Cell volume and the regulation of apoptotic cell death

Apoptosis is a physiological mechanism allowing for the removal of abundant or potentially harmful cells. The hallmarks of apoptosis include degradation of cellular DNA, exposure of phosphatidylserine at the outer leaflet of the cell membrane and cell shrinkage. Phosphatidylserine exposure favours adhesion to macrophages with subsequent phagocytosis of the shrunken apoptotic particles. The interaction of cell volume regulatory mechanisms and apoptosis is illustrated in two different model systems, i.e. (a) lymphocyte apoptosis following stimulation of CD95 receptor and (b) erythrocyte apoptosis upon cell shrinkage. (a) Triggering of CD95 in Jurkat T lymphocytes is paralleled by activation of cell volume regulatory Cl- channels, inhibition of the Na+/H+ exchanger and osmolyte release. The latter coincides with cell shrinkage, DNA fragmentation and phosphatidylserine exposure. CD95 stimulation leads to early inhibition of the voltage gated K+ channel Kv1.3, which may contribute to the inhibition of the Ca2+ release activated Ca2+ channel I(CRAC). (b) Osmotic shock of erythrocytes activates a cell volume regulatory cation conductance allowing the entry not only of Na+ but of Ca2+ as well. Increased cytosolic Ca2+ stimulates a scramblase which disrupts the phosphatidylserine asymmetry of the cell membrane, leading to phosphatidylserine exposure. The cation conductance is further activated by oxidative stress and energy depletion and inhibited by Cl-. Shrinkage of erythrocytes stimulates in addition a sphingomyelinase with subsequent formation of ceramide which potentiates the effect of cytosolic Ca2+ on phosphatidylserine. In conclusion, cell volume-sensitive mechanisms participate in the triggering of apoptosis following receptor stimulation or cell injury.     

Discovery of novel aspartyl ketone dipeptides as potent and selective caspase-3 inhibitors

The discovery of a series of potent, selective and reversible dipeptidyl caspase-3 inhibitors are reported. The iterative discovery process of using combinatorial chemistry, parallel synthesis, moleculare modelling and structural biology will be discussed.     

Bayesian analysis of binary prediction tree models for retrospectively sampled outcomes

Classification tree models are flexible analysis tools which have the ability to evaluate interactions among predictors as well as generate predictions for responses of interest. We describe Bayesian analysis of a specific class of tree models in which binary response data arise from a retrospective case-control design. We are also particularly interested in problems with potentially very many candidate predictors. This scenario is common in studies concerning gene expression data, which is a key motivating example context. Innovations here include the introduction of tree models that explicitly address and incorporate the retrospective design, and the use of nonparametric Bayesian models involving Dirichlet process priors on the distributions of predictor variables. The model specification influences the generation of trees through Bayes' factor based tests of association that determine significant binary partitions of nodes during a process of forward generation of trees. We describe this constructive process and discuss questions of generating and combining multiple trees via Bayesian model averaging for prediction. Additional discussion of parameter selection and sensitivity is given in the context of an example which concerns prediction of breast tumour status utilizing high-dimensional gene expression data; the example demonstrates the exploratory/explanatory uses of such models as well as their primary utility in prediction. Shortcomings of the approach and comparison with alternative tree modelling algorithms are also discussed, as are issues of modelling and computational extensions.     

Hantavirus pulmonary syndrome-associated hantaviruses contain conserved and functional ITAM signaling elements

Hantaviruses infect human endothelial and immune cells, causing two human diseases, hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS). We have identified key signaling elements termed immunoreceptor tyrosine-based activation motifs (ITAMs) within the G1 cytoplasmic tail of all HPS-causing hantaviruses. ITAMs direct receptor signaling within immune and endothelial cells and the presence of ITAMs in all HPS-causing hantaviruses provides a means for altering normal cellular responses which maintain vascular integrity. The NY-1 G1 ITAM was shown to coprecipitate a complex of phosphoproteins from cells, and the G1 ITAM is a substrate for the Src family kinase Fyn. The hantavirus ITAM coprecipitated Lyn, Syk, and ZAP-70 kinases from T or B cells, while mutagenesis of the ITAM abolished these interactions. In addition, G1 ITAM tyrosines directed intracellular interactions with Syk by mammalian two-hybrid analysis. These findings demonstrate that G1 ITAMs bind key cellular kinases that regulate immune and endothelial cell functions. There is currently no means for establishing the role of the G1 ITAM in hantavirus pathogenesis. However, the conservation of G1 ITAMs in all HPS-causing hantaviruses and the role of these signaling elements in immune and endothelial cells suggest that functional G1 ITAMs are likely to dysregulate normal immune and endothelial cell responses and contribute to hantavirus pathogenesis.     

Molecular evolution of the Escherichia coli chromosome. VI. Two regions of high effective recombination

Two 6- to 8-min regions, centered respectively near 45 min (O-antigen region) and 99 min (restriction-modification region) on the Escherichia coli chromosome, display unusually high variability among 11 otherwise very similar strains. This variation, revealed by restriction fragment length polymorphism (RFLP) and nucleotide sequence comparisons, appears to be due to a great local increase in the retention frequency of recombinant replacements. We infer a two-step mechanism. The first step is the acquisition of a small stretch of DNA from a phylogenetically distant source. The second is the successful retransmission of the imported DNA, together with flanking native DNA, to other strains of E. coli. Each cell containing the newly transferred DNA has a very high selective advantage until it reaches a high frequency and (in the O-antigen case) is recognized by the new host's immune system. A high selective advantage increases the probability of retention greatly; the effective recombination rate is the product of the basic recombination rate and the probability of retention. Nearby nucleotide sequences clockwise from the O-antigen (rfb) region are correlated with specific O antigens, confirming local hitchhiking. Comparable selection involving imported restriction endonuclease genes is proposed for the region near 99 min.     

The VirB4 family of proposed traffic nucleoside triphosphatases: common motifs in plasmid RP4 TrbE are essential for conjugation and phage adsorption

Proteins of the VirB4 family are encoded by conjugative plasmids and by type IV secretion systems, which specify macromolecule export machineries related to conjugation systems. The central feature of VirB4 proteins is a nucleotide binding site. In this study, we asked whether members of the VirB4 protein family have similarities in their primary structures and whether these proteins hydrolyze nucleotides. A multiple-sequence alignment of 19 members of the VirB4 protein family revealed striking overall similarities. We defined four common motifs and one conserved domain. One member of this protein family, TrbE of plasmid RP4, was genetically characterized by site-directed mutagenesis. Most mutations in trbE resulted in complete loss of its activities, which eliminated pilus production, propagation of plasmid-specific phages, and DNA transfer ability in Escherichia coli. Biochemical studies of a soluble derivative of RP4 TrbE and of the full-length homologous protein R388 TrwK revealed that the purified forms of these members of the VirB4 protein family do not hydrolyze ATP or GTP and behave as monomers in solution.