BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed

Seismological Structures on Bimodal Distribution of Deep Tectonic Tremor

Deep tectonic tremors occur at the downdip extent of the seismogenic zone due to fluid processes. Beneath the northeastern Kii Peninsula, southwestern Japan, there is an along-dip bimodal distribution of tremor. However, no constraint exists on the structures controlling that distribution. We extract detailed seismological structures from multi-band receiver functions and evaluate conditional differences in the distribution. To achieve high resolution images along the plate interface, we utilize records of regional deep-focus earthquakes from the Pacific slab. Cross-section images show the subducting oceanic plate with depth-dependent phases along the bimodal distribution, revealing a conspicuous plate interface at the updip portion and an inconspicuous interface below the mantle wedge at the downdip portion. This indicates that episodic tremors occur in the high pore-fluid plate interface below the impermeable forearc crust, and that continual tremors occur at the permeable mantle wedge corner, owing to continuous fluid supply from the oceanic crust. [Plain Language Summary] Deep slow earthquakes have mainly been detected at the deeper extent of estimated large-slip regions of large-scale regular earthquakes in the Nankai subduction zone, southwestern Japan. Epicenters of tectonic tremors are also downdip-aligned. However, some clusters of continual tremor with frequent small bursts were found at further downdip portions beneath the northeastern Kii Peninsula. The complexity of the bimodal tremor distribution poses a structural question regarding whether the tectonic tremor occurs below a mantle wedge or below the continental crust. We utilize a receiver function method that surveys subsurface velocity boundaries and evaluate detailed seismological structures around the plate interface using a multi-band analysis. Furthermore, regional deep-focus earthquake records are effectively utilized for receiver function mapping. The high-frequency cross section exhibits depth dependence of plate-interface phases, which demarcates active regions of updip events and downdip continual tremor, thus revealing that episodic tremor occurs below the continental crust and continual tremor occurs at the mantle wedge corner. The high-contrast updip interface reveals that a large amount of fluid is confined at the plate interface below the impermeable forearc crust, which may lead to active episodic slow earthquakes at updip portions

Control of plasma membrane lipid homeostasis by the extended synaptotagmins

Acute metabolic changes in plasma membrane (PM) lipids, such as those mediating signalling reactions, are rapidly compensated by homeostatic responses whose molecular basis is poorly understood. Here we show that the extended synaptotagmins (E-Syts), endoplasmic reticulum (ER) proteins that function as PtdIns(4,5)P2- and Ca2+-regulated tethers to the PM, participate in these responses. E-Syts transfer glycerolipids between bilayers in vitro, and this transfer requires Ca2+ and their lipid-harbouring SMP domain. Genome-edited cells lacking E-Syts do not exhibit abnormalities in the major glycerolipids at rest, but exhibit enhanced and sustained accumulation of PM diacylglycerol following PtdIns(4,5)P2 hydrolysis by PLC activation, which can be rescued by expression of E-Syt1, but not by mutant E-Syt1 lacking the SMP domain. The formation of E-Syt-dependent ER–PM tethers in response to stimuli that cleave PtdIns(4,5)P2 and elevate Ca2+ may help reverse accumulation of diacylglycerol in the PM by transferring it to the ER for metabolic recycling.Accepted versio

Control of plasma membrane lipid homeostasis by the extended synaptotagmins

Acute metabolic changes of plasma membrane (PM) lipids, such as those mediating signaling reactions, are rapidly compensated by homeostatic responses whose molecular basis is poorly understood. Here we show that the Extended-Synaptotagmins (E-Syts), ER proteins which function as PI(4,5)P(2) and Ca(2+)-regulated tethers to the PM, participate in these responses. E-Syts transfer glycerolipids between bilayers in vitro and such transfer requires Ca(2+) and their SMP domain, a lipid-harboring module. Genome edited cells lacking E-Syts do not exhibit abnormalities in the major glycerolipids at rest, but display enhanced and sustained accumulation of PM diacylglycerol (DAG) upon PI(4,5)P(2) hydrolysis by PLC activation, which can be rescued by expression of E-Syt1, but not by mutant E-Syt1 lacking the SMP domain. The formation of E-Syts-dependent ER-PM tethers in response to stimuli that cleave PI(4,5)P(2) and elevate Ca(2+) may help reverse accumulation of DAG in the PM by transferring it to the ER for metabolic recycling