Bioinformatics-based assessment of the relevance of candidate genes for mutation discovery

The bioinformatics resources provide a wide range of tools that can be applied in different areas of mutation screening. The enormous and constantly increasing amount of genomic data obtained in plant-oriented molecular studies requires the development of efficient techniques for its processing. There is a wide range of bioinformatics tools which can aid in the course of mutation discovery. The following chapter focuses mainly on the application of different tools and resources to facilitate a Targeting-Induced Local Lesions in Genomes (TILLING) analysis. TILLING is a technique of reverse genetics that applies a traditional mutagenesis to create DNA libraries of mutagenised individuals that are then subjected to high-throughput screening for the identification of mutations. The bioinformatics tools have shown to be useful in supporting the process of candidate gene selection for mutation screening. The availability of bioinformatics software and experimental data repositories provides a powerful tool which enables a process of multi-database mining. The existing raw experimental data (genomics-related information, expression data, annotated ontologies) can be interpreted in terms of a new biological context. This may help in selecting the proper candidate gene for mutation discovery that is controlling the target phenotype. The mutation screening using a TILLING strategy requires a former knowledge of the full genomic sequence of the gene which is of interest. Depending on whether a fully sequenced genome of a particular species is available, different bioinformatics tools can facilitate this process. Specific tools can be also useful for the identification of possible gene paralogs which may mask the effect of mutated gene. Bioinformatics resources can also support the selection of gene fragments most prone to acquire a deleterious nucleotide change. Finally, there are available tools enabling a proper design of oligonucleotide primers for the amplification of a gene fragment for the purpose of mutation screening

Thalamocortical Connectivity Correlates with Phenotypic Variability in Dystonia

Dystonia is a brain disorder characterized by abnormal involuntary movements without defining neuropathological changes. The disease is often inherited as an autosomal-dominant trait with incomplete penetrance. Individuals with dystonia, whether inherited or sporadic, exhibit striking phenotypic variability, with marked differences in the somatic distribution and severity of clinical manifestations. In the current study, we used magnetic resonance diffusion tensor imaging to identify microstructural changes associated with specific limb manifestations. Functional MRI was used to localize specific limb regions within the somatosensory cortex. Microstructural integrity was preserved when assessed in subrolandic white matter regions somatotopically related to the clinically involved limbs, but was reduced in regions linked to clinically uninvolved (asymptomatic) body areas. Clinical manifestations were greatest in subjects with relatively intact microstructure in somatotopically relevant white matter regions. Tractography revealed significant phenotype-related differences in the visualized thalamocortical tracts while corticostriatal and corticospinal pathways did not differ between groups. Cerebellothalamic microstructural abnormalities were also seen in the dystonia subjects, but these changes were associated with genotype, rather than with phenotypic variation. The findings suggest that the thalamocortical motor system is a major determinant of dystonia phenotype. This pathway may represent a novel therapeutic target for individuals with refractory limb dystonia

Expansion of the Gene Ontology knowledgebase and resources

The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developments that facilitate access to, and application of, the GO knowledgebase, and 2) extensions to the resource as well as increasing support for descriptions of causal models of biological systems and network biology. To learn more, visit http://geneontology.org/

Visualizing Multivariate Hierarchic Data Using Enhanced Radial Space-Filling Layout

Currently, visualization tools for large ontologies (e.g., pathway and gene ontologies) result in a very flat wide tree that is difficult to fit on a single display. This paper develops the concept of using an enhanced radial space-filling (ERSF) layout to show biological ontologies efficiently. The ERSF technique represents ontology terms as circular regions in 3D. Orbital connections in a third dimension correspond to non-tree edges in the ontology that exist when an ontology term belongs to multiple categories. Biologists can use the ERSF layout to identify highly activated pathway or gene ontology categories by mapping experimental statistics such as coefficient of variation and overrepresentation values onto the visualization. This paper illustrates the use of the ERSF layout to explore pathway and gene ontologies using a gene expression dataset from E. coli

Nitrogen abundances in Planet-harbouring stars

We present a detailed spectroscopic analysis of nitrogen abundances in 91 solar-type stars, 66 with and 25 without known planetary mass companions. All comparison sample stars and 28 planet hosts were analysed by spectral synthesis of the near-UV NH band at 3360 \AA observed at high resolution with the VLT/UVES,while the near-IR NI 7468 \AA was measured in 31 objects. These two abundance indicators are in good agreement. We found that nitrogen abundance scales with that of iron in the metallicity range -0.6 <[Fe/H]< +0.4 with the slope 1.08 \pm 0.05. Our results show that the bulk of nitrogen production at high metallicities was coupled with iron. We found that the nitrogen abundance distribution in stars with exoplanets is the high [Fe/H] extension of the curve traced by the comparison sample of stars with no known planets. A comparison of our nitrogen abundances with those available in the literature shows a good agreement.Comment: 15 pages, 7 figures, Accepted for publication in A&

The visual perception of natural motion: abnormal task-related neural activity in DYT1 dystonia

Although primary dystonia is defined by its characteristic motor manifestations, non-motor signs and symptoms have increasingly been recognized in this disorder. Recent neuroimaging studies have related the motor features of primary dystonia to connectivity changes in cerebello-thalamo-cortical pathways. It is not known, however, whether the non-motor manifestations of the disorder are associated with similar circuit abnormalities. To explore this possibility, we used functional magnetic resonance imaging to study primary dystonia and healthy volunteer subjects while they performed a motion perception task in which elliptical target trajectories were visually tracked on a computer screen. Prior functional magnetic resonance imaging studies of healthy subjects performing this task have revealed selective activation of motor regions during the perception of \u27natural\u27 versus \u27unnatural\u27 motion (defined respectively as trajectories with kinematic properties that either comply with or violate the two-thirds power law of motion). Several regions with significant connectivity changes in primary dystonia were situated in proximity to normal motion perception pathways, suggesting that abnormalities of these circuits may also be present in this disorder. To determine whether activation responses to natural versus unnatural motion in primary dystonia differ from normal, we used functional magnetic resonance imaging to study 10 DYT1 dystonia and 10 healthy control subjects at rest and during the perception of \u27natural\u27 and \u27unnatural\u27 motion. Both groups exhibited significant activation changes across perceptual conditions in the cerebellum, pons, and subthalamic nucleus. The two groups differed, however, in their responses to \u27natural\u27 versus \u27unnatural\u27 motion in these regions. In healthy subjects, regional activation was greater during the perception of natural (versus unnatural) motion (P \u3c 0.05). By contrast, in DYT1 dystonia subjects, activation was relatively greater during the perception of unnatural (versus natural) motion (P \u3c 0.01). To explore the microstructural basis for these functional changes, the regions with significant interaction effects (i.e. those with group differences in activation across perceptual conditions) were used as seeds for tractographic analysis of diffusion tensor imaging scans acquired in the same subjects. Fibre pathways specifically connecting each of the significant functional magnetic resonance imaging clusters to the cerebellum were reconstructed. Of the various reconstructed pathways that were analysed, the ponto-cerebellar projection alone differed between groups, with reduced fibre integrity in dystonia (P \u3c 0.001). In aggregate, the findings suggest that the normal pattern of brain activation in response to motion perception is disrupted in DYT1 dystonia. Thus, it is unlikely that the circuit changes that underlie this disorder are limited to primary sensorimotor pathways

Extending the Implicit Association Test (IAT): Assessing Consumer Attitudes Based on Multi-Dimensional Implicit Associations

Background: The authors present a procedural extension of the popular Implicit Association Test (IAT; [1]) that allows for indirect measurement of attitudes on multiple dimensions (e.g., safe–unsafe; young–old; innovative–conventional, etc.) rather than on a single evaluative dimension only (e.g., good–bad). Methodology/Principal Findings: In two within-subjects studies, attitudes toward three automobile brands were measured on six attribute dimensions. Emphasis was placed on evaluating the methodological appropriateness of the new procedure, providing strong evidence for its reliability, validity, and sensitivity. Conclusions/Significance: This new procedure yields detailed information on the multifaceted nature of brand associations that can add up to a more abstract overall attitude. Just as the IAT, its multi-dimensional extension/application (dubbed md-IAT) is suited for reliably measuring attitudes consumers may not be consciously aware of, able to express, or willing to share with the researcher [2,3].Product Innovation ManagementIndustrial Design Engineerin

Gaseous emissions during concurrent combustion of biomass and non-recyclable municipal solid waste

Background: Biomass and municipal solid waste offer sustainable sources of energy; for example to meet heat and electricity demand in the form of combined cooling, heat and power. Combustion of biomass has a lesser impact than solid fossil fuels (e. g. coal) upon gas pollutant emissions, whilst energy recovery from municipal solid waste is a beneficial component of an integrated, sustainable waste management programme. Concurrent combustion of these fuels using a fluidised bed combustor may be a successful method of overcoming some of the disadvantages of biomass (high fuel supply and distribution costs, combustion characteristics) and characteristics of municipal solid waste (heterogeneous content, conflict with materials recycling). It should be considered that combustion of municipal solid waste may be a financially attractive disposal route if a 'gate fee' value exists for accepting waste for combustion, which will reduce the net cost of utilising relatively more expensive biomass fuels. Results: Emissions of nitrogen monoxide and sulphur dioxide for combustion of biomass are suppressed after substitution of biomass for municipal solid waste materials as the input fuel mixture. Interactions between these and other pollutants such as hydrogen chloride, nitrous oxide and carbon monoxide indicate complex, competing reactions occur between intermediates of these compounds to determine final resultant emissions. Conclusions: Fluidised bed concurrent combustion is an appropriate technique to exploit biomass and municipal solid waste resources, without the use of fossil fuels. The addition of municipal solid waste to biomass combustion has the effect of reducing emissions of some gaseous pollutants