Subtraction of background damage in PFGE experiments on DNA fragment-size distributions

The non-random distribution of DNA breakage in pulsed-field gel electrophoresis (PFGE) experiments poses a problem of proper subtraction of the background damage to obtain a fragment-size distribution due to radiation only. As been pointed out by various authors, a naive bin-to-bin subtraction of the background signal will not result in the right DNA mass distribution histogram, and may even result in negative values. Previous more systematic subtraction methods have been based mainly on random breakage, appropriate for low-LET radiation but problematic for high LET. Moreover, an investigation is needed whether the background breakage itself is random or non-random. Previously a new generalized formalism based on stochastic processes for the subtraction of the background damage in PFGE experiments for any LET and any background was proposed, and as now applied it to a set of PFGE data for Fe ions. We developed a Monte Carlo algorithm to compare the naïve subtraction procedure in artificial data sets to the result produced by the new formalism. The simulated data corresponded to various cases, involving non-random (high-LET) or random radiation breakage and random or non-random background breakage. The formalism systematically gives better results than naïve bin-by-bin subtraction in all these artificial data sets.     

Protective properties of certain external proteins of group B streptococci

On the basis of genes, which control synthesis of externally localized proteins of group B streptococci (bac and scaAB), recombinant polypeptides P6 and ScaAB were obtained. Data on protective activity of these polypeptides during experimental infection of immunized mice as well as in opsonophagocytic test on cultivated peritoneal macrophages are presented. It has been shown that protective effect of specific antibodies to P6 was dependent from intensity of immune response. Titer of specific IgG to P6 equal 1:25000 was protective for mice during challenge with LD50. During sublethal challenge level of humoral immunity determined both rate of microorganism elimination and degree of decrease of concentration of streptococci in the spleen. Recombinant polypeptide ScaAB also had marked protective activity and protective titer ScaAB-specific IgG was significantly lower compared with the first polypeptide (1:1600). It has been established that both types of antibodies have opsonizing activity against different strains of group B streptococci. Opsonizing properties of antibodies to P6 were restricted to Bac protein-producing streptococci whereas specificity of antibodies to ScaAB was not restricted by type and group borders. Opsonization of both group B and group A streptococci was revealed. It has been established that protective efficacy mediated by antibodies was dependent not only from their opsonizing characteristics but also from availability of protein antigens, which under certain conditions can be shielded by capsular polysaccharide. It has been assumed that vaccine preparation developed on the basis of polypeptides P6 and ScaAB is promising for further research.     

Relationship between insertion/deletion (indel) frequency of proteins and essentiality

Background  

In a previous study, we demonstrated that some essential proteins from pathogenic organisms contained sizable insertions/deletions (indels) when aligned to human proteins of high sequence similarity. Such indels may provide sufficient spatial differences between the pathogenic protein and human proteins to allow for selective targeting. In one example, an indel difference was targeted via large scale in-silico screening. This resulted in selective antibodies and small compounds which were capable of binding to the deletion-bearing essential pathogen protein without any cross-reactivity to the highly similar human protein. The objective of the current study was to investigate whether indels were found more frequently in essential than non-essential proteins.     

Voltammetric studies of glutathione transfer across arrays of liquid–liquid microinterfaces for sensing applications

Amino Acids - The simple and facilitated transfer of tripeptide glutathione across the water/2-nitrophenyl octhyl ether interface was studied via cyclic voltammetry at interface between two...     

Mechanism of heat stress-induced cellular senescence elucidates the exclusive vulnerability of early S-phase cells to mild genotoxic stress

Heat stress is one of the best-studied cellular stress factors; however, little is known about its delayed effects. Here, we demonstrate that heat stress induces p21-dependent cellular senescence-like cell cycle arrest. Notably, only early S-phase cells undergo such an arrest in response to heat stress. The encounter of DNA replication forks with topoisomerase I-generated single-stranded DNA breaks resulted in the generation of persistent double-stranded DNA breaks was found to be a primary cause of heat stress-induced cellular senescence in these cells. This investigation of heat stress-induced cellular senescence elucidates the mechanisms underlying the exclusive sensitivity of early S-phase cells to ultra-low doses of agents that induce single-stranded DNA breaks.     

Mapping the protein interaction network in methicillin-resistant Staphylococcus aureus

Mortality attributable to infection with methicillin-resistant Staphylococcus aureus (MRSA) has now overtaken the death rate for AIDS in the United States, and advances in research are urgently needed to address this challenge. We report the results of the systematic identification of protein-protein interactions for the hospital-acquired strain MRSA-252. Using a high-throughput pull-down strategy combined with quantitative proteomics to distinguish specific from nonspecific interactors, we identified 13,219 interactions involving 608 MRSA proteins. Consecutive analyses revealed that this protein interaction network (PIN) exhibits scale-free organization with the characteristic presence of highly connected hub proteins. When clinical and experimental antimicrobial targets were queried in the network, they were generally found to occupy peripheral positions in the PIN with relatively few interacting partners. In contrast, the hub proteins identified in this MRSA PIN that are essential for network integrity and stability have largely been overlooked as drug targets. Thus, this empirical MRSA-252 PIN provides a rich source for identifying critical proteins essential for network stability, many of which can be considered as prospective antimicrobial drug targets.