Xeml Lab: a tool that supports the design of experiments at a graphical interface and generates computer-readable metadata files, which capture information about genotypes, growth conditions, environmental perturbations and sampling strategy

Data mining depends on the ability to access machine-readable metadata that describe genotypes, environmental conditions, and sampling times and strategy. This article presents Xeml Lab. The Xeml Interactive Designer provides an interactive graphical interface at which complex experiments can be designed, and concomitantly generates machine-readable metadata files. It uses a new eXtensible Mark-up Language (XML)-derived dialect termed XEML. Xeml Lab includes a new ontology for environmental conditions, called Xeml Environment Ontology. However, to provide versatility, it is designed to be generic and also accepts other commonly used ontology formats, including OBO and OWL. A review summarizing important environmental conditions that need to be controlled, monitored and captured as metadata is posted in a Wiki ( http://www.codeplex.com/XeO ) to promote community discussion. The usefulness of Xeml Lab is illustrated by two meta-analyses of a large set of experiments that were performed with Arabidopsis thaliana during 5 years. The first reveals sources of noise that affect measurements of metabolite levels and enzyme activities. The second shows that Arabidopsis maintains remarkably stable levels of sugars and amino acids across a wide range of photoperiod treatments, and that adjustment of starch turnover and the leaf protein content contribute to this metabolic homeostasis.     

Photosynthesis in flashing light in soybean leaves grown in different conditions. I. Photosynthetic induction state and regulation of ribulose-1,5-bisphosphate carboxylase activity

The photosynthetic induction state under conditions of different lightfleck frequencies or durations, or different shade periods was studied in soybean leaves in order to examine how it might limit utilization of sunflecks in leaf canopies. Induction following an increase in photon flux density (PFD) from strongly limiting to saturating PFDs exhibited two phases; a fast-inducing one, requiring about 1 min and a slow one, requiring up to 60 min for completion. Transfer of fully induced leaves to low light resulted in a rapid decrease in the fast-inducing component, a slower decrease in the slow-inducing component and an even slower decrease in stomatal conductance. Therefore, the decreases in extent of induction appeared to be due to biochemical factors and not to stomatal closure. Under flashing light regimes consisting of 1-s lightflecks given at different frequencies for long periods, a constant induction state was achieved, the measure of induction state increased with the frequency of the lightflecks. This constant induction state also depended on the growth conditions, with shade leaves having a higher value than those grown at high light at any particular lightfleck frequency. The measure of induction state was mostly lower in flashing light as compared to constant light of the same mean PFD, particularly in leaves with a low light saturation point and in short lightflecks. Initial activities of ribulose-1,5-bisphosphate carboxylase (rubisco) were also higher in continuous light and were highly correlated with the measure of induction state. The rapid decrease in extent of induction of soybean leaves during shade periods is an important limitation to the ability of the leaves to respond to light increases similar to those occurring with sunflecks. At least part of the limitation on carbon assimilation during sunflecks due to photosynthetic induction is based on regulation of rubisco activity.     

Drought stress and cereal aphid performance

The performance of clones of Rhopalosiphum padi and Sitobion avenae from England and Spain was examined on drought-stressed tillering winter wheat in an environment chamber at 14 ± 1°C. Two different levels of drought stress and an unstressed control were established by different watering regimes which resulted in drought-stressed plants being smaller at the end of the experiment. The effect of drought stress to plants on aphid performance was not significantly different between the clones tested. Drought stress had no effect on aphid development time, nymphal mortality, the weight of teneral adults and the number of embryos in teneral adults up to the onset of reproduction in the first F₁ generation. The subsequent reproductive capacity, as measured by the effective and potential fecundity, and the reproductive rate, were much reduced on drought-stressed plants. However, there was only a small decrease in the intrinsic rate of increase (r_m). Overall the clone of R. padi from Spain performed better than that from England, the development and prereproductive times being shorter and the fecundity higher in the Spanish clone, giving a higher r_m. There were no differences in the fecundity and the r_m between the Spanish and the English clones of S. avenae. The proportion of the F₂ generation that was alate differed greatly between clones, and only the English S. avenae produced significantly more alatae on drought-stressed than on unstressed plants.     

Possible significance of changes in the light requirement of Cirsium palustre seeds after dispersal in ash coppice

Abstract. It is demonstrated that after the feelling of ash coppice Cirsium palustre becomes established from seed that was produced during the previous coppice cycle and has lain underground for several years. These seeds are light-requiring and it is probable that their germination is triggered by exposure to light during coppicing in winter.
It is assumed that the seeds become light-requiring because phytochrome in the far-red absorbing form high. This facilitates their incorporation in the seed bank in summer. However, the disappearance of Pfr is inhibited at low temperatures; this means that the seeds can store the light stimulus in winter and will not germinate until they experience higher temperatures in spring. The significance of the inhibition of seed germination under a leaf canopy is that it enhances the seeds chance of being incorporated in the soil seed bank.     

The structure of the outer shell layer in radiolitid rudists, a morphoconstructional approach

Radiolitids (Bivalvia, Radiolitidae) built the calcite outer layer of their shell with compact structure as many other bivalves, or with repetitively layered non-compact structure following different patterns: continuous radial ridges, discontinuous radial ridges, normal cellular, cellular with radially elongate cells, discontinuous cellular, and discontinuous cellular with elongate cells. Some special structures may develop in localized parts: radial structures and inner-marginal or radial grooves. All these structures are currently used in the diagnosis of the family and for the characterization of subfamilies. Constructional morphology analyses and re-evaluation of all these structures reveal that they were misunderstood in some important aspects in the bivalve Treatise and that, consequently, the diagnosis of the family has to be emended and their subfamilies reconsidered. All outer shell layer structure related characters are described, illustrated, and interpreted under a constructional approach, some characters are proposed to emend the diagnosis of the family, and two possible clades are preliminarily distinguished.     

Association between DRD4 gene polymorphism and personality variation in great tits: a test across four wild populations

Polymorphisms in the dopamine receptor D4 gene (DRD4) have been related to individual variation in novelty‐seeking or exploratory behaviour in a variety of animals, including humans. Recently, the human DRD4 orthologue was sequenced in a wild bird, the great tit (Parus major) and a single nucleotide polymorphism in exon 3 of this gene (SNP830) was shown to be associated with variation in exploratory behaviour of lab‐raised individuals originating from a single wild population. Here we test the generality of this finding in a large sample of free‐living individuals from four European great tit populations, including the originally sampled population. We demonstrate that the association between SNP830 genotype and exploratory behaviour also exists in free‐living birds from the original population. However, in the other three populations we found only limited evidence for an association: in two populations the association appeared absent; while in one there was a nonsignificant tendency. We could not confirm a previously demonstrated interaction with another DRD4 polymorphism, a 15 bp indel in the promoter region (ID15). As yet unknown differences in genetic or environmental background could explain why the same genetic polymorphism (SNP830) has a substantial effect on exploratory behaviour in one population, explaining 4.5–5.8% of the total variance—a large effect for a single gene influencing a complex behavioural trait—but not in three others. The confirmation of an association between SNP830 genotype and personality‐related behaviour in a wild bird population warrants further research into potential fitness effects of the polymorphism, while also the population differences in the strength of the association deserve further investigation. Another important future challenge is the identification of additional loci influencing avian personality traits in the wild.     

Taxonomical and biostratigraphical significance of the North African radiolitid rudist bivalve Praeradiolites biskraensis (Coquand, 1880)

Abstract: The revision of the radiolitid rudist bivalve Praeradiolites biskraensis (Coquand), including shell morphology and structure, taxonomical status, and palaeogeographical and stratigraphical distribution, was undertaken. We studied Coquand’s collection, other specimens from the type locality, Col de Sfa, and other Algerian fossil localities, as well as recently collected material from the Gafsa region in Tunisia. A neotype from Col de Sfa is proposed. The stratigraphical distribution of the species is bracketed in the Upper Cenomanian, using the distribution of co‐occurring ammonites in Tunisia and microfossils in Algeria. The palaeogeographical distribution is verified for Algeria and Tunisia based on all records in North Africa. Survey of the taxonomical status and problems of related radiolitid genera has resulted in revised diagnoses of Praeradiolites Douvillé, Eoradiolites Douvillé, Sphaerulites Lamarck and Radiolites Lamarck and revealed problems with Radiolites fleuriaui d’Orbigny, which is being the type species of Praeradiolites. Maghrebites gen. nov. is proposed for the North African radiolitid rudist Praeradiolites biskraensis (Coquand).