Fast automatic registration of images using the phase of a complex wavelet transform: application to proteome gels

Image registration describes the process of manipulating a distorted version of an image such that its pixels overlay the equivalent pixels in a clean, master or reference image. The need for it has assumed particular prominence in the analysis of images of electrophoretic gels used in the analysis of protein expression levels in living cells, but also has fundamental applications in most other areas of image analysis. Much of the positional information of a data feature is carried in the phase of a complex transform, so a complex transform allows explicit specification of the phase, and hence of the position of features in the image. Registration of a test gel to a reference gel is achieved by using a multiresolution movement map derived from the phase of a complex wavelet transform (the Q-shift wavelet transform) to dictate the warping directly via movement of the nodes of a Delaunay-triangulated mesh of points. This warping map is then applied to the original untransformed image such that the absolute magnitude of the spots remains unchanged. The technique is general to any type of image. Results are presented for a simple computer simulated gel, a simple real gel registration between similar "clean" gels with local warping vectors distributed about one main direction, a hard problem between a reference gel and a "dirty" test gel with multi-directional warping vectors and many artifacts, and some typical gels of present interest in post-genomic biology. The method compares favourably with others, since it is computationally rapid, effective and entirely automatic.     

Phase Coexistence in a Dynamic Phase Diagram

Metastability and phase coexistence are important concepts in colloidal science. Typically, the phase diagram of colloidal systems is considered at the equilibrium without the presence of an external field. However, several studies have reported phase transition under mechanical deformation. The reason behind phase coexistence under shear flow is not fully understood. Here, multilamellar vesicle (MLV)‐to‐sponge (L₃) and MLV‐to‐L_α transitions upon increasing temperature are detected using flow small‐angle neutron scattering techniques. Coexistence of L_α and MLV phases at 40 °C under shear flow is detected by using flow NMR spectroscopy. The unusual rheological behavior observed by studying the lamellar phase of a non‐ionic surfactant is explained using ²H NMR and diffusion flow NMR spectroscopy with the coexistence of planar lamellar–multilamellar vesicles. Moreover, a dynamic phase diagram over a wide range of temperatures is proposed.     

Phase behavior of diblock copolymers; pressure and temperature dependence studied by small-angle neutron scattering

The structure factor of a poly(ethylene-propylene)poly(dimethylsiloxane) diblock copolymer has been measured by SANS as a function of temperature and pressure. In contradiction to the random phase approximation the conformational compressibility exhibits a pronounced maximum at the order-disorder phase transition. The phase boundary shows an unusual shape: with increasing pressure it first decreases and then increases. Its origin is an increase in, respectively, the entropic and the enthalpic part of the Flory-Huggins interaction parameter. The Ginzburg parameter describing the limit of the mean-field approximation is not influenced by pressure.     

Ab initio studies of chemical equilibria. Equilibria containing first row hydrides AH2, AH3, and AH4 and their positive ions

Equilibrium constants were calculated for fourteen simple reactions involving AH₂, AH₃, and AH₄ first row hydrides and their positive ions. Except for the “experimental” correlation energies used, the theoretical approach is entirely non-empirical in character. The results suggest that if the correlation effects were accounted for in a more sophisticated way, most of the calculated equilibrium constants would be more reliable than the available experimental data.     

Global study of myoglobin-surfactant interactions

Surfactants interact with proteins in multifarious ways which depend on surfactant concentration and structure. To obtain a global overview of this process, we have analyzed the interaction of horse myoglobin (Mb) with an anionic (SDS) and cationic (CTAC) surfactant, using both equilibrium titration techniques and stopped-flow kinetics. Binding and kinetics of conformational changes can be divided into a number of different regions (five below the cmc and one above) with very distinct features (broadly similar between the two surfactants, despite their difference in head group and chain length), which nuance the classical view of biphasic binding prior to micellization. In stage A, fairly weak interactions lead to a linear decrease in thermal stability. This gives way to a more cooperative process in stage B, where aggregates (presumably hemimicelles) start to form on the protein surface, leading to global denaturation (loss of a thermal transition) and biphasic unfolding kinetics. This is consolidated in stage C with titratable surfactant adsorption. Adsorption of this surfactant species leads to significant changes in kinetics, namely, inhibition of unfolding kinetics in CTAC and altered unfolding amplitudes in SDS, though the process is still biphasic in both surfactants. Stage D commences the reduction in exothermic binding signals, leading to further uptake of 5 (SDS) or 31 (CTAC) surfactant molecules without any major changes in protein conformation. In stage E many more surfactant molecules (46 SDS and 39 CTAC) are bound, presumably as quasi-micellar structures, and we observe a very slow unfolding phase in SDS, which disappears as we reach the cmc. Above the cmc, the unfolding rates remain essentially constant in SDS, but increase significantly in CTAC, possibly because binding of bulk micelles removes the inhibition by hemimicellar aggregates. Our work highlights the fascinating richness of conformational changes that proteins can undergo in the presence of molecules with self-assembling properties.     

Metabolic profiling using direct infusion electrospray ionisation mass spectrometry for the characterisation of olive oils

There is a continuing need for improved methods for assessing the adulteration of foodstuffs. We report some highly encouraging data, where we have developed direct infusion electrospray ionisation mass spectrometry (ESI-MS) together with chemometrics as a novel, rapid (1 min per sample) and powerful technique to elucidate key metabolite differences in vegetable and nut oils. Principal components analysis of these ESI-MS spectra show that the reproducibility of this approach is high and that olive oil can be discriminated from oils which are commonly used as adulterants. These adulterants include refined hazelnut oil, which is particularly challenging given its chemical similarity to olive oils.     

Vancomycin architecture dependence on the capture efficiency of antibody-modified microbeads by magnetic nanoparticles

We show that the ability to control the architecture/orientation of vancomycin on the surface of magnetic nanoparticles has a drastic effect on the ability of the nanoparticles to magnetically confine vancomycin-antibody modified polystyrene microbeads.