A simple method to calculate the accessible volume of protein-bound ligands: application for ligand selectivity

We here present a method for estimating the accessible volume surrounding each atom of a ligand when bound to a receptor. The accessible volumes are calculated as the volume of a sphere with fixed radius, centered on each ligand atom, not simultaneously occupied by the volume of the receptor. The method is capable of describing the packing of the ligand in the binding pocket. Moreover, where structural models of several receptors in complex with the same ligand are available, a comparative study discriminating on accessible volumes can be performed. For these cases, a relatively large accessible volume in a particular receptor might indicate that this receptor has a unique cavity that might be exploited to develop a selective ligand analog. The ligand atoms showing variation in surrounding volume accessibility when bound to different receptors constitute attractive anchor points where one might want to attach substituents that modify the selectivity of the ligand. We have applied the described method to two different enzyme-ligand systems that bind tetrahydrobiopterin, i.e. the aromatic amino acid hydroxylases and nitric oxygen synthases. Our results yield new insights into the specificity of cofactor binding to these protein families.     

Lipid entrapment and cellular changes in the rat myocard, lung and liver after long-term parenteral nutrition with lipid emulsion. A light microscopic and ultrastructural study

We have demonstrated organ damage after long-term administration of lipid-based parenteral nutrition, possibly initiated by intravascular pooling of lipid and phagocytes, in both rats and pigs. To evaluate whether accumulation of lipid could simply be caused by mechanical filtration, a comparative study of three separate capillary beds was performed. Rats were given lipid emulsion (n = 5) or isotonic saline (n = 4) through central venous catheters for 3 weeks. Using both light and electron microscopy, lipid accumulation and structural changes in the rat myocard were compared to those in the lung and liver. The study provides evidence that within myocardial capillaries both peripheral blood monocytes and endothelial cells performed phagocytosis of lipid droplets following administration of lipid emulsion, but no large-scale intravascular pooling of lipid resulted. Morphometry of the myocard detected no lipid increase in the myocytes from the rats given lipid emulsion compared with controls and in neither were there any stigmata of vasculitis or myocardial damage, in contrast to the lung and liver, where intravascular pooling of lipid and phagocytes was seen. This indicates that phagocytosis was an important mechanism involved in entrapment and elimination of lipid.     

NMR structure of Escherichia coli glutaredoxin 3-glutathione mixed disulfide complex: implications for the enzymatic mechanism

Glutaredoxins (Grxs) catalyze reversible oxidation/reduction of protein disulfide groups and glutathione-containing mixed disulfide groups via an active site Grx-glutathione mixed disulfide (Grx-SG) intermediate. The NMR solution structure of the Escherichia coli Grx3 mixed disulfide with glutathione (Grx3-SG) was determined using a C14S mutant which traps this intermediate in the redox reaction. The structure contains a thioredoxin fold, with a well-defined binding site for glutathione which involves two intermolecular backbone-backbone hydrogen bonds forming an antiparallel intermolecular beta-bridge between the protein and glutathione. The solution structure of E. coli Grx3-SG also suggests a binding site for a second glutathione in the reduction of the Grx3-SG intermediate, which is consistent with the specificity of reduction observed in Grxs. Molecular details of the structure in relation to the stability of the intermediate and the activity of Grx3 as a reductant of glutathione mixed disulfide groups are discussed. A comparison of glutathione binding in Grx3-SG and ligand binding in other members of the thioredoxin superfamily is presented, which illustrates the highly conserved intermolecular interactions in this protein family.     

Parallel Dantzig–Wolfe decomposition for real-time optimization—Applied to a complex oil field

This paper studies Dantzig–Wolfe decomposition for real-time optimization of process systems with a decentralized structure. The idea is to improve computational efficiency and transparency of a solution. The contribution lies in the application of the Dantzig–Wolfe method which allows us to efficiently decompose an optimization problem into parts. Moreover, we show how the algorithm can be parallelized for even higher efficiency. The nonlinear system is modeled by piecewise linear models with the added benefit that error bounds can be computed. In this context alternative parameterizations are discussed.The properties of the method are studied by applying it to a model of a complex petroleum field with severe production optimization challenges due to rate dependent gas-coning wells. The model resembles the Troll west oil rim, a huge gas and oil field on the Norwegian Continental shelf.Finally, the paper discusses workflows in production optimization as a means to explain how the proposed methodology can be applied in practice.     

Automated approaches for analysis of multimodal MRI acquisitions in a study of cognitive aging

In this work we describe an integrated and automated workflow for a comprehensive and robust analysis of multimodal MR images from a cohort of more than hundred subjects. Image examinations are done three years apart and consist of 3D high-resolution anatomical images, low resolution tensor-valued DTI recordings and 4D resting state fMRI time series. The integrated analysis of the data requires robust tools for segmentation, registration and fiber tracking, which we combine in an automated manner. Our automated workflow is strongly desired due to the large number of subjects. Especially, we introduce the use of histogram segmentation to processed fMRI data to obtain functionally important seed and target regions for fiber tracking between them. This enables analysis of individually important resting state networks. We also discuss various approaches for the assessment of white matter integrity parameters along tracts, and in particular we introduce the use of functional data analysis (FDA) for this task.     

A novel approach to acoustic liquid density measurements using a buffer rod based measuring cell

A new method for measuring the pressure reflection coefficient in a buffer rod configuration is presented, together with experimental results for acoustic measurements of the liquid density, based on the measurement of the liquid's acoustic impedance. The method consists of using 2 buffers enclosing the liquid in a symmetrical arrangement with a transducer fixed to each buffer. One of the transducers is used in a pulse-echo mode while the other transducer operates as a receiver. The echo amplitudes leading to the pressure reflection coefficient as found by this method possess advantages such as reduced attenuation due to a shorter liquid transmission path and reduced interference, as compared with the ABC method. Measurements with distilled water and with special density calibration oil qualities have been performed using both the new method and the ABC method and are shown for the new method to give a density span within +/- 0.15% of the reference values. A comparison of the measured densities based on both a time-domain and a l(2)-norm frequency domain integration signal processing approach is given, along with a recommendation as to how the signal processing should be performed.     

Measurement of minimum ignition energies of dust clouds in the <1mJ region

The lower energy limit of current standard test apparatus for determining the minimum ignition energy (MIE) of dust clouds is in the range of 1-3mJ. This is a quite severe limitation because many dusts ignite readily at this energy level. A new spark generator, capable of producing synchronised sparks of very low energies and with an integrated system for measurement of spark energy, has therefore been developed and employed to a number of easily ignitable dusts. Before testing the MIE of dust clouds, it was considered essential to calibrate the new spark generator against a gas of known MIE. For this purpose, a mixture of propane and air was selected. However, a comprehensive literature review revealed that the reported MIEs of this gas mixture vary significantly, depending on the spark discharge characteristics, including discharge duration. When taking these factors into account, it was concluded that the new spark generator yielded reasonable results for propane/air. Applying the new spark generator to explosive dust clouds showed that a number of dusts do in fact have MIEs that are one to two orders of magnitude lower than 1mJ. The new spark generator may therefore offer a basis for developing a standard test apparatus in the low-energy region. When using a method of triggering the spark by the explosive dust cloud itself, which probably is a more industrially relevant process than synchronisation between the dust dispersion and sparkover, somewhat higher MIEs were found compared to those determined when using synchronised sparks. However, even with this method of spark triggering, MIEs below 1mJ were found.     

Subminimal Inhibitory Concentrations of the Disinfectant Benzalkonium Chloride Select for a Tolerant Subpopulation of Escherichia coli with Inheritable Characteristics

Exposure of Escherichia coli to a subminimal inhibitory concentration (25% below MIC) of benzalkonium chloride (BC), an antimicrobial membrane-active agent commonly used in medical and food-processing environments, resulted in cell death and changes in cell morphology (filamentation). A small subpopulation (1-5% of the initial population) survived and regained similar morphology and growth rate as non-exposed cells. This subpopulation maintained tolerance to BC after serial transfers in medium without BC. To withstand BC during regrowth the cells up regulated a drug efflux associated gene (the acrB gene, member of the AcrAB-TolC efflux system) and changed expression of outer membrane porin genes (ompFW) and several genes involved in protecting the cell from the osmotic- and oxidative stress. Cells pre-exposed to osmotic- and oxidative stress (sodium chloride, salicylic acid and methyl viologen) showed higher tolerance to BC. A control and two selected isolates showing increased BC-tolerance after regrowth in BC was genome sequenced. No common point mutations were found in the BC- isolates but one point mutation in gene rpsA (Ribosomal protein S1) was observed in one of the isolates. The observed tolerance can therefore not solely be explained by the observed point mutation. The results indicate that there are several different mechanisms responsible for the regrowth of a tolerant subpopulation in BC, both BC-specific and general stress responses, and that sub-MIC of BC may select for phenotypic variants in a sensitive E. coli culture.