The signaling hubs at the crossroad of longevity and age-related disease networks

The established human age-related disease proteins (ARDPs) and longevity-associated proteins (LAPs) together with their first-order interacting partners form scale-free networks which significantly overlap. About half of the common proteins are involved in signal transduction. These proteins are strongly interconnected and in turn form a common signaling network which comprises over 40% of all hubs (proteins with multiple interactions) in the human interactome. Along with the insulin pathway, the common signaling network is remarkably enriched with the focal adhesion and adherens junction proteins whose relation to the control of lifespan is yet to be fully addressed. The examples of such candidate proteins include several hubs, focal adhesion kinase PTK2 and the extracellular proteins fibronectin FN1, paxillin PXN, and vinculin VCL. The results of the network-based analysis highlight the potential importance of these pathways, especially hubs, in linking the human longevity and age-related diseases.     

A Novel Approach for Ovine Primary Alveolar Epithelial Type II Cell Isolation and Culture from Fresh and Cryopreserved Tissue Obtained from Premature and Juvenile Animals

The in vivo ovine model provides a clinically relevant platform to study cardiopulmonary mechanisms and treatments of disease; however, a robust ovine primary alveolar epithelial type II (ATII) cell culture model is lacking. The objective of this study was to develop and optimize ovine lung tissue cryopreservation and primary ATII cell culture methodologies for the purposes of dissecting mechanisms at the cellular level to elucidate responses observed in vivo. To address this, we established in vitro submerged and air-liquid interface cultures of primary ovine ATII cells isolated from fresh or cryopreserved lung tissues obtained from mechanically ventilated sheep (128 days gestation—6 months of age). Presence, abundance, and mRNA expression of surfactant proteins was assessed by immunocytochemistry, Western Blot, and quantitative PCR respectively on the day of isolation, and throughout the 7 day cell culture study period. All biomarkers were significantly greater from cells isolated from fresh than cryopreserved tissue, and those cultured in air-liquid interface as compared to submerged culture conditions at all time points. Surfactant protein expression remained in the air-liquid interface culture system while that of cells cultured in the submerged system dissipated over time. Despite differences in biomarker magnitude between cells isolated from fresh and cryopreserved tissue, cells isolated from cryopreserved tissue remained metabolically active and demonstrated a similar response as cells from fresh tissue through 72 hr period of hyperoxia. These data demonstrate a cell culture methodology using fresh or cryopreserved tissue to support study of ovine primary ATII cell function and responses, to support expanded use of biobanked tissues, and to further understanding of mechanisms that contribute to in vivo function of the lung.     

Spectral reflectance and integrity of cell membranes and chlorophyll relative to the concentration of airborne mineral elements in a lichen

To determine the environmental impact of oil-combustion pollutants and soil dust on a lichen, we examined the spectral reflectance of thalli of the epiphytic fruticose lichen, Ramalina duriaei , expressed as values of NDVI (the normalized difference vegetation index). We analyzed electrolyte leakage caused by degradation of cell membranes in terms of electric conductivity of water, apart from chlorophyll degradation, the latter expressed as changes in the A435 nm/A415 nm ratio to indicate the physiological status of the lichen. The concentrations of Al, Cr, Fe, K, Ni, P, sulfate-S, Ti and V in the lichen thallus were measured to quantify the degree of pollution. Thalli of R. duriaei , growing in a nature reserve on the periphery of a 40-year-old industrial town, Ashdod, in southwest Israel were compared with thalli of R. duriaei from an unpolluted forest in the northeastern part of the country transplanted to the polluted areas in and around the town. After an exposure for 10 months, many transplants exhibited lower NDVI values, higher electric conductivity values as well as a lower A435 nm/A415 nm ratio. The three physical/physiological parameters thus reflected severe injury in the lichen transplants. The concentrations of Al, Cr, Fe, Ni, sulfate-S, Ti and V in the lichen transplants were found to correlate inversely with the NDVI values, whereas the concentrations of Fe, Ni, Ti and V were found to correlate with electric conductivity. The decrease in the A435 nm/A415 nm ratio was found to correlate with high concentrations of Al, Fe, Ni, sulfate-S, Ti and V in the lichen transplants, whereas the concentration of K and P correlated with both the NDVI value and the A435 nm/A415 nm ratio. It is concluded that in situ thalli of R. duriaei , the only indigenous fruticose lichen growing in the region of Ashdod, are endangered by the presence of pollutants and by acid rain due to the combustion of heavy fuel oil.     

Approaching the CAPRI challenge with an efficient geometry-based docking

The last 3 rounds (3-5) of CAPRI included a wide range of docking targets. Several targets were especially challenging, since they involved large-scale movements and symmetric rearrangement, while others were based on homology models. We have approached the targets with a variety of geometry-based docking algorithms that include rigid docking, symmetric docking, and flexible docking with symmetry constraints. For all but 1 docking target, we were able to submit at least 1 acceptable quality prediction. Here, we detail for each target the prediction methods used and the specific biological data employed, and supply a retrospective analysis of the results. We highlight the advantages of our techniques, which efficiently exploit the geometric shape complementarity properties of the interaction. These enable them to run only few minutes on a standard PC even for flexible docking, thus proving their scalability toward computational genomic scale experiments. We also outline the major required enhancements, such as the introduction of side-chain position refinement and the introduction of flexibility for both docking partners.