Native Sites (native + site)

Distribution by Scientific Domains


Selected Abstracts


New algorithms and an in silico benchmark for computational enzyme design

PROTEIN SCIENCE, Issue 12 2006
Alexandre Zanghellini
Abstract The creation of novel enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Here we describe two new algorithms for enzyme design that employ hashing techniques to allow searching through large numbers of protein scaffolds for optimal catalytic site placement. We also describe an in silico benchmark, based on the recapitulation of the active sites of native enzymes, that allows rapid evaluation and testing of enzyme design methodologies. In the benchmark test, which consists of designing sites for each of 10 different chemical reactions in backbone scaffolds derived from 10 enzymes catalyzing the reactions, the new methods succeed in identifying the native site in the native scaffold and ranking it within the top five designs for six of the 10 reactions. The new methods can be directly applied to the design of new enzymes, and the benchmark provides a powerful in silico test for guiding improvements in computational enzyme design. [source]


The regulation of ecosystem functions by ecotypic variation in the dominant plant: a Spartina alterniflora salt-marsh case study

JOURNAL OF ECOLOGY, Issue 1 2002
Denise M. Seliskar
Summary 1Genetic differences among populations of a keystone species may affect ecosystem functional properties. We tested this by planting Spartina alterniflora from different geographical regions in a newly created salt marsh in Delaware, USA. 2Spartina alterniflora plants from morphologically distinct short-form (back marsh) populations were originally collected from Massachusetts (41°34, N), Delaware (38°47, N), and Georgia (31°25, N) in the USA and vegetatively propagated for 6 years in a salt water-irrigated common garden in Delaware before transfer to a newly created salt marsh. 3The magnitude of the expression of marsh functions in the created marsh, measured over 5 years, remained distinct in patches of each ecotype. End of season aerial biomass, below-ground biomass, root and rhizome distribution, canopy height, stem density, and carbohydrate reserves were closer to values reported for the plants' native sites than to those typical of Delaware. Thus, many of the plant features characteristic of particular latitudes appear to be under genetic control. Such ecotypic differentiation influences ecosystem function through keystone resource and keystone modifier activities. 4Respiration of the microbial community associated with either dead shoots or the soil varied with plant ecotype in the created wetland and the patterns reflected those reported for their native sites. High edaphic respiration under the Massachusetts ecotype was correlated with the high percentage of sugar in the rhizomes. Edaphic chlorophyll was greater under the canopies of the Massachusetts and Delaware ecotypes than under the Georgia canopy and exhibited a relationship similar to that of algal production rates reported for the native sites. Larval fish were most abundant in pit traps in the Massachusetts ecotype. [source]


Effect of an exotic Acacia (Fabaceae) on ant assemblages in South African fynbos

AUSTRAL ECOLOGY, Issue 4 2001
Kristine French
Abstract Ant assemblages in South African fynbos invaded by Acacia saligna were compared with ant assemblages in undisturbed fynbos to determine whether ant assemblages change under exotic plants that produce ant-dispersed seeds. Overall, no differences in the species richness of ants were found between weed-infested and native sites but there were differences in both ant abundance and the composition of the ant assemblage. Ants were much less abundant in weed-infested sites. To investigate whether changes in ant assemblages in weed-infested areas could be due to a preference for native seeds over exotic seeds, seeds of a range of species were offered to ants and ants that handled seeds were identified. Thirteen species of ants handled A. saligna seeds and there was no evidence to suggest that the ant assemblage as a whole preferred native seeds to A. saligna seeds. Hypotheses that may account for this pattern are discussed. [source]