A New Analysis Method for Simulations Using Node Categorizations

Most research concerning the influence of network structure on phenomena taking place on the network focus on relationships between global statistics of the network structure and characteristic properties of those phenomena, even though local structure has a significant effect on the dynamics of some phenomena. In the present paper, we propose a new analysis method for phenomena on networks based on a categorization of nodes. First, local statistics such as the average path length and the clustering coefficient for a node are calculated and assigned to the respective node. Then, the nodes are categorized using the self-organizing map (SOM) algorithm. Characteristic properties of the phenomena of interest are visualized for each category of nodes. The validity of our method is demonstrated using the results of two simulation models. The proposed method is useful as a research tool to understand the behavior of networks, in particular, for the large-scale networks that existing visualization techniques cannot work well.Comment: 9 pages, 8 figures. This paper will be published in Social Network Analysis and Mining(www.springerlink.com

Novel regulation of mitotic exit by the Cdc42 effectors Gic1 and Gic2

Copyright @ The Rockefeller University PressThe guanine nucleotide exchange factor Cdc24, the GTPase Cdc42, and the Cdc42 effectors Cla4 and Ste20, two p21-activated kinases, form a signal transduction cascade that promotes mitotic exit in yeast. We performed a genetic screen to identify components of this pathway. Two related bud cortex–associated Cdc42 effectors, Gic1 and Gic2, were obtained as factors that promoted mitotic exit independently of Ste20. The mitotic exit function of Gic1 was dependent on its activation by Cdc42 and on the release of Gic1 from the bud cortex. Gic proteins became essential for mitotic exit when activation of the mitotic exit network through Cdc5 polo kinase and the bud cortex protein Lte1 was impaired. The mitotic exit defect of cdc5-10 Δlte1 Δgic1 Δgic2 cells was rescued by inactivation of the inhibiting Bfa1-Bub2 GTPase-activating protein. Moreover, Gic1 bound directly to Bub2 and prevented binding of the GTPase Tem1 to Bub2. We propose that in anaphase the Cdc42-regulated Gic proteins trigger mitotic exit by interfering with Bfa1-Bub2 GTPase-activating protein function.The work of E. Schiebel is supported by Cancer Research UK

Functional diversification of Argonautes in nematodes:an expanding universe

In the last decade, many diverse RNAi (RNA interference) pathways have been discovered that mediate gene silencing at epigenetic, transcriptional and post-transcriptional levels. The diversity of RNAi pathways is inherently linked to the evolution of Ago (Argonaute) proteins, the central protein component of RISCs (RNA-induced silencing complexes). An increasing number of diverse Agos have been identified in different species. The functions of most of these proteins are not yet known, but they are generally assumed to play roles in development, genome stability and/or protection against viruses. Recent research in the nematode Caenorhabditis elegans has expanded the breadth of RNAi functions to include transgenerational epigenetic memory and, possibly, environmental sensing. These functions are inherently linked to the production of secondary siRNAs (small interfering RNAs) that bind to members of a clade of WAGOs (worm-specific Agos). In the present article, we review briefly what is known about the evolution and function of Ago proteins in eukaryotes, including the expansion of WAGOs in nematodes. We postulate that the rapid evolution of WAGOs enables the exceptional functional plasticity of nematodes, including their capacity for parasitism

Effects of ocean acidification on invertebrate settlement at volcanic CO<inf>2</inf> vents

We present the first study of the effects of ocean acidification on settlement of benthic invertebrates and microfauna. Artificial collectors were placed for 1 month along pH gradients at CO2 vents off Ischia (Tyrrhenian Sea, Italy). Seventy-nine taxa were identified from six main taxonomic groups (foraminiferans, nematodes, polychaetes, molluscs, crustaceans and chaetognaths). Calcareous foraminiferans, serpulid polychaetes, gastropods and bivalves showed highly significant reductions in recruitment to the collectors as pCO2 rose from normal (336-341 ppm, pH 8.09-8.15) to high levels (886-5,148 ppm) causing acidified conditions near the vents (pH 7.08-7.79). Only the syllid polychaete Syllis prolifera had higher abundances at the most acidified station, although a wide range of polychaetes and small crustaceans was able to settle and survive under these conditions. A few taxa (Amphiglena mediterranea, Leptochelia dubia, Caprella acanthifera) were particularly abundant at stations acidified by intermediate amounts of CO2 (pH 7. 41-7.99). These results show that increased levels of CO2 can profoundly affect the settlement of a wide range of benthic organisms. © 2010 Springer-Verlag

XDJ1, a gene encoding a novel non-essential DnaJ homologue from Saccharomyces cerevisiae

The gene encoding a novel DnaJ-like protein, termed Xdj1, has been identified by amplification of Saccharomyces cerevisiae genomic DNA. An open reading frame of 1380 bp was detected. Disruption of XDJ1 did not yield any detectable new phenotype. A double-deletion strain containing a disruption of both XDJ1 and YDJ1, another gene coding for a DnaJ-like protein, was still viable. Under a variety of growth conditions, no XDJ1 transcripts could be detected by Northern blot analysis and no translation product was found by immunoblotting with antibody against Xdj1 produced in Escherichia coli. Thus, XDJ1 is either expressed only under very specific conditions or represents a silent gene

Environmental issues and the geological storage of CO2 : a discussion document

Increasing CO2 emissions will lead to climate change and ocean acidification with severe consequences for ecosystems and for human society. Strategies are being sought to reduce emissions including the geological storage of CO2. Existing studies operate within existing oil and gas regulatory frameworks, but if other non-oil reservoir geological formations are used these existing regulations may not apply. At UK and European levels the potential environmental impacts of uncontrolled CO2 releases from storage sites have been highlighted to be of significance for regulators. Thus a new regulatory framework may be needed. The precautionary principle is likely to be adopted by regulators, so it is important that the effects of acute and chronic exposures of ecosystems to CO2 leakages are evaluated. Consequently, existing regulations are likely to be developed to include specific recommendations concerning leakages. This review shows that many basic data simply do not exist to assist regulators in this process

Subtle but significant effects of CO<inf>2</inf> acidified seawater on embryos of the intertidal snail, Littorina obtusata

Our understanding of the effects of ocean acidification on whole organism function is growing, but most current information is for adult stages of development. Here, we show the effects of reduced pH seawater (pH 7.6) on aspects of the development, physiology and behaviour of encapsulated embryos of the marine intertidal gastropod Littorina obtusata. We found reduced viability and increased development times under reduced pH conditions, and the embryos had significantly altered behaviours and physiologies. In acidified seawater, embryos spent more time stationary, had slower rotation rates, spent less time crawling, but increased their movement periodicity compared with those maintained under control conditions. Larval and adult heart rates were significantly lower in acidified seawater, and hatchling snails had an altered shell morphology (lateral length and spiral shell length) compared to control snails. Our findings show that ocean acidification may have multiple, subtle effects during the early development of marine animals that may have implications for their survival beyond those predicted using later life stages. © Inter-Research 2009

A method to compensate head movements for mobile eye tracker using invisible markers

Although mobile eye-trackers have wide measurement range of gaze, and high flexibility, it is difficult to judge what a subject is actually looking at based only on obtained coordinates, due to the influence of head movement. In this paper, a method to compensate for head movements while seeing the large screen with mobile eye-tracker is proposed, through the use of NIR-LED markers embedded on the screen. The head movements are compensated by performing template matching on the images of view camera to detect the actual eye position on the screen. As a result of the experiment, the detection rate of template matching was 98.6%, the average distance between the actual eye position and the corrected eye position was approximately 16 pixels for the projected image (1920 x 1080)