Influence of the extraction mode on the yield of some furanocoumarins from Pastinaca sativa fruits

Analysis of plant material is an important task in chemotaxonomical investigations, in search of plants with pharmacological activity or in standardisation of plant drugs. The choice of optimal conditions for the analysis of plant material and effect of extraction method on the yield of furanocoumarins from Pastinaca sativa fruits were examined. The following extraction methods were used in experiments: exhaustive extraction in Soxhlet apparatus, ultrasonification (USAE) at 25 and 60 degrees C, microwave-assisted solvent extraction in open and closed system (MASE) and accelerated solvent extraction (ASE). In most cases, the yield of furanocoumarins was highest by use of ASE method as well as by ultrasonification at 60 degrees C.     

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods

Background

Protein-protein interactions play a critical role in protein function. Completion of many genomes is being followed rapidly by major efforts to identify interacting protein pairs experimentally in order to decipher the networks of interacting, coordinated-in-action proteins. Identification of protein-protein interaction sites and detection of specific amino acids that contribute to the specificity and the strength of protein interactions is an important problem with broad applications ranging from rational drug design to the analysis of metabolic and signal transduction networks.

Results

In order to increase the power of predictive methods for protein-protein interaction sites, we have developed a consensus methodology for combining four different methods. These approaches include: data mining using Support Vector Machines, threading through protein structures, prediction of conserved residues on the protein surface by analysis of phylogenetic trees, and the Conservatism of Conservatism method of Mirny and Shakhnovich. Results obtained on a dataset of hydrolase-inhibitor complexes demonstrate that the combination of all four methods yield improved predictions over the individual methods.

Conclusions

We developed a consensus method for predicting protein-protein interface residues by combining sequence and structure-based methods. The success of our consensus approach suggests that similar methodologies can be developed to improve prediction accuracies for other bioinformatic problems.     

A multiparent advanced generation inter-cross population for genetic analysis in wheat

We present the first results from a novel multiparent advanced generation inter-cross (MAGIC) population derived from four elite wheat cultivars. The large size of this MAGIC population (1579 progeny), its diverse genetic composition and high levels of recombination all contribute to its value as a genetic resource. Applications of this resource include interrogation of the wheat genome and the analysis of gene-trait association in agronomically important wheat phenotypes. Here, we report the utilization of a MAGIC population for the first time for linkage map construction. We have constructed a linkage map with 1162 DArT, single nucleotide polymorphism and simple sequence repeat markers distributed across all 21 chromosomes. We benchmark this map against a high-density DArT consensus map created by integrating more than 100 biparental populations. The linkage map forms the basis for further exploration of the genetic architecture within the population, including characterization of linkage disequilibrium, founder contribution and inclusion of an alien introgression into the genetic map. Finally, we demonstrate the application of the resource for quantitative trait loci mapping using the complex traits plant height and hectolitre weight as a proof of principle.     

A HYPOTHESIS FOR IMPORT OF THE NUCLEAR‐ENCODED PsaE PROTEIN OF PAULINELLA CHROMATOPHORA (CERCOZOA,RHIZARIA) INTO ITS CYANOBACTERIAL ENDOSYMBIONTS/PLASTIDS VIA THE ENDOMEMBRANE SYSTEM1

The cyanobacterial endosymbionts of Paulinella chromatophora can shed new light on the process of plastid acquisition. Their genome is devoid of many essential genes, suggesting gene transfer to the host nucleus and protein import back into the endosymbionts/plastids. Strong evidence for such gene transfer is provided by the psaE gene, which encodes a PSI component that was efficiently transferred to the Paulinella nucleus. It remains unclear, however, how this protein is imported into the endosymbionts/plastids. We reanalyzed the sequence of Paulinella psaE and identified four potential non‐AUG translation initiation codons upstream of the previously proposed start codon. Interestingly, the longest polypeptide, starting from the first UUG, contains a clearly identifiable signal peptide with very high (90%) predictability. We also found several downstream hairpin structures that could enhance translation initiation from the alternative codon. These results strongly suggest that the PsaE protein is targeted to the outer membrane of Paulinella endosymbionts/plastids via the endomembrane system. On the basis of presence of respective bacterial homologs in the Paulinella endosymbiont/plastid genome, we discuss further trafficking of PsaE through the peptidoglycan wall and the inner envelope membrane. It is possible that other nuclear‐encoded proteins of P. chromatophora also carry signal peptides, but, alternatively, some may be equipped with transit peptides. If this is true, Paulinella endosymbionts/plastids would possess two distinct targeting systems, one cotranslational and the second posttranslational, as has been found in higher plant plastids. Considering the endomembrane system‐mediated import pathway, we also discuss homology of the membranes surrounding Paulinella endosymbionts/plastids.     

Isolation by distance in saproxylic beetles may increase with niche specialization

Species confined to temporally stable habitats are usually susceptible to habitat fragmentation, as living in long-lasting habitats is predicted to constrain evolution of dispersal ability. In Europe, saproxylic invertebrates associated with tree hollows are currently threatened due to the severe fragmentation of their habitat, but data on the population genetic consequences of such habitat decline are still scarce. By employing AFLP markers, we compared the spatial genetic structure of two ecologically and taxonomically related beetle species, Osmoderma barnabita and Protaetia marmorata (Cetoniidae). Both species are exclusively associated with tree hollows, but O. barnabita has a more restricted host preferences compared to P. marmorata. Analyses of spatial autocorrelation showed, in line with the predicted low dispersal potential of these saproxylic beetles, that both species are characterized by a strong kinship structure, which was more pronounced in the specialist O. barnabita than in the generalist P. marmorata. Individuals of both species sampled within single trees showed high relatedness (≈0.50 in O. barnabita and ≈0.15 in P. marmorata). Interestingly, groups of pheromone-emitting O. barnabita males sampled on the same tree trunk were found to be full brothers. Whether this result can be explained by kin selection to increase attraction of conspecific females for mating or by severe inbreeding of beetles within individual tree hollows needs further study. Although our studied populations were significantly inbred, our results suggest that the dispersal ability of Osmoderma beetles may be one order of magnitude greater than suggested by previous dispersal studies and acceptable levels of habitat fragmentation for metapopulation survival may be bigger than previously thought.     

Morphological Variation in Daphnia Cucullata Sars with Progressive Eutrophication of a Polymictic Lowland Reservoir

Morphological variation in Daphnia cucullata Sars was studied from 1994 to 2001 when fast increasing water trophy of the Siemianówka Reservoir was related to high TP and chlorophyll concentrations. During this period, D. cucullata biomass, as well as its contribution to the total cladocerans biomass clearly decreased. We found that among the six morphological parameters analyzed in D. cucullata, body length, height of the head and length of the tail spine had a tendency to decrease. The maximum values of these traits and carapace length also decreased. The morphology of D. cucullata appeared to be influenced by factors such as food availability, fish predation and an exclusive presence of D. cucullata among Daphniidae species. Increased water mixing in the reservoir may have also affected the changes in the head inclination of D. cucullata.     

Toward the insulin-IGF-I intermediate structures: functional and structural properties of the [TyrB25NMePheB26] insulin mutant

The origins of differentiation of insulin from insulin-like growth factor I (IGF-I) are still unknown. To address the problem of a structural and biological switch from the mostly metabolic hormonal activity of insulin to the predominant growth factor activities of IGF-I, an insulin analogue with IGF-I-like structural features has been synthesized. Insulin residues Phe(B25) and Tyr(B26) have been swapped with the IGF-I-like Tyr(24) and Phe(25) sequence with a simultaneous methylation of the peptide nitrogen of residue Phe(B26). These modifications were expected to introduce a substantial kink in the main chain, as observed at residue Phe(25) in the IGF-I crystal structure. These alterations should provide insight into the structural origins of insulin-IGF-I structural and functional divergence. The [Tyr(B25)NMePhe(B26)] mutant has been characterized, and its crystal structure has been determined. Surprisingly, all of these changes are well accommodated within an insulin R6 hexamer. Only one molecule of each dimer in the hexamer responds to the structural alterations, the other remaining very similar to wild-type insulin. All alterations, modest in their scale, cumulate in the C-terminal part of the B-chain (residues B23-B30), which moves toward the core of the insulin molecule and is associated with a significant shift of the A1 helix toward the C-terminus of the B-chain. These changes do not produce the expected bend of the main chain, but the fold of the mutant does reflect some structural characteristics of IGF-1, and in addition establishes the CO(A19)-NH(B25) hydrogen bond, which is normally characteristic of T-state insulin.