Prediction of protein-protein interaction types using association rule based classification

This article has been made available through the Brunel Open Access Publishing Fund - Copyright @ 2009 Park et alBackground: Protein-protein interactions (PPI) can be classified according to their characteristics into, for example obligate or transient interactions. The identification and characterization of these PPI types may help in the functional annotation of new protein complexes and in the prediction of protein interaction partners by knowledge driven approaches. Results: This work addresses pattern discovery of the interaction sites for four different interaction types to characterize and uses them for the prediction of PPI types employing Association Rule Based Classification (ARBC) which includes association rule generation and posterior classification. We incorporated domain information from protein complexes in SCOP proteins and identified 354 domain-interaction sites. 14 interface properties were calculated from amino acid and secondary structure composition and then used to generate a set of association rules characterizing these domain-interaction sites employing the APRIORI algorithm. Our results regarding the classification of PPI types based on a set of discovered association rules shows that the discriminative ability of association rules can significantly impact on the prediction power of classification models. We also showed that the accuracy of the classification can be improved through the use of structural domain information and also the use of secondary structure content. Conclusion: The advantage of our approach is that we can extract biologically significant information from the interpretation of the discovered association rules in terms of understandability and interpretability of rules. A web application based on our method can be found at http://bioinfo.ssu.ac.kr/~shpark/picasso/SHP was supported by the Korea Research Foundation Grant funded by the Korean Government(KRF-2005-214-E00050). JAR has been supported by the Programme Alβan, the European Union Programme of High level Scholarships for Latin America, scholarship E04D034854CL. SK was supported by Soongsil University Research Fund

Orientation of tabular mafic intrusions controls convective vigour and crystallization style

The microstructure in basaltic dykes is significantly different to that in sills and lava lakes of the same bulk composition. For a given width of intrusion (or depth of lava lake), vertical tabular bodies are coarser-grained than horizontal bodies, with an invariant plagioclase shape across the intrusion. When comparing samples from sills and dykes for which the average grain size is the same, the dyke samples contain fewer small grains and fewer large grains than the sill samples. In contrast, the variation of median clinopyroxene-plagioclase-plagioclase dihedral angles in dykes correlates precisely with that observed in sills and is a function of the rate of diffusive heat loss. These patterns can be accounted for if the early stages of crystallization in dykes primarily involve the growth of isolated grains suspended in a well-mixed convecting magma, with the final stage (during which dihedral angles form) occurring in a crystal-rich static magma during which heat loss is primarily diffusive. In contrast, crystallization in sills occurs predominantly in marginal solidification fronts, suggesting that any convective motions are insufficient to entrain crystals from the marginal mushy layers and to keep them suspended while they grow. An exception to this general pattern is provided by members of the Mull Solitary Dykes, which propagated 100-1000 km SE from the Mull Palaeogene Igneous Centre, Scotland, through the shallow crust. These dykes, where sampled > 100 km from Mull, have a microstructure indistinguishable from that of a sill of comparable thickness. We suggest that sufficient nucleation and crystallization occurred in these dykes to increase the viscosity sufficiently to damp convection once unidirectional flow had ceased

Pyrosequencing of Mytilus galloprovincialis cDNAs: tissue-specific expression patterns.

BACKGROUND: Mytilus species are important in marine ecology and in environmental quality assessment, yet their molecular biology is poorly understood. Molecular aspects of their reproduction, hybridisation between species, mitochondrial inheritance, skewed sex ratios of offspring and adaptation to climatic and pollution factors are priority areas. METHODOLOGY/PRINCIPAL FINDINGS: To start to address this situation, expressed genetic transcripts from M. galloprovincialis were pyrosequenced. Transcripts were isolated from the digestive gland, foot, gill and mantle of both male and female mussels. In total, 175,547 sequences were obtained and for foot and mantle, 90% of the sequences could be assembled into contiguous fragments but this reduced to 75% for the digestive gland and gill. Transcripts relating to protein metabolism and respiration dominated including ribosomal proteins, cytochrome oxidases and NADH dehydrogenase subunits. Tissue specific variation was identified in transcripts associated with mitochondrial energy metabolism, with the digestive gland and gill having the greatest transcript abundance. Using fragment recruitment it was also possible to identify sites of potential small RNAs involved in mitochondrial transcriptional regulation. Sex ratios based on Vitelline Envelop Receptor for Lysin and Vitelline Coat Lysin transcript abundances, indicated that an equal sex distribution was maintained. Taxonomic profiling of the M. galloprovincialis tissues highlighted an abundant microbial flora associated with the digestive gland. Profiling of the tissues for genes involved in intermediary metabolism demonstrated that the gill and digestive gland were more similar to each other than to the other two tissues, and specifically the foot transcriptome was most dissimilar. CONCLUSIONS: Pyrosequencing has provided extensive genomic information for M. galloprovincialis and generated novel observations on expression of different tissues, mitochondria and associated microorganisms. It will also facilitate the much needed production of an oligonucleotide microarray for the organism

Satellite remote sensing data can be used to model marine microbial metabolite turnover

Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters to create a system-scale model of marine microbial metabolism for 5904 grid cells (49 km2) in the Western English Chanel, across 3 years of weekly averages. Thirteen environmental variables predicted the relative abundance of 24 bacterial Orders and 1715 unique enzyme-encoding genes that encode turnover of 2893 metabolites. The genes’ predicted relative abundance was highly correlated (Pearson Correlation 0.72, P-value <10−6) with their observed relative abundance in sequenced metagenomes. Predictions of the relative turnover (synthesis or consumption) of CO2 were significantly correlated with observed surface CO2 fugacity. The spatial and temporal variation in the predicted relative abundances of genes coding for cyanase, carbon monoxide and malate dehydrogenase were investigated along with the predicted inter-annual variation in relative consumption or production of ~3000 metabolites forming six significant temporal clusters. These spatiotemporal distributions could possibly be explained by the co-occurrence of anaerobic and aerobic metabolisms associated with localized plankton blooms or sediment resuspension, which facilitate the presence of anaerobic micro-niches. This predictive model provides a general framework for focusing future sampling and experimental design to relate biogeochemical turnover to microbial ecology

Sex-biased parental care and sexual size dimorphism in a provisioning arthropod

The diverse selection pressures driving the evolution of sexual size dimorphism (SSD) have long been debated. While the balance between fecundity selection and sexual selection has received much attention, explanations based on sex-specific ecology have proven harder to test. In ectotherms, females are typically larger than males, and this is frequently thought to be because size constrains female fecundity more than it constrains male mating success. However, SSD could additionally reflect maternal care strategies. Under this hypothesis, females are relatively larger where reproduction requires greater maximum maternal effort – for example where mothers transport heavy provisions to nests. To test this hypothesis we focussed on digger wasps (Hymenoptera: Ammophilini), a relatively homogeneous group in which only females provision offspring. In some species, a single large prey item, up to 10 times the mother’s weight, must be carried to each burrow on foot; other species provide many small prey, each flown individually to the nest. We found more pronounced female-biased SSD in species where females carry single, heavy prey. More generally, SSD was negatively correlated with numbers of prey provided per offspring. Females provisioning multiple small items had longer wings and thoraxes, probably because smaller prey are carried in flight. Despite much theorising, few empirical studies have tested how sex-biased parental care can affect SSD. Our study reveals that such costs can be associated with the evolution of dimorphism, and this should be investigated in other clades where parental care costs differ between sexes and species

Embodying self-compassion within virtual reality and its effects on patients with depression

Background: Self-criticism is a ubiquitous feature of psychopathology and can be combatted by increasing levels of self-compassion. However, some patients are resistant to self-compassion. Aims: To investigate whether the effects of self-identification with virtual bodies within immersive virtual reality could be exploited to increase self-compassion in patients with depression. Method: We developed an 8-minute scenario in which 15 patients practised delivering compassion in one virtual body and then experienced receiving it from themselves in another virtual body. Results: In an open trial, three repetitions of this scenario led to significant reductions in depression severity and self-criticism, as well as to a significant increase in self-compassion, from baseline to 4-week follow-up. Four patients showed clinically significant improvement. Conclusions: The results indicate that interventions using immersive virtual reality may have considerable clinical potential and that further development of these methods preparatory to a controlled trial is now warranted

Protection and mechanism of action of a novel human respiratory syncytial virus vaccine candidate based on the extracellular domain of small hydrophobic protein

Infections with human respiratory syncytial virus (HRSV) occur globally in all age groups and can have devastating consequences in young infants. We demonstrate that a vaccine based on the extracellular domain (SHe) of the small hydrophobic (SH) protein of HRSV, reduced viral replication in challenged laboratory mice and in cotton rats. We show that this suppression of viral replication can be transferred by serum and depends on a functional IgG receptor compartment with a major contribution of FcRI and FcRIII. Using a conditional cell depletion method, we provide evidence that alveolar macrophages are involved in the protection by SHe-specific antibodies. HRSV-infected cells abundantly express SH on the cell surface and are likely the prime target of the humoral immune response elicited by SHe-based vaccination. Finally, natural infection of humans and experimental infection of mice or cotton rats does not induce a strong immune response against HRSV SHe. Using SHe as a vaccine antigen induces immune protection against HRSV by a mechanism that differs from the natural immune response and from other HRSV vaccination strategies explored to date. Hence, HRSV vaccine candidates that aim at inducing protective neutralizing antibodies or T-cell responses could be complemented with a SHe-based antigen to further improve immune protection

'I Once Stared at Myself in the Mirror for Eleven Hours.' Exploring mirror gazing in participants with body dysmorphic disorder

This study provides insight into the lived experience of mirror gazing using Interpretative Phenomenological Analysis and Photo Elicitation. A total of 10 participants who identified themselves as suffering from body dysmorphic disorder took photographs that related to their body dysmorphic disorder experience. Photographs were discussed in interviews. It was found that mirror gazing in body dysmorphic disorder is an embodied phenomenon. Motivations for mirror gazing were confusing, complex and masochistic. Overall, participants described mirrors as being controlling, imprisoning and disempowering forces that had a crippling and paralysing effect on life. It is argued that health psychologists must ask clients about their embodied experiences when looking in the mirror

A proton-cyclotron wave storm generated by unstable proton distribution functions in the solar wind

We use audification of 0.092 s cadence magnetometer data from the Wind spacecraft to identify waves with amplitudes >0.1 nT near the ion gyrofrequency (~0.1 Hz) with duration longer than 1 hr during 2008. We present one of the most common types of event for a case study and find it to be a proton-cyclotron wave storm, coinciding with highly radial magnetic field and a suprathermal proton beam close in density to the core distribution itself. Using linear Vlasov analysis, we conclude that the long-duration, large-amplitude waves are generated by the instability of the proton distribution function. The origin of the beam is unknown, but the radial field period is found in the trailing edge of a fast solar wind stream and resembles other events thought to be caused by magnetic field footpoint motion or interchange reconnection between coronal holes and closed field lines in the corona

The importance of metagenomic surveys to microbial ecology: or why Darwin would have been a metagenomic scientist

Scientific discovery is incremental. The Merriam-Webster definition of 'Scientific Method' is "principles and procedures for the systematic pursuit of knowledge involving the recognition and formulation of a problem, the collection of data through observation and experiment, and the formulation and testing of hypotheses". Scientists are taught to be excellent observers, as observations create questions, which in turn generate hypotheses. After centuries of science we tend to assume that we have enough observations to drive science, and enable the small steps and giant leaps which lead to theories and subsequent testable hypotheses. One excellent example of this is Charles Darwin's Voyage of the Beagle, which was essentially an opportunistic survey of biodiversity. Today, obtaining funding for even small-scale surveys of life on Earth is difficult; but few argue the importance of the theory that was generated by Darwin from his observations made during this epic journey. However, these observations, even combined with the parallel work of Alfred Russell Wallace at around the same time have still not generated an indisputable 'law of biology'. The fact that evolution remains a 'theory', at least to the general public, suggests that surveys for new data need to be taken to a new level