Bridging natural and social sciences: a framework for identify strategies and actions for the conservation of biodiversity.

The Atlantic Forest is one of the most diverse areas in the world and considered a hotspot. Several actions are needed for its preservation, among them the implementation of the Biodiversity Corridors. The Atlantic Forest has three biodiversity corridors and the Rio de Janeiro State, which harbors huge species diversity, is in the Serra do Mar Corridor. We developed socioeconomic, political and environmental indicators to present conservation strategies supported by a wide database. These indicators complemented the previous surveys of priority areas which emphasized biotic elements, and their integration allowed the elaboration of strategies for the conservation and management, regionally directed, to support actions to be implemented by the Government. The analysis was done considering three subjects: Anthropic Pressure, Physical and Biotic State, and Present Ability of Response. Data analysis followed a synthesis-aggregation schedule and the resulting database was taken to a workshop, where specialists proposed strategies and actions for the conservation. These strategies were discussed considering vegetation remnant distribution, biological relevance, environmental vulnerability, kind of anthropic pressure in the region and potential for success of the actions proposed, based on the ability of response. Rio de Janeiro State is very diverse in biotic, physical, political, socioeconomic and cultural aspects which demand specific actions for each region. So, depending on the present situation of the natural and anthropic environments and on the present and future sources of degradation, regionally directed actions are applicable. This specificity in conservation actions will enable that the State remnants will be more successfully protected.

Protein cutoff scanning: a comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins.

In this study, we carried out a comparative analysis between two classical methodologies to prospect residue contacts in proteins: the traditional cutoff dependent (CD) approach and cutoff free Delaunay tessellation (DT). In addition, two alternative coarse-grained forms to represent residues were tested: using alpha carbon (CA) and side chain geometric center (GC). A database was built, comprising three top classes: all alpha, all beta, and alpha/beta. We found that the cutoff value? at about 7.0 A emerges as an important distance parameter.? Up to 7.0 A, CD and DT properties are unified, which implies that at this distance all contacts are complete and legitimate (not occluded). We also have shown that DT has an intrinsic missing edges problem when mapping the first layer of neighbors. In proteins, it may produce systematic errors affecting mainly the contact network in beta chains with CA. The almost-Delaunay (AD) approach has been proposed to solve this DT problem. We found that even AD may not be an advantageous solution. As a consequence, in the strict range up ? to 7.0 A, the CD approach revealed to be a simpler, more complete, and reliable technique than DT or AD. Finally, we have shown that coarse-grained residue representations may introduce bias in the analysis of neighbors in cutoffs up to ? 6.8 A, with CA favoring alpha proteins and GC favoring beta proteins. This provides an additional argument pointing to ? the value of 7.0 A as an important lower bound cutoff to be used in contact analysis of proteins.