On the Prediction of the Enantioselectivity of Candida rugosa Lipase by Comparative Molecular Field Analysis

Comparative molecular field analysis (CoMFA) was used to derive a quantitative substrate model for the enzymatic resolution of norbornanol esters by the lipase of Candida rugosa. Within these calculations, the steric and electrostatic interactions of both enantiomers and the differences in the corresponding two fields were used for the correlation of the substrate structure with the enantioselectivity of the hydrolysis. Different alignments of the molecules were used to improve the model.     

Plant communities of the montane mesophilous grasslands (Polygono bistortae–Trisetion flavescentis alliance) in central Europe: Formalized classification and syntaxonomical revision

Abstract

The research conducted here presents a syntaxonomical revision of the montane mesophilous meadows of the Polygono bistortae-Trisetion flavescentis alliance in central Europe – the Slovak part of the western and eastern Carpathians. These typical semi-natural grasslands occur mainly as small islands over the calcareous bedrocks. Associations of this alliance have tight relationships to the Arrhenatherion, Mesobromion and Nardo-Agrostion alliances. Formal definitions based on combination of the species groups were used regarding the diversity and geographical range of the Polygono bistortae-Trisetion flavescentis alliance. Following the formal definitions from the eight associations reported previously for Slovakia, only four of them can be placed within the Polygono bistortae-Trisetion flavescentis: Campanulo glomeratae-Geranietum sylvatici, Geranio sylvatici-Trisetetum, Crepido mollis-Agrostietum capillaries and Geranio-Alchemilletum crinitae. A comparison of traditional and formalized classification, and the advantages/disadvantages of the formalized classification are discussed.     

Genetic diversity inferred from AFLP fingerprinting in populations of Onosma echioides (Boraginaceae) from serpentine and calcareous soils

Abstract

Onosma echioides is a non-obligate serpentinophytic borage occurring discontinuously on calcareous and serpentine outcrops at the northwest limit of its range. Mean concentrations of Ca, Mg and heavy metals in root and shoot samples of eight populations from the two soil types were first determined. Subsequently, the genetic polymorphism of the same accessions was estimated by means of Amplified Fragment Length Polymorphism (AFLP) fingerprinting technique. Root and shoot samples from serpentine outcrops showed higher levels of Ni, Cr and Mg, and lower Ca/Mg ratios compared with those from calcareous soils. Based on 353 polymorphic AFLP bands, the two edaphic groups of populations showed comparable levels of genetic diversity. A remarkable genetic differentiation between populations and a high level of within-population genetic variance were found. Results of Mantel's test supported a significant correlation between genetic and geographical distances, while no difference in relation to the edaphic factor was detected. Molecular data suggested isolation as the key factor shaping the infraspecific genetic structure of O. echioides, which may be in relation with the short-distance, zoochorous systems of seed dispersal and pollination of this species.     

Ecogeographic and genetic evaluation of endemic species in the Maritime Alps: the case of Moehringia lebrunii and M. sedoides (Caryophyllaceae)

Abstract

The Maritime Alps are one of the ‘hot spots’ in the Mediterranean basin. This study investigated two endemic plants, Moehringia lebrunii and Moehringia sedoides (Caryophyllaceae) in order to increase knowledge of the vegetation of this region, and to investigate possible conservation strategies. Ecogeographic surveys and molecular analyses were undertaken. Gene diversity, the Shannon index and G_ST were calculated within and among populations of the two species based on ISSR data. The populations of M. lebrunii had a density ranging between 0.04 and 0.86 individual/m² and a rather low inner genetic variability value. According to IUCN Red List Criteria, the current status of M. lebrunii is Endangered [EN B2ab(ii, iv)]. M. sedoides is an endemic of the SW Alps (not exclusive of the Maritime Alps), and is very abundant within the core of the range. Its range of occurrence is smaller than previously reported; nevertheless, the species is not under threat. This taxon showed a population density ranging between 0.03 and 0.58 individual/m². Genetic variability values revealed a high variation among the species. Only peripheral populations seemed to suffer from their segregated position. Thus, M. sedoides is to be considered Critically Endangered [CR B1ab(i, ii, iii, iv) + 2ab(i, ii, iii, iv)] for Italy according to Regional Guidelines.     

Dopamine Receptor Microdomains Involved in Molecular Recognition and the Regulation of Drug Affinity and Function

A cationic protonatable amine moiety on dopaminergic ligands forms a high affinity reinforced ionic bond with an anionic aspartic acid at position 3.32 of dopamine receptors. When present, catechol hydroxyls of the ligands form hydrogen bonds with serines at position 5.42, 5.43, and 5.46, and this network of hydrogen bonds serves to orient ligands in the binding-site crevice and increase their binding affinity. A steric clash between aromatic moieties of the ligands and aromatic amino acids of the receptor (e.g., H6.55, F6.52 or F6.51 and W6.48) is likely to be propagated in domino-like fashion along the length of TM6, which is believed to trigger activation of the receptor. Specifically, it is the change in the conformation of W6.48 from an orientation perpendicular to the plane of the lipid membrane to one that is parallel that is believed to result in activation. Molecular determinants that mediate the D4/D2-selectivity of many extremely D4-selective 1,4-DAP ligands, include a nonconserved cluster of bulky amino acids at the TM2/TM3 interface (positions 2.61, 3.28 and 3.29).     

Turbellarian assemblages in freshwater lagoons in southern Brazil

Turbellarians, which typically feed on bacteria, algae, rotifers, oligochaetes, dipteran larvae, microcrustaceans, and other organisms, are abundant in diverse types of wetlands. Despite their importance, abundance, and species richness in freshwater environments, turbellarians are seldom considered in studies on biodiversity. We analyzed the structure of turbellarian communities in shore areas of three categories of permanent wetlands classified according to their perimeter as small, intermediate, and large during an annual cycle. In total, 1847 turbellarians were collected representing 42 species and 15 genera, from the orders Catenulida, Macrostomida, Lecithoepitheliata, Rhabdocoela, and Tricladida. Sixteen species were common to the three categories of wetlands, whereas nineteen species were unique to a particular category. Species composition varied among wetlands of different sizes; small, intermediate, and large wetlands had different dominant species. We found seasonal differences in community composition over the year, but no significant differences in mean values of observed species richness among wetlands with different sizes and among seasonal samples. The estimated species richness was, however, higher in the small wetlands, followed by the large and intermediate wetlands. In the summer, abundance was significantly lower in the small water bodies than in the intermediate and large bodies of water. Our results reinforce the need for conservation of wetlands of different sizes.     

Computational Studies of Ligand-Receptor Interactions in Bitter Taste Receptors

Phenylthiocarbamide tastes intensely bitter to some individuals, but others find it completely tasteless. Recently, it was suggested that phenylthiocarbamide elicits bitter taste by interacting with a human G protein-coupled receptor (hTAS2R38) encoded by the PTC gene. The phenylthiocarbamide nontaster trait was linked to three single nucleotide polymorphisms occurring in the PTC gene. Using the crystal structure of bovine rhodopsin as template, we generated the 3D structure of hTAS2R38 bitter taste receptor. We were able to map on the receptor structure the amino acids affected by the genetic polymorphisms and to propose molecular functions for two of them that explained the emergence of the nontaster trait. We used molecular docking simulations to find that phenylthiocarbamide exhibited a higher affinity for the target receptor than the structurally similar molecule 6-n-propylthiouracil, in line with recent experimental studies. A 3D model was constructed for the hTAS2R16 bitter taste receptor as well, by applying the same protocol. We found that the recently published experimental ligand binding affinity data for this receptor correlated well with the binding scores obtained from our molecular docking calculations.     

ANALYSIS OF LIGAND–RECEPTOR INTERACTIONS IN CELLS BY ATOMIC FORCE MICROSCOPY

ABSTRACT

Atomic force microscopy (AFM) increasingly has been used to analyse “receptor” function, either by using purified proteins (“molecular recognition microscopy”) or, more recently, in situ in living cells. The latter approach has been enabled by the use of a modified commercial AFM, linked to a confocal microscope, which has allowed adhesion forces between ligands and receptors in cells to be measured and mapped, and downstream cellular responses analysed. We review the application of AFM to cell biology and, in particular, to the study of ligand–receptor interactions and draw examples from our own work and that of others to show the utility of AFM, including for the exploration of cell surface functionalities. We also identify shortcomings of AFM in comparison to “standard” methods, such as receptor auto-radiography or immuno-detection, that are widely applied in cell biology and pharmacological analysis.     

Relationship between environmental variables and surface activity of scorpions in the Arid Chaco ecoregion of Argentina

Many environmental factors may influence the activity of scorpions in arid ecosystems. In this study, we examined the effects of such factors on scorpion activity at a mature and a secondary forest site in the Chancaní Reserve (Arid Chaco ecoregion in Córdoba, Argentina). Scorpions were collected using pitfall traps, and their nocturnal activity was observed by means of UV light during 14 nights. Temperature, air humidity, atmospheric pressure, and wind velocity were measured, and the percentage of visible moon was estimated. A total of 440 scorpions, representing seven species belonging to two families (Bothriuridae and Buthidae), were observed in the study area. Brachistosternus ferrugineus was the species most commonly observed using both methods. Mature and secondary forest shared slightly more than 50% of species. Surface activity of scorpions observed with the two methods differed significantly between the two areas. Surface activity of all scorpions and of B. ferrugineus were negatively related to the phase of the moon and positively related to air temperature. Physical factors thus have important effects on scorpion activity.