Nonradioisotopic PCR heteroduplex analysis: a rapid, reliable method of detecting minor gene mutations

A geographically diverse set of isolates indicates two phylogenetic lineages withinStachybotrys chartarum

Stachybotrys chartarum is a black mitosporic fungus capable of dense colonization of cellulose-based building materials such as drywall. The presence of S. chartarum in indoor environments has been reported as linked to a variety of alleged environment-related illnesses including infant acute idiopathic pulmonary hemorrhage, although there continues to be insufficient (especially exposure) data to support such associations. We investigated genetic variation among 52 morphologically and geographically diverse, indoor and outdoor isolates of S. chartarum sensu lato using molecular markers based on β-tubulin, calmodulin, elongation factor-1 alpha, and trichodiene synthase genes, as well as the internal transcribed spacer region of nuclear ribosomal DNA. Gene genealogies proved concordant in dividing all isolates into two strongly supported clades. The majority of the variable sites separating these lineages were fixed within each of these clades, and there was no evidence of recombination between genotypes. The results of this study therefore provide strong support for the recognition of two phylogenetic species within S. chartarum sensu lato, and further demonstrate the limitations of morphological characters in delineating monophyletic taxa among morphologically simple fungi.Key words: Stachybotrys atra, cryptic speciation, calmodulin, elongation factor-1 alpha, trichodiene synthase.

Identification of two LDL receptor mutations causing familial hypercholesterolemia in Indian subjects

Familial hypercholesterolemia (FH) is a genetic disorder caused by numerous mutations in the low-density lipoprotein receptor (LDLR) gene. Mutational analyses of Indians in South Africa suggest the possibility of a high frequency of FH in India. This study aimed at identifying mutations in exons 3, 4, 9, and 14 of the LDLR gene among Indians and at eventually developing population-directed molecular-based screening assays. DNA samples from 25 hypercholesterolemic patients with clinical features of FH and 25 normal controls were analyzed for four known point mutations: W66G (exon 3), E207K (exon 4), E387K (exon 9), and P664L (exon 14), which are those most reported among Indian immigrants in South Africa. Subsequently, samples were screened for other mutations by modified heteroduplex analysis in these exons. Point mutations predicted to be common among Indians were absent in the samples analyzed. Heteroduplex analysis and sequencing revealed the presence of novel insertion mutations in two patients. Both mutations are single-nucleotide "G" insertions at position 242 in exon 3 and position 397 in exon 4. The observed mutations are predicted to cause a translational frameshift, encoding truncated LDLR proteins due to premature termination. The mutant proteins are likely to be degraded intracellularly and, therefore, are pathogenic.

Rapid characterization of mutations in amplified human hprt cDNA by polyacrylamide gel electrophoresis

Compiling hprt mutation spectra involves the isolation and analysis of numerous 6-thioguanine-resistant clones for identifying characteristic point mutations. Since cDNA amplificates are compulsory intermediates in most mutant classification protocols, we suggest their preliminary characterization by polyacrylamide gel electrophoresis for the rapid distinction of clonal and independent mutants and for streamlining mutant analysis procedures. Based on the human hprt cDNA sequence a strategy was developed for mapping missing exons by analytical digests with a small panel of restriction enzymes. In mutant classification schemes, polyacrylamide gel electrophoresis of AluI-digested cDNA amplificates increased the sensitivity for detecting RT-PCR products of reduced size, e.g., in the case of missing exon 5. Restriction analysis of cDNA amplificates from 109 independent mutant clones showed a significant increase of exon loss after NNK induction as compared to spontaneous or BaP-induced mutants. The determination of exon loss from cDNA amplificates, as carried out for 39 independent mutant PCR products, might direct towards the genomic target sequences carrying the point mutations, that caused the aberrant splicing, thus eliminating the need of laborious multiplex PCR comprising all exons. For single-strand conformation polymorphism (SSCP) analysis of five known point mutations, sub-amplificates comprising exons 7 and 8 of hprt cDNA were obtained. After a combined heat and alkali denaturation of the double-stranded PCR products, the samples were separated in pre-cast polyacrylamide gels under non-denaturing conditions. Five known nucleotide substitutions within the amplified region, including the C508T hot spot mutation, resulted in mobility shifts of single-strand bands relative to the wild type pattern.