bluuebunny/crossref_metadata_2025_split huggingface dataset:
A region of Haemophilus influenzae Rd hybridizes with repetitive human DNA
Authors: Mody Rashna B. , Joshi Vasudha P. 
Published: May 2005

AbstractA 17.7 kbp EcoR1 fragment of Haemophilus influenzae Rd (wild‐type strain) DNA containing repeats has been cloned together with the DNA repair gene uvr3. The region containing repetitive DNA was subcloned on a 13 kbp EcoR1 fragment (pHi13). The insert hybridizes with restriction enzyme digests of H. influenzae Rd and H. parainfluenzae and exhibits a repetitive pattern. Discrete bands superimposed upon a polydisperse background were observed when pHi13 hybridizes with restriction digests of human DNA. The hybridization patterns indicate that H. parainfluenzae and human DNA contain cross‐hybridizing sequences. The repeats of pHi13 are present on a 2.6 kbp PvuII fragment.
DNA fingerprinting for forensic identification: Some statistical issues
Authors: Majumder Partha P. 
Published: May 2005

AbstractIn DNA fingerprinting work, it is well known that, although fragment lengths of a sample are uncorrelated, measurement errors of fragment lengths are correlated. Unless the fragment length is very large, the measurement errors are directly proportional to fragment lengths. In the currently practiced matching procedures for forensic identification, these facts are ignored or inadequately used. Some of these issues are addressed in this study. Based on available empirical observations, an appropriate statistical model and techniques are proposed. These techniques lead to the definition and construction of elliptical match windows, instead of independent interval (linear) windows currently used. Simulation experiments indicate that the performance of the proposed procedure is superior to the current procedures. Further, the proposed procedure does not make use of some assumptions underlying the current procedures. Extensions of the procedure to utilize replicate measurements of crimescene and/or suspect's samples are indicated.
Application of DNA fingerprinting to the taxonomy of European blackberry species
Authors: Nybom Hilde , Kraft Thomas 
Published: May 2005

AbstractThousands of blackberry species (Rubus subgenus Rubus) have been described from Central and Northern Europe. These species are usually polyploid and pseudogamous. Since apomixis is only facultative, the species have retained the possibility to produce some offspring by sexual recombination. Hybridization of restriction‐enzyme‐digested DNA samples to the M13, (AC)/(TG) and 33.15 probes has yielded valuable information on the occurrence and distribution of genetic variation in Rubus. Intraspecific variation proved to be very restricted, with identical DNA fingerprints sometimes being exhibited by Swedish, Danish and German populations of the same species. By comparison, interspecific variation was usually pronounced, suggesting that most species have been derived through genetic recombination. Speciation through interspecific hybridization was demonstrated in one case. Several critical taxa were investigated; some of these proved to have unique DNA fingerprints, whereas others appear to be identical with previously described species. Evaluation of raspberry cultivars, obtained through several generations of vegetative propagation or with various in vitro techniques, failed to detect any DNA fingerprint variation, suggesting that the fingerprints are somatically stable. Blackberry seedlings, obtained by pollinating various species as well as interspecific hybrids with pollen from yet other species, were successfully evaluated with DNA fingerprinting to determine the relative proportions of the apomictic and sexual seed set.
One‐dimensional genome scanning: Identification of the basis of a mouse mutation and identification of genomic changes in ovarian carcinoma
Authors: Brilliant Murray H. , Gondo Yoichi , Magliocco Anthony 
Published: May 2005

AbstractWe have developed a simple one‐dimensional electrophoretic method, genome scanning, that can be used to identify large‐scale genomic differences between two or more DNA samples. Genome scanning is especially useful in the detection of genetic amplifications, deletions, and rearrangements. The assay is essentially a high‐resolution Southern analysis, comparing equivalent amounts of genomic DNA samples that are variant for a given trait. The Southern blots are hybridized to a probe sequence derived from a medium copy number repetitive element (1000–2000 copies per haploid genome) naturally dispersed throughout the genome. The hybridization pattern that results is complex and consists of hundreds of bands. If the DNA samples are otherwise equivalent, a net difference in hybridization intensity between homologous bands of different samples indicates a genetic change. In this report, we discuss the origin of the method, its premise, and review its application to mouse mutational analysis and to human cancer research (a more detailed discussion of the theory is presented elsewhere in this issue; Y. Gondo and M. H. Brilliant, Electrophoresis 1995, 16, 174–178).
The potential of microsatellites for hybridization‐ and polymerase chain reaction‐based DNA fingerprinting of chickpea (Cicer arietinum L.) and related species
Authors: Sharma Prakash C. , Hüttel Bruno , Winter Peter , Kahl Günter , Gardner Richard C. , Weising Kurt 
Published: May 2005

AbstractThe genetic variability in agronomically important chickpea accessions (Cicer arietinum L.) as detected by single‐locus restriction fragment length polymorphism (RFLP) probes, random amplified polymorphic DNA (RAPD) and isoenzyme markers, is rather low. Recently, highly polymorphic microsatellites became the markers of choice for linkage mapping and population studies. We are currently following two main strategies to exploit the variability of microsatellites and adjacent sequences for genetic studies in chickpea. (i) In an approach referred to as oligonucleotide fingerprinting, microsatellite‐complementary oligonucleotides were employed as multilocus probes for in‐gel hybridization. A total of 38 different probes representing di‐, tri‐ and tetranucleotide repeats were used to analyze variability between and within four accessions of C. arietinum. Hybridization signals were obtained with 35 probes. While the abundance and level of polymorphism of the different target sequences varied considerably, distinct, intraspecifically informative banding patterns were obtained with the majority of probes and all restriction enzymes tested. No obvious correlation existed between abundance, fingerprint quality, and sequence characteristics of a particular motif. (ii) In a recently developed strategy called microsatellite primed polymerase chain reaction (MP‐PCR), micro‐satellite‐complementary oligonucleotides serve as single PCR primers for genomic DNA templates. We tested the general applicability of MP‐PCR by amplifying DNA samples from tomato, chickpea and two related annual Cicer species with a variety of di‐, tri‐ and tetranucleotide repeat primers. Most but not all primers generated distinct fingerprint‐like banding patterns after agarose gel electrophoresis and ethidium bromide staining of the amplification products. Since the method proved to be sensitive to reaction conditions in a way similar to RAPD analysis, we increased the PCR specificity by the introduction of a modified “touch‐down” protocol. In chickpea, touch‐down MP‐PCR generated highly reproducible banding patterns which predominantly revealed interspecific polymorphisms. The potential of different microsatellite‐based strategies for genome analysis in chickpea is discussed.
DNA fingerprinting in captive population of the endangered Siberian crane (Grus leucogeranus)
Authors: Tokarskaya Olga N. , Petrosyan Varos G. , Kashentseva Tatiana , Panchenko Vladimir G. , Ryskov Aleksei P. 
Published: May 2005

AbstractDNA fingerprinting was used to estimate genetic diversity within the endangered Siberian crane (Grus leucogeranus) captive population consisting of several dozens of founders originating from the two wild populations of eastern and western Siberia. Similarity and difference among captive individuals were demonstrated by the unweighted pair‐group (UPGMA) clustering procedure. Quantitative characteristics of the eastern and western captive population groups such as average percentage differences (APD) and heterozygosity showed a high extent of genetic variability of 77.9–79.3% and heterozygosity of 0.85–0.72 within each group. Genetic heterogeneity of the captive population structure observed here provides guidelines for management of the species gene pool in captivity. These data also indicate that monitoring of genetic diversity through DNA fingerprinting can facilitate the efforts of Siberian crane management and restoration.
Size‐selected genomic libraries: The distribution and size‐fractionation of restricted genomic DNA fragments by gel electrophoresis
Authors: Gondo Yoichi 
Published: May 2005

AbstractBy using one‐dimensional genome scanning, it is possible to directly identify the restricted genomic DNA fragment that reflects the site of genetic change. The subsequent strategies to obtain the molecular clones of the corresponding restriction fragment are usually as follows: (i) the restriction of a mass quantity of an appropriate genomic DNA, (ii) the size‐fractionation of the restricted DNA on a preparative electrophoresis gel in order to enrich the corresponding restriction fragment, (iii) the construction of the size‐selected libraries from the fractionated genomic DNA, and (iv) the screening of the library to obtain an objective clone which is identified on the analytical genome scanning gel. A knowledge of the size distribution pattern of restriction fragments of the genomic DNA makes it possible to calculate the heterogeneity or complexity of the restriction fragment in each size‐fraction. This manuscript first describes the distribution of the restriction fragments with respect to their length. Some examples of the practical application of this theory to genome scanning is then discussed using presumptive genome scanning gels. The way to calculate such DNA complexities in the prepared size‐fractionated samples is also demonstrated. Such information should greatly facilitate the design of experimental strategies for the cloning of a certain size of genomic DNA after digestion with restriction enzyme(s) as is the case with genome scanning.
A discontinuous buffer system increasing resolution and reproducibility in DNA sequencing on high voltage horizontal ultrathin‐layer electrophoresis
Authors: Carninci Piero , Volpatti Federico , Schneider Claudio 
Published: May 2005

AbstractA novel discontinuous buffer system for DNA sequencing based on horizontal ultrathin‐layer gel electrophoresis is described. The optimized system, named unbuffered stacking gel/discontinuous borate EDTA‐buffer system, is composed of a 0.5 mm thick stacking gel, where standard sequencing reactions (1 μL volume) are easily loaded, and a 50 μm ultrathin running gel, where DNA fragments are separated. The novel discontinuous buffer system allows for sample concentration and efficient injection from the stacking gel into the capillary slab gel. Increased resolution, assessed by autoradiography, can be achieved within 25 min running time already over a 10.1 cm distance from the gel slot compared to the conventional gel system. An advantage of the new system is the capacity to resolve compressions in GC‐rich regions, usually causing migrating artifacts in standard gels. The described system affords a major improvement in speed, resolution and reproducibility in DNA sequencing.
Three‐dimensional imaging of DNA fragments during electrophoresis using a confocal detector
Authors: Brewer Laurence R. , Davidson J. Courtney , Balch Joseph W. , Carrano Anthony V. 
Published: May 2005

AbstractWe have measured the three‐dimensional distribution of DNA fragments within an electrophoretic band confined by a glass microchannel. The measurements were made using a confocal microscope and a photon‐counting photo‐multiplier detector. A DNA sequencing standard was loaded into glass micro‐channel plates containing polyacrylamide gel. The measurements were made by scanning the plates in three dimensions using a mechanical stage under computer control, while electrophoresis was taking place. We found that the distribution of DNA was the same for all the bands measured in the sequencing ladder with an approximate Gaussian distribution along all three axes. These measurements are important to understand what physical forces shape electrophoretic bands confined by a channel and they also aid in the design of high throughput DNA sequencers.
Preparative separation of nucleosome core particles containing defined‐sequence DNA in multiple translational phases
Authors: Harp Joel M. , Palmer Elise L. , York Melissa H. , Gewiess Andreas , Davis Matthew , Bunick Gerard J. 
Published: May 2005

AbstractThe nucleosome core particle is composed of an octamer of core histone proteins and about 146 bp of DNA. When reconstituted from purified histone octamer and defined‐sequence, nucleosome positioning DNA fragments, the DNA will bind to the histone core in a number of translational phases with respect to the dyad symmetry axis of the histone octamer. Only one of these phases contains symmetrically bound DNA, and it is this species which is required for crystallization and X‐ray diffraction studies. We have developed a technique for separating nucleosome core particles, containing defined‐sequence 146 bp DNA, which differ only in translational phasing of the DNA with respect to the histone octamer core.
A simple and rapid technique for postelectrophoretic detection of proteases using azocasein
Authors: Peyronel Daniel Vázquez , Cantera Ana María B. 
Published: May 2005

AbstractAzocasein, diffused into gels after polyacrylamide gel electrophoresis, provides a useful substrate for simple and rapid protease detection. After electrophoresis, the gels are incubated in an azocasein solution, immersed in trichloroacetic acid and then treated with NaOH. Proteolytic zones appear as uncolored bands on an orange background. The gels can be stored in trichloroacetic acid for months. This technique gives good results with serine proteases, acid proteases and metalloproteases. The method can be used under nondenaturing conditions and in the presence of sodium dodecyl sulfate. The sensitivity of this method is at the submicrogram protein level for trypsin.
Feasibility study of a drug immunoassay based on micellar electrokinetic capillary chromatography with laser induced fluorescence detection: Determination of theophylline in serum
Authors: Steinmann Lone , Caslavska Jitka , Thormann Wolfgang 
Published: May 2005

AbstractThis paper presents principle and first results of a novel competitive binding immunoassay for monitoring of theophylline in human serum. The assay is based upon short time incubation of a mixture of antiserum, containing the antibody raised against theophylline, fluorescein labelled theophylline (tracer) and serum prior to injection of a few nanoliter of this mixture onto a fusedsilica capillary for subsequent separation and analysis of free tracer and the antibody‐tracer‐complex by micellar electrokinetic capillary chromatography with laser induced fluorescence detection. Quantitation based upon multi‐level calibration using the height of the peak produced by the free tracer is shown to provide theophylline serum levels which are in agreement with those obtained by a commercial fluorescence polarization immunoassay and with those determined by micellar elektrokinetic capillary chromatography with direct serum injection and on‐column UV absorption detection.
Multilocus genomic mapping with intracisternal A‐particle proviral oligonucleotide probes hybridized to mouse DNA in dried agarose gels
Authors: Lueders Kira K. 
Published: May 2005

AbstractRecently, oligonucleotide probes that detect intracisternal A‐particle (IAP) gene subfamilies with a limited number of proviral copies have been shown to be useful multilocus markers. A procedure for hybridization of these probes has been developed and is described. In summary, the main features of the method are the following: (i) A pulse controller is used during agarose gel electrophoresis to improve resolution of restriction fragments in genomic DNA. (ii) Hybridization is performed in a dried gel. (iii) The hybridized gel is washed in tetramethylammonium chloride to eliminate differences in oligonucleotide composition on hybrid stability. Use of the prodecure is demonstrated by genomic mapping of IAP loci in the AXB BXA recombinant inbred mouse strains, identification of hypomethylated loci in tumor cells, and detection of a transposed IAP provirus previously identified as the basis for a mutation at the agouti locus.
Theory of zone separation in isotachophoresis: A diffusional approach
Authors: Gebauer Petr , Boček Petr 
Published: May 2005

AbstractThe qualitative characteristics of isotachophoresis differ substantially from “classical” separation methods such as chromatography or zone electrophoresis. Self‐sharpening zone boundaries and step‐like concentration profiles are the most specific features of this method, which does not allow the description of the isotachophoretic separation in usual “chromatographic” terms, such as resolution or number of theoretical plates. A theory is presented in this paper, combining the usual isotachophoretic separation characteristics with the theory of isotachophoretic zone boundary, which is the only element of the isotachophoretic system with dispersional properties. This allows us to consider situations near the limits of the isotachophoretic method as far as both selectivity and sample amount (i.e., zone size) are concerned. Based on a simplified expression of the concentration profiles across the isotachophoretic zone boundary, separation and separation limits are described and discussed in terms of resolution, selectivity and zone capacity. Equations are derived showing the relationships between resolution, boundary width, selectivity, sample amount, and column and electrolyte conditions. A simple phenomenological equation is presented, expressing isotachophoretic resolution as a function of only sample amount (or sample zone length) and boundary width. A thermo‐dynamic form of this equation is derived, which is shown to be similar to such an expression for resolution in zone electrophoresis. In both cases resolution is a function of sample selectivity, electric field strength and column length. A simple theoretical model for zone capacity is presented, making it possible to estimate the separation performance of isotachophoretic systems. Based on the presented theory, parallels between isotachophoresis and zone electrophoresis are discussed and both methods are compared.
Gene and genome scanning by two‐dimensional DNA typing
Authors: Uitterlinden André G. 
Published: May 2005

AbstractA major effort in the analysis of DNA currently focuses on identifying genes and their pathological variants underlying disease. Once such disease genes have been isolated a major task of molecular medicine is to identify the spectrum of DNA sequence variations responsible for the aberrant function of such genes. These efforts, however, are hindered by the vast amount of genetic information to scan for variations and the limited capacity of analytical techniques in terms of accuracy and speed. Recently, a number of techniques were developed, so‐called “genome scanning” techniques, which allow complete genomes to be analyzed for sequence variation in parallel, i.e., at multiple sites or loci simultaneously rather than serially at predefined loci. Here we present the background and applications of a particular electrophoretic parallel processing approach, generically termed two‐dimensional DNA typing. The approach is based on separating DNA fragments by two‐dimensional electrophoresis [1], including denaturing gradient gel electrophoresis, thus allowing hundreds of fragments to be simultaneously assessed by comparative analysis for variations in size and sequence. The method is suitable for hybridization analysis with locus‐specific and multilocus probes of genomic DNA restriction fragments derived from human and other DNA, and for analysis of polymerase chain reaction (PCR) fragments derived from large genes. Two‐dimensional DNA typing has been applied, e.g., in linkage analysis of pedigrees, analysis of tumor genomes for rearrangements, and to scan the cystic fibrosis transmembrane regulator gene for sequence variations such as point mutations.
Model of isotachophoresis (displacement electrophoresis) in tapered capillaries
Authors: Šlais Karel 
Published: May 2005

AbstractThe principle and theoretical description of boundary focusing under electrophoretic migration in a tapered capillary are presented. The model describes the gradual volume decrease of a moving boundary between weak electrolytes or ampholytes. The relations between the departure from the local steady state, the ratio of inlet to outlet capillary cross section, the effective mobilities and the selectivity are formulated. They allow the selection of operating conditions such that the departure from the local steady state can be decreased to an acceptable level. The relations predict that isotachophoresis (displacement electrophoresis) in a capillary with a shallow taper can maintain a constant ratio of actual boundary width to local steady state width, provided that the local capillary cross section decreases linearly with length. The significance of some assumptions needed for the model formulation is analyzed. Numerical examples are given indicating the method feasibility.
Dynamic control to improve the separation performance in capillary electrophoresis
Authors: Chang Huan‐Tsung , Yeung Edward S. 
Published: May 2005

AbstractDynamic control in capillary electrophoresis (CE) is able to provide better resolution, shorter separation time, reduced band broadening and better reproducibility for the separations of organic and inorganic ions and large molecules such as proteins and DNA. This article provides an overview of dynamic control in CE by several techniques: pH, temperature, external electric field, and field amplification. These techniques take advantage of the changes in electroosmotic flow coefficient, electrophoretic mobilities of the analytes due to changes in equilibrium, viscosity of the buffer solution, and/or electric field strength. The basic theories and applications to the improvement of the separation performance for standard samples in CE by using these dynamic control techniques are presented. Finally, the advantages and shortcomings of these techniques and the future trends of dynamic control for the separations of real samples are discussed.