The genetic dynamics of the rapid and recent colonization of Denmark by Arion lusitanicus (Mollusca, Pulmonata, Arionidae).

We describe the genetic dynamics of the recent establishment of the 'Iberian slug', Arion lusitanicus J. Mabille 1868, in Denmark and compare its population structure to two other members of the 'large Arion complex', Arion ater ater, native to Denmark, and Arion ater rufus, introduced into Denmark in the early 1900s. Assaying allozyme polymorphism at seven enzyme loci, we found that: (1) None of the three taxa reproduce primarily by self-fertilization. Differences among loci and colonies in the pattern of deviation from Hardy-Weinberg equilibrium are most consistent with isolate mixing and perhaps with low amounts of selfing. (2) For both A. lusitanicus and A. a. rufus, gene diversity is lower in Danish colonies than in southern German colonies, implying population bottlenecks in the establishment of Danish colonies. (3) Significant linkage disequilibrium values usually involve the same three loci, viz. PGI, MDH-1 and MDH-2, suggesting physical linkage among these loci. (4) For both A. a. rufus and A. lusitanicus, the overall gene frequencies from Denmark and southern Germany are homogeneous, while variation among colonies within these regions ranges from around 15 to 28% for the three taxa. This indicates strong, local population genetic subdivision but with little restriction to gene flow from possible source areas. The heterogeneity in measures of diversity and differentiation indicates that population structure for all three taxa is dominated by ongoing founder effects, local extinction/colonisation dynamics, and genetic drift processes.

Prospective comparison of PCR-based vs late mRNA-based preemptive antiviral therapy for HCMV infection in patients after allo-SCT.

Human CMV (HCMV)-directed preemptive therapy has helped to improve the outcome following allo-SCT. In this study, we evaluated the safety and efficacy of a late mRNA-based (NucliSens CMV pp67) anti-HCMV treatment strategy. A prospective randomized multicenter pilot trial was performed comparing PCR-based, with late mRNA-based preemptive HCMV-directed antiviral therapy in patients after allo-SCT. In all, 133 patients were randomized in three different centers at the time of transplant, 130 of whom are evaluable. Viral screening was performed weekly. Antiviral therapy was initiated at the second consecutive positive PCR result, or at the first detection of late mRNA. The therapy was stopped if clearance of HCMV DNA or late mRNA was demonstrated after 14 days of antiviral therapy. If HCMV infection persisted, antiviral therapy was continued in a reduced dose. The median duration of antiviral therapy during the first treatment episode was 28 days for PCR-, and 19 days for mRNA-screened patients (P<0.02). However, the overall duration of antiviral therapy, as well as the incidence of HCMV disease and the OS at day 100 after transplantation was comparable between the two study groups. We conclude that late mRNA-based anti-HCMV therapy may show comparable safety and efficacy with PCR-based therapy in patients after allo-SCT.

Avian Clock gene polymorphism: evidence for a latitudinal cline in allele frequencies.

In comparison with most animal behaviours, circadian rhythms have a well-characterized molecular genetic basis. Detailed studies of circadian clock genes in 'model' organisms provide a foundation for interpreting the functional and evolutionary significance of polymorphic circadian clock genes found within free-living animal populations. Here, we describe allelic variation in a region of the avian Clock orthologue which encodes a functionally significant polyglutamine repeat (ClkpolyQcds), within free-living populations of two passerine birds, the migratory bluethroat (Luscinia svecica) and the predominantly nonmigratory blue tit (Cyanistes caeruleus). Multiple ClkpolyQcds alleles were found within populations of both species (bluethroat: 12 populations, 7 alleles; blue tit: 14 populations, 9 alleles). Some populations of both species were differentiated at the ClkpolyQcds locus as measured by F(ST) and R(ST) values. Among the blue tit, but not bluethroat populations, we found evidence of latitudinal clines in (i) mean ClkpolyQcds repeat length, and (ii) the proportions of three ClkpolyQcds genotype groupings. Parallel analyses of microsatellite allele frequencies, which are considered to reflect selectively neutral processes, indicate that interpopulation allele frequency variation at the ClkpolyQcds and microsatellite loci does not reflect the same underlying demographic processes. The possibility that the observed interpopulation ClkpolyQcds allele frequency variation is, at least in part, maintained by selection for microevolutionary adaptation to photoperiodic parameters correlated with latitude warrants further study.

Maintenance of clonal diversity in Dipsa bifurcata (Fallén, 1810) (Diptera: Lonchopteridae). I. Fluctuating seasonal selection moulds long-term coexistence.

The deterministic maintenance of clonal diversity in thelytokous taxa can be seen as a model for understanding how environmental heterogeneity both can stabilize genetic diversity and can allow coexistence of competing species. We here analyze the temporal fluctuations in clonal diversity in the thelytokous Lonchopterid fly, Dipsa bifurcata (Fallén, 1810), at four localities in Sweden over an 8-year period. Estimated fitness values for clones are cyclical, synchronous among populations and correlated with seasonal changes in the environment. Differential winter viability and emergence from overwintering along with differential reproductive rate during the summer appear to be the selective mechanisms by which long-term clonal diversity is maintained. In a companion paper (Tomiuk et al, 2004), we present a model for the maintenance of clonal diversity through the mechanism of differential diapause among clones, utilizing fitness values estimated from the data presented here. In general, our results imply that fluctuating seasonal fitnesses can maintain stable genetic polymorphism within populations, as well as coexistence between closely related competitors, when coupled with differences in diapause phenology.

Maintenance of clonal diversity in Dipsa bifurcata (Fallén, 1810) (Diptera: Lonchopteridae). II. Diapause stabilizes clonal coexistence.

We analyze a selection model analogous to a one-locus, two-allele haploid system that can explain recurrent seasonal changes in diversity for communities with diapausing species or populations with diapausing clones. The model demonstrates the potential influence of differential diapause on the stability of species and clonal coexistence and, by extension, on the maintenance of genetic polymorphism in general. Using estimates of clonal fitness values from populations of the parthenogenetic spear-winged fly Dipsa bifurcata (Fallén, 1810) (Diptera: Lonchopteridae), the model explains the long-term stable oscillation of clonal frequencies exhibited by these populations. In general, clones or species that share the same spatial habitat can persist in stable coexistence if there are differences not only in their temporarily fluctuating fitness values but also in their dormancy patterns.

Simultaneous analysis of interleukin-10 gene microsatellites and single-nucleotide polymorphisms in parallel with tumour necrosis factor and interferon-gamma short tandem repeats by fluorescence-based polymerase chain reaction.

Different cytokine genotypes exist in the population, for example, as a result of selective pressure of infectious diseases. It may be that specific cytokine genotypes that are beneficial by creating a 'proinflammatory' phenotype predispose to severe inflammatory disease with worse clinical outcome. There is individual variation in the production of certain cytokines in relation to their genotypes. IL-10, IFN-gamma and TNF-alpha are key components in the regulation of immune responses and the balance of their expression levels is predictive in certain diseases. To describe cytokine genotypes, a one-tube PCR reaction was developed to analyse simultaneously DNA sequence variations of cytokine genes IL-10, IFN-gamma, and TNF. This multiplex PCR approach was used to provide genotypic data for two geographically independent donor groups from Germany and Gabon. Significant differences were obtained for the majority of sequence variations comparing both populations. However, the SNPs within the 5'-flanking region of the IL-10 gene at position -1087 and -6208 are comparable in their genic and genotypic behaviour. Comparing allelic and genotypic disequilibrium between pairs of loci revealed different association patterns for both populations according to the geographical polymorphism. This assay may improve immunogenetic studies in disease, characterized by disbalanced IL-10, IFN-gamma and TNF-alpha expression.

Genetic variations of the SLC7A9 gene: allele distribution of 13 polymorphic sites in German cystinuria patients and controls.

Cystinuria is a hereditary disorder of cystine and dibasic amino acid transport across the luminal membrane of renal tubules and intestine, resulting in recurrent nephrolithiasis. While mutations in the SLC3A1 gene cause type I cystinuria, patients with non-type I cystinuria carry mutations in the SLC7A9 gene. Both gene products form the renal amino acid transporter rBAT/b0,+AT affected in cystinuria. In the present study a total of 59 patients with different ethnic background were screened for sequence variations in SLC7A9, out of these 32 were of German origin. For determination of allele frequencies of detected polymorphisms, 58 healthy German controls were investigated. Molecular-genetic analysis was performed using single-strand conformation polymorphism analysis, restriction assays and sequencing. Allele frequencies were analyzed statistically for the detected polymorphisms. In addition to the 6 already known variants we identified 7 new polymorphisms. Statistical analyses showed a significantly different distribution of alleles between German patients and German controls in case of the polymorphisms c. 147C>T (exon 2), c.386C>T (exon 3), IVS3+22T>G, c.584C>T (exon 4), c.610T>C (exon 4), c.692C>T (exon 5), c.852C>A (exon 6) and c.872C>T (exon 6). In summary, our results show that cystinuria is a complex disease which is not only caused by mutations in SLC7A9 and SLC3A1, but also influenced by other modifying factors such as variants in SLC7A9.

Analysis of the genes SLC7A9 and SLC3A1 in unclassified cystinurics: mutation detection rates and association between variants in SLC7A9 and the disease.

Cystinuria is a common inherited disorder of defective renal reabsorption of cystine and dibasic amino acids. Recently, 2 responsible genes have been identified: mutations in the SLC3AI gene encoding the glycoprotein rBAT cause cystinuria type I, while variants in the SLC7A9 gene have been demonstrated in non-type I cystinuria; its gene product b(0)+AT is the light chain of the renal cystine transport system rBAT/b(0),+-AT. To estimate the role of both genes in the etiology of cystinuria, we searched for sequence alterations in SLC7A9 and SLC3AI: 30 unclassified cystinurics were investigated. In 50% of patients (15/30), point mutations in SLC3A1 were detected. Screening of the SLC7A9 gene revealed 10 mutations in 8 patients corresponding to a frequency of 27%. In addition to previously published mutations in the SLC7A9 gene, we detected 2 new mutations (F 140S, c747delG). An overall detection rate of 73% (22/30) in unclassified patients is delineated for mutations in both genes. In 33% (10/30), 2 mutations were detected, in 40% (12/30) 1 mutation. Furthermore, 5 new polymorphic sites were identified in SLC7A9. While the base pair variation in intron 9 is homogeneously distributed in patients and control individuals, the allelic and genotypic distributions of the polymorphisms in 3 exons of SLC7A9--exons 2, 5 and 6--and intron 3 differ significantly between both groups. Our results suggest that some haplotypes defined through the exons 2, 5 and 6 and intron 3 might be markers of a functional variant in the SLC7A9 gene. Evidently, since the mutation detection rates in the 2 so far known cystinuria genes never reach 100%, further genes and modulating factors should influence the phenotype in a subset of patients. However, the presented data show that testing for mutations in the 2 currently known cystinuria genes is already a meaningful approach to the molecular diagnostics of the disease.

Semiautomated and simultaneous analysis of the interleukin-10 gene microsatellites IL-10G and IL-10R by fluorescence-based polymerase chain reaction reveals significant differences in allele distributions between Caucasians (Germany) and Africans (Gabon).

Interleukin-10 (IL-10) is an important immunoregulatory cytokine influencing many aspects of the adaptive and inflammatory immune response. Two dinucleotide repeats have been identified in the 5'-UTR of IL-10 and shown to be useful genetic markers in several diseases. A simple, two-colour fluorescence assay was developed for determination of microsatellite fragment length by an automatic sequencer. Using this method polymorphisms at the IL-10G and IL-10R loci of the 5' flanking region of the IL-10 gene can be identified simultaneously. A unified standard nomenclature was applied to the known IL-10G and IL-10R microsatellites. The multiplex PCR approach was used to compare the allele frequencies in two independent donor groups from Germany (Caucasian), comprising 112 and 106 cases, respectively, and one group from Gabon (African) including 91 donors. Significant differences in the allele distribution were found. Both Caucasian populations tested showed no significant differences in their allele and genotype distribution. Whereas in Africans, allele IL-10G25 is rare at 3% compared to 21% in Caucasian, alleles IL-10G22 and G23 are more prevalent in Africans than in Caucasians (22% versus 10% and 26% versus 7%, respectively). Within the IL-10R locus, the allele R13 was observed at 88% in the African group compared to 69% in Caucasians. These data may help immunogenetic studies in diseases, where IL-10 is thought to be deregulated.

Case populations must match the respective disease model: Genotype diversity causes linkage disequilibrium mapping failure in monogenic disorders.

Traditional linkage analysis in large families is the most promising approach for mapping disease genes of monogenic heritable disorders when the number of informative meioses is sufficient. With rare diseases, however, the low availability of informative pedigrees poses a significant limitation. As an adjunct to family linkage methods, association studies based on the investigation of individual haplotypes from a number of unrelated patients (i.e. linkage disequilibrium analysis) have recently been employed in mapping hereditary disease loci. However, such haplotype analysis is hampered by a number of effects that influence statistical evaluation, e.g. i) population history and size, ii) allele and haplotype frequencies in the respective population(s), iii) heterogeneous mutation and natural selection processes, and iv) small sample sizes of patient groups. The purpose of the present study was to determine the utility and limitations of haplotype-based genetic mapping in estimating the location of the NYX gene, which has recently been identified as the causative gene for a rare inherited retinal disorder known as the complete type of X-linked congenital stationary night blindness (CSNB1). For this purpose we recapitulated haplotypes and tested for linkage disequilibrium in 20 unrelated male CSNB1 patients from three European populations and 44 healthy individuals. All subjects were genotyped for 17 polymorphic microsatellite loci covering the Xp11.4 region with an average marker density of approximately 0.29 cM. We found that a precise model to describe mutations at loci that erroneously break up linkage is highly required, and that the case population must match the respective disease model.

Complete form of X-linked congenital stationary night blindness: refined mapping and evidence of genetic homogeneity.

A number of distinct, partly non-overlapping genetic loci have been reported for the complete type of X-linked congenital stationary night blindness (CSNB1), suggesting genetic heterogeneity. In order to refine the localization of the CSNB1 gene and to demonstrate genetic homogeneity, linkage analysis was performed in two large CSNB1 families. Clinical features consistent with the diagnosis of CSNB1 were documented in five patients from a German seven-generation kindred by full ophthalmological examination including psychophysical and electroretinographical testing. Haplotype analysis in 30 members of the large German family was performed with 38 polymorphic markers predominantly covering the critical region. Linkage analyses defined a locus for CSNB1 with flanking markers DXS8042 and DXS228, refining the interval to 2.5 cM in Xp11.4. In addition, two-point linkage analysis was carried out using the MLINK computer program. In agreement with meiotic breakpoints, lod scores of 3.0 and greater were obtained for markers located to the proximal site of the former 5 cM CSNB consensus interval. A large Dutch CSNB1 family was re-evaluated with markers from the Xp11.4 region, and supports the CSNB1 minimal interval found in the German family. Together with previous results from three unrelated families from Sweden, Sardinia and Great Britain, our results provide evidence of genetic homogeneity in the disorder. Subsequent mutation analyses in CSNB1 patients revealed no pathogenic sequence alterations in DFFRX and CASK genes, but retain candidates for other diseases mapping to that region.

Screening for mutations in the promoter and the coding region of the IGFBP1 and IGFBP3 genes in Silver-Russell syndrome patients.

In the present study we sought to identify genetic variation in genes for insulin-like growth factor binding proteins 1 and 3 (IGFBP1, IGFBP3) in 7p12-13 which through alteration of protein function or level of expression might contribute to the manifestation of Silver-Russell syndrome. Genomic DNA samples from 49 Silver-Russell syndrome (SRS) patients and from unaffected controls were investigated by single-strand conformation analysis. Overlapping polymerase chain reaction fragments covered the whole coding sequences as well as the 5' untranslated region of the IGFBP1 and IGFBP3 genes. We detected 3 new polymorphisms in the transcribed sequence of IGFBP1, one amino acid polymorphism in exon 1 of IGFBP3 and four variants in its promotor region and in intron 1. They all occurred in similar frequencies in SRS patients and in controls. Thus, paternally inherited mutations in the promoter and coding regions of IGFBP1 and IGFBP3 genes play neither a major nor a minor role in the etiology of SRS. The newly detected polymorphisms in the coding region are powerful tools for analysis of imprinting status and for detection of possible changes in the imprinting patterns of the two genes.

Population differentiation through mutation and drift--a comparison of genetic identity measures.

Different genetic identity or distance measures are compared that consider allelic variation within and between populations. Particularily we analyse those suggested by Nei (IS, DS), Rogers (DR), Reynolds, Weir and Cockerham (D theta), Nei, Tajima and Tateno (DA), Tomiuk and Loeschcke (ITL, DTL) and Goldstein et al. ((delta mu)2). The simulations focus on the influence of non-equilibrium conditions on the stability of these measures. The degree of homozygosity of an ancestral population before it splits into two sister populations is most important for the stability of the different estimates of genetic identity. If populations are not close to their equilibrium homozygosity, a considerable bias can occur and, thereby, provide very misleading estimates of the time span since divergence. The ITL-measure based on estimates of ancestral alleles is more robust than other measures of genetic identity, especially for large population sizes and high mutation rates. For the infinite allele model, the analysis shows that more precise estimates of the frequency of ancestral alleles can greatly improve the reliability of the estimate of genetic identity in the case of ITL. For the stepwise mutation model, the TL-measure combines the attributes of the DA- and (delta mu)2-measures. The TL-measure is efficient for the construction of the correct tree topology of related populations as well as for the estimation of the branch length when protein or microsatellite data are analysed.

The evaluation of gonosomal mosaics: lymphocyte interphase nuclei analyzed by FISH.

The reliable evaluation of chromosomal mosaics is still considered to be difficult in clinical diagnosis if aberrant metaphases are only present at low frequencies. Classical cytogenetic findings cannot significantly exclude low mosaic levels, obviously, because of the relatively low number of analyzed metaphases. To study this problem, the number of gonosomes in lymphocyte interphase nuclei was determined by FISH (fluorescence in situ hybridization) application of two satellite DNA probes. DXZI and DYZI. The results obtained with this method from lymphocytes of clinically and cytogenetically inconspicuous persons showed a high degree of reliability. The DNA probe yielded correct signals in more than 95% of the analyzed nuclei. Additionally, patients were examined who showed cytogenetically confirmed numerical gonosome aberrations. These results were compared with those obtained from the control group of inconspicuous patients and discussed with respect to the evaluation of gonosomal mosaics.

A maximum-likelihood estimator of the genetic identity between polyploid species.

Based on a recently proposed method for estimating the genetic identity between polyploid species, maximum-likelihood estimators are given for the genetic identity between polyploid species, for the ancestral degree of homozygosity and their variances. As an example, the genetic identity, the ancestral degree of homozygosity and their variances were estimated from data sets of populations of two species, the weevil Polydrusus mollis and the salamander Ensatina complex. It was found that other indices of the genetic identity between species obviously underestimate genetic identity due to the pooling of differences caused by mutation and drift.