bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electrophoretic mobility of composite objects in free solution: Application to DNA separation
Authors: Long Didier , Ajdari Armand 
Published: May 2005

AbstractWe propose here a simple procedure to estimate the electrophoretic mobility of composite objects obtained by linking two charged subunits, stressing that this electrophoretic mobility is in general different from the ratio of the total charge to the total friction coefficient. We focus especially on the situation where at least one of the subunits is a polyelectrolyte. Our remarks in particular correct the existing theoretical analysis of separation capabilities of devices in which a buoy (sphere, protein, polymer) is attached to a DNA chain. We also predict that, in some cases, the direction of electrophoretic motion can be reversed by increasing the electric field amplitude.
Theory of electrophoretic mobility of a polyelectrolyte in semidilute solutions of neutral polymers
Authors: Muthukumar Murugappan 
Published: May 2005

AbstractAn explicit formula is derived for the electrophoretic mobility of a polyelectrolyte molecule in a semidilute solution of neutral polymers in terms of the molecular weight N of a polyelectrolyte, concentration c of neutral polymers, Debye length and solvent quality. The nature of the crossover between different regimes, as c, N, and the salt concentration are varied, is presented. The calculations show that one progressively enters into regimes of no‐separation, separation, and no‐separation in the electrophoresis of polyelectrolytes as c is increased. If c is very high, one returns to the mechanism of separation in gel electrophoresis.
Use of neutral surfactants for the capillary electrophoretic separation of hydrophobically modified poly(acrylic acids)
Authors: Collet Jérǒme , Tribet Christophe , Gareil Pierre 
Published: May 2005

AbstractHydrophobically modified poly(acrylic acids) (HMPAs) are random copolymers of sodium acrylate and dodecyl acrylamide, containing 0–10% mol/mol of dodecyl grafts. The hydrophobic character of different HMPAs of average molecular weight 150 000 was studied by capillary electrophoresis (CE), using neutral surfactants as buffer additives. The differentiation of the electrophoretic mobilities of HMPAs with their hydrophobicity was achieved through the use of nonionic Brij 35 and zwitterionic DAPS surfactants. A nearly baseline separation of the precursor and three HMPAs derivatives was obtained in a poly(ethylene glycol)‐coated capillary with a background electrolyte containing 10 mM N‐dodecyl‐N,N‐dimethyl‐3‐ammonio‐1‐propanesulfonate (DAPS) and 10 mM borax (pH 9.2). In addition to CE experiments, the polymer‐surfactant interactions were also investigated by means of quasi‐elastic light scattering (QELS) and viscosimetric measurements. According to the latter results, the separation mechanism was interpreted as an expansion of the polymer coil in the presence of micelles and subsequent change of its frictional properties. A true micellar electrokinetic capillary chromatography (MEKC) partitioning model was discarded on the basis of the relative sizes of the macromolecule and the micelles.
Determination of denatured serum proteins in the casein fraction of heat‐treated milk by capillary zone electrophoresis
Authors: Recio Isidra , Olieman Cornelis 
Published: May 2005

AbstractThe amount of heat‐denatured serum proteins in heat‐treated milk could be estimated by analyzing the casein fraction, obtained by isoelectric precipitation at pH 4.6, by capillary zone electrophoresis. A hydrophilically coated capillary was used in combination with 6 M urea in a citrate buffer at pH 3. Optimization of the sample and running buffer minimized adsorption of serum proteins, especially that of bovine serum albumin (BSA). This afforded a detection limit down to ca. 5–65 μg/mL of the three main serum proteins in milk. The detector response (UV at 214 nm) was linear in the range of 0.05–0.35 and 0.05–0.85 mg/mL for α‐lactalbumin and β‐lactoglobulin, respectively. BSA showed a slightly less linear behavior, due to residual adsorption to the capillary wall. The recovery of serum proteins was in the range of 89–107%. The method was evaluated by analyzing Dutch commercial milks and cheese milk, which had received increasing heat loads. The additions of milk powder to pasteurized milk could be detected by this method as well as the serum protein to casein ratio in various products.
Computer optimization of background electrolyte composition in the separation of metal ions by capillary electrophoresis
Authors: Billiet Hugo A. H. , Andersson Per E. , Haddad Paul R. 
Published: May 2005

AbstractThe iterative regression design developed earlier for high performance liquid chromatography (HPLC) has been applied successfully to the optimization of the separation of 11 metal ions by capillary electrophoresis. The parameters used for optimization were pH (over the range 3.5–5.0) and the concentration of 2‐hydroxyisobutyric acid (HIBA) (2–20 mM) used as the complex‐forming ligand added to the background electrolyte. Five initial experiments were performed and the response surface was calculated using the relative resolution product as criterion. Three additional experiments were sufficient to establish a stable optimum, with which all 11 metal ions were separated and well spread in the electropherogram. The total analysis time was less than 5 min.
Fish species identification by isoelectric focusing of parvalbumins in immobilized pH gradients
Authors: Esteve‐Romero Josep S. , Yman Ingrid Malmheden , Bossi Alessandra , Righetti Pier Giorgio 
Published: May 2005

AbstractIsoelectric focusing in immobilized pH gradients (IPG) is reported for unequivocal identification of fish species. Three orders of fishes have been analyzed: salmons, flat and cod fishes. In each family, four closely related species have been analyzed. For clear‐cut species identification, two strategies have been adopted: (i) to perform IPGs in very narrow (1 pH unit and less) acidic gradients, typically spanning the pH 4–5 range, where fewer proteins are present and the pattern is much clearer; (ii) to focus the analysis on the parvalbumins, since this protein class is highly species‐specific and resistant to heat. Thus, not only fresh muscle could be analyzed, but also boiled fish samples. In all cases unambiguous determination of each species could be performed, either by simple visual band inspection or, in the most difficult cases, by densitometric evaluation of the Coomassie‐blue stained profiles. The analysis was performed in extracts of single species and also in mixtures of the most closely related species.
The construction of the World Wide Web‐accessible myocardial two‐dimensional gel electrophoresis protein database “HEART‐2DPAGE”: A practical approach
Authors: Pleißner Klaus‐Peter , Sander Stefan , Oswald Helmut , Regitz‐Zagrosek Vera , Fleck Eckart 
Published: May 2005

AbstractThe construction of the two‐dimensional electrophoresis (2‐DE) gel protein database “HEART‐2DPAGE” for human heart proteins, accessible via the World Wide Web (WWW), is described. This database provides the opportunity to retrieve descriptive information interactively by mouse clicking on a protein spot within a 2‐DE gel image or to retrieve the position of a protein if its protein name or a search expression is given. The realization of searching for proteins, the creation of clickable spots, marked by crosses or textual information, and interactive viewing opportunities are discussed from a softwareoriented point of view. The database takes into account that some human heart proteins are chamber specific. Several Common Gateway Interface (CGI) scripts are described and some practical experience is discussed.
High‐performance field inversion capillary electrophoresis of 0.1–23 kbp DNA fragments with low‐gelling, replaceable agarose gels
Authors: Chen Nong , Wu Lijuan , Palm Anders , Srichaiyo Tasanee , Hjertén Stellan 
Published: May 2005

AbstractField inversion capillary gel electrophoresis (FICGE) has been used for the separation of 0.1–23 kbp DNA fragments in a low‐melting, low‐gelling agarose gel. The influence of the amplitude of the voltage pulses, the pulse times and gel concentrations on the separation factor has been studied and found to be similar to that of polyacrylamide gels. Very high resolution can be obtained by altering continuously the pulse times and/or voltage according to a program tailor‐made for the size of the DNA molecules to be separated (programmed FICGE). The advantage of these agarose gels in comparsion with polyacrylamide gels is that they are nontoxic, easy to prepare and they have high UV transmission. They give a resolution that is equivalent to or better than that of polyacrylamide gels, and the risk of bubble formation in the gel is small. In addition, they are replaceable and, therefore, very convenient for automated analyses.
Capture in the gel: Intermoleculare triplex formation during gel electrophoresis
Authors: Belotserkovskii Boris P. , Johnston Brian H. 
Published: May 2005

AbstractAnalysis of unusual gel mobility patterns formed by certain DNA triplexes has revealed that intermolecular triplex formation can occur during gel electrophoresis when a faster migrating single strand overtakes a slower migrating band containing a duplex of appropriate sequence. Control experiments showed that this capture of the third strand occurs by sequence‐specific hybridization rather than some nonspecific retardation. This phenomenon can be used to detect triplexes by a gel‐shift assay even if their lifetime is much shorter than the time of gel electrophoresis.
Quantitation of glycated hemoglobins in human adult blood by capillary isoelectric focusing
Authors: Conti Monica , Gelfi Cecilia , Bosisio Adriana Bianchi , Righetti Pier Giorgio 
Published: May 2005

AbstractA precise and reproducible method for assessment of glycated hemoglobin in human adult red blood cells is reported, based on capillary isoelectric focusing (IEF). In order to obtan baseline resolution between adult hemoglobin (Hb A) and its glycated form (Hb A1c), two species which differ by minute ΔpI values, < 0.03 pH units, the following procedure was adopted: the focusing mixture consisted of 5% Ampholine, pH 6–8, 0.5% Pharmalyte, pH 3–10, 3% short‐chain liquid polyacrylamide and an equimolar mixture of two “separators”, 0.33 M β‐alanine and 0.33 M 6‐aminocaproic acid. The last two compounds flatten the pH gradient in the pI region of the two Hbs, thus allowing full separation. Additionally, the Hb samples, instead of being pulse‐loaded, are uniformly distributed in the background electrolyte. A longer capillary lifetime is obtained if all nonbuffering ions are eliminated; thus, as catholyte, 50 mM Lys (pH 9.7) is utilized and as anolyte 50 mM acetic acid (pH 3.5) is adopted. The percentages of Hb A1c, as obtained by capillary IEF, are in good agreement (±6%) with data obtained by one of the standard zone electrophoretic methods in clinical chemistry, i.e., the Helena REP Glyco gel system.
Selecting and amplifying one fragment from a DNA fragment mixture by polymerase chain reaction with a pair of selective primers
Authors: Matsunaga Hiroko , Kohara Yoshinobu , Okano Kazunori , Kambara Hideki 
Published: May 2005

AbstractA new method for selecting and amplifying a single DNA fragment from a mixture is proposed. This method is applicable for the rapid classification of DNA fragments from a mixture and for preparation of sequencing templates. DNAs of several to tens of kilobases (kb) are digested with a four‐base recognition restriction enzyme to produce smaller fragments. The complementary strand extension reactions are then carried out to produce fluorophore‐labeled DNA fragments from the digestion products. These fragments can be rapidly classified accrording to their terminal‐base sequences and their sizes are analyzed by capillary‐array gel electrophoresis (CAGE). Electropherograms are used to characterize the fragments and to select polymerase chain reaction (PCR) primers. Any fragment in a digestion mixture can be amplified by PCR with a pair of primers selected from a primer pool by referring to the electropherograms of the fragments. This method was successfully used to compare the electropherograms of two different DNA strands and to sequence a several‐kb DNA fragment without subcloning. Combined with CAGE, this method could be used to dramatically simplify DNA fragment analysis.
DNA sequencing using a four‐color confocal fluorescence capillary array scanner
Authors: Kheterpal Indu , Scherer James R. , Clark Steven M. , Radhakrishnan Arun , Ju Jingyue , Ginther Charles L. , Sensabaugh George F. , Mathies Richard A. 
Published: May 2005

AbstractThe design, construction and operation of a four‐color capillary array electrophoresis scanner are presented. The use of sensitive energy transfer primers facilitates four‐color detection of the DNA sequencing fragments following excitation at a single laser wavelength (488 nm). This scanner collects fluorescence data from up to 25 capillaries in parallel. The resulting four‐color image files are automatically reduced to four‐color line plots, and a base‐calling program (Sax) is used to call the sequence. The performance of this system for DNA sequencing is demonstrated by examining twelve different motifs of the hypervariable region I of human mitochondrial (mt) DNA obtained from a Sierra Leone population.
Factors that affect the stability of protein‐DNA complexes during gel electrophoresis
Authors: Fried Michael G. , Bromberg Jennifer L. 
Published: May 2005

AbstractThe gel electrophoresis mobility shift assay is widely used for qualitative and quantitative characterization of protein complexes with nucleic acids. Often it is found that complexes persist within electrophoresis gels for much longer than expected on the basis of their free‐solution lifetimes. Volume exclusion, direct interaction with gel matrices and the reduction of water activity by the gel have been proposed as mechanisms enhancing the stability of complexes during electrophoresis. We have used the well‐characterized interaction of the E. coli cyclic AMP receptor protein (CAP) with lactose promoter DNA to test these proposals. We found that the activity of water within polyacrylamide gels differs little from that of the buffer in which they were cast and that the dependence of the dissociation rate constant on water activity is too small for osmotic stabilization to contribute significantly to the lifetimes of CAP‐DNA complexes. In addition, we found that a cross‐linked gel matrix is not required for the stabilization of CAP‐DNA complexes, that comparable stabilization is produced by three dissimilar polymers (linear polyacrylamide, dextran and polyethylene glycol), and that these polymers stabilize complexes more effectively than equivalent weight concentrations of their cognate monomers. While these results challenge the notion that direct interaction with the gel matrix contributes to the stability of protein‐DNA complexes, they are all features expected of excluded volume mechanisms.
Detection of conformation bias between the complementary strands of deoxynucleotide repeat (TG/AC)n
Authors: Dobi Albert , Mahan Mark A. , Agoston Denes V. 
Published: May 2005

AbstractAntiparallel complementary strands of DNA contribute symmetrically to the helical structure and its stability; rough conformational differences between complementary strands would interfere with this symmetric contribution and the stability. To detect conformational differences between complementary strands, we challenged the complementary strands to different “pore size” of acrylamide gels and measured differences in migration during electrophoretic mobility analysis. Changes in migration differences revealed a significant structural bias between the complementary strands of the dinucleotide repeat deoxy‐(TG/AC)n.
Gel electrophoretic mobility of charged particles in a medium with curved channels
Authors: Fridrikh Serguei , Gotlib Yulii , Belenkij Boris 
Published: May 2005

AbstractA model of electrophoretic mobility of small charged particles (for example short DNA fragments) in media with curved channels is proposed. The medium is represented by a dense material embedding the curved channels accessible to the charged particles. The steady flow method is used to obtain an analytical expression of the particles' electrophoretic mobility as a function of the channel's shape. The analogy between the statistical properties of the channels and polymer chains (free‐jointed and with the persistent mobility mechanism) is used.
Rapid and enhanced detection of mitochondrial DNA variation using single‐strand conformation analysis of superposed restriction enzyme fragments from polymerase chain reaction‐amplified products
Authors: Barros Francisco , Lareu María Victoria , Salas Antonio , Carracedo Angel 
Published: May 2005

AbstractA strategy is described for detecting mitochondrial (mt) DNA variation which permits rapid and straightforward screening for forensic purposes. The method is based on the selection of fragments with adequate length for performing single strand conformation polymorphism (SSCP) analysis selecting a set of restriction enzymes (RE) which yield fragments with prefixed lengths. After digestion of mtDNA by the appropriate enzyme or set of enzymes, SSCP analysis is performed in a semiautomatic electrophoretic system using a silver staining detection method. The conformational changes due to single mutations were therefore found not to change the electrophoretic protocol but to change the relative position of the mutations within the fragment. The discrimination power of this method is estimated to be 90% when two restriction enzymes (MspI and Hinfl) are used, but it is considerably higher when other enzymes are added.
Cytosolic proteins from neutrophilic granulocytes: A comparison between patients with severe chronic neutropenia and healthy donors
Authors: Kasper Brigitte , Thole Hubert H. , Patterson Scott D. , Welte Karl 
Published: May 2005

AbstractA modified technique of two‐dimensional gel electrophoresis (2‐DE) was used to investigate differences in the pattern of cytosolic proteins of neutrophilic granulocytes from patients with severe congenital neutropenia, cyclic neutropenia, and idiopathic neutropenia in comparison with healthy donors. At the time of study, all patients tested received treatment with a recombinant human granulocyte colony‐stimulating factor (r‐metHuG‐CSF; Filgrastim, Amgen). Using the Investigator 2‐D Electrophoresis System™ (Millipore) we were able to detect more than 1000 protein spots in the cytosol of neutrophilic granulocytes from both patients and healthy controls. We investigated six patients with severe congenital neutropenia, five patients with cyclic neutropenia, four patients with idiopathic neutropenia, and 13 healthy donors. In the cytosol of neutrophilic granulocytes from patients we found an additional protein spot. This protein spot (molecular mass approximately 32.4 kDa, pI about 5.5) could be identified by internal sequencing after in‐gel digestion with endoproteinase Lys‐C as tropomyosin. The importance of the overexpression of tropomyosin in neutrophilic granulocytes from patients with severe chronic neutropenia is not yet understood.
Analysis of host‐induced response in the rice blast fungus Magnaporthe grisea using two‐dimensional polyacrylamide gel electrophoresis
Authors: Kachroo Pradeep , Lee Kelvin H. , Schwerdel Cornelia , Bailey James E. , Chattoo Bharat B. 
Published: May 2005

AbstractTwo‐dimensional (2‐D) polyacrylamide gel electrophoresis of proteins was used to study the response of the rice blast fungus to extracts prepared from resistant and susceptible rice cultivars. A protein of molecular mass 31 kDa was induced by a susceptible host extract, while the fungus exposed to extract from the resistant cultivar and the untreated samples did not show the presence of this protein. Levels of this 31 kDa protein increased 30‐fold, 72h after treatment with plant extracts, with the concomitant appearance of at least sixteen other novel proteins. Fungus treated with extracts of resistant host or the untreated samples did not show any of these proteins while the proteins specific to different growth stages appeared as expected. Analysis of the extracellular samples showed induction of a 17 kDa protein after 72h in the culture treated with susceptible host extract. Since the resistant host extract does not cause induction of any protein it is likely that the proteins induced in response to the susceptible host are expressed during the disease process and/or its establishment. Our study demonstrates usefulness of 2‐D analysis in understanding host‐pathogen interactions.
Micellar electrokinetic capillary chromatography as a method for the determination of n‐octanol/water partition coefficients of pesticides
Authors: Dinelli Giovani , Mallegni Roberto , Vicari Alberto 
Published: May 2005

AbstractMicellar electrokinetic capillary chromatography (MEKC) was used to determine the n‐octanol/water partition coefficient (Kow) of nonionic and ionic organic chemicals, mainly herbicides. Three electrolyte buffer systems with different organic modifiers were tested to evaluate their effect on the linear relationship between log Kow and log ḱ. The effect of the pH value of injected samples on linear log Kow/log ḱ relationship of ionic chemicals was also evaluated. Since a good correlation was found between log Kow values and the logarithms of the capacity factor (ḱ) of each tested organic solvent, other parameters were considered to evaluate the efficacy of the method, such as the rate of electroosmotic flow, the efficiency and reproducibility of the separation, and the separation number (n). The method was found to be applicable over a range of log Kow values from 0.72 to 5.1 and demonstrated a good predictive capability, giving similar results to direct experimental measures, at least within classes of compounds with similar physico‐chemical properties.
Phosphated surfactants as pseudostationary phase for micellar electrokinetic chromatography: Separation of polycyclic aromatic hydrocarbons
Authors: Akbay Cevdet , Shamsi Shahab A. , Warner Isiah M. 
Published: May 2005

AbstractA double alkyl chain di(2‐ethylhexyl)phosphate (DEHP) is introduced as a potential anionic micellar pseudophase for a wide range of benzene derivatives and/or polycylic aromatic hydrocarbons (PAHs). Several parameters such as concentration of phosphated surfactant, type and concentration of organic solvents (acetonitrile, isopropanol, and methanol), as well as capillary electrophoresis separation voltage were optimized to enhance resolution, efficiency and selectivity as well as to maximize peak capacities. The migration times and selectivity order for a number of PAHs differ significantly, depending on the type of organic solvent added to the DEHP surfactant. Acetonitrile at a concentration of 30% V/V in combination with 100 mM DEHP gave optimum separation for a mixture of 21 benzene derivatives and PAHs in under 16 min.
pH Changes in Immobiline gels due to low‐molecular mass ion adsorption and condition for salt front formation during electrophoretic desorption
Authors: Stoyanov Alexander V. , Righetti Pier Giorgio 
Published: May 2005

AbstractA simple theoretical model of low molecular mass ion adsorption on a weak exchanger is proposed. For a system containing immobilized charges in uniform concentration the pH change values connected with neutral salt addition and followed by further washing and voltage application are evaluated. The question of stability of the moving boundary, arising in the area near the electrodes, is considered for the constant current stabilization at different values of Immobiline concentration, pK values of Immoboline and salt concentration. The threshold values of ion mobility capable of providing a sharp salt front formation are also evaluated for conditions of strong adsorption. We found that, with extremely acidic Immobilines, a sharp salt front does not arise under the latter condition, even in the case of very high Immobiline concentrations.