RNA isolation from yeast using silica matrices.

RNA isolation from yeast is complicated by the need to initially break the cell wall. While this can be accomplished by glass bead disruption or enzyme treatment, these approaches result in DNA contamination and/or the need for incubation periods. We have developed a protocol for the isolation of RNA samples from yeast that minimizes degradation by RNases and incorporates two purification steps: acid phenol extraction and binding to a silica matrix. The procedure requires no precipitation steps, facilitating automation, and can be completed in less than 90 min. The RNA quality is ideal for microarray analysis.     

Quantitative floral phenology at the landscape scale: Is a comparative spatio-temporal description of ‘‘flowering landscapes’’ possible?

Entomophilous flowers form the food resources for insect pollinators. Many pollinator species forage at the landscape scale and depend on floral resources that are highly variable in space and time. We present a general model approach in which the floral resources of plant communities are estimated by the floral phenology and the cover of entomophilous plant species. We applied this landscape model in a case study for three landscape sections (1.5–2.2 km²) with strongly differing land-use patterns. The comparison between a conservation area and two agricultural landscapes shows extreme differences in the quantities and in the course of floral resources.

In a stepwise simplification of the landscape model we tested the effects of input data with lower spatio-temporal resolution. Even if input data for floral phenology and vegetation have a low resolution, the landscape model allows a ranking of landscape-specific floral resource potentials. The results of the case study encourage the use of landscape models to estimate floral resource potentials. The assessment of floral resource potentials may help to define this essential landscape quality for evaluation in practical nature conservation.     

Spatial patterns of Yucatan reef fish communities: Testing models using a multi-scale survey design

Using a hierarchical multi-scale survey design, we examined the spatial patterns of reef fish communities and tested ecological models concerning the relative importance of reef geomorphology and anthropogenic pressure possibly driving community structure. Canonical redundancy analysis was used as a form of multivariate analysis of variance (MANOVA) to asses differences in reef fish community composition at two spatial scales: broad (10⁵ m) and intermediate (10⁴ m). Surveys were conducted on the east coast of the Yucatan Peninsula (Mexican Caribbean fringing reef), including regions and reefs which differed in geomophologic structure and human use. Seven hundred and fourteen line transects were distributed among 13 reef localities belonging to different regions established a priori. Transects covered four types of reef habitat: lagoon, front, slope, and terrace. Tests of significance were based on permutation procedures. Significant differences among regions were found for the lagoon, slope, and terrace fish communities, consistent with the geomorphologic model, but it is only in the reef lagoon that they were consistent with the anthropogenic model, which may indicate an effect of coastal human activities. Significant differences among reefs within regions were observed, which could be associated with local environmental gradients. Canonical nested MANOVA was an appropriate method for testing ecological hypotheses about the functioning of complex biological systems. The use of a surveying strategy that explicitly incorporated the spatial structure represents an important contribution of this paper to coral reef fish ecology.     

A study of protein structure changes during hydration by diffuse X-ray scattering: II. Fourier transform analysis of diffuse X-ray scattering data

Radial distribution functions were deduced by Fourier transform analysis of the angular dependences of diffuse X-ray scattering intensities for the following proteins with different hydration degrees: water-soluble α-protein myoglobin, water-soluble (α + β) protein lysozyme, and transmembrane proteins from the photosynthetic reaction centers of purple bacteria Rhodobacter sphaeroides and Blastochlorii (Rhodopseudomonas) viridis. The results of Fourier transform analysis of X-ray scattering intensities give quantitative characteristics of the mechanism underlying the influence of water on the formation of biological macromolecules. On the one hand, water loosens the network of hydrogen bonds, which results in a considerable conformational mobility in the molecules of lysozyme and myoglobin and the reaction centers. On the other hand, water stabilizes and orders the protein globule. A strict correlation was found between the shift of the “first” maximum of the radial distribution function, loosening of the intraglobular hydrogen bonds, increase in the intramolecular mobility, and appearance of pronounced functional activity in macromolecules. The pattern of behavior of the first maximum in the transmembrane proteins of the reaction center was similar to that observed for the water-soluble proteins. However, the first maximum reached the limiting value of 2.9 Å at a considerably lower hydration degree compared with the water-soluble proteins. A quick transition of the protein complex of the reaction center to its native state is due to the fact that the dehydrated conformation of this complex is very close to the native conformation. Comparison of the radial distribution function for water, water-soluble proteins, and transmembrane proteins suggests a quantitative conclusion that water is the least densely packed and ordered system, the water-soluble proteins are more densely packed than water, and the transmembrane proteins are the most densely packed and ordered system.     

Wild gathered food plants in the European mediterranean: A comparative analysis

The Mediterranean basin has a long and multifaceted cultural history and harbors a high biodiversity. Epidemiological studies have drawn attention to certain traditional Mediterranean diets. However, wild gathered food species, which are an important, but fast disappearing element of these diets, so far have been largely neglected in scientific studies. In this study we compare ethnobotanical data obtained from field studies conducted in Southern Italy, Southern Spain, mainland Greece, and Crete resulting in the identification of a core group of 18 culinary used wild gathered plant species. This group comprises species likePapaver rhoeas L.,Sonchus asper L.,S. oleraceus L., andSilene vulgaris L. We argue that the culinary use of wild gathered weedy greens evolved together with the neolithization process, since this offered the necessary ecological niches for them to thrive, thereby enriching and securing the diets of European agriculturalists. Especially wild gathered Asteraceae species seem to form a sort of proto-nutraceutical, which accounts for a significant input of biologically active compounds in the diet.     

Interactions of amphipathic CPPs with model membranes

We have investigated the interactions between two carrier peptides and model membrane systems as well as the conformational consequences of these interactions. Studies performed with lipid monolayers at the air-water interface have enabled identification of the nature of the lipid-peptide interactions and characterization of the influence of phospholipids on the ability of these peptides to penetrate into lipidic media. Penetration experiments reveal that both peptides interact strongly with phospholipids. Conformational investigations indicate that the lipid-peptide interaction govern the conformational state of the peptides. Based on the ability of both peptides to promote ion permeabilization of both natural and artificial membranes, we propose a model illustrating the translocation process. For MPG, it is based on the formation of a β-barrel pore-like structure, while for Pep-1, it is based on association of helices.     

Phylogeny of anoxygenic filamentous phototrophic bacteria of the family Oscillochloridaceae as inferred from comparative analyses of the rrs, cbbL, and nifH genes

Phylogeny of anoxygenic filamentous phototrophic bacteria (AFPB) of the family Oscillochloridaceae (Oscillochloris trichoides DG6^T and the recently isolated strains Oscillochloris sp. R and C6) was studied based on comparative analyses of the genes coding for 16S rRNA (rrs), ribulose-1,5-bisphosphate carboxylase/oxygenase (cbbL), and nitrogenase (nifH). The sequences of the genes studied proved to be identical in the three strains, which is in agreement with data obtained earlier that showed a lack of differentiating phenotypic distinctions between these strains; therefore, it is proposed that the new strains should be identified as representatives of the species O. trichoides. Using an earlier designed system of oligonucleotide primers and a specially designed additional primer, fragments of the cbbL genes of the “red-like” form I RuBisCO were amplified and sequenced for all of the O. trichoides strains. Analysis of the cbbL genes suggested a separate position of the bacteria studied in the phylogenetic tree, where O. trichoides strains formed an independent branch, which, apart from this species, also included the only studied species of gram-positive facultatively chemoautotrophic bacteria, Sulfobacillus acidophilus. In the phylogenetic tree inferred from the analysis of nifH genes, the bacteria under study also formed a new separate branch, deviating near the root, which indicated a lack of relatedness between them and other phototrophic bacteria. The data obtained support the conclusion that AFPB has an ancient origin and their allocation as one of the main evolutionary lineages of eubacteria, which was made based on the analysis of ribosomal genes.     

Development of a novel roving-treatment process employing sequential chelating agent and enzymatic stages, utilising thermal analysis for assessment of fibre and yarn quality

Despite the potential benefits of utilising enzyme-based treatments to remove specific non-cellulosic polysaccharide components from flax fibre prior to spinning, attempts to date have not proved successful. At present, techniques employing conventional chemical reagents are solely employed within this industry. To establish the feasibility of incorporating an enzyme treatment stage within a novel process sequence, small-scale laboratory test protocols have been developed and employed to screen the performance of a range of commercial enzyme formulations on commercial dew-retted flax rovings. Thermal analysis and physical testing permitted rapid assessment and the best-performing treatment sequences, based on Pectinex AR and Pentopan 500 BG, respectively (Novozymes A/S, Bagsvaerd, Denmark) were then successfully scaled-up for industrial spinning trials. The results of these trials have shown that treatment with a chelating agent followed by pectinase and peroxide bleaching processes is capable of producing good quality yarn. The compositional and structural changes occurring in the fibre at each stage of treatment were detected using derivative thermogravimetry, and revealed quantitative changes in weight loss, decomposition temperature and peak widths in response to process steps. Assessment of chemical and physical performance data for the yarns obtained indicates that such a process may have commercial applications, supplementing the repertoire of traditional techniques and reagents available to the industry.