Blue copper proteins: a comparative analysis of their molecular interaction properties

Blue copper proteins are type-I copper-containing redox proteins whose role is to shuttle electrons from an electron donor to an electron acceptor in bacteria and plants. A large amount of experimental data is available on blue copper proteins; however, their functional characterization is hindered by the complexity of redox processes in biological systems. We describe here the application of a semiquantitative method based on a comparative analysis of molecular interaction fields to gain insights into the recognition properties of blue copper proteins. Molecular electrostatic and hydrophobic potentials were computed and compared for a set of 33 experimentally-determined structures of proteins from seven blue copper subfamilies, and the results were quantified by means of similarity indices. The analysis provides a classification of the blue copper proteins and shows that (I) comparison of the molecular electrostatic potentials provides useful information complementary to that highlighted by sequence analysis; (2) similarities in recognition properties can be detected for proteins belonging to different subfamilies, such as amicyanins and pseudoazurins, that may be isofunctional proteins; (3) dissimilarities in interaction properties, consistent with experimentally different binding specificities, may be observed between proteins belonging to the same subfamily, such as cyanobacterial and eukaryotic plastocyanins; (4) proteins with low sequence identity, such as azurins and pseudoazurins, can have sufficient similarity to bind to similar electron donors and acceptors while having different binding specificity profiles.     

Dynamics of genotypic structure in clonal Rhododendron ferrugineum (Ericaceae) populations

Two populations of Rhododendron ferrugineum growing at subalpine level in the Pyrenees (France) were studied in two sites (Bethmale and Mourtis). Identification and delimitation of genets were inferred from amplified fragment length polymorphism (AFLP) markers, along a closure gradient (from meadow to more closed heath) in each site. Surface and age of genets, genotypic diversity (Simpson's index D), 'proportion distinguishable' genotypes and genetic relationships between genets were then estimated. Amplification of the 312 DNA samples with three selective primer pairs gave a mean of 98 detectable peaks (i.e. bands) per sample, with size ranging from 60 to 300 bp. In total 60% (Bethmale) and 70% (Mourtis) of the peaks were polymorphic, and a total of 31 and 23 multilocus genotypes were identified, in Bethmale and Mourtis, respectively. We inferred that pioneer genotypes began arriving 110 years ago mainly over a 40-year period in the Mourtis meadow, and began about 130 years ago over a 100-year period in the Bethmale meadow. After this pioneer stage, populations extended vegetatively. Two different patterns of genotypic dynamics can be identified. At Bethmale, population closure could have led to a dramatic loss of genets and to the selection of highly genetically related genotypes. In contrast, at Mourtis, genotypic diversity and genet density did not change fundamentally along the closure gradient. However the range of genetic diversity diminished from the open to the closed situation, suggesting that thinning could have occurred in the past.     

Seed protein electrophoresis of some cultivated and wild species of <Emphasis Type="Italic">Chenopodium</Emphasis>

Seed protein profiles of 40 cultivated and wild taxa of Chenopodium have been compared by sodium dodecyl sulfate polyacrylamide gel electrophoresis. The relative similarity between various taxa, estimated by Jaccard’s similarity index and clustered in UPGMA dendrogram, is generally in accordance with taxonomic position, crossability relationships and other biochemical characters. Eight accessions of C. quinoa studied are clustered together and show genetic similarity with closely related C. bushianum and C. berlandieri subsp. nuttalliae. The taxa included under C. album complex are clustered in two groups which show that these taxa are a heterogenous assemblage and their taxonomic affinities need a reassessment. Other wild species studied are placed in the dendrogram more or less according to their taxonomic position.     

Alteration of Fish Diversity Downstream from Petit-Saut Dam in French Guiana. Implication of Ecological Strategies of Fish Species

Dams are expected to decrease fish diversity because they deeply alter downstream environment. However, such decline has not been consistently observed although profound modifications in the structure and/or composition of fish communities were generally recorded, and were linked to modifications of the downstream environment. In this work we analyze data from observations made before and almost 10 years after the completion of a hydroelectric dam in the neotropics. We monitored fish diversity below that dam and compared the taxonomic and functional structures of the samples between the pre- and post-dam periods. A significant decrease in species richness was evidenced. Taxonomic and trophic structures were significantly different between the two periods. Conversely, the functional structure of samples based on reproductive traits did not change significantly after the damming. Concerning feeding habits, a large increase in relative abundance of detritivores and a parallel decrease of fish species feeding on terrestrial food sources were observed in samples taken 6–9 years after closure of the dam as compared with samples taken before the dam.     

Evolutionary transition from resprouter to seeder life history in two Erica (Ericaceae) species: insights from seedling axillary buds

BACKGROUND AND AIMS: The genus Erica represents the epitome of plant biodiversity in the South African Cape region. It includes seeder and resprouter species, but both species diversity and narrow endemism are tightly associated with the seeder habit. It also includes 'mixed' species, in which both seeder and resprouter life histories are found. This intraspecific variation in life history is genetically based. METHODS: The cotyledonary region and basal stem of seeder and resprouter seedlings of two 'mixed' species, Erica calycina and E. coccinea, were examined to detect morphological and anatomical differences in axillary bud development between regeneration forms. KEY RESULTS: While at least some bud activity was observed for resprouter seedlings, none was detected for seeder seedlings. A closer examination allowed the detection of some axillary buds in seeder seedlings of the two species, but they appeared in an unequivocally atrophied state. CONCLUSIONS: The seeder and resprouter life histories are two character states and the seeder one (i.e. loss of resprouting) is derived within these two Erica species. Results allow the hypothesis that the loss of resprouting in a fire-prone scenario such as the Cape fynbos has promoted high diversification rates in seeder Erica lineages.     

Variation in fish density,assemblage composition and relative rates of predation among mangrove,seagrass and coral reef habitats

We tested the hypothesis for several Caribbean reef fish species that there is no difference in nursery function among mangrove, seagrass and shallow reef habitat as measured by: (a) patterns of juvenile and adult density, (b) assemblage composition, and (c) relative predation rates. Results indicated that although some mangrove and seagrass sites showed characteristics of nursery habitats, this pattern was weak. While almost half of our mangrove and seagrass sites appeared to hold higher proportions of juvenile fish (all species pooled) than did reef sites, this pattern was significant in only two cases. In addition, only four of the six most abundant and commercially important species (Haemulon flavolineatum, Haemulon sciurus, Lutjanus apodus, Lutjanus mahogoni, Scarus iserti, and Sparisoma aurofrenatum) showed patterns of higher proportions of juvenile fish in mangrove and/or seagrass habitat(s) relative to coral reefs, and were limited to four of nine sites. Faunal similarity between reef and either mangrove or seagrass habitats was low, suggesting little, if any exchange between them. Finally, although relative risk of predation was lower in mangrove/seagrass than in reef habitats, variance in rates was substantial suggesting that not all mangrove/seagrass habitats function equivalently. Specifically, relative risk varied between morning and afternoon, and between sites of similar habitat, yet varied little, in some cases, between habitats (mangrove/seagrass vs. coral reefs). Consequently, our results caution against generalizations that all mangrove and seagrass habitats have nursery function.     

Disturbance-Mediated Drift in Tree Functional Groups in Amazonian Forest Fragments

The interactive effects of forest disturbance and fragmentation on tropical tree assemblages remain poorly understood. We examined the effects of forest patch and landscape metrics, and levels of forest disturbance on the patterns of floristic composition and abundance of tree functional groups within 21 forest fragments and two continuous forest sites in southern Brazilian Amazonia. Trees were sampled within 60 (10 × 250 m) plots placed in the core areas of the fragments. Tree assemblage composition and abundance were summarized using nonmetric multidimensional scaling (NMDS). Forest patch size explained 36.2 percent and 30 percent of the variance in the proportion of small-seeded softwood and hardwood stems in the 21 forest patches, respectively. Large fragments retained a higher abundance of hardwood tree species whereas small-seeded softwood trees appear to proliferate rapidly in small disturbed fragments. Generalized linear mixed models showed that time since fragmentation had both positive and negative effects on the density of different functional groups of trees and on the ordination axes describing tree abundance. The composition and abundance of different tree genera were also related to time since fragmentation, distance to the nearest edge, and fire severity, despite the recent post-isolation history of the forest patches surveyed. Both the proliferation of fast-growing pioneer trees and the decline of hardwood trees found in our forest plots have profound consequences on the floristic composition, forest dynamics, carbon storage, and nutrient cycling in Amazonian forest fragments.     

Riqueza y Distribución Ecológica de Especies de Pteridofitas en la Zona del Río Yavarí-Mirín, Amazonía Peruana

We studied the ecological distribution of pteridophytes (ferns and fern allies) along eight 8-km transects covering 12.7 ha in Peruvian Amazonia. Subunits of 200 m² of the transects have previously been classified into four different forest types, and here we document and quantify the floristic differences among these forest types. Pteridophytes have been suggested as an indicator group to classify rain forest habitats, but this requires that the ecological preferences of the species are well documented and consistent across geographic regions. Here we analyzed in detail the distribution and diversity patterns of 130 species across the four rain forest types. Relative species abundance and species diversity were similar among some of the forest types and differed among others, but the species composition differed markedly. Our results largely confirmed the earlier interpretation of the edaphic preferences of the pteridophyte species in western Amazonia. This supports the proposition that deterministic processes have an important role in influencing the floristic composition of Amazonian forests.     

Helminth parasitism in the coyote, Canis latrans, from the Rolling Plains of Texas

Eighteen helminth species were recovered from 150 coyotes necropsied in West Texas: 2 trematodes, Alaria marcianae (12% of hosts infected) and Alaria sp. (0.6%); 3 cestodes, Taenia pisiformis (39%), T. serialis (4%) and Mesocestoides corti (58%); 2 acanthocephalans, Oncicola canis (26%) and Pachysentis canicola (23%); and 11 nematodes, Physaloptera rara (60%), Pterygondermatites cahirensis (37%), Spirocerca lupi (83%), Subulura s.p. (1.3%), Filaroides osleri (28%), Ancylostoma caninum (87%), Toxascaris leonina (89%), Dermatoxys veligera (1.3%), Syphacia sp. (0.6%), Dirofilaria immitis (0.6%), and Trichuris sp. (0.6%). All hosts were infected with from 1 to 10 helminth species (-x = 5.5 species). Simpson's index was very low (0.12) indicating a diverse helminth fauna. The helminth fauna of West Texas coyotes demonstrated only low similarity with those from other geographic regions in North America. Significant positive relationships were found between pairs of prevalent helminth species in terms of frequency of occurrence. Comparison of mean levels of infection between pairs of helminth species indicated 6 significant relationships. A clumped distribution was indicated in those helminths utilizing arthropod intermediate hosts or paratenic hosts. Analysis of prevalence of helminth species in terms of host sex by frequency of occurrence and mean levels of infection revealed only one significant relationship; T. leonina occurred more frequently in females than males. Similar analysis of age relationships ( ? 1 year and ? 2 years) and helminth parasitism indicated P. rara occurred more frequently in older animals while A. caninum and P. cahirensis occurred more frequently and with higher levels of infection in younger animals. The results of these findings are discussed in terms of food niche and behavioral aspects of this host from the Rolling Plains of Texas.