bluuebunny/crossref_metadata_2025_split huggingface dataset:
A set of electrophoretic molecular markers for strain typing and population genetic studies of Histoplasma capsulatum
Authors: Carter Deidre A. , Burt Austin , Taylor John W. , Koenig Gina L. , Dechairo Bryan M. , White Thomas J. 
Published: May 2005

AbstractA set of eleven biallelic and three multiallelic molecular markers have been developed to analyze populations of Histoplasma capsulatum. All markers are amplified by polymerase chain reaction (PCR) and can be readily scored using minimal amounts of template DNA. The 11 biallelic loci have polymorphic restriction endonuclease sites or small insertions or deletions which may be assessed by agarose gel electrophoresis. These markers are inherited in an unambiguous manner and are ideal for assessing structure and gene flow within US populations of H. capsulatum, but are monomorphic in non‐US populations. Both length and sequence variation are present in the multiallelic loci, which can be scored by direct sequencing, polyacrylamide gel electrophoresis, or single‐strand conformation polymorphism (SSCP): As they are hyper‐variable, the multiallelic loci can be used to type isolates and to assess the level of genetic variation within populations. Preliminary results indicate that the three multiallelic markers presented are sufficient to distinguish isolates at the individual level and are polymorphic in both US and non‐US populations. This collection of molecular markers will be a useful tool in population and epidemiology studies of H. capsulatum.
A simple and fast procedure for high quality DNA isolation from gels using laundry detergent and inverted columns
Authors: Pusch Carsten 
Published: May 2005

AbstractA quick method for the recovery of DNA from agarose and polyacrylamide gels with high efficiency and quality is described. Excised gel slices, containing at least 10 ng DNA, are incubated for 15 min at 60°C in the presence of laundry detergents. An “inverted column” is obtained by covering the extraction liquid by a layer of cotton wool, Sephadex G‐50 and another layer of cotton wool. Following centrifugation the supernatant containing the DNA is recovered by aspiration and the DNA is precipitated with isopropanol and tRNA, washed with ethanol and air‐dried. The yield of reisolated DNA does not depend on DNA fragment size and small quantities of gel volume. Thus, the technique may prove useful in a broad range of applications in the methodology of molecular biology.
Oriented macroporous polyacrylamide gels
Authors: Charlionet Roland , Machour‐Merlet Nadine , Leclerc Stéphane , Malandain Jean‐Jacques 
Published: May 2005

AbstractMacroporous gels with huge cavities and partition walls result from controlled microsyneresis during gelation. In this report we show that the microsyneresis process can be further controlled: it is possible to orient the partition walls of macropores by the use of an electric field throughout polymerization. Our oriented macroporous polyacrylamide gels offer a specific structure: a set of parallel channels of about 2 μm inner diameter, with polyacrylamide walls including acidic groups linked to the aggregated matter.
Fast separation of underivatized carbohydrates by coelectroosmotic capillary electrophoresis
Authors: Zemann Andreas , Nguyen Duc Tuan , Bonn Günther 
Published: May 2005

AbstractA method for the rapid quantitative analysis of underivatized acidic sugars, monosaccharides and disaccharides using coelectroosmotic capillary electrophoresis was developed. Indirect UV detection at 254 nm using sorbate as background electrolyte was employed for monitoring the analytes. A highly alkaline pH value of the electrolyte system was chosen in order to achieve an electrophoretic mobility of the saccharides towards the anode. A dynamic reversal of the electroosmotic flow and, by this means, a codirectional movement of the negatively charged analytes and the electroosmotic flow is accomplished by employing a polycationic surfactant (hexadimethrine bromide), which is added to the background electrolyte. To further improve the resolution of specific carbohydrates, acetone is used as organic modifier. A practical application of the developed method for the fast determination of fructose, glucose, and sucrose in various soft drinks is provided.
Separation of disaccharides as their borate complexes by capillary electrophoresis with indirect detection in visible range
Authors: Plocek Jiří , Chmelík Josef 
Published: May 2005

AbstractBorate complexation was used to make possible the separation of disaccharides by capillary electrophoresis with indirect detection. A high borate concentration did not affect the indirect detection sensitivity in as negative a way as predicted previously. The concentration sensitivity for sucrose was determined to be 2 mM at the borate concentration of 200 mM in running electrolyte. The newly introduced backround chromophore, p‐nitrophenol, allows the monitoring of the separation process in a visible range at 400 nm. This also enables the indirect detection of UV‐absorbing compounds in complex mixtures in which they would be impossible to detect with a UV‐absorbing backround chromophore.
Sulfobutylether‐β‐cyclodextrin‐mediated capillary electrophoresis for separation of chlorinated and substituted phenols
Authors: Groom Carl A. , Luong John H. T. 
Published: May 2005

AbstractCyclodextrin‐mediated capillary electrophoresis has been developed for separation and analysis of chlorinated as well as substituted phenolic compounds. The procedure used a negatively charged sulfobutylether‐β‐cyclodextrin (SB‐βCD) to effect differential partitioning of the phenols between the buffer and CD phases. In 50 mM phosphate buffer containing as low as 1 mM SB‐β‐CD, 25 phenolic compounds including 11 Environmental Protection Agency (EPA) priority phenols were separated with theoretical plate numbers well above 100 000, for 50 cm of effective length in most cases. An equilibrium complexation model was used for investigating the effect of pH as well as different cyclodextrin concentrations on the electrophoretic mobility. The cyclodextrin‐mediated capillary electrophoresis system was also applicable for separating and quantifying the level of pentachlorophenol in contaminated soil samples.
Isoelectric properties of the soluble matrices in relation to the chemical composition of some Scleractinian skeletons
Authors: Dauphin Yannicke , Cuif Jean‐Pierre 
Published: May 2005

AbstractSoluble matrices of four Scleractinian skeletons (Madrepora, Favia, Leptastrea and Fungia), were extracted and studied by isoelectric focusing (IEF). The main part of the extracted matrices is acidic. IEF gels are poorly stained or unstained by Coomassie Blue and silver. The positive Alcian Blue staining is indicative of a sulfated and acidic nature of the glycoproteins. Chemical analysis shows high S contents in Scleractinian skeletons. These results are supported by the comparison with IEF and chemical contents of Molluscan shells.
Proteomic ‘contigs’ of Ochrobactrum anthropi, application of extensive pH gradients
Authors: Wasinger Valerie C. , Bjellqvist Bengt , Humphery‐Smith Ian 
Published: May 2005

AbstractThe most extensive linear pH gradients yet employed in combination with two‐dimensional gel electrophoresis are described, along with their application in proteome analysis. A significant proportion of the protein compliment of bacterial species is believed to be accessible using an extended linear pH gradient of 2.3 to 11.0. Protein standards with predicted isoelectric points (pI) ranging from 3.24 to 9.56 were used to confirm focusing positions with respect to the immobilised pH gradients (IPG) prior to mapping studies of Ochrobactrum anthropi. Multiple gel images were used to construct contiguous windows of protein expression (‘proteomic contigs’) within 18 cm pH gradients 2.3–5, 4–7, and 6–11 in conjunction with 15%T and 7.5%T acrylamide gels, the latter being used to resolve higher molecular weight (Mr) proteins. Each IPG had a 5 cm region of similar pH gradient overlap at pH 4–5 and pH 6–7 that was used to construct an image of protein expression characteristic of whole cell lysates. This is reminiscent of genomic sequencing initiatives whereby portions are combined to form a contiguous picture of the whole. The protein maps obtained demonstrated a means of resolving the many tens of thousands of cellular proteins likely to occur in eukarvotic systems, but also highlighted the need to further optimise protein extraction, equilibration buffers, and separation conditions of higher Mr proteins occurring at extreme pI. Theoretical 2‐D protein maps were constructed for five organisms for which the total DNA sequence is now available. In all cases, higher Mr acidic and basic proteins were shown to be common.
Spontaneous and induced minisatellite instability
Authors: Jeffreys Alec J. , Bois Philippe , Buard Jérǒme , Collick Andrew , Dubrova Yuri , Hollies Caroline R. , May Celia A. , Murray John , Neil David L. , Neumann Rita , Stead John D. H. , Tamaki Keiji , Yardley Jane 
Published: May 2005

AbstractMinisatellites provide not only the basis for DNA fingerprinting and DNA profiling but also extremely informative systems for analysing processes of tandem repeat turnover in the human genome. Minisatellite instability appears to involve distinct mutation processes in somatic and germline cells; in the germline, mutation is frequently dominated by inter‐allelic conversion‐like events most likely occurring at meiosis and apparently regulated by cis‐acting mutation initiator elements. Attempts to define these initiators in transgenic mice have so far been thwarted by what appears to be a major human/mouse barrier to the inter‐species transfer of repeat instability. Minisatellites not only show high frequency spontaneous mutation in the germline, but also appear to be very sensitive to mutation induction by ionizing radiation, both in experimentally irradiated mice and in human populations exposed following the Chernobyl disaster; the mechanisms of mutation induction by radiation remain enigmatic.
Mitochondrial D‐loop diversity in Australian riverine and Australian desert aborigines
Authors: van Holst Pellekaan Sheila , Frommer Marianne , Sved John , Boettcher Barry 
Published: May 2005

AbstractPopulation structure has been revealed in mitochondrial D‐loop segment 1 (mt DLS1) sequences from Australian Aboriginal people in the Darling River region of NSW (Riverine) and from Yuendumu in central Australia (Desert). Comparison with five published global studies reveals that these Australians demonstrate greatest divergence from some Africans, least from Papua New Guinea (PNG) highlanders, and only slightly more divergence from some Pacific groups (Indonesian, Asian, Samoan, and coastal PNG). A median networks approach [1] demonstrates that several hypervariable nucleotide sites within the DLS1 are likely to have undergone mutation independently. A comprehensive evaluation of specific nucleotide variants with the large amount of global sequence data now available has been achieved in three stages of analysis: (i) identification of key nucleotide variants (from the Cambridge reference sequence [2]) in the Aboriginal Australian by pairwise comparison and construction of a ‘local’ median network, (ii) identification of key nucleotide variants in a selected global sample including Australian mtDLS1 types most different from each other, and (iii) calculation of the frequency with which these key nucleotide sites occur as variants in a greatly extended global sample. The third stage of the analysis revealed that nucleotides 16287 and 16356 are unique markers for representatives from the northern Riverine region. A ‘thymine’ at nucleotide 16223 is an informative signature of African and several identifiable non‐African DLS1 types, whereas the ‘cytosine’ form is a marker for European, Pacific, and some Asian populations.
Genome analysis of the fungal plant pathogen, Leptosphaeria maculans using pulsed field gel electrophoresis
Authors: Howlett Barbara J. 
Published: May 2005

AbstractPulsed field gel electrophoresis (PFGE), or electrophoretic karyotyping, separates chromosomal‐sized pieces of DNA in agarose gels where the orientation of the electric field is periodically altered. This technique has revealed that many fungi have a high degree of chromosomal length polymorphisms. Often the only isolates with identical karyotypes are derived from a single clone, thus PFGE provides a ‘genetic fingerprint’ for them. The size range and number of chromosomes within isolates of a particular species are usually constant, hence PFGE can distinguish between morphologically similar fungi. This technique can also be used to follow inheritance of chromosomal length polymorphisms and shows that in some fungi novel‐sized chromosomes are produced during meiosis. As well as resolving the nuclear (A‐type) chromosomes, it can also resolve dispensable (B‐type) chromosomes and cytoplasmic genomes including mitochondrial DNA and linear plasmids. The application of this technique to Australian isolates of Leptosphaeria maculans, which causes blackleg disease of canola (Brassica napus), is discussed.
Identification of pathogenic yeasts of the imperfect genus Candida by polymerase chain reaction fingerprinting
Authors: Meyer Wieland , Latouche G. Nicolas , Daniel Heide‐Marie , Thanos Marcus , Mitchell Thomas G. , Yarrow David , Schönian Gabriele , Sorrell Tania C. 
Published: May 2005

AbstractWith the increase in the number of immunocompromised hosts, the number of fungal pathogens has increased markedly. Identification and classification, especially of yeast species and strains, is often difficult when based solely on phenotypic characteristics. Since it became clear that different fungal pathogens require specific treatment strategies, there is a need for simple, rapid and reliable methods to identify fungal isolates. Polymerase chain reaction (PCR) fingerprinting was successfully applied here to identify yeast isolates Microsatellite [(GTG)5; (GACA)4] and minisatellite [(5′GAGGGTGGCGGTTCT 3′), derived from the core‐sequence of the phage M13] specific primers were used as single primers in the PCR to amplify hypervariable interrepeat DNA sequences from over 200 European, American and Australian clinical isolates within the genus Candida. Each species, represented by its type strain, could be identified by a specific multilocus pattern, allowing for the assignment of all the isolates to the appropriate species. Intra‐species variation in the multilocus profiles was about 20% compared to inter‐species variation, which was up to 80%. Anamorph‐teleomorph pairs could be identified by highly homologous PCR fingerprint patterns. PCR fingerprinting was more discriminatory when compared with routinely used biochemical tests (Vitek YBC and API ID 32C). PCR fingerprinting has proven to be a powerful tool for the identification of medically important yeasts. It is rapid, sensitive, reliable, highly reproducible, stable in vitro and in vivo, and applicable to large‐scale experiments. Potential applications include: yeast taxonomy, epidemiology, environmental surveys, and improvement of the diagnosis of mycotic diseases.
Polymerase chain reaction‐linked single‐strand conformation polymorphism of ribosomal DNA to fingerprint parasites
Authors: Gasser Robin B. , Monti Jennifer R. , Zhu Xingquan , Chilton Neil B. , Hung Guo‐Chiuan , Guldberg Per 
Published: May 2005

AbstractTo overcome limitations of the morphological identification of some parasites (and their different developmental stages) to species, we have established a polymerase chain reaction‐linked single‐strand conformation polymorphism technique (PCR‐SSCP) utilizing the second internal transcribed spacer (ITS‐2) of ribosomal (r)DNA. This spacer was specifically chosen in the study of strongylid and ascarid nematodes because it is known to provide reliable species markers. The ITS‐2 from individual parasites was amplified by PCR, then denatured and subjected to electrophoresis on a mutation detection enhancement (MDE) (nondenaturing) gel matrix. PCR‐SSCP analysis showed that the single‐strand ITS‐2 patterns produced allowed the accurate identification of species. The method also allowed the display of (low‐level) variation in patterns within some species between different geographical isolates. These findings demonstrate the usefulness of PCR‐SSCP of ITS‐2 for the identification of nematode species and indicate its potential for resolving variation in the ITS‐2 sequence within species.
An evaluation of selected DNA extraction strategies for short tandem repeat typing
Authors: Vandenberg Nicholas , van Oorschot Roland. A. H. , Mitchell Robert J. 
Published: May 2005

AbstractOrganic and Chelex extraction methods are compared to five commercially available DNA extraction kits. For forensic purposes, comparison of different extraction strategies is based on the ability of the methods to economically recover high yields of amplifiable DNA from small blood samples in a quick, simple and safe manner. The findings of this study indicate that resin‐based methods, such as Chelex, are best able to meet these criteria.
Linkage analysis of bronchial hyperreactivity and atopy with chromosome 11q13
Authors: Wong Zilla Y. H. , Tsonis Dina , van Herwerden Lynne , Raven Joan , Forbes Andrew , Abramson Michael J. , Walters E. Haydn , Harrap Stephen B. 
Published: May 2005

AbstractThere are two key clinical features of asthma: allergy and bronchial hyperreactivity (BHR). Some pedigree studies of atopy have indicated linkage with the high affinity IgE receptor (FcϵRI‐β) gene on chromosome 11q13, but others failed to confirm this linkage. We examined the genetic linkage of three polymorphic microsatellite markers to atopy and BHR in 120 affected sibling pairs recruited from the general community. We found no linkage to atopy at any of the three 11q13 loci studied. Our findings also do not favour linkage between BHR and loci approximately 8–9 cM either side of the FcϵRI‐β gene.
Genetic analysis of the freshwater crayfish Cherax tenuimanus
Authors: Imgrund John , Groth David , Wetherall John 
Published: May 2005

AbstractThe marron (Cherax tenuimanus) is one of the few species of freshwater crayfish native to Australia that is suitable for aquaculture and occurs only in the southwest of Western Australia. This study describes polymorphic microsatellite markers which differentiate marron populations from several geographically distinct regions (including rivers and streams, dams, and commercial marron farms) throughout Western Australia. Twenty microsatellite loci, primarily of the (CA)n. (GT)n type, were isolated and sequenced from a marron cosmid library. Three of these loci were characterised further. Two loci exhibited extensive polymorphism and one was monomorphic. The polymorphic loci exhibited Mendelian codominant inheritance in the family group comprising two individual parents and approximately 100 offspring bred for this study. These loci permitted differentiation between the five geographically distinct populations studied and thus provide a basis for genetic characterisation of marron stock in Western Australia.
Minisatellite DNA markers reveal hybridisation between the endangered black robin and tomtit
Authors: Ma Wei , Lambert David 
Published: May 2005

AbstractWe have used multilocus minisatellite DNA profiling to assess genetic variation in the endangered and highly inbred black robins and the closely related tomtits. These species are restricted to wild populations on the Chatham Islands, off the east coast of New Zealand. DNA profiles revealed a remarkable degree of genetic similarity among black robins, as well as among the tomtits sampled, although the typical profiles of these two species were clearly distinct. The parentage of two putative hybrid chicks and one putative hybrid adult was established for a ‘black robin’ adult male and an adult tomtit female which were found nesting together. The ‘black robin’ male, despite being morphologically a typical black robin, was found to possess a number of minisatellite‐containing restriction fragments not recorded from the black robin population (n = 103). These fragments were however detected in tomtits. Consequently, this bird appeared to be an F1 hybrid and his three offspring were F2 hybrids. Mitochondrial DNA sequencing of members of this family showed that the ‘black robin’ male had cytochrome b and 16S of black robin, rather than tomtit, haplotypes. This indicates that the black robin adult male hybrid was the result of a black robin female mating with a tomtit male. These findings are particularly important since tomtits had been used as cross‐foster parents for black robins, as part of an earlier conservation recovery program The existence of any hybrids thus detected would have important implications for cross‐fostering programs generally, since may such programs are now being implemented in conservation programs worldwide.
Clinical potential of microchip capillary electrophoresis systems
Authors: Colyer Christa L. , Tang Thompson , Chiem Nqhia , Harrison D. Jed 
Published: May 2005

AbstractClinical interest in the use of capillary electrophoresis (CE) has recently been extended to the microchip environment. Clinical analyses demand careful handling of complex samples that are often limited in quantity and in concentration. The integrated sample handling and analysis capabilities of microchip substrates thus seem ideally suited to clinical applications. This review surveys the development of sample handling (injection, mixing, and reaction) and separation elements on‐chip. The integration of these elements to create a variety of clinical analyzers has been demonstrated. The application of microchip CE systems to human serum protein analysis, immunoassay, and DNA studies is reviewed, along with various other clinical applications. In addition, the clinical potential of the lab‐on‐a‐chip concept is discussed.
Comparison of serum protein electrophoresis by agarose gel and capillary zone electrophoresis in a clinical setting
Authors: Jolliff Carl R. , Blessum Cynthia R. 
Published: May 2005

AbstractCapillary zone electrophoresis (CZE) offers the potential for automating serum protein electrophoretic analysis traditionally performed on standard thin‐layer agarose gels. The following describes the use of CZE compared to agarose gel electrophoresis (AGE) for the detection of dysproteinemia and paraproteinemia in a clinical study involving 240 patients. The study includes within‐run and between‐run reproducibility data on the Paragon CZE® 2000 Clinical Capillary Electrophoresis System, in addition to concordance data between the two methodologies. Paraprotein quantitation studies comparing AGE versus CZE were also performed. Reproducibility for the automated CZE system was superior to the AGE system. Improved reproducibility for the CZE method is largely due to measuring protein absorbance directly at 214 nm versus the traditional AGE method that measures the amount of dye adsorbed to protein. Reproducibility data as percent coefficient of variance (% CV) for the five classic bands in a normal control serum for between‐run precision ranged from 1.2 to 4.5% for CZE compared to AGE, which ranged from 3.8 to 8.0% CV. Concordance studies between AGE and CZE involving dysproteinemias including hypogammaglobulinemia, polyclonal and monoclonal gammopathies, acute and chronic inflammation, nephrosis, hepatodegenerative disease, cirrhosis, and iron deficiency anemia showed 96% agreement. Paraprotein classification, which compared the CZE immunosubtraction method to immunofixation electrophoresis (IFE) on agarose, showed 100% agreement. Certain dysproteinemias involving beta lipoprotein were in partial concordance due to the inability of the CZE procedure to detect this component. Detection limits for monoclonal gammopathies, providing they were not comigrating with other proteins, were IgG 50 mg/dL, IgM 75 mg/dL, and IgA 75 mg/dL. Paraprotein quantitative studies between the two methods showed less than a ± 0.2 g/dL variation.