tis9, pcDNA-Tis10, Tis9 and Tis10) or combined vaccines (pcDNA-Tis9 + pcDNA-Tis10 and Tis9 + Tis10) by intramuscular injection and intraperitoneal injection for DNA and protein vaccines, respectively. Negative controls were injected with PBS or a naked pcDNA3.1 vector in the same manner. An experimental challenge with TiLV was carried out at 4 weeks post-vaccination (wpv) by intraperitoneal injection with a dose of 1 × 105 TCID50 per fish. Relative percent survival (RPS) ranged from 16.67 ± 00.00 to 61.11 ± 9.62%. The Tis10 and pcDNA-Tis10 vaccines conferred better protection compared to Tis9 and pcDNA-Tis9. Highest levels of protection were observed in pcDNA-Tis9 + pcDNA-Tis10 (61.11 ± 9.62%) and Tis9 + Tis10 (55.56 ± 9.62%) groups. Specific antibody was detected in all vaccinated groups at 1-4 wpv by Dot Blot method, with the highest integrated density at 2 and 3 wpv. In silico analysis of Tis9 and Tis10 revealed a number of B-cell epitopes in their coil structure, possibly reflecting their immunogenicity. Findings suggested that the combination of Tis9 and Tis10 in DNA and recombinant protein vaccine showed high efficacy for the prevention of TiLV disease in hybrid red tilapia.

Evolution of the Membrane Transport Protein Domain.

Membrane transport proteins are widely present in all living organisms, however, their function, transported substrate, and mechanism of action are unknown. Here we use diverse bioinformatics tools to investigate the evolution of MTPs, analyse domain organisation and loop topology, and study the comparative alignment of modelled 3D structures. Our results suggest a high level of conservancy between MTPs from different taxa on both amino acids and structural levels, which imply some degree of functional similarities. The presence of loop/s of different lengths in various positions suggests tax-on-specific adaptation to transported substrates, intracellular localisation, accessibility for post-translation modifications, and interaction with other proteins. The comparison of modelled structures proposes close relations and a common origin for MTP and Na/H exchanger. Further, a high level of amino acid similarity and identity between archaeal and bacterial MTPs and Na/H exchangers imply conservancy of ion transporting function at least for archaeal and bacterial MTPs.

Evidence suggesting common mechanisms underlie contralateral and ipsilateral negative BOLD responses in the human visual cortex

The task-evoked positive BOLD response (PBR) to a unilateral visual hemi-field stimulation is often accompanied by robust and sustained contralateral as well as ipsilateral negative BOLD responses (NBRs) in the visual cortex. The signal characteristics and the neural and/or vascular mechanisms that underlie these two types of NBRs are not completely understood. In this paper, we investigated the properties of these two types of NBRs. We first demonstrated the linearity of both NBRs with respect to stimulus duration. Next, we showed that the hemodynamic response functions (HRFs) of the two NBRs were similar to each other, but significantly different from that of the PBR. Moreover, the subject-wise expressions of the two NBRs were tightly coupled to the degree that the correlation between the two NBRs was significantly higher than the correlation between each NBR and the PBR. However, the activation patterns of the two NBRs did not show a high level of interhemispheric spatial similarity, and the functional connectivity between them was not different than the interhemispheric functional connectivity between the NBRs and PBR. Finally, while attention did modulate both NBRs, the attention-related changes in their HRFs were similar. Our findings suggest that the two NBRs might be generated through common neural and/or vascular mechanisms involving distal/deep brain regions that project to the two hemispheres.

Rhodohalobacter sulfatireducens sp. nov., isolated from a marine solar saltern.

A novel Gram-stain-negative, oxidase-positive, catalase-positive, non-motile, facultatively anaerobic, rod-shaped bacterium, designated WB101T, was isolated from a marine solar saltern located in Wendeng, PR China. Strain WB101T shared a high level of 16S rRNA gene sequence similarity with Rhodohalobacter barkolensis 15182T (93.5%), R.halophilus JZ3C29T (93.2%), and 'R. mucosus' 8A47T (92.1%). Strain WB101T formed a species-level branch within the genus Rhodohalobacter in both phylogenetic and phylogenomic topologies. The DNA G + C content was 42.0%. Strain WB101T was found to have menaquinone-7 as the only respiratory quinone. The dominant cellular fatty acid (≥ 10%) was iso-C15:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylcholine. Characterisation based on phylogenetic, physiological, and biochemical properties indicated that strain WB101T represents a novel species of the genus Rhodohalobacter, and the name Rhodohalobacter sulfatireducens sp. nov. is proposed. The type strain is WB101T (= KCTC 92204T = MCCC 1H00518T).

Deficits in implementing integrated water resources management in South Africa: The role of institutional interplay

Integrated Water Resources Management (IWRM) has been transferred from the Global North to the Global South. Decades after adopting IWRM in formal policies, countries in the Global South in particular are struggling to implement it in practice. We believe the interplay of formal and informal institutions to be a reason for the failed transfer, but institutional interplay is rarely considered when policies are transferred. Based on a case study of water governance in the uMngeni river basin in South Africa, we investigate how specific types of informal institutions affect the practical implementation of selected aspects of IWRM: subsidiarity, stakeholder involvement, and securing access to water and sanitation. We explore (1) informal institutions that supported previous formal legislation and are still actively reproduced, (2) bureaucratic cultures operationalised through governance modes, and (3) traditional governance as part of a dual governance system. We find that in most cases, a higher level of similarity between formal and informal institutions leads to the more frequent implementation of formal provisions, and hence converging interplay between institutions. Passed-down power structures, another aspect of informal institutions, proved particularly resistant to institutional change. We conclude that analysing the setting of informal institutions before making policy reforms would provide a more realistic assessment of the results to be expected. Understanding institutional interplay in policy transfer processes is hence essential to designing more effective policies and avoiding the pitfalls inherent to blueprint solutions.

Investigation of genetic polymorphism of Russian rape and turnip rape varieties using SSR and SRAP markers.

Rapeseed (Brassica napus L.) and turnip rape (B. rapa L. subsp. campestris (L.)) are important agricultural plants widely used for food, fodder and technical purposes and as green manure. Over the past decades, a large number of perspective varieties that are being currently cultivated in every region of Russia have been developed. To increase the breeding eff iciency and facilitate the seed production, modern molecular-genetic techniques should be introduced as means to estimate species and varietal diversity. The objective of the presented research study was to investigate DNA polymorphism of the rapeseed and turnip rape varieties developed at Federal Williams Research Center of Forage Production and Agroecology and detect informative markers for varietal identif ication and genetic certif ication. To genotype 18 gDNA samples, 42 and 25 combinations of respective SSR and SRAP primers were used. The results obtained demonstrate that SRAP markers were more effective for polymorphism analysis: 36 % of the tested markers revealed genetic polymorphism compared with only 16.7 % of microsatellite loci. Molecular markers to detect differences at interspecif ic and intervarietal levels have also been found. For the investigated set, such microsatellite loci as Na12A02, Ni2C12, Ni02-D08a, Ra02-E01, Ni03H07а and SRAP-marker combinations as F13-R9, Me4- R7, F11-Em2, F10-R7, F9-Em2 and F9-R8 proved to be informative. Application of the two marker techniques made it possible to detect a higher level of DNA polymorphism in plants of different types (spring and winter varieties) if compared against the intervarietal differences within a species or a group. According to Nei’s genetic diversity index, in the cluster of winter rapeseed, VIK 2 and Gorizont varieties had the longest genetic distance, and in the spring cluster, these were Novosel and Veles. A high level of similarity was found between Vikros and Bizon winter rapeseed varieties. The results obtained have a high practical value for varietal specif ication of seed material and genetic certif ication of rapeseed and turnip rape varieties.

Functional Diversity Based on Morphometric Analysis and Identification of the Algerian Carob Tree (Ceratonia siliqua L.) Cultivars

Sixty-six carob accessions from 19 sites throughout Algeria were analysed by leaf, pod and seed characteristics to assess their genetic diversity and identify the first Algerian carob cultivars that could be used as germplasms for breeding programmes. We compared Algerian accessions with carobs from different Mediterranean countries, and our results showed a high level of morphological similarity between Algerian and Spanish carob pods. Analysis of variance showed highly significant differences (p ˂ 0.001) between accessions for all the quantitative traits. Correlation analysis between variables indicated that seed yield could be improved by selecting light, thin and narrow carob pods. Multiple correspondence analysis explained a total variance of 30.22 % and illustrated three distinct leaf classes. Principal component analysis proposed two main groups of variables, one based on seed performance and the other targeting pod potential. Hierarchical classification with seven clusters revealed considerable genetic diversity among the Algerian carob accessions studied, and indicated that the type of bioclimate did not influence their distribution, suggesting that morphometric traits are probably controlled more by genes that by bioclimate. Linear discriminant analysis, clustering and heatmap plotting identified 11 potential cultivars, 10 female and one hermaphroditic.

Validation of an established deep learning auto-segmentation tool for cardiac substructures in 4D radiotherapy planning scans.

Emerging data suggest that dose-sparing several key cardiac regions is prognostically beneficial in lung cancer radiotherapy. The cardiac substructures are challenging to contour due to their complex geometry, poor soft tissue definition on computed tomography (CT) and cardiorespiratory motion artefact. A neural network was previously trained to generate the cardiac substructures using three-dimensional radiotherapy planning CT scans (3D-CT). In this study, the performance of that tool on the average intensity projection from four-dimensional (4D) CT scans (4D-AVE), now commonly used in lung radiotherapy, was evaluated. The 4D-AVE of n=20 patients completing radiotherapy for lung cancer 2015-2020 underwent manual and automated cardiac substructure segmentation. Manual and automated substructures were compared geometrically and dosimetrically. Two senior clinicians also qualitatively assessed the auto-segmentation tool's output. Geometric comparison of the automated and manual segmentations exhibited high levels of similarity across parameters, including volume difference (11.8% overall) and Dice similarity coefficient (0.85 overall), and were consistent with 3D-CT performance. Differences in mean (median 0.2Gy, range -1.6-0.3Gy) and maximum (median 0.4Gy, range -2.2-0.9Gy) doses to substructures were generally small. Nearly all structures (99.5%) were deemed to be appropriate for clinical use without further editing. Cardiac substructure auto-segmentation using a deep learning-based tool trained on a 3D-CT dataset was feasible on the 4D-AVE scan, meaning this tool is suitable for use on 4D-CT radiotherapy planning scans. Application of this tool would increase the practicality of routine clinical cardiac substructure delineation, and enable further cardiac radiation effects research.

Using communication networks to assess the level of sharing of wildlife health data and information among wildlife professionals in Ontario, Canada

ABSTRACT There is a need for wildlife professionals to work together to more effectively protect wildlife health; however, collaboration between people of different professions and institutions can be challenging. Our objective was to examine and compare how the conservation and animal health fields share wildlife health data and information in Ontario, Canada. Fifty-five (50%) of 110 invited participants completed an online questionnaire about their wildlife health communication network over the previous 12 months. The professional communication networks (i.e., ego-networks) of practitioners were compared with respect to data sharing between institutions and professions. Results showed low levels of tie dispersion and high levels of ego-alter similarity. There was more data and information sharing occurring between people of different institutions than between people of different professions based on comparing tie dispersion and ego-alter similarity values for these categories. This study highlights opportunities for improved networking between wildlife conservation and health practitioners in Ontario.

Characterization of Leptin (LEP) gene in Indian dromedary camel (Camelus dromedarius)

Information on the camel leptin gene when compared to other domestic livestock species is very limited. Hence, thepresent study was undertaken to characterize the leptin gene of the Indian dromedary camel (Camelus dromedarius).Five overlapping primer pairs were designed utilizing the available Lama Glama leptin gene sequence. Through theassembly, alignment, and editing of the five overlapping nucleotide sequences, a 2425 bp long leptin gene sequence(Accession no. MT103545.1) of dromedary camel covering partial exon-2, intron-2, exon-3, and partial-3’ UTRregion was characterized. The study successfully amplified the leptin gene, including intron-2 and 3’UTR of camelleptin gene for the first time using genomic DNA samples. The Indian dromedary camel leptin gene at the nucleotide level shared more than 97% similarity with llama and more than 80% similarity with major domesticated species like cattle, buffalo, sheep, and goat. The evolutionary relationship study based on amino acid sequences showed a close relationship between dromedary and bactrian camel species followed by llama. The high level of similarity between camel leptin gene amino acid sequence and other species showed the conserved nature of leptin protein.

Demystifying the impact of customer participation on citizenship behaviors through interpersonal attraction and its contingencies

This paper addresses the lack of clarity on the linkage between customer participation (CP) and customer citizenship behavior (CCB) by using reinforcement theory to investigate the mediating role of interpersonal attraction (IPA) and the moderating effect of three types of reinforcers (people, task, and environment) in the impact of CP on CCB. Dyadic data from a field survey of both customers and designers from an interior design institute confirms the mediating role of IPA, particularly under high level of shared similarity between customers and employees, and when the task outcomes are better than expected. Moreover, the effect of IPA on CCB is stronger when customers perceive the organizational climate as highly customer-oriented. Besides extending the CP and CCB literature by exploring the impact of IPA on CCB with CP as a mediator and several reinforcers as moderator, this paper also suggests how service firms may influence their customers’ citizenship behaviors.

Comparative Analysis of the Results of Mine Surveying and Numerical Studies of the Running Tunnel of the Kyiv Metro

Purpose. The article is aimed to perform a comparative analysis of the results of mine surveying and numerical studies of the running tunnel of the Kyiv metro and obtain the reliability of the author’s system of parametric analysis. Methodology. The comparative analysis of the results of research on the displacements of the running tunnel was carried out in two directions. In the first direction, the movement of the lining of the running tunnels between the stations «Slavutych» – «Osokorky», «Osokorky» – «Pozniaky» and «Pozniaky» – «Kharkivska» obtained in the course of mine surveying studies was analyzed. In the second direction, a numerical analysis using the finite element method was performed. For this analysis, models of three lining rings were created. These rings were chosen because the maximum level of vertical movements was observed in them. Their reason is the influence of the engineering and geological conditions of the part of the Syretsko-Pecherska line on the left bank of the Dnipro River. These conditions are characterized by the layering of weak and water-saturated soils (sands of various sizes and densities, sandy loams, light loams and clays). The lining of the real tunnel is a standard structure used for shield tunneling of the Kyiv metro. The models reflect the geometric dimensions of the running tunnels, as well as the deformation characteristics and soil density of the surrounding layered massif. Findings. The authors analyzed the characteristics of the layered massif and the maximum displacements of the running tunnels of the part of the Syretsko-Pecherska line on the left bank of the Dnipro River. In the course of the numerical analysis, the vertical displacements of the models of the three lining rings were obtained. A comparative analysis of the results of mine surveying and numerical studies was carried out. The obtained level of error (up to 15 %) between the results of mine surveying and numerical studies proves that the developed bases of parametric analysis are reliable. Originality. For the first time, the theoretical foundations of parametric analysis for a real underground object were introduced. The author’s developments related to the creation of finite-element models based on the real characteristics of the soils of the layered massif provide a high level of similarity to the results of theoretical developments and instrumental mine surveying measurements. Practical value. It consists in the substantiation of the parameters of the deformed state that occurs in the horizontal working during shield tunneling.

Discovery of deoxyribonuclease II-like proteins in bacteria

Deoxyribonuclease II (DNase II) is one of the earliest enzymes discovered in the history of biochemistry. Its role in apoptosis and development has been documented with great detail in eukaryotes. Prior in silico analyses showed its complete absence in bacterial genomes, with the exception of single bacterial genus: Burkholderia. It is therefore considered to be a eukaryotic enzyme. Here we show that the presence of DNase II is not limited to Burkholderia, as we find over one hundred DNase II-like sequences spanning 90 bacteria species belonging to 54 different genera and seven phyla. The majority of the significant hits (85%) come from Bacteroidetes and Proteobacteria phyla. Sequence analyses reveal that bacterial DNase II-like proteins possess a signature catalytic motif of eukaryotic DNase II. In phylogenetic analyses, we find that bacterial DNase II-like proteins are divided into two distinct clades. Our structural analyses reveal high levels of similarity between experimentally determined crystal structures of recombinant Burkholderia thailandensis DNase II and candidate bacterial DNase II-like proteins. We also biochemically show that Chromobacterium violaceum cell lysate possesses acidic DNase II-like activities. Collectively, our results indicate that DNase II has deeper evolutionary roots than previously thought. We argue that either some prokaryotic lineages have undergone losses of DNase II genes, resulting in rare conservation, or some lineages have acquired DNase II genes from eukaryotes through lateral gene transfer. We also discuss the possible involvement of DNase II as a part of an anti-phage defense system in bacteria.

Exploring Mitogenomes Diversity of Fusarium musae from Banana Fruits and Human Patients.

Fusarium musae has recently been described as a cross-kingdom pathogen causing post-harvest disease in bananas and systemic and superficial infection in humans. The taxonomic identity of fungal cross-kingdom pathogens is essential for confirming the identification of the species on distant infected hosts. Understanding the level of variability within the species is essential to decipher the population homogeneity infecting human and plant hosts. In order to verify that F. musae strains isolated from fruits and patients are part of a common population and to estimate their overall diversity, we assembled, annotated and explored the diversity of the mitogenomes of 18 F. musae strains obtained from banana fruits and human patients. The mitogenomes showed a high level of similarity among strains with different hosts’ origins, with sizes ranging from 56,493 to 59,256 bp. All contained 27 tRNA genes and 14 protein-coding genes, rps3 protein, and small and large ribosomal subunits (rns and rnl). Variations in the number of endonucleases were detected. A comparison of mitochondrial endonucleases distribution with a diverse set of Fusarium mitogenomes allowed us to specifically discriminate F. musae from its sister species F. verticillioides and the other Fusarium species. Despite the diversity in F. musae mitochondria, strains from bananas and strains from human patients group together, indirectly confirming F. musae as a cross-kingdom pathogen.

Agreement attraction error and timing profiles in continuous speech

Studies of agreement attraction in language production have shown that speakers systematically produce verb agreement errors in the presence of a local noun whose features differ from that of the agreement controller. However, in attraction experiments, these errors only ever occur in a subset of trials. In the present study, we applied a naturalistic scene-description paradigm to investigate how attraction affects the distribution of errors and the time-course of correctly inflected verbs. We conducted our experiment both in the lab and in an unsupervised web-based setting. The results were strikingly similar across the experimental settings for both the error and timing analyses, demonstrating that it is possible to conduct production experiments via the internet with a high level of similarity to those done in the lab. The experiments replicated the basic number attraction effect, though they elicited comparable interference from both singular and plural local nouns, challenging common assumptions about a strong plural markedness effect in attraction. We observed slowdowns before correct verbs that paralleled the distribution of agreement errors, suggesting that the process resulting in attraction can be active even when no error is produced. Our results are easily captured by a model of agreement attraction in which errors arise at the point of computing agreement, rather than reflecting earlier errors made during initial encoding of the subject number.

Simulation Analysis of LED Stripes Drivers’ Influence on Electric Energy Quality

This paper presents a comparative simulation study of the operation of various types of drivers dedicated for use in light-emitting diode (LED)-based light stripes. The study comprises an experimentally verified simulation in view of their influence on harmonic content generation and impact on electric energy quality. The simulation models were optimized in order to precisely reflect the currents and voltage waveforms recorded in the frame of laboratory measurements. The simulation parameters were adjusted in view of harmonic generation analysis and high-frequency (HF) transient presence resulting from circuit principles of operation. Two driver circuit types were analyzed in the framework of the study—a voltage stabilization circuit based on a Zener diode, and a current stabilization integrated circuit (IC) based on an AL8806 chip. The study results entail an analysis executed for light stripes comprising various numbers of LEDs connected to each driver and various numbers of each of the tested drivers equipped with the same number of LEDs used as load. Based on the simulation, THD factors, harmonic components spectrum, waveform factors, power factors analysis and HF transient parameters were determined. The obtained simulations results are characterized by a high level of similarity in relation to results gained by means of measurements.

Genomic analysis of qnr-harbouring IncX plasmids and their transferability within different hosts under induced stress

BackgroundConjugative plasmids play a major role in the dissemination of antibiotic resistance genes. Knowledge of the plasmid characteristics and behaviour can allow development of control strategies. Here we focus on the IncX group of plasmids carrying genes conferring quinolone resistance (PMQR), reporting their transfer and persistence within host bacteria of various genotypes under distinct conditions and levels of induced stress in form of temperature change and various concentrations of ciprofloxacin supplementation.MethodsComplete nucleotide sequences were determined for eight qnr-carrying IncX-type plasmids, of IncX1 (3), IncX2 (3) and a hybrid IncX1-2 (2) types, recovered from Escherichia coli of various origins. This data was compared with further complete sequences of IncX1 and IncX2 plasmids carrying qnr genes (n = 41) retrieved from GenBank and phylogenetic tree was constructed. Representatives of IncX1 (pHP2) and IncX2 (p194) and their qnrS knockout mutants, were studied for influence of induced stress and genetic background on conjugative transfer and maintenance.ResultsA high level of IncX core-genome similarity was found in plasmids of animal, environmental and clinical origin. Significant differences were found between the individual IncX plasmids, with IncX1 subgroup plasmids showing higher conjugative transfer rates than IncX2 plasmids. Knockout of qnr modified transfer frequency of both plasmids. Two stresses applied simultaneously were needed to affect transfer rate of wildtype plasmids, whereas a single stress was sufficient to affect the IncX ΔqnrS plasmids. The conjugative transfer was shown to be biased towards the host phylogenetic proximity. A long-term cultivation experiment pointed out the persistence of IncX plasmids in the antibiotic-free environment.ConclusionsThe study indicated the stimulating effect of ciprofloxacin supplementation on the plasmid transfer that can be nullified by the carriage of a single PMQR gene. The findings present the significant properties and behaviour of IncX plasmids carrying antibiotic resistance genes that are likely to play a role in their dissemination and stability in bacterial populations.