Gene expression profiles in rat brain disclose CNS signature genes and regional patterns of functional specialisation

Background: The mammalian brain is divided into distinct regions with structural and neurophysiological differences. As a result, gene expression is likely to vary between regions in relation to their cellular composition and neuronal function. In order to improve our knowledge and understanding of regional patterns of gene expression in the CNS, we have generated a global map of gene expression in selected regions of the adult rat brain (frontomedial-, temporal- and occipital cortex, hippocampus, striatum and cerebellum; both right and left sides) as well as in three major non-neural tissues (spleen, liver and kidney) using the Applied Biosystems Rat Genome Survey Microarray. Results: By unsupervised hierarchical clustering, we found that the transcriptome within a region was highly conserved among individual rats and that there were no systematic differences between the two hemispheres (right versus left side). Further, we identified distinct sets of genes showing significant regional enrichment. Functional annotation of each of these gene sets clearly reflected several important physiological features of the region in question, including synaptic transmission within the cortex, neurogenesis in hippocampus and G-protein-mediated signalling in striatum. In addition, we were able to reveal potentially new regional features, such as mRNA transcription- and neurogenesis-annotated activities in cerebellum and differential use of glutamate signalling between regions. Finally, we determined a set of 'CNSsignature' genes that uncover characteristics of several common neuronal processes in the CNS, with marked overrepresentation of specific features of synaptic transmission, ion transport and cell communication, as well as numerous novel unclassified genes. Conclusion: We have generated a global map of gene expression in the rat brain and used this to determine functional processes and pathways that have a regional preference or ubiquitous distribution within the CNS, respectively. The existence of shared specialised neuronal activities in CNS is interesting in a context of potential functional redundancy, and future studies should further explore the overall characteristics of CNS-specific versus region-specific gene profiles in the brain

Statistical Properties of mechanically generated surface gravity waves: a laboratory experiment in a three-dimensional wave basin

A wave basin experiment has been performed in the MARINTEK laboratories, in one of the largest existing three-dimensional wave tanks in the world. The aim of the experiment is to investigate the effects of directional energy distribution on the statistical properties of surface gravity waves. Different degrees of directionality have been considered, starting from long-crested waves up to directional distributions with a spread of ±30° at the spectral peak. Particular attention is given to the tails of the distribution function of the surface elevation, wave heights and wave crests. Comparison with a simplified model based on second-order theory is reported. The results show that for long-crested, steep and narrow-banded waves, the second-order theory underestimates the probability of occurrence of large waves. As directional effects are included, the departure from second-order theory becomes less accentuated and the surface elevation is characterized by weak deviations from Gaussian statistics

Experimental study of freak wave impacts on a tension-leg platform

This study investigates the freak wave impinging on a tension-leg platform through wave flume experiments. The freak waves are generated using the focused wave theory. By adjusting the wave focusing location, different incident wave scenarios at the structure location are produced. Simultaneous measurements of wave shape evolutions upon impingement, wave impact pressures on the platform deck, platform motions and tether forces are carried out for synchronized analyses of the wave kinematics/dynamics and structural responses. The variation of these parameters with the incident wave profile is studied. It is found that although applying less intensive local impact pressures as compared to the highly-breaking freak wave, the slightly-breaking or non-breaking freak wave imposes the same level of adverse effect on the platform's global stability in terms of motions and tether forces. In addition, the high-crest freak wave causes violent motions of the floating platform, which are likely to induce snap loads of large amplitude and high occurrence frequency in tethers. The published results would provide useful benchmarks for validating numerical and analytical models

Demonstrating public value to funders and other stakeholders—the journey of ELIXIR, a virtual and distributed research infrastructure for life science data

Open Science is a founding principle of ELIXIR, a pan-European research infrastructure for life science data, with 21 Member countries plus the European Molecular Biology Laboratory. The mission of ELIXIR is to coordinate bioinformatics resources so that they form a single, integrated and pan-European infrastructure, which can be used freely by academic and private-sector researchers across the globe. As a recipient of public and charitable funding, ELIXIR must demonstrate its value, and the need to produce evidence in support of this is intensifying. Our practice-led journey towards demonstrating public value is articulated around five main challenges and, for each, we present our pragmatic approach for tackling it. We begin by showing how we are working towards demystifying what research infrastructures do. We then shed light on the sort of evidence our funders and other stakeholders are asking us for, how this evidence varies in nature and scope, and our tactics to satisfy them. We follow-on by providing our thoughts on possible barriers and solutions to embedding impact evaluation in our activities. Finally, we provide lessons learned, which we believe are sufficiently transferable and will be inspirational to other research infrastructures as they embark on their own journeys to demonstrate public value.publishedVersio

Gene expression in the rat brain: High similarity but unique differences between frontomedial-, temporal- and occipital cortex

<p>Abstract</p> <p>Background</p> <p>The six-layered neocortex of the mammalian brain may appear largely homologous, but is in reality a modular structure of anatomically and functionally distinct areas. However, global gene expression seems to be almost identical across the cerebral cortex and only a few genes have so far been reported to show regional enrichment in specific cortical areas.</p> <p>Results</p> <p>In the present study on adult rat brain, we have corroborated the strikingly similar gene expression among cortical areas. However, differential expression analysis has allowed for the identification of 30, 24 and 11 genes enriched in frontomedial -, temporal- or occipital cortex, respectively. A large proportion of these 65 genes appear to be involved in signal transduction, including the ion channel <it>Fxyd6</it>, the neuropeptide <it>Grp </it>and the nuclear receptor <it>Rorb</it>. We also find that the majority of these genes display increased expression levels around birth and show distinct preferences for certain cortical layers and cell types in rodents.</p> <p>Conclusions</p> <p>Since specific patterns of expression often are linked to equally specialised biological functions, we propose that these cortex sub-region enriched genes are important for proper functioning of the cortical regions in question.</p

Gene-Based Analysis of Regionally Enriched Cortical Genes in GWAS Data Sets of Cognitive Traits and Psychiatric Disorders

Background: Despite its estimated high heritability, the genetic architecture leading to differences in cognitive performance remains poorly understood. Different cortical regions play important roles in normal cognitive functioning and impairment. Recently, we reported on sets of regionally enriched genes in three different cortical areas (frontomedial, temporal and occipital cortices) of the adult rat brain. It has been suggested that genes preferentially, or specifically, expressed in one region or organ reflect functional specialisation. Employing a gene-based approach to the analysis, we used the regionally enriched cortical genes to mine a genome-wide association study (GWAS) of the Norwegian Cognitive NeuroGenetics (NCNG) sample of healthy adults for association to nine psychometric tests measures. In addition, we explored GWAS data sets for the serious psychiatric disorders schizophrenia (SCZ) (n = 3 samples) and bipolar affective disorder (BP) (n = 3 samples), to which cognitive impairment is linked. Principal Findings: At the single gene level, the temporal cortex enriched gene RAR-related orphan receptor B (RORB) showed the strongest overall association, namely to a test of verbal intelligence (Vocabulary, P = 7.7E-04). We also applied gene set enrichment analysis (GSEA) to test the candidate genes, as gene sets, for enrichment of association signal in the NCNG GWAS and in GWASs of BP and of SCZ. We found that genes differentially expressed in the temporal cortex showed a significant enrichment of association signal in a test measure of non-verbal intelligence (Reasoning) in the NCNG sample. Conclusion: Our gene-based approach suggests that RORB could be involved in verbal intelligence differences, while the genes enriched in the temporal cortex might be important to intellectual functions as measured by a test of reasoning in the healthy population. These findings warrant further replication in independent samples on cognitive traits

A comparison of four clustering methods for brain expression microarray data

Background DNA microarrays, which determine the expression levels of tens of thousands of genes from a sample, are an important research tool. However, the volume of data they produce can be an obstacle to interpretation of the results. Clustering the genes on the basis of similarity of their expression profiles can simplify the data, and potentially provides an important source of biological inference, but these methods have not been tested systematically on datasets from complex human tissues. In this paper, four clustering methods, CRC, k-means, ISA and memISA, are used upon three brain expression datasets. The results are compared on speed, gene coverage and GO enrichment. The effects of combining the clusters produced by each method are also assessed. Results k-means outperforms the other methods, with 100% gene coverage and GO enrichments only slightly exceeded by memISA and ISA. Those two methods produce greater GO enrichments on the datasets used, but at the cost of much lower gene coverage, fewer clusters produced, and speed. The clusters they find are largely different to those produced by k-means. Combining clusters produced by k-means and memISA or ISA leads to increased GO enrichment and number of clusters produced (compared to k-means alone), without negatively impacting gene coverage. memISA can also find potentially disease-related clusters. In two independent dorsolateral prefrontal cortex datasets, it finds three overlapping clusters that are either enriched for genes associated with schizophrenia, genes differentially expressed in schizophrenia, or both. Two of these clusters are enriched for genes of the MAP kinase pathway, suggesting a possible role for this pathway in the aetiology of schizophrenia. Conclusion Considered alone, k-means clustering is the most effective of the four methods on typical microarray brain expression datasets. However, memISA and ISA can add extra high-quality clusters to the set produced by k-means, so combining these three methods is the method of choice

LFCS Review report – Model testing Model testing of large structures in a wave basin

This document describes previous model tests on large structures in general and long pontoon bridges in particular. Furthermore, this report highlights the challenges related to model testing of these type of structures. Work to improve the capability of doing this type of model testing is suggested. In addition, possible model test setups for a long segment of a floating pontoon bridge is elaborated.publishedVersio

Wave Drift Forces and Low Frequency Damping on the Exwave Semi-Submersible

The paper presents realistic horizontal wave drift force coefficients and low frequency damping coefficients for the Exwave semi-submersible under severe seastates. The analysis includes conditions with collinear waves and current. Model test data is used to identify the difference frequency wave exciting force coefficients based on a second order signal analysis technique. First, the slowly varying excitation is estimated from the relationship between the incoming wave and the low frequency motion using a linear oscillator. Then, the full quadratic transfer function (QTF) of the difference frequency wave exciting forces is defined from the relationship between the incoming waves and the second order force response. The process identifies also the linear low frequency damping. The paper presents results from cases selected from the EXWAVE JIP test matrix. The empirical wave drift coefficients are compared to potential flow predictions and to coefficients from a semi-empirical formula. The results show that the potential flow predictions largely underestimate the wave drift forces, especially at the low frequency range where severe seastates have most of the energy.acceptedVersio