The chicken or the egg? Adaptation to desiccation and salinity tolerance in a lineage of water beetles

Transitions from fresh to saline habitats are restricted to a handful of insect lineages, as the colonization of saline waters requires specialized mechanisms to deal with osmotic stress. Previous studies have suggested that tolerance to salinity and desiccation could be mechanistically and evolutionarily linked, but the temporal sequence of these adaptations is not well established for individual lineages. We combined molecular, physiological and ecological data to explore the evolution of desiccation resistance, hyporegulation ability (i.e., the ability to osmoregulate in hyperosmotic media) and habitat transitions in the water beetle genus Enochrus subgenus Lumetus (Hydrophilidae). We tested whether enhanced desiccation resistance evolved before increases in hyporegulation ability or vice versa, or whether the two mechanisms evolved in parallel. The most recent ancestor of Lumetus was inferred to have high desiccation resistance and moderate hyporegulation ability. There were repeated shifts between habitats with differing levels of salinity in the radiation of the group, those to the most saline habitats generally occurring more rapidly than those to less saline ones. Significant and accelerated changes in hyporegulation ability evolved in parallel with smaller and more progressive increases in desiccation resistance across the phylogeny, associated with the colonization of meso‐ and hypersaline waters during global aridification events. All species with high hyporegulation ability were also desiccation‐resistant, but not vice versa. Overall, results are consistent with the hypothesis that desiccation resistance mechanisms evolved first and provided the physiological basis for the development of hyporegulation ability, allowing these insects to colonize and diversify across meso‐ and hypersaline habitats.     

Crop-to-crop Gene Flow using Farm Scale Sites of Oilseed Rape (<Emphasis Type="Italic">Brassica napus</Emphasis>) in the UK

From 2000–2003 a range of Farm Scale Evaluation (FSE) trials were established in the UK to assess the effect of the release and management of herbicide tolerant (HT) crops on the abundance and diversity of farmland wildlife compared with their conventionally managed non-GM-equivalents. The objective of this research project was to investigate gene flow within the winter (WOSR) and spring oilseed rape (SOSR) FSE trials and to develop a statistical model for the prediction of cross-pollination frequency that can be used to evaluate current separation distance guidelines. Seed samples were collected from the non-GM half of the trial sites and were tested for evidence of cross-pollination from the GM HT halves using a quantitative PCR assay specific to the HT (bar) gene. Rates of cross-pollination were found to decrease rapidly with increasing distance from the GM source. The quantitative data were subjected to statistical analysis and a two-step model was found to provide the best fit for the data. Significant differences were found between the results for WOSR, SOSR and varietal association (VA) crops. The model predicted that the %GM content (including upper 95% confidence limits) of a sample taken at a distance of 50 m away from the GM source would be 0.04% (0.84%) for WOSR, 0.02% (0.39%) for SOSR, 0.77% (21.72%) for WOSR VA and 0.37% (5.18%) for SOSR VA. The data and models presented here are discussed in the context of necessary separation distances to meet various possible thresholds for adventitious presence of GM in OSR. The British Crown's right to retain a non-exclusive, royalty-free licence in and to any copyright is acknowledged.     

The effect of geographical scale of sampling on DNA barcoding

Eight years after DNA barcoding was formally proposed on a large scale, CO1 sequences are rapidly accumulating from around the world. While studies to date have mostly targeted local or regional species assemblages, the recent launch of the global iBOL project (International Barcode of Life), highlights the need to understand the effects of geographical scale on Barcoding's goals. Sampling has been central in the debate on DNA Barcoding, but the effect of the geographical scale of sampling has not yet been thoroughly and explicitly tested with empirical data. Here, we present a CO1 data set of aquatic predaceous diving beetles of the tribe Agabini, sampled throughout Europe, and use it to investigate how the geographic scale of sampling affects 1) the estimated intraspecific variation of species, 2) the genetic distance to the most closely related heterospecific, 3) the ratio of intraspecific and interspecific variation, 4) the frequency of taxonomically recognized species found to be monophyletic, and 5) query identification performance based on 6 different species assignment methods. Intraspecific variation was significantly correlated with the geographical scale of sampling (R-square = 0.7), and more than half of the species with 10 or more sampled individuals (N = 29) showed higher intraspecific variation than 1% sequence divergence. In contrast, the distance to the closest heterospecific showed a significant decrease with increasing geographical scale of sampling. The average genetic distance dropped from > 7% for samples within 1 km, to < 3.5% for samples up to > 6000 km apart. Over a third of the species were not monophyletic, and the proportion increased through locally, nationally, regionally, and continentally restricted subsets of the data. The success of identifying queries decreased with increasing spatial scale of sampling; liberal methods declined from 100% to around 90%, whereas strict methods dropped to below 50% at continental scales. The proportion of query identifications considered uncertain (more than one species < 1% distance from query) escalated from zero at local, to 50% at continental scale. Finally, by resampling the most widely sampled species we show that even if samples are collected to maximize the geographical coverage, up to 70 individuals are required to sample 95% of intraspecific variation. The results show that the geographical scale of sampling has a critical impact on the global application of DNA barcoding. Scale-effects result from the relative importance of different processes determining the composition of regional species assemblages (dispersal and ecological assembly) and global clades (demography, speciation, and extinction). The incorporation of geographical information, where available, will be required to obtain identification rates at global scales equivalent to those in regional barcoding studies. Our result hence provides an impetus for both smarter barcoding tools and sprouting national barcoding initiatives-smaller geographical scales deliver higher accuracy.     

Use of a deformable atlas to identify cryptic critical structures in the treatment of glioblastoma multiforme

Dose constraints for traditional neural critical structures (e.g. optic chiasm, brain stem) are a standard component of planning radiation therapy to the central nervous system. Increasingly, investigators are becoming interested in accounting for the dose delivered to other non-target neural structures (e.g. hippocampi), which are not easily identified on axial imaging. In this pilot study, a commercially available digital atlas was used to identify cryptic neural structures (hippocampus, optic radiations, and visual cortices) in 6 patients who received intensity modulated radiation therapy (IMRT) as part of multimodal management of glioblastoma multiforme (GBM). The patient's original IMRT plans were re-optimized, with avoidance parameters for the newly identified critical structures. Re-optimization was able to reduce both mean and maximum dose to the volumes of interest, with a more pronounced effect for contralateral structures. Mean dose was reduced by 11% and 3% to contralateral and ipsilateral structures, respectively, with comparable reduction in maximum dose of 10% and 2%, respectively. Importantly, target coverage was not compromised, with an average change in coverage of 0.2%. Overall, our results demonstrate the feasibility of incorporating tools for cryptic critical structure identification into the treatment planning process for GBM.     

SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools

Background  

Deluged by the rate and complexity of completed genomic sequences, the need to align longer sequences becomes more urgent, and many more tools have thus been developed. In the initial stage of genomic sequence analysis, a biologist is usually faced with the questions of how to choose the best tool to align sequences of interest and how to analyze and visualize the alignment results, and then with the question of whether poorly aligned regions produced by the tool are indeed not homologous or are just results due to inappropriate alignment tools or scoring systems used. Although several systematic evaluations of multiple sequence alignment (MSA) programs have been proposed, they may not provide a standard-bearer for most biologists because those poorly aligned regions in these evaluations are never discussed. Thus, a tool that allows cross comparison of the alignment results obtained by different tools simultaneously could help a biologist evaluate their correctness and accuracy.     

Does macrophyte fractal complexity drive invertebrate diversity,biomass and body size distributions?

Habitat structure is one of the fundamental factors determining the distribution of organisms at all spatial scales, and vegetation is of primary importance in shaping the structural environment for invertebrates in many systems. In the majority of biotopes, invertebrates live within vegetation stands of mixed species composition, making estimates of structural complexity difficult to obtain. Here we use fractal indices to describe the structural complexity of mixed stands of aquatic macrophytes, and these are employed to examine the effects of habitat complexity on the composition of free-living invertebrate assemblages that utilise the habitat in three dimensions. Macrophytes and associated invertebrates were sampled from shallow ponds in southwest England, and rapid digital image analysis was used to quantify the fractal complexity of all plant species recorded, allowing the complexity of vegetation stands to be reconstructed based on their species composition. Fractal indices were found to be significantly related to both invertebrate biomass–body size scaling and overall invertebrate biomass; more complex stands of macrophytes contained a greater number of small animals. Habitat complexity was unrelated to invertebrate taxon richness and macrophyte surface area and species richness were not correlated with any of the invertebrate community parameters. The biomass–body size scaling relationship of lentic macroinvertebrates matched those predicted by models incorporating both allometric scaling of resource use and the fractal dimension of a habitat, suggesting that both habitat fractal complexity and allometry may control density–body size scaling in lentic macroinvertebrate communities.     

The degradation of beta-sitosterol by Pseudomonas sp. NCIB 10590 under aerobic conditions

The bacterial degradation of beta-sitosterol by Pseudomonas sp NCIB 10590 has been studied. Major biotransformation products included 24-ethylcholest-4-en-3-one, androsta-1,4-diene-3,17-dione, 3-oxochol-4-en-3-one-24-oic acid and 3-oxopregn-4-en-3-one-20-carboxylic acid. Minor products identified were 26-hydroxy-24-ethylcholest-4-en-3-one, androst-4-ene-3,17-dione, 3-oxo-24-ethylcholest-4-en-26-oic acid, 3-oxochola-1,4-dien-3-one-24-oic acid, 3-oxopregna-1,4-dien-3-one-20 carboxylic acid and 9 alpha-hydroxyandrosta-1,4-diene-3,17-dione. Studies with selected inhibitors have enabled the elucidation of a comprehensive pathway of beta-sitosterol degradation by bacteria.