Optimized oligonucleotide probes for DNA fingerprinting

Sex chromosome polymorphism in guppies

Sex chromosomes differ from autosomes by dissimilar gene content and, at a more advanced stage of their evolution, also in structure and size. This is driven by the divergence of the Y or W from their counterparts, X and Z, due to reduced recombination and the resulting degeneration as well as the accumulation of sex-specific and sexually antagonistic genes. A paradigmatic example for Y-chromosome evolution is found in guppies. In these fishes, conflicting data exist for a morphological and molecular differentiation of sex chromosomes. Using molecular probes and the previously established linkage map, we performed a cytogenetic analysis of sex chromosomes. We show that the Y chromosome has a very large pseudoautosomal region, which is followed by a heterochromatin block (HCY) separating the subtelomeric male-specific region from the rest of the chromosome. Interestingly, the size of the HCY is highly variable between individuals from different population. The largest HCY was found in one population of Poecilia wingei, making the Y almost double the size of the X and the largest chromosome of the complement. Comparative analysis revealed that the Y chromosomes of different guppy species are homologous and share the same structure and organization. The observed size differences are explained by an expansion of the HCY, which is due to increased amounts of repetitive DNA. In one population, we observed also a polymorphism of the X chromosome. We suggest that sex chromosome-linked color patterns and other sexually selected genes are important for maintaining the observed structural polymorphism of sex chromosomes.

DNA fingerprinting in forensics: past, present, future

DNA fingerprinting, one of the great discoveries of the late 20th century, has revolutionized forensic investigations. This review briefly recapitulates 30 years of progress in forensic DNA analysis which helps to convict criminals, exonerate the wrongly accused, and identify victims of crime, disasters, and war. Current standard methods based on short tandem repeats (STRs) as well as lineage markers (Y chromosome, mitochondrial DNA) are covered and applications are illustrated by casework examples. Benefits and risks of expanding forensic DNA databases are discussed and we ask what the future holds for forensic DNA fingerprinting.

DNA fingerprinting in cattle using oligonucleotide probes

Oligonucleotide probes specific for simple tandem repeat sequences produce individual specific DNA fingerprints in man and all animal species tested so far. Here 11 different synthetic probes were hybridized to bovine genomic DNAs which had been digested with the restriction endonucleases HinfI, AluI and HaeIII. Two of these probes gave DNA fingerprint patterns which were analysed for three German breeds. Different parameters were calculated, such as the average number of bands per individual or the probability of finding identical fingerprints in two unrelated individuals. The number of polymorphic bands varies from 11 to 23 in the different breeds and the probability of finding the same banding pattern in two unrelated individuals ranges from 1.5 x 10(-7) to 2.4 x 10(-7). Hence this DNA fingerprinting procedure allows precise identification of individuals. It is also a useful additional method for paternity testing in cattle.

Analysis of systemic sclerosis in twins reveals low concordance for disease and high concordance for the presence of antinuclear antibodies

OBJECTIVE

To examine concordance for systemic sclerosis (SSc) in monozygotic (MZ) and dizygotic (DZ) twins.

METHODS

MZ and DZ twins were recruited nationwide. Zygosity was confirmed by DNA fingerprint analysis. The presence of antinuclear antibodies (ANAs) was determined using indirect immunofluorescence with HEp-2 cells as substrate. Identification of SSc-associated serum autoantibodies was performed by immunoprecipitation and double immunodiffusion. Major histocompatibility complex class II alleles were identified by polymerase chain reaction-restriction fragment length polymorphism analysis.

RESULTS

Concordance for SSc was found to be similar in MZ and DZ twins. Overall concordance for SSc was low in the twins (4.7%). Concordance for the presence of ANAs was significantly higher in MZ twins compared with DZ twins. SSc-associated serum autoantibodies occurred exclusively in patients with SSc. The distribution of SSc-associated serum autoantibodies was similar to that observed in our large database of SSc patients. Increased HLA allele sharing was detected in DZ twins, irrespective of disease concordance.

CONCLUSION

These results indicate that inherited genetic factors are not sufficient to explain the development of SSc. Rather, these data indicate that inheritance may play a role in the development of serum autoantibodies in the "healthy" twin sibling of an SSc patient.

A shared TCR CDR3 sequence in NOD mouse autoimmune diabetes

T cells involved in autoimmune diseases have been characterized by the genetic elements used to construct their autoimmune TCR. In the present study, we sequenced the alpha and beta chains of the TCR expressed by a CD4(+) T cell clone, C9, functional in NOD mouse diabetes. Clone C9 can adoptively transfer diabetes or, when attenuated, C9 can be used to vaccinate NOD mice against diabetes. Clone C9 recognizes a peptide epitope (p277) of the 60 kDa heat shock protein (hsp60) molecule. We now report that the C9 TCR beta chain features a CDR3 peptide sequence that is prevalent among NOD mice. This CDR3 element is detectable by 2 weeks of age in the thymus, and later in the spleen and in the autoimmune insulitis. Thus, a TCR CDR3beta sequence appears to be a common idiotope associated with mouse diabetes.

Preferential accumulation of single-stranded regions in telomeres of human fibroblasts

We have demonstrated recently that chronic hyperoxic treatment accelerates the rate of aging of fibroblasts and the rate of telomere shortening in parallel. It was hypothesized that accelerated telomere shortening is due to preferential accumulation of oxidative damage in telomeres. To test this hypothesis, we measured the accumulation of sites sensitive to S1 nuclease treatment in telomeres, in minisatellites, and in the bulk of the genome of fibroblasts under different models of oxidative stress as well as after treatment with the alkylating agent, N-methyl-N'-nitro-N-nitrosoguanidine. A comparison with qualitative data obtained by alkaline electrophoresis reveals that the sites transferred to double-strand breaks by treatment with low concentrations of S1 nuclease are, in fact, single-stranded regions in the DNA. These regions may resemble single-stranded overhangs, gaps, or conventional single-strand breaks. The frequency of single-stranded regions is significantly higher in telomeres than in minisatellites or in the bulk of the genome under all conditions tested. Those regions induced in minisatellites or in the overall genome by a bolus dose of hydrogen peroxide are completely repaired within 24 h. On the other hand, 50 +/- 12% of H2O2-induced single-stranded regions remain unrepaired for at least 19 days in telomeres of human fibroblasts, leading to a significant increase of the telomeric steady-state level of these lesions. This preferential accumulation might significantly contribute to telomere shortening.

Oligonucleotide DNA fingerprinting optimized to determine parentage in three beetle species

Oligonucleotide fingerprinting was performed on three beetle species from different families (Coleoptera: Staphylinidae: Aleochara curtula; Silphidae: Nicrophorus vespilloides; Tenebrionidae: Blaps lethifera) to obtain detailed information on parentage in mating systems. We report variations in the number of hybridizing fragments for the different species depending on the combinations of probes and restriction enzymes used. In addition to conventional multilocus fingerprint patterns, we established a single locus system for A. curtula (GTG5; HinfI) and described an oligolocus system in N. vespilloides (GATA4; HaeIII).

A detailed linkage map of rainbow trout produced using doubled haploids

We report the first detailed genetic linkage map of rainbow trout (Oncorhynchus mykiss). The segregation analysis was performed using 76 doubled haploid rainbow trout produced by androgenesis from a hybrid between the "OSU" and "Arlee" androgenetically derived homozygous lines. Four hundred and seventy-six markers segregated into 31 major linkage groups and 11 small groups (< 5 markers/group). The minimum genome size is estimated to be 2627.5 cM in length. The sex-determining locus segregated to a distal position on one of the linkage groups. We analyzed the chromosomal distribution of three classes of markers: (1) amplified fragment length polymorphisms, (2) variable number of tandem repeats, and (3) markers obtained using probes homologous to the 5' or 3' end of salmonid-specific small interspersed nuclear elements. Many of the first class of markers were clustered in regions that appear to correspond to centromeres. The second class of markers were more telomeric in distribution, and the third class were intermediate. Tetrasomic inheritance, apparently related to the tetraploid ancestry of salmonid fishes, was detected at one simple sequence repeat locus and suggested by the presence of one extremely large linkage group that appeared to consist of two smaller groups linked at their tips. The double haploid rainbow trout lines and linkage map present a foundation for further genomic studies.

A paternity case with apparently conflicting multilocus and single-locus DNA typing results

A paternity case is presented in which DNA typing with thirteen variable number of tandem repeat (VNTR) systems was in apparent conflict with an initial multilocus DNA analysis using oligonucleotide probe (CAC)5. A dual approach was necessary, because the multilocus analysis yielded a proportion of aberrant nonmaternal offspring bands far too small and level of band-sharing too high for non-paternity. The case could finally be solved by reference to the joint likelihood ratio combining both approaches. Arguments are presented that summation of log likelihoods is indeed valid even if no information is available regarding linkage between the VNTR loci and the loci contributing to a multilocus DNA fingerprint.

A simple and effective chemiluminescent DNA fingerprinting technique using digoxigenin-labelled minisatellite probes

DNA fingerprinting has become a powerful tool in behaviourial and evolutionary ecology. However, investigators have been limited in their access to this technique because of the need for special radioisotope facilities. We present an alternative, non-isotopic DNA fingerprinting technique based on chemiluminescent detection of digoxigenin-labelled minisatellite probes. This methodology should provide a greater number of researchers with access to DNA fingerprinting without the need for special laboratory facilities.

Arthrogryposis multiplex congenita in a monozygotic twin. An intrauterine lesion?

Arthrogryposis multiplex congenita is a specific, well-defined congenital deformity which primarily affects muscles of limbs resulting in secondary joint deformities. The aetiology is still uncertain. One of monozygotic twin brothers with classical arthrogryposis multiplex congenita is presented, proving that this specific condition is not genetically transmitted.

On sex determination in the Turkish desert woodlouse Hemilepistus elongatus (Crustacea, Isopoda, Oniscidea): searching for sex chromosomes and for sex-specific differences in simple DNA repeats

The karyotype of male and female Hemilepistus elongatus was investigated by means of C-banding. The diploid chromosome number in both sexes is 2n = 50. By scrutinizing general morphology and localization of the constitutive heterochromatin, no heteromorphic sex chromosomes were found. All chromosome pairs in males are well paired during diakinesis. Hybridization of genomic DNA with (GACA)4 and (GATA)4 oligonucleotides revealed no sex-specific patterns. Key words : karyotype, C-banding, sex determination, simple DNA-repeats, Isopoda.

Genomic instability in colorectal carcinomas: comparison of different evaluation methods and their biological significance

In order to demonstrate the relationship between microsatellite instability and other types of genomic instability, a series of 56 sporadic colorectal carcinomas was investigated by flow cytometrical ploidy analysis, oligonucleotide fingerprinting, and microsatellite polymerase chain reaction (PCR). Stabilization of the p53 gene product was analysed by immunohistochemistry and proliferative activity was determined flow cytometrically and by silver staining of nucleolar organizer regions (AgNORs). Of the 56 carcinomas, 11 (19 per cent) exhibited microsatellite instability; 33 of the cases were aneuploid (59 per cent) and 29 (52 per cent) showed alterations of the oligonucleotide fingerprints. There was a significant correlation of microsatellite instability with localization of these tumours proximal to the splenic flexure, diploid DNA content, and less frequent p53 stabilization. A solid growth pattern, mucinous differentiation, and a Crohn's-like lymphoid infiltrate were also characteristic for those tumours. The results demonstrate for the first time a significantly lower proliferative activity in tumours with microsatellite instability. Data obtained from DNA flow cytometry or from oligonucleotide fingerprinting did not correlate with such tumour characteristics. It is proposed that the use of microsatellite PCR facilitates specifically the detection of a group of colorectal cancers which may differ in pathogenesis and perhaps prognosis.

SINE sequences detect DNA fingerprints in salmonid fishes

DNA probes homologous to two previously described salmonid short interspersed nuclear elements (SINEs) detected DNA fingerprint patterns in 14 species of salmonid fishes. The probes showed more homology to some species than to others and little homology to three nonsalmonid fishes. The DNA fingerprint patterns derived from the SINE probes are individual-specific and inherited in a Mendelian manner. Probes derived from different regions of the same SINE detect only partially overlapping banding patterns, reflecting a more complex SINE structure than has been previously reported. Like the human Alu sequence, the SINEs found in salmonids could provide useful genetic markers and primer sites for PCR-based techniques. These elements may be more desirable for some applications than traditional DNA fingerprinting probes that detect tandemly repeated arrays.

DNA fingerprinting detects genetic variability in the pearl millet downy mildew pathogen (Sclerospora graminicola)

Genetic variability in six host genotype-specific pathotypes of pearl millet downy mildew pathogen S. graminicola was studied at the molecular level using mini- and micro-satellites. Our results indicated that microsatellites (GAA)6, (GACA)4, and especially (GATA)4 were quite informative and showed high levels of polymorphism among the pathotypes. The six pathotypes could be classified into five groups based on the cluster analysis of their genetic similarities, thereby confirming the existence of distinct host genotype-specific virulence in S. graminicola pathotypes. We demonstrate, for the first time, the use of DNA fingerprinting to detect genetic variation in downy mildew fungus of pearl millet.

Oligonucleotide (CAC)5 fingerprinting: validity and reliability in paternity testing

Following the development of DNA fingerprinting (Jeffreys et al., Nature 1985, 314, 67-73) using the minisatellite probes 33.15 and 33.6, many other fingerprinting probes have been described. The wide type M13 phage, 3' HVR region of alpha globin gene, F10 and various synthetic oligonucleotide probes have been shown to produce multiallelic and individual specific DNA fingerprints. The two probes developed by Jeffreys et al. have been extensively used in forensic and paternity determination in various laboratories, however, for the use of DNA fingerprints produced by synthetic oligonucleotide probes, still need critical evaluation. In this paper the statistical evaluations of the fingerprinting probes (CAC)5 was carried out by comparing the results produced by Jeffreys et al., using probes 33.15 and 33.6. The mutation rate calculated for (CAC)5 as 0.015 is nearly similar to the probe 33.15 (0.011) but higher than the probe 33.6 (0.005). The data obtained using (CAC)5 fingerprint in paternity cases from the northeast of England are presented.

DNA fingerprinting of Brassica juncea cultivars using microsatellite probes

The genetic variability in the Brassica juncea cultivars was detected by employing in-gel hybridization of restricted DNA to simple repetitive sequences such as (GATA)4, (GACA)4 and (CAC)5. The most informative probe/enzyme combination was (GATA)4/EcoRI, yielding highly polymorphic fingerprint patterns for the B. juncea cultivars. This technique was found to be dependable for establishing the variety specific patterns for most of the cultivars studied, a prerequisite for germplasm preservation. The results of the present study were compared with those reported in our earlier study in which random amplification of polymorphic DNA (RAPD) was used for assessing the genetic variability in the B. juncea cultivars.

Parallel genome analysis by one- and two-dimensional DNA fingerprinting in human gliomas

The detection of DNA variation in cancers is an important step in elucidating the mechanism of tumorigenesis. Using the strategy of multipoint genome analysis we detected many differences between glioma-derived and constitutional DNA by customary DNA fingerprinting with simple repetitive oligonucleotide probes. Amplification of the epidermal growth factor receptor (EGFR) gene has been found to be easily detectable as new or highly intensified bands in one-dimensional (1-D) DNA fingerprints of glioblastoma DNA generated with probes (GTG)5 or (GT)8. However, in most low-grade astrocytomas, 1-D DNA fingerprinting has failed to reveal any genomic abnormalities. In these cases a two-dimensional (2-D) technique was successfully employed that is based on size separation in neutral gels followed by sequence-dependent separation in denaturing gradient gels and hybridization with several mini- and microsatellite core probes. The hundreds of spots visualized with this technique were used to detect subtle changes probably occurring as the initial steps of tumorigenesis in human gliomas. On average, five of the approximately 580 spots generated by probes CAC and 33.6 were found to be altered in tumor DNA; 80% of the alterations were spot losses, the rest being spot gains or amplifications. Computer-based image analysis using an external lambda marker provided a stringent way to compare spot patterns generated by 2-D DNA fingerprinting. In comparisons performed between typing patterns generated on the same gel, 99% of truly identical spots were confirmed by the software. In intergel comparisons 84% of identical spots were matched on the basis of the marker information alone.

Genetic self-management in a captive colony of mandrills (Mandrillus sphinx) as revealed by DNA minisatellite fingerprints

DNA fingerprints using three oligonucleotide probes, a (GTG)5 short tandem repeat sequence, and 2 corresponding to the core sequences of minisatellites 33.15 and 33.6, have been used to generate DNA fingerprints of a captive colony of mandrills (Mandrillus sphinx) housed at the Centre International de Recherches Médicales de Franceville (CIRMF), in order to monitor paternity. A colony of 6 males and 7 females was established in a 6 ha. rain-forested enclosure in 1983. Band sharing scores indicated that none of the founders were related. By April 1994 the colony had increased to 84 individuals. Forty-nine of the 77 births were first-generation infants, a further 27 were second-generation offspring, and one was a third-generation mandrill. Five animals died during the study, and one was removed for husbandry reasons. Overall band sharing between individuals increased markedly and the power to discriminate between first- and second-generation infants was reduced; the probability of two individuals sharing the same pattern increased 1000-fold from 10(-6) to 10(-3). The dominant male in the group effectively guards access to all receptive females during the annual breeding season. Paternity analysis confirmed that the dominant male is the father of the great majority of offspring born during this term of dominance. Daughters born before 1991 to either of the two dominant males reached sexual maturity during this tenure. Incestual inbreeding occurred with both males, but only 25% of all possible cases resulted in the birth of a viable infant; one male fathered infants on 3 of 13 possible occasions and a second male on 2 of 7 occasions. Female avoidance strategies and shifts in male dominance in this closed mandrill colony appeared to be timed in a way that reduces incest.

The bovine interleukin-4 gene: genomic organization, localization, and evolution

Interleukin-4 (IL4) is involved in the immune response to certain parasites and possibly in the development of some atopic diseases since it triggers the T helper 2 lymphocyte response. Therefore, IL4 is a candidate gene, for example, for disease association studies and gene mapping. We isolated bovine IL4 cosmids and determined the genomic organization. Fragments carrying the exons as well as 725 base pairs (bp) from the 5' flanking and 190 bp from the 3' flanking region were cloned and sequenced. The first 481 base pairs of the 5' flanking region, including the putative promoter sequences, are surprisingly similar (92%) between cattle and human. In addition, we cloned and sequenced a mixed [(t/g)a]m(ca)n repeat located approximately 35 kilobases upstream from the IL4 gene. It showed seven repeat length alleles in a limited number of animals. The IL4 gene has been assigned to 7q15-q21 by fluorescence in situ hybridization in cattle. Evolutionary aspects are discussed on the basis of sequence data as well as interspecies chromosomal homologies.

The use of genomic DNA probes for in-gel hybridization

Hybridization within agarose gels using oligonucleotide probes has been described in several publications; genomic DNA probes, however, have been used rarely and only with limited success. Here we present a simple and convenient procedure for in-gel hybridization using radiolabeled genomic DNA fragments. The protocol was improved by the use of formamide in the hybridization as well as in the washing step. This method was compared with the conventional Southern blotting technique and was shown to produce good results in restriction pattern analysis, as well as in chromosomal localization with the help of pulsed field gel electrophoresis.

Multilocus DNA fingerprints in seven species of salmonids

DNA fingerprinting is a molecular biological technique that is widely used for identifying parentage and relatedness in plants and animals. To identify new DNA fingerprinting probes for use with salmonids, Southern blots of genomic DNA from chinook salmon (Oncorhynchus tshawytscha) were hybridized at low stringencies with 12 different oligonucleotides designed from published core sequences of variable number of tendem repeats. Seven of the 12 oligonucleotides produced highly variable fingerprint-like patterns; however, only 3 of these had clear, distinct bands. The estimated heterozygosity for one population of chinook salmon using the three oligonucleotides as probes ranged from 0.64 to 0.77. Those three oligonucleotides were further hybridized with DNA from two unrelated individuals from six other species of salmonids. A single-locus DNA fingerprint probe originally developed for chinook salmon was also hybridized with DNA from the other six species at moderate stringency. There were differences in the complexity and signal strength of the resulting banding pattern between species for a given probe. Estimates of variability (heterozygosity and band sharing) for the three oligonucleotide probes and OtSL1 were high, indicating that the probes were potentially useful genetic markers. The availability of these additional DNA fingerprint probes should assist in ecological and evolutionary studies in salmonids, as well as in efforts to estimate genetic diversity of populations.

DNA fingerprint analysis in acute leukemias

Restriction fragment length polymorphism (RFLP) analysis by Southern blotting or direct in-gel hybridization is a routine procedure in any genetic laboratory. Minisatellites and simple repeat probes for RFLP analysis have proved to be highly informative genetic markers, depending on their degree of homology and index of heterozygosity. Several of these probes have considerable individualization potential, thus yielding 'fingerprint' pattern. In the setting of acute leukemia DNA fingerprint (DNA-F) analysis is able to provide considerable information concerning the genetic instability of the leukemic clone. DNA-F is capable of detecting randomly occurring genetic alterations of unknown localization and to identify new hotspots of malignant transformation. As DNA-F analysis is not likely to be hampered by the effects of chemotherapy or DNA methylation, altered fingerprints may be regarded as characteristic of the leukemic clone. With the introduction of polymerase chain reaction (PCR) and increasing sensitivity, DNA-F analysis is likely to be of significant importance in monitoring minimal residual disease in human leukemia.

Randomly amplified polymorphic DNA fingerprinting identifies subgroups of Trichoderma viride and other Trichoderma sp. capable of chestnut blight biocontrol

Eleven strains of Trichoderma viride, 2 strains of the putative teleomorph Hypocrea rufa and 9 of several other Trichoderma sp. were characterized by random polymorphic DNA amplification (RAPD) fingerprinting and screened for their ability to antagonize growth of European strains of the chestnut blight causing fungus Cryphonectria parasitica, using a dual-culture assay. The best strains were found in the species T. harzianum, T. parceramosum, a distinguishable subgroup of T. viride and a not named Trichoderma sp. The successful application of these strains against chestnut blight in vivo is demonstrated.

Autosomal sex reversal and campomelic dysplasia are caused by mutations in and around the SRY-related gene SOX9

A human autosomal XY sex reversal locus, SRA1, associated with the skeletal malformation syndrome campomelic dysplasia (CMPD1), has been placed at distal 17q. The SOX9 gene, a positional candidate from the chromosomal location and expression pattern reported for mouse Sox9, was isolated and characterized. SOX9 encodes a putative transcription factor structurally related to the testis-determining factor SRY and is expressed in many adult tissues, and in fetal testis and skeletal tissue. Inactivating mutations on one SOX9 allele identified in nontranslocation CMPD1-SRA1 cases point to haploinsufficiency for SOX9 as the cause for both campomelic dysplasia and autosomal XY sex reversal. The 17q breakpoints in three CMPD1 translocation cases map 50 kb or more from SOX9.

The incidence of mini- and micro-satellite repetitive DNA in the canine genome

We have estimated the incidence of microand mini-satellites in the dog genome. A genomic phage library from canine liver, with an average insert size of 16 kb, was screened to detect potentially polymorphic microand mini-satellite sequences, which may be useful for the development of markers of inherited diseases, for fingerprinting, or for population genetics. Synthetic oligonucleotide probes were used to search for microsatellite sequences, and minisatellites were investigated with eight heterologous VNTR probes. (CA)n.(GT)n sequences were by far the most frequent, with a calculated average distance between consecutive loci of 42 kb. The average distance between loci of tri- or tetra-nucleotide repeats was about 330 kb. Mean inter-locus distances were 320 kb for (GGC)n, 205 kb for (GTG)n, 563 kb for (AGG)n, 320 kb for (TCG)n, 233 kb for (TTA)n, 384 kb for (CCTA)n, 368 kb for (CTGT)n, 122 kb for (TTCC)n, 565 kb for (TCTA)n, and 229 kb for (TAGG)n. Cross-hybridization with eight human minisatellite probes was found at average distances of 1400 kb; only one did not hybridize at all. We conclude that the di-, tri and tetra-nucleotide short tandem repeats, as well as some minisatellite sequences, are potentially useful as genetic markers, for mapping of the canine genome, and also for paternity testing and the analysis of population characteristics.

Oligonucleotide fingerprinting detects genetic diversity among Ascochyta rabiei isolates from a single chickpea field in Tunisia

Fifty isolates of Ascochyta rabiei (Pass.) Labr. were hierarchically sampled from four well-separated locations of a single chickpea field in Beja (Tunisia), and single-spored. DNA was isolated from in-vitro-grown mycelia, digested with HinfI or RsaI, and hybridized to a set of synthetic oligonucleotides complementary to simple repetitive sequences. According to the fingerprint patterns derived from the probes (CA)8, (CAA)5, (CAT)5 and (GATA)4, 12 different fungal haplotypes were found at various frequencies within the investigated field. Seven haplotypes were confined to one location only, four occurred at two, one at three, and none at all four locations. Most of the genetic variability originated from diversity within, rather than between, locations. In some cases, more than one haplotype was isolated from the same lesion of a single host plant. Genetic distances between isolates, as calculated from band-sharing data, varied between 0.05 and 0.22. Relatedness between the different haplotypes was evaluated by cluster analysis using UPGMA.

Gene expression of the cardiac Na(+)-Ca2+ exchanger in end-stage human heart failure

The regulation of cytosolic Ca2+ concentration during excitation-contraction coupling is altered in the failing human heart. Previous studies have focused on disturbances in Ca2+ release and reuptake from the sarcoplasmic reticulum (SR), whereas functional studies of the cardiac Na(+)-Ca2+ exchanger, another important determinant of myocyte homeostasis, are lacking for the failing human heart. Using a cardiac Na(+)-Ca2+ exchanger cDNA recently cloned from a guinea pig cDNA library, we investigated the gene expression of the cardiac Na(+)-Ca2+ exchanger in relation to the SR Ca(2+)-ATPase. Expression of both genes was quantified in left ventricular myocardium from 24 failing human cardiac explants and 7 control heart samples in relation to beta-myosin heavy chain mRNA by slot blot analysis. Compared with patients with nonfailing hearts, patients with dilated cardiomyopathy (DCM, n = 13) showed a 55% increase in Na(+)-Ca2+ exchanger mRNA levels (P < .05 versus control value) and a 41% increase in patients with coronary artery disease (CAD, n = 11). In the same hearts, SR Ca(2+)-ATPase mRNA levels were decreased by 50% in DCM and by 45% in CAD (P < .05 for both versus control value). There was a positive correlation between Na(+)-Ca2+ exchanger and SR Ca(2+)-ATPase mRNA levels both in normal and failing human hearts, albeit with different slopes and intercepts of the regression line. The Na(+)-Ca2+ exchanger protein levels as assessed by Western blot analysis and normalized to beta-myosin heavy chain protein were increased in DCM and CAD (P < .05 and P < .01 versus control value, respectively), whereas SR Ca(2+)-ATPase protein levels were reduced (P < .05 for both groups versus control values). Thus, the Na(+)-Ca2+ exchanger gene expression is enhanced in failing human hearts and may, in part, compensate for the depressed SR function with regard to diastolic Ca2+ removal.

Increased angiotensin-I converting enzyme gene expression in the failing human heart. Quantification by competitive RNA polymerase chain reaction

Local activation of the components of the renin angiotensin system in the heart is regarded as an important modulator of cardiac phenotype and function; however, little is known about their presence, regulation, and potential activation in the human heart. To investigate the gene expression of major angiotensin-II-forming enzymes in left ventricles of normal (n = 9) and failing human hearts (n = 20), we established a competitive RNA-polymerase chain reaction (PCR) for mRNA quantification of angiotensin-I converting enzyme (ACE) and human heart chymase. For each gene, competitor RNA targets with small internal deletions were used as internal standards to quantify the original number of transcripts and to control reverse transcription and PCR. In PCR, each target and the corresponding competitor were amplified by competing for the same primer oligonucleotides. The variability of ACE RNA-PCR was 11% indicating a high reproducibility of this method. In addition, ACE mRNA levels obtained by competitive RNA-PCR correlated favorably with traditional slot blot hybridization (r = 0.69, n = 10; P < 0.05). Compared with nonfailing hearts, the number of ACE transcripts referred to 100 ng of total RNA was increased threefold in patients with chronic heart failure (4.2 +/- 2.5 vs. 12.8 +/- 6 x 10(5); P < 0.0005). In contrast, no significant difference was found in chymase gene expression between normal and failing hearts. Thus, the expression of the cardiac ACE but not of human heart chymase is upregulated in failing human heart indicating an activation of the cardiac renin-angiotensin system in patients with advanced heart failure.

A multilocus DNA fingerprint with built-in security devices

An unusual case of paternity testing is reported in which determination of paternity was an essential part of a genetic diagnosis. A Y-chromosomal abnormality, observed in a 33-year-old male whose wife had experienced a series of spontaneous abortions, was not found in his alleged father. DNA fingerprinting with the oligonucleotide multilocus probe (CAC)5 yielded two aberrant bands for the proband, i.e. bands exhibited by neither parent. This finding resulted in a comparatively low paternity probability of 0.02934 which is suggestive of, but does not unequivocally prove, false paternity. Subsequent analysis with other multi- and single-locus systems, however, failed to confirm this preliminary result. The paternity probability computed on the basis of the single-locus systems was 0.99997, providing compelling evidence in favour of true paternity. The present case thus demonstrates that even when two mutations turn up in a DNA fingerprint, these may be readily recognized as such.

DNA fingerprinting in rice using oligonucleotide probes specific for simple repetitive DNA sequences

In this report we describe the use of five oligonucleotide probes, namely (GATA)4, (GACA)4, (GGAT)4, (GAA)6 and (CAC)5, to reveal highly polymorphic DNA regions in rice. With each of the oligonucleotide probes, the level of polymorphism was high enough to distinguish several rice genotypes. Moreover, individual plants of one cultivar showed the same cultivar-specific DNA fingerprint. The multilocus fingerprint patterns were somatically stable. Our study demonstrates that microsatellite-derived DNA fingerprints are ideally suited for the identification of rice genotypes. As the majority of the probes detected a high level of polymorphism, they can be very useful in monitoring and aiding gene introgression from wild rice into cultivars.

Multilocus DNA fingerprinting: the independence problem in quantitative paternity testing

A simulation study was performed in order to determine whether or not the assumption of independence, made in the quantitative analysis of multilocus DNA fingerprints, represents an inadmissible over-simplification. A total of 10,000 cases of true and false paternity, respectively, were simulated in twenty replicas of various genetic models. Log-likelihood ratios (paternity vs. non-paternity; LR) were calculated using published likelihood formulae and assuming position-wise independence. The resulting LR distributions were compared to (i) the results of a classical analysis of the underlying genotype data, and (ii) the distributions expected from the likelihood model employed in the LR calculations. Although considerable discrepancies were observed between these distributions, decision making about paternity appeared to be only marginally affected, especially when only a fraction of each multilocus DNA fingerprint was analyzed.

(CAC)5 detects DNA fingerprints and sequences homologous to gene transcripts in rice

In the present report the potential of (CAC)5 is demonstrated for DNA fingerprinting in rice. Based on the fingerprint data, (CAC)5 was estimated to differentiate up to 6.3 x 10(8) genotypes of rice. In a search for homologous sequences in rice transcripts, four oligonucleotide probes, namely, (CAC)5, (GATA)4, (GACA)4, and (TG)10, were used. Among these probes, (CAC)5 showed hybridization to total rice RNA in a tissue-specific manner; while a band at 1.2 kb was common in both seed and leaf RNA, there were additional prominent bands at 1.9 and 2.3 kb in seed and leaf RNA, respectively. When (CAC)5 was hybridized to poly(A)+ RNA, in addition to a band at 1.2 kb in seed and leaf, hybridization was observed only in seed to heterogeneously sized RNAs.

Multiple hepatocellular carcinomas at the early stage have different clonality

BACKGROUND

The clonality of hepatocellular carcinoma is still controversial. To evaluate the clonality of this cancer, mostly small multiple hepatocellular carcinomas of 18 patients were analyzed by DNA fingerprinting.

METHODS

DNA from the liver tissues was digested with HinfI. After gel electrophoresis, in gel-hybridization with a synthetic oligonucleotide probe GTGGTGGTGGTGGTG was performed. The band patterns were compared among the tumors and the nontumor part. In patients positive for hepatitis B surface antigen (HBsAg), the integration pattern of hepatitis B viral DNA in liver tissues was also analyzed.

RESULTS

Seven of the 9 HBsAg-positive patients had tumors with different clonalities by both methods. In the remaining 9 HBsAg-negative patients, 4 had different band patterns in their tumors by DNA fingerprinting.

CONCLUSIONS

Multiple hepatocellular carcinomas frequently have different clonalities; this finding reiterates the importance of eliminating the underlying cause and the contributing factors of hepatocarcinogenesis.

The Pearson product-moment correlation coefficient is better suited for identification of DNA fingerprint profiles than band matching algorithms

A database of DNA fingerprint profiles from permanently established human and animal cell lines was prepared with a computer program originally designed for numerical taxonomy of bacteria. Identifications of cell line DNA profiles were performed, both by the Pearson product-moment correlation coefficient and by band matching. Under the conditions used the Pearson product-moment correlation coefficient was consistently more reliable.

Paternity testing with oligonucleotide multilocus probe (CAC)5/(GTG)5: a multicenter study

The statistical analysis is reported of 256 paternity cases referred to seven different German laboratories for multilocus DNA fingerprinting with oligonucleotide probe (CAC)5/(GTG)5 and restriction enzyme HinfI. All parameters characteristic of multilocus DNA fingerprints were found to differ significantly between the contributing centres: the number of analyzed gel positions, the number of bands scored per individual, the probability of occurrence of a band at a particular position, and the band-sharing probabilities between the mother and both child and alleged father. Despite these differences, paternity cases could be divided clearly into two distinct subgroups on the basis of (i) offspring bands that could not be assigned to either the mother or the alleged father and (ii) the extent of band-sharing between child and alleged father. This partitioning, which is likely to correspond to true and false paternity, confirms previous findings for other multilocus probes. A goodness-of-fit test on the normalized number of bands scored per individual revealed no systematic deviations from commonly adopted analytical models regarding electrophoretic bands as independent entities. Log10-likelihood ratios of paternity vs. non-paternity were calculated utilizing one of these models, and a clear-cut partitioning was again obtained which coincides with that mentioned before. Only one case could not be decided unambiguously, and was either due to two independent mutations or to a close relative of the alleged father being the true father.

Inverted and satellited Y chromosome in the orangutan (Pongo pygmaeus)

An inverted and satellited Y chromosome of almost acrocentric appearance was detected in seven of 14 male orangutans. In the remaining seven animals a submetacentric Y chromosome without NORs occurred. The high frequency with which the satellited Y chromosomes were associated with acrocentric autosomes and the positive AgNO3-staining of their satellite stalks clearly indicate the active state of the NOR on the Y chromosomes. DNA fingerprinting in two orangutan families showed that the inverted and satellited Y chromosomes in carrier orangutan males do not interfere with normal fertility. Within our sample of male orangutans studied, the inverted and satellited Y chromosome is restricted to Sumatran animals; all Bornean specimens possessed the submetacentric Y chromosome. The question arises whether these two kinds of Y chromosome differ constitutively between the Pongo pygmaeus subpopulations.

Primitive sex chromosomes in poeciliid fishes harbor simple repetitive DNA sequences

The demonstration of the chromosomal mode of sex determination via genetic experiments as well as the absence of heteromorphic sex chromosomes affirm poeciliid fishes as a unique group among vertebrates that are endowed with the most primitive form of sex chromosomes. In many different taxa the evolutionary process involved in the differentiation of advanced sex chromosomes is outlined through sex specifically organized repetitive sequences. In this investigation hybridization of synthetic probes specific to genomic simple repeat motifs uncovers a sex-specific hybridization pattern in certain viviparous fishes of the family Poeciliidae. The hybridization pattern together with specific staining of the constitutive heterochromatin by C-banding reveals heterogamety in males (Poecilia reticulata) as well as in females (P. sphenops). In P. velifera, however, C-banding alone fails to unravel the heterogametic status. The female specific W-chromosome can be detected by simple repetitive sequence probes. Therefore, the principal significance of heterochromatization as a means of generating differentiated sex chromosomes is evident.