Spatio-structural granularity of biological material entities

<p>Abstract</p> <p>Background</p> <p>With the continuously increasing demands on knowledge- and data-management that databases have to meet, ontologies and the theories of granularity they use become more and more important. Unfortunately, currently used theories and schemes of granularity unnecessarily limit the performance of ontologies due to two shortcomings: (i) they do not allow the integration of multiple granularity perspectives into one granularity framework; (ii) they are not applicable to cumulative-constitutively organized material entities, which cover most of the biomedical material entities.</p> <p>Results</p> <p>The above mentioned shortcomings are responsible for the major inconsistencies in currently used spatio-structural granularity schemes. By using the Basic Formal Ontology (BFO) as a top-level ontology and Keet's general theory of granularity, a granularity framework is presented that is applicable to cumulative-constitutively organized material entities. It provides a scheme for granulating complex material entities into their constitutive and regional parts by integrating various compositional and spatial granularity perspectives. Within a scale dependent resolution perspective, it even allows distinguishing different types of representations of the same material entity. Within other scale dependent perspectives, which are based on specific types of measurements (e.g. weight, volume, etc.), the possibility of organizing instances of material entities independent of their parthood relations and only according to increasing measures is provided as well. All granularity perspectives are connected to one another through overcrossing granularity levels, together forming an integrated whole that uses the <it>compositional object perspective </it>as an integrating backbone. This granularity framework allows to consistently assign structural granularity values to all different types of material entities.</p> <p>Conclusions</p> <p>The here presented framework provides a spatio-structural granularity framework for all domain reference ontologies that model cumulative-constitutively organized material entities. With its multi-perspectives approach it allows querying an ontology stored in a database at one's own desired different levels of detail: The contents of a database can be organized according to diverse granularity perspectives, which in their turn provide different <it>views </it>on its content (i.e. data, knowledge), each organized into different levels of detail.</p

Bridging Crystal Engineering and Drug Discovery by Utilizing Intermolecular Interactions and Molecular Shapes in Crystals

Most structure-based drug discovery methods utilize crystal structures of receptor proteins. Crystal engineering, on the other hand, utilizes the wealth of chemical information inherent in small-molecule crystal structures in the Cambridge Structural Database (CSD). We show that the interaction surfaces and shapes of molecules in experimentally determined small-molecule crystal structures can serve as effective tools in drug discovery. Our description of the shape and interaction propensities of molecules in their crystal structures can be used to screen them for specific binding compatibility with protein targets, as demonstrated through the high-throughput profiling of around 138 000 small-molecule structures in the CSD and a series of drug-protein crystal structures. Electron-density-based intermolecular boundary surfaces in small-molecule crystal structures and in target-protein pockets are utilized to identify potential ligand molecules from the CSD based on 3D shape and intermolecular interaction matching

Supramolecular interactions between hexabromoethane and cyclopentadienyl ruthenium bromides: Halogen bonding or electrostatic organisation?

The interaction between hexabromoethane and [CpRu(CO)2Br] (Cp = (η-C5H5), results in the deposition of two different isostoichiometric co-crystals, 2[CpRu(CO)2Br]·C2Br6, one crystallising in space group P (Z = 1) and the other in P21/n (Z = 4). These were produced in the reaction of HCBr3 and [(CpRu(CO)2)2] under indoor illumination, following a slight modification of the literature procedure. The origin of the hexabromoethane is as yet unknown but it appears to have been formed in the reaction rather than being an impurity in the bromoform. We have analysed the structures using the Hirshfeld surface approach and electrostatic potentials, supported by DFT theoretical calculations to better define the nature of intermolecular interactions in the solid state. The results indicate that the most significant interactions within both crystal forms arise not from the closest van der Waals contacts but, rather, from more distant interactions between the unsymmetrical electron distributions about the bromine atoms in the solvate and substrate molecules

Seemingly simple group 8 cyclopentadienyl dicarbonyl metal halides: From little things, interesting things grow

Single crystal X-ray studies are presented for the ‘piano-stool’ structures [CpRu,Os(CO)2Cl], [Cp′Ru(CO)2X] (X = Cl, Br, I (redetermination)), [Cp*Ru(CO)2Cl] (two phases), enabling the assembly of comparative geometric data for the [CpM(CO)2Cl] (M = Fe, Ru, Os), [Cp,Cp′Ru(CO)2X] (X = Cl, Br, I) and [CpxRu(CO)2Cl] (Cpx = Cp (η–C5H5), Cp′ (η–C5H4CH3), Cp* (η–C5CH3)5,CpPh (η–C5(C6H5)5)). In the [Cp′Ru(CO)2X] arrays, the methyl groups are found to consistently lie ‘eclipsed’ vis-a-vis the halogen substituents, with a concomitant tilt of the Cp ring; the reasons for this are explored theoretically

Encroachment of upland Mediterranean plant species in riparian ecosystems of southern Portugal

Riparian ecosystems have unique biodiversity, are highly sensitive to disturbance and anthropogenic influence. As world water resources become scarcer, scientists predict greater competition among species for water resources. Indeed, increased encroachment of upland plants into the riparian zone is already occurring, irreversibly changing riparian plant communities. Since semi-arid regions such as Mediterranean-type ecosystems are likely to follow this same trajectory, assessing the contributions of riparian versus upland (sclerophyllous) plants to community composition is important. A survey of seventy 2 km-long riparian transects on the Sado and Guadiana watersheds in southern Portugal assessed (1) the woody riparian plant community composition, (2) how much richness is due to strictly riparian plants versus sclerophyllous upland plants, and (3) which combinations of biotic and abiotic factors allow higher species richness in the strictly riparian, sclerophyllous, and overall plant communities. The survey detected 53 different woody plant species (28 endemic) across all communities. Riparian community richness was on average 16 species, seven of which were strictly riparian and the remainder being sclerophyllous, exotic species or fruit trees. Sclerophyllous plant species occurred consistently across sampling units (90% of transects). On average, 46% of the total woody plant community richness was due to strictly riparian plants and 28% was due to sclerophyllous plants. Community richness was positively affected by the area of shrubs in the riparian zone and by the absence of human activities and goats. Surrounding landscape pattern only affected the strictly riparian plant richness. These results suggest that natural and human-mediated disturbances in riparian ecosystems create gaps and clearings for which riparian and sclerophyllous plants compete. Establishment success seems to be related to the propagule pressure of the neighbouring landscape, its diversity and density, as well as the presence of herbivores. Preserving strictly riparian plants, removing exotic species, preventing grazing, and promoting riparian values (recreation, aesthetics and the provision of ecosystem services) will aid the future conservation of the unique biodiversity of riparian ecosystems