bluuebunny/crossref_metadata_2025_split huggingface dataset:
The investigation of glycosaminoglycan mimotope structure using capillary electrophoresis and other complementary electrophoretic techniques
Authors: Carney Stephen L. , Caterson Bruce , Penticost Helen R. 
Published: May 2005

AbstractWe have used various electrophoretic techniques to analyse glycosaminoglycan structure. Capillary electrophoresis has been particularly useful in the determination of the sulphation of glycosaminoglycans (GAG) and the sulphation of partly desulphated glycosaminoglycans produced by methanolysis. This, in conjuction with preparative electrophoresis and enzyme linked immunosorbent assay (ELISA) has permitted us to ascertain the length of the oligosaccharide required for binding and sulphate ester groups required for optimal binding and those essential for antibody binding. From these preliminary studies, we have demonstrated that the minimum length of oligosaccharide required for binding was about 12–14 monosaccharides in length. It appears likely that 6 sulphation is required for strong binding but 4 sulphation is not involved in mimotope binding. We propose on the basis of this evidence that the mimotope does not contain 4‐sulphate residues but 3‐4 6‐sulphate ester groups are essential for binding.
Purity of glycosaminoglycan‐related compounds using capillary electrophoresis
Authors: Malsch Reinhard , Harenberg Job 
Published: May 2005

AbstractHigh performance capillary electrophoresis was used to determine impurities in glycosaminoglycans. The counterion of glycosaminoglycans was analyzed with indirect UV‐detection using a 40 mM 4‐aminopyridine buffer. Calcium, lithium, potassium and sodium could be resolved. A linear correlation between the area under the curve and the concentration of sodium (r2 = 0.98) and calcium (r2 = 0.99) was found. Using enzymatic depolymerization, chondroitin sulfates were cleaved to disaccharides. The resulting disaccharides, with the structure 4‐deoxy‐α‐L‐threo‐hex‐4‐enopyranosyl uronic acid (ΔUA) 2 × (1 → 3)‐D‐GalNY6X (X = H, sulfate and Y = acetyl, sulfate) for dermatan sulfate, were detected selectively at 230 nm using capillary electrophoresis. Dermatan sulfate disaccharides were analyzed using a 50 cm long fused silica capillary (75 μm ID). The buffer used was 10 mM sodium tetraborate and 50 mM SDS, pH 8.8. The detection was at 230 nm. Using the main peak ΔUA (1 → 3)‐D‐GalNAc4S as standard, between 1 and 80% dermatan sulfate in heparin preparations were analyzed. The disaccharide showed a linear correlation of the peak area versus the concentration with a correlation coefficient r2 = 0.98. The methods are useful in characterizing the identity and concentration of the counterion of glycosaminoglycans after chondroitinase degradation.
Electrophoretic separation of biopolymers in a matrix of polyacrylamide covalently linked to agarose
Authors: Chiari Marcella , Campoleoni Andrea , Conti Paola , Felli Chiara , Patrosso Maria C. , Brogren Carl H. 
Published: May 2005

AbstractA new type of agarose polyacrylamide mixed‐bed gel, obtained by simultaneous gelation of a novel type of allyl‐activated agarose and its copolymerization with acrylamide, has pore sizes intermediate between those of polyacrylamide and agarose. The process used to activate the agarose chains enables the substitution to be controlled. As indicated by nuclear magnetic resonance (NMR), only one allyl group was inserted per agarose basic unit. Several formulations of mixed‐bed gels, containing different percentages of acrylamide, were compared with conventional polyacrylamide or agarose gels. Resolution, migration distance and band sharpness of different molecular mass fragments were evaluated, with two types of gel run side‐by‐side in a vertical or horizontal system. The faster electrophoretic mobility of DNA in dilute mix‐bed gels and the improved separation of the component of high molecular mass (1 to 6 kbp) of the 1 kbp ladder indicate that these matrices have larger porosity than any dilute polyacrylamide formulations. Sodium dodecyl sulfate (SDS)‐protein complexes migrate in the mixed gels faster than in polyacrylamide gels of the same %T.
Interaction of lectins with their ligand carbohydrate of α‐fetoprotein: Analysis by mixed‐lectin affinity electrophoresis
Authors: Taketa Kazuhisa , Liu Miao , Taga Hiroko 
Published: May 2005

AbstractSerum or ascites α‐fetoprotein (AFP) from patients with hepatocellular carcinoma and from a cord blood were analyzed by affinity electrophoresis with two lectins mixed in agarose gel in a combination of concanavalin A (Con A) and Lens culinaris agglutinin A (LCA‐A) or of erythroagglutinating phytohemagglutinin (E‐PHA) and Allomyrina dichotoma lectin (allo A). Con A‐ and LCA‐A‐reactive AFP‐C2‐L3 was not further retarded by mixing with either of the other lectin. It showed a mobility identical with that of AFP‐C2 or AFP‐L3. E‐PHA‐ and allo A‐reactive AFP‐P4‐A3 showed similar results. It migrated with intermediate mobilities of AFP‐P4 and AFP‐A3 depending on the concentrations of the two lectins mixed in the gel. the results indicate that the two mixed lectins compete with each other for the topologically different lectin‐binding sites on the oligosaccharide of AFP molecule.
Identification of glycosylated forms of wheat storage proteins using two‐dimensional electrophoresis and blotting
Authors: Laurière Michel , Bouchez Isabelle , Doyen Christine , Eynard Lucia 
Published: May 2005

AbstractTwo‐dimensional electrophoresis with acid‐polyacrylamide gel electrophoresis (PAGE), followed by sodium dodecyl sulfate (SDS)‐PAGE and SDS‐PAGE of unreduced polypeptides followed by SDS‐PAGE under reducing conditions, were used to separate and identify the different subgroups of gliadins and glutenins and to distinguish between covalent and noncovalent polymers of glutenins. Gels were blotted under semidry conditions according to Laurière (Anal. Biochem. 1993, 212, 206–211) to allow large polymers of glutenins to be transferred efficiently. Glycosylated polypeptides were detected on blots using either the method of Haselbeck and Hösel (Glycoconjugate J. 1990, 7, 63–74), or using anti‐(xylose‐containing N‐glycan) antibodies (Laurière et al., Plant Physiol 1989, 90, 1182–1188). High and low molecular weight glutenin subunits were shown to aggregate through both disulfide bridges and noncovalent protein‐to‐protein interactions. Aggregated γ‐gliadins were also demonstrated. Glycans were detected on both gliadin and gluteinin polypeptides. Covalently aggregated low molecular weight glutenins were shown to contain N‐glycans with xylose, which demonstrated their sorting in the Golgi apparatus.
Soldium dodecyl sulphate‐polyacrylamide gel electrophoresis of human parotid salivary proteins: Comparison of dansylation, Coomassie Blue R‐250 and silver detection methods
Authors: Beeley Josie A. , Newman Frances , Wilson Paul H. R. , Shimmin Ian C. 
Published: May 2005

AbstractDetection of human parotid salivary proteins by dansylation and UV‐transillumination after sodium dodecyl sulphate‐polyacrylamide gel electrophoresis (SDS‐PAGE) has been compared with Coomassie Blue R‐250 and silver staining procedures. Dansylation gives superior results in terms of both resolution and sensitivity, especially with basic proline‐rich proteins (PRPs).
Electrophoretic fingerprinting and multiparameter analysis of cells and particles
Authors: Budde Axel , Knippel Eberhard , Grümmer Gerald , Treichler Jens , Brockmann Hannes , Donath Edwin , Bäumler Hans 
Published: May 2005

AbstractA recently developed electrophoretic instrumentation based on a real‐time image processing system has been applied to electrophoretic fingerprinting and multiparameter analysis of cells and other particles. The comparison between theoretical and experimental electrophoretic fingerprints, completed by the analysis of differences between measured fingerprints, offers a new methodology for better understanding and controlling of the processes at solid/liquid interfaces. Moreover, the multi‐parameter analysis including electrophoretic mobility, size, density and shape of cells can complete the diagnosis and prognosis of diseases.
Two‐dimensional electrophoretic patterns of acute‐phase human serum proteins in the course of bacterial and viral diseases
Authors: Bini Luca , Magi Barbara , Marzocchi Barbara , Cellesi Carla , Berti Brunilde , Raggiaschi Roberto , Rossolini Aldo , Pallini Vitaliano 
Published: May 2005

AbstractAcute‐phase serum proteins were analyzed by two‐dimensional electrophoresis with isoelectric focusing in 3‐10 immobilized pH gradients. Most spots were identified by reference to the plasma map in the SWISS‐2DPAGE database. Serum amyloid A protein spots were identified by immunoblotting with specific antiserum and by matching determined with predicted values of electrophoretic parameters. Changes in the concentrations of α1‐antitrypsin, leucinerich glycoprotein, haptoglobin, serum retinol‐binding protein and transthyretin were quantitated by densitometry of silver‐stained gels. Electrophoretic patterns from 18 patients with bacterial diseases and 16 patients with viral diseases were compared. The incidence of serum amyloid A protein spots was 18/18 in bacterial diseases and 6/16 in viral diseases. As for the other reactants studied, variations were simultaneous in bacterial disease and tended to be staggered in viral diseases.
Electrophoretic analysis of biliary proteins: Application of high resolution two‐dimensional polyacrylamide gel electrphoresis with immobilized pH gradient in the first dimension
Authors: He Chang , Jüngst Dieter 
Published: May 2005

AbstractNative bile samples, dialyzed against double distilled water, fractionated by Sepharose 2B column chromatography, concentrated by ultrafiltration and lyophilized, were solubilized in lysis buffer and studied by two‐dimensional electrophoresis (2‐DE) with immobilized pH gradients in the first dimension. We counted 70, and 7 spots in 2‐DE patterns of bile from patients with cholesterol gallstones and pigment gallstones, respectively.
Marker pattern instabilities as a major cause of reproducibility problems in two‐dimensional DNA fingerprinting
Authors: Hampe Jochen , Marczinek Karola , Preuss André , Nürnberg Peter 
Published: May 2005

AbstractTwo‐dimensional (2‐D) DNA fingerprinting is a promising technique for multilocus analysis of eukaryotic genomes. It has been successfully applied to the detection of DNA variation in tumors, to linkage analyses and to genomic comparisons of inbred mouse strains. However, there are still problems with inter‐gel comparisons of 2‐D DNA typing patterns as documented by the intergel reproducibility rates reported in the literature, which range from 84 to 98%. The basis for standardization in almost all of these studies has been a set of lambda fragments (digested separately with the restriction enzymes HaeIII, RsaI, Bg/I) that produces a spot pattern scattered across the gel. These spots are used as markers for gel comparisons. Since we noticed considerable variations in the marker spot paterns, we evaluated the properties of the lambda marker using both computer simulation and an empirical analysis of forty independent consecutive gels from our laboratory. We explain the instabilities of the spot pattern on the basis of the melting properties of the individual lambda fragments. A subset of spots is presented that has been stable in all our experiments. Only this set of spots should be used for gel standardization purposes until a new, completely reproducible marker becomes available. Finally, suggestions for an improved marker system are made.
Molecular analysis of Salmonella enterica serotype Dublin: Building bridges between population genetic and molecular epidemiological studies
Authors: Platt David J. , Browning Lynda M. , Candlish Denise 
Published: May 2005

AbstractPopulation genetic studies of Salmonella enterica serotype Dublin using multilocus enzyme electrophoresis have recognised two dominant clones termed Du1 and Du3. The characterisation of plasmids in Dublin suggests greater strain diversity. The application of restriction enzyme fragmentation pattern (REFP) analysis of genomic DNA using Sau3A and HincII together with plasmid subtractive analysis can resolve anomalies in earlier comparisons. Twenty‐six isolates were selected for inclusion in the study. All had been previously characterised with respect to their plasmids, and were isolated from the USA, Canada and five European countries. On the basis of plasmid profiles, 17 were predicted to correspond with Du1 and Du3. Sau3A digestion generated two distinct REFPs (A and B) of < 70% similarity, which corresponded with Du1 and Du3. After the contribution of plasmid‐derived bands was subtracted, two variants of A (A1 and A2) and four of B (B1, B2, B3 and B4) were recognised. Seventeen were concordant with predictions from population genetic studies. Nine that could not be predicted on the basis of atypical plasmid profiles all showed REFP A1 (Du1) and were consistent with the incursion of additional plasmids or plasmid cointegration. REFPs from HincII digests generally corroborated Sau3A data but showed greater overall similarity between the strains and more influence from plasmid DNAPresented at the British Electrophoresis Society Meeting, Maidstone Kent, UK, July 13–14, 1995.
.
Improved conditions for the analysis of large variable number of tandemly repeated (VNTR) unit polymorphisms
Authors: Vandenbroeck Koen , Consiglio Antonella , Martino Gianvito , Grimaldi Luigi M. E. 
Published: May 2005

AbstractLarge variable number of tandemly repeated (VNTR) unit polymorphisms were identified by amplification of genomic DNA with appropriate primers, followed by agarose gel electrophoresis and ethidium bromide staining. However, when genomic DNA was extracted using paramagnetic beads, we found that the efficiency of polymerase chain reaction amplification of VNTR's was affected by the purity of the solid phase‐eluted DNA. Here we report that VNTR's located in the human interleukin‐1 receptor antagonist and interleukin‐4 genes are clearly and reliably amplified only when more stringent conditions are used in order to obtain purer DNA eluates from DNA‐bead complexes. In addition, polyacrylamide gel electrophoresis followed by silver staining is superior to ethidium bromide staining of agarose gels in visualizing the different allelic bands of heterozygous carriers.
From image processing to classification: IV. Classification of electrophoretic patterns by neural networks and statistical methods enable quality assessment of wheat varieties for breadmaking
Authors: Jensen Kristen , Kesmir Can , Søndergaard Ib 
Published: May 2005

AbstractThe end‐use quality of products made from doughs consisting of wheat flour and water is often dependent upon the storage (gluten) proteins of the grain endosperm. Today the electrophoretic patterns of the high molecular weight (HMW) glutenin subunits are used for quality selections in wheat breeding programs in several countries. In this study, we used two multivariate techniques to classify digitized patterns from isoelectric focusing of gliadins and glutenins: a two‐layered neural network architecture consisting of a self‐organizing feature map and a feed‐forward classifier [1], and discriminant analysis [2, 3]. Three groups of seven wheat varieties (Triticum aestivum L.), associated with poor, medium or good properties in relation to bread‐making quality, were used. The best classification results were otained by the neural network model, based on data from the gliadin fraction: it was possible to classify varieties associated with poor or good quality, with recognition rates of 70 and 69%, respectively. The statistical method was better suited to solve the classification problem when the data was based on the glutenin fraction: if a specific variety was already known to be non‐poor, this method enabled us to classify the medium‐ and good‐quality classes with recognition rates of 90 and 88%, respectively. The results obtained were confirmed by correlation coefficients.
Quantitation of the water channel protein aquaporin (CHIP28) from red blood cell membranes by densitometry of silver stained polyacrylamide gels
Authors: Benga Gheorghe , Banner Malcolm , Wrigglesworth John M. 
Published: May 2005

AbstractA protein determination procedure which involves the densitometry of silver stained polyacrylamide gels is described. It involves calibration with bovine serum albumin and molecular weight markers on the same gel with the protein to be quantitated. The procedure is simple, rapid, reproducible and accurate and is more sensitive than other procedures for protein determination. The procedure is particularly useful in quantitating proteins purified in small amounts since the determination can be performed on the same gel used to check the purification. It avoids interference by detergents and other substances usually present in solutions of purified proteins. The procedure has been applied to the quantitation of a recently identified protein, aquaporin (CHIP28), assumed to be a major water channel in the red blood cell membrane. A quantitative analysis of a purified fraction of this protein shows that the 28 kDa component represents approximately two thirds of the protein content of the sample, with the remainder comprising a glycosylated, high molecular mass component. The procedure may be useful for quantitating proteins revealed on silver stained gels and could be included as a standard part of any protocol for protein purification.
The role of pH and membrane porosity in preparative electrophoresis
Authors: Corthals Garry L. , Margolis Joel , Williams Keith L. , Gooley Andrew A. 
Published: May 2005

AbstractThe Gradiflow is a preparative electrophoresis apparatus, allowing fractionation based on a combination of size and charge of proteins in their native (unreduced) form. The prepative fractionation of two proteins of similar size and isoelectric point is demonstrated using the Gradiflow. A separation membrance of appropriate pore size was chosen and then fractionation was “fine tuned” by selecting an appropriate buffer pH to accentuate charge differences between the proteins of interest. Complete separation of mg quantities of bovine serum albumin and ovalbumin was achieved within 40 minPresented at the Second Annual Meeting of the Australian Electrophoresis Society, Sydney, April 29–30, 1995.
.
Thermostable variants of subtilisin selected by temperature‐gradient gel electrophoresis
Authors: Sättler Andrea , Kanka Susanne , Maurer Karl‐Heinz , Riesner Detlev 
Published: May 2005

AbstractRegion‐specific random mutagenesis in the weak calcium binding site of subtilisin Carlsberg and subsequent screening for variants with enhanced heat stability revealed two variants, which showed significantly enhanced residual activity at 68°C, 0.1 mM CaCl2, pH 8.0. Preselected variants have been studied by temperature‐gradient gel electrophoresis (TGGE) and were found to be stabilized due to different effects. Whereas the point mutation (Ser188Pro) mainly enhanced autoproteolytic stability of subtilisin, the double mutation (Ser188Pro; Ala194Glu) additionally increased the apparent Tm‐value of the molecule for 2–3°C under a variety of conditions. It was possible to differentiate between the effects of autoproteolysis and structural unfolding to a certain degree by TGGE and to show the complex influence of changed calcium affinity on thermal stability for the double variant.
Determination of the C‐terminal form of an anemone toxin using capillary electrophoresis and mass spectrometry
Authors: Forest Eric , Pétillot Yves , Gagnon Jean , Cotton Joël , Vita Claudio 
Published: May 2005

AbstractTo identify the form of the C‐terminal amino acid of a sea anemone toxin, the native protein was compared with two synthetic proteins comprising the same sequence and a free or an amide C‐terminal form. Using electrospray ionization‐mass spectrometry, capillary electrophoresis and the coupling of both techniques, we assigned the C‐terminus of the native protein to be in the free carboxyl form.
Deterministic model of DNA gel electrophoresis in strong electric fields
Authors: Lee Namkyoung , Obukhov Sergei , Rubinstein Michael 
Published: May 2005

AbstractWe present a new model for the motion of a megabase‐long DNA molecule undergoing gel electrophoresis. We assume that the dynamics of large segments of DNA is almost deterministic and can be described by a set of simple mechanical equations. This allows the numerical study of gel electrophoresis of ultra‐high molecular weight DNA. A strong electric field forces DNA in a gel into a tree‐like structure with branches – loops of different sizes. We determined the loop‐size distribution function. This distribution has a power law form, confirming the hypothesis of the statistical self‐similarity of a moving polymer. We find periodic configuration changes in the motion of a circular polymer, with the average period proportional to the molecular weight. During the period, a polymer goes through three distinct phases: a simple V‐shape configuration, a growing tree, and a decaying tree. For a linear polymer this periodicity is much less pronounced because of additional perturbations to the dynamics caused by free ends. A circular polymer stays in a simple V‐shaped configuration about 30% of the time, independent of molecular weight (10% for a linear polymer).
Polyacrylamide solutions for DNA sequencing by capillary electrophoresis: Mesh sizes, separation and dispersion
Authors: Wu Chunhung , Quesada Mark A. , Schneider Dieter K. , Farinato Raymond , Studier F. William , Chu Benjamin 
Published: May 2005

AbstractTwo preparations of linear polyacrylamide with average molecular weights of 0.37 million and 1.14 million Da, and a deuterated preparation with an average molecular weight of 1.71 million Da, were used to study the effects of molecular weight, polydispersity, and concentration on the mesh size of entangled polymers in a DNA sequencing buffer solution and their ability to resolve DNA sequencing reactions by capillary electrophoresis. The polyacrylamide concentrations were above the overlap threshold C*, the concentration above which an entangled polymer network is expected to form. Small angle neutron scattering experiments showed that between 1% and 8% polyacrylamide, the mesh size (ζ) can be expressed by the relation ζ = 2.09C−0.76, where ζ is in Å and C is the polymer concentration in g/mL. The mesh size depended only on the concentration and was independent of the average molecular weight of the polyacrylamide. Consistent with this result, electrophoretic mobilities of DNA moving through the polymer network depended almost entirely on the polyacrylamide concentration and not on its molecular weight or polydispersity. Although separation was little affected, band sharpness persisted to longer DNAs when the polymer network contained a higher fraction of larger polyacrylamide molecuels. We postulate a dispersive effect that depends on the size of the DNA and the resiliency of the polymer network. This interpretation provides a rationale for optimizing the design of polymer solutions to sieve DNA for sequencing by capillary electrophoresis.