Calcium Sensing by Recoverin : Effect of Protein Conformation on Ion Affinity

The detailed functional mechanism of recoverin, which acts as a myristoyl switch at the rod outer-segment disk membrane, is elucidated by direct and replica-exchange molecular dynamics. In accord with NMR structural evidence and calcium binding assays, simulations point to the key role of enhanced calcium binding to the EF3 loop of the semiopen state of recoverin as compared to the closed state. This 2-4-order decrease in calcium dissociation constant stabilizes the semiopen state in response to the increase of cytosolic calcium concentration in the vicinity of recoverin. A second calcium ion then binds to the EF2 loop and, consequently, the structure of the protein changes from the semiopen to the open state. The latter has the myristoyl chain extruded to the cytosol, ready to act as a membrane anchor of recoverin.Peer reviewe

X-ray microscopy of living multicellular organisms with the Prague Asterix Iodine Laser System

Soft X-ray contact microscopy (SXCM) experiments have been performed using the Prague Asterix Iodine Laser System (PALS). Laser wavelength and pulse duration were λ = 1.314 μm and τ (FWHM) = 450 ps, respectively. Pulsed X rays were generated using teflon, gold, and molybdenum targets with laser intensities I ≥ 1014 W/cm2. Experiments have been performed on the nematodes Caenorhabditis elegans. Images were recorded on PMMA photo resists and analyzed using an atomic force microscope operating in contact mode. Our preliminary results indicate the suitability of the SXCM for multicellular specimens

Elevational species richness gradients in a hyperdiverse insect taxon: a global meta-study on geometrid moths

AIMS: We aim to document elevational richness patterns of geometrid moths in a globally replicated, multi-gradient setting, and to test general hypotheses on environmental and spatial effects (i.e. productivity, temperature, precipitation, area, mid-domain effect and human habitat disturbance) on these richness patterns. LOCATION: Twenty-six elevational gradients world-wide (latitudes 28° S to 51° N). METHODS: We compiled field datasets on elevational gradients for geometrid moths, a lepidopteran family, and documented richness patterns across each gradient while accounting for local undersampling of richness. Environmental and spatial predictor variables as well as habitat disturbance were used to test various hypotheses. Our analyses comprised two pathways: univariate correlations within gradients, and multivariate modelling on pooled data after correcting for overall variation in richness among different gradients. RESULTS: The majority of gradients showed midpeak patterns of richness, irrespective of climate and geographical location. The exclusion of human-affected sampling plots did not change these patterns. Support for univariate main drivers of richness was generally low, although there was idiosyncratic support for particular predictors on single gradients. Multivariate models, in agreement with univariate results, provided the strongest support for an effect of area-integrated productivity, or alternatively for an elevational area effect. Temperature and the mid-domain effect received support as weaker, modulating covariates, while precipitation-related variables had no explanatory potential. MAIN CONCLUSIONS: Despite the predicted decreasing diversity–temperature relationship in ectotherms, geometrid moths are similar to ants and salamanders as well as small mammals and ferns in having predominantly their highest diversity at mid-elevations. As in those comparative analyses, single or clear sets of drivers are elusive, but both productivity and area appear to be influential. More comparative elevational studies for various insect taxa are necessary for a more comprehensive understanding of elevational diversity and productivity

Treatment of synthetic textile wastewater containing dye mixtures with microcosms

The aim was to assess the ability of microcosms (laboratory-scale shallow ponds) as a post polishing stage for the remediation of artificial textile wastewater comprising two commercial dyes (basic red 46 (BR46) and reactive blue 198 (RB198)) as a mixture. The objectives were to evaluate the impact of Lemna minor L. (common duckweed) on the water quality outflows; the elimination of dye mixtures, organic matter, and nutrients; and the impact of synthetic textile wastewater comprising dye mixtures on the L. minor plant growth. Three mixtures were prepared providing a total dye concentration of 10 mg/l. Findings showed that the planted simulated ponds possess a significant (p < 0.05) potential for improving the outflow characteristics and eliminate dyes, ammonium-nitrogen (NH4-N), and nitrate-nitrogen (NO3-N) in all mixtures compared with the corresponding unplanted ponds. The removal of mixed dyes in planted ponds was mainly due to phyto-transformation and adsorption of BR46 with complete aromatic amine mineralisation. For ponds containing 2 mg/l of RB198 and 8 mg/l of BR46, removals were around 53%, which was significantly higher than those for other mixtures: 5 mg/l of RB198 and 5 mg/l of BR46 and 8 mg/l of RB198 and 2 mg/l of BR46 achieved only 41 and 26% removals, respectively. Dye mixtures stopped the growth of L. minor, and the presence of artificial wastewater reduced their development

Molecular Characterisation of Trimethoprim Resistance in Escherichia coli and Klebsiella pneumoniae during a Two Year Intervention on Trimethoprim Use

BACKGROUND: Trimethoprim resistance is increasing in Enterobacteriaceae. In 2004-2006 an intervention on trimethoprim use was conducted in Kronoberg County, Sweden, resulting in 85% reduction in trimethoprim prescriptions. We investigated the distribution of dihydrofolate reductase (dfr)-genes and integrons in Escherichia coli and Klebsiella pneumoniae and the effect of the intervention on this distribution. METHODOLOGY/PRINCIPAL FINDINGS: Consecutively isolated E. coli (n = 320) and K. pneumoniae (n = 54) isolates phenotypically resistant to trimethoprim were studied. All were investigated for the presence of dfrA1, dfrA5, dfrA7, dfrA8, dfrA12, dfrA14, dfrA17 and integrons class I and II. Isolates negative for the seven dfr-genes (n = 12) were also screened for dfr2d, dfrA3, dfrA9, dfrA10, dfrA24 and dfrA26. These genes accounted for 96% of trimethoprim resistance in E. coli and 69% in K. pneumoniae. The most prevalent was dfrA1 in both species. This was followed by dfrA17 in E. coli which was only found in one K. pneumoniae isolate. Class I and II Integrons were more common in E. coli (85%) than in K. pneumoniae (57%). The distribution of dfr-genes did not change during the course of the 2-year intervention. CONCLUSIONS/SIGNIFICANCE: The differences observed between the studied species in terms of dfr-gene and integron prevalence indicated a low rate of dfr-gene transfer between these two species and highlighted the possible role of narrow host range plasmids in the spread of trimethoprim resistance. The stability of dfr-genes, despite large changes in the selective pressure, indirectly suggests a low fitness cost of dfr-gene carriage

Fluorocarbon evaporative cooling developments for the ATLAS pixel and semiconductor tracking detectors

Heat transfer coefficients 2-5.103 Wm-2K-1 have been measured in a 3.6 mm I.D. heated tube dissipating 100 Watts - close to the full equivalent power (~110 W) of a barrel SCT detector "stave" - over a range of power dissipations and mass flows in the above fluids. Aspects of full-scale evaporative cooling circulator design for the ATLAS experiment are discussed, together with plans for future development

Accounting fraud, business failure and creative auditing: A microanalysis of the strange case of the Sunbeam Corporation

This article closely examines the Sunbeam Corporation’s path to failure and explores the reasons for its singularity. From the analysis of US fraud cases included in the UCLA-LoPucki Bankruptcy Research Database, this corporate case appears as an outlier. For Sunbeam, the time-lapse between fraud disclosure and its final bankruptcy is the longest of the entire sample; it is unique because of its length. This article uses a historical microanalysis to evaluate different hypotheses about the Sunbeam Corporation’s path to failure. The relationships between acquisitions and fraud, ‘scapegoat dynamics’ and ‘creative auditing’ are identified as the most relevant issues to be examined against a changing institutional context. The resulting reconstruction of the events provides unexpected insights and recommendations for future research on auditing and accounting fraud

A structure filter for the Eukaryotic Linear Motif Resource

<p>Abstract</p> <p>Background</p> <p>Many proteins are highly modular, being assembled from globular domains and segments of natively disordered polypeptides. Linear motifs, short sequence modules functioning independently of protein tertiary structure, are most abundant in natively disordered polypeptides but are also found in accessible parts of globular domains, such as exposed loops. The prediction of novel occurrences of known linear motifs attempts the difficult task of distinguishing functional matches from stochastically occurring non-functional matches. Although functionality can only be confirmed experimentally, confidence in a putative motif is increased if a motif exhibits attributes associated with functional instances such as occurrence in the correct taxonomic range, cellular compartment, conservation in homologues and accessibility to interacting partners. Several tools now use these attributes to classify putative motifs based on confidence of functionality.</p> <p>Results</p> <p>Current methods assessing motif accessibility do not consider much of the information available, either predicting accessibility from primary sequence or regarding any motif occurring in a globular region as low confidence. We present a method considering accessibility and secondary structural context derived from experimentally solved protein structures to rectify this situation. Putatively functional motif occurrences are mapped onto a representative domain, given that a high quality reference SCOP domain structure is available for the protein itself or a close relative. Candidate motifs can then be scored for solvent-accessibility and secondary structure context. The scores are calibrated on a benchmark set of experimentally verified motif instances compared with a set of random matches. A combined score yields 3-fold enrichment for functional motifs assigned to high confidence classifications and 2.5-fold enrichment for random motifs assigned to low confidence classifications. The structure filter is implemented as a pipeline with both a graphical interface via the ELM resource <url>http://elm.eu.org/</url> and through a Web Service protocol.</p> <p>Conclusion</p> <p>New occurrences of known linear motifs require experimental validation as the bioinformatics tools currently have limited reliability. The ELM structure filter will aid users assessing candidate motifs presenting in globular structural regions. Most importantly, it will help users to decide whether to expend their valuable time and resources on experimental testing of interesting motif candidates.</p

A Field Guide to Pandemic, Epidemic and Sporadic Clones of Methicillin-Resistant Staphylococcus aureus

In recent years, methicillin-resistant Staphylococcus aureus (MRSA) have become a truly global challenge. In addition to the long-known healthcare-associated clones, novel strains have also emerged outside of the hospital settings, in the community as well as in livestock. The emergence and spread of virulent clones expressing Panton-Valentine leukocidin (PVL) is an additional cause for concern. In order to provide an overview of pandemic, epidemic and sporadic strains, more than 3,000 clinical and veterinary isolates of MRSA mainly from Germany, the United Kingdom, Ireland, France, Malta, Abu Dhabi, Hong Kong, Australia, Trinidad & Tobago as well as some reference strains from the United States have been genotyped by DNA microarray analysis. This technique allowed the assignment of the MRSA isolates to 34 distinct lineages which can be clearly defined based on non-mobile genes. The results were in accordance with data from multilocus sequence typing. More than 100 different strains were distinguished based on affiliation to these lineages, SCCmec type and the presence or absence of PVL. These strains are described here mainly with regard to clinically relevant antimicrobial resistance- and virulence-associated markers, but also in relation to epidemiology and geographic distribution. The findings of the study show a high level of biodiversity among MRSA, especially among strains harbouring SCCmec IV and V elements. The data also indicate a high rate of genetic recombination in MRSA involving SCC elements, bacteriophages or other mobile genetic elements and large-scale chromosomal replacements

A Field Guide to Pandemic, Epidemic and Sporadic Clones of Methicillin-Resistant Staphylococcus aureus

In recent years, methicillin-resistant Staphylococcus aureus (MRSA) have become a truly global challenge. In addition to the long-known healthcare-associated clones, novel strains have also emerged outside of the hospital settings, in the community as well as in livestock. The emergence and spread of virulent clones expressing Panton-Valentine leukocidin (PVL) is an additional cause for concern. In order to provide an overview of pandemic, epidemic and sporadic strains, more than 3,000 clinical and veterinary isolates of MRSA mainly from Germany, the United Kingdom, Ireland, France, Malta, Abu Dhabi, Hong Kong, Australia, Trinidad & Tobago as well as some reference strains from the United States have been genotyped by DNA microarray analysis. This technique allowed the assignment of the MRSA isolates to 34 distinct lineages which can be clearly defined based on non-mobile genes. The results were in accordance with data from multilocus sequence typing. More than 100 different strains were distinguished based on affiliation to these lineages, SCCmec type and the presence or absence of PVL. These strains are described here mainly with regard to clinically relevant antimicrobial resistance- and virulence-associated markers, but also in relation to epidemiology and geographic distribution. The findings of the study show a high level of biodiversity among MRSA, especially among strains harbouring SCCmec IV and V elements. The data also indicate a high rate of genetic recombination in MRSA involving SCC elements, bacteriophages or other mobile genetic elements and large-scale chromosomal replacements