On the potential of simple repetitive DNA for fingerprinting in clinical, forensic, and evolutionary dynamic studies

Chloride conductance and genetic background modulate the cystic fibrosis phenotype of Delta F508 homozygous twins and siblings

To investigate the impact of chloride (Cl(-)) permeability, mediated by residual activity of the cystic fibrosis transmembrane conductance regulator (CFTR) or by other Cl(-) channels, on the manifestations of cystic fibrosis (CF), we determined Cl(-) transport properties of the respiratory and intestinal tracts in Delta F508 homozygous twins and siblings. In the majority of patients, cAMP and/or Ca(2+)-regulated Cl(-) conductance was detected in the airways and intestine. Our finding of cAMP-mediated Cl(-) conductance suggests that, in vivo, at least some Delta F508 CFTR can reach the plasma membrane and affect Cl(-) permeability. In respiratory tissue, the expression of basal CFTR-mediated Cl(-) conductance, demonstrated by 30% of Delta F508 homozygotes, was identified as a positive predictor of milder CF disease. In intestinal tissue, 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid-insensitive (DIDS-insensitive) Cl(-) secretion, which is indicative of functional CFTR channels, correlated with a milder phenotype, whereas DIDS-sensitive Cl(-) secretion was observed mainly in more severely affected patients. The more concordant Cl(-) secretory patterns within monozygous twins compared with dizygous pairs imply that genes other than CFTR significantly influence the manifestation of the basic defect.

Residual chloride secretion in intestinal tissue of deltaF508 homozygous twins and siblings with cystic fibrosis. The European CF Twin and Sibling Study Consortium

BACKGROUND & AIMS

Cholinergic stimulation of chloride secretion is impaired in the intestines of patients with cystic fibrosis (CF). However, intestinal chloride secretion has been observed in patients with mild CF mutations. The aim of this study was to investigate residual Cl(-) secretion in the intestine of DeltaF508 homozygous CF patients, and examine the contribution of cystic fibrosis transmembrane conductance regulator (CFTR) and alternative Cl(-) conductances. Twins and siblings with identical CFTR genotypes were investigated to determine the impact of factors other than CFTR on chloride secretion.

METHODS

Chloride secretion in rectal tissue was investigated by applying Ca(2+) and adenosine 3',5'-cyclic monophosphate (cAMP)-linked agonists before and after the inhibition of alternative Cl(-) conductances with 4,4'-diisothiocyanostilbene-2, 2'-disulfonic acid (DIDS).

RESULTS

cAMP-mediated Cl(-) secretion was observed in 73% of patients, and 20% showed DIDS-sensitive Ca(2+)-activated Cl(-) secretion. This DIDS-sensitive alternative chloride conductance was seen only in CF patients who also responded to cAMP agonists. Chloride secretion was more concordant within monozygous twins than within dizygous pairs.

CONCLUSIONS

These results suggest the presence of CFTR-mediated Cl(-) secretion in a subgroup of patients, implying that a portion of deltaF508 CFTR can be processed in vivo and function as a chloride channel in the apical membrane of intestinal cells. Moreover, a considerable number of deltaF508 homozygous patients express chloride conductances other than CFTR in their intestinal epithelia.

Five cases of forensic short tandem repeat DNA typing

In medicolegal samples DNA is often broken into fragments. In many cases, only the amplification of short tandem repeated DNA stretches (STRs), which are located in noncoding regions, allows DNA typing of such degraded materials. To demonstrate the high diversity of biological materials which forensic biologists have to deal with, and to outline the success rates and limits of the method, we describe five cases (minute amount of tissue on barrel, tissue in decay, tumor tissue, sperm after multiple rape, stored urine samples) in which forensic DNA typing was successfully performed by use of the short tandem repeats HUMDHFRP2, HUMD8S306, HUMCD4, HUMF13A1, HUMTH01, HUMVWA, and HUMFES.

A repetitive DNA sequence 5' to the human myelin basic protein gene may be linked to MS in Danes

The myelin basic protein (MBP) gene is a candidate locus for disease susceptibility in multiple sclerosis (MS). In the present study a part of the tetranucleotide (TGGA)n repeat polymorphism 5' to the MBP gene was examined in 90 Danish MS patients and 106 controls. Lymphocyte DNA was isolated and used in PCR assay. The PCR fragments produced were separated by agarose and acrylamide electrophoresis. Hereby we found three different bandpatterns i.e. a homozygote with a 450 bp fragment, a homozygote with a fragment 375 bp and a heterozygote with both bands present. The 450 bp fragment occurred significantly more often among MS than in the control group and the 375 bp fragment was underrepresented among MS than in the control group. The differences between incidence of the three band pattern in the MS and the control group were significant different at 1% level. Our study thus indicate that there is an association between MS and a length polymorphism of the 5' end to the MBP gene in Danish MS patients.

Direct hybridization and amplification applications for the diagnosis of infectious diseases

We are entering an exciting new era of molecular diagnostics in the clinical microbiology laboratory. A number of perspectives are presented in this review. First presented was a discussion of molecular diagnostics for detection of the bacterium, Chlamydia trachomatis. This is especially relevant since the tests available for this organism represent the forefront of commercial systems. Also, these tests exemplify the difficulties and advantages inherent to future molecular diagnostics for all types of disease processes. Next, a discussion of the techniques thus far employed in the field of clinical microbiology is presented. Obvious overlap exists with other areas of molecular pathology. However, the emphasis is on which techniques have proven most useful in identifying infectious agents. Finally, the features of a successful clinical microbiology diagnostics laboratory are presented, including test component requirements, laboratory personnel, quality assurance techniques, and physical laboratory setting. It is hoped that helpful advice and references are provided that will assist individual clinical laboratories as they enter the field of molecular diagnostics of infectious diseases.

Identification of the most represented repeated motifs in Arabidopsis thaliana microsatellite loci

The major simple sequence repeats present in the Arabidopsis genome were identified by Southern hybridizations with 49 oligonucleotide probes matching all the possible combinations of motifs up to 4 nucleotides long. The method used allowed us to perform all the hybridizations under the same temperature conditions. A good correlation was observed with the data obtained from database analysis, indicating that the method can be useful for identifying the major classes of microsatellite loci in species for which few or no sequence data are available. AG/CT, AAG/CTT, ATG/CAT and GTG/CAC are the major motifs present in the Arabidopsis genome that can be used as convenient probes to isolate microsatellite loci by screening libraries. AAG/CTT is the more frequent of these motifs, and its relative frequency in Arabidopsis is much higher than averagely found in the plant kingdom. About 8% of the cDNA clones from an immature silique library contains AG/CT, AAG/CTT or ATG/CAT microsatellite loci. Several microsatellite loci were isolated by screening genomic and cDNA libraries. Twenty-six tri-nucleotide loci were PCR amplified from four different ecotypes, and polymorphism was observed for 12 of them; 10 loci showing two alleles and 2 loci showing three alleles.

Simple repetitive DNA sequences from primates: compilation and analysis

Simple repeats composed of tandemly repeated units 1-6 nucleotides (nt) long have been extracted from a selected set of primate genomic DNA sequences. Of the 501 theoretically possible, different types of repeats only 67 were present in the analyzed database in at least two different size ranges over 12 nt. They include all simple repeats known to be polymorphic in the primate genome. A list of moderately expanding and nonexpanding oligonucleotide patterns has also been included. Furthermore, we have compiled statistical data with emphasis on the overall variability of the most abundant 67 types of repeats. We have demonstrated that the expandability of at least some simple repeats may be affected by the overall base composition and by flanking sequences. In particular, the occurrence of tandemly repeated CAG and GCC triplets in exons positively correlates with their G+C content. We also noted that in the vicinity of Alu sequences tetrameric repeats are more abundant than in the total genomic DNA. This paper can be used as a comprehensive guide in identification of the most abundant and potentially polymorphic simple repeats. It is also of broader significance as a step toward understanding the contribution of flanking sequences and the overall sequence composition to variability of simple repeats.