Comparative genomics of Pseudomonas fluorescens subclade III strains from human lungs

Abstract Background While the taxonomy and genomics of environmental strains from the P. fluorescens species-complex has been reported, little is known about P. fluorescens strains from clinical samples. In this report, we provide the first genomic analysis of P. fluorescens strains in which human vs. environmental isolates are compared. Results Seven P. fluorescens strains were isolated from respiratory samples from cystic fibrosis (CF) patients. The clinical strains could grow at a higher temperature (>34 °C) than has been reported for environmental strains. Draft genomes were generated for all of the clinical strains, and multi-locus sequence analysis placed them within subclade III of the P. fluorescens species-complex. All strains encoded type- II, −III, −IV, and -VI secretion systems, as well as the widespread colonization island (WCI). This is the first description of a WCI in P. fluorescens strains. All strains also encoded a complete I2/PfiT locus and showed evidence of horizontal gene transfer. The clinical strains were found to differ from the environmental strains in the number of genes involved in metal resistance, which may be a possible adaptation to chronic antibiotic exposure in the CF lung. Conclusions This is the largest comparative genomics analysis of P. fluorescens subclade III strains to date and includes the first clinical isolates. At a global level, the clinical P. fluorescens subclade III strains were largely indistinguishable from environmental P. fluorescens subclade III strains, supporting the idea that identifying strains as ‘environmental’ vs ‘clinical’ is not a phenotypic trait. Rather, strains within P. fluorescens subclade III will colonize and persist in any niche that provides the requirements necessary for growth.http://deepblue.lib.umich.edu/bitstream/2027.42/116129/1/12864_2015_Article_2261.pd

The human keratins: biology and pathology

The keratins are the typical intermediate filament proteins of epithelia, showing an outstanding degree of molecular diversity. Heteropolymeric filaments are formed by pairing of type I and type II molecules. In humans 54 functional keratin genes exist. They are expressed in highly specific patterns related to the epithelial type and stage of cellular differentiation. About half of all keratins—including numerous keratins characterized only recently—are restricted to the various compartments of hair follicles. As part of the epithelial cytoskeleton, keratins are important for the mechanical stability and integrity of epithelial cells and tissues. Moreover, some keratins also have regulatory functions and are involved in intracellular signaling pathways, e.g. protection from stress, wound healing, and apoptosis. Applying the new consensus nomenclature, this article summarizes, for all human keratins, their cell type and tissue distribution and their functional significance in relation to transgenic mouse models and human hereditary keratin diseases. Furthermore, since keratins also exhibit characteristic expression patterns in human tumors, several of them (notably K5, K7, K8/K18, K19, and K20) have great importance in immunohistochemical tumor diagnosis of carcinomas, in particular of unclear metastases and in precise classification and subtyping. Future research might open further fields of clinical application for this remarkable protein family

Comparative study of 7 fluorescent pseudomonad clinical isolates.

International audienceThere is some debate about the potential survival of Pseudomonas fluorescens at temperatures above 37 degrees C and its consequences for infectious potential, owing to the heterogeneity of clinical strains. Seven clinical strains growing at 37 degrees C or more were submitted for polyphasic identification; 2 were identified as Pseudomonas mosselii and 4 were precisely characterized as P. fluorescens bv. I or II. The binding indexes on glial cells of the strains identified as P. fluorescens bv. I and P. mosselii were compared with that of a reference psychrotrophic strain, P. fluorescens MF37 (bv. V). Clinical P. fluorescens had a similar adherence potential range than strain MF37. Conversely, the binding indexes for P. mosselii strains were 3 times greater than that for strain MF37. These data, and those obtained by comparing the cytotoxic activities of P. fluorescens clinical strains, suggest the existence of different virulence mechanisms, leading either to a low infectious form or to a microorganism with cytotoxic activity in the same range as that of P. mosselii or even Pseudomonas aeruginosa

INDI 67. Developments of Indicators to improve monitoring of MSFD descriptors 6 and 7 (INDI67) : final report

Context To protect the marine environment more effectively, the European Union adopted the Marine Strategy Framework Directive (MSFD) in 2008, aiming to achieve the Good Environmental Status (GES) of the EU's marine waters by 2020 and to protect the resource base upon which marine-related economic and social activities depend. A major challenge in the implementation of the MSFD is to achieve the necessary scientific knowledge on the marine environment, its processes and the methods to monitor them. The focus of INDI67 is on the evaluation and development of indicators to monitor GES of descriptor 6 and 7. Seafloor integrity (descriptor 6) refers to the structure and functions of the benthic ecosystems. It relates to the comprises physical, chemical and biological properties as well as to spatial and temporal connectedness, avoiding artificial fragmentation of habitats or temporal sealing due to ephemeral sediment deposits or armouring. Hydrographic conditions (descriptor 7) imply that the nature and scale of any long-term changes to the prevailing hydrographical conditions resulting from anthropogenic activities (individual and cumulative), do not lead to significant negative impacts on the benthic and pelagic habitats, functioning or on hydro-geomorphological impacts on the seabed. Objectives The overall objective of INDI67 is to develop and evaluate tools and methods to support the monitoring of MSFD descriptors 6 and 7. The subject is the monitoring of seafloor integrity and hydrography using both modelling and measurements of hydro- and sediment dynamic processes and seabed characteristics. Three parameters have been selected as key indicator, i.e. turbidity, bottom shear stress and seabed/habitat type. These parameters are all related to sea floor dynamics and are strongly linked as changes in seafloor integrity and turbidity occur as a result of the combined force that waves and currents exert on the sea floor. Furthermore, they are witnesses of changes induced by human activities (dredging/disposal, aggregate extraction, constructions, fishery). Turbidity (used both in terms of suspended particulate matter(SPM) concentration and light availability) and bottom shear stress are currently measured and modelled. Bottom shear stress and seabed/habitat type are included in the Belgian MSFD monitoring programme, while turbidity is not yet included as GES indicator. Conclusions The major conclusion with respect to the measuring and modelling of the key indicators turbidity/SPMC, bottom shear stress and seabed/habitat type are: 1) Despite calibration to a reference solution and the use of ISO-normed optical turbidity sensors, model calibration may vary considerably in recorded turbidity for a same SPMC solution across different instruments resulting in instrument-specific turbidity-SPMC relation. Turbidity (or dB for acoustic sensors) should therefore not be used as it is not standardized and will diminish the comparability of the data. Instead, the optical and acoustic sensor output should be transformed into a mass concentration, a unit that is comparable in time and between regions. Monitoring in situ SPMC should follow common guidance and protocols to restrict their measurement uncertainties. The main challenge is now to evaluate model results uncertainty and improve the formulation of natural processes, such as flocculation and bottom shear stress, together with the effects of pressures in the models