Biomedical subjects

Walther Parson

Publications and source records attributed to Walther Parson.

52 records · Page 3Linked to original sources

PubMed2004

Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database.

Large forensic mtDNA databases which adhere to strict guidelines for generation and maintenance, are not available for many populations outside of the United States and western Europe. We have established a high quality mtDNA control region sequence database for urban Nairobi as both a reference database for forensic investigations, and as a tool to examine the genetic variation of Kenyan sequences in the context of known African variation. The Nairobi sequences exhibited high variation and a low random match probability, indicating utility for forensic testing. Haplogroup identification and frequencies were compared with those reported from other published studies on African, or African-origin populations from Mozambique, Sierra Leone, and the United States, and suggest significant differences in the mtDNA compositions of the various populations. The quality of the sequence data in our study was investigated and supported using phylogenetic measures. Our data demonstrate the diversity and distinctiveness of African populations, and underline the importance of establishing additional forensic mtDNA databases of indigenous African populations.

Black People↗

PubMed2004

Applicability of tandem mass spectrometry to the automated comparative sequencing of long-chain oligonucleotides.

An algorithm for the comparative sequencing (COMPAS) of oligonucleotides is shown to be suitable for the sequence verification of nucleic acids ranging in length from a few to 80 nucleotides. The algorithm is based on the matching of a fragment ion spectrum generated by collision-induced dissociation to m/z values predicted from a known reference sequence employing established fragmentation pathways. Prior to mass spectrometric investigation, the oligonucleotides were on-line purified by ion-pair reversed-phase high-performance liquid chromatography using monolithic separation columns. This study evaluated the potential and the limits of COMPAS regarding the length and the charge state of oligonucleotides, the selected collision energy, and the analyzed amount of sample using a quadrupole ion trap mass spectrometer. The results revealed that oligonucleotides could be very reliably re-sequenced up to 60-mers, although the algorithm was successfully used to even verify sequences up to 80-mers. The relative collision energy was typically in the range between 13 and 20%, which allowed in most cases a verification of the reference sequence in a window of at least three consecutive collision energies. To select a proper charge state for fragmentation, a compromise had to be found between high signal intensity and low charge state. Furthermore, by reducing the eluent flow rate during elution of the oligonucleotide, the sequence of a 50-mer was successfully verified from the analysis of 295 fmol of the raw product. COMPAS was proven to be reproducible and was applied to the genotyping of the polymorphic, Y-chromosomal locus M9 contained in a 62-base pair polymerase chain reaction product.

Algorithms↗

PubMed2004

Optimized suppression of adducts in polymerase chain reaction products for semi-quantitative SNP genotyping by liquid chromatography-mass spectrometry.

While electrospray ionization mass spectrometry has shown great potential for the identification of genotypes in DNA sequences amplified by polymerase chain reaction (PCR), the quantitative determination of allele frequencies remains challenging because of the presence of cationic adducts in the mass spectra which severely impairs accuracy of quantitation. We report here on the elaboration of an optimized desalting protocol for ion-pair reversed-phase high-performance liquid chromatography-electrospray ionization mass spectrometry (ICEMS) of PCR amplicons which facilitates the genotyping of single nucleotide polymorphisms (SNPs). Chromatographic purification at temperatures between 50 and 70 degrees C using monolithic reversed-phase columns and acetonitrile gradients in aqueous, 20-30 mmol/l butyldimethylammonium bicarbonate enabled the mass spectrometric analysis of nucleic acid solutions containing up to 1.7 mol/l sodium chloride. A further improvement in removal of metal cations was achieved upon the addition of 5-10 mmol/l ethylenediaminetetraacetic acid (EDTA) to the sample solution prior to liquid chromatography. ICEMS was used for the semi-quantitative genotyping of SNPs amplified from the tetraploid genome of potato cultivars. Using a quadrupole ion trap mass spectrometer, allele frequencies were determined with an accuracy of 2-9% by measuring the relative intensities of the signals corresponding to the molecular mass of each of the alleles in the deconvoluted mass spectra. ICEMS results correlated well with those obtained by pyrosequencing, single nucleotide primer extension, and conventional dideoxy sequencing.

Chromatography, High Pressure Liquid↗

PubMed2003

Molecular characterization and Austrian Caucasian population data of the multi-copy Y-chromosomal STR DYS464.

DYS464 is a multi-copy STR system with four positions on the Y-chromosome (DYS464a, b, c, and d) which was recently identified and characterized [Forensic Sci. Int. 130 (2002) 97]. The aims of our study were to perform a population study, to estimate the mutation rate and an extensive sequence analysis in order to confirm the nomenclature. Fourteen different alleles were found in an Austrian population sample with an allele length varying from 9 to 19 repeats. All alleles were cloned and sequenced. Alleles 9-19 showed the general repeat structure (CCTT)n...(CCTT)2...(CCTT)3...(CCTT)4...(CCTT)2...(CCTT)2. The nomenclature is based on the number of repeated units of the variable (CCTT)n-stretch only. In 13% of the samples intermediate alleles, namely 14.3A, 14.3B and 15.3 were detected. In these alleles the variable repeat block is interrupted by a CTT motif (14.3A: (CCTT)3CTT(CCTT)11; 14.3B and 15.3: (CCTT)7CTT(CCTT)7/8). A comparison with GenBank entries revealed the existence of a length variant due to a deletion of one cytosine in the 5' flanking region of the first repeat block. We designed an alternative forward primer to circumvent possible ambiguities in the allele designation. A total of 54 different genotypes were identified in 135 men corresponding to a discrimination capacity (DC) of 40% and a gene diversity (GD) of 0.97. These values are much higher than those of other Y-chromosomal short tandem repeats (Y-STRs). DYS464 has the same haplotype diversity (HD) as the combination of the five Y-STR loci with the lowest gene diversities of the Y-STR core set. On the other hand, a combination of the three most diverse loci (DYS464, DYS385 and DYS390) has the same capacity to distinguish between paternal lineages than the complete minimal haplotype (minHT) consisting of eight Y-STR loci. In our population sample the addition of DYS464 to the minHT increases the number of different haplotypes from 110 to 122. The mutation-rate estimate based on the 70 meioses analyzed amounts to 2.86 x 10(-2) (95% confidence interval 3.5 x 10(-3) to 9.95 x 10(-2)). This value is approximately 10 times higher than the average mutation-rate estimate for Y-STRs.

Alleles↗

PubMed2003

Rapid screening of mtDNA coding region SNPs for the identification of west European Caucasian haplogroups.

This work presents a selection of 16 SNPs from the coding region of the human mitochondrial DNA. The selected markers are used for the assignment of individuals to one of the nine major European Caucasian mitochondrial haplogroups. The selected SNPs are targeted in two multiplex systems, via the application of the SNaPshot kit, a multiplex method based on the dideoxy single-base extension of unlabeled oligonucleotide primers. The method is conceived as a rapid screening technique prior to sequencing analysis, in order to eliminate multiple suspects from an inquiry or to discriminate between stains in a high volume casework example. Moreover, the ability to assign an unknown sample to an mtDNA type of known Caucasian origin could be of probative value in some investigations. A database of 277 Austrian Caucasians has been constructed, and the probability of a chance match between two unrelated individuals is calculated as 11.4%. This novel multiplex PCR amplification and typing system for mtDNA coding region SNPs promises to be a convenient and informative new DNA profiling system in the forensic field.

DNA, Mitochondrial↗

PubMed2003

Localization and quantification of Cd- and Cu-specific metallothionein isoform mRNA in cells and organs of the terrestrial gastropod Helix pomatia.

A quantitative assay based on real-time detection polymerase chain reaction (rtdPCR) was applied to analyze basal and metal-induced mRNA levels of two metallothionein (MT) isoforms (Cd-MT and Cu-MT) in organs of the terrestrial gastropod Helix pomatia. The results show that specific Cd-MT mRNA levels increase with Cd tissue burden, identifying hepatopancreas and gut as the main organs of Cd accumulation and, accordingly, the predominant organs of Cd-MT mRNA expression. In situ hybridization localized this isoform in epithelial cells of hepatopancreas, gut, and kidney. In contrast to the observed Cd-dependent inducibility of the Cd-binding MT isoform, gene expression of the Cu-binding MT could not be induced by either Cd or Cu exposure. Only very low mRNA amounts of the Cu-MT isoform were found in snail hepatopancreas and kidney, whereas the mantle exhibited high basal mRNA levels of this isoform. In situ localization revealed that the Cu-MT gene expression was restricted to one cell type, the so-called rhogocytes, which are present to various extents in the different organs examined. These results suggest a metal-specific sharing of functions between the two MT isoforms. The Cd-MT isoform apparently plays a crucial role in Cd detoxification, as demonstrated by the inducibility of this isoform, as well as its specific localization in the main metabolic and Cd storing organs. The predominant presence of Cu-MT in rhogocytes of snail mantle strengthens the hypothesis that this isoform may regulate Cu availability in hemocyanin synthesis.

Animals↗

PubMed2003

Characterization of the Aspergillus nidulans transporters for the siderophores enterobactin and triacetylfusarinine C.

The filamentous ascomycete Aspergillus nidulans produces three major siderophores: fusigen, triacetylfusarinine C, and ferricrocin. Biosynthesis and uptake of iron from these siderophores, as well as from various heterologous siderophores, is repressed by iron and this regulation is mediated in part by the transcriptional repressor SREA. Recently we have characterized a putative siderophore-transporter-encoding gene ( mirA ). Here we present the characterization of two further SREA- and iron-regulated paralogues (mirB and mirC ), including the chromosomal localization and the complete exon/intron structure. Expression of mirA and mirB in a Saccharomyces cerevisiae strain, which lacks high affinity iron transport systems, showed that MIRA transports specifically the heterologous siderophore enterobactin and that MIRB transports exclusively the native siderophore triacetylfusarinine C. Construction and analysis of an A. nidulans mirA deletion mutant confirmed the substrate specificity of MIRA. Phylogenetic analysis of the available sequences suggests that the split of the species A. nidulans and S. cerevisiae predates the divergence of the paralogous Aspergillus siderophore transporters.

Amino Acid Sequence↗

PubMed2003

Mitochondrial DNA heteroplasmy or artefacts--a matter of the amplification strategy?

We compared two different PCR strategies for the amplification of mtDNA hypervariable region 1 (HV1) with regard to the detection and interpretation of point mutation heteroplasmy in human hair roots. We monitored the level of detected heteroplasmy using direct sequence analysis. PCR amplifications were performed in duplicate on each hair root, using 62 cycles of nested PCR versus 35 cycles of direct PCR. As a previous publication reported different sensitivities of heteroplasmy detection based on the number of PCR cycles used, we were interested in whether and how different PCR amplification strategies would impact sequence quality and the detection of point heteroplasmy. We identified 12 out of 93 hair roots as heteroplasmic (7 out of 31 persons) with direct PCR, whereas 2 of these heteroplasmic events could not be identified with the nested PCR approach. Generally, the quality of the sequence electropherograms in terms of background noise was significantly lower for the nested PCR amplification strategy, leading to ambiguous results in some of the nucleotide positions. Thus, the ability to clearly distinguish a genuine mixture of two nucleotides from background noise at a heteroplasmic position was substantially greater with direct PCR amplification, which generally resulted in higher quality sequence electopherograms.

Artifacts↗

PubMed2003

Improved specificity of Y-STR typing in DNA mixture samples.

Y-STR loci are beneficial for the analysis of forensic samples especially in sexual assault cases or other situations where mixtures of male and female cells are present. However, the amplification of Y-chromosomal STRs is also known to result in the formation of artefactual amplification products, mainly due to insufficient PCR specificity. This is a major drawback of the method, as the sensitivity as well as the correct Y-STR interpretation are affected. In our study, the addition of a PCR enhancer to the reaction master-mix resulted in a significant increase of specificity of Y-STR typing. This was clearly demonstrated by a loss of artefactual signal with increasing enhancer concentration, while the peak heights of the Y-STR alleles were not significantly affected by the enhancer. Mixtures of up to 1:500 (200 pg male and 100 ng female DNA) gave correct Y-STR profiles when the PCR enhancer was added to the reaction, while artefactual amplification succeeded over Y-specific amplification when no PCR enhancer was present.

Chromosomes, Human, Y↗

PubMed2003

Phylogeography of the vairone (Leuciscus souffia, Risso 1826) in Central Europe.

The vairone Leuciscus souffia is a cyprinid fish that inhabits river systems in and around the Alps. The complete mitochondrial DNA control region (945 bp) was sequenced in 295 vairone from 22 populations in Central Europe. A total of 51 haplotypes were identified with a maximum pairwise distance between haplotypes of 5.6%. Phylogenetic analyses revealed two major clades in L. souffia, an 'Italian' clade, and an 'Alpine' clade. Two hybrid zones exist, in the Mediterranean Alps and in the Soca basin. The position of the sister species of L. souffia, L. turskyi, to the 'Alpine' and the 'Italian' clade could not be resolved unambiguously. However, a linearized tree analysis indicated that L. turskyi represents a third lineage, that originated at the same time as the 'Alpine' and the 'Italian' clades of L. souffia. In the 'Alpine' clade two groups were resolved, a subclade with haplotypes from the Rhône and Var basins and a cluster with haplotypes from the Danube and Rhine systems. Our data suggest a long history of the vairone in Central Europe, predating Pleistocene glacial cycles. Two main refugia during glaciations must have existed, one in Italy and another one most probably in the Danube system. However, age estimates based on molecular clock calibrations suggest the survival of 'Alpine' haplotypes in several drainages during the last glaciation cycles. The Rhine system was only recently colonized.

Animals↗

PubMed2003

Systematic study on STR profiling on blood and saliva traces after visualization of fingerprint marks.

This paper describes a systematic study of the influence of optical, physical, and chemical methods used for fingerprint enhancement on subsequent DNA analysis of biological stains. Latent fingerprints as well as fingerprints in contact with blood and saliva on different surfaces were treated with dactyloscopic methods. As a general finding, subsequent STR profiling of the blood/saliva traces led to good results after all the enhancement methods included in this study. Concerning blood enhancement procedures, the airbrush technique showed deleterious effects on subsequent STR analysis in some cases. We therefore recommend the implementation of the layer technique, as it brings advantages for fingerprint enhancement as well. It could also be shown that, as can be necessary in practical casework, two enhancement methods can be performed on a single stain without having influence on STR profiling. In terms of methodological variety, this paper reflects a comprehensive study performed on STR profiling after fingerprint enhancement methods, including rare methods and variations of techniques, which can be a useful alternative in certain case scenarios.

Blood Stains↗

PubMed2002

Single nucleotide polymorphism genotyping by on-line liquid chromatography-mass spectrometry in forensic science of the Y-chromosomal locus M9.

A method is described for genotyping alleles of the Y-chromosomal locus M9, incorporating DNA extraction, amplification by polymerase chain reaction (PCR), sample purification by ion-pair reversed-phase high-performance liquid chromatography (IP-RP-HPLC), and allele identification by on-line hyphenation to electrospray ionization mass spectrometry (ESI-MS). The alleles G and C were differentiated in 114 base pair amplicons on the basis of intact molecular mass measurements with a mass accuracy between 0.007 and 0.017%. The accuracy of mass determination was significantly reduced to less than 0.0036% upon amplification of a short, 61 bp fragment. The application of steep gradients of acetonitrile in 25 mM butyldimethylammonium bicarbonate not only enabled the efficient separation of non-target components from the PCR product in a monolithic, poly-(styrene-divinylbenzene)-based capillary column, but also allowed the high-throughput analysis of the PCR products with cycle times of 2 min. The new method was compared to a conventional restriction fragment length polymorphism assay with capillary gel electrophoretic analysis. In a blind study, 90 samples of unrelated individuals were genotyped. The high accuracy (<0.004%) and small relative standard deviation (<0.007%, n=20) of mass measurements, which enables even the differentiation of A and T alleles with a mass difference of 9 mass units, make IP-RP-HPLC-ESI-MS a potent tool for the routine characterization of SNPs in forensic science.

Base Sequence↗

PubMed2002

Lack of antibody production following immunization in old age: association with CD8(+)CD28(-) T cell clonal expansions and an imbalance in the production of Th1 and Th2 cytokines.

Although it is generally recognized that the function of the immune system declines with age, the nature of the underlying defects is still poorly understood. We now demonstrate the predominance of CD8(+)CD28(-) T cell clonal expansions in elderly persons who fail to produce specific Abs following influenza vaccination. These clones express effector cell markers and are mostly CD45RA(+). When isolated and put into culture, they are unable to proliferate, but produce IFN-gamma (but no IL-5) upon stimulation with anti-CD3 or autoantigen. These autoreactive CD8(+) type 1 effector cells seem to trigger a Th1 polarization, as CD4(+) T cells from elderly persons without in vivo Ab production produce Th1, but only low amounts of Th2 cytokines upon in vitro stimulation with PHA. Therefore, the increased occurrence of CD8(+)CD28(-) clonal expansions may be decisive for the development of immune deficiency in the elderly.

Aged↗

PubMed2002

Microsatellite alterations in human bladder cancer: detection of tumor cells in urine sediment and tumor tissue.

OBJECTIVES: Bladder cancer is the result of clonal expansion of cancer cells in which multiple genetic alterations have occurred. Loss of heterozygosity (LOH) studies have demonstrated that alterations in microsatellite regions are common in bladder cancer. This observation offers the possibility of early tumor detection by examining the DNA of urinary sediment. METHODS: We investigated alterations of 17 microsatellite loci in urinary bladder carcinomas of different stages and grades. Per locus, 19-30 specimens were evaluated. DNA was isolated from tumor specimens, urinary sediment and peripheral blood lymphocytes. DNA fragments of 17 microsatellite loci were amplified by PCR and analyzed for genomic alterations. RESULTS: Microsatellite alterations were detected in tumor tissue and urine sediment from 27 out of 31 patients (87%). Urine sediment analysis alone proved positive in 24 out of 31 patients (77%). The type of lesions most frequently detected was LOH (74% of all alterations), followed by length alteration (24%) and additional alleles (2%). On average, the alteration frequency was 22% per locus. The loci at chromosomes 9 and 18 proved most informative. No alterations were found in grade I tumors. The study revealed a correlation between microsatellite alterations and the respective grades and stages of the tumors. Average alteration frequencies per locus were: 27.4% in grade III versus 19.3% in grade II tumors, 26.5% in invasive versus 12.3% in superficial tumors. CONCLUSIONS: Our results demonstrate that microsatellite alterations are common in bladder cancer and that analysis of genomic instabilities in urine samples should be further evaluated as a method for bladder cancer screening in a high-risk group. Especially, when a set of microsatellites is used that shows a high probability of detecting alterations and allows easy handling, this could be an alternative or a completion to currently available methods.

Carcinoma, Transitional Cell↗

PubMed2002

Regulation of freA, acoA, lysF, and cycA expression by iron availability in Aspergillus nidulans.

In the filamentous fungus Aspergillus nidulans, iron homeostasis is regulated at the transcriptional level by the negative-acting GATA factor SREA. In this study the expression of a putative heme-containing metalloreductase-encoding gene, freA, was found to be upregulated by iron limitation independently of SREA, demonstrating the existence of an iron-regulatory mechanism which does not involve SREA. In contrast to freA, various other genes encoding proteins in need of iron-containing cofactors-acoA, lysF, and cycA-were downregulated in response to iron depletion. Remarkably, SREA deficiency led to increased expression of acoA, lysF, and cycA under iron-replete growth conditions.

Amino Acid Sequence↗

PubMed2001

On-Line Liquid Chromatography Mass Spectrometry: A Useful Tool for the Detection of DNA Sequence Variation This work was financially supported by the Austrian Science Fund (P-14133-PHY) and the National Institutes of Health (HG01932). The suggestion of Dr. Jeff van Ness from the Keck Graduate Institute of Applied Life Sciences in Claremont, CA, USA, to utilize butyldimethylamine for IP-RP-HPLC separations is gratefully acknowledged.

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Journal Article↗