bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numerical technique and computational procedure for isotachophoresis
Authors: Palusinski Olgierd A. , Su Yu , Fife Paul C. 
Published: May 2005

AbstractThis paper presents a new numerical method for computation of solutions of prototypical equations of isotachophoresis. Numerical computation is complicated because the Poisson equation, which relates electrostatic potential to space charge density, contains a small parameter. This parameter is usually assumed to have the value of zero. Under this assumption the Poisson differential equation is replaced by an algebraic equation, which is often called the equation of electroneutrality, because it indeed states that the electrolyte is electrically neutral this assumption were not studied in the past. Here we propose an iterative procedure which allows for computation of solutions without the assumption of electroneutrality. The accuracy is controlled by a number of iterations and is limited by a computer round‐off error only. The method is based on our previously published theory of existence and uniqueness of solutions of isotachophoretic equations. Details of the computational algorithm for prototypical equations of isotachophoresis are given. A numerical example and comparison with previously published data are also provided.
Conditions for purification of proteins by free‐flow zone electrophoresis
Authors: Clifton Michael J. , Jouve Nicolas , Balmann Hélène De , Sanchez Victor 
Published: May 2005

AbstractThe separation of proteins by free‐flow zone electrophoresis is generally impaired by a number of secondary effects which cause spreading of the protein streams with resultant loss in resolution. A strategy is outlined, based on experimental observations and numerical modeling, which allows the operating conditions and separation chamber dimensions to be chosen so as to obtain complete separation of two proteins of known mobility. This approach takes into account some dispersive phenomena such as molecular diffusion, electroosmosis and residence time gradients. In some cases, the right operating conditions cannot be achieved on earth and electrophoresis separations in microgravity may then be justified.
The development of recycle zone electrophoresis
Authors: Ivory Cornelius F. 
Published: May 2005

AbstractMilan Bier′s contributions to preparative electrophoresis and, in particular, his work in „recycling”︁, have had an enormous impact on the development of scaling strategies for continuous flow electrophoresis. This paper reviews my early work on the theory of recycle applied to zone electrophoresis and reports the results of several recent experiments in which proteins were purified from complex feed mixtures using recycle zone electrophoresis.
Membrane active plasma factor in multiple sclerosis: Characterization and isolation by recycling isoelectric focusing
Authors: Tamblyn Cherry H. , Seaman Geoffrey V. F. , Egen Ned B. , Bier Milan 
Published: May 2005

AbstractRecycling isoelectric focusing is a rapid, high resolution technique that has the capability of fractionating complex mixtures of proteins on a preparative scale on the basis of their isoelectric points (pIs). For this reason, it appeared to be an ideal tool to further characterize and isolate the surface active plasma component(s) which is abnormal in multiple sclerosis(MS). The normal control and the abnormal MS plasma components, or factors, proved to be stable under the conditions used in this technique, including deionization by electrodialysis, dialysis against distilled water, lyophilization and the presence of 3M urea and carrier distilled water, lyophilization and the presence of 3M urea and carrier ampholytes. The presence or absence of plasma factor activity was determined by incubating red blood cells in a test plasma, or plasma fraction, followed by the determination of the red blood cell electrophoretic mobility in the presence and absence of linoleic acid. Both the normal and MS factor had a pI of 4.0 ± 0.1 under the conditions used. A high degree of purification was achieved and albumin was eliminated as a possible candidate for the factor(s).
Gene‐Protein database of Escherichia coli K ‐ 12: Edition 3
Authors: Vanbogelen Ruth A. , Hutton M. Elizabeth , Neidhardt Frederick C. 
Published: May 2005

AbstractThe first two editions of the E. coli Gene‐Protein Index were published to provide identifications of protein spots resolved by two‐dimensional gel electrophoresis as the products of known genes. This third edition has been expanded to include information about genes and proteins gained directly from two‐dimensional gel analysis – including information about protein spots not yet characterized genetically or biochemically – and is therefore more properly called a cellular proteins database. An alpha‐numeric designation has been uniquely assigned to each of the 616 polypeptide spots in the current database. To this, information is linked about the polypeptide′s identification (protein name, gene name, Enzyme Commission – EC number), location on reference gels (x‐y coordinates), genetics (Genbank code, DNA sequence reference), biochemistry (molecular weight, isoelectric point), and physiology (steady state level of the protein as a function of media and temperature, membership in various regulons and stimulons).
The distribution of particles characterized by size and free mobility within polydisperse populations of protein‐polysaccharide conjugates, determined from two‐dimensional agarose electropherograms
Authors: Tietz Dietmar , Aldroubi Akram , Schneerson Rachel , Unser Michael , Chrambach Andreas 
Published: May 2005

AbstractNew approaches for the characterization of polydisperse particle populations are presentedPreliminary reports of this study were presented at the American Electrophoresis Society Meeting, Washington DC, USA, July 6–11, 1989; at the NIH/ADAMHA‐Industry Collaboration Forum, Bethesda, Maryland, USA, October 3, 1989; at the Electrophoresis Forum '89, Munich Germany, October 23–25, 1989; and at Frontiers in Bioprocessing II, Boulder, Colorado, USA, June 17–21, 1990.
. The investigated samples contain virus‐sized protein‐polysaccharide conjugates which had previously been prepared as immunogens against bacterial meningitis (Hib). The analysis is based on two‐dimensional agarose electrophoresis (Serwer‐type). This method, like the one of O'Farrell, achieves a separation according to size and charge. It relies on a different principle, however, and is applicable to nondenatured particles which are 100 to more than 1000 times larger in mass than regular uncrosslinked proteins. Data from stained gel patterns are evaluated by the computer program ELPHOFIT, which makes it possible to standardize the gel and to construct a nomogram which defines every position on the gel in terms of particle size and free mobility (related to surface net charge density). The output of ELPHOFIT, consisting of nomogram parameters, is transferred to the image processing program GELFIT. This software is used to evaluate the computer images obtained by digitizing the stained gel patterns: (i) The nomogram is electronically superimposed on the computer image. (ii) The gel pattern is transformed from a curvilinear to a rectangular coordinate system of particle size and free mobility. The center of gravity as well as density maxima are given in coordinates of particle size and free mobility. Ranges of grey levels can be accentuated by adding 16 pseudocolors. (iii) Using surface‐stripping techniques, GELFIT provides an estimate for the number of major subpopulations within each preparation. (iv) Numerical values or the distribution of particle size and free mobility are determined. Using program IMAGE, the quantitative physical assessment of a given conjugate preparation is presented in the form of a computer‐generated three‐dimensional plot, the shape of which serves to identify and characterize the preparation visually. The data analysis based on digitized two‐dimensional gel patterns is automated to an extent that a technician can perform routine evaluations. It uses the Macintosh II personal computer.
A rapid and economical method for hybrid purity testing of tomato (Lycopersicon esculentum L.) F1 hybrids using ultrathin‐layer isoelectric focusing of alcohol dehydrogenase variants from seeds
Authors: van den Berg Bartel M. 
Published: May 2005

AbstractIn the cultivated tomato (Lycopersicon esculentum L.), two electrophoretic variants of the enzyme alcohol dehydrogenase (ADH) encoded by the alleles Adh‐1+ and Adh‐11 are found. A rapid and economic method for testing the hybrid purity of tomato F 1 seeds, based on the expected presence of Adh‐1 alleles, was developed. The method is based on the analysis of the ADH variants by ultrathin‐layer isoelectric focusing, pH range 3–10, of crude extracts from imbibed seeds followed by enzyme activity staining. The isoelectric points (pIS) of the ADH variants were estimated to be 5.5 and 5.7 for Adh‐1+ and Adh‐11; respectively. Using the procedure described and a newly developed sample applicator strip, it is Possible for one person to routinely analyze 1152 seeds per day using only a single electrophoresis unit. An investigation of a large number of inbred lines, both experimental and commercial hybrids, together with open‐pollinated varieties, showed the potential of the method. Among F1 hybrids, a higher frequency of the Adh‐11 allele was found than among open pollinated varieties, suggesting that F1 hybrid breeding has resulted in a higher frequency of Adh‐11 alleles by selection of linked genes.
Analysis of two‐dimensional electrophoretic patterns of proteins obtained from the sera of normal and tumorbearing nude rats
Authors: Yoshida Motoko , Itoh Michio , Imai Toshio , Tanimoto Yoshifumi , Sakurabayashi Ikunosuke , Furuya Shin 
Published: May 2005

AbstractTo classify two‐dimensional electrophoresis (2‐DE) patterns of normal and abnormal samples, a new parameter, named shift value, is introduced. The shift value is defined by the product of three indices; differences in density, differences in area, and the Euclid distance between peaks of matched glycoprotein spots in the 2‐DE patterns. Shift values obtained from the differences between the 2‐DE patterns of tumorbearing and normal sera (control) were always found to be larger than those obtained from two control patterns. The shift value obtained from glycoprotein spots could be more effectively used to distinguish normal and abnormal patterns than that obtained from simple proteins. In our earlier attempts to compare serum proteins of normal and tumor patients, we could not discriminate differences caused by genetic background. In order to circumvent this difficulty, we employed an inbred strain of nude rats into which various types of human cancer had been implanted. Reliability of the analysis is enhanced by using a polyacrylamide gel backed with a silanized glass support and an automatic 2‐DE apparatus.
Genome scanning by two‐dimensional DNA typing: The use of repetitive DNA sequences for rapid mapping of genetic traits
Authors: Uitterlinden André G. , Slagboom Eline P. , Mullaart Erick , Meulenbelt Ingrid , Vijg Jan 
Published: May 2005

AbstractThe existence of repetitive DNA sequences offers the possibility to assess the mammalian genome for individual variation in its entirety rather than at one or only a few sites. In order to fully explore the various sets of mammalian repeat sequences for this purpose, analytical tools are required which allow many if not all individual members of sets of repetitive elements to be resolved and identified in terms of location and allelic variation. We have applied and further developed an electrophoretic system, two‐dimensional DNA typing, which may fulfill these requirements. The two‐dimensional system combines separation of DNA fragments is by size in a neutral gel, with separation by sequence composition in a denaturing gradient gel. By hybridization with minisatellite‐ and simple‐sequence core probes and by inter‐repeat polymerase chain reaction techniques, it is possible to obtain individual ‐ and even chromosomespecific separation patterns that consist of hundreds of spots. Computerized image analysis and matching of such spot patterns allow the rapid assesment of multiple polymorphisms, spread over the genome, to monitor genetic variability in populations. When coupled to databases of polymorphic DNA markers with a known genomic location, two‐dimensional DNA typing can greatly accellerate the mapping of genetic traits in humans, animals, and plants.
Highly instable (GATA)n‐containing sequences of the mouse during the cloning process
Authors: Studer Roland , Kammerbauer Claudia , Zischler Hans , Hnkkanen Ari 
Published: May 2005

AbstractMouse DNA fingerprints were obtained by HaeIII digestion of genomic DNA and ingel hybridization with the (GATA)4 oligonucleotide probe. In order to obtain locusspecific probes that hybridize with only one fragment of the (GATA)4 DNA fingerprint, a genomic library of size‐selected inserts was constructed using a system of direct subcloning from the phage clones. During the cloning procedure, the phage as well as the plasmid insert DNAs changed primarily within their repetitive DNA but also within adjacent nonrepetitive sequences, as was demonstrated for several clones by in‐gel hybridization with the (GATA)4 probe as well as by sequence analysis. Isolated subclones varied within their (GATA)n repeats, resulting in different insert lengths. Several “metastable” as well as stable (GATA)4‐positive subclones could be isolated. Also, vector sequences were affected by alterations during the cloning process. These phenomena are discussed within the context of possible mechanisms for cloning artifacts.
Plant DNA fingerprinting with radioactive and digoxigenated oligonucleotide probes complementary to simple repetitive DNA sequences
Authors: Weising Kurt , Beyermann Birgit , Ramser Juliane , Kahl Günter 
Published: May 2005

AbstractThe existence of hypervariable DNA sequences in nuclear genomes, and the use of appropriate “fingerprinting” probes to detect them, has gained widespread scientific interest, and also led to multiple applications in diverse areas. Two years ago, the new technique of “DNA fingerprinting” was also introduced into the analysis and characterization of plant genomes, initially by using human or M 13 minisatellites as probes. In the present article, we demonstrate the applicability for plant DNA fingerprinting of oligonucleotide probes specific for simple repetitive DNA sequences. We show that various levels of intra‐ and interspecific polymorphisms can be detected; the information to be gained depends on the optimal combination of probe and species. Variety‐specific patterns were obtained in several cases. Some probes revealed variability between individuals. Somatic variability was not observed. Different DNA isolation and purification procedures were tested in order to introduce a fast and easy‐to‐perform isolation method suitable for a large variety of plant species. Nonradioactive fingerprinting was performed using digoxigenated oligonucleotides as probes. Banding patterns obtained with radioactive and digoxigenin‐based labeling techniques proved to be of similar quality.
On paternity determination from multilocus DNA profiles
Authors: Yassouridis Alexander , Epplen Jorg T. 
Published: May 2005

AbstractVarious approaches have been worked out to calculate to the probability of paternity from DNA multilocus profiles. Despite promising results, the application and practicability of these approaches are often restricted (due to, e.g., the equality assumption of the a priori probabilities by using Bayes theorem, no allowance of mutations, etc). Here we present two methods for paternity determination, one of which is an extension of the well‐known procedure of Evett et al. J. Forens. Sci. Soc. 1988, 28, 249–254. These methods depend on fewer assumption sand therefore maybe applied to a wide spectrum of disputed paternity cases.
Free mobility determination by electrophoresis in polyacrylamide containing agarose at a nonrestrictive concentration
Authors: Pospichal Jan , Vicchio Domenick , Chrambach Andreas 
Published: May 2005

AbstractIn the determination of the free mobility, related to the surface net charge, by quantitative gel electrophoresis, the previous arbitrary extrapolation of Ferguson plots from the lowest gel concentrations that give a mechanically stable gel to 0 %T has recently been replaced by measurement of mobilities across that concentration range, using the addition of 0.5 % agarose to polyacrylamide at the various low concentrations in application to a DNA fragment 155 bp in size (Orbán, L. et al., in preparation). The present study applies that approach to several proteins and DNA fragments smaller than 1300 bp, using 0.4 % agarose in polyacrylamide gels of varying concentration. The intercepts of the plots with the mobility axis provide experimental data by which the free mobility in polyacrylamide gel electrophoresis can be estimated for molecules not significantly retarded in their migration at the agarose concentration admixed to polyacrylamide. Across the gel concentration range below 3 %T, in the presence of agarose, the Ferguson plots of proteins and DNA fragments are convex. It was shown by mass spectrometry that this convex curvature of the plots in the mixed polymer is not significantly due to low polymerization efficiency in the concentration range of liquid polyacrylamide (below 3 %T).
Estimation of polyacrylamide gel pore size from Ferguson plots of normal and anomalously migrating DNA fragments. I. Gels containing 3 % N, N′‐methylenebisacrylamide
Authors: Holmes Diana L. , Stellwagen Nancy C. 
Published: May 2005

AbstractThe mobilities of normal and anomalously migrating DNA fragments were determined in polyacrylamide gels of different acrylamide concentrations, polymerized with 3 % N, N′‐methylenebisacrylamide as the crosslinker. The DNA samples were a commercially available 123‐bp ladder and two molecular weight ladders containing multiple copies of two 147‐base pair (bp) restriction fragments, obtained from the MspI digestion of plasmid pBR322. One of the 147 bp fragments is known to migrate anomalously slowly in polyacrylamide gels. Ferguson plots were constructed for all multimer ladders, using both absolute mobilities and relative mobilities with respect to the smallest DNA molecule in each data set. If the retardation coefficients were calculated from the relative mobilities, and the rms radius of gyration was used as the measure of DNA size, the Ogston equations were obeyed and the gel fiber parameters could be calculated. The effective pore sizes of the gels were estimated from the gel concentration at which the mobility of a given DNA molecule was reduced to one‐half its mobility at zero gel concentration. The estimated pore radii ranged from ∼ 130 nm for 3.5 % gels to ∼ 70 nm for 10.5 % gels. These values are much larger than the pore sizes previously determined for the polyacrylamide matrix.
Separation of human alloalbumain variants by isoelectric focusing
Authors: Rocha Jorge , Kömpf Jost , Ferrand Nuno , Amorim António , Ritter Horst 
Published: May 2005

AbstractA technique for the separation of human alloalbumin variants by means of isoelectric focusing in the presence of 8M urea and 60 mM L‐serine is described. The potential usefulness of this technique in the detection and classification of genetic heterogeneity at the albumin locus is demonstrated by the differentiation of three human alloalbumin variants of European origin.
Structural basis of electrophoretic variants of rat α‐fetoprotein
Authors: Ehara Akira , Nishi Shinzo 
Published: May 2005

AbstractThe molecular basis for electrophoretic variations of rat α‐fetoprotein was studied. Stepwise deglycosylations of proteins and radiolabeling of the sugars indicated that the number of such chains per molecule is two and one for the slow and fast variants, respectively.
Luminography – a new, highly sensitive visualization method for electrophoresis
Authors: Schneppenheim Reinhard , Budde Ulrich , Dahlmann Nicolaus , Rautenberg Peter 
Published: May 2005

AbstractA highly sensitive method for protein visualization following electrophoresis and protein blotting was developed. The method is based on the light‐emitting reaction of luminol and hydrogen peroxide catalyzed by horseradish peroxidase. The luminescent assay can be applied either to the native gel or after protein blotting, and it has a sensitivity two orders of magnitude higher than that achieved with chromogenic detection systems. Analogous to autoradiography the luminescent signal is recorded on an X‐ray film with similar sensitivity. We present several examples of application emphasizing the general versatility of this innovative method.
Oxidation of cysteine to cysteic acid in proteins by peroxyacids, as monitored by immobilized pH gradients
Authors: Chiari Marcella , Ettori Claudia , Righetti Pier Giorgio , Colonna Stefano , Gaggero Nicoletta , Negri Armando 
Published: May 2005

AbstractIt has often been debated whether the presence of persulfate in a polyacrylamide gel could lead to the oxidation of cysteine (Cys) in proteins to cysteic acid. In fact, direct incubation of bovine serum albumin (BSA) with peroxodisulfate and periodate barely alters the isoelectric point (pI) and does not produce any cysteic acid. In contrast, caroate (peroxomonosulfate) and perphathalate strongly lower the pI of BSA. In the former case it as demonstrated that 4‐ Cys (of a total of 35) were converted into cysteic acid. Perphthalate was found to be, by far, the strongest oxidant: 15 (of 35) Cys residues were oxidized to cysteic acid and all methionine groups were destroyed.
Description of a new variant in the gluamateoxaloacetate transaminase system by thin‐layer agarose gel isoelectric focusing
Authors: Farnbacher Oliver , Weidinger Sebastian 
Published: May 2005

AbstractThin‐layer isoelectric focusing in agarose within the pH range of 4.0–6.5 has shown a high resolution of the soluble cytoplasmic glutamate‐oxaloacetate transaminase (GOT1) banding pattern. The complex pattern of the common GOT1 phenotype consists of eight bands with different intesities. A genetic variant of GOT1, which has been designated GOT1 Mexico, could tentatively be identified.
Fluctuating bond model of DNA gel electrophoresis
Authors: Schönherr Götz , Noolandi Jaan 
Published: May 2005

AbstractWe present a Monte Carlo algorithm that allows a small length scale numerical study of DNA gel electrophoresis in high electric fields, similar to the fluctuating bond model for dynamical properties of polymeric systems. This approach combines advantages of lattice Monte Carlo method with those from continuous Brownian dynamics algorithms, and also takes into account the persistence length of DNA, as well as the random nature of the gel. The initial orientation and acceleration of a random‐walk DNA conformation shows a number of features that can be related to experimental results. The detailed description of DNA motion provided by this approach may lead to a first realistic computer study of the process of DNA sequencing.
Application of schlieren optics to, real‐time monitoring of protein electrophoresis in crosslinker‐free linear polyacrylamide solution
Authors: Takagi Toshio , Kubota Hidehiro , Oishi Seizo 
Published: May 2005

AbstractMolecular sieving effect of crosslinker‐free linear polyacrylamide solutions could be visualized in a real‐time mode using schlieren optics for electrophoresis of proteins. Since linear polymer solutions are going to find application in capillary electrophoresis (Zhu, M., et al., J. Chromatogr. 1989, 480, 311–319), the above approach may be useful for obtaining basic data of electrophoresis of proteins and nucleic acids in such media under conditions free from the predominant wall effect pertinent to the use of a capillary.