Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification

Fast and efficient DNA fingerprinting of crop cultivars and individuals is frequently used in both theoretical population genetics and in practical breeding. Numerous DNA marker technologies exist and the ratio of speed, cost and accuracy are of importance. Therefore even in species where highly accurate and polymorphic marker systems are available, such as microsatellite SSR (simple sequence repeats), also alternative methods may be of interest. Thanks to their high abundance and ubiquity, temporary mobile retrotransposable elements come into recent focus. Their properties, such as genome wide distribution and well-defined origin of individual insertions by descent, predetermine them for use as molecular markers. In this study, several Ty3-gypsy type retrotransposons have been developed and adopted for the inter-retrotransposon amplified polymorphism (IRAP) method, which is suitable for fast and efficient pea cultivar fingerprinting. The method can easily distinguish even between genetically closely related pea cultivars and provide high polymorphic information content (PIC) in a single PCR analysis.     

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.     

Altered HLA Class I Profile Associated with Type A/D Nucleophosmin Mutation Points to Possible Anti-Nucleophosmin Immune Response in Acute Myeloid Leukemia

Nucleophosmin 1 (NPM1) mutations are frequently found in patients with acute myeloid leukemia (AML) and the newly generated sequences were suggested to induce immune response contributing to the relatively favorable outcome of patients in this AML subset. We hypothesized that if an efficient immune response against mutated nucleophosmin can be induced in vivo, the individuals expressing HLA alleles suitable for presenting NPM-derived peptides should be less prone to developing AML associated with NPM1 mutation. We thus compared HLA class I frequencies in a cohort of patients with mutated NPM1 (63 patients, NPMc+), a cohort of patients with wild-type NPM1 (94 patients, NPMwt) and in normal individuals (large datasets available from Allele Frequency Net Database). Several HLA allelic groups were found to be depleted in NPMc+ patients, but not in NPMwt compared to the normal distribution. The decrease was statistically significant for HLA B*07, B*18, and B*40. Furthermore, statistically significant advantage in the overall survival was found for patients with mutated NPM1 expressing at least one of the depleted allelic groups. The majority of the depleted alleles were predicted to bind potent NPM-derived immunopeptides and, importantly, these peptides were often located in the unmutated part of the protein. Our analysis suggests that individuals expressing specific HLA allelic groups are disposed to develop an efficient anti-AML immune response thanks to aberrant cytoplasmic localization of the mutated NPM protein.     

Leaving uncut refuges during meadow harvesting increases the functional diversity of Orthoptera

In the past, insect species richness was high in Central European seminatural grasslands, which were characterized by low‐intensity land use. Currently, however, the hay in most of these grasslands is mechanically harvested, which negatively impacts insect biodiversity. One way to reduce this negative effect is to leave unmown patches as refuges. In the current research we evaluated the short‐term effects of leaving an unmown patch on the taxonomic and functional diversity of the Orthoptera assemblage in a meadow. We found that orthopteran species richness and abundance were significantly reduced by mowing, whether or not a patch was left uncut. In contrast, functional evenness, indicating distribution of species abundances in a niche space, was reduced by mowing only if the plot lacked an uncut refuge. Functional richness, indicating the amount of niche space occupied by species, was elevated if the plot had an uncut refuge. Larger species were negatively affected by mowing, while habitat specialists, mobile species and soil‐ovipositing species benefitted from it. We infer that the presence of an uncut patch increased the diversity of habitats available to orthopterans and maintained even distribution of species among niche space. In summary, leaving an unmown refuge in grasslands could increase the functional diversity of orthopterans, even if it does not preserve taxonomic diversity.     

Transmembrane adaptor protein WBP1L regulates CXCR4 signalling and murine haematopoiesis

WW domain binding protein 1‐like (WBP1L), also known as outcome predictor of acute leukaemia 1 (OPAL1), is a transmembrane adaptor protein, expression of which correlates with ETV6‐RUNX1 (t(12;21)(p13;q22)) translocation and favourable prognosis in childhood leukaemia. It has a broad expression pattern in haematopoietic and in non‐haematopoietic cells. However, its physiological function has been unknown. Here, we show that WBP1L negatively regulates signalling through a critical chemokine receptor CXCR4 in multiple leucocyte subsets and cell lines. We also show that WBP1L interacts with NEDD4‐family ubiquitin ligases and regulates CXCR4 ubiquitination and expression. Moreover, analysis of Wbp1l‐deficient mice revealed alterations in B cell development and enhanced efficiency of bone marrow cell transplantation. Collectively, our data show that WBP1L is a novel regulator of CXCR4 signalling and haematopoiesis.     

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.     

A new insight into solid-state conformation of macrolide antibiotics

Quantitative analysis of the molecular conformations of the 14-membered macrolide antibiotics erythromycin A and B, clarithromycin, and roxithromycin in the solid state was performed. While the erythronolide macrocycle adopts a very similar folded-out conformation in all the macrolides studied, the proximity of the monosaccharide moieties, L-cladinose and D-desosamine, to each other is demonstrated to be the distinctive feature of their molecular conformations, based on atom-atom interaction energy analysis. More surprisingly, the common features in the relative orientation of the monosaccharide moieties (in terms of non-bonded atom-atom interactions) were revealed between the 14- and 15-membered (azithromycin) macrolide antibiotics. Herein we report on the details of the spatial arrangement of the monosaccharide moieties in these structurally related drug molecules and their influence on the biopharmaceutical properties of erythromycin derivatives.     

Alien plant invasions in tropical and sub-tropical savannas: patterns,processes and prospects

Biological invasions affect virtually all ecosystems on earth, but the degree to which different regions and biomes are invaded, and the quality of information from different regions, varies greatly. A large body of literature exists on the invasion of savannas in the Neotropics and northern Australia where invasive plants, especially African grasses, have had major impacts. Less has been published on plant invasions in African savannas, except for those in South Africa. Negative impacts due to plant invasions in African savannas appear to be less severe than in other regions at present. As savannas cover about 60% of the continent, with tens of millions of people relying on the services they provide, it is timely to assess the current status of invasions as a threat to these ecosystems. We reviewed the literature, contrasting the African situation with that of Neotropical and Australian savannas. A number of drivers and explanatory factors of plant invasions in savannas have been described, mostly from the Neotropics and Australia. These include herbivore presence, residence time, intentional introductions for pasture improvements, fire regimes, the physiology of the introduced species, and anthropogenic disturbance. After comparing these drivers across the three regions, we suggest that the lower extent of alien plant invasions in African savannas is largely attributable to: (1) significantly lower rates of intentional plant introductions and widespread plantings (until recently); (2) the role of large mammalian herbivores in these ecosystems; (3) historical and biogeographical issues relating to the regions of origin of introduced species; and (4) the adaptation of African systems to fire. We discuss how changing conditions in the three regions are likely to affect plant invasions in the future.     

Evaluating the stability of the classification of community data

We propose a method for a posteriori evaluation of classification stability which compares the classification of sites in the original data set (a matrix of species by sites) with classifications of subsets of its sites created by without‐replacement bootstrap resampling. Site assignments to clusters of the original classification and to clusters of the classification of each subset are compared using Goodman‐Kruskal's lambda index. Many resampled subsets are classified and the mean of lambda values calculated for the classifications of these subsets is used as an estimation of classification stability. Furthermore, the mean of the lambda values based on different resampled subsets, calculated for each site of the data set separately, can be used as a measure of the influence of particular sites on classification stability. This method was tested on several artificial data sets classified by commonly used clustering methods and on a real data set of forest vegetation plots. Its strength lies in the ability to distinguish classifications which reflect robust patterns of community differentiation from unstable classifications of more continuous patterns. In addition, it can identify sites within each cluster which have a transitional species composition with respect to other clusters.