Allelic diversity and population structure in Vibrio cholerae O139 Bengal based on nucleotide sequence analysis

Comparative analysis of gene fragments of six housekeeping loci, distributed around the two chromosomes of Vibrio cholerae, has been carried out for a collection of 29 V. cholerae O139 Bengal strains isolated from India during the first epidemic period (1992 to 1993). A toxigenic O1 ElTor strain from the seventh pandemic and an environmental non-O1/non-O139 strain were also included in this study. All loci studied were polymorphic, with a small number of polymorphic sites in the sequenced fragments. The genetic diversity determined for our O139 population is concordant with a previous multilocus enzyme electrophoresis study in which we analyzed the same V. cholerae O139 strains. In both studies we have found a higher genetic diversity than reported previously in other molecular studies. The results of the present work showed that O139 strains clustered in several lineages of the dendrogram generated from the matrix of allelic mismatches between the different genotypes, a finding which does not support the hypothesis previously reported that the O139 serogroup is a unique clone. The statistical analysis performed in the V. cholerae O139 isolates suggested a clonal population structure. Moreover, the application of the Sawyer's test and split decomposition to detect intragenic recombination in the sequenced gene fragments did not indicate the existence of recombination in our O139 population

Collecting high-order interactions in an effective pairwise intermolecular potential using the hydrated ion concept: The hydration of Cf3+

This work proposes a new methodology to build interaction potentials between a highly charged metal cation and water molecules. These potentials, which can be used in classical computer simu- lations, have been fitted to reproduce quantum mechanical interaction energies (MP2 and BP86) for a wide range of [M(H2O)n]m+(H2O)l clusters (n going from 6 to 10 and l from 0 to 18). A flexible and polarizable water shell model (Mobile Charge Density of Harmonic Oscillator) has been coupled to the cation-water potential. The simultaneous consideration of poly-hydrated clusters and the polarizability of the interacting particles allows the inclusion of the most important many-body effects in the new polarizable potential. Applications have been centered on the californium, Cf(III) the heaviest actinoid experimentally studied in solution. Two different strategies to select a set of about 2000 structures which are used for the potential building were checked. Monte Carlo simulations of Cf(III)+500 H2O for three of the intermolecular potentials predict an aquaion structure with coordination number close to 8 and average RCf–O in the range 2.43–2.48 Å, whereas the fourth one is closer to 9 with RCf–O = 2.54 Å. Simulated EXAFS spectra derived from the structural Monte Carlo distribution compares fairly well with the available experimental spectrum for the simulations bearing 8 water molecules. An angular distribution similar to that of a square antiprism is found for the octa-coordination.Ministerio de Ciencia e Innovación CTQ2011-2593

Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

BACKGROUND: The bacterial flagellum is the most important organelle of motility in bacteria and plays a key role in many bacterial lifestyles, including virulence. The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space. As if to stress its importance, plants and animals produce receptors specifically dedicated to the recognition of flagella. Aside from motility, the flagellum also moonlights as an adhesion and has been adapted by humans as a tool for peptide display. Flagellar sequence variation constitutes a marker with widespread potential uses for studies of population genetics and phylogeny of bacterial species. RESULTS: We sequenced the complete flagellin gene (flaA) in 18 different species and subspecies of Aeromonas. Sequences ranged in size from 870 (A. allosaccharophila) to 921 nucleotides (A. popoffii). The multiple alignment displayed 924 sites, 66 of which presented alignment gaps. The phylogenetic tree revealed the existence of two groups of species exhibiting different FlaA flagellins (FlaA1 and FlaA2). Maximum likelihood models of codon substitution were used to analyze flaA sequences. Likelihood ratio tests suggested a low variation in selective pressure among lineages, with an omega ratio of less than 1 indicating the presence of purifying selection in almost all cases. Only one site under potential diversifying selection was identified (isoleucine in position 179). However, 17 amino acid positions were inferred as sites that are likely to be under positive selection using the branch-site model. Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence. CONCLUSION: The models applied to our set of sequences allowed us to determine the possible evolutionary pathway followed by the flaA gene in Aeromonas, suggesting that this gene have probably been evolving independently in the two groups of Aeromonas species since the divergence of a distant common ancestor after one or several episodes of positive selection. REVIEWERS: This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst)

Tear fluid biomarkers in ocular and systemic disease: potential use for predictive, preventive and personalised medicine

In the field of predictive, preventive and personalised medicine, researchers are keen to identify novel and reliable ways to predict and diagnose disease, as well as to monitor patient response to therapeutic agents. In the last decade alone, the sensitivity of profiling technologies has undergone huge improvements in detection sensitivity, thus allowing quantification of minute samples, for example body fluids that were previously difficult to assay. As a consequence, there has been a huge increase in tear fluid investigation, predominantly in the field of ocular surface disease. As tears are a more accessible and less complex body fluid (than serum or plasma) and sampling is much less invasive, research is starting to focus on how disease processes affect the proteomic, lipidomic and metabolomic composition of the tear film. By determining compositional changes to tear profiles, crucial pathways in disease progression may be identified, allowing for more predictive and personalised therapy of the individual. This article will provide an overview of the various putative tear fluid biomarkers that have been identified to date, ranging from ocular surface disease and retinopathies to cancer and multiple sclerosis. Putative tear fluid biomarkers of ocular disorders, as well as the more recent field of systemic disease biomarkers, will be shown

Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

<p>Abstract</p> <p>Background</p> <p>The bacterial flagellum is the most important organelle of motility in bacteria and plays a key role in many bacterial lifestyles, including virulence. The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space. As if to stress its importance, plants and animals produce receptors specifically dedicated to the recognition of flagella. Aside from motility, the flagellum also moonlights as an adhesion and has been adapted by humans as a tool for peptide display. Flagellar sequence variation constitutes a marker with widespread potential uses for studies of population genetics and phylogeny of bacterial species.</p> <p>Results</p> <p>We sequenced the complete flagellin gene <it>(flaA</it>) in 18 different species and subspecies of <it>Aeromonas</it>. Sequences ranged in size from 870 (<it>A. allosaccharophila</it>) to 921 nucleotides (<it>A. popoffii</it>). The multiple alignment displayed 924 sites, 66 of which presented alignment gaps. The phylogenetic tree revealed the existence of two groups of species exhibiting different FlaA flagellins (FlaA1 and FlaA2). Maximum likelihood models of codon substitution were used to analyze <it>flaA </it>sequences. Likelihood ratio tests suggested a low variation in selective pressure among lineages, with an ω ratio of less than 1 indicating the presence of purifying selection in almost all cases. Only one site under potential diversifying selection was identified (isoleucine in position 179). However, 17 amino acid positions were inferred as sites that are likely to be under positive selection using the branch-site model. Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence.</p> <p>Conclusion</p> <p>The models applied to our set of sequences allowed us to determine the possible evolutionary pathway followed by the <it>flaA </it>gene in <it>Aeromonas</it>, suggesting that this gene have probably been evolving independently in the two groups of <it>Aeromonas </it>species since the divergence of a distant common ancestor after one or several episodes of positive selection.</p> <p>Reviewers</p> <p>This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst).</p

The second victim phenomenon: A qualitative study among bachelor’s degree nursing students within the clinical learning environment

Aim: This study explores and describes the second victim phenomenon in nursing students in association with the characteristics of the clinical learning environment and the clinical supervision process. Design: Qualitative design using conventional content analysis and summative content analysis approaches. Methods: From September 2022 to July 2023, in-depth semi-structured individual interviews were conducted with a purposive sample of 10 undergraduate nursing students. Results: Six main themes were developed: ‘defining the physical and psychological responses after the most significant patient safety incident’, ‘analyzing the characteristics of patient safety incidents’, ‘creating a safe learning environment to provide the best care for patients’, ‘developing mentorship capabilities and qualities for an ideal follow up of students as a second victim’, ‘providing resources and integrating support structures to second victim nursing students during their clinical learning’, and ‘considering the cooperation and coordination between the health institution and the higher education institutions.’ Conclusion: Nursing students become second victims during their clinical placement. The clinical learning environment and mentoring characteristics influence the second victim experience.The authors thank the University of Alicante for the provision of financial support to this research

Prediction of whole-genome DNA G+C content within the genus Aeromonas based on housekeeping gene sequences

Different methods are available to determine the G+C content (e.g. thermal denaturation temperature or high performance liquid chromatography, HPLC), but obtained values may differ significantly between strains, as well as between laboratories. Recently, several authors have demonstrated that the genomic DNA G+C content of prokaryotes can be reliably estimated from one or several protein coding gene nucleotide sequences. Few G+C content values have been published for the Aeromonas species described and the data, when available, are often incomplete or provide only a range of values. Our aim in this current work was twofold. First, the genomic G+C content of the type or reference strains of all species and subspecies of the genus Aeromonas was determined with a traditional experimental method in the same laboratory. Second, we wanted to see if the sequence-based method to estimate the G+C content described by Fournier et al. [7] could be applied to determine the G+C content of the different species of Aeromonas from the sequences of the genes used in taxonomy or phylogeny for this genus

The reference strain Aeromonas hydrophicla CIP 57.50 should be reclassified as Aeromonas salmonicida CIP 57.50

The use of reference strains is a critical element for the quality control of different assays, from the development of molecular methods to the evaluation of antimicrobial activities. Most of the strains used in these assays are not type strains and some of them are cited erroneously because of subsequent reclassifications and descriptions of novel species. In this study, we propose that the reference strain Aeromonas hydrophila CIP 57.50 be reclassified as Aeromonas salmonicida CIP 57.50 based on phenotypic characterization and sequence analyses of the cpn60, dnaJ, gyrB and rpoD genes

Biochemical identification and numerical taxonomy of Aeromonas spp. isolated from environmental and clinical samples in Spain

Aims: To study the phenotypic characteristics of Aeromonas spp. from environmental and clinical samples in Spain and to cluster these strains by numerical taxonomy. Methods and Results: A collection of 202 Aeromonas strains isolated from bivalve molluscs, water and clinical samples was tested for 64 phenotypic properties; 91% of these isolates were identified at species level. Aeromonas caviae was predominant in bivalve molluscs and Aerom. bestiarum in freshwater samples. Cluster analyses revealed eight different phena: three containing more than one DNA-DNA hybridization group but including strains that belong to the same phenospecies complex (Aerom. hydrophila, Aerom. sobria and Aerom. caviae), Aerom. encheleia, Aerom. trota and three containing unidentified Aeromonas strains isolated from bivalve molluscs. Conclusions: Aeromonas spp. are widely distributed in environmental and clinical sources. A selection of 16 of the phenotypical tests chosen allowed the identification of most isolates (91%), although some strains remain unidentified, mainly isolates from bivalve molluscs, suggesting the presence of new Aeromonas species. Numerical taxonomy was not in total concordance with the identification of the studied strains. Significance and Impact of the Study: Numerical taxonomy of Aeromonas strains isolated from different sources revealed the presence of potentially pathogenic Aeromonas spp., especially in bivalve molluscs, and phena with unidentified strains that suggest new Aeromonas species