Errata corrige

Abstract

Ecological research on extreme environments can be applied to exobiological problems such as the question of life on Mars. If life forms (fossil or extant) are found on Mars, their study will help to solve fundamental questions about the nature of life on Earth. Extreme environments that are beyond the range of adaptability of their inhabitants are defined as “absolute extreme.” Such environments can serve as terrestrial models for the last stages of life in the history of Mars, when the surface cooled down and atmosphere and water disappeared. The cryptoendolithic microbial community in porous rocks of the Ross Desert in Antarctica and the microbial mats at the bottom of frozen Antarctic lakes are such examples. The microbial communities of Siberian permafrost show that, in frozen but stable communities, long-term survival is possible. In the context of terraforming Mars, selected microorganisms isolated from absolute extreme environments are considered for use in creation of a biological carbon cycle.     

Comparative Study of Plasmonic Properties of Cysteine-Functionalized Gold and Silver Nanoparticle Aggregates

The absorptance spectra of gold and silver nanoparticle (NP) aqueous dispersions were measured by UV–visible spectroscopy and computed numerically by finite element method. Both NPs were functionalized by l-cysteine amino acid (Cys) in order to develop aggregate-based localized surface plasmon resonance biosensors. Absorptance spectra measured at an analogous pH value of ～4.9 were compared, where Au-Cys conjugates have moderately split spectra with two commensurate maxima, while Ag-Cys conjugates exhibit the most pronounced secondary peak according to the highest degree of aggregation. The purpose of our theoretical study was to determine the simplest linear chain-like and wavy aggregate geometries, which result in maxima matching the measured peaks. The aggregates were characterized by N number and d diameter of NPs, g gap between the NPs, and t thickness of the l-cysteine covering. By tuning the angle of incidence and E -field oscillation direction in p-polarized light with respect to the aggregates, the contribution of longitudinal and transversal modes was varied. The comparison of measurements and computations revealed that spectra measured on bioconjugate dispersions include effects of numerous aggregates with various geometries, illuminated from different directions and are influenced by inter-aggregate coupling. Inspecting the normalized E -field distribution surrounding the aggregates, it was shown that fundamentally different multipolar modes can be identified at primary and secondary absorptance maxima, due to coupled plasmonic resonances on NPs.     

Metschnikowia Species Share a Pool of Diverse rRNA Genes Differing in Regions That Determine Hairpin-Loop Structures and Evolve by Reticulation

Modern taxonomy of yeasts is mainly based on phylogenetic analysis of conserved DNA and protein sequences. By far the most frequently used sequences are those of the repeats of the chromosomal rDNA array. It is generally accepted that the rDNA repeats of a genome have identical sequences due to the phenomenon of sequence homogenisation and can thus be used for identification and barcoding of species. Here we show that the rDNA arrays of the type strains of Metschnikowia andauensis and M. fructicola are not homogenised. Both have arrays consisting of diverse repeats that differ from each other in the D1/D2 domains by up to 18 and 25 substitutions. The variable sites are concentrated in two regions that correspond to back-folding stretches of hairpin loops in the predicted secondary structure of the RNA molecules. The substitutions do not alter significantly the overall hairpin-loop structure due to wobble base pairing at sites of C-T transitions and compensatory mutations in the complementary strand of the hairpin stem. The phylogenetic and network analyses of the cloned sequences revealed that the repeats had not evolved in a vertical tree-like way but reticulation might have shaped the rDNA arrays of both strains. The neighbour-net analysis of all cloned sequences of the type strains and the database sequences of different strains further showed that these species share a continuous pool of diverse repeats that appear to evolve by reticulate evolution.     

Tumor movements detected by multi-slice CT-based image fusion in the radiotherapy of lung cancer patients

The aim of our study was to detect the possible uncertainties arising from tumor movements in the daily routine treatment planning, in extreme breathing conditions. Ten patients with lung cancer were enrolled into the study. According to tumor location, five patients had peripheral and five had central tumor. After the normal planning CT scan, two more scans were made with the same CT parameters in maximal exhalation and in maximal inhalation. For planning, the normal breathing scans were used with the fusion of the maximal inhalation and maximal exhalation scans. After the fusion in all breathing phases the gross tumor volumes were contoured (GTV1, GTV2, GTV3). Around the GTV1 (normal breathing phase GTV) 3 planning target volumes (PTV) were generated with the margin of 0.5 cm, 1.5 cm and 2.5 cm (PTV1, PTV2, PTV3). Individual plans were generated to all PTVs. All GTV volumes were registered. In all cases volume deviations were registered in different breathing phases (min: 1.5%, max: 35.6%). For GTV coverage comparison the coverage index (CI) was used. In case of extreme breathing conditions, using 0.5 cm margin was sufficient to reach good coverage for central tumors. For peripheral tumors 1.5 cm margin had to be used for the acceptable coverage (CI: 0.85-1.00). In our study, extreme breathing conditions were analyzed. According to our results, CT scans used in the daily routine do not exactly represent the tumor midposition and the true tumor volume. Due to breathing synchronous tumor movements, 0.5 cm margin must be used for planning in central location. In peripheral tumors wider margin should be used.     

Cystein cathepsin and Hsp90 activities determine the balance between apoptotic and necrotic cell death pathways in caspase-compromised U937 cells

Caspase-inhibited cells induced to die may exhibit the traits of either apoptosis or necrosis or both, simultaneously. However, mechanisms regulating the commitment to these distinct forms of cell death are barely identified. We found that staurosporine induced both apoptotic and necrotic traits in U937 cells exposed to the caspase inhibitor benzyloxycarbonyl-Val-Ala-DL-Asp(OMe)-fluoromethylketone. Morphology and flow cytometry revealed that individual cells exhibited either apoptotic or necrotic traits, but not the mixed phenotype. Inhibition of cathepsin activity by benzyloxycarbonyl-Phe-Ala-fluoromethylketone rendered caspase-compromised cells resistant to staurosporine-induced apoptosis, but switched the cell death form to necrosis. Inhibition of heat shock protein 90 kDa (Hsp90) chaperon activity by geldanamycin conferred resistance to necrosis in caspase-compromised cells but switched the cell death form to apoptosis. Combination of benzyloxycarbonyl-Phe-Ala-fluoromethylketone and geldanamycin halted the onset of both forms of cell death by saving mitochondrial trans-membrane potential and preventing acidic volume (lysosomes) loss. These effects of benzyloxycarbonyl-Phe-Ala-fluoromethylketone and/or geldanamycin on cell death were restricted to caspase-inhibited cells exposed to staurosporine but influenced neither only the staurosporine-provoked apoptosis nor hydrogen peroxide (H2O2)-generated necrosis. Our results demonstrate that the staurosporine-induced death pathway bifurcates in caspase-compromised cells and commitment to apoptotic or necrotic phenotypes depends on cathepsin protease or Hsp90 chaperon activities.     

Radiative and non-radiative charge recombination pathways in Photosystem II studied by thermoluminescence and chlorophyll fluorescence in the cyanobacterium Synechocystis 6803

The mechanism of charge recombination was studied in Photosystem II by using flash induced chlorophyll fluorescence and thermoluminescence measurements. The experiments were performed in intact cells of the cyanobacterium Synechocystis 6803 in which the redox properties of the primary pheophytin electron acceptor, Phe, the primary electron donor, P(680), and the first quinone electron acceptor, Q(A), were modified. In the D1Gln130Glu or D1His198Ala mutants, which shift the free energy of the primary radical pair to more positive values, charge recombination from the S(2)Q(A)(-) and S(2)Q(B)(-) states was accelerated relative to the wild type as shown by the faster decay of chlorophyll fluorescence yield, and the downshifted peak temperature of the thermoluminescence Q and B bands. The opposite effect, i.e. strong stabilization of charge recombination from both the S(2)Q(A)(-) and S(2)Q(B)(-) states was observed in the D1Gln130Leu or D1His198Lys mutants, which shift the free energy level of the primary radical pair to more negative values, as shown by the retarded decay of flash induced chlorophyll fluorescence and upshifted thermoluminescence peak temperatures. Importantly, these mutations caused a drastic change in the intensity of thermoluminescence, manifested by 8- and 22-fold increase in the D1Gln130Leu and D1His198Lys mutants, respectively, as well as by a 4- and 2.5-fold decrease in the D1Gln130Glu and D1His198Ala mutants, relative to the wild type, respectively. In the presence of the electron transport inhibitor bromoxynil, which decreases the redox potential of Q(A)/Q(A)(-) relative to that observed in the presence of DCMU, charge recombination from the S(2)Q(A)(-) state was accelerated in the wild type and all mutant strains. Our data confirm that in PSII the dominant pathway of charge recombination goes through the P(680)(+)Phe(-) radical pair. This indirect recombination is branched into radiative and non-radiative pathways, which proceed via repopulation of P(680)(*) from (1)[P(680)(+)Ph(-)] and direct recombination of the (3)[P(680)(+)Ph(-)] and (1)[P(680)(+)Ph(-)] radical states, respectively. An additional non-radiative pathway involves direct recombination of P(680)(+)Q(A)(-). The yield of these charge recombination pathways is affected by the free energy gaps between the Photosystem II electron transfer components in a complex way: Increase of DeltaG(P(680)(*)<-->P(680)(+)Phe(-)) decreases the yield of the indirect radiative pathway (in the 22-0.2% range). On the other hand, increase of DeltaG(P(680)(+)Phe(-)<-->P(680)(+)Q(A)(-)) increases the yield of the direct pathway (in the 2-50% range) and decreases the yield of the indirect non-radiative pathway (in the 97-37% range).     

New validated method for piracetam HPLC determination in human plasma

The new method for HPLC determination of piracetam in human plasma was developed and validated by a new approach. The simple determination by UV detection was performed on supernatant, obtained from plasma, after proteins precipitation with perchloric acid. The chromatographic separation of piracetam under a gradient elution was achieved at room temperature with a RP-18 LiChroSpher 100 column and aqueous mobile phase containing acetonitrile and methanol. The quantitative determination of piracetam was performed at 200 nm with a lower limit of quantification LLQ=2 microg/ml. For this limit, the calculated values of the coefficient of variation and difference between mean and the nominal concentration are CV%=9.7 and bias%=0.9 for the intra-day assay, and CV%=19.1 and bias%=-7.45 for the between-days assay. For precision, the range was CV%=1.8/11.6 in the intra-day and between-days assay, and for accuracy, the range was bias%=2.3/14.9 in the intra-day and between-days assay. In addition, the stability of piracetam in different conditions was verified. Piracetam proved to be stable in plasma during 4 weeks at -20 degrees C and for 36 h at 20 degrees C in the supernatant after protein precipitation. The new proposed method was used for a bioequivalence study of two medicines containing 800 mg piracetam.     

Highly potent dUTPase inhibition by a bacterial repressor protein reveals a novel mechanism for gene expression control

Transfer of phage-related pathogenicity islands of Staphylococcus aureus (SaPI-s) was recently reported to be activated by helper phage dUTPases. This is a novel function for dUTPases otherwise involved in preservation of genomic integrity by sanitizing the dNTP pool. Here we investigated the molecular mechanism of the dUTPase-induced gene expression control using direct techniques. The expression of SaPI transfer initiating proteins is repressed by proteins called Stl. We found that Φ11 helper phage dUTPase eliminates SaPIbov1 Stl binding to its cognate DNA by binding tightly to Stl protein. We also show that dUTPase enzymatic activity is strongly inhibited in the dUTPase:Stl complex and that the dUTPase:dUTP complex is inaccessible to the Stl repressor. Our results disprove the previously proposed G-protein-like mechanism of SaPI transfer activation. We propose that the transfer only occurs if dUTP is cleared from the nucleotide pool, a condition promoting genomic stability of the virulence elements.     

The Strong In Vivo Anti-Tumor Effect of the UIC2 Monoclonal Antibody Is the Combined Result of Pgp Inhibition and Antibody Dependent Cell-Mediated Cytotoxicity

P-glycoprotein (Pgp) extrudes a large variety of chemotherapeutic drugs from the cells, causing multidrug resistance (MDR). The UIC2 monoclonal antibody recognizes human Pgp and inhibits its drug transport activity. However, this inhibition is partial, since UIC2 binds only to 10–40% of cell surface Pgps, while the rest becomes accessible to this antibody only in the presence of certain substrates or modulators (e.g. cyclosporine A (CsA)). The combined addition of UIC2 and 10 times lower concentrations of CsA than what is necessary for Pgp inhibition when the modulator is applied alone, decreased the EC₅₀ of doxorubicin (DOX) in KB-V1 (Pgp⁺) cells in vitro almost to the level of KB-3-1 (Pgp^-) cells. At the same time, UIC2 alone did not affect the EC₅₀ value of DOX significantly. In xenotransplanted severe combined immunodeficient (SCID) mice co-treated with DOX, UIC2 and CsA, the average weight of Pgp⁺ tumors was only ∼10% of the untreated control and in 52% of these animals we could not detect tumors at all, while DOX treatment alone did not decrease the weight of Pgp⁺ tumors. These data were confirmed by visualizing the tumors in vivo by positron emission tomography (PET) based on their increased ¹⁸FDG accumulation. Unexpectedly, UIC2+DOX treatment also decreased the size of tumors compared to the DOX only treated animals, as opposed to the results of our in vitro cytotoxicity assays, suggesting that immunological factors are also involved in the antitumor effect of in vivo UIC2 treatment. Since UIC2 binding itself did not affect the viability of Pgp expressing cells, but it triggered in vitro cell killing by peripheral blood mononuclear cells (PBMCs), it is concluded that the impressive in vivo anti-tumor effect of the DOX-UIC2-CsA treatment is the combined result of Pgp inhibition and antibody dependent cell-mediated cytotoxicity (ADCC).