Genotypic and phenotypic diversity of Ralstonia pickettii and Ralstonia insidiosa isolates from clinical and environmental sources including High-purity Water. Diversity in Ralstonia pickettii

<p>Abstract</p> <p>Background</p> <p><it>Ralstonia pickettii </it>is a nosocomial infectious agent and a significant industrial contaminant. It has been found in many different environments including clinical situations, soil and industrial High Purity Water. This study compares the phenotypic and genotypic diversity of a selection of strains of <it>Ralstonia </it>collected from a variety of sources.</p> <p>Results</p> <p><it>Ralstonia </it>isolates (fifty-nine) from clinical, industrial and environmental origins were compared genotypically using i) Species-specific-PCR, ii) PCR and sequencing of the 16<it>S-</it>23<it>S </it>rRNA Interspatial region (ISR) iii) the <it>fliC </it>gene genes, iv) RAPD and BOX-PCR and v) phenotypically using biochemical testing. The species specific-PCR identified fifteen out of fifty-nine designated <it>R. pickettii </it>isolates as actually being the closely related species <it>R. insidiosa</it>. PCR-ribotyping of the 16<it>S-</it>23<it>S </it>rRNA ISR indicated few major differences between the isolates. Analysis of all isolates demonstrated different banding patterns for both the RAPD and BOX primers however these were found not to vary significantly.</p> <p>Conclusions</p> <p><it>R. pickettii </it>species isolated from wide geographic and environmental sources appear to be reasonably homogenous based on genotypic and phenotypic characteristics. <it>R. insidiosa </it>can at present only be distinguished from <it>R. pickettii </it>using species specific PCR. <it>R. pickettii </it>and <it>R. insidiosa </it>isolates do not differ significantly phenotypically or genotypically based on environmental or geographical origin.</p

Novel Tn4371-ICE like element in Ralstonia pickettii and Genome mining for comparative elements

peer-reviewedBackground: Integrative Conjugative Elements (ICEs) are important factors in the plasticity of microbial genomes. An element related to the ICE Tn4371 was discovered during a bioinformatic search of the Ralstonia pickettii 12J genome. This element was analysed and further searches carried out for additional elements. A PCR method was designed to detect and characterise new elements of this type based on this scaffold and a culture collection of fifty-eight Ralstonia pickettii and Ralstonia insidiosa strains were analysed for the presence of the element. Results: Comparative sequence analysis of bacterial genomes has revealed the presence of a number of uncharacterised Tn4371-like ICEs in the genomes of several beta and gamma Proteobacteria. These elements vary in size, GC content, putative function and have a mosaic-like structure of plasmid- and phage-like sequences which is typical of Tn4371-like ICEs. These elements were found after a through search of the GenBank database. The elements, which are found in Ralstonia, Delftia, Acidovorax, Bordetella, Comamonas, Acidovorax, Congregibacter, Shewanella, Pseudomonas Stenotrophomonas, Thioalkalivibrio sp. HL-EbGR7, Polaromonas, Burkholderia and Diaphorobacter sp. share a common scaffold. A PCR method was designed (based on the Tn4371-like element detected in the Ralstonia pickettii 12J genome) to detect and characterise new elements of this type. Conclusion: All elements found in this study possess a common scaffold of core genes but contain different accessory genes. A new uniform nomenclature is suggested for ICEs of the Tn4371 family. Two novel Tn4371-like ICE were discovered and characterised, using the novel PCR method described in two different isolates of Ralstonia pickettii from laboratory purified water.PUBLISHEDpeer-reviewe

Drug release mechanisms of chemically cross-linked albumin microparticles: effect of the matrix erosion

Albumin (BSA) microparticles were developed as a biotechnological alternative for drug delivery. Vitamin B12 (Vit-B12) was used as a model drug. The microparticles were obtained from maleic anhydride-functionalized BSA and N′,N′-dimethylacrylamide (DMAAm) in a W/O emulsion without and with PVA. The microparticles produced at 15 min of stirring without PVA showed the best results in terms of size, homogeneity, and sphericity. In such a case, BSA played a role as a surface active agent, replacing PVA. For longer stirring times, BSA was unable to act as an emulsifier. These microparticles showed an uncommon release profile, consisting of a two-step release mechanism, at the pH range studied. Considering that a two-step release mechanism is occurring, the experimental data were adjusted by applying modified power law and Weibull equations in order to describe release mechanism n and release rate constant k, respectively. Each one of the release stages was related to a specific value of n and k. The second stage was driven by a super case II transport mechanism, as a result of diffusion, macromolecular relaxation, and erosion. A third model, described by Hixson–Crowell, confirmed the erosion mechanism. Vit-B12 diffusion kinetics in aqueous solutions (i.e., without the microparticles) follows a one-step process, being k dependent on the pH, confirming that the two-step release mechanism is a characteristic profile of the developed microparticles. The microparticles released only 2.70% of their initial drug load at pH 2, and 58.53% at pH 10

SNAPSHOT USA 2020: A second coordinated national camera trap survey of the United States during the COVID-19 pandemic

Managing wildlife populations in the face of global change requires regular data on the abundance and distribution of wild animals, but acquiring these over appropriate spatial scales in a sustainable way has proven challenging. Here we present the data from Snapshot USA 2020, a second annual national mammal survey of the USA. This project involved 152 scientists setting camera traps in a standardized protocol at 1485 locations across 103 arrays in 43 states for a total of 52,710 trap-nights of survey effort. Most (58) of these arrays were also sampled during the same months (September and October) in 2019, providing a direct comparison of animal populations in 2 years that includes data from both during and before the COVID-19 pandemic. All data were managed by the eMammal system, with all species identifications checked by at least two reviewers. In total, we recorded 117,415 detections of 78 species of wild mammals, 9236 detections of at least 43 species of birds, 15,851 detections of six domestic animals and 23,825 detections of humans or their vehicles. Spatial differences across arrays explained more variation in the relative abundance than temporal variation across years for all 38 species modeled, although there are examples of significant site-level differences among years for many species. Temporal results show how species allocate their time and can be used to study species interactions, including between humans and wildlife. These data provide a snapshot of the mammal community of the USA for 2020 and will be useful for exploring the drivers of spatial and temporal changes in relative abundance and distribution, and the impacts of species interactions on daily activity patterns. There are no copyright restrictions, and please cite this paper when using these data, or a subset of these data, for publication

Phosphatidylinositol 3-kinase (PI3K) pathway activation in bladder cancer

The phosphatidylinositol 3-kinase (PI3K) pathway is a critical signal transduction pathway that regulates multiple cellular functions. Aberrant activation of this pathway has been identified in a wide range of cancers. Several pathway components including AKT, PI3K and mTOR represent potential therapeutic targets and many small molecule inhibitors are in development or early clinical trials. The complex regulation of the pathway, together with the multiple mechanisms by which it can be activated, make this a highly challenging pathway to target. For successful inhibition, detailed molecular information on individual tumours will be required and it is already clear that different tumour types show distinct combinations of alterations. Recent results have identified alterations in pathway components PIK3CA, PTEN, AKT1 and TSC1 in bladder cancer, some of which are significantly related to tumour phenotype and clinical behaviour. Co-existence of alterations to several PI3K pathway genes in some bladder tumours indicates that these proteins may have functions that are not related solely to the known canonical pathway

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology