A Possible Role for Short Introns in the Acquisition of Stroma-Targeting Peptides in the Flagellate Euglena gracilis

The chloroplasts of Euglena gracilis bounded by three membranes arose via secondary endosymbiosis of a green alga in a heterotrophic euglenozoan host. Many genes were transferred from symbiont to the host nucleus. A subset of Euglena nuclear genes of predominately symbiont, but also host, or other origin have obtained complex presequences required for chloroplast targeting. This study has revealed the presence of short introns (41–93 bp) either in the second half of presequence-encoding regions or shortly downstream of them in nine nucleus-encoded E. gracilis genes for chloroplast proteins (Eno29, GapA, PetA, PetF, PetJ, PsaF, PsbM, PsbO, and PsbW). In addition, the E. gracilis Pbgd gene contains two introns in the second half of presequence-encoding region and one at the border of presequence-mature peptide-encoding region. Ten of 12 introns present within presequence-encoding regions or shortly downstream of them identified in this study have typical eukaryotic GT/AG borders, are T-rich, 45–50 bp long, and pairwise sequence identities range from 27 to 61%. Thus single recombination events might have been mediated via these cis-spliced introns. A double crossing over between these cis-spliced introns and trans-spliced introns present in 5′-UTRs of Euglena nuclear genes is also likely to have occurred. Thus introns and exon-shuffling could have had an important role in the acquisition of chloroplast targeting signals in E. gracilis. The results are consistent with a late origin of photosynthetic euglenids.     

Indicating Soil Acidity Using Vegetation Relevés in Spatially Limited Areas – Case Study from the Považský Inovec, Slovakia

A fine-scaled approach for predicting soil acidity using plant species in a spatially limited area (?epú?ky Nature Reserve, Slovakia) is presented here. This approach copes with some specific limitations: i) a limited pool of vegetation data may make the predictions too sensitive to the lack of species information, and ii) the predictions may be sensitive to the narrow pH gradient. Vegetation relevés and soil reaction (pH-H₂O and pH-CaCl₂) were systematically recorded. A set of species indicator values and amplitudes was calibrated with physical pH data using the Weighted Averaging (WA), HOF modelling and Non-Metric Multidimensional Scaling (NMDS) methods, along with Ellenberg indicator values. Two prediction methods were tested: i) WA and ii) Amplitude Overlap (AO). WA prediction with Ellenberg’s and WA-calibrated species indicator values were the most powerful technique (R ²?=?68.4–68.7% and 53.4–59.1% for pH-CaCl₂ and pH-H₂O, respectively). WA-prediction with HOF-based indicator values was less effective (R ²?=?61.7% and 50.7%) due to the decrease in species’ information because with HOF modelling many species are assumed indifferent or too rare. The NMDS method does not bring any significant gain to the calibration, though it avoids the lack of species information. The AO method was proven to be less powerful under studied circumstances, because it is sensitive both to the lack of species’ information and to the truncation of species responses. The results prove that a spatially explicit approach can provide significant indices to estimate changes in soil acidity – pH-CaCl₂ better than pH-H₂O.     

Physiological evidence for the involvement of peptide YY in the regulation of energy homeostasis in humans

Objective: To explore the potential role of the endogenous peptide YY (PYY) in the long‐term regulation of body weight and energy homeostasis. Research Methods and Procedures: Fasting and postprandial plasma PYY concentrations were measured after an overnight fast and 30 to 180 minutes after a standardized meal in 29 (21 men/8 women) non‐diabetic subjects, 16 of whom had a follow‐up visit 10.8 ± 1.4 months later. Ratings of hunger and satiety were collected using visual analog scales. Resting metabolic rate (RMR) (15‐hour RMR) and respiratory quotient (RQ) were assessed using a respiratory chamber. Results: Fasting PYY concentrations were negatively correlated with various markers of adiposity and negatively associated with 15‐hour RMR (r = ?0.46, p = 0.01). Postprandial changes in PYY (area under the curve) were positively associated with postprandial changes in ratings of satiety (r = 0.47, p = 0.01). The maximal PYY concentrations achieved after the meal (peak PYY) were negatively associated with 24‐hour RQ (r = ?0.41, p = 0.03). Prospectively, the peak PYY concentrations were negatively associated with changes in body weight (r = ?0.58, p = 0.01). Discussion: Our data indicate that the endogenous PYY may be involved in the long‐term regulation of body weight. It seems that this long‐term effect was not exclusively driven by the modulation of food intake but also by the control of energy expenditure and lipid metabolism.     

Gabčíkovo River Barrage System: The Ecological Disaster and Economic Calamity for the Inland Delta of the Middle Danube

The Gabíkovo Water Project (GWP), a major construction of damming and canalizing on the upper part of the middle Danube was completed and put into operation in October 1992. It destroyed most of the 230km2 of wetlands. Two-thirds of the wetlands are becoming dry, discontinuous or severely changed which will ultimately destroy the original ecosystem and lead to a decline in biological diversity. Based upon detailed knowledge of the limnology and fish biology of this section of the Danube River the effects of the GWP were predicted as early as 1964. All the recent post-construction impact studies of the GWP report few negative effects and so the planners and builders defend the project. It is difficult to believe that all sides in the current GWP legal controversy have overlooked the most important point. Any effects immediately after construction are purely transitory. A large body of published empirical and theoretical information clearly shows that the mostly negative effects of such large water projects become apparent only several years or decades after construction. The value of the destroyed wetland and river floodplain is at least US $ 520 million per year, and clearly incriminates the VV (Vodohospodárska výstavba) of fraudulent representation of 'benefits'. The enormous flood of devious publications glorifying the work of the VV in recent years should be interpreted as a cover up for the bad conscience of the builders. The International Court of Justice in the Hague delivered its judgement on the GWP case on 25 September 1997. There were no winners in this case as both Slovakia and Hungary were said to have acted inappropriately: it was illegal for Hungary to stop its part on the project according to the treaty of 1977, and Slovakia had no right to put Gabíkovo into operation unilaterally. As the Court dealt little with the social, environmental and economic aspects of the GWP, the true losers became the inland delta of the Danube, the last large wetland of Europe, and the local inhabitants.     

Combined affinity and rate constant distributions of ligand populations from experimental surface binding kinetics and equilibria

The present article considers the influence of heterogeneity in a mobile analyte or in an immobilized ligand population on the surface binding kinetics and equilibrium isotherms. We describe strategies for solving the inverse problem of calculating two-dimensional distributions of rate and affinity constants from experimental data on surface binding kinetics, such as obtained from optical biosensors. Although the characterization of a heterogeneous population of analytes binding to uniform surface sites may be possible under suitable experimental conditions, computational difficulties currently limit this approach. In contrast, the case of uniform analytes binding to heterogeneous populations of surface sites is computationally feasible, and can be combined with Tikhonov-Phillips and maximum entropy regularization techniques that provide the simplest distribution that is consistent with the data. The properties of this ligand distribution analysis are explored with several experimental and simulated data sets. The resulting two-dimensional rate and affinity constant distributions can describe well experimental kinetic traces measured with optical biosensors. The use of kinetic surface binding data can give significantly higher resolution than affinity distributions from the binding isotherms alone. The shape and the level of detail of the calculated distributions depend on the experimental conditions, such as contact times and the concentration range of the analyte. Despite the flexibility introduced by considering surface site distributions, the impostor application of this model to surface binding data from transport limited binding processes or from analyte distributions can be identified by large residuals, if a sufficient range of analyte concentrations and contact times are used. The distribution analysis can provide a rational interpretation of complex experimental surface binding kinetics, and provides an analytical tool for probing the homogeneity of the populations of immobilized protein.     

Induced cell death of preimplantation mouse embryos cultured in vitro evaluated by comet assay

The occurrence of apoptosis in mouse preimplantation embryos was analyzed using DNA staining (Hoechst 33342, PI) for the visualization of nuclear changes and by the comet assay, a single-cell gel electrophoresis assay, modified for the analysis of blastocysts. Mouse preimplantation embryos isolated 56 h after superovulation were cultured in vitro for 64 h. Apoptosis was induced by treatment with camptothecin and actinomycin D during the first 15 h of culture. After culture in vitro, a number of embryos were stained and analyzed using morphological criteria. The remaining embryos were examined using the comet assay for the detection of DNA fragmentation. The proportion of damaged embryos in experimental groups, in comparison to controls, was dependent on the dose of apoptosis inductor. At high doses (camptothecin, microg/ml and actinomycin D, 0.05 microg/ml) over 90% (chi-square test, P<0.001) of embryos had apoptotic comets, at medium doses (camptothecin, 0.01 microg/ml and actinomycin D, 0.005 microg/ml) comets appeared only in 30-70% of embryos (camptothecin, P<0.01 and actinomycin D, P<0.001). At low doses (camptothecin, 0.001 microg/ml and actinomycin D, 0.0005 microg/ml) the increase in damaged embryos was not statistically significant. Hoechst/PI staining showed a higher percentage of damaged blastomeres at high doses. Morphological changes correlated with the outcome of the comet assay. Our results show that comet assay is an appropriate method for studying apoptosis in preimplantation embryos, and it appears to be more sensitive than the classically used morphological analyses.     

Molecular cloning and 3D structure prediction of the first raw-starch-degrading glucoamylase without a separate starch-binding domain

Raw-starch-degrading glucoamylases have been known as multidomain enzymes consisting of a catalytic domain connected to a starch-binding domain (SBD) by an O-glycosylated linker region. A molecular genetics approach has been chosen to find structural differences between two related glucoamylases, raw-starch-degrading Glm and nondegrading Glu, from the yeasts Saccharomycopsis fibuligera IFO 0111 and HUT 7212, respectively. We have found that Glm and Glu show a high primary (77%) and tertiary structure similarity. Glm, although possessing a good ability for raw starch degradation, did not show consensus amino acid residues to any SBD found in glucoamylases or other amylolytic enzymes. Raw starch binding and digestion by Glm must thus depend on the existence of a site(s) lying within the intact protein which lacks a separate SBD. The enzyme represents a structurally new type of raw-starch-degrading glucoamylase.     

Essential role of MCM proteins in premeiotic DNA replication

A critical event in eukaryotic DNA replication involves association of minichromosome maintenance (MCM2-7) proteins with origins, to form prereplicative complexes (pre-RCs) that are competent for initiation. The ability of mutants defective in MCM2-7 function to complete meiosis had suggested that pre-RC components could be irrelevant to premeiotic S phase. We show here that MCM2-7 proteins bind to chromatin in fission yeast cells preparing for meiosis and during premeiotic S phase in a manner suggesting they in fact are required for DNA replication in the meiotic cycle. This is confirmed by analysis of a degron mcm4 mutant, which cannot carry out premeiotic DNA replication. Later in meiosis, Mcm4 chromatin association is blocked between meiotic nuclear divisions, presumably accounting for the absence of a second round of DNA replication. Together, these results emphasize similarity between replication mechanisms in mitotic and meiotic cell cycles.     

High-performance liquid chromatographic analysis and separation of N-feruloylserotonin isomers

The N-feruloylserotonin containing fraction was isolated from seeds of Leuzea carthamoides (Willd.) DC by solvent extraction followed by column chromatography on silica gel or on Sephadex LH-20. Nuclear magnetic resonance spectroscopic analysis of the isolated fraction showed the presence of four structurally related compounds. These compounds were identified as four isomers of N-feruloylserotonin: N-(Z)-feruloylserotonin, N-(Z)-isoferuloylserotonin, N-(E)-feruloylserotonin and N-(E)-isoferuloylserotonin. They were analyzed by HPLC on Separon SGX C18, Separon SGX and Separon SGX phenyl, using various mobile phases. Separon SGX phenyl phase was found the most efficient for a rapid analysis and for the final separation of the N-feruloylserotonin isomers.