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Publication year - 2010
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201090062
Subject(s) - snail , biology , chemistry , ecology
Following the firebomb The ancients got one thing right with their Aristotelian elements: Fire. Reactive oxygen species (ROS) are a universal element of life. The spark of fire that creates ATP is the result of completing the last hand‐off in the relay of electrons that consumes our food in exchange for chemical energy. But, as Prometheus discovered, there was a price to be paid for giving man fire. But I digress; that's for Ancient History 101. Federova et al. chose to use rat legmuscle proteins as a system for studying the damage caused by and recovery from oxidative stress directed primarily at the amino acid tryptophan. Knowing the crystal structure of actin and tropomyosin, they were able to use MS/MS to determine the sensitivity of each trp residue to damage and the rate at which the cell repaired the damage caused by X‐irradiation. pp. 2692–2700Little snails grow up Snails are escargot in some parts of the world, but mostly they are agricultural pests. They are not enough of a pest to put them on the “genome to be sequenced” list, so Sun et al. took it upon themselves to at least get some proteomic data on early development of one species. Pomacea canaliculata , the golden apple snail, lays up to 8000 eggs per year. Development goes through several stages, initially without a shell, then developing a fully formed shell as it transitions from stage II to stage III. A number of other changes occur at the same time. Using 2‐DE MS/MS, they detected ∼700 spots, 125 of which were abundant enough to examine further. They were sequenced then MS‐BLASTed and MASCOTed; over 50% were identified. Some look like potential targets for control of the pests. pp. 2701–2711Does your model lose its flavor in the forced layout overnight? Do your nodes and edges seem to all look alike? Do you get a headache after trying to remember differences between, say, the third and fourth layouts? Do you stop when you should GO? Then you need the smooth new clustered circular layout (CCL) software (Fung et al. ). Compared with graphs generated by the old‐fashioned force directed layout, the CCL does not suffer from irregularity in final layout and it does treat complementary information, e.g. Gene Ontology data, as real information, not simply as a name tag, and it can use colors intelligently for nodes and edges. The visibility of GO information also reveals the location of protein‐protein clusters, bottleneck points at interfaces, and localization of proteins in organelles. pp. 2723–2727

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