Simulation of diffusion time of small molecules in protein crystals

A simple model for evaluation of diffusion times of small molecule into protein crystals has been developed, which takes into account the physical and chemical properties both of protein crystal and the diffusing molecules. The model also includes consideration of binding and the binding affinity of a ligand to the protein. The model has been validated by simulation of experimental set-ups of several examples found in the literature. These experiments cover a wide range of situations: from small to relatively large diffusing molecules, crystals having low, medium, or high protein density, and different size. The reproduced experiments include ligand exchange in protein crystals by soaking techniques. Despite the simplifying assumptions of the model, theoretical and experimental data are in agreement with available data, with experimental diffusion times ranging from a few seconds to several hours. The method has been used successfully for planning intermediate cryotrapping experiments in maltodextrin phosphorylase crystals.     

Effect of environmental parameters on biodiversity of the fungal component in lithic Antarctic communities

Extremophiles - A wide sampling of rocks, colonized by microbial epi–endolithic communities, was performed along an altitudinal gradient from sea level to 3600 m asl and sea distance...     

Co-management and Spatial Features Contribute to Secure Fish Abundance and Fishing Yields in Tropical Floodplain Lakes

Empirical data are needed to show the efficacy of co-management, which is regarded as a promising approach to achieve conservation goals. In this study, we addressed the potential influence of fisheries co-management to increase fish abundance and fishing yields in the lower Tocantins River Basin (Brazilian Amazon), downstream from a large dam. We analyzed 590 fish landings (6.7 t of fish) from five fishing villages and 48 fish samples obtained using gillnets (10,378 fish from 101 species) in 12 floodplain lakes in four regions: two with incipient co-management and two unmanaged. The fish species richness did not differ among the regions, but the lakes in the regions that were co-managed had higher fish abundance (biomass and number of individuals) and a higher mean proportion of fish reproducing during the high water season. Fishers had higher catches per unit of effort in the co-managed regions than fishers in the non-managed regions. These results were also influenced by geographic factors (distance and accessibility of lakes), as fish biomass was higher in lakes that were distant from the main river and from the main city in the region. Managers should thus consider strategic selection of the geographic locations of managed sites, even in remote areas. However, the fish biomass sampled in lakes was more related to region than to the lakes’ geographical location. Therefore, co-management has at least partially contributed to increased fish abundance and fishing yields in the studied region, through the protection of an important fish habitat (lakes). We provide empirical evidence that co-management can contribute to the maintenance of fish abundance, sustainability of fisheries, and food security in large tropical rivers impacted by damming.     

Identifying DNA splice sites using hypernetworks with artificial molecular evolution

Identifying DNA splice sites is a main task of gene hunting. We introduce the hyper-network architecture as a novel method for finding DNA splice sites. The hypernetwork architecture is a biologically inspired information processing system composed of networks of molecules forming cells, and a number of cells forming a tissue or organism. Its learning is based on molecular evolution. DNA examples taken from GenBank were translated into binary strings and fed into a hypernetwork for training. We performed experiments to explore the generalization performance of hypernetwork learning in this data set by two-fold cross validation. The hypernetwork generalization performance was comparable to well known classification algorithms. With the best hypernetwork obtained, including local information and heuristic rules, we built a system (HyperExon) to obtain splice site candidates. The HyperExon system outperformed leading splice recognition systems in the list of sequences tested.     

Interleukin-15 plays a central role in human kidney physiology and cancer through the γc signaling pathway

The ability of Interleukin-15 (IL-15) to activate many immune antitumor mechanisms renders the cytokine a good candidate for the therapy of solid tumors, particularly renal cell carcinoma. Although IL-15 is being currently used in clinical trials, the function of the cytokine on kidney's components has not been extensively studied; we thus investigated the role of IL-15 on normal and tumor renal epithelial cells. Herein, we analyzed the expression and the biological functions of IL-15 in normal renal proximal tubuli (RPTEC) and in their neoplastic counterparts, the renal clear cell carcinomas (RCC). This study shows that RPTEC express a functional heterotrimeric IL-15Rαβγc complex whose stimulation with physiologic concentrations of rhIL-15 is sufficient to inhibit epithelial mesenchymal transition (EMT) commitment preserving E-cadherin expression. Indeed, IL-15 is not only a survival factor for epithelial cells, but it can also preserve the renal epithelial phenotype through the γc-signaling pathway, demonstrating that the cytokine possess a wide range of action in epithelial homeostasis. In contrast, in RCC in vitro and in vivo studies reveal a defect in the expression of γc-receptor and JAK3 associated kinase, which strongly impacts IL-15 signaling. Indeed, in the absence of the γc/JAK3 couple we demonstrate the assembly of an unprecedented functional high affinity IL-15Rαβ heterodimer, that in response to physiologic concentrations of IL-15, triggers an unbalanced signal causing the down-regulation of the tumor suppressor gene E-cadherin, favoring RCC EMT process. Remarkably, the rescue of IL-15/γc-dependent signaling (STAT5), by co-transfecting γc and JAK3 in RCC, inhibits EMT reversion. In conclusion, these data highlight the central role of IL-15 and γc-receptor signaling in renal homeostasis through the control of E-cadherin expression and preservation of epithelial phenotype both in RPTEC (up-regulation) and RCC (down-regulation).     

Plasticity in the Rat Prefrontal Cortex: Linking Gene Expression and an Operant Learning with a Computational Theory

The plasticity in the medial Prefrontal Cortex (mPFC) of rodents or lateral prefrontal cortex in non human primates (lPFC), plays a key role neural circuits involved in learning and memory. Several genes, like brain-derived neurotrophic factor (BDNF), cAMP response element binding (CREB), Synapsin I, Calcium/calmodulin-dependent protein kinase II (CamKII), activity-regulated cytoskeleton-associated protein (Arc), c-jun and c-fos have been related to plasticity processes. We analysed differential expression of related plasticity genes and immediate early genes in the mPFC of rats during learning an operant conditioning task. Incompletely and completely trained animals were studied because of the distinct events predicted by our computational model at different learning stages. During learning an operant conditioning task, we measured changes in the mRNA levels by Real-Time RT-PCR during learning; expression of these markers associated to plasticity was incremented while learning and such increments began to decline when the task was learned. The plasticity changes in the lPFC during learning predicted by the model matched up with those of the representative gene BDNF. Herein, we showed for the first time that plasticity in the mPFC in rats during learning of an operant conditioning is higher while learning than when the task is learned, using an integrative approach of a computational model and gene expression.     

Survival and redox activity of Friedmanniomyces endolithicus, an Antarctic endemic black meristematic fungus,after gamma rays exposure

Despite living organisms are not exposed to acute ionizing radiation under natural conditions, some exhibit a high radiation resistance. Understanding this phenomenon is important for assessing the impact of radiation-related accidents, occupational exposures and space missions. In this context, in this study we analyzed the effect of gamma rays on the Antarctic cryptoendolithic melanized fungus Friedmanniomyces endolithicus CCFEE 5208 and demonstrated its resistance to acute doses of gamma radiation (up to 400 Gy), accompanied by increase in metabolic activity.