bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determining consanguinity by oligonucleotide fingerprinting with (GTG)5/(CAC)5
Authors: Pöche Hubert , Peters Christian , Wrobel Gudrun , Schneider Volkmar , Epplen Jörg T. 
Published: May 2005

AbstractSimple tandemly organized (GTG)n/(CAC)n sequences are spread throughout the human chromosomes. The most informative DNA fingerprints for the testing of pedigrees and/or paternity were obtained with the simple triplet repeat probe (GTG)5 or its complement (CAC)5. These hypervariable simple‐repeat fragments are stably inherited in a Mendelian fashion. Using these highly discriminating probes, all human individuals could, theoretically, be differentiated, except for genetically identical monozygotic twins. Examples from actual case work are reported and pertinent advantages of this methodology are discussed.
Effect of hair dyes and bleach on the hair protein patterns as revealed by isoelectric focusing
Authors: Nagai Atsushi , Komoriya Hideou , Bunai Yasuo , Yamada Sadao , Jiang Xiuyan , Ohya Isao 
Published: May 2005

AbstractThe effect of hair dyes. i.e., temporary, semi‐permanent, or permanent hair dyes, or hair bleach on the isoelectric focusing (IEF) hair protein patterns was studied. A permanent hair dye (metallic, alkaline oxidative, or acidic oxidative) and hair bleach induced changes in the IEF hair protein patterns and in the intensity of hair protein bands. The changes in the IEF patterns, caused by the alkaline oxidative dye or the bleach, are considered to result from the combined effect of an alkaline agent and an oxidative agent in the alkaline oxidative dye and in the hair bleach.
A practicable two‐dimensional electrophoresis of urinary proteins as a useful tool in medical diagnosis
Authors: Lapin Alexander , Feigl Walter 
Published: May 2005

AbstractPractical experience with a rapid two‐dimensional electrophoresis technique for routine analysis of urinary proteins is discussed. The method consists of cellulose acetate electrophoresis in combination with sodium dodecyl sulfate (SDS) electrophoresis, performed together with Coomassie Blue gel staining on “PhastSystem”. Over 400 analyses were performed within the time of two years. Most patients were from nephrological, urological and kidney‐transplant departments. Some of them were from obstetric, pediatric or oncological departments. A systematic discussion and evaluation of the two‐dimensional protein pattern with typical examples is outlined.
Analysis of circulating immune complexes isolated from plasma, cerebrospinal fluid and urine
Authors: Wiederkehr Felix , Büeler Martin R. , Vonderschmitt Dieter J. 
Published: May 2005

AbstractThe protein nature of soluble immune complexes (IC) from fresh plasma, cerebrospinal fluid (CSF), and urine was studied by combining several analytical and biochemical techniques. In plasma and CSF, free immunoglobulins G were separated from larger IC by gel filtration with a fast protein liquid chromatographic system. In urine, IC were separated by precipitation with polyethylene glycol. IC were further purified by protein‐A and protein‐G affinity chromatography and analyzed by two‐dimensional gel electrophoresis. Apart from plasma samples from healthy donors, IC from cases with macrocreatine kinase type 1 and multiple sclerosis were analyzed. For CSF two cases of multiple sclerosis and for urine one case with urinary tract infection are shown. The method can be used for the examination of IC of unknown protein composition in body fluids.
A comparative analysis of alterations in protein expression after activation or human immunodeficiency virus, type 1 infection of human CD4+ T cells
Authors: Van de Keere Fabienne , Willard‐Gallo Karen E. 
Published: May 2005

AbstractWe have previously described an in vitro model for studying human immunodeficiency virus, type 1 (HIV‐1) infection in CD4+ T cells [1]. This model employs the WE17/10 cell line, which loses expression of its T cell receptor/CD3 (TCR/CD3) after several months of productive infection. We have used this model to analyze the synthesis and posttranslational modification of viral and cellular proteins after HIV‐1 infection and to determine the relationship of these changes to TCR/CD3 expression. Mainly we observe positive changes in protein expression after infection. A phosphoprotein, referred to as WH:1, appears in infected cells that still express their TCR/CD3 complex, and its persistence is linked to the presence of the complex. We examined whether loss of the TCR/CD3 complex could be associated with alterations in the T cell activation pathway as a result of infection. We used T cell activators and inhibitors to determine whether there were common elements between the two events. Quantitative enhancement in one spot, Cs:1, occurred after both Cyclosporin A treatment of uninfected cells and HIV‐1 infection of untreated cells. Taken altogether, these data suggest that a correlation exists between negative regulation of late events in the T cell activation pathway and down regulation of the TCR/CD3 complex after HIV‐1 infection.
Analysis of limiting factors of DNA band separation by a DNA sequencer using fluorescence detection
Authors: Nishikawa Tetsuo , Kambara Hideki 
Published: May 2005

AbstractThe factors affecting the electrophoretic separation of DNA bands in DNA base sequencing using fluorescence detection are analyzed. All the factors contributing to DNA band spacing and band width are evaluated; DNA diffusion and thermal effects on gels are the main considerations. The dependence of the gel's electrical resistivity on gel temperature and the variation of temperature over gel thickness are associated with a broadening of DNA band width. As a result of the analyses the maximum separable base number is represented as a function of various electrophoretic variables. The best separations are possible with an electric field strength corresponding to gel thickness. The maximum separable base number increases as the gel thickness decreases. It also increases as the migration distance increases, but it becomes saturated and has an upper limit when the migration distance is long. This upper limit increases as gel thickness decreases. DNA fragments with 600 and 601 bases can be completely separated from each other under optimum conditions for a 0.2 mm thick gel plate. Furthermore, using the band spacing information, under the same conditions, 750 bases could be assigned separately.
Capillary zone electrophoresis for the quantitation of oligosaccharides formed through the action of chitinase
Authors: Lee Kyung‐Bok , Kim Yeong‐Shik , Linhardt Robert J. 
Published: May 2005

AbstractCapillary zone electrophoresis with fluorescence detection was used to analyze the products formed by chitinase acting on N‐acetylchitooligosaccharide‐fluorescent conjugates. Six oligosaccharides of the structure [N‐acetylglucosamine(1→4)]n (where n = 1–6) were conjugated to 7‐amino‐1,3‐naphthalene disulfonic acid by reductive amination. Each oligosaccharide‐fluorescent conjugate was purified by preparative gradient polyacrylamide gel electrophoresis, semi‐dry electrotransfer to a positively‐charged nylon membrane and recovered by washing the membrane with salt solution. The products formed by treating each oligosaccharide‐fluorescent conjugate with chitinase were analyzed by capillary zone electrophoresis. The chitinase treatment hexasaccharide‐fluorescent conjugate was also examined kinetically to study the action pattern of this enzyme.
Increased selectivity in the detection of glycoproteins on nitrocellulose membranes by washing with sodium hydroxide solution
Authors: Kondo Maki , Harada Hiroshi , Sunada Saburo , Yamaguchi Takashi 
Published: May 2005

AbstractWe increased selectivity in the detection of glycoproteins on nitrocellulose membranes by introducing a washing step using sodium hydroxide solution. Glycoproteins on the nitrocellulose membrane were first oxidized by sodium periodate; biotin hydrazide was then coupled to the aldehyde groups generated in the sugar moiety of the glycoproteins. The membrane was washed twice using sodium hydroxide solution, and avidin‐horseradish peroxidase was then coupled to the remaining biotin. This system allows the detection of nanograms of glycoproteins on nitrocellulose membranes, and its specificity allows the clear distinction of glycoproteins from the nonglycosylated protein of bovine serum albumin.
The rat liver epithelial (RLE) cell protein database
Authors: Wirth Peter J. , Luo Lin‐di , Fujimoto Yoshinori , Bisgaard Hanne C. , Olson Arthur D. 
Published: May 2005

AbstractComputer databases of rat liver epithelial (RLE) cellular polypeptides have been established using high resolution two‐dimensional gel electrophoresis and computer‐assisted analysis. Databases have been constructed utilizing both [35S]methionine‐ and [32P]orthophosphate‐labeled as well as silver‐stained polypeptides from normal RLE cells. The RLE database, which contains both qualitative and quantitative annotations, includes experiments with normal, chemically and oncogene transformed as well as spontaneously transformed cell lines. A total of 2537 [35S]methionine‐labeled polypeptides from whole cell lysates (1920 acidic and 617 basic, separated in the first dimension using isoelectric focusing and nonequilibrium pH gradient electrophoresis, respectively) were analyzed and databases constructed using the Elsie 5 gel analysis system. To increase the “viewing window” and hence the usefulness of the RLE database, subcellular fractionation of whole cell preparations was performed and high resolution two‐dimensional maps of the individual subcellular components were constructed. Databases representing 1229 cytosolic, 1539 acidic and 674 basic nuclear, 1746 membrane‐associated, 415 mitochondrial, 773 in vitro translated and 350 phosphoproteins were established from these maps. The RLE databases contain the Elsie 5 identification number, protein name (if known), molecular weight and pI information, quantitative and spot shape data, and specific information regarding transformation‐sensitive, growth‐related (exponentially proliferating versus confluent) cell populations as well as those polypeptides modulated by specific growth factors. The RLE databases represent initial efforts toward the establishment of comprehensive databases of rat liver proteins and serve as a vital resource for on‐going as well as future studies regarding the regulation of growth and differentiation as well as transformation of RLE cells.
Immobilized metal ion affinity electrophoresis: A preliminary report
Authors: Goubran‐Botros Hany , Vijayalakshmi Mookambeswaran A. 
Published: May 2005

AbstractThe ligand “Sepharose‐IDA‐Cu(II)” was entrapped into an agarose gel used for afinity electrophoresis. The binding of three closely related proteins, namely α‐chymotrypsinogen A, α‐chymotrypsin, and α‐chymotrypsin inactivated with disopropyl fluorophosphate (DIFP) to the affinity gel, was investigated. When the protein having affinity for the ligand was run in the presence of small amounts of the ligand, the retention of the protein by the ligand caused “tailing” of the sample. This pattern was changed in the presence of increasing amounts of the ligand, leading to a “rocket” shape due to the stronger binding of the protein to the chelated metal ligand entrapped in the gel. The degree of retardation in the gel with the ligand is an expression of the affinity between the protein and the ligand. The migration distance of α‐chymotrypsin and α‐chymotrypsin treated with DIFP at a given concentration of the ligand is linearly related to the protein amount deposited on the gel. The dissociation constant for the tested proteins were calculated from the Bøg‐Hansen‐Takeo plot. The difference in the affinity strength of these structurally related proteins towards the ligand suggests the involvement of the surface topography of histidine residues on their binding to the ligand.
Irreversible trapping of DNA during crossed‐field gel electrophoresis
Authors: Viovy Jean‐Louis , Miomandre Fabien , Miquel Marie‐Cecile , Caron François , Sor Frédéric 
Published: May 2005

AbstractUsing an original protocol with a rotating gel electrophoresis apparatus, it is shown that duplex DNA undergoing crossed‐field electrophoresis in agarose gets trapped in the gel when the field is increased above a threshold value which decreases with the chain length and depends on the angle between the fields in a non‐monotonous manner. This trapping is irreversible, i.e. once trapped at a high field strength, chains are unable to resume their motion when the field is returned to a lower value at which they moved prior to trapping. A model of trapping by “tight knots” is proposed. It predicts a trapping threshold proportional to the inverse square of the electric field, in qualitative agreement with the data. The implications of our results for the separation of large DNA molecules are discussed.
Use of cyclodextrins for the enantioselective separation of ergot alkaloids by capillary zone electrophoresis
Authors: Fanali Salvatore , Flieger Mirko , Steinerova Nadezda , Nardi Annalise 
Published: May 2005

AbstractErgot alkaloid enantiomer derivatives were resolved using capillary zone electrophoresis. The effect of cyclodextrins, added to the background electrolyte, on the migration time and the resolution was studied. Good separation for epimericergot alkaloid derivatives was also obtained using phosphate buffer at pH 2.5. Separation was improved by supplementing the background electrolyte with 30 mM of γ‐cyclodextrin. Good resolution of racemic ergot alkaloid derivatives in their enantiomers was achieved in a background electrolyte containing either β‐cyclodextrin or its derivative, or γ‐cyclodextrin.
Traveling‐wave dielectrophoresis of microparticles
Authors: Hagedorn Rolf , Fuhr Günter , Müller Torsten , Gimsa Jan 
Published: May 2005

AbstractThe traveling‐wave‐induced linear transfer of dielectric particles like living cells and artificial objects of microscopic dimensions is analyzed. It is shown that the electrode geometries must correspond to particle sizes to allow an effective manipulation of particles immersed in weakly electrolytic solutions by high frequency traveling waves. The theoretical model elaborated in this paper is in good agreement with experimental results obtained in microfabricated chambers of linearly arranged electrodes. It explains the behavior of homogeneous cellulose spheres as well as that of membrane‐covered pine polls. The traveling‐wave‐driven electrodes are described by a superposition of time‐dependent point charges. Subsequently, each of these point charges has to be considered as polarizing the dielectric particle and interacting with the polarized particle. This results in forces which effectively translocate the particle.
Stability of capillary gels for automated sequencing of DNA
Authors: Swerdlow Harold , Dew‐Jager Kerry E. , Brady Kevin , Grey Ronda , Dovichi Norman J. , Gesteland Raymond 
Published: May 2005

AbstractRecent interest in capillary gel electrophoresis has been fueled by the Human Genome Project and other large‐scale sequencing projects. Advances in gel polymerization techniques and detector design have enabled sequencing of DNA directly in capillaries. Efforts to exploit this technology have been hampered by problems with the reproducibility and stability of gels. Gel instability manifests itself during electrophoresis as a decrease in the current passing through the capillary under a constant voltage. Upon subsequent microscopic examination, bubbles are often visible at or near the injection (cathodic) end of the capillary gel. Gels have been prepared with the polyacrylamide matrix covalently attached to the silica walls of the capillary. These gels, although more stable, still suffer from problems with bubbles. The use of actual DNA sequencing samples also adversely affects gel stability. We examined the mechanisms underlying these disruptive processes by employing polyacrylamide gel‐filled capillaries in which the gel was not attached to the capillary wall. Three sources of gel instability were identified. Bubbles occurring in the absence of sample introduction were attributed to electroosmotic force; replacing the denaturant urea with formamide was shown to reduce the frequency of these bubbles. The slow, steady decline in current through capillary sequencing gels interferes with the ability to detect other gel problems. This phenomenon was shown to be a result of ionic depletion at the gel‐liquid interface. The decline was ameliorated by adding denaturant and acrylamide monomers to the buffer reservoirs. Sample‐induced problems were shown to be due to the presence of template DNA; elimination of the template allowed sample loading to occur without complications. The improved samples permitted multiple consecutive DNA sequencing runs on the same capillary.
Compensation for mobility inequalities between lanes computed from band signals in on‐line fluorescence DNA sequencing
Authors: Fujii Hidehiko , Kashiwagi Katsuya 
Published: May 2005

AbstractAmong on‐line fluorescence DNA sequencing systems, the four‐lane method exhibits the potential for reporting an erroneous sequence due to nonuniform mobility of the DNA fragments migrating among the four lanes. This error is manifest in phenomenon commonly called smiling. This paper presents a computational algorithm which compensates for the mobility inequalities between lanes using signal data obtained from the shorter DNA fragments forming the faster migrating bands. The program mainly consists of two routines: (i) calculation of calibration coefficients (mobility ratios between lanes), and (ii) examination of the coefficients by applying them to a later domain of the same signals. Both routines are connected with several feed‐back branches for recalculation. Homology analysis of final sequences has shown that the accuracy rate is maximized with this algorithm and any ambiguous result can be assigned to the residual error inherent in the band identification method used.
Movement of fluorescence pattern after photobleaching: An accelerated procedure for DNA electrophoretic mobility analysis
Authors: Chu Benjamin , Wang Zhulun 
Published: May 2005

AbstractA new approach which is compatible with many of the existing procedures for the analysis of DNA species in gel electrophoresis is being demonstrated. It takes advantage of fluorescence photobleaching in order to create a sharp boundary between the stained and the (partially) photobleached DNA. By arbitrarily creating a stained DNA band of narrower width, the sensitivity to detect (averaged) DNA band movements has been increased. This feature permits measurements of time‐dependent electrophoretic mobility over very short time periods. The approach can be used to shorten the running time of gel electrophoresis experiment and to increase the resolution because of the sharper boundary and narrower band width. With faster running time, diffusion of both DNA and dye in the gel also becomes less serious. Movement of fluorescence pattern after photobleaching also permits measurements of localized motions when the gel pores are small in comparison with DNA sizes. Experiments demonstrating some aspects of the proposed technique, as well as the anticipated limitations, are presented and discussed.
Molecular sieving of lambda phage DNA in polyacrylamide solutions as a function of the molecular weight of the polymer
Authors: Pulyaeva Helena , Wheeler David , Garner Mark M. , Chrambach Andreas 
Published: May 2005

AbstractElectrophoresis of lambda phage DNA was carried out in solutions at various concentrations of uncrosslinked polyacrylamide of 0.6, 1, 5 and 9 × 106 molecular weight (Mw) with narrow Mw distribution. By inspection of mobilities in the various concentration ranges, it appears that mobilities decrease, and retardation increases, with increasing Mw. The relation between electrophoretic retardation and the Mw of the polymer was also interpreted (i) in the manner previously applied to nonlinear Ferguson plots and compatible with the Ogston model; and (ii) empirically, on the basis of the first derivatives of the functions describing the Ferguson plots at the polymer concentrations used. Interpretation (i) shows that the retardation increases linearly in the order of 0.6, 1, 5 and 9 × 106 Mw of polyacrylamide. Interpretation (ii) shows a nonlinear increase of retardation in the Mw range 5 to 9 × 106, and a decrease in retardation as Mw is raised from 0.6 to 5.0 × 106. Hypothetically, interpretation (ii) can be explained mechanistically by a progressive change, as the polymer size is increased, from a collision with the surface of the polymer fiber to one occurring after permeation in the interior of a randomcoiled fiber. Interpretation (i) may fail to detect that change due to the large difference between DNA mobility in solutions of the smallest polymer and the free mobility. DNA peak detection in all of the four size classes of polyacrylamide in solution is limited to relatively narrow ranges of polymer concentration. For the electrophoresis of lambda DNA, polyacrylamide of 5 × 10−6 Mw represents an optimum due to a compromise between small mobility differences at various concentrations of the polymer with Mw 0.6 × 106, either little retardation (interpretation (i)) or insufficient responsiveness of the Ferguson plot to concentration changes (interpretation (ii)) in presence of the polymer of 1 × 106 Mw and an excessively narrow available concentration range at 9 × 106 Mw. A highly disperse solution of polyacrylamide of 18 × 106 molecular weight retarded lambda DNA only slightly. Retardation decreased upon ultrafiltration of the polymer solutions, presumably through the decrease of their concentrations or adsorption of the largest chains within the size distribution.
Advances in DNA electrophoresis in polymer solutions
Authors: Tietz Dietmar , Aldroubi Akram , Pulyaeva Helena , Guszczynski Tadeusz , Garner Mark M. , Chrambach Andreas 
Published: May 2005

AbstractDNA electrophoresis in gels and solutions of agarose and polyacrylamide was objectively evaluated with regard to separation efficiency at optimal polymer concentrations. In application to DNA fragments, polyacrylamide gels were superior for separating fragments of less than 7800 bp, and agarose gels are the best choice for larger fragments. Agarose solutions are nearly as good as polyacrylamide gels for small DNA (< 300 bp). Agarose solutions have a higher efficiency than polyacrylamide solutions for DNA of less than 1200 bp. Separation efficiency sharply decreases with increasing length of DNA. Retardation in polyacrylamide solutions was found to depend on polymer length in a biphasic fashion. The choice of resolving polymer concentrations depends on the progressive stretching of DNA in proportion to polymer concentration. The rate of that stretching appears higher in polyacrylamide solution than in gels or in liquid or gelled agarose. Application of polymer solutions to capillary electrophoresis raises further problems concerning agarose plugs, DNA interactions with the polymers, operation at low field strength and long durations as well as detection sensitivity.