Estimation of the diversity between DNA calorimetric profiles,differential melting curves and corresponding melting temperatures

The Poland–Fixman–Freire formalism was adapted for modeling of calorimetric DNA melting profiles, and applied to plasmid pBR 322 and long random sequences. We studied the influence of the difference (H_GC?H_AT) between the helix‐coil transition enthalpies of AT and GC base pairs on the calorimetric melting profile and on normalized calorimetric melting profile. A strong alteration of DNA calorimetrical profile with H_GC?H_AT was demonstrated. In contrast, there is a relatively slight change in the normalized profiles and in corresponding ordinary (optical) normalized differential melting curves (DMCs). For fixed H_GC?H_AT, the average relative deviation (S) between DMC and normalized calorimetric profile, and the difference between their melting temperatures (T_cal?T_m) are weakly dependent on peculiarities of the multipeak fine structure of DMCs. At the same time, both the deviation S and difference (T_cal?T_m) enlarge with the temperature melting range of the helix‐coil transition. It is shown that the local deviation between DMC and normalized calorimetric profile increases in regions of narrow peaks distant from the melting temperature.     

Molecular analysis of Gigaspora (Glomales, Gigasporaceae)

This work presents a cooperative effort to integrate new molecular (isozyme and SSU analyses) characters into the morphological taxonomy of the genus Gigaspora (Glomales). Previous analyses of published Gigaspora SSU sequences indicated the presence of a few polymorphic nucleotides in the region delimited by primers NS71-SSU 1492'. In our study, the SSU of 24 isolates of arbuscular mycorrhizal (AM) fungi from the Gigasporaceae were amplified and the NS71-SSU 1492' region was directly sequenced. The corresponding sequences of four more isolates of AM fungi from Gigasporaceae, already published, were also included in our analyses. Three Gigaspora groups were identified on the basis of a 6 nucleotide-long 'molecular signature': Gigaspora rosea group ( G. rosea + G. albida ), Gigaspora margarita group ( G. margarita + G. decipiens ) and Gigaspora gigantea , which constituted a group by itself. The isozyme profiles (malate dehydrogenase, MDH) of 12 of these 28 isolates, and seven other isolates not sequenced, were compared. The results obtained further supported the grouping of isolates provided by the SSU analysis. Both SSU and MDH analysis indicated that two out of the 35 isolates had been misidentified, which was confirmed when their morphology was reassessed. The use of the Gigaspora intrageneric molecular signature as a quick, unambiguous and objective method to recognize Gigaspora isolates under any (field or laboratory) experimental conditions is suggested.     

Molecular weight distribution and functional group profiles of TEMPO-oxidized lyocell fibers

The effects of TEMPO-mediated oxidation, performed with NaClO, a catalytic amount of NaBr, and 2,2′,6,6′-tetramethylpiperidine-1-oxy radical (TEMPO), were studied on lyocell fibers by means of GPC using multiple detection and group-selective fluorescence labeling according to the CCOA and FDAM methodology. The applied method determines functional group content as a sum parameter, as well as functional group profiles in relation to the molecular weight of the cellulose fibers. Both the CHO and COOH profiles, as well as molecular weight alterations, were analyzed. A significant decrease in the average molecular weight was obtained during the first hour of TEMPO-mediated oxidation, but prolonged oxidation time resulted in no strong additional chain scission. Significant amounts of COOH groups were introduced in the high molecular weight fractions by the oxidation with higher concentrations of NaClO (2.42–9.67 mmol NaClO/g fiber) after modification times of 1 h or longer.     

Environmental monitoring through functional biodiversity tools

The foundational concept for our research, which is largely shared by statisticians and ecologists, is that biodiversity is one of the most important indicators for environmental assessment. Because this indicator decreases in relation to ecosystem stressors, its measurement is essential for predicting future biological impacts of environmental damages. Although many indices have been proposed, no universally accepted measure for biodiversity has yet been established. In this context, the use of diversity profiles allows the analyst to display a family of indices in a single graph. However, this approach presents two critical limitations: first, a community composition is not always interpretable; second, the diversity profiles could lead to ranking issues when the curves intersect each other. The aim of this paper is to resolve these limitations by introducing functional biodiversity tools. In particular, three functional measures are proposed: the derivatives, the radius of curvature and the curve length. The analysis of derivatives and of the radius of curvature addresses the first limitation and highlights the characteristics, the differences and the similarities among communities. Arc length addresses the second limitation, providing a scalar measure that leads to a unique communities ranking for a given pattern of richness even if profiles intersect. The proposed functional models are applied to a real data set involving lichen biodiversity in the province of Genoa, Italy. Our approach allowed us to analyze the characteristics of lichen communities and to identify the biodiversity ranking. The combined use of these tools provides a useful method for identifying areas of high environmental risk, with the potential to address the monitoring of environmental policies.     

New insights into the binding mode of pyridine-3-carboxamide inhibitors of E. coli DNA gyrase

Previously we have reported on a series of pyridine-3-carboxamide inhibitors of DNA gyrase and DNA topoisomerase IV that were designed using a computational de novo design approach and which showed promising antibacterial properties. Herein we describe the synthesis of additional examples from this series aimed specifically at DNA gyrase, along with crystal structures confirming the predicted mode of binding and in vitro ADME data which describe the drug-likeness of these compounds.     

High throughput measure of diversity in cytoplasmic and nuclear traits for unravelling geographic distribution of rosemary

In the present work, variability of both cytoplasmic and nuclear microsatellite traits was investigated with the aim of characterizing a set of rosemary germplasm resources (Salvia rosmarinus). Most of the materials were collected in Italy and France. High‐resolution melting curves were compared each other computing their Euclidean distances and estimating the differences within their principal component as a measure of genetic diversity. Mantel correlation results combined to linear discriminant analysis allowed examined populations to be divided in four principal groups corresponding to four geographic areas, with few interesting and discussed exceptions. As rosemary propagates by seeds coming from insect mediated pollination, steady wild populations can be expected to be in panmictic equilibrium. Gained results confirmed and extended precedent characterization of rosemary genotypes and are compatible with the distribution of other Mediterranean species, as well as with the presence of a glacial refugium in the north‐east area of Sardinia previously described. As the officinal use of this aromatic shrub is spreading, characterization and conservation of wild Mediterranean germplasm is gaining strategic importance. A core collection of 100 genotypes was pointed out as suitable for a cheaper biodiversity ex situ preservation as well as for subsequent metabolic and linkage disequilibrium analyses.     

Effect of low-energy microwaves on DNA stability in solution

DNA isolated from liver of healthy and tumor-bearing (sarcoma 45) rats was irradiated in water-salt solution with weak microwaves (64.5 GHz, 50 μW/cm²). The heat stability of DNA increased with irradiation time (a raise of 1.5°C in T _m for “tumor” DNA after 90 min, without changes in ΔT), which may be associated with dehydration of the surrounding Na⁺ ions.     

Comparative chemical profiling of three TCM drugs in the Paeoniaceae family by UPLC-MS/MS combined with chemometric methods

Paeoniae Radix Rubra (Chi-Shao in Chinese) and Paeoniae Radix Alba (Bai-Shao in Chinese) are two valuable traditional Chinese medicine (TCM) drugs, usually indicated for menstrual disorders and viral infections. Paeonia anomala subsp. anomala (Xinjiang-Shaoyao in Chinese) is taken as Chi-Shao substitute in Xinjiang, China. Due to the diverse growing conditions, there are some differences in chemical compositions of three TCM drugs. An UPLC fingerprint analysis with chemometric methods, including similarity analysis and hierarchical clustering analysis, was applied in the study. By virtue of UPLC-QTOF-MS, 29 components including 18 monoterpene glycosides, 5 galloyl glucoses and 6 phenolic compounds were simultaneously identified. It could be concluded that the UPLC-QTOF-MS combined with chemometric methods could efficiently identify the three TCM drugs, and was a powerful approach for the chemical profiling of three TCM drugs. The developed method provide an available approach for quality control of three TCM drugs.     

On the Vertical Distribution of the Metazoan Meiofauna in Shelf Break and Upper Slope Habitats of the NE Atlantic

The metazoan meiofauna of nine stations in shelf break and upper slope areas (70 to 1500 m water depth) of the N.E. Atlantic were investigated in order to assess which environmental factors are important in the control of densities and sediment profiles. Total meiofaunal densities (ranging between 368 and 1523 ind/10 cm²) were correlated with bacterial densities, an important food source for meiofauna. However, considering sediment vertical distribution profiles, the relative importance of both food and oxygen on the meiofauna became obvious. A combination of both bacterial densities and oxygen supply could explain about 95% of the variability in the vertical profiles of the meiofauna densities. Meiofauna numbers increase in proportion to food availability in the surface sediment layers, but this relationship breaks down in deeper sediment layers where the oxygen supply is often limiting, particularly in fine sediments.