EU environmental principles: Implementation in Germany

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Differentielle Effekte von Prava- und Simvastatin auf das Lungenödem post reanimationem und die Endothelzellfunktion

Es konnte gezeigt werden, dass Pravastatin die Ausprägung eines Lungenödems post reanimationem abmildert. Zudem wirkt sich Pravastatin günstig auf die Endothelzellfunktion in vitro aus. Simvastatin hingegen wirkt sich negativ auf die Angiogenese in vitro aus und induziert als Ausdruck einer Inflammation hohe endotheliale COX-2-Proteinlevel

Preoperative plasma growth-differentiation factor-15 for prediction of acute kidney injury in patients undergoing cardiac surgery

Covariate plot of the predictions from the random forest model. Four variables are displayed. Within each box, the x-axis denotes plasma creatinine (Îźmol/l), the y-axis the probability of developing cardiac-surgery-associated acute kidney injury (CSA-AKI). Within each column of plots, the additive Euroscore increases from bottom to top (legend, right). Within each row of plots the growth-differentiation factor-15 (GDF-15) levels increase from left to right. Significant non-linear interaction takes place between GDF-15 and creatinine. Within each additive Euroscore category (row of plots), increases in GDF-15 (plots more to the right within each row) increase the probability of developing CSA-AKI. However, this effect is more prominent in patients with normal creatinine (x-axis label of each plot). (TIFF 3197 kb

Prospects for harnessing biocide resistance for bioremediation and detoxification

Prokaryotes in natural environments respond rapidly to high concentrations of chemicals and physical stresses. Exposure to anthropogenic toxic substancessuch as oil, chlorinated solvents, or antibioticsfavors the evolution of resistant phenotypes, some of which can use contaminants as an exclusive carbon source or as electron donors and acceptors. Microorganisms similarly adapt to extreme pH, metal, or osmotic stress. The metabolic plasticity of prokaryotes can thus be harnessed for bioremediation and can be exploited in a variety of ways, ranging from stimulated natural attenuation to bioaugmentation and from wastewater treatment to habitat restoration.We thank H. Stroo (Stroo Consulting) and C. Aziz (Ramboll) for providing photographs of bioaugmentation with OHRB, and H. Patzelt (Mazoon Environmental and Technological Services) for providing photographs of bioaugmentation with halophilic microorganisms. Funding: S.A., I.S.-A., and A.J.M.S. are supported by the Netherlands Ministry of Education, Culture and Science (project 024.002.002) and advanced ERC grant (project 323009). H.S. and S.A. were supported by a grant of BE-Basic-FES funds from the Dutch Ministry of Economic Affairs. H.S., J.R.v.d.M., and H.J.H. were supported by the European Commission (BACSIN, contract 211684; P4SB, contract 633962).info:eu-repo/semantics/publishedVersio

Isolation and characterization of <i>Magnetospirillum</i> sp strain 15-1 as a representative anaerobic toluene-degrader from a constructed wetland model

Previously, Planted Fixed-Bed Reactors (PFRs) have been used to investigate microbial toluene removal in the rhizosphere of constructed wetlands. Aerobic toluene degradation was predominant in these model systems although bulk redox conditions were hypoxic to anoxic. However, culture-independent approaches indicated also that microbes capable of anaerobic toluene degradation were abundant. Therefore, we aimed at isolating anaerobic-toluene degraders from one of these PFRs. From the obtained colonies which consisted of spirilli-shaped bacteria, a strain designated 15-1 was selected for further investigations. Analysis of its 16S rRNA gene revealed greatest similarity (99%) with toluene-degrading Magnetospirillum sp. TS-6. Isolate 15-1 grew with up to 0.5 mM of toluene under nitrate-reducing conditions. Cells reacted to higher concentrations of toluene by an increase in the degree of saturation of their membrane fatty acids. Strain 15-1 contained key genes for the anaerobic degradation of toluene via benzylsuccinate and subsequently the benzoyl-CoA pathway, namely bssA, encoding for the alpha subunit of benzylsuccinate synthase, bcrC for subunit C of benzoyl-CoA reductase and bamA for 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase. Finally, most members of a clone library of bssA generated from the PFR had highest similarity to bssA from strain 15-1. Our study provides insights about the physiological capacities of a strain of Magnetospirillum isolated from a planted system where active rhizoremediation of toluene is taking place

Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches

Aptamers are oligonucleotide ligands, either RNA or ssDNA, selected for high-affinity binding to molecular targets, such as small organic molecules, proteins or whole microorganisms. While reports of new aptamers are numerous, characterization of their specific interaction is often restricted to the affinity of binding (KD). Over the years, crystal structures of aptamer-protein complexes have only scarcely become available. Here we describe some relevant technical issues about the process of crystallizing aptamer-protein complexes and highlight some biochemical details on the molecular basis of selected aptamer-protein interactions. In addition, alternative experimental and computational approaches are discussed to study aptamer-protein interactions.

<i>Delftia</i> sp LCW, a strain isolated from a constructed wetland shows novel properties for dimethylphenol isomers degradation

BACKGROUND: Dimethylphenols (DMP) are toxic compounds with high environmental mobility in water and one of the main constituents of effluents from petro- and carbochemical industry. Over the last few decades, the use of constructed wetlands (CW) has been extended from domestic to industrial wastewater treatments, including petro-carbochemical effluents. In these systems, the main role during the transformation and mineralization of organic pollutants is played by microorganisms. Therefore, understanding the bacterial degradation processes of isolated strains from CWs is an important approach to further improvements of biodegradation processes in these treatment systems. RESULTS: In this study, bacterial isolation from a pilot scale constructed wetland fed with phenols led to the identification of Delftia sp. LCW as a DMP degrading strain. The strain was able to use the o-xylenols 3,4-DMP and 2,3-DMP as sole carbon and energy sources. In addition, 3,4-DMP provided as a co-substrate had an effect on the transformation of other four DMP isomers. Based on the detection of the genes, proteins, and the inferred phylogenetic relationships of the detected genes with other reported functional proteins, we found that the phenol hydroxylase of Delftia sp. LCW is induced by 3,4-DMP and it is responsible for the first oxidation of the aromatic ring of 3,4-, 2,3-, 2,4-, 2,5- and 3,5-DMP. The enzyme may also catalyze both monooxygenation reactions during the degradation of benzene. Proteome data led to the identification of catechol meta cleavage pathway enzymes during the growth on ortho DMP, and validated that cleavage of the aromatic rings of 2,5- and 3,5-DMPs does not result in mineralization. In addition, the tolerance of the strain to high concentrations of DMP, especially to 3,4-DMP was higher than that of other reported microorganisms from activated sludge treating phenols. CONCLUSIONS: LCW strain was able to degraded complex aromatics compounds. DMPs and benzene are reported for the first time to be degraded by a member of Delftia genus. In addition, LCW degraded DMPs with a first oxidation of the aromatic rings by a phenol hydroxylase, followed by a further meta cleavage pathway. The higher resistance to DMP toxicity, the ability to degrade and transform DMP isomers and the origin as a rhizosphere bacterium from wastewater systems, make LCW a suitable candidate to be used in bioremediation of complex DMP mixtures in CWs systems

Calculation of partial isotope incorporation into peptides measured by mass spectrometry

<p>Abstract</p> <p>Background</p> <p>Stable isotope probing (SIP) technique was developed to link function, structure and activity of microbial cultures metabolizing carbon and nitrogen containing substrates to synthesize their biomass. Currently, available methods are restricted solely to the estimation of fully saturated heavy stable isotope incorporation and convenient methods with sufficient accuracy are still missing. However in order to track carbon fluxes in microbial communities new methods are required that allow the calculation of partial incorporation into biomolecules.</p> <p>Results</p> <p>In this study, we use the characteristics of the so-called 'half decimal place rule' (HDPR) in order to accurately calculate the partial¹³C incorporation in peptides from enzymatic digested proteins. Due to the clade-crossing universality of proteins within bacteria, any available high-resolution mass spectrometry generated dataset consisting of tryptically-digested peptides can be used as reference.</p> <p>We used a freely available peptide mass dataset from <it>Mycobacterium tuberculosis </it>consisting of 315,579 entries. From this the error of estimated versus known heavy stable isotope incorporation from an increasing number of randomly drawn peptide sub-samples (100 times each; no repetition) was calculated. To acquire an estimated incorporation error of less than 5 atom %, about 100 peptide masses were needed. Finally, for testing the general applicability of our method, peptide masses of tryptically digested proteins from <it>Pseudomonas putida </it>ML2 grown on labeled substrate of various known concentrations were used and¹³C isotopic incorporation was successfully predicted. An easy-to-use script <abbrgrp><abbr bid="B1">1</abbr></abbrgrp> was further developed to guide users through the calculation procedure for their own data series.</p> <p>Conclusion</p> <p>Our method is valuable for estimating¹³C incorporation into peptides/proteins accurately and with high sensitivity. Generally, our method holds promise for wider applications in qualitative and especially quantitative proteomics.</p

The BRCA2 c.68-7T > A variant is not pathogenic: A model for clinical calibration of spliceogenicity.

Although the spliceogenic nature of the BRCA2 c.68-7T>A variant has been demonstrated, its association with cancer risk remains ontroversial. In this study, we accurately quantified by real-time PCR and digital PCR the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636 individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families. Exon 3 exclusion rate was 4.5-fold higher in variant carriers (13%) than controls (3%), indicating an exclusion rate for the c.68-7T>A allele of approximately 20%. The posterior probability of pathogenicity was 7.44 x 10-115. There was neither evidence for increased risk of breast cancer (OR 1.03; 95% CI 0.86-1.24), nor for a deleterious effect of the variant when co-occurring with pathogenic variants. Our data provide for the first time robust evidence of the non-pathogenicity of the BRCA2 c.68-7T>A. Genetic and quantitative transcript analyses together inform the threshold for the ratio between functional and altered BRCA2 isoforms compatible with normal cell function. These findings might be exploited to assess the relevance for cancer risk of other BRCA2 spliceogenic variants