Enchytraeus albidus Microarray: Enrichment, Design, Annotation and Database (EnchyBASE)

Enchytraeus albidus (Oligochaeta) is an ecologically relevant species used as standard test organisms for risk assessment. Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints. The assessment of transcriptomic responses can be very useful e.g. to understand underlying mechanisms of toxicity with gene expression fingerprinting. In the present paper the following is being addressed: 1) development of suppressive subtractive hybridization (SSH) libraries enriched for differentially expressed genes after metal and pesticide exposures; 2) sequencing and characterization of all generated cDNA inserts; 3) development of a publicly available genomic database on E. albidus. A total of 2100 Expressed Sequence Tags (ESTs) were isolated, sequenced and assembled into 1124 clusters (947 singletons and 177 contigs). From these sequences, 41% matched known proteins in GenBank (BLASTX, e-value≤10-5) and 37% had at least one Gene Ontology (GO) term assigned. In total, 5.5% of the sequences were assigned to a metabolic pathway, based on KEGG. With this new sequencing information, an Agilent custom oligonucleotide microarray was designed, representing a potential tool for transcriptomic studies. EnchyBASE (http://bioinformatics.ua.pt/enchybase/) was developed as a web freely available database containing genomic information on E. albidus and will be further extended in the near future for other enchytraeid species. The database so far includes all ESTs generated for E. albidus from three cDNA libraries. This information can be downloaded and applied in functional genomics and transcription studies

Long-term and realistic global change manipulations had low impact on diversity of soil biota in temperate heathland

In a dry heathland ecosystem we manipulated temperature (warming), precipitation (drought) and atmospheric concentration of CO(2) in a full-factorial experiment in order to investigate changes in below-ground biodiversity as a result of future climate change. We investigated the responses in community diversity of nematodes, enchytraeids, collembolans and oribatid mites at two and eight years of manipulations. We used a structural equation modelling (SEM) approach analyzing the three manipulations, soil moisture and temperature, and seven soil biological and chemical variables. The analysis revealed a persistent and positive effect of elevated CO(2) on litter C:N ratio. After two years of treatment, the fungi to bacteria ratio was increased by warming, and the diversities within oribatid mites, collembolans and nematode groups were all affected by elevated CO(2) mediated through increased litter C:N ratio. After eight years of treatment, however, the CO(2)-increased litter C:N ratio did not influence the diversity in any of the four fauna groups. The number of significant correlations between treatments, food source quality, and soil biota diversities was reduced from six to three after two and eight years, respectively. These results suggest a remarkable resilience within the soil biota against global climate change treatments in the long term

Cancer Biomarker Discovery: The Entropic Hallmark

Background: It is a commonly accepted belief that cancer cells modify their transcriptional state during the progression of the disease. We propose that the progression of cancer cells towards malignant phenotypes can be efficiently tracked using high-throughput technologies that follow the gradual changes observed in the gene expression profiles by employing Shannon's mathematical theory of communication. Methods based on Information Theory can then quantify the divergence of cancer cells' transcriptional profiles from those of normally appearing cells of the originating tissues. The relevance of the proposed methods can be evaluated using microarray datasets available in the public domain but the method is in principle applicable to other high-throughput methods. Methodology/Principal Findings: Using melanoma and prostate cancer datasets we illustrate how it is possible to employ Shannon Entropy and the Jensen-Shannon divergence to trace the transcriptional changes progression of the disease. We establish how the variations of these two measures correlate with established biomarkers of cancer progression. The Information Theory measures allow us to identify novel biomarkers for both progressive and relatively more sudden transcriptional changes leading to malignant phenotypes. At the same time, the methodology was able to validate a large number of genes and processes that seem to be implicated in the progression of melanoma and prostate cancer. Conclusions/Significance: We thus present a quantitative guiding rule, a new unifying hallmark of cancer: the cancer cell's transcriptome changes lead to measurable observed transitions of Normalized Shannon Entropy values (as measured by high-throughput technologies). At the same time, tumor cells increment their divergence from the normal tissue profile increasing their disorder via creation of states that we might not directly measure. This unifying hallmark allows, via the the Jensen-Shannon divergence, to identify the arrow of time of the processes from the gene expression profiles, and helps to map the phenotypical and molecular hallmarks of specific cancer subtypes. The deep mathematical basis of the approach allows us to suggest that this principle is, hopefully, of general applicability for other diseases

The toxicity of copper contaminated soil using a gnotobiotic soil multi-species test system (SMS)

A gnotobiotic multi-species study was designed to consist of a food-web of soil-dwelling animals. The food-web was exposed to five concentrations copper (Cu) spiked soil for three exposure durations i.e. 28, 56 and 84 days. Based on multivariate analysis the food-web was significantly affected by Cu exposure at and above 300 mg Cu kg(-1) soil (lowest tested concentration). The number of animals present in the 2500 mg Cu kg(-1) (highest tested concentration) was at all sampling occasions below the starting point level. Based on analysis of the individual species the lowest 10% effect concentration (EC10) observed was 50 mg Cu kg(-1) soil, for Enchytraeus crypticus. Using the EC10 for the individual species the HC5 (Hazard Concentration at the 5% level) was estimated to be between 25 and 36 mg Cu kg(-1) soil, depending on the exposure duration. A similar experiment but using a reduced design was performed employing soil contaminated with Cu in the field more than 80 years ago. The trend in the field-contaminated soil was similar to that observed for the spiked soil

Increased frequency of drought reduces species richness of enchytraeid communities in both wet and dry heathland soils

Studies of biological responses in the terrestrial environment to rapid changes in climate have mostly been concerned with above-ground biota, whereas less is known of belowground organisms. The present study focuses on enchytraeids (Oligochaeta) of heathland ecosystems and how the enchytraeid community has responded to simulated climate change in a long-term field experiment. Either increased temperature or repeated drought was applied for 13 years to field plots located in Wales, The Netherlands and Denmark representing a gradient in precipitation and annual temperature fluctuations thereby providing an opportunity to study biological responses on a local (within sites) and regional scale. Warming treatments increasing night-time temperature (0.5e1 �C higher than ambient at 5 cm soil depth) had no detectable effects on the enchytraeid communities. Increased intensity and frequency of drought had rather weak persistent effects on total enchytraeid abundance suggesting that ecosystem functions of enchytraeids may only be transiently impacted by repeated spring or summer drought. However, drought treatment had persistent negative effects on species richness and community structure across sites. Drought treated plots harboured only 35e65% of the species present in control plots, and the reduction of species richness was most pronounced at the driest sites. It is discussed that soil invertebrates, due to their weak migratory potential, may be more liable to extinction under changing climatic conditions than above-ground species, and therefore consequences of climate change to soil organisms need particular attention in future research