Subcellular proteomic characterization of the high-temperature stress response of the cyanobacterium Spirulina platensis

The present study examined the changes in protein expression in Spirulina platensis upon exposure to high temperature, with the changes in expression analyzed at the subcellular level. In addition, the transcriptional expression level of some differentially expressed proteins, the expression pattern clustering, and the protein-protein interaction network were analyzed. The results obtained from differential expression analysis revealed up-regulation of proteins involved in two-component response systems, DNA damage and repair systems, molecular chaperones, known stress-related proteins, and proteins involved in other biological processes, such as capsule formation and unsaturated fatty acid biosynthesis. The clustering of all differentially expressed proteins in the three cellular compartments showed: (i) the majority of the proteins in all fractions were sustained tolerance proteins, suggesting the roles of these proteins in the tolerance to high temperature stress, (ii) the level of resistance proteins in the photosynthetic membrane was 2-fold higher than the level in two other fractions, correlating with the rapid inactivation of the photosynthetic system in response to high temperature. Subcellular communication among the three cellular compartments via protein-protein interactions was clearly shown by the PPI network analysis. Furthermore, this analysis also showed a connection between temperature stress and nitrogen and ammonia assimilation

Comparative analysis of the Spirulina platensis subcellular proteome in response to low- and high-temperature stresses: uncovering cross-talk of signaling components

The present study focused on comparative proteome analyses of low- and high-temperature stresses and potential protein-protein interaction networks, constructed by using a bioinformatics approach, in response to both stress conditions

Progress Report : CEq Emergence Assistant (the tool support for the CEq formal method)

JAIST 21世紀COEシンポジウム2008「検証進化可能電子社会」= JAIST 21st Century COE Symposium 2008 Verifiable and Evolvable e-Society, 開催：2008年3月3日～4日, 開催場所：北陸先端科学技術大学院大学GRP研究員発表会　セッションB-2発表資

Lambdoid emergence

We analyse lambdoid gene regulation using the CEq formal method for inferring emergent properties from modal influence graphs. In addition to presenting the most comprehensive mathematical modelling of Bacteriophage lambda to date, our approach allows us to articulate and explore rigourously stated and algebraically concise properties of the way the virus works, and to propose novel explanations of the nature of lambdoid switching, stability, anti-immunity, and more.リサーチレポート（北陸先端科学技術大学院大学情報科学研究科

Rewriting game theory applied to protein signalling in MAPK cascades

We propose the recent notion of rewriting game theory as a tool for studying biochemical systems. Rewriting game theory is based on a discrete and dynamic notion of Nash-style equilibria for games without structural constraints and with arbitrary payoff values. Our aim here is to show how the formalism can be used to characterise biological information as logical properties of a purely chemical model. Specifically, we address MAPK cascades through a compendium of the involved chemical reactions, with particular focus on the known signalling pathways. We also present preliminary computerised support for our methodology.リサーチレポート（北陸先端科学技術大学院大学情報科学研究科

SpirPep: an in silico digestion-based platform to assist bioactive peptides discovery from a genome-wide database

Abstract Background Bioactive peptides, including biological sources-derived peptides with different biological activities, are protein fragments that influence the functions or conditions of organisms, in particular humans and animals. Conventional methods of identifying bioactive peptides are time-consuming and costly. To quicken the processes, several bioinformatics tools are recently used to facilitate screening of the potential peptides prior their activity assessment in vitro and/or in vivo. In this study, we developed an efficient computational method, SpirPep, which offers many advantages over the currently available tools. Results The SpirPep web application tool is a one-stop analysis and visualization facility to assist bioactive peptide discovery. The tool is equipped with 15 customized enzymes and 1–3 miscleavage options, which allows in silico digestion of protein sequences encoded by protein-coding genes from single, multiple, or genome-wide scaling, and then directly classifies the peptides by bioactivity using an in-house database that contains bioactive peptides collected from 13 public databases. With this tool, the resulting peptides are categorized by each selected enzyme, and shown in a tabular format where the peptide sequences can be tracked back to their original proteins. The developed tool and webpages are coded in PHP and HTML with CSS/JavaScript. Moreover, the tool allows protein-peptide alignment visualization by Generic Genome Browser (GBrowse) to display the region and details of the proteins and peptides within each parameter, while considering digestion design for the desirable bioactivity. SpirPep is efficient; it takes less than 20 min to digest 3000 proteins (751,860 amino acids) with 15 enzymes and three miscleavages for each enzyme, and only a few seconds for single enzyme digestion. Obviously, the tool identified more bioactive peptides than that of the benchmarked tool; an example of validated pentapeptide (FLPIL) from LC-MS/MS was demonstrated. The web and database server are available at http://spirpepapp.sbi.kmutt.ac.th. Conclusion SpirPep, a web-based bioactive peptide discovery application, is an in silico-based tool with an overview of the results. The platform is a one-stop analysis and visualization facility; and offers advantages over the currently available tools. This tool may be useful for further bioactivity analysis and the quantitative discovery of desirable peptides

Additional file 4: of SpirPep: an in silico digestion-based platform to assist bioactive peptides discovery from a genome-wide database

Table S1. Dataset and output comparison between SpirPep and BIOPEP, the identified bioactive peptides obtained from temperature stress – expressed protein [30] digested with trypsin and no miscleavage. (XLSX 18 kb

Additional file 2: of SpirPep: an in silico digestion-based platform to assist bioactive peptides discovery from a genome-wide database

Figure S2. SpirPep sequence diagram: SpirPep was designed into a three-tier system (front-end, queuing, and back-end). The front-end sends the queries to SpirPepDB (FrontendDB and SpirPepApps) and responds to the users. The queries are queued by the Redis server and sent to Resque worker(s) in the back-end. When the analysis is complete, the system will send an email notification with the link to the results page to users. The results will be stored in the database temporary table and exported to the GFF file format, which can be internally used by the SpirPep visualizer. (JPEG 466 kb