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.     

A rigid cavity containing tetra-cobalt(III) [2 x 2] grid complex

The synthesis and structure of a rigid, cavity containing tetra-cobalt(III) [2 x 2] grid complex using an unusual bis(bipyridine)dimethoxynaphthyridine ligand is described.     

Electrogenerated chemiluminescence using solution phase and immobilized tris(4,7-diphenyl-1,10-phenanthrolinedisulfonic acid)ruthenium(II)

Electrogenerated chemiluminescence (ECL) with tris(4,7-diphenyl-1,10-phenanthrolinedisulfonic acid)rathenium(II) (RuBPS) in solution and immobilized on an electrode surface is investigated. Flow injection analysis with a thin layer electrochemical cell modified for ECL detection is used to determine the analytical utility of solution phase RuBPS and RuBPS immobilized in a cationic polypyrrole derivative. The solution phase reaction of RuBPS with oxalate is investigated with regard to the dependence of ECL emission on RuBPS concentration, carrier stream flow rate, and pH. In the parameter range studied, ECL intensity is not linear with the concentration of RuBPS in the sample. A maximum ECL intensity is observed with a RuBPS concentration of approximately 250 M. Slower linear velocities give greater ECL intensities which is the opposite of what is observed for Ru(bpy) ₃ ³⁺ and oxalate. Greater ECL intensity is observed at lower pHs for oxalate and at higher pHs for proline. RuBPS ECL with oxalate yields a working curve with a linear range from 0.1–100 M oxalate. Solution phase ECL is observed for RuBPS and other amines such as NADH, proline, tripropylamine, and antibiotics including streptomycin and gentamicin. RuBPS is also immobilized by electrochemical polymerization of 1-methyl-3-(pyrrol-1-ylmethyl)pyridinium chloride (MPP) in the presence of RuBPS. This polymer-modified electrode yields ECL for oxalate and for amines.Deceased     

Preconcentration of trace metal ions by combined complexation-anion exchange : Part 2. Cobalt,zinc, cadmium and lead with 8-hydroxyquinoline-5-sulfonic acid [1]

The ligand, 8-hydroxyquinoline-5-sulfonic acid, forms anionic complexes with cobalt(II), zinc(II), cadmium(II), and lead(II), each resulting complex showing a high affinity for anion-exchange resins. The effect of pH, ligand/metal ratio, volume, and concentration on percent retention of the anionic complexes by an anion-exchange resin are reported. At optimum conditions, all four metals are quantitatively retained by the column. Zinc, cadmium and lead(II) ions are completely eluted with 11 ml or less of 2 M HN0₃; cobalt(II) is totally removed by 12 M HCl and 2 M HNO₃. Concentration enhancements of 100-fold are easily achieved. All four anionic complexes can be left on the column for 7 days and still be quantitatively (99%) recovered. A ligand-loaded resin column can also remove all four metals quantitatively. Distribution coefficients for the metal complexes and their ligand/metal ratios were determined by using batch methods that may also serve as the isolation procedure.     

Mndo study of bond orders in some conjugated BI- and tri-cyclic hydrocarbons

MNDO calculations have been carried out on a number of conjugated bicyclic and tricyclic hydrocarbons. For reference purposes some acenes and monocyclic non-benzenoid hydrocarbons are also mentioned. While the influence of 2 or 6 π-electron systems in stabilising, and of 4 π-electron systems in destabilising, structures is readily evident, it is clear that arrays of 10 or more π-electrons have markedly less effect, and the balance between fixation of bonds and delocalisation in many compounds possessing such systems is subtle.     

Octaphenylbiphenylene and dodecaphenyltriptycene

Octaphenylbiphenylene, the expected dimer of tetraphenylbenzyne, has been prepared in low yield by diazotization of 3,4,5,6-tetraphenylanthranilic acid, and its X-ray structure has been determined. The X-ray structure of a second, abnormal dimer of tetraphenylbenzyne, 1,2,3,8,9,10-hexaphenyldibenzo[fg,op]naphthacene has also been determined; this is a saddle-shaped polycyclic aromatic hydrocarbon. 1,2,3,4,5,6,7,8,13,14,15,16-Dodecaphenyltriptycene, perhaps the most crowded triptycene derivative yet prepared, has been made by the reaction of tetraphenylbenzyne with 1,2,3,4,5,6,7,8-octaphenylanthracene, which in turn was synthesized in two steps from commercial starting materials. The X-ray structure of the dodecaphenyltriptycene nonabenzene solvate is a remarkable channel containing structure in which more than 50% of the unit cell volume is occupied by the benzene molecules.     

Frequency Response Method for Measuring Mass Transfer Rates in Adsorbents via Pressure Perturbation

A new apparatus for the measurement of equilibria and dynamics for gas-phase adsorption systems is utilized to examine the adsorption of carbon dioxide on BPL activated carbon. The apparatus has a flow-through configuration. For dynamics, with constant inlet flow, pressure within the adsorbent-containing section is varied sinusoidally, and the time-dependent outlet flow rate is measured to determine an amplitude ratio and phase lag. Studies are made of temperature effects and particle size effects. Results are compared with several mathematical models. Frequency response data show that the BPL system follows surface (or micropore) diffusion kinetics. The rate of adsorption for the activated carbon is found to be only weakly dependent on the bulk particle size.     

Polymerization of aromatic nuclei. XXVI. Poly(p-phenylene): Friedel–crafts alkylation,molecular weight,and propagation mechanism

Poly(p-phenylene) was alkylated with n-propyl bromide, n-propyl chloride, and isopropyl bromide in the presence of aluminum chloride. Apparently, the reactions involve dialkylation with n-propyl halides and alternating mono- and dialkylation with isopropyl bromide. Alkylation with ethyl or n-butyl bromide was unsuccessful. The dialkylated polymer was sufficiently soluble to allow molecular weight determination. Mechanistic aspects of alkylation and propagation are treated.     

Influence of ignored and well-known zone distortions on the separation performance of proteins in capillary free zone electrophoresis with special reference to analysis in polyacrylamide-coated fused silica capillaries in various buffers. I. Theoretical studies

Distortion of the starting zone upon its electrophoretic migration toward the detection window gives rise to both symmetrical zones caused by diffusion, sedimentation in the horizontal section of the capillary and the curvature of the capillary, and asymmetrical zones having their origin in Joule heating, sedimentation in the vertical section of the capillary, pH and conductivity differences between the sample zone and the surrounding buffer, solute adsorption onto the capillary wall, and association-dissociation of complexes between the analyte and a buffer constituent or between analytes. Interestingly and importantly a theoretical study shows that moderate pH and conductivity differences as well as adsorption and all of the above interactions when they are characterized by a fast on/off kinetics do not increase the zone broadening (or only slightly), because the sharpening of one boundary of the zone is about the same as the broadening of the other boundary. In addition the peak symmetry caused by a conductivity difference is in most experiments counteracted by a pH difference. The experimentally determined plate numbers in the absence of electroosmosis exceeded one million per meter in some experiments (Part II). These plate numbers are among the highest reported [Z. Zhao, A. Malik, M.L. Lee, Anal. Chem. 65 (1993) 2747; M. Gilges, K. Kleemiss, G. Schomburg, Anal. Chem. 66 (1994) 2038; H. Wan, M. Ohman, L.G. Blomberg, J. Chromatogr. A 924 (2001) 591 (plate numbers determined in the presence of electroosmosis may be higher, although the width of the zone in the capillary may be larger) [p. 680 in S. Hjertén, Electrophoresis 11 (1990) 665]). Capillary free zone electrophoresis is perhaps the only separation method, which, under optimum conditions, gives a plate number not far from the theoretical limit. A prerequisite for this high performance is that the polyacrylamide-coated capillary is washed with 2 M HCl between the runs and stored in water over night (Part II). The difference between the experimentally determined total variance and the sum of the calculated variances originating from the width of the starting zone, longitudinal diffusion, Joule heating, sedimentation in the vertical section of the capillary, curvature of the capillary (i.e., the sum of all other variances) was in our most successful experiments about 28% of the variance of diffusion. The zone broadening, 2sigma, caused by diffusion was estimated at 0.77 mm. The total zone width (2sigma) calculated from the experimentally determined plate number was as small as 1 mm when the migration distance was 40 cm. Accordingly, the only efficient way to reduce drastically the total zone width is to decrease the analysis time and, thereby, the diffusional broadening. An important finding was that the variance originating from the loops of the capillary is not always negligible in high-performance runs. Therefore, one should employ straight capillaries and avoid CE apparatus with cartridges that require a strong curvature of the capillary, common in most commercial instruments. Mathematical formulas have been derived for the sedimentation of the solute zone, the enrichment factor, and the migration time in experiments where the solute is dissolved in a dilute running buffer. This zone sharpening method gave very narrow starting zones (0.04-0.4 mm). However, upon high dilution of the buffer the enrichment becomes so strong that part of the sample zone probably sediments out of the capillary; the almost inevitable change in pH may decrease the mobility of the proteins and, thus, cause the enrichment factor to become still lower than expected. Diffusion of the protein in the very narrow starting zone (located close to the tip of the capillary) and sometimes the thermal expansion of the buffer in the capillary contributes to additional loss of protein in the enrichment step. In some buffers, the interaction between the protein and the buffer constituents is so slow that the peaks become broad. Therefore, different types of buffers should be tested when high resolution is required. The relation sigma2 (the variance of the interaction between a protein and the buffer constituents) = constant x u (the mobility) seems to be valid for all proteins in the applied sample, at least when they have similar molecular masses. To facilitate the understanding of the progress of a free zone electrophoresis experiment, we have discussed in simple terms how the concentrations of the background electrolytes become rearranged during a run and why the difference between the mobilities of the proteins and the mobilities of the background electrolyte determines whether a peak exhibits fronting or tailing. A theoretical analysis of zone broadening in capillary zone electrophoresis, chromatography, and electrochromatography indicates that electrochromatography in homogeneous gels might be the only chromatographic technique which can compete in performance with free electrophoresis. Using an equation, valid not only for electrophoresis, but also for chromatography and centrifugation, the mobility of a concentration boundary has been calculated for the first time and was, as expected, low. Equations based on the Kohlrausch regulating function do not permit such calculations. Another regulating function (the H function) and some of its characteristics are briefly discussed. The theoretical discussions in this paper and the experimental studies in Part II show that high-performance electrophoresis deserves its prefix when the runs are designed to give minimum zone broadening. Some guidelines are given to facilitate this optimization. The plate numbers are so high that the resolution cannot be increased by more than 30% even if they approach the theoretically maximum values.     

Surface modification of an ethylene-acrylic acid copolymer film: grafting amine-terminated linear and branched architectures

Polymer films can be tailored for a specific application by modifying their surface properties. In this study, linear and branched architectures were grafted to ethylene-acrylic acid (EAA) copolymer films using the so-called grafting from approach. Dicyclohexylcarbodiimide was used to activate the carboxylic acid functionality on the surface of the EAA copolymer film before reacting it with selected di- and tri-amine compounds. The carboxylic acid functionality was subsequently regenerated by reacting the amine-grafted film with succinic anhydride. These reaction steps were then repeated to create the linear and branched architectures on the EAA film surface. The film surface resulting from each reaction step was analyzed using attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy and contact angle measurements. A systematic analysis of the ATR-FTIR results was performed to estimate the average conversion of the reaction schemes and to explain the observed contact angle results. A significant reduction in water contact angle for the EAA film grafted with a branched architecture was observed. The EAA film grafted with a linear architecture showed a marginal reduction in water contact angle when ethanol was used as a solvent for ethylenediamine. When the solvent for ethylenediamine was changed to water, the contact angle decreased noticeably. However, analysis of control films showed that the reduction in the contact angles was due to the solvent treatment. In the case of branched architectures, such reduction in contact angle due to the solvent treatment was not observed. Several control experiments were performed to ensure that the reduction in the contact angles was in fact due to the grafted species and not due to exposure to various solvents used in the reaction scheme.