Biomedical subjects

Doris Lechner

Publications and source records attributed to Doris Lechner.

5 recordsLinked to original sources

PubMed2004

High-Density SNP genotyping defines 17 distinct haplotypes of the TNF block in the Caucasian population: implications for haplotype tagging.

The region spanning the tumor necrosis factor (TNF) cluster in the human major histocompatibility complex (MHC) has been implicated in susceptibility to numerous immunopathological diseases, including type 1 diabetes mellitus and rheumatoid arthritis. However, strong linkage disequilibrium across the MHC has hampered the identification of the precise genes involved. In addition, the observation of "blocks" of DNA in the MHC within which recombination is very rare, limits the resolution that may be obtained by genotyping individual SNPs. Hence a greater understanding of the haplotypes of the block spanning the TNF cluster is necessary. To this end, we genotyped 32 human leukocyte antigen (HLA)-homozygous workshop cell lines and 300 healthy control samples for 19 coding and promoter region SNPs spanning 45 kb in the central MHC near the TNF genes. The workshop cell lines defined 11 SNP haplotypes that account for approximately 80% of the haplotypes observed in the 300 control individuals. Using the control individuals, we defined a further six haplotypes that account for an additional 10% of donors. We show that the 17 haplotypes of the "TNF block" can be identified using 15 SNPs.

Cell Line, Transformed↗

PubMed2004

The antimycobacterial components of hops (Humulus lupulus) and their dereplication.

Bioassay-guided fractionation of a hexane extract of strobile hops (Humulus lupulus) was undertaken to isolate and characterize the antimycobacterial constituents using the fast-growing mycobacterial species Mycobacterium fortuitum. Activity was associated with a low polarity fraction and 1H NMR spectra indicated the presence of a fatty acid mixture with unsaturated components. GC-MS of the derivatives indicated the presence of palmitic, stearic and oleic acids with small quantities of lignoceric, arachidic, behenic and linoleic acids. These compounds were assessed against M. fortuitum and all saturated fatty acids were inactive at concentrations greater than 256 microg/ml, whereas the unsaturated fats oleic and linoleic acids displayed minimum inhibitory concentrations of between 4 and 16 microg/ml against the fast-growing species tested. The widespread occurrence of these components could render screening for antimycobacterials from natural sources highly problematic without adequate dereplication. We propose that GC-MS of derivatised components of lipophilic extracts be a first step before any antimycobacterial bioassay-guided study, as this technique is the method of choice for dereplication of fatty acids.

Antitubercular Agents↗

PubMed2004

The anti-staphylococcal activity of Angelica dahurica (Bai Zhi).

Bioassay-guided fractionation of a hexane extract prepared from the roots of the Chinese drug Angelica dahurica (Bai Zhi) led to the isolation of the polyacetylenic natural product falcarindiol (1). The absolute stereochemistry of this compound was confirmed by careful 1H NMR analysis of its (R)- and (S)-Mosher ester derivatives as the 3(R), 8(S) isomer. Activity was tracked using a Mycobacterium fortuitum screening assay and the purified product was evaluated against multidrug-resistant and methicillin-resistant strains of Staphylococcus aureus (MRSA). The minimum inhibitory concentrations (MIC) of this metabolite ranged from 8 to 32 microg/ml highlighting the potential of the acetylene natural product class as antibiotic-lead compounds. These MIC values compare favourably with some of the newest agents in development for the treatment of MRSA infection and indicate that further evaluation of the antibiotic activity of acetylenes is warranted.

Angelica↗

PubMed2002

Molecular haplotyping at high throughput.

Reconstruction of haplotypes, or the allelic phase, of single nucleotide polymorphisms (SNPs) is a key component of studies aimed at the identification and dissection of genetic factors involved in complex genetic traits. In humans, this often involves investigation of SNPs in case/control or other cohorts in which the haplotypes can only be partially inferred from genotypes by statistical approaches with resulting loss of power. Moreover, alternative statistical methodologies can lead to different evaluations of the most probable haplotypes present, and different haplotype frequency estimates when data are ambiguous. Given the cost and complexity of SNP studies, a robust and easy-to-use molecular technique that allows haplotypes to be determined directly from individual DNA samples would have wide applicability. Here, we present a reliable, automated and high-throughput method for molecular haplotyping in 2 kb, and potentially longer, sequence segments that is based on the physical determination of the phase of SNP alleles on either of the individual paternal haploids. We demonstrate that molecular haplotyping with this technique is not more complicated than SNP genotyping when implemented by matrix-assisted laser desorption/ionisation mass spectrometry, and we also show that the method can be applied using other DNA variation detection platforms. Molecular haplotyping is illustrated on the well-described beta(2)-adrenergic receptor gene.

Alleles↗

PubMed2002

Large-scale genotyping by mass spectrometry: experience, advances and obstacles.

Single nucleotide polymorphism (SNP) genotyping has become a key technology for genetic studies. In recent years, matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry has emerged as a very powerful method for SNP genotyping. Here, we discuss our experience in implementing a high-throughput SNP genotyping facility based on MALDI, and the issues encountered in adapting this to large-scale genetic studies. Most of these issues are not specific to using MALDI approaches, and they will also serve as valuable pointers for establishing high-throughput genotyping with other methods.

Genetic Testing↗