DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins

Abstract Despite efforts during the past decades, loop modeling remains a difficult part of protein structure modeling. Several approaches have been developed in the framework of crystal structures. However, for homology models, the modeling of loops is still far from being solved. We propose DaReUS-Loop, a data-based approach that identifies loop candidates mining the complete set of experimental structures available in the Protein Data Bank. Candidate filtering relies on local conformation profile-profile comparison, together with physico-chemical scoring. Applied to three different template-based test sets, DaReUS-Loop shows significant increase in the number of high-accuracy loops, and significant enhancement for modeling long loops. A special advantage is that our method proposes a prediction confidence score that correlates well with the expected accuracy of the loops. Strikingly, over 50% of successful loop models are derived from unrelated proteins, indicating that fragments under similar constraints tend to adopt similar structure, beyond mere homology

Herbivory among habitats on the Neotropical tree Cnidoscolus quercifolius Pohl. in a seasonally deciduous forest

Our goal was to identify herbivory patterns from two insect guilds associated with Cnidoscolus quercifolius in a tropical deciduous forest in northeastern Brazil. We sampled four different habitats: (1) forest edge, (2) mesic (near to the perennial water source), (3) forest interior and (4) rupestrian fields. Habitat edge had lower leaf damage than rupestrian, mesic and forest interior habitats. Nevertheless, abundance of galls at the edge habitat was higher than at mesic, forest interior and/or rupestrian habitats. There was no difference in gall mortality by natural enemies among the four habitats sampled, demonstrating the absence of any influence of top-down controls related to abundance of galls. Trophic relationships were not related to the patterns of distribution among habitats of two insect herbivorous guilds associated with C. quercifolius. Our results demonstrated that environmental heterogeneity of dry forests can significantly alter important ecological interactions and experimental studies are needed to better understand the mechanisms responsible for differences in herbivory among habitats

Palm species richness, latitudinal gradients, sampling effort, and deforestation in the Amazon region

ABSTRACT Palms are most diverse in warm and humid regions near the equator. Though palms remain relatively well conserved, they are under increasing pressure from deforestation. Here, we analyze patterns of palm species richness relative to latitudinal gradient, sampling effort, and deforestation in the Amazon, and compare patterns of richness and floristic similarity among Amazonian sub-regions. We built a database of 17,310 records for 177 species. The areas with the greatest richness were in the western, central and northeastern Amazon, principally at latitudes 0-5ºS. Species richness and the number of records were highly correlated (R2=0.76, P2000 km2) were found in the southern and eastern Amazon of Brazil, which coincide with low richness and gaps in records. Similarity analyzes resulted in two groups of sub-regions: the first included the Amazon s.s., the Andes and the Guiana, while the second included the Plateau and Gurupi. We conclude that the highest species richness is at low latitudes, and observed richness is affected by sampling effort and is vulnerable to deforestation. Therefore, areas with low species richness, especially areas with data deficiency, need to be further studied for a better understanding of their patterns of diversity and richness