Ground beetle assemblages and distribution of functional traits in olive orchards and vineyards depend on the agricultural management practice

BioControl - Biodiversity in the Mediterranean is undergoing a decline resulting in reduced ecosystem service provisions. Here we analysed the functional diversity of ground beetles in...     

Dynamics and binding modes of free cdk2 and its two complexes with inhibitors studied by computer simulations

This article presents a molecular dynamics (MD) study of the cdk2 enzyme and its two complexes with the inhibitors isopentenyladenine and roscovitine using the Cornell et al. force field from the AMBER software package. The results show that inserting an inhibitor into the enzyme active site does not considerably change enzyme structure but it seemingly changes the distribution of internal motions. The inhibitor causes differences in the domain motions in free cdk2 and in its complexes. It was found out that repulsion of roscovitine N9 substituent causes conformational change on Lys 33 side chain. Isopentenyladenine forms with Lys 33 side chain terminal amino group a hydrogen bond. It implies that the cavity, where N9 substituent of roscovitine is buried, can adopt larger substituent due to Lys 33 side chain flexibility. The composition of electrostatic and van der Waals interactions between the inhibitor and the enzyme were also calculated along both cdk2/inhibitor MD trajectories together with MM-PB/GBSA analysis. These results show that isopentenyladenine-like inhibitors could be more effective after modifications leading to an increase in their van der Waals contact with the enzyme. We suggest that a way leading to better inhibitors occupying isopentenyladenine binding mode could be: to keep N9 and N7 purine positions free, to keep 3,3-dimethylallylamino group at C6 position, and to add, e.g., benzylamino group at C2 position. The results support the idea that the isopentenyladenine binding mode can be used for cdk2 inhibitors design and that all possibilities to improve this binding mode were not uncovered yet.     

A liquid chromatographic-mass spectrometric evidence of dihydrosanguinarine as a first metabolite of sanguinarine transformation in rat

Adult rats were orally administered with a single dose of sanguinarine (10 mg SA per 1 kg body weight) in 1.0 ml water. In the plasma and the liver, dihydrosanguinarine (DHSA) was identified as a SA metabolite by high performance liquid chromatography-electrospray ionization mass spectrometry (HPLC/ESI-MS). Significantly higher levels of DHSA were found in both the plasma and the liver in comparison with those of SA. SA and DHSA were not detected in the urine. The formation of DHSA might be the first step of SA detoxification in the organism and its subsequent elimination in phase II reactions. Benz[c]acridine (BCA), in the literature cited SA metabolite, was found neither in urine nor in plasma and liver.     

Evaluation of a Purification Procedure for the Muscarinic Receptor for the Purpose of Quantitative Receptor Assays of Anticholinergics

Abstract

The presented purification procedure for the muscarinic receptor from calf striatum includes the extraction of lipids with hexane in the first step and the removal of 39% of non-receptor proteins with 2 M NaCl in the second step. The simplicity of such an approach to the purification of the receptor warrants its use in the routine practice for quantitative purposes. The high affinity binding of tertiary ³H-dexetimide (³H-DEX) and quaternary ³H-N-methylscopolamine (³H-NMS) is preserved after the removal of irrelevant lipids and proteins from the P2-pellet.

The overall yield of receptors - 80%, when labelled with ³H-NMS, was satisfactory. Moreover, the final product, the NaCl-pellet, exerts a higher density of ³H-NMS binding sites per mg proteins by a factor of about 1.7. The overall yield of receptors and purification factor were lower, when measured with ³H-DEX. The total yield of ³H-DEX binding sites amounted to about 40% and the receptor density per mg protein decreased by a factor of 0.85.

We did not succeed in the improvement of the ratio specific/non-specific binding, neither for ³H-DEX nor for ³H-NMS for the purified receptor preparations. The use of ³H-NMS is preferable to ³H-DEX in plasma sample assays because of a negligible effect of plasma on ligand binding when compared with ³H-DEX.     

Rapd fingerprinting of diploid Lolium perenne × hexaploid Festuca arundinacea hybrid genomes

We tested the application of RAPD technology for identification of hybrid genomes originated from a maternal clone of Lolium perenne L. (2n = 2x = 14) bearing cytoplasmic male sterility, which was pollinated separately by five clones of Festuca arundinacea Schreb. cv. Barocco (2n = 6x = 42). Six classes of RAPD markers were recognized, specific to: 1) Festuca genome and inherited into F1 hybrid genomes, 2) Lolium genome inherited into F1 hybrid genomes, 3) Lolium-specific bands not found in F1 progeny, 4) Festuca-specific bands not found in F1 progeny, 5) new bands found only in F1 hybrid profiles, 6) bands common to all parental and F1 hybrid genotypes. RAPD data were shown to have full potential a) to serve as an unequivocal proof of genome recombination in perennial ryegrass × tall fescue hybrids, b) to identify hybrid genomes, c) to reveal phenetic relationships of the accessions from crossing families, d) to enhance, by fingerprinting, the selection of superior hybrid material for further breeding. RAPD data were found to be consistent with the festucoid phenotype of F1 hybrids. This revised version was published online in July 2006 with corrections to the Cover Date.     

Adaptive evolution and effective population size in wild house mice

Estimates of the proportion of amino acid substitutions that have been fixed by selection (α) vary widely among taxa, ranging from zero in humans to over 50% in Drosophila. This wide range may reflect differences in the efficacy of selection due to differences in the effective population size (N(e)). However, most comparisons have been made among distantly related organisms that differ not only in N(e) but also in many other aspects of their biology. Here, we estimate α in three closely related lineages of house mice that have a similar ecology but differ widely in N(e): Mus musculus musculus (N(e) ～ 25,000-120,000), M. m. domesticus (N(e) ～ 58,000-200,000), and M. m. castaneus (N(e) ～ 200,000-733,000). Mice were genotyped using a high-density single nucleotide polymorphism array, and the proportions of replacement and silent mutations within subspecies were compared with those fixed between each subspecies and an outgroup, Mus spretus. There was significant evidence of positive selection in M. m. castaneus, the lineage with the largest N(e), with α estimated to be approximately 40%. In contrast, estimates of α for M. m. domesticus (α = 13%) and for M. m. musculus (α = 12 %) were much smaller. Interestingly, the higher estimate of α for M. m. castaneus appears to reflect not only more adaptive fixations but also more effective purifying selection. These results support the hypothesis that differences in N(e) contribute to differences among species in the efficacy of selection.