The relative flexibility of B-DNA and A-RNA duplexes: database analysis

An extensive analysis of structural databases is carried out to investigate the relative flexibility of B-DNA and A-RNA duplexes in crystal form. Our results show that the general anisotropic concept of flexibility is not very useful to compare the deformability of B-DNA and A-RNA duplexes, since the flexibility patterns of B-DNA and A-RNA are quite different. In other words, ‘flexibility’ is a dangerous word for describing macromolecules, unless it is clearly defined. A few soft essential movements explain most of the natural flexibility of A-RNA, whereas many are necessary for B-DNA. Essential movements occurring in naked B-DNAs are identical to those necessary to deform DNA in DNA–protein complexes, which suggest that evolution has designed DNA–protein complexes so that B-DNA is deformed according to its natural tendency. DNA is generally more flexible, but for some distortions A-RNA is easier to deform. Local stiffness constants obtained for naked B-DNAs and DNA complexes are very close, demonstrating that global distortions in DNA necessary for binding to proteins are the result of the addition of small concerted deformations at the base-pair level. Finally, it is worth noting that in general the picture of the relative deformability of A-RNA and DNA derived from database analysis agrees very well with that derived from state of the art molecular dynamics (MD) simulations.     

Variable Surface Glycoprotein RoTat 1.2 PCR as a specific diagnostic tool for the detection of Trypanosoma evansi infections

Background  

Based on the recently sequenced gene coding for the Trypanosoma evansi (T. evansi) RoTat 1.2 Variable Surface Glycoprotein (VSG), a primer pair was designed targeting the DNA region lacking homology to other known VSG genes. A total of 39 different trypanosome stocks were tested using the RoTat 1.2 based Polymerase Chain Reaction (PCR).     

Investigation of the use of immobilised metal affinity chromatography for the on-line sample clean up and pre-concentration of nucleotides prior to their determination by ion pair liquid chromatography-electrospray mass spectrometry: a pilot study

This study explored an alternative way to enrich and pre-purify biological samples containing nucleoside mono-, di- and triphosphates. These compounds were trapped by immobilised metal affinity chromatography (IMAC) on a Poros 20 MC IMAC-column, which was conditioned with Fe3+. The IMAC-column was implemented in a column switching set-up separating nucleoside mono-, di- and triphosphates on a Hypersil ODS 35 mm x 0.3 mm capillary column hyphenated to electrospray mass spectrometry resulting in the first miniaturised column switching liquid chromatography-mass spectrometry (LC-MS) system for nucleotides.     

FT-IR spectroscopic characteristics of differently cultivated Bacillus subtilis

Bacillus subtilis is an aerobic endospore forming bacterium widely spread in different environments. Because it represents a biological agent of some health relevance, its rapid detection and identification is highly desirable. By using FT-IR spectroscopy for this purpose slightly different characteristics were obtained from cell mass grown in differently composed cultural media, and harvested in different phases of bacterial growth. If cultivated uniformly, i.e., 24h at 30 degrees C in a minimum-strength nutrient broth, cell mass of B. subtilis delivered a well differentiated spectrum with major absorption bands of nucleic acid structures at 3300cm(-1), cell wall constituents at 3000-2800cm(-1), proteinaceous structures at 1660, 1544 and 1235cm(-1), and some aliphatic structural units at 1080cm(-1). Attenuated total reflectance, and absorption/transmission scanning techniques, delivered structurally identical spectra but those obtained by the former technique were more expressed.     

Degradation phase of apoptosis during the early stages of human metanephros development

Apoptosis as a vital process is necessary for human intrauterine development. Not only the induction and course of apoptosis, but engulfment of the apoptotic cells (bodies) were the centre of our interest. Macrophages were detected in the early stages of human intrauterine development and the role of macrophages in the clearance of apoptotic cells in the early stages of human metanephros development was confirmed.     

Activation of serotonin (5-HT)1A receptors inhibits amphetamine sensitization in mice

The effects of serotonin (5-HT)1A drugs on the development and expression of sensitization to the locomotor effect of amphetamine (AMPH) were studied in mice. 8-Hydroxy-2-(di-n-propylamino)tetralin (8-OH-DPAT), a 5-HT1A agonist, dose-dependently reduced the expression of AMPH (2.5 mg/kg)-induced sensitization. The latter inhibitory effect of 8-OH-DPAT was reversed by (S)-N-tert-butyl-3-(4-(2-methoxyphenyl)piperazin-1-yl)-2-phenyl propamine (WAY 100135), a 5-HT1A antagonist. WAY 100135 given alone did not affect expression of AMPH sensitization. Combined injections of 8-OH-DPAT, but not WAY 100135, with AMPH (2.5 mg/kg) during the development of sensitization, protected against the expression of sensitization to a challenge dose of AMPH (2.5 mg/kg) 3 days after withdrawal. The above inhibitory effect of 8-OH-DPAT on the development of AMPH sensitization was blocked by pretreatment with WAY 100135. The AMPH-induced conditioned locomotion was unaffected by pretreatment with 8-OH-DPAT. These results indicate that 5-HT1A receptors are not involved in AMPH-induced sensitization per-se, whereas their pharmacological activation leads to the inhibition of both the development and the expression of AMPH-induced sensitization.     

Evolutionary epidemiology of schistosomiasis: linking parasite genetics with disease phenotype in humans

Here we assess the role of parasite genetic variation in host disease phenotype in human schistosomiasis by implementing concepts and techniques from environmental association analysis in evolutionary epidemiology. Schistosomiasis is a tropical disease that affects more than 200 million people worldwide and is caused by parasitic flatworms belonging to the genus Schistosoma. While the role of host genetics has been extensively studied and demonstrated, nothing is yet known on the contribution of parasite genetic variation to host disease phenotype in human schistosomiasis. In this study microsatellite genotypes of 1561 Schistosoma mansoni larvae collected from 44 human hosts in Senegal were linked to host characteristics such as age, gender, infection intensity, liver and bladder morbidity by means of multivariate regression methods (on each parasite locus separately). This revealed a highly significant association between allelic variation at the parasite locus L46951 and host infection intensity and bladder morbidity. Locus L46951 is located in the 3′ untranslated region of the cGMP-dependent protein kinase gene that is expressed in reproductive organs of adult schistosome worms and appears to be linked to egg production. This putative link between parasite genetic variation and schistosomiasis disease phenotype sets the stage for further functional research.     

Ecological niche and phylogeny explain distribution of seed mass in the central European flora

Seed size is a crucial life‐history trait determining the amount of reserves that are available to establishing seedlings. The most frequently observed patterns in seed size distribution are a higher frequency of large‐seeded species in shaded habitats and a positive correlation of seed size with plant size. We analysed to what extent realised niche dimensions, as expressed by Ellenberg indicator values and plant functional traits such as plant height and life form, explained seed mass variation in the central European flora. By including information on phylogenetic relatedness of the species, not only contemporary ecology but also the evolutionary history of plant species could be taken into account. Seed mass evolution was slow and was best explained by selection‐inertia models with multiple adaptive peaks as a function of either habitat or life form. The highest seed mass optima were observed in the deciduous forest and saltwater and seashore habitats, and in phanerophytes in case of models with optima as a function of life form. The analyses showed that Ellenberg values were more important than habitat and life form in explaining seed mass distribution in the central European flora. The often observed relation between shade and large seeds was also evident in our study, but we found an equally important relation between large seeds and drought and a positive relation between seed mass and salinity. Our results indicate that not only plant size and competition for light but a complex set of factors influence the ecology of seed size, and that a more precise delineation of species’ niches improves the understanding of seed size evolution.     

Effects of long-term nitrogen addition on phosphorus cycling in organic soil horizons of temperate forests

High atmospheric nitrogen (N) deposition is expected to impair phosphorus (P) nutrition of temperate forest ecosystems. We examined N and P cycling in organic soil horizons of temperate forests exposed to long-term N addition in the northeastern USA and Scandinavia. We determined N and P concentrations, enzyme activities and net N and P mineralization rates in organic soil horizons of two deciduous (Harvard Forest, Bear Brook) and two coniferous (Klosterhede, Gårdsjön) forests which had received experimental inorganic N addition between 25 and 150 kg N ha^?1 year^?1 for more than 25 years. Long-term N addition increased the activity of phosphatase (+?180%) and the activity of carbon (C)- and N-acquiring enzymes (cellobiohydrolase: +?70%, chitinase: +?25%). Soil N enrichment increased the N:P ratio of organic soil horizons by up to 150%. In coniferous organic soil horizons, net N and P mineralization were small and unaffected by N addition. In deciduous organic soil horizons, net N and P mineralization rates were significantly higher than at the coniferous sites, and N addition increased net N mineralization by up to 290%. High phosphatase activities concomitant with a 40% decline in P stocks of deciduous organic soil horizons indicate increased plant P demand. In summary, projected future global increases in atmospheric N deposition may induce P limitation in deciduous forests, impairing temperate forest growth.     

Binary similarity measures for fingerprint analysis of qualitative metabolomic profiles

Introduction

Contemporary metabolomic fingerprinting is based on multiple spectrometric and chromatographic signals, used either alone or combined with structural and chemical information of metabolic markers at the qualitative and semiquantitative level. However, signal shifting, convolution, and matrix effects may compromise metabolomic patterns. Recent increase in the use of qualitative metabolomic data, described by the presence (1) or absence (0) of particular metabolites, demonstrates great potential in the field of metabolomic profiling and fingerprint analysis.

Objectives

The aim of this study is a comprehensive evaluation of binary similarity measures for the elucidation of patterns among samples of different botanical origin and various metabolomic profiles.

Methods

Nine qualitative metabolomic data sets covering a wide range of natural products and metabolomic profiles were applied to assess 44 binary similarity measures for the fingerprinting of plant extracts and natural products. The measures were analyzed by the novel sum of ranking differences method (SRD), searching for the most promising candidates.

Results

Baroni-Urbani–Buser (BUB) and Hawkins–Dotson (HD) similarity coefficients were selected as the best measures by SRD and analysis of variance (ANOVA), while Dice (Di1), Yule, Russel-Rao, and Consonni-Todeschini 3 ranked the worst. ANOVA revealed that concordantly and intermediately symmetric similarity coefficients are better candidates for metabolomic fingerprinting than the asymmetric and correlation based ones. The fingerprint analysis based on the BUB and HD coefficients and qualitative metabolomic data performed equally well as the quantitative metabolomic profile analysis.

Conclusion

Fingerprint analysis based on the qualitative metabolomic profiles and binary similarity measures proved to be a reliable way in finding the same/similar patterns in metabolomic data as that extracted from quantitative data.