Responsive microsecond-lifetime photoluminescent probes for analysis of protein kinases and their inhibitors

Responsive ARC-Lum probes were used for measurement of the concentration of active protein kinases (PKs) and determination of affinity of inhibitors of PKs. ARC-Lum probes incorporate thiophene or a selenophene heterocycle and a fluorophore conjugated to the lysine residue in the peptide fragment. In the complex with a PK, ARC-Lum probes emit long-lifetime (microsecond-scale) luminescence at the emission wavelengths of the fluorescent label if the complex is illuminated at the excitation wavelength of the thiophene- or selenophene-containing phosphorescence donors. Bisubstrate ARC-Lum probes bind with sub-nanomolar affinity with several PKs of the AGC group. This article is part of a Special Issue entitled: Inhibitors of Protein Kinases (2012).     

Intestinal lactoflora in Estonian and Norwegian patients with antibiotic associated diarrhea

The disruption of intestinal microbiota is an important risk factor for the development of Clostridium difficile caused antibiotic associated diarrhea (AAD). The role of intestinal lactoflora in protection against C. difficile is unclear. Fecal samples (n = 74) from AAD patients were investigated for C. difficile and lactobacilli by culture and real-time PCR. Lactobacilli were identified by enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) and sequencing of 16S rRNA. In C. difficile negative cases we found somewhat higher counts of intestinal Lactobacilli (5.02 vs. 2.15 CFU log₁₀/g; p = 0.053) by culture and more frequently Lactobacillus plantarum (33.3% vs. 9.4%; p = 0.03) as compared with positive ones. Results of total counts of lactobacilli comparing Estonian and Norwegian samples were conflicting by culture and PCR. We found higher colonization of Norwegian AAD patients with L. plantarum (21% vs. 5%, p = 0.053) and Estonians with Lactobacillus gasseri (19% vs. 2%, p = 0.023). Particular lactobacilli (e.g. L. plantarum) may have a role in protection against C. difficile, whereas the meaning of total counts of lactobacilli remains questionable. In different persons and nations, different lactobacilli species may have a protective role against C. difficile.     

The Rcs phosphorelay modulates the expression of plant cell wall degrading enzymes and virulence in Pectobacterium carotovorum ssp. carotovorum

Production of plant cell wall degrading enzymes, the major virulence factors of soft-rot Pectobacterium species, is controlled by many regulatory factors. Pectobacterium carotovorum ssp. carotovorum SCC3193 encodes an Rcs phosphorelay system that involves two sensor kinases, RcsC(Pcc) and RcsD(Pcc), and a response regulator RcsB(Pcc) as key components of this system, and an additional small lipoprotein RcsF(Pcc). This study indicates that inactivation of rcsC(Pcc), rcsD(Pcc) and rcsB(Pcc) enhances production of virulence factors with the highest effect detected for rcsB(Pcc). Interestingly, mutation of rcsF(Pcc) has no effect on virulence factors synthesis. These results suggest that in SCC3193 a parallel phosphorylation mechanism may activate the RcsB(Pcc) response regulator, which acts as a repressor suppressing the plant cell wall degrading enzyme production. Enhanced production of virulence factors in Rcs mutants is more pronounced when bacteria are growing in the absence of plant signal components.     

FRET-based screening assay using small-molecule photoluminescent probes in lysate of cells overexpressing RFP-fused protein kinases

An assay was developed for the characterization of protein kinase inhibitors in lysates of mammalian cells based on the measurement of FRET between overexpressed red fluorescent protein (TagRFP)-fused protein kinases (PKs) and luminophore-labeled small-molecule inhibitors (ARC-Photo probes). Two types of the assay, one using TagRFP as the photoluminescence donor together with ARC-Photo probes containing a red fluorophore dye as acceptor, and the other using TagRFP as the acceptor fluorophore in combination with a terbium cryptate-based long-lifetime photoluminescence donor, were used for FRET-based measurements in lysates of the cells overexpressing TagRFP-fused PKs. The second variant of the assay enabled the performance of the measurements under time-resolved conditions that led to substantially higher values of the signal/background ratio and further improved the reliability of the assay.     

Hybrid ecosystems can contribute to local biodiversity conservation

Calcareous grasslands have become severely threatened habitats in Europe. The aim of this study was to investigate the changes in plant species richness, and functional and phylogenetic diversity in northern Estonian calcareous (alvar) grasslands resampled after 90 years of land-use change. Functional traits characterizing species that have benefited most from decreased habitat area and altered environmental conditions, and additional species that can potentially inhabit the remaining grassland patches were identified. Also changes in the relative amount of habitat-specific species were studied to detect a possible decrease in habitat integrity. Although grasslands in the studied region had lost most of their original area (~90 %), species richness had substantially increased due to invasion by more competitive, nutrient-demanding native species. Functional diversity generally increased, whereas phylogenetic diversity showed no response to altered conditions. Overall, these grasslands have lost their integrity as calcareous grassland habitat type in the region, because the relative amount of habitat-specific characteristic species has declined significantly. However, although the grasslands have transformed to a ‘hybrid’ habitat type and restoration to their previous state is likely not reasonable, such degraded species-rich grassland fragments can still be recognized as important habitats to preserve high local biodiversity and several characteristic species of calcareous grasslands. As current landscapes consist of an increasing number of hybrid and novel communities, new tools to supplement traditional conservation or restoration practices are necessary to recognize and maintain regions and habitats of high local biodiversity.     

Alternatively activated macrophages regulate extracellular levels of the hormone placental lactogen via receptor-mediated uptake and transcytosis

Alternatively activated (M2) macrophages regulate immune responses and tissue remodelling. In many tissues including placenta, M2 express stabilin-1, a multidomain protein that exerts a dual role as a scavenger receptor for acetylated low density lipoprotein (acLDL) and SPARC (secreted protein acidic and rich in cysteine) and as an intracellular cargo carrier for SI-CLP. Using yeast two-hybrid screening, we identified the developmental hormone placental lactogen (PL) as a novel ligand of stabilin-1. In Chinese hamster ovary-stabilin-1 cells and M2, FACS and confocal microscopy demonstrated that stabilin-1 mediates internalization and endosomal sorting of PL. In M2 macrophages, PL was partially degraded in lysosomes; part of PL escaped degradation and was delivered to novel PL+ storage vesicles lacking endosomal/lysosomal markers. During formation, PL+ vesicles underwent transient interaction with the trans-Golgi network (TGN). Upon placement of PL-loaded M2 into PL-free medium, PL was secreted into the supernatant. Leupeptin, an inhibitor of lysosomal hydrolases, reduced PL degradation, enhanced sorting of PL into the TGN/storage vesicle pathway and increased PL secretion. Thus, processing of PL in M2 macrophages occurs either by the classical lysosomal pathway or by a novel TGN-associated trans-secretory pathway. Macrophages isolated from human placental villi efficiently endocytosed PL-FITC and transported it to the storage vesicles. Our data show that extracellular PL levels are determined by uptake, degradation, storage, and release in M2. During pregnancy PL concentration reaches 10 microg/ml in maternal circulation and stays below 0.5 microg/ml in fetal circulation. We propose that stabilin-1-positive macrophages determine the difference in PL levels between maternal and fetal circulation.     

Sulfate-reducing anaerobic ammonium oxidation as a potential treatment method for high nitrogen-content wastewater

After sulfate-reducing ammonium oxidation (SRAO) was first assumed in 2001, several works have been published describing this process in laboratory-scale bioreactors or occurring in the nature. In this paper, the SRAO process was performed using reject water as a substrate for microorganisms and a source of NH(4) (+), with SO(4) (2-) being added as an electron acceptor. At a moderate temperature of 20°C in a moving bed biofilm reactor (MBBR) sulfate reduction along with ammonium oxidation were established. In an upflow anaerobic sludge blanket reactor (UASBR) the SRAO process took place at 36°C. Average volumetric TN removal rates of 0.03?kg-N/m3/day in the MBBR and 0.04?kg-N/m3/day in the UASBR were achieved, with long-term moderate average removal efficiencies, respectively. Uncultured bacteria clone P4 and uncultured planctomycete clone Amx-PAn30 were detected from the biofilm of the MBBR, from sludge of the UASBR uncultured Verrucomicrobiales bacterium clone De2102 and Uncultured bacterium clone ATB-KS-1929 were found also. The stoichiometrical ratio of NH(4) (+) removal was significantly higher than could be expected from the extent of SO(4) (2-) reduction. This phenomenon can primarily be attributed to complex interactions between nitrogen and sulfur compounds and organic matter present in the wastewater. The high NH(4) (+) removal ratio can be attributed to sulfur-utilizing denitrification/denitritation providing the evidence that SRAO is occurring independently and is not a result of sulfate reduction and anammox. HCO(3) (-) concentrations exceeding 1,000?mg/l were found to have an inhibiting effect on the SRAO process. Small amounts of hydrazine were naturally present in the reaction medium, indicating occurrence of the anammox process. Injections of anammox intermediates, hydrazine and hydroxylamine, had a positive effect on SRAO process performance, particularly in the case of the UASBR.