Managing contradictory evidence

The paper draws on the theory of mass assignment to refine the underlying semantics of intuitionistic fuzzy sets. Inconsistency can arise from several sources and it is dealt with in different ways. All the representations of inconsistency and contradiction in this paper arise from considering restricting and positive evidence lattices. In particular this paper formally addresses the operators, intersection and conjunction in detail. Because union and disjunction are required to compute the values for intersection and conjunction these are also covered as part of the analysis

Semantic transfer and contradictory evidence in intuitionistic fuzzy sets

The relationship between object level intuitionistic fuzzy sets and predicate based intuitionistic fuzzy sets is explored. Mass assignment uses a process called semantic unification to evaluate the degree to which one set supports another, the inverse function is semantic separation. Intuitionistic fuzzy sets are mapped onto a mass assignment framework and the semantic unification operator is generalised to support both mass assignment and intuitionistic fuzzy sets, as is semantic separation. Transfer of inconsistent and contradictory evidence are also dealt with

Reasoning consistently about inconsistency

Patching et al. and Hinde et al. in their work on truth-space mass assignments, presented a semantic unification function and a semantic separation function for mass assignment logic that dealt with inconsistency. This paper takes these two functions and while preserving the outside inconsistencies shows how inconsistency can be reasoned about in a consistent manner. This means that inconsistency that arises outside the system need not enter the system, but needs to be represented within the system, and can therefore be extracted appropriately as output from the system to emerge as inconsistency on the outside. The internal reasoning system need therefore only concern itself with belief in truth, falsity and uncertainty

Managing contradictory evidence

The paper draws on the theory of mass assignment to refine the underlying semantics of intuitionistic fuzzy sets. Inconsistency can arise from several sources and it is dealt with in different ways. All the representations of inconsistency and contradiction in this paper arise from considering restricting and positive evidence lattices. In particular this paper formally addresses the operators, intersection and conjunction in detail. Because union and disjunction are required to compute the values for intersection and conjunction these are also covered as part of the analysis

Reasoning Consistently about Inconsistency

Patching et al. and Hinde et al. in their work on truth-space mass assignments, presented a semantic unification function and a semantic separation function for mass assignment logic that dealt with inconsistency. This paper takes these two functions and while preserving the outside inconsistencies shows how inconsistency can be reasoned about in a consistent manner. This means that inconsistency that arises outside the system need not enter the system, but needs to be represented within the system, and can therefore be extracted appropriately as output from the system to emerge as inconsistency on the outside. The internal reasoning system need therefore only concern itself with belief in truth, falsity and uncertainty

Purification of bacterial membrane sensor kinases and biophysical methods for determination of their ligand and inhibitor interactions

This article reviews current methods for the reliable heterologous overexpression in Escherichia coli and purification of milligram quantities of bacterial membrane sensor kinase (MSK) proteins belonging to the two-component signal transduction family of integral membrane proteins. Many of these methods were developedatLeedsalongsideProfessor SteveBaldwintowhomthisreviewisdedicated.Italsoreviewstwo biophysical methods that we have adapted successfully for studies of purified MSKs and other membrane proteins – synchrotron radiation circular dichroism (SRCD) spectroscopy and analytical ultracentrifugation (AUC), both of which are non-immobilization and matrix-free methods that require no labelling strategies. Other techniques such as isothermal titration calorimetry (ITC) also share these features but generally require high concentrations of material. In common with many other biophysical techniques, both of these biophysical methods provide information regarding membrane protein conformation, oligomerization state and ligand binding, but they possess the additional advantage of providing direct assessments of whether ligand binding interactions are accompanied by conformational changes. Therefore, both methods provide a powerful means by which to identify and characterize inhibitor binding and any associated protein conformational changes, thereby contributing valuable information for future drug intervention strategies directed towards bacterial MSKs

Microbial transformations of selenite by methane-oxidizing bacteria

Abstract Methane oxidizing bacteria are well known for their role in the global methane cycle and their potential for microbial transformation of wide range of hydrocarbon and chlorinated hydrocarbon pollution. Recently, it has also emerged that methane-oxidizing bacteria interact with inorganic pollutants in the environment. Here we report what we believe to be the first study of the interaction of pure strains of methane-oxidizing bacteria with selenite. Results indicate that the commonly used laboratory model strains of methane oxidizing bacteria, Methylococcus capsulatus (Bath) and Methylosinus trichosporium OB3b are both able to reduce the toxic selenite (SeO32-) but not selenate (SeO42-) to red spherical nanoparticulate elemental selenium (Se0), which was characterised via EDX and EXAFS. The cultures also produced volatile selenium-containing species, which suggests that both strains may have an additional activity that can either transform Se0 or selenite into volatile methylated forms of selenium. Transmission electron microscopy (TEM) measurements and experiments with the cell fractions: cytoplasm, cell wall and cell membrane show that the nanoparticles are formed mainly on the cell wall. Collectively these results are promising for the use of methane-oxidizing bacteria for bioremediation or suggest possible uses in the production of selenium nanoparticles for biotechnology

Efficiency of Purine Utilization by Helicobacter pylori: Roles for Adenosine Deaminase and a NupC Homolog

The ability to synthesize and salvage purines is crucial for colonization by a variety of human bacterial pathogens. Helicobacter pylori colonizes the gastric epithelium of humans, yet its specific purine requirements are poorly understood, and the transport mechanisms underlying purine uptake remain unknown. Using a fully defined synthetic growth medium, we determined that H. pylori 26695 possesses a complete salvage pathway that allows for growth on any biological purine nucleobase or nucleoside with the exception of xanthosine. Doubling times in this medium varied between 7 and 14 hours depending on the purine source, with hypoxanthine, inosine and adenosine representing the purines utilized most efficiently for growth. The ability to grow on adenine or adenosine was studied using enzyme assays, revealing deamination of adenosine but not adenine by H. pylori 26695 cell lysates. Using mutant analysis we show that a strain lacking the gene encoding a NupC homolog (HP1180) was growth-retarded in a defined medium supplemented with certain purines. This strain was attenuated for uptake of radiolabeled adenosine, guanosine, and inosine, showing a role for this transporter in uptake of purine nucleosides. Deletion of the GMP biosynthesis gene guaA had no discernible effect on mouse stomach colonization, in contrast to findings in numerous bacterial pathogens. In this study we define a more comprehensive model for purine acquisition and salvage in H. pylori that includes purine uptake by a NupC homolog and catabolism of adenosine via adenosine deaminase

Deuterated detergents for structural and functional studies of membrane proteins: Properties, chemical synthesis and applications

Detergents are amphiphilic compounds that have crucial roles in the extraction, purification and stabilization of integral membrane proteins and in experimental studies of their structure and function. One technique that is highly dependent on detergents for solubilization of membrane proteins is solution-state NMR spectroscopy, where detergent micelles often serve as the best membrane mimetic for achieving particle sizes that tumble fast enough to produce high-resolution and high-sensitivity spectra, although not necessarily the best mimetic for a biomembrane. For achieving the best quality NMR spectra, detergents with partial or complete deuteration can be used, which eliminate interfering proton signals coming from the detergent itself and also eliminate potential proton relaxation pathways and strong dipole-dipole interactions that contribute line broadening effects. Deuterated detergents have also been used to solubilize membrane proteins for other experimental techniques including small angle neutron scattering and single-crystal neutron diffraction and for studying membrane proteins immobilized on gold electrodes. This is a review of the properties, chemical synthesis and applications of detergents that are currently commercially available and/or that have been synthesized with partial or complete deuteration. Specifically, the detergents are sodium dodecyl sulphate (SDS), lauryldimethylamine-oxide (LDAO), n-octyl-?-D-glucoside (?-OG), n-dodecyl-?-D-maltoside (DDM) and fos-cholines including dodecylphosphocholine (DPC). The review also considers effects of deuteration, detergent screening and guidelines for detergent selection. Although deuterated detergents are relatively expensive and not always commercially available due to challenges associated with their chemical synthesis, they will continue to play important roles in structural and functional studies of membrane proteins, especially using solution-state NMR