Mosaic Genotype Research Articles

Testing Introgressive Hybridization Hypotheses Using Statistical Network Analysis of Nuclear and Cytoplasmic Haplotypes in the Leaf Beetle Timarcha goettingensis Species Complex

Previous studies of leaf beetles (Chrysomelidae) in the Timarcha goettingensis species complex using mitochondrial (cox2) and nuclear (ITS-2 rRNA) markers revealed two main clades confined to the Iberian Peninsula and the rest of Europe but showing incongruent distributions indicative of gene exchange between both groups. Because of the anastomosing nature of hybridization, which disrupts the cladistic structure of character variation, phylogenetic trees might be inappropriate to represent and study this process. Here we test for evidence of hybridization in the T. goettingensis complex by analyzing the extra homoplasy arising in hybrid genomes from the simultaneous analysis of genetically independent markers. Haplotype networks obtained by Templeton's statistical parsimony analysis were generated for combined (concatenated) cox2 and ITS-2 sequences from 167 individuals of the T. goettingensis complex. Networks were used to detect runs of homoplasious characters physically clustered along a nucleotide sequence, as evidence for recombination between both gene partitions. A hypergeometric tail probability for the chance occurrence of physically clustered character changes on the connections linking networks of genotypes was applied. The test recognized two instances of statistically significant clustering, indicating the presence of cox2-ITS-2 mosaic genotypes and reticulation of both main T. goettingensis clades, supporting the reticulate origin of samples of T. maritima in southwestern France and T. sinuatocollis/T. monserratensis in the eastern Pyrenees. Although the assessment of reticulation in DNA sequences does not provide direct proof for hybridization, the geographical distribution of mosaic genotypes in the vicinity of "pure" genotypes supports the effect of gene flow between the two divergent lineages. The study demonstrates the utility of statistical parsimony networks for the detection of hybrids in the growing number of phylogeographic studies based on multiple gene markers.

Mottled coloration of haploid-diploid and diploid-triploid mosaic amago salmon Oncorhynchus masou ishikawae

Mottled amago salmon Oncorhynchus masou ishikawe with both yellow- and dark-pigmented skin occurred together with typical albino individuals in a commercial farm. Out of 12 mottled fish examined by DNA content flow-cytometry and erythrocytic nucleus size, three were diploid, eight were haploid-diploid mosaic and one was diploid-triploid mosaic. This fact indicates that the mottled coloration might link to polyploid mosaicism. Genotype of diploid and non-diploid cells at the albino locus was estimated in nine mature mottled fish by observing the frequency of wild-type and albino progeny when mating to homozygous albino (aa). One diploid and three haploid-diploid mosaic mottled fish were presumed to have mosaic genotype with both hemizygous ‘a’ and heterozygous ‘Aa’ cells (a/Aa), because the segregation ratio between two phenotypes was 1∶1. Three other haploid-diploid mosaic fish were presumed to have mosaic genotype with both hemizygous ‘a’ and homozygous ‘AA’ cells (a/AA), because of exclusive occurrence of wild-type phenotype in the progeny. The diploid-triploid mosaic mottled fish was presumed to have mosaic genotypes ‘aa/AAA’, ‘aa/AAa’ or ‘aa/Aaa’, because this fish yielded only albino progeny. One diploid mottled fish produced both two phenotypes but albino mebryos appeared with much more frequency than the expectation, when assuming the genotype ‘Aa’. Thus, this fish was considered to have mosaic genotype ‘Aa/aa’.

Mosaic Turner Syndrome and Hyperinsulinaemic Hypoglycaemia

A common and well recognised feature of Turner's syndrome (partial or total monosomy X) is impaired glucose tolerance or type 2 diabetes mellitus. A small percentage of patients with Turner's syndrome have a complex mosaic karyotype with atypical clinical features and mental retardation. METHODS/PATIENT: We report the first case of a child with a complex mosaic Turner genotype and hyperinsulinaemic hypoglycaemia responsive to diazoxide therapy. Cytogenetic analysis showed four cell lines: one with 45,X; the others with an additional small ring chromosome, a small marker chromosome, and both the ring and marker chromosomes, respectively. FISH studies showed the abnormal chromosomes to originate from an X. The X inactivation locus (XIST) was present in the ring, but not in the marker chromosome. The recognition of hypoglycaemia in children with atypical Turner's syndrome is important as persistent hypoglycaemia may lead to brain damage in addition to the risk of mental retardation. Further studies are required to understand whether the mosaic over--or underexpression of unidentified X chromosome gene(s) in the pancreatic beta-cells leads to hyperinsulinaemic hypoglycaemia.

The putative recombination of hepatitis B virus genotype B with pre-C/C region of genotype C.

Among hepatitis B virus (HBV) genotypes the B and C are most prevalent in China. To further study on the inside story of the intertypes, the genotype of 136 sequences from Chinese patients were analyzed either by restriction fragment length polymorphism on fragments or by phylogenetic analysis and bootscanning on full genome. The 22 complete sequences of genotype B clustered with different genotypes depending on gene fragments analyzed, which indicated that recombinant events occurred during HBV evolutionary history. To locate the recombinant regions, the sequences of HBV entire genome were analyzed by SimPlot program. The recombinant regions of B genotype with recombination were mapped in the pre-C/C region with relatively less varied size. Besides, three sequences of genotype C have recombination with genotype B or D in different regions. However, among all of the 136 sequences, none of authentic genotype B was identified. To investigate the possible mechanism responsible for intertype recombination, the selection pressure on the recombinant region was estimated by using CODEML program. All models allow for positively selected sites suggest existence of positive selection pressure. In conclusion, the genotype B with recombination was exclusive subgroup of genotype B in China. The mosaic genotype B might result from immune pressure on the pre-C/C gene.

Global identification of three major genotypes of varicella-zoster virus: longitudinal clustering and strategies for genotyping.

By analysis of a single, variable, and short DNA sequence of 447 bp located within open reading frame 22 (ORF22), we discriminated three major varicella-zoster virus (VZV) genotypes. VZV isolates from all six inhabited continents that showed nearly complete homology to ORF22 of the European reference strain Dumas were assigned to the European (E) genotype. All Japanese isolates, defined as the Japanese (J) genotype, were identical in the respective genomic region and proved the most divergent from the E strains, carrying four distinct variations. The remaining isolates carried a combination of E- and J-specific variations in the target sequence and thus were collectively termed the mosaic (M) genotype. Three hundred twenty-six isolates collected in 27 countries were genotyped. A distinctive longitudinal distribution of VZV genotypes supports this approach. Among 111 isolates collected from European patients, 96.4% were genotype E. Consistent with this observation, approximately 80% of the VZV strains from the United States were also genotype E. Similarly, genotype E viruses were dominant in the Asian part of Russia and in eastern Australia. M genotype viruses were strongly dominant in tropical regions of Africa, Indochina, and Central America, and they were common in western Australia. However, genotype M viruses were also identified as a minority in several countries worldwide. Two major intertypic variations of genotype M strains were identified, suggesting that the M genotype can be further differentiated into subgenotypes. These data highlight the direction for future VZV genotyping efforts. This approach provides the first simple genotyping method for VZV strains in clinical samples.

Prenatal diagnosis of fetal hydrops associated with Down's syndrome in a 40-year-old woman with a mosaic Turner's karyotype (45,X/47,XXX)

Prenatal diagnosis of fetal hydrops associated with Down's syndrome in a 40-year-old woman with a mosaic Turner's karyotype (45,X/47,XXX)

Molecular relationships of Helicobacter pylori strains in a family with gastroduodenal disease

Objective: Few studies have examined the genetic relationships of Helicobacter pylori strains affecting family members. Our aim was to do so. Methods: We characterized H. pylori isolates obtained from members of a single family presenting with various gastroduodenal diseases to examine H. pylori bacterial genetic similarity. Endoscopic evaluation with gastric mapping was performed on each individual to establish clinical and histological disease. Genomic DNA extracted from each H. pylori isolate was used to generate DNA fingerprints for each strain by REP-PCR. vacA genotypes and cagA presence were established by PCR. Results: Gastrointestinal diseases among the five members of this family included gastric adenocarcinoma in a 52-yr-old man (index patient), gastric MALT-lymphoma in the 73-yr-old mother; intestinal metaplasia (IV) and atrophic gastritis in the 48-yr-old brother; intestinal metaplasia (I-III) in the 47-yr-old brother, and a duodenal ulcer scar in the 42-yr-old sister. REP-PCR DNA fingerprints of H. pylori isolates from the index patient, his mother, and both of his brothers were identical or highly similar. By contrast, the H. pylori DNA fingerprint from the sister was markedly different from the H. pylori DNA fingerprints from the other family members. All isolates had the genotype cagA-positive and vacA slb/ml mosaic genotype. Conclusions: The DNA fingerprints of H. pylori strains obtained from members of this family with malignancy or premalignant histological disease were identical or highly similar and markedly different from the H. pylori DNA fingerprint from the sibling with duodenal ulcer disease. All H. pylori isolates within the family possessed genetic markers of enhanced virulence (presence of the cagA gene and vacA sl/ml mosaicism). In addition to host genetics and environmental factors, these findings suggest that infection with genetically similar H. pylori strains is a significant factor in determining the clinical outcome of an infection with H. pylori.

Molecular characterization of FRAXE-positive subjects with mental impairment in two unrelated Italian families

The FRAXE fragile site, 600 Kb distal to the more common FRAXA, has been reported to be expressed in subjects with mild nonsyndromal mental retardation. Amplification of more than 200 GCC repeats associated with methylation of the adjacent CpG island at Xq28 is responsible for FRAXE fragility. We describe two unrelated, mentally retarded males identified during a screening for fragile X syndrome. Both index cases underwent FRAXE molecular analysis, following cytogenetic expression of the fra X site and negative FRAXA test. In family 1, we were able to investigate other 13 subjects over three generations, identifying two additional FRAXE-positive males, one with a fully mutated allele and one with a mosaic genotype. Detailed evaluation of physical traits and psychometric tests was performed on three retarded males from family 1 and the propositus from family 2. All of them were found to lack a definite phenotype, and showed different degrees of mental retardation. Slight mental retardation was evident in the mosaic male, suggesting that methylation might be an important determinant of mental impairment.

Relationship between Reaction to Infection with Barley Yellow Mosaic Virus Strains and Genotypes for Esterase Isozymes in Two-rowed Barley(Hordeum distichum L.) Cultivars.

The authors evaluated the reaction of the major Japanese two-rowed barley cultivars to infection with strains I, II and III of barley yellow mosaic virus (BaYMV) (Table 1). Out of 50 cultivars tested, 44, 18 and 47 cultivars were susceptible to strain I, II and III respectively (Table 2). Although almost all of the two-rowed barley cultivars were susceptible to strains I and III, many cultivars were resistant to strain II. 44 cultivars susceptible to strain I could be classified into two groups, susceptible or resistant to strain II. The old cultivars, for instance Kirin Choku 1, Tochigi Golden Melon and Golden Melon Sai 1, were susceptible to strain II, while the introduced or recently improved cultivars, for instance Prior, Svanhals, Haruna Nijo and Amagi Nijo were mainly resistant to it. It could be considered that the resistance gene(s) to strain 11 was mainly incorporated into Japanese two-rowed barley cultivars from Prior, Plumage Archer and Sapporo 7, especially Prior played an important role in the transmission of this resistance gene(s) (Fig. 1).

Molecular studies of the fragile X syndrome.

We have studied families segregating for the fragile X syndrome for the presence of amplification of the CGG repeat sequence adjacent to the HpaII Tiny Fragment (HTF) island in the FMR-1 gene. We demonstrate that 138/143 fragile X positive, mentally retarded males show a characteristic smear of fragments corresponding to somatic variation in the amplification of the CGG sequence. In 7/8 normal transmitting males (NTM's), we show that there is a small amplification of sequence but no evidence for somatic variation. Defined mutated fragments in the size range found in NTM's are seen in daughters of NTM's. The daughters of these female carriers show either a defined fragment in the NTM size range, a defined larger fragment or a heterogeneous pattern of fragments. In the latter 2 cases the clinical phenotype of the females cannot easily be predicted, presumably because of variable X inactivation. In some families, the observed DNA genotype does not correlate with the phenotype; in others we demonstrate the occurrence of individuals with a mosaic DNA genotype. The implications of these data for diagnosis of the disease are discussed.

Random/nonrandom X-chromosome inactivation in <i>Nesokia indica: </i>possible influence of heterochromatin

Five types of X chromosomes with different amounts of heterochromatin have been observed in Nesokia indica, the Indian mole rat. They have been found in both mosaic and nonmosaic individuals. The influence, if any, of heterochromatin on the kinetics of X-chromosome DNA replication was evaluated in bone marrow cells and peripheral blood lymphocytes of Nesokia females with variant X chromosomes. In bone marrow cells of nonmosaic females a random X-chromosome inactivation (XCI) pattern was observed, except when there was a total loss of heterochromatin from the variant X chromosome, resulting in predominantly early replication. A nonrandom pattern was observed, however, in blood and bone marrow cells of all individuals with mosaic genotypes. In these females the X chromosome with the lesser amount of heterochromatin was predominantly the active one. The amount of heterochromatin per se or, more likely, specific sequences contained in the heterochromatic region seem to influence the XCI pattern in a cis-acting manner. The observations also seem to support a process of cell selection in individuals with variant X chromosomes.

Does heterochromatin variation potentiate speciation?

An increasing incidence of sex-chromosome variation in constitutive heterochromatin, including individuals with mosaic genotypes, has been observed in a single natural population of Nesokia indica, the Indian mole rat. Variations in the heterochromatic areas of the X chromosome are largely due to deletions at R-band-positive regions corresponding to folate-sensitive fragile sites. All individuals with either a pre- or post-zygotic loss or gain of sex-chromosome heterochromatin have so far proved to be infertile. Whether such F1 sterility is due to abnormal gonadal development, gametic incompetence, or other factors is not clear. More important is the indication that the constitutive heterochromatin of this species may contain coding DNA sequences with putative regulatory functions.

Disease expression in ±/± ↔ [formula omitted] mouse chimeras: Evidence for an extramuscular component in the pathogenesis of both dysgenic abnormal diaphragm innervation and skeletal muscle 16 S acetylcholinesterase deficiency

Homozygous mdg mdg mice die at birth and express a syndrome of abnormalities, the most striking of which is a gross failure of skeletal muscle development. Recently, additional abnormalities in the development of nerve-muscle relationships have been recognized; in particular, on muscle fibers within the diaphragm, motor end plates are inappropriately dispersed and, in all muscles, there is a paucity of the 16 S form of acetylcholinesterase (AChE). These abnormalities could result entirely as secondary consequences of the primary muscle defect or from expression of the mdg defect in additional cell types, e.g., motor neurons. To determine if the muscle genotype alone is responsible for these defects in dysgenic mice, chimeras composed of both dysgenic and normal cells have been investigated. Different glucosephosphate isomerase variants existed in the mdg mdg and normal cells comprising these chimeras and the mutant, normal, or mosaic genotypes of chimera diaphragm and skeletal muscle was estimated by measuring the relative proportions of each isozyme. In two chimeras, the diaphragm innervation pattern was revealed by AChE cytochemistry and in both, discrete regions of abnormally dispersed and normally restricted motor end-plate zones were observed. No correlation between these patterns of innervation and the assessed genotype of the muscle fibers existing in each area was observed. The relative 16 S AChE content in the limbs of four chimeras was found to range from 2.5 to 42.0%. Here also, no correlation between 16 S AChE content and the muscle genotype was observed. The results of these investigations are not consistent with a model of mdg mdg pathogenesis in which only the skeletal muscle is primarily affected; an extramuscular deficiency responsible for at least part of the full mdg mdg syndrome is therefore suggested.