Biology
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Item GRASP [Genomic Resource Access for Stoichioproteomics]: comparative explorations of the atomic content of 12 Drosophila proteomes(Springer Nature, 2013-09-04) Gilbert, James D J; Acquisti, Claudia; Martinson, Holly M; Elser, James J; Kumar, Sudhir; Fagan, William F“Stoichioproteomics” relates the elemental composition of proteins and proteomes to variation in the physiological and ecological environment. To help harness and explore the wealth of hypotheses made possible under this framework, we introduce GRASP (http://www.graspdb.net), a public bioinformatic knowledgebase containing information on the frequencies of 20 amino acids and atomic composition of their side chains. GRASP integrates comparative protein composition data with annotation data from multiple public databases. Currently, GRASP includes information on proteins of 12 sequenced Drosophila (fruit fly) proteomes, which will be expanded to include increasingly diverse organisms over time. In this paper we illustrate the potential of GRASP for testing stoichioproteomic hypotheses by conducting an exploratory investigation into the composition of 12 Drosophila proteomes, testing the prediction that protein atomic content is associated with species ecology and with protein expression levels. Elements varied predictably along multivariate axes. Species were broadly similar, with the D. willistoni proteome a clear outlier. As expected, individual protein atomic content within proteomes was influenced by protein function and amino acid biochemistry. Evolution in elemental composition across the phylogeny followed less predictable patterns, but was associated with broad ecological variation in diet. Using expression data available for D. melanogaster, we found evidence consistent with selection for efficient usage of elements within the proteome: as expected, nitrogen content was reduced in highly expressed proteins in most tissues, most strongly in the gut, where nutrients are assimilated, and least strongly in the germline. The patterns identified here using GRASP provide a foundation on which to base future research into the evolution of atomic composition in Drosophila and other taxa.Item Transient windows for connectivity in a changing world(Springer Nature, 2014-01-13) Zeigler, Sara L; Fagan, William FThe primary focus of studies examining metapopulation processes in dynamic or disturbance-dependent landscapes has been related to spatiotemporal changes in the habitat patches themselves. However, like the habitat patches, opportunities for movement between patches can also exist intermittently in dynamic landscapes, creating transient connectivity windows – which we define as a period of time during which matrix conditions increase the probability of one or more individuals moving successfully between habitat patches. Far less is known about the implications of dynamic changes in connectivity per se, and, to our knowledge, there are no connectivity metrics or metapopulation models that explicitly consider intermittent changes to connectivity between habitat patches. Consequently, in this paper, we examined the peer-reviewed, published literature up to November 2013 to better understand the consequences of variability in connectivity and to highlight knowledge gaps on this topic. First, we describe how connectivity per se can vary along a temporal gradient, offering examples of ecological systems that fall along this gradient. Second, we examine how temporal variability in connectivity is important for metapopulation dynamics, particularly given likely alterations to disturbance regimes as a result of global change. We conclude our review by briefly discussing key avenues for future connectivity-related research, all of which hinge on the need to perceive connectivity as a transient feature.