Structural characterizations of lipids A by MS/MS of doubly charged ions on a hybrid linear ion trap/orbitrap mass spectrometer

Here, a new 'one pot' and fast approach is described, based on electrospray ionization (ESI) of negative ions by using a hybrid linear ion trap/orbitrap mass spectrometer (LTQ/orbitrap) for MS and MS/MS analysis. By this method the distribution of the primary and secondary acyl residues of the intact lipid A is inferred by analysis of the ESI spectra measured in positive and negative mode. The analysis of these data allows an unequivocal assignment of the fatty acid distribution. This methodology was successfully tested on two different lipid A with known structures, deriving from the Agrobacterium tumefaciens and Escherichia coli lipopolysaccharides (LPS).     

Computer-assisted protein domain boundary prediction using the DomPred server

Domain prediction from sequence is a particularly challenging task, and currently, a large variety of different methodologies are employed to tackle the task. Here we try to classify these diverse approaches into a number of broad categories. Completely automatic domain prediction from sequence alone is currently fraught with problems, but this should not be so surprising since human experts currently have significant disagreement on domain assignment even when given the structures. It can be argued that we should only test the domain prediction methods on benchmark data that human experts agree upon and this is the approach we take in this paper. Even for the data sets on which human experts agree, automatic structure-based domain assignment still cannot always agree, and so again it is still unlikely that domain prediction methods will reliably obtain correct results completely automatically. We make the argument that computer-assisted domain prediction is a more achievable goal. With this aim in mind, we present the DomPred server. This server provides the user with the results from two completely different categories of method (DPS and DomSSEA). In this paper, each method is individually benchmarked against one of the latest domain prediction benchmarks to provide information about their respective reliabilities. A variety of different benchmark scores are employed since the accuracy of a domain prediction method depends critically on what types of results one wishes to obtain (single/multi-domain classification, domain number, residue linker positions, etc.). Also both of these methods, implemented within the DomPred server, can suggest alternative domain predictions, allowing the user to make the final decision based on these results and applying their own background knowledge to the problem. The DomPred server is available from the URL:http://bioinf.cs.ucl.ac.uk/software.html.     

EQUILIBRIUM MODELING OF PSEUDOMONAD AGGREGATION AND PARTITIONING TO DOLOMITE†

Bioremediation is a common treatment technology considered for the remediation of many toxic and hazardous waste sites. In order for this technology to be successfully implemented, the mobility and adhesion characteristics of the microorganisms must be understood. This study explored the surface and adhesion characteristics of two pseudomonads: Pseudomonas aeruginosa Olin and P. fluorescens rib:lux. In general, the Lewis acid/base character of these microorganisms dominated surface thermodynamics. In both cases partitioning to dolomite, a common mineral, was predicted to be greatest in the stationary phase. In the log growth and decay phases, the Lewis acid/base interaction energy was repulsive for both organisms. The stationary phase for both microbes exhibited a reversal of the Lewis acid/base energy to attractive. Although the magnitude of the various surface energy components differed between the microorganism, it is remarkable that the Lewis acid/base energy exhibited similar behavior.     

On the connection between energy velocity, reverberation time and angular momentum

The decay of a steady acoustic field in an enclosure is studied both theoretically and experimentally. Our main result is that the initial part of any local sound decay is driven by an exponential function of time whose rate constant is equal in modulus to the inverse of the mean energy velocity divergence. This is empirically demonstrated by experimental analysis of both 1-D and 3-D case studies, thus showing that the reverberation time is strictly connected with the sound energy velocity field and can be determined from its differential properties. A further property of the mean energy velocity is found: it is related not only with the reverberation time, but also with the angular momentum density and with the non-uniform distribution of energy.