Processing of DNA lesions by archaeal DNA polymerases from Sulfolobus solfataricus

Spontaneous damage to DNA as a result of deamination, oxidation and depurination is greatly accelerated at high temperatures. Hyperthermophilic microorganisms constantly exposed to temperatures exceeding 80°C are endowed with powerful DNA repair mechanisms to maintain genome stability. Of particular interest is the processing of DNA lesions during replication, which can result in fixed mutations. The hyperthermophilic crenarchaeon Sulfolobus solfataricus has two functional DNA polymerases, PolB1 and PolY1. We have found that the replicative DNA polymerase PolB1 specifically recognizes the presence of the deaminated bases hypoxanthine and uracil in the template by stalling DNA polymerization 3–4 bases upstream of these lesions and strongly associates with oligonucleotides containing them. PolB1 also stops at 8-oxoguanine and is unable to bypass an abasic site in the template. PolY1 belongs to the family of lesion bypass DNA polymerases and readily bypasses hypoxanthine, uracil and 8-oxoguanine, but not an abasic site, in the template. The specific recognition of deaminated bases by PolB1 may represent an initial step in their repair while PolY1 may be involved in damage tolerance at the replication fork. Additionally, we reveal that the deaminated bases can be introduced into DNA enzymatically, since both PolB1 and PolY1 are able to incorporate the aberrant DNA precursors dUTP and dITP.     

Simple plasma work-up for a fast chromatographic analysis of homocysteine,cysteine, methionine and aromatic amino acids

Simplified sample workup obviating protein precipitation and eluent evaporation commonly employed in earlier reports using chloroformate-mediated derivatization of aminothiols prior to mass spectrometric (MS) detection is presented. The reduction of disulfides in plasma is accomplished with dithiothreitol within minutes. A simultaneous derivatization with ethyl chloroformate (ECF) and extraction of derivatives into organic phase takes place within seconds. Along with S-amino acids, also aromatic amino acids can be determined during a 5-min run. Gas chromatography with flame ionization detection (GC-FID) proved to be sensitive enough to reach plasma homocysteine levels. A prerequisite for a reliable quantitation was fulfilled under the given conditions. Intra-assay precision was <5%, recoveries from spiked plasma complete (101.2%), detection and quantitation limits for homocysteine came to <1 and 3 micro mol/l. Our results were in full agreement with those obtained by liquid chromatography (r=0.999 for homocysteine and 0.987 for cysteine), and were close to two homocysteine immunoassays (r=0.991 and 0.939, respectively).     

Growth response of Bolboschoenus maritimus ssp. maritimus and B. maritimus ssp. compactus to different trophic conditions

Bolboschoenus maritimus (L.) Palla (=Scirpus maritimus L.) forms extensive stands in the littoral zone of small fishponds and as a weed in rice and maize fields. Within the species, two subspecies are distinguished: Bolboschoenus maritimus subsp. maritimus, B. maritimus subsp. compactus. They differ in ecology, especially in their relationships with trophic conditions and salinity of habitats. To determine growth response of these two types to different nutrient levels, we compared their seasonal development under experimental cultivation at four controlled nutrient levels. Some differences between the subspecies were found to be stable, regardless of nutrient level, namely greater amount of smaller underground tubers and more extensive rhizome system in subsp. compactus compared to less numerous larger tubers and simpler rhizome system in subsp. maritimus. In response to trophic conditions,the plants of subsp. compactus were more resistant to the conditions of the highest trophic level than those of subsp. maritimus, which were stressed. This demonstrates better adaptability and spreading ability of B. maritimus subsp. compactus at high trophic levels.     

The biology of Butomus umbellatus in shallow waters with fluctuating water level

Butomus umbellatus L. is a plant species typical of littoral communities of river and stream shores. It can form continuous stands in shallow reservoirs with fluctuating water level. Their expansion is promoted by: (a) intensive vegetative reproduction of plants, (b) crowded sprouting from rhizome fragments on emerged pond bottom, (c) shallow water layer in the year following summer drainage. Expansion of B. umbellatus depends on ploidy level: two cytotypes were found in the Czech and Slovak Republics, differing in their reproductive ability. Seed production of triploids is strongly limited (they are self-incompatible within clones), while diploids can be fully fertile. Nevertheless, even in diploids, the efficiency of seed reproduction under natural conditions is low. Triploids spread by intensive vegetative reproduction, which is decisive for clonal growth of populations and their regeneration after scraping of bottom surface. During seasonal development, maximum of aboveground biomass is produced in early summer, while underground biomass increases till autumn. Growth of the plants is limited by cutting before maximum underground biomass is attained, or by duck grazing.     

The effect of submergence on tuber production and dormancy in two subspecies ofBolboschoenus maritimus

Two subspecies ofBolboschoenus maritimus (L.)Palla were cultivated in submerged and non-submerged conditions. The production of tubers, the proportion of tubers remaining dormant and the time between production and reactivation were investigated. Total tuber production was found to be dependent on subspecies and may be considered a biological character of the subspecies.Bolboschoenus maritimus ssp.compactus, a subspecies of less, flooded habitats, produced more tubers with a greater capacity for growth leaving a smaller proportion of dormant tubers. Inactivity of tubers and their reactivation after one or two years were enhanced by submergence in both subspecies. The proportion of tubers that are permanently dormant as well as the dormancy of the whole plant are important features influencing the survival of populations ofB. maritimus over periods of unfavourable conditions.     

Analysis of articulation of fricative praealveolar sibilant "S" in control population

Defective pronunciation of one or more mother language phones, i.e. dyslalia, represents the most frequent speech impairment both in children and adult people. Cases of persisting speech disorder need professional approach and help. The aim of the study was to obtain a model of physiological articulation of the sibilant "s" in children. The method of FFT spectral analysis was made use of. Results will serve for further use in evaluation of speech impairment.     

Regulation of growth,nutritive, phytochemical and antioxidant potential of cultivated <Emphasis Type="Italic">Drimiopsis maculata</Emphasis> in response to biostimulant (vermicompost leachate,VCL) application

The effect of vermicompost leachate (VCL, low-cost biostimulant) on the growth, elemental (macro and micro-nutrients) and phytochemical content as well as the antioxidant potential of Drimiopsis maculata was evaluated. Three dilutions (1:5; 1:10 and 1:20) of VCL were tested and the cultivation lasted for 3 months. In addition to the recorded growth parameters, dried and ground plant materials (leaves and bulbs) were evaluated for nutrients, phenolic acids and antioxidant capacity. Vermicompost leachate application enhanced the growth of D. maculata, particularly, the leaves (VCL 1:10) and bulbs (VCL 1:20) which were significantly bigger than the controls. Apart from the concentration of phosphorus which was significantly lower in the leaves of VCL (1:20)-treated plants, the quantity of all four macro-nutrients analysed were similar with and without VCL. Similar observations were also demonstrated in the majority of quantified micro-nutrients in D. maculata. Relative to the control, VCL-treated plants had higher concentrations of the 10 phenolic acids quantified in the leaves. However, the majority of the quantified phenolic acids were not significantly enhanced in bulbs. Antioxidant activity of D. maculata extracts was generally higher in leaves than in the bulbs. The leaf extract from VCL (1:10 and 1:20)-treated plants exhibited lower oxygen radical absorbance capacity (ORAC) when compared to the control. However, bulbs from VCL (1:5) treatment had significantly higher ORAC than the control. From a conservational perspective, the current findings provided insight on viable approaches useful for mitigating challenges associated with over-harvesting of highly utilized but slow-growing plant species.     

Identifying a minimal rheological configuration: a tool for effective and efficient constitutive modeling of soft tissues

We describe a modeling methodology intended as a preliminary step in the identification of appropriate constitutive frameworks for the time-dependent response of biological tissues. The modeling approach comprises a customizable rheological network of viscous and elastic elements governed by user-defined 1D constitutive relationships. The model parameters are identified by iterative nonlinear optimization, minimizing the error between experimental and model-predicted structural (load-displacement) tissue response under a specific mode of deformation. We demonstrate the use of this methodology by determining the minimal rheological arrangement, constitutive relationships, and model parameters for the structural response of various soft tissues, including ex vivo perfused porcine liver in indentation, ex vivo porcine brain cortical tissue in indentation, and ex vivo human cervical tissue in unconfined compression. Our results indicate that the identified rheological configurations provide good agreement with experimental data, including multiple constant strain rate load/unload tests and stress relaxation tests. Our experience suggests that the described modeling framework is an efficient tool for exploring a wide array of constitutive relationships and rheological arrangements, which can subsequently serve as a basis for 3D constitutive model development and finite-element implementations. The proposed approach can also be employed as a self-contained tool to obtain simplified 1D phenomenological models of the structural response of biological tissue to single-axis manipulations for applications in haptic technologies.     

Generalization of Mimics Imperfect in Colour Patterns: The Point of View of Wild Avian Predators

Current research of imperfect mimicry brings ambiguous results. Experiments simulating more natural conditions rather than laboratory experiments show lower willingness of avian predators to attack less perfect mimics. We decided to simulate a natural situation by testing responses of wild‐caught adult avian predators (Great tit – Parus major) to variously perfect mimics of the red firebug (Pyrrhocoris apterus), which were in previous studies shown to elicit avoidance in Great tits. Presented mimics were perfect in all traits (firebug with its own colour pattern), imperfect in colour pattern (firebug with modified colour pattern), perfect in colour pattern, but imperfect in other visual traits (cockroach with firebug colour pattern), and imperfect in colour pattern as well as in other visual traits (cockroach with modified colour patterns). Modification of the pattern focused on the rounded spots on firebug's hemielytra, which is a conspicuous trait within the pattern. The pattern modification had no influence on the number of birds attacking the prey; nevertheless, birds spent more time observing the cockroaches that displayed the perfect firebug colour pattern than in the case of any other prey. Moreover, firebugs that displayed the perfect firebug colour pattern were observed for the shortest time (equal to that of the model – unmodified firebug). Cockroaches were attacked more often than firebugs, which suggest that birds were able to use additional visual cues (shape of legs and antennae) in prey recognition. Given these result, we conclude that differences in morphological traits characteristic for used prey taxa (true bugs, cockroaches) seem to be more important in the prey's protection than its colour pattern.     

Genetic engineering of cytokinin metabolism: Prospective way to improve agricultural traits of crop plants

Cytokinins (CKs) are ubiquitous phytohormones that participate in development, morphogenesis and many physiological processes throughout plant kingdom. In higher plants, mutants and transgenic cells and tissues with altered activity of CK metabolic enzymes or perception machinery, have highlighted their crucial involvement in different agriculturally important traits, such as productivity, increased tolerance to various stresses and overall plant morphology. Furthermore, recent precise metabolomic analyses have elucidated the specific occurrence and distinct functions of different CK types in various plant species. Thus, smooth manipulation of active CK levels in a spatial and temporal way could be a very potent tool for plant biotechnology in the future. This review summarises recent advances in cytokinin research ranging from transgenic alteration of CK biosynthetic, degradation and glucosylation activities and CK perception to detailed elucidation of molecular processes, in which CKs work as a trigger in model plants. The first attempts to improve the quality of crop plants, focused on cereals are discussed, together with proposed mechanism of action of the responses involved.