bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic typing with HUMTH01, HUMVWA31A and HUMFES/FPS short tandem repeat loci, D1S80 variable number tandem repeat locus and HLA‐DQα of recent and from XII–XIII centuries spongy bone
Authors: de Pancorbo Marian M. , Castro Azucena , Alonso Santos , Fernández‐Fernández Isabel , Barbero Carmen , García‐Orad Africa , Izaguirre Neskuts , Iriondo Mikel , de la Rúa Concepción 
Published: May 2005

AbstractThe genetic analysis of ancient populations through DNA from bone remains, requires the use of short sized loci that can be amplified by polymerase chain reaction (PCR) for which the short tandem repeat (STR) loci are most suitable. These techniques can also be applied to genetic identification in forensic casework. In this study three STR loci, HUMFES/FPS, HUMTH01 and HUMVWA31A, were selected to estimate their usefulness when applied to recent and ancient spongy bone DNA typing. In addition, loci D1S80 and HLA DQα were also tested in the analysis of recent spongy bone DNA. The recent remains studied were constituted by ten spongy bone samples of postmortem material from one individual buried for 1 year. The ancient remains are composed by 8 spongy bone samples from the heads of left femurs from a XII–XIII Centuries Basque Country population. Adequate amplification and typing results could only be obtained with cetyltrimethyl ammonium bromide (CTAB)‐extracted DNA, without any further purification after precipitation. Genotypes of the one year post‐mortem material and those of his son and his wife were obtained at the D1S80, HLA‐DQα, and STR loci. In all these systems, no exclusion was observed, with a combined probability of paternity of 0.9997. This demonstrates the reliability of the obtained results. The genetic typing of HUMTH01 in spongy bone from the XII–XIII Centuries Basque Country individuals was also performed. This will allow the genetic analysis on ancient bone remains and therefore, to carry out evolutionary population studies.
Genome fingerprinting of the silkworm, Bombyx mori, using random arbitrary primers
Authors: Nagaraja Ganachari M. , Nagaraju Javaregowda 
Published: May 2005

AbstractThe random amplified polymorphic DNA (RAPD) technique was used to study DNA profiling of thirteen silkworm genotypes. The genotypes included six diapausing and seven nondiapausing varieties that represent a high degree of divergence with respect to geographic origin, and morphological, qualitative, quantitative and biochemical characters. Two hundred sixteen amplified products were generated using 40 random primers. Genotype‐specific amplification products were identified. Amplification products specific to diapausing genotypes were also identified. Segregation of the RAPD marker was analyzed in a backcross population and found to be inherited as dominant Mendelian traits. Based on pairwise comparison of amplified products, the genetic similarity coefficient was calculated using the NeiLi similarity coefficient, and cluster analysis was performed by a hierarchical clustering technique. Silkworm genotypes were clustered into two groups, one consisting of six diapausing and the other of seven nondiapausing genotypes. The results of our study suggest that the RAPD technique could be used as a powerful tool to generate genetic markers that are linked to traits of interest in the silkworm.
Intra‐ and inter‐population diversity at short tandem repeat loci in diverse populations of the world
Authors: Deka Ranjan , Shriver Mark D. , Yu Ling M. , Ferrell Robert E. , Chakraborty Ranajit 
Published: May 2005

AbstractTo study the level of intra‐ and inter‐population variation at hypervariable DNA loci, we have characterized 15 human populations of diverse ethnic and geographic origins at six short tandem repeat loci by using the polymerase chain reaction. Even though the spectrum of allelic variation is quite broad and there are substantial differences in allele frequency distributions among populations, in general, populations within a major racial group show a greater degree of similarity. This observation is reflected in the analysis of gene diversity. When the total diversity is apportioned, the maximum variation becomes attributable to inter‐individual differences within a population; of the variation that is attributable to differences between populations within a racial group and differences between racial groups, the former is smaller than the latter. Separate analysis of gene diversity for each of the major population groups based on geographic and ethnic relationship shows that the total gene diversity is higher for the larger racial groups, namely, African, Caucasian and Mongoloid, than the American Indians and the Pacific Islanders. As expected, a reciprocal relationship between gene diversity and FST levels is observed. Higher values of FST in the American Indian and the Pacific Islanders may reflect smaller population size and a higher level of isolation. An analysis of genetic distance encompassing the populations belonging to the three major racial groups recognizes three distinct clusters – all the populations of African affiliation cluster together, as do the Caucasian affiliated and the Mongoloid groups, in two distinct clusters. Interestingly, three broadly classified cosmopolitan US populations, namely, US White, US Black and US Asian, cluster with their ancestrally related populations. This study dispels some of the concerns regarding the applicability of DNA typing data for forensic use.
Trinucleotide repeat expansion and human disease
Authors: Hummerich Holger , Lehrach Hans 
Published: May 2005

AbstractTrinucleotide repeat expansions have been identified as the underlying mutation in an increasing number of human genetic diseases, such as fragile site syndromes, myotonic dystrophy and several neurodegenerative disorders including Huntington's disease. By an unknown mechanism, polymorphic GC‐rich triplet repeats expand in all these diseases. The expansions of a CCG repeat in fragile‐site‐associated disorders and the CTG repeat (in the 3′‐untranslated region of the myotonin kinase gene) causing myotonic dystrophy are very large, whereas small expansions of CAG repeats have been identified in the open reading frame of genes in a number of neurological genetic disorders.
DNA polymorphism analysis in five endangered species of Meconopsis (Himalayan poppy) using multi‐copy sequence‐based probes
Authors: Sulaiman Irshad M. , Hasnain Seyed E. 
Published: May 2005

AbstractAn attempt to understand the genetic basis of extinction of Meconopsis (Himalayan poppy), an endangered genus of ornamental value and confined to alpine Himalayas, is described. Multicopy DNA sequences were isolated from a Sau3A partial genomic plasmid library of M. simplicifolia and M. paniculata. Genetic polymorphism between five species of Meconopsis belonging to geographically isolated populations was evident, albeit at a low level, in genomic Southerns when probed with repetitive DNA clones isolated from this library. Intra‐population monomorphic band patterns for different populations of a species was evident with respect to a number of enzymes suggesting very low or no genetic variability and/or low mutation rate within a given population of Meconopsis.
Why ontogeny recapitulates phylogeny
Authors: Ohno Susumu 
Published: May 2005

AbstractIn development, mammalian embryos successively develop notochord, somites, gill pouches and three sets of kidneys: pronephros, mesonephros and metanephros. Hence, Ernst Haeckel's dictum “ontogeny recapitulates phylogeny.” The reason for this dictum appears to be the immortality of genes. Genes, once well entrenched, appear to linger for a long time even after the forfeiture of their raison d'ětre. The genes for dental enamel and dentin of the chicken are good examples. Furthermore, genes once doomed may resurrect themselves. For example, genes for red and green opsins of higher primates arose as alleles of the once doomed but resurrected red opsin locus.
An electrophoretic approach to the assessment of the spatial distribution of DNA double‐strand breaks in mammalian cells
Authors: Friedl Anna A. , Kraxenberger Alfred , Eckardt‐Schupp Friederike 
Published: May 2005

AbstractAn approach is presented making it possible to investigate whether breaks in fragmented mammalian chromosomal DNA were induced randomly and independently from each other. Genomic DNA isolated from mammalian cells irradiated with γ‐rays or restriction enzyme‐treated human DNA was resolved according to size using pulsed field gel electrophoresis, and the resulting DNA mass distributions were measured in ethidium bromide‐stained gels. The DNA profiles thus obtained were compared to the predictions on DNA fragment size distribution which follow from a so‐called random breakage model to test whether the experimental outcome is compatible with the assumption of a random localization of breaks. Comparisons of fragment distributions may be performed utilizing two equivalent representations that are linked by an adequate transformation. Considering either directly measurable DNA mass profiles in units of migration distances along a gel lane or transformed distributions in units of molecular length, we show for γ‐irradiated samples that the predictions derived from the employed models agree well with the observed data, thus allowing an immediate quantification of double‐strand breaks (DSB). Using restriction enzyme‐treated DNA as a paradigm, the disagreement of predicted and observed data shows the applicability of our approach to the detection of a non‐random distribution of DSB. Therefore, we suppose that our approach may also be useful to reveal a clustering of DSB, which is postulated to occur after damage induction by densely ionizing radiation. Furthermore, investigations on the spatial distribution of chemically or endogenously produced DSB, as well as residual DSB after repair, may be attempted.
Analysis of microsatellites by direct blotting electrophoresis and chemiluminescence detection
Authors: Mekus Frauke , Dörk Thilo , Deufel Thomas , Morral Núria , Tümmler Burkhard 
Published: May 2005

AbstractWe describe a fast and reliable method for the nonradioactive analysis of microsatellites. For three dinucleotide repeats within the cystic fibrosis transmebrane conductance regulator (CFTR) gene, the separation of polymerase chain reaction (PCR) products generated with biotinylated primers on a direct blotting electrophoresis system and subsequent chemiluminescence detection is shown. In direct blotting electrophoresis, the separation of DNA fragments depended linearly on size. The reproducible resolution allowed reliable assignment of allele lengths to a given signal. The nonradioactive detection protocol was advantageous compared to radioactive methods: samples could be analyzed within one day due to the fast signal development by 3‐(4‐meth‐oxyspiro{1,2‐dioxetane‐3,2′‐(5′‐chloro)tricyclo[3.3.1.1.3,7]decan}‐4‐yl)phenylphosphate disodium salt (CSPD). Variation of exposure times enabled differentiation between major bands and byproducts of comparable intensity that are due to the slippage of the Taq polymerase during PCR amplification.
Specific staining of glycine N‐methyltransferase
Authors: Santos Fátima , Amorim António , Kömpf Jost 
Published: May 2005

AbstractGlycine N‐methyltransferase from rabbit, human, rat and pig livers was separated by isoelectric focusing and a specific functional staining method was developed through the detection of sarcosine produced from the methylation of glycine. Isozyme patterns obtained in the various species tested differ both in the number of bands and apparent isoelectric points. These differences may explain the contradictory data on the subunit structure and glycosylation status of the enzyme reported so far.
Capillary gel electrophoresis separation of high‐mannose type oligosaccharides derivatized by 1‐aminopyrene‐3,6,8‐trisulfonic acid
Authors: Guttman András , Pritchett Tom 
Published: May 2005

AbstractIn this paper we report the capillary gel electrophoresis separation of 1‐amino‐pyrene‐3,6,8‐trisulfonic acid (APTS) labeled oligosaccharides, released enzymatically from bovine pancreatic ribonuclease B. The released and labeled high‐mannose structures were identified by spiking the separated peaks with the appropriate commercially available individual oligosaccharides. Baseline separation of the three positional isomers of the mannose‐7 and mannose‐8 oligosaccharides was attained. Comparison of the electrophoretic mobilities of the high‐mannose type branched carbohydrates to the linear molecules of malto‐oligosaccharides (glucose oligomers) have been shown using different gel concentrations in the running buffer system. We observed that increasing gel concentration in the running buffer causes an increase in the relative mobility values of the high‐mannose type carbohydrate molecules compared to the linear glucose oligomers. Analysis of our data indicated that this increase in relative migration time was not due to sieving, but seemed to be related to the mannose content and hydrodynamic volume of the branched glycans as well as to the viscosity of the separation medium.
Fractionation of carrier ampholytes in multicompartment electrolyzers with isoelectric membranes
Authors: Bossi Alessandra , Righetti Pier Giorgio 
Published: May 2005

AbstractMulticompartment electrolyzers with isoelectric membranes can be successfully utilized for the preparation of carrier ampholytes of narrow pH ranges from commercially available wider pH intervals. An example is given on the preparation of a 0.6 pH unit (pH 6.7–7.3) range from a standard pH 6–8 interval. A 10% Ampholine solution is focused in an electrolyzer equipped with the following isoelectric membranes: pI 6.0, 6.7, 7.3 and 8.0. The narrow pH 6.7–7.3 cut can be efficiently utilized for base‐line separation and quantitation of hemoglobin A from its glycated form, Hb A1c. This analysis is important for the screening and follow up of diabetic patients. The advantage of multicompartment electrolyzers are: (i) precision in the preparation of narrow pH cuts, due to the presence of membranes with defined pI values; (ii) ability to perform in both small‐ and large‐scale operations and (iii) absence of contaminants leaching from granulated supports, as typical of some previous techniques.
An updated two‐dimensional gel database of rat liver proteins useful in gene regulation and drug effect studies
Authors: Anderson N. Leigh , Esquer‐Blasco Ricardo , Hofmann Jean‐Paul , Meheus Lydie , Raymackers Jos , Steiner Sandra , Witzmann Frank , Anderson Norman G. 
Published: May 2005

AbstractWe have improved upon the reference two‐dimensional (2‐D) electrophoretic map of rat liver proteins originally published in 1991 (N. L. Anderson et al., Electrophoresis 1991, 12, 907–930). A total of 53 proteins (102 spots) are now identified, many by microsequencing. In most cases, spots cut from wet, Coomassie Blue stained 2‐D gels were submitted to internal tryptic digestion [2], and individual peptides, separated by high‐performance liquid chromatography (HPLC), were sequenced using a Perkin‐Elmer 477A sequenator. Additional spots were identified using specific antibodies.
Steady‐state models in electrophoresis: From isotachophoresis to capillary zone electrophoresis
Authors: Beckers Jozef L. 
Published: May 2005

AbstractAlthough all electrophoretic techniques are closely allied and controlled by the same rules, we often distinguish between steady‐state and dynamic models in the modeling of electrophoretic processes, whereby steady‐state models are applied for isotachophoresis (ITP) and dynamic models are applied for other electrophoretic processes, wherein a steady‐state is not reached. This paper shows how, starting from a mathematical model for the steady‐state in ITP, mathematical models can be derived for several modifications of ITP and that even nonsteady‐state processes can be estimated by a repeated application of a steady‐state model. In this way all parameters in sample zones in capillary zone electrophoresis (CZE), through which temporal electropherograms can be simulated, can be calculated. Realistic simulations can be obtained for zone electrophoretic processes, for which the electrodispersive character is the dominating peak broadening mechanism, and simulated electropherograms resemble measured electropherograms concerning migration times, peak shapes, fronting or tailing character and the question of peaks and dips.
Capillary electrophoresis with polymeric separation media: Considerations for theory
Authors: Smisek David L. 
Published: May 2005

AbstractThe theory of capillary electrophoresis with polymeric separation media is reviewed. Some of the major theories of gel electrophoresis are examined in terms of the experimental observations that they support. The considerations and difficulties in applying these theories to capillary electrophoresis with polymeric separation media are investigated, particularly the use of high electric field strengths and low concentration polymer solutions. Recent advances in this area, including some empirically‐derived relationships and models currently found in the literature, and future directions for theory development are discussed.
Study of high‐field dispersion in micellar electrokinetic chromatography
Authors: Yu Lixin , Davis Joe M. 
Published: May 2005

AbstractThe anomalous dispersion of hydrophobic, highly retained analytes at high electric field strengths E in micellar electrokinetic chromatography (MEKC) is experimentally and theoretically quantified. A simple model for plate number N is proposed, in which only plug size and longitudinal diffusion govern dispersion. This model describes well the dispersion of acetone, 2′‐deoxyadenosine, and 2′‐deoxyadenosine‐5′‐monophosphate (dAMP) in MEKC buffers and also dAMP in capillary‐electrophoresis buffers. However, the model describes the dispersion of 1‐nitropyrene, pyrene, perylene, and the 4‐chloro‐7‐nitrobenzofuran (NBD) derivative of cyclohexylamine only at low E's; for these analytes, a nonequilibrium‐like dispersion causes N to decrease rapidly at high E's. Furthermore, the dispersion of NBD‐cyclohexylamine has a dependence on capillary diameter. Theoretical arguments are proposed, which show that this additional dispersion cannot be explained quantitatively by mass‐transfer kinetics, micellar polydispersity, hydrodynamic flow, Joule heating, or the radial variation of partition coefficient. In addition, experiments are performed suggesting that wall adsorption and sample inhomogeneity are not responsible for the efficiency loss. Other dispersion sources are suggested for future exploration.
Capillary isoelectric focusing: A routine method for protein analysis?
Authors: Schwer Christine 
Published: May 2005

AbstractAlthough isoelectric focusing (IEF) in the slab gel format is a widely used technique in protein analysis, capillary isoelectric focusing (CIEF) is not yet a method used routinely, despite major advantages. This may be due to the fact that several methods for performing IEF in the capillary can be found in the literature, differing in the manner of mobilizing the focused protein zones for detection. We therefore discuss and compare the three most widely used CIEF techniques – using chemical, pressure, or electroosmotic flow (EOF) mobilization – with respect to linearity of the calibration curve, resolution, and reproducibility.
Electroosmotic control of chiral separation in capillary zone electrophoresis
Authors: Hong Shencai , Lee Cheng S. 
Published: May 2005

AbstractThe resolution in capillary zone electrophoresis (CZE), with the assumption of diffusion control only, is strongly dependent on the direction and magnitude of electroosmotic flow. In fact, excellent separation resolution will be obtained if the electroosmotic flow is in the opposite direction of the electrophoretic migration. By applying various radial electric potential gradients across the capillary wall, the direct control of the ζ potential and the electroosmotic flow results in a great enhancement of chiral resolution in cyclodextrin‐modified CZE. All 12 basic chiral drugs, including (+/−)‐ephedrine, (+/−)‐pseudoephe‐drine, (+/−)‐norephedrine, (+/−)‐epinephrine, (+/−)‐norepinephrine, and (+/−)‐isoproterenol, are separated and resolved within 22 min of the analysis time. There is no additional band broadening and dispersion introduced by the direct control of electroosmosis with the application of various radial electric potential gradients.
On the measurements of electrophoretic mobilities by means of capillary isotachophoresis at a constant voltage
Authors: Ermakov Sergey V. , Zhukov Michael Y. , Capelli Laura , Righetti Pier Giorgio 
Published: May 2005

AbstractA method for measuring electrophoretic mobilities by means of isotachophoresis (ITP) at a constant voltage as described by H. Carchon and E. Eggermont (Electrophoresis, 1982, 3, 263–274) is analyzed. An error made in this work, disregarding the pH shift arising at the initial discontinuity on the leader‐terminator boundary, has been corrected. This method has been carefully studied and generalized for the presence of constant electroosmotic flow in a capillary. The limits of its applicability and the diffusionless ITP theory in general are discussed. A detailed study of the evolution of initial discontinuity (stationary boundary) showed some anomalies not reported previously, particularly nonmonotonic concentration profiles in the vicinity of stationary boundaries. Moreover, in some cases, diffusion effects and the contribution of H+ ions can also strongly influence the behavior of moving boundaries. Computer modelling (confirmed by experimental data) showed that these effects could lead to the decay of the ITP train, despite the fact that the steady state diffusionless ITP theory predicts its stability.
Some variables affecting reproducibility in capillary electrophoresis
Authors: Shihabi Zakariya K. , Hinsdale Mark E. 
Published: May 2005

AbstractSeveral variables that can affect reproducibility of both the peak height and the migration time in capillary electrophoresis (CE) were investigated here. A great part of the imprecision in CE for migration time is related to the interaction of the analyte with the capillary wall. Within a run, acidic compounds with long migration times have a higher relative standard deviation. In general, conditions that decreased the migration time, such as a short capillary length, tended to enhance the reproducibility of the migration time. Sample size also affected the reproducibility of peak height. Too small or too large an injection volume diminished the reproducibility. Sample matrix, such as high levels of proteins or salts in the sample, decreased the reproducibility. Furthermore, improvement in reproducibility can be achieved by using internal standards (especially for migration time), thorough washing of the capillary, or removing the excess proteins by acetonitrile deproteinization. Acetonitrile has an added effect of producing sample stacking. Depending on the migration time and analyte concentration, the peak height and area yielded different reproducibility results.