Start-to-end processing of two-dimensional gel electrophoretic images

Gel electrophoresis serves as a basic analytical tool in the proteomic studies. However, processing of gel electrophoretic images is still the main bottleneck of data analysis, and there is an increasing need for the fully automated approaches. The proposed start-to-end strategy of analyzing the gel images consists of chemometric tools, which allow their effective preprocessing, automatic warping, and data modeling. The image preprocessing techniques: denoising in the wavelet domain and the penalized asymmetric least squares approach for the background estimation are proposed. Matching of images is based on fuzzy warping of features, extracted from the gel images. For the classification or calibration purpose, multivariate approaches such, as partial least squares (PLS) or kernel-PLS methods are used. Performance of the proposed strategy is demonstrated on the real set of the two-dimensional gel images.     

Warping two-dimensional electrophoresis gel images to correct for geometric distortions of the spot pattern

A crucial step in two-dimensional gel based protein expression analysis is to match spots in different gel images that correspond to the same protein. It still requires extensive and time-consuming manual interference, although several semiautomatic techniques exist. Geometric distortion of the protein patterns inherent to the electrophoresis procedure is one of the main causes of these difficulties. An image warping method to reduce this problem is presented. A warping is a function that deforms images by mapping between image domains. The method proceeds in two steps. Firstly, a simple physicochemical model is formulated and applied for warping of each gel image to correct for what might be one of the main causes of the distortions: current leakage across the sides during the second-dimensional electrophoresis. Secondly, the images are automatically aligned by maximizing a penalized likelihood criterion. The method is applied to a set of ten gel images showing the radioactively labeled proteome of yeast Saccharomyces cerevisiae during normal and steady-state saline growth. The improvement in matching when given the warped images instead of the original ones is exemplified by a comparison within a commercially available software.     

Superimposing two-dimensional gels to study genetic variation in malaria parasites.

Two-dimensional polyacrylamide gel electrophoresis is a valuable tool for studying genetic variation in the human malaria parasite, Plasmodium falciparum. It involves examining the position of protein spots in gel produced from different isolates. Some spots have been seen to vary, while others have had a constant position in all isolates so far examined. These invariant spots provide a reference frame to compare variations in other spots. This paper discusses the usefulness of digital image handling, warping and superimposition in a personal computer environment. Rather than produce a fully automatic interpretation system, we show how the computer may be used as a tool for manipulating gel images, although interpretation of the gels' features remains with the human expert. Autoradiographs are scanned on a desktop scanner, and the images in digital form can be displayed on a monitor attached to a personal computer. The coordinates of the invariant spots on each of several gels are identified by the user. Each of the gels is then warped so that the invariant spots of all the gels coincide as closely as possible. The variable spots are then examined. We have used both affine warping transformations, which match the invariant spots as closely as possible, and thin plate spline transformations, which match them exactly. Colour superimposition proved a useful way of examining the gels.     

A review of the CLIP system for the quantitative analysis of two-dimensional electrophoresis gels

This paper reviews the CLIP image processing system for the complete analysis of two-dimensional electrophoresis images. The analysis problem for two-dimensional gel images can be broken down into three issues: segmentation of individual gel images, alignment and comparison of pairs of gel images, and information storage and retrieval. This paper describes these problems and reviews how the CLIP system handles each of them. Segmentation is the location and isolation of each protein spot on an individual gel image and also the extraction of individual spot data such as position, area and volume. There are three basic stages: background field correction, noise filtering, spot detection and information extraction. Alignment and comparison of gel images involves matching protein spots between two gels. This can be quite difficult because there is not a simple relationship which can transform one gel image onto another. The database issues concern storing all the information which has been obtained from the above operations such that retrieval of this information can be readily performed. The advantage of the CLIP system over others is speed of processing. CLIP series computers use one processor for every pixel of the camera image such that image processing algorithms run in parallel. The main disadvantage is in the cost of these machines. With the declining trend in the cost of parallel processors, these machines will become more and more viable alternatives. This papers reviews the algorithms for the analysis of two-dimensional gels. It is shown that CLIP is flexible enough to perform more than one type of algorithm for a particular operation.     

Sodium dodecyl sulphate-polyacrylamide gel electrophoresis of proteins in dry-cured hams: data registration and multivariate analysis across multiple gels

This study investigates whether dry-cured hams from two European countries can be distinguished using SDS-PAGE. Thirty-seven commercial hams (19 Spanish, 18 French) were used in the study. Four protein fractions were extracted from each sample, with sufficient material prepared to allow each fraction to be analysed in triplicate lanes. The complete extraction process was carried out in duplicate. The 24 specimens originating from each ham sample were randomly allocated to different lane positions and gels, as were at least two reference lanes (for reference proteins). In total, 118 gels were prepared. Mathematical routines were developed using a matrix language to process the gel image files. Procedures were written to carry out 'within-gel' image correction, lane extraction and normalization, 'between-gel' data registration and linear discriminant analysis (LDA) of each fraction's data to establish whether the provenance could be systematically distinguished. The between-gel registration was carried out using a genetic algorithm (GA). Feature selection was also performed using a GA, to pass subsets of features to the LDA routine. Cross-validated classification success rates were 84, 91, 81 and 85%, respectively, for the four fractions. We conclude that SDS-PAGE can be conducted in a sufficiently quantitative manner and can potentially verify the provenance of regional speciality dry-cured hams.     

Automatic registration for images of two-dimensional protein gels.

Two-dimensional polyacrylamide gel electrophoresis 1 (2-D PAGE 1) is currently the method of choice for separating complex mixtures of cellular proteins. Despite its usefulness, 2-D PAGE is not being applied to its full potential because of difficulties with both the method and analysis of the results. One of the key problems is the difficulty and slowness of image analysis, especially registration (image alignment), which is laborious and the results unsatisfactory. We have developed a novel system for analysis of 2-D PAGE images, called Z3, that performs the analysis faster and more precisely. The Z3 system employs novel approaches to image registration, image display, computation of differential expression, and the design and analysis of 2-D gel experiments. This paper describes in detail the registration algorithm, and briefly discusses the merits of complementary pseudocolor display. The registration algorithm is novel in that for the first time raw-image-based registration technology is applied to 2-D gel analysis.     

Information transfer between large and small two-dimensional polyacrylamide gel electrophoresis

To determine the feasibility of data transfer, an interlaboratory comparison was conducted on colon carcinoma cell line (DLD-1) proteins resolved by two-dimensional polyacrylamide gel electrophoresis either on small (6 x 7 cm) or large (16x18 cm) gels. The gels were silver-stained and scanned by laser densitometry, and the image obtained was analyzed using Melanie software. The number of spots detected was 1337+/-161 vs. 2382+/-176 for small vs. large format gels, respectively. After gel calibration using landmarks determined using pl and Mr markers, large- and small-format gels were matched and 712+/-36 proteins were found on both types of gels. Having performed accurate gel matching it was possible to acquire additional information after accessing a 2-D PAGE reference database (http://www.expasy.ch/ cgibin/map2/def?DLD1_HUMAN). Thus, the difference in gel size is not an obstacle for data transfer. This will facilitate exchanges between laboratories or consultation concerning existing databases.     

On the use of wavelet filtering and correlation techniques in atmospheric condensed phase spectroscopy

The application of wavelet filtering and analysis in spectroscopy is discussed in relation to the analysis of complex atmospheric spectra, where contributions from condensed phase particles and gas phase molecules are present in the form of broad-band features and narrow lines, respectively. The broad-band contribution can be extracted as the 'smooth signal' component of the wavelet transform, with a large reduction in the size of the corresponding data files. This procedure is applied to an investigation of the H2SO4 aerosol content of a series of atmospheric spectra measured in the ATMOS missions. The sulfate content of the smooth signal is analysed by means of correlation techniques, using a set of laboratory reference spectra of varying sulfuric acid concentration and temperature. Correlation density maps and correlation curves are used to select the most appropriate spectral zones for sulfate analysis and to assess the sulfate aerosol content in the atmosphere subsequent to the eruption of the Mount Pinatubo volcano.     

Mass spectrometric imaging of immobilized pH gradient gels and creation of "virtual" two-dimensional gels

We have developed a matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) based technique for the detection of intact proteins directly from immobilized pH gradient gels (IPGs). The use of this technique to visualize proteins from IPGs was explored in this study. Whole cell Escherichia coli extracts of various loadings were separated on IPGs. These IPGs were processed to remove contaminants and to achieve matrix/analyte cocrystallization on the surface of the gel. Mass spectra were acquired by scanning the surface of the gel and were assimilated into a "virtual" two dimensional (2-D) gel. This virtual 2-D gel is analogous to a "classical" 2-D gel, except that the molecular weight information is acquired by mass spectrometry rather than by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). This mass spectrometry (MS) based technology exemplifies a number of desirable characteristics, some of which are not attainable with classical two-dimensional electrophoresis (2-DE). These include high sensitivity, high reproducibility, and an inherently higher resolution and mass accuracy than 2-D gels. Furthermore, there is a difference in selectivity exhibited between virtual 2-D gels and classical 2-D gels, as a number of proteins are visible in the virtual gel image that are not present in the stained gels and vice versa. In this report, virtual 2-D gels will be compared to classical 2-D gels to illustrate these features.     

Comparative fluorescence two-dimensional gel electrophoresis using a gel strip sandwich assembly for the simultaneous on-gel generation of a reference protein spot grid

The comparison of proteins separated on 2DE is difficult due to gel-to-gel variability. Here, a method named comparative fluorescence gel electrophoresis (CoFGE) is presented, which allows the generation of an artificial protein grid in parallel to the separation of an analytical sample on the same gel. Different fluorescent stains are used to distinguish sample and marker on the gel. The technology combines elements of 1DE and 2DE. Special gel combs with V-shaped wells are placed in a stacking gel above the pI strip. Proteins separated on the pI strip are electrophoresed at the same time as marker proteins (commercially available purified protein of different molecular weight) placed in V-wells. In that way, grids providing approximately 100 nodes as landmarks for the determination of protein spot coordinates are generated. Data analysis is possible with commercial 2DE software capable of warping. The method improves comparability of 2DE protein gels, because they are generated in combination with regular in-gel anchor points formed by protein standards. This was shown here for two comparative experiments with three gels each using Escherichia coli lysate. For a set of 47 well-defined samples spots, the deviation of the coordinates was improved from 7% to less than 1% applying warping using the marker grid. Conclusively, as long as the same protein markers, the same size of pI-strips and the same technology are used, gel matching is reproducibly possible. This is an important advancement for projects involving comparison of 2DE-gels produced over several years and in different laboratories.     

IPAAm凝胶在丙酮水溶液中溶胀行为的关联与预报

基于Maurer和Prausnitz的凝胶相平衡条件，建立了凝胶的溶胀模型.模型假设凝胶是以凝胶组分及凝胶吸收的溶液为核心，以弹性半渗透膜为壳的复合体.并采用UNIQUAC方程计算凝胶相及与之共存液相的Gibbs过剩自由能，采用“phantomnetwork”理论计算凝胶的弹性自由能，采用“自由体积”计算分子的尺度效应.同时以N-异丙基丙烯酰胺（IPAAm）为单体合成了IPAAm凝胶.研究了25 ℃时IPAAm凝胶在丙酮水溶液中的溶胀行为，并测定了丙酮在胶体相和与之共存液相中的分配，以检验模型的关联与预报能力.结果表明,模型预报的单体总量和交联剂浓度对凝胶溶胀的影响与实验符合得很好.而且凝胶溶胀时，能很好地预测丙酮在两相中的分配,表明模型具有很好的关联和预报能力.     

Continuous swelling pressure equilibria of the systemκ-carrageenan/water

The deformation of -carrageenan/water gels in a centrifugal field leading to a continuous equilibrium is described. These gels form three-dimensional physical networks. The concentration gradient and the movement of the meniscus gel/solvent during the change of the concentration in the gel phase is measured with a Schlieren optical system of an analytical ultracentrifuge. The gel is considered to be a binary elastic mixture of crosslinked polymer and solvent and is assumed to remain isotropic during the deformation. The concentration dependence of the swelling pressure in the concentration range between the maximum swollen gel and that at the cell bottom can be obtained in a single equilibrium experiment. For the avaluation of the experiments, the weight fraction of the polymer in the maximum swollen gel has been determined separately by a gravimetric method.By means of the swelling pressure-concentration curves the thermodynamic properties of the investigated -carrageenan/water gels can be calculated. The system can be described semi-empirically with a slightly modified Flory-Huggins equation with an interaction parameter _w in the weight fraction scale, which depends linearly on the concentration. The dependence of the static shear modulusG on the polymer concentration follows the scalling theory of De Gennes.Dedicated to Prof. Dr. Ronald Koningsveld on the occasion of his 70th birthday     

Giant Complex Modulus Reduction of κ‐Carrageenan Magnetic Gels

Summary: Effects of magnetization on the complex modulus of κ‐carrageenan magnetic gels have been investigated. The magnetic gel was made of a natural polymer, κ‐carrageenan, and a ferromagnetic particle, barium ferrite. The complex modulus of the magnetic gel was investigated by dynamic viscoelastic measurements with a compressional strain. It was first observed that the magnetic gels showed giant storage modulus reduction ≈10⁷ Pa before and after magnetization. The reduction was nearly independent of the frequency, and it increased with increasing the volume fraction of the ferrite. The maximum reduction in the storage modulus reached 14.9 MPa which corresponds to 76.5% of the modulus before magnetization. It was also found that the change in the modulus was nearly independent of a magnetization direction. Magnetism and morphology of the magnetic gels were also presented.

Strain dependence of the storage modulus at 1 Hz for κ‐carrageenan gel (□) and its magnetic gel before (○) and after (•) magnetization (ϕ = 0.39). The geometry of magnetization and strain directions is perpendicular.     

The Application of Complex Wavelet Transform to Spectral Signals Background Deduction

The accuracy of spectrograms may be affected by baseline excursion or drift when infrared spectrometers are used in the analyses of gases. Background deduction or baseline correction is one of the effective pretreatment methods that can improve measurement accuracy. This paper presents a novel methodology based on complex wavelet transform algorithm to perform background deduction. The complex wavelet transform methodology establishes a complex wavelet filter to decompose the spectral signals first, and set the decomposition coefficients in the high-frequency section to zero, and then reconstruct the background signals; finally, the background deduction can be realized by deducting the background signals. In this study, the complex wavelet established by Daubechies was selected to demonstrate background deduction aiming at simulative spectral signals with different backgrounds and the real spectral signal of SF6 decomposition gases. Compared with the results done by the real wavelet transform in the same conditions, the results indicate that complex wavelet transform methodology can perform background deduction more efficiently than real wavelet transform methodology, thus improving the effectiveness and precision of spectrogram measurements greatly, which is useful for SF6 gas decomposition compositions analysis     

An improved pixel-based approach for analyzing images in two-dimensional gel electrophoresis

An improved pixel-based approach for analyzing 2-DE images is presented. The key feature of the method is to create a mask based on all gels in the experiment using image morphology, followed by multivariate analysis on the pixel level. The method reduces the impact of noise and background by identifying regions in the image where protein spots are present, but make no assumption on individual spot boundaries for isolated spots. This makes it possible to detect significant changes in complex regions, and visualize these changes over multiple gels in an easy way. False missing values and spot volumes caused by imposing erroneous spot boundaries are thus circumvented. The approach presented gives improved pixel-based information from the gels, and is also an alternative to existing methods for data-reduction, significance testing and visualization of 2-DE data. Results are compared with software using a common spot boundary approach on an experiment consisting of 35 full size gel images. Gel alignment is required before analysis.     

Rheoreversible polymeric organogels: the art of science for art conservation

A new category of gels where gelification and breaking of the gels are chemically induced is presented. In particular, the latent gellant polyallylamine produced stable gels with some organic solvents after reaction with CO2 at room temperature, giving the gellant polyallylammonium carbamate. The rheological behavior switches from solution-type to gel-type. After weak acid-catalyzed displacement of CO2, the gel character disappears in a few seconds, making these polymeric organogels rheoreversible by a simple chemical action. This "intelligent" chemical switch between solution-type and gel-type rheological behavior has been exploited to clean pictorial surfaces in art conservation. In fact, during the cleaning procedure, there is a need for the gel supporting the cleaning solvent to have a very high viscosity. After cleaning has been successful, there is a strong necessity to reduce the viscosity, to better eliminate traces of the gellant that must be completely removed from the work of art. In the present study, we show that the art of science, in the sense of designing new physicochemical systems exploiting the "science palette", can lead to an improvement in the techniques used to protect and conserve the results of the "artists' palette".     

Thermoanalytical investigations on the sol-gel synthesis of YBa2Cu3O72212;δ

The high temperature superconducting compound YBa₂Cu₃O_72212; (Y-123) is synthesised by sol-gel process using various precursors viz., acetate, acetate-citrate, nitrate-citrate and acrylamide. The phase purity of the final product depends on the homogeneity of the gels which intern depends on the bonding of the metal ions in the gels. The samples prepared by acrylamide and nitrate-citrate gel routes yielded phase pure Y-123 compound with better superconducting properties. The mechanism of formation of Y-123 in all these four gel routes is established by characterising the gels and intermediate phases using TG, DTA and XRD techniques. Kinetic analysis is carried out on the mass loss data using the method proposed by Phadni's and Deshpande. Avrami-Erofeev nuclei growth in case of acrylamide, diffusion controlled process in nitrate-citrate and phase boundary reaction mechanisms in case of acetate-citrate gels are found to be responsible for the formation of Y-123 phase.The authors are grateful to Dr. Baldev Raj, Director, Metals and Materials Group, for his constant encouragement and support. We thank Prof. G. V. Subba Rao, Director, Central Electrochemical Research Institute, Karaikudi for his keen interest in this work. Thanks are also due to Dr. Sundaram, CECRI, Karaikudi for his help in thermal analysis experiments.     

The remarkable role of hydrogen bond,halogen, and solvent effect on self-healing supramolecular gel

Self-healing supramolecular gels of low-molecular-weight (LMW) molecules are smart soft materials; however, the development of self-healing LMW gelator is still a challenging task because of the lack of in-depth studies about self-healing mechanisms of LMW gels and the solvent effect on gel properties. Therefore, herein a different perspective was used to study a family of D-gluconic acetal-based gelators with variable structural fragments in 14 different solvents, and a more detailed understanding of self-assembly and self-healing mechanism of supramolecular gels was attained. Based on the critical gelation concentration, phase transition temperature, and rheological data, A8 bearing an amide group in side chain and two chlorine atoms linked to benzene ring was found to be an outstanding gelator, which could form gels with good self-healing ability in a variety of solvents. Interestingly, A8 gel formed in n-BuOH demonstrates high transparency, good mechanical strength, self-supporting behavior, and great self-healing ability from mechanical damage. Based on the Fourier transform infrared spectroscopy, nuclear magnetic resonance spectroscopy, X-ray photoelectron spectroscopy, X-ray diffraction, and theoretical calculation analysis, the self-assembly and self-healing mechanisms of A8 gel were proposed, indicating that a combination of hydrogen bonding and halogen effect was responsible for the efficient self-healing behavior of supramolecular gel. Furthermore, the analysis of solvent parameters indicated that the dispersion force of solvent favored gelators to self-assemble, hydrogen bonding donor ability of solvent mainly affected the formation of one-dimensional assembly, and hydrogen bonding receptor ability and polarity of solvent mainly influenced the supramolecular interactions among assemblies, significantly intervening the self-healing ability of gels. Overall, this study provides a new perspective to the understanding of gelator structure–property correlation in solvents and sheds light for future development of self-healing supramolecular gels.     

Wavelet transforms in separation science for denoising and peak overlap detection

Wavelet transform is a versatile time‐frequency analysis technique, which allows localization of useful signals in time or space and separates them from noise. The detector output from any analytical instrument is mathematically equivalent to a digital image. Signals obtained in chemical separations that vary in time (e.g., high‐performance liquid chromatography) or space (e.g., planar chromatography) are amenable to wavelet analysis. This article gives an overview of wavelet analysis, and graphically explains all the relevant concepts. Continuous wavelet transform and discrete wavelet transform concepts are pictorially explained along with their chromatographic applications. An example is shown for qualitative peak overlap detection in a noisy chromatogram using continuous wavelet transform. The concept of signal decomposition, denoising, and then signal reconstruction is graphically discussed for discrete wavelet transform. All the digital filters in chromatographic instruments used today potentially broaden and distort narrow peaks. Finally, a low signal‐to‐noise ratio chromatogram is denoised using the procedure. Significant gains (>tenfold) in signal‐to‐noise ratio are shown with wavelet analysis. Peaks that were not initially visible were recovered with good accuracy. Since discrete wavelet transform denoising analysis applies to any detector used in separation science, researchers should strongly consider using wavelets for their research.