On Branching Processes and the Early Stages of the Spread of an Epidemic

Branchingprocess(BP)isusedtomodeltheearlystagesofthespreadofasexuallytransmitteddisease.TheearlystagesofAIDSspreadwhichistransmittedbothhomosexuallyandheterosexuallyarestudiedasaBP.     

Influence of agar and activated charcoal on uptake of gibberellin and plant morphogenesis In vitro

Summary Agar and activated charcoal (AC) are commonly used in tissue culture. However, their deeper actions and functions are largely unknown. This experiment investigated the effect of agar and AC, singly and jointly, on gibberellin (GA) uptake by corn shoots. Corn seeds were germinated on Murashige and Skoog medium (MS). Shoot excised from 1-wk-old seedlings were cultured on liquid (0.0 g l⁻¹ agar) or solid (8 g l⁻¹ agar) MS containing 3 μM indole-3-acetic acid, 13.3 μM N⁶-benzyladenine, and 6000 CPM ml⁻¹ [³H]GA₄ as tracer. Both liquid and solid media had two treatments, one without AC and one supplemented with 5 g l⁻¹AC. Uptake of [³H]GA₄ and morphogenesis of corn shoots were recorded after 2 wk of culture. Corn explants cultured in AC-free media acquired high levels of [³H]GA₄, while explants from AC-containing media showed only traces of [³H]GA₄. Explants cultured in AC-free liquid medium contained about twice the amount of [³H]GA₄ as those from AC-free solid medium. Addition of agar reduced shoot length, while addition of AC increased both shool and root length. It is concluded that: (1) agar reduced the uptake of GA₄; and (2) GA₄ was irreversibly adsorbed by AC, and thus became unavailable to corn explants.     

A regio- and stereo-controlled approach to triazoloquinoxalinyl C-nucleosides

The synthesis of a new series of acyclic triazoloquinoxalinyl C-nucleosides and their transformation to their cyclic analogs are described following protection, activation, and deprotection with subsequent intramolecular nucleophilic substitution protocol. The antibacterial potency of the new compounds was determined using an inhibition zone diameter test. The results show that 3a and 2b exhibit good activity against Escherichiacoli and Candidaalbicans. On the other hand, the cyclic mesylated C-nucleoside 13 showed activity against the Gram-positive bacteria (Staphylococcusaureus) and antifungal activity against C. albicans.     

Identification of Embryonic Neural Plate Border Stem Cells and Their Generation by Direct Reprogramming from Adult Human Blood Cells

1. Download high-res image (202KB)
2. Download full-size image

     

Topological analysis and interactive visualization of biological networks and protein structures

Computational analysis and interactive visualization of biological networks and protein structures are common tasks for gaining insight into biological processes. This protocol describes three workflows based on the NetworkAnalyzer and RINalyzer plug-ins for Cytoscape, a popular software platform for networks. NetworkAnalyzer has become a standard Cytoscape tool for comprehensive network topology analysis. In addition, RINalyzer provides methods for exploring residue interaction networks derived from protein structures. The first workflow uses NetworkAnalyzer to perform a topological analysis of biological networks. The second workflow applies RINalyzer to study protein structure and function and to compute network centrality measures. The third workflow combines NetworkAnalyzer and RINalyzer to compare residue networks. The full protocol can be completed in ～2 h.     

Computing topological parameters of biological networks

Rapidly increasing amounts of molecular interaction data are being produced by various experimental techniques and computational prediction methods. In order to gain insight into the organization and structure of the resultant large complex networks formed by the interacting molecules, we have developed the versatile Cytoscape plugin NetworkAnalyzer. It computes and displays a comprehensive set of topological parameters, which includes the number of nodes, edges, and connected components, the network diameter, radius, density, centralization, heterogeneity, and clustering coefficient, the characteristic path length, and the distributions of node degrees, neighborhood connectivities, average clustering coefficients, and shortest path lengths. NetworkAnalyzer can be applied to both directed and undirected networks and also contains extra functionality to construct the intersection or union of two networks. It is an interactive and highly customizable application that requires no expert knowledge in graph theory from the user. AVAILABILITY: NetworkAnalyzer can be downloaded via the Cytoscape web site: http://www.cytoscape.org     

Somatic embryogenesis from leaf of witloof chicory through suspension culture

A procedure for regeneration of somatic embryogenesis from witloof chicory leaf has been developed. Explants were taken from the distal third part of leaf vein and cultured on Murashige and Skoog medium (MS) containing 100 mg/1 casein hydrolysate 1.3 M 2,4-D, and 1.3 M kinetin. A pale yellowisl nodular callus was formed after 4 weeks which was maintained in the same medium for 8–12 weeks with one change to a fresh medium every 4 weeks. Callus was then suspended in the same medium without agar for 4–6 weeks with one change to a fresh medium every 2 weeks. Embryo-like structures appeared upon transfer to liquid MS containing 1.8 M benzyladenine. Embryo germination was accomplished in half strength MS medium with or without 1 g/l activated charcoal.Abbreviations AC activated charcoal - BA benzyladenine - MS Murashige & Skoog (1962) medium     

Rapid propagation of tuna (Opuntia ficus-indica) and plant establishment in soil

Explants from young joints of mature plants of tuna (Opuntia ficus-indica Mill.) were cultured on Murashige and Skoog (MS) medium containing 8.8 M benzyladenine (BA) and 0.5 M naphthaleneacetic acid (NAA). Shoots produced were utilized as secondary explants. Each shoot was cut longitudinally from apex to base into two explants, and some of these explants were cut transversely into proximal and distal explants. The size and number of shoots produced was affected by size and position of the explant within its source. The shoots were rooted in vitro or ex vitro and plants were successfully established in soil from both rooting methods.Abbreviations AC activated charcoal - BA benzyladenine - IBA indolebutyric acid - MS Murashige & Skoog (1962) medium - NAA naphthaleneacetic acid     

A promoter DNA demethylation landscape of human hematopoietic differentiation

Global mechanisms defining the gene expression programs specific for hematopoiesis are still not fully understood. Here, we show that promoter DNA demethylation is associated with the activation of hematopoietic-specific genes. Using genome-wide promoter methylation arrays, we identified 694 hematopoietic-specific genes repressed by promoter DNA methylation in human embryonic stem cells and whose loss of methylation in hematopoietic can be associated with gene expression. The association between promoter methylation and gene expression was studied for many hematopoietic-specific genes including CD45, CD34, CD28, CD19, the T cell receptor (TCR), the MHC class II gene HLA-DR, perforin 1 and the phosphoinositide 3-kinase (PI3K) and results indicated that DNA demethylation was not always sufficient for gene activation. Promoter demethylation occurred either early during embryonic development or later on during hematopoietic differentiation. Analysis of the genome-wide promoter methylation status of induced pluripotent stem cells (iPSCs) generated from somatic CD34(+) HSPCs and differentiated derivatives from CD34(+) HSPCs confirmed the role of DNA methylation in regulating the expression of genes of the hemato-immune system, and indicated that promoter methylation of these genes may be associated to stemness. Together, these data suggest that promoter DNA demethylation might play a role in the tissue/cell-specific genome-wide gene regulation within the hematopoietic compartment.