Induction of a Citrus gene highly homologous to plant and yeast thi genes involved in thiamine biosynthesis during natural and ethylene-induced fruit maturation

Maturing citrus fruit undergo pigment changes which can be enhanced by exogenous ethylene. In order to identify genes induced by ethylene in citrus fruit peel, we cloned the gene c-thi1. mRNA corresponding to c-thi1 increased gradually in the peel during natural fruit maturation and in response to ethylene. GA₃ pretreatment reduced the inductive effect of ethylene. Levels of c-thi1 increased also in juice sacs but the effect of ethylene was much less prominent. c-thi1 is homologous to yeast and plant genes encoding for an enzyme belonging to the pathway of thiamine biosynthesis. The data suggest that thiamine is involved in citrus fruit maturation.     

Evidence against superoxide involvement in tyrosine hydroxylation by mushroom tyrosinase

The possible involvement of superoxide anions in the hydroxylation of tyrosine by mushroom tyrosinase was studied. Superoxide dismutase and scavengers of superoxide ions of smaller MW than superoxide dismutase, such as nitroblue tetrazolium and copper salicylate, had no direct effect on the monohydroxyphenolase activity of mushroom tyrosinase. The kinetics of tyrosine hydroxylation, but not of DOPA oxidation, by mushroom tyrosinase was atrected by the addition of a xanthine-xanthine oxidase system. In the presence of the xanthine-xanthine oxidase system, the lag period of tyrosine hydroxylation was shortened compared to the lag period in the absence of the xanthine-xanthine oxidase system. The xanthine- xanthine oxidase system alone (without mushroom tyrosinase) had no effect on tyrosine conversion to dopachrome. Superoxide dismutase, catalase and hydroxyl radical scavengers counteracted to some extent the shortening of the lag period of tyrosine hydroxylation by mushroom tyrosinase caused by the xanthin e-xanthine oxidase system. It is suggested that the shortening of the lag period is due mainly to hydroxyl radicals generated by the xanthine-xanthine oxidase system via interaction of O₂^?. and hydrogen paroxide (a Haber-Weiss type reaction). The data do not support the direct participation of superoxide anions in tyrosine hydroxylation by mushroom tyrosinase.     

Senescent cells and the incidence of age‐related diseases

Age‐related diseases such as cancer, cardiovascular disease, kidney failure, and osteoarthritis have universal features: Their incidence rises exponentially with age with a slope of 6–8% per year and decreases at very old ages. There is no conceptual model which explains these features in so many diverse diseases in terms of a single shared biological factor. Here, we develop such a model, and test it using a nationwide medical record dataset on the incidence of nearly 1000 diseases over 50 million life‐years, which we provide as a resource. The model explains incidence using the accumulation of senescent cells, damaged cells that cause inflammation and reduce regeneration, whose level rise stochastically with age. The exponential rise and late drop in incidence are captured by two parameters for each disease: the susceptible fraction of the population and the threshold concentration of senescent cells that causes disease onset. We propose a physiological mechanism for the threshold concentration for several disease classes, including an etiology for diseases of unknown origin such as idiopathic pulmonary fibrosis and osteoarthritis. The model can be used to design optimal treatments that remove senescent cells, suggeting that treatment starting at old age can sharply reduce the incidence of all age‐related diseases, and thus increase the healthspan.     

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods

Background  

The availability of microarrays measuring thousands of genes simultaneously across hundreds of biological conditions represents an opportunity to understand both individual biological pathways and the integrated workings of the cell. However, translating this amount of data into biological insight remains a daunting task. An important initial step in the analysis of microarray data is clustering of genes with similar behavior. A number of classical techniques are commonly used to perform this task, particularly hierarchical and K-means clustering, and many novel approaches have been suggested recently. While these approaches are useful, they are not without drawbacks; these methods can find clusters in purely random data, and even clusters enriched for biological functions can be skewed towards a small number of processes (e.g. ribosomes).     

A flexible method for the fabrication of gold nanostructures using oligonucleotide derivatives

Several linear and branched DNA structures from 80-200 nm with a biotine molecule in the middle have been prepared. These structures have been decorated by addition of positively charged gold nanoparticles carrying 4-(dimethylamino)pyridine ligands. Streptavidin binds to the central biotine molecule introducing a 20 nm gap in the structure in which a biotinylated nanoparticle can be introduced. The simplest structure (80 nm, linear) is formed by 4 oligonucleotides. By changing some of these components changes on length, shape, and recognition system easily can be introduced.     

Short communication direct effect of Cd on glutathione S-transferase and glutathione reductase from Calystegia sepium

Interactions between heavy metals, glutathione, glutathione S-transferase (GST), and glutathione reductase (GR) are being investigated by many working groups, but evaluation of the direct effect of Cd+ on these enzymes in vitro is lacking. We report here the effect of cadmium (10, 50, 100, 250 microM CdSO4) on partially purified enzymes from Calystegia sepium. Plants were grown under normal field conditions without metals and the enzymes were extracted by Tris buffer and partially purified by ammonium sulphate fractionation and gel filtration. Glutathione S-transferase activity was measured with different substrates, i.e., 1-chloro-2,4-dinitrobenzene (CDNB), p-nitrobenzylchloride (NBC), and the herbicide Fluorodifen. GST activity was significantly lower in leaf compared to stem, flower, and rhizome and the inhibitory effect of Cd was obtained with NBC and Fluorodifen substrates at 250 microM. There was no effect of Cd on GR activity up to 250 microM.     

AVIS: AJAX viewer of interactive signaling networks

MOTIVATION: Increasing complexity of cell signaling network maps requires sophisticated visualization technologies. Simple web-based visualization tools can allow for improved data presentation and collaboration. Researchers studying cell signaling would benefit from having the ability to embed dynamic cell signaling maps in web pages. SUMMARY: AVIS is a Google gadget compatible web-based viewer of interactive cell signaling networks. AVIS is an implementation of AJAX (Asynchronous JavaScript with XML) with the usage of the libraries GraphViz, ImageMagic (PerlMagic) and overLib. AVIS provides web-based visualization of text-based signaling networks with dynamical zooming, panning and linking capabilities. AVIS is a cross-platform web-based tool that can be used to visualize network maps as embedded objects in any web page. AVIS was implemented for visualization of PathwayGenerator, a tool that displays over 4000 automatically generated mammalian cell signaling maps; NodeNeighborhood a tool to visualize first and second interacting neighbors of yeast and mammalian proteins; and for Genes2Networks, a tool to connect lists of genes and protein using background protein interaction networks. AVAILABILITY: A demo page of AVIS and links to applications and distributions can be found at http://actin.pharm.mssm.edu/AVIS2. Detailed instructions for using and configuring AVIS can be found in the user manual at http://actin.pharm.mssm.edu/AVIS2/manual.pdf.     

Functional atlas of the integrin adhesome

A detailed depiction of the 'integrin adhesome', consisting of a complex network of 156 components linked together and modified by 690 interactions is presented. Different views of the network reveal several functional 'subnets' that are involved in switching on or off many of the molecular interactions within the network, consequently affecting cell adhesion, migration and cytoskeletal organization. Examination of the adhesome network motifs reveals a relatively small number of key motifs, dominated by three-component complexes in which a scaffolding molecule recruits both a signalling molecule and its downstream target. We discuss the role of the different network modules in regulating the structural and signalling functions of cell-matrix adhesions.     

Complex effects of scale on the relationships of landscape pattern versus avian species richness and community structure in a woodland savanna mosaic

Landscape pattern metrics are widely used for predicting habitat and species diversity. However, the relationship between landscape pattern and species diversity is typically measured at a single spatial scale, even though both landscape pattern, and species occurrence and community composition are scale‐dependent. While the effects of scale on landscape pattern are well documented, the effects of scale on the relationships between spatial pattern and species richness and composition are not well known. Here, our main goal was to quantify the effects of cartographic scale (spatial resolution and extent) on the relationships between spatial pattern and avian richness and community structure in a mosaic of grassland, woodland, and savanna in central Wisconsin. Our secondary goal was to evaluate the effectiveness of a newly developed tool for spatial pattern analysis, multiscale contextual spatial pattern analysis (MCSPA), compared to existing landscape metrics. Landscape metrics and avian species richness had quadratic, exponential, or logarithmic relationships, and these patterns were generally consistent across two spatial resolutions and six spatial extents. However, the magnitude of the relationships was affected by both resolution and extent. At the finer resolution (10‐m), edge density was consistently the best predictor of species richness, followed by an MCSPA metric that measures the standard deviation of woody cover across extents. At the coarser resolution (30‐m), NDVI was the best predictor of species richness by far, regardless of spatial extent. Another MCSPA metric that denotes the average woody cover across extents, together with percent of woody cover, were always the best predictors of variation in avian community structure. Spatial resolution and extent had varying effects on the relationships between spatial pattern and avian community structure. We therefore conclude that cartographic scale not only affects measures of landscape pattern per se, but also the relationships among spatial pattern, species richness, and community structure, often in complex ways, which reduces the efficacy of landscape metrics for predicting the richness and diversity of organisms.