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PubMed1978

[The smallpox vaccination strain MVA: marker, genetic structure, experience gained with the parenteral vaccination and behavior in organisms with a debilitated defence mechanism (author's transl)].

The MVA virus is a lab virus ideally suited for vaccination of both man and animal which can be differentiated from the known Vaccinia strains by the use of numerous biological markers. Its reduced virulence for the chick embryo, for experimental animals and for man is a particularly characteristic feature. With the exception of chick embryo fibroblasts, the MVA virus grows in cell cultures only abortively. This applies particularly to cells of human origin in which the cytopathic effect and plaque formation are completely missing. The restriction analysis of the DNS of the MVA virus demonstrates that its genetic structure differs from that of the CVA basic virus and other orthopox viruses. In contrast to the WHO reference strain Elstree, the MVA virus has a genome shortened by about 9 per cent. The use of the MVA virus for human vaccination is particularly indicated in persons to be vaccinated for the first time and likely to entail a risk (on account of allergies etc.) because it brings about a state of revaccination without complications. The MVA virus can be administered in intracutaneous, subcutaneous or intramuscular injections. Innocuoursness and successful vaccination have been demonstrated in more than 120000 persons. While other Vaccinia strains, such as the Elstree virus, experience a drastic increase of virulence in the immunosuppressed organism (subjected to whole-body irradiation), the MVA virus cannot be activated not even in this situation.

Animals↗
PubMedDate not supplied

[Phage T4 partial diploidy obtained with the method of DNA interrupted injection. I. Analysis of the genetic structure and phage progeny reproduction process].

Phage T4 chromosome fragmentation is shown to take place when DNA injection is interrupted, a fragment length being strictly controlled by the interval from the moment of adsorbtion till the moment of an interruption. Populations of the bacteria cells infected by the phage T4 partial diploids are produced with the method of DNA interrupted injection. In the population a merodiploid involves some phage T4 amber mutant and a phage "wild" type chromosome fragment of the size controlled. To construct merodiploids the amber mutant in gene 43 and the mutant in gene 32 with the higher and the lower recombination frequency, accordingly, are used. Every merodiploid which is the heterozygote by one of these genes or which is the heterozygote by the late genes is determined to reproduce mixed phage progeny. Both the mean of the burst and the parent genotypes ratio in progeny either in the E. coli CR-63 cells or in the E. coli B depend on neither the heterozygote genetic structure nor the diploid region size. The results obtained conclude that phage genes express their function in the small fragments and the fragment recombination with the mutant partner whole chromosome follows their autonomous replication.

Chromosomes↗
PubMed1994

Genetic structures associated with spread of the type Ia trimethoprim-resistant dihydrofolate reductase gene amongst Escherichia coli strains isolated in the Nottingham area of the United Kingdom.

DNA probes for specific integrase genes were used to study 122 R plasmids encoding the predominant trimethoprim-insusceptible type Ia dihydrofolate reductase (DHFR) found in clinical isolates of Escherichia coli. The predominance of the type Ia DHFR was thought to result from the location of its gene on transposon Tn7, but of trimethoprim R plasmids carrying this gene that were collected between 1978 and 1983, between 1987 and 1988, and during 1992, only 49/60 (81.6%), 30/43 (69.8%) and 9/19 (47.4%) respectively hybridized with a probe for the Tn7 integrase gene. It has been suggested that novel genetic elements termed 'integrons' may play an important role in the dissemination of antibiotic resistance genes. Known integrons encode an integrase similar to that encoded by transposon Tn21, and 28 Tn7-negative plasmids (10/60 from 1978-83, 10/43 from 1987-8 and 8/19 from 1992) showed homology with a probe specific for the Tn21 integrase gene. Six plasmids were negative with both probes. It is concluded that Tn7 has played an important role in the dissemination of the gene encoding the type Ia DHFR amongst clinical isolates of E. coli in the Nottingham region of the UK, but that other genetic structures, some of which seem to have an integrase function similar to that of known integrons, may be playing an increasingly significant role.

Bacteriuria↗
PubMedDate not supplied

Founder effects and the genetic structure of Coulter pine.

Mean expected heterozygosity at 33 isozyme loci decreased with latitude from 0.193 near the southern extreme of Coulter pine's range to 0.107 at its northern extreme. This decrease was paralleled by a loss of alleles north of the Peninsular Ranges of southern California. Fifteen alleles dropped out along the roughly lineal range, at points coincident with large gaps in the species' distribution. The pattern may reflect a cascading series of founder events as Coulter pine invaded the Trans. verse Ranges and the South Coast Ranges from Pleistocene refugia. Alleles were not replaced following colonization, probably because migration, Nm, among populations is only 0.74-1.27, depending on estimator, the lowest values reported in any pines. Wright's (F(ST)) indicated that 16.5% of the total genic diversity is among populations. The fixation index, (F(IS)) of 0.072 indicated only a moderate excess of homozygotes. However, the northernmost outlier had significant excess homozygosity (F = 0.253). Hybridization may also play a role in the genetic structure of Coulter pine: 16 alleles were novel, or private, occurring only where Coulter pine was sympatric with Jeffrey pine, particularly at San Benito Mountain. Some of these novel alleles could be the result of introgression from Jeffrey pine, or possibly represent hybrizymes, products of intragenic recombination between genomes.

Alleles↗
PubMed1995

Evolution of ribosomal DNA (rDNA) genetic structure in colonial Californian populations of Avena barbata.

DNA samples from 980 plants of Avena barbata from 48 ecologically diverse sites in California and Oregon were assayed to determine their genotype for two duplicated loci governing rDNA variants. More than 40 different rDNA genotypes were observed among which 5 made up 96% of our sample in environmentally homogeneous sites; predominant genotypes were less frequent and recombinant genotypes were more frequent in environmentally heterogeneous sites. The spatial distribution of each predominant rDNA genotype was nearly an exact overlay on both macro- and microgeographical scales of a distinctive habitat and also of the distribution of an eight-locus morphological-allozyme variant genotype. In all, seven different habitat-genotype combinations (ecotypes) were distinguishable on the basis of their morphological-allozyme-rDNA genotypes. None of these seven genotypes has been found in ancestral Spanish populations; thus the above predominant multilocus genotypes (ecotypes) of the colonial populations evidently evolved subsequent to the recent introduction (within 150-200 generations) of A. barbata to California. The precise associations of specific alleles and genotypes of the morphological allozyme and rDNA loci with different specifiable habitats leads us to the conclusion that natural selection favoring particular multilocus combinations of alleles in different habitats was the main guiding force in shaping the internal genetic structure of local populations as well as the overall adaptive landscape of A. barbata over California and Oregon.

Avena↗
PubMed1993

Evolution of multilocus genetic structure in Avena hirtula and Avena barbata.

Avena barbata, an autotetraploid grass, is much more widely adapted than Avena hirtula, its diploid ancestor. We have determined the 14-locus genotype of 754 diploid and 4751 tetraploid plants from 10 and 50 Spanish sites, respectively. Allelic diversity is much greater in the tetraploid (52 alleles) than in the diploid (38 alleles): the extra alleles of the tetraploid were present in nonsegregating heteroallelic quadriplexes. Seven loci were monomorphic for the same allele (genotypically 11) in all populations of the diploid: five of these loci were also monomorphic for the same allele (genotypically 1111) in all populations of the tetraploid whereas two loci each formed a heteroallelic quadriplex (1122) that was monomorphic or predominant in the tetraploid. Seven of the 14 loci formed one or more highly successful homoallelic and/or heteroallelic quadriplexes in the tetraploid. We attribute much of the greater heterosis and wider adaptedness of the tetraploid to favorable within-locus interactions and interlocus (epistatic) interactions among alleles of the loci that form heteroallelic quadriplexes. It is difficult to account for the observed patterns in which genotypes are distributed ecogeographically except in terms of natural selection favoring particular alleles and genotypes in specific habitats. We conclude that natural selection was the predominant integrating force in shaping the specific genetic structure of different local populations as well as the adaptive landscape of both the diploid and tetraploid.

Alleles↗
PubMed2006

Field and microcosm experiments to evaluate the effects of agricultural Cu treatment on the density and genetic structure of microbial communities in two different soils.

The effects of Cu amendment on indigenous soil microorganisms were investigated in two soils, a calcareous silty clay (Ep) and a sandy soil (Au), by means of a 1-year field experiment and a two-month microcosm incubation. Cu was added as 'Bordeaux mixture' [CuSO(4), Ca(OH)(2)] at the standard rate used in viticulture (B1=16 kg Cu kg(-1) soil) and at a higher level of contamination (B3=48 kg Cu ha(-1) soil). More extractable Cu was observed in sandy soil (Au) than in silty soil (Ep). Furthermore, total Cu and Cu-EDTA declined with time in Au soil, whereas they remained stable in Ep soil. Quantitative modifications of the microflora were assessed by C-biomass measurements and qualitative modifications were assessed by the characterization of the genetic structure of bacterial and fungal communities from DNA directly extracted from the soil, using B- and F-ARISA (bacterial and fungal automated ribosomal intergenic spacer analysis). In the field study, no significant modifications were observed in C-biomass whereas microcosm incubation showed a decrease in B3 contamination only. ARISA fingerprinting showed slight but significant modifications of bacterial and fungal communities in field and microcosm incubation. These modifications were transient in all cases, suggesting a short-term effect of Cu stress. Microcosm experiments detected the microbial community modifications with greater precision in the short-term, while field experiments showed that the biological effects of Cu contamination may be overcome or hidden by pedo-climatic variations.

Anti-Infective Agents↗
PubMed2005

Genetic structure and chromosomal integration site of the cryptic prophage CP-1639 encoding Shiga toxin 1.

The sequence of 50 625 bp of chromosomal DNA derived from Shiga-toxin (Stx)-producing Escherichia coli (STEC) O111: H- strain 1639/77 was determined. This DNA fragment contains the cryptic Stx1-encoding prophage CP-1639 and its flanking chromosomal regions. The genome of CP-1639 basically resembles that of lambdoid phages in structure, but contains three IS629 elements, one of which disrupts the gene of a tail fibre component. The prophage genome lacks parts of the recombination region including integrase and excisionase genes. Moreover, a capsid protein gene is absent. CP-1639 is closely associated with an integrase gene of an ancient integrative element. This element consists of three ORFs of unknown origin and a truncated integrase gene homologous to intA of CP4-57. By PCR analysis and sequencing, it was shown that this integrative element is present in a number of non-O157 STEC serotypes and in non-STEC strains, where it is located at the 3'-end of the chromosomal ssrA gene. Whereas in most E. coli O111: H- strains, prophages are inserted in this site, E. coli O26 strains contain the integrative element not connected to a prophage. In E. coli O103 strains, the genetic structure of this region is variable. Comparison of DNA sequences of this particular site in E. coli O157: H7 strain EDL933, E. coli O111: H- strain 1639/77 and E. coli K-12 strain MG1655 showed that the ssrA gene is associated in all cases with the presence of foreign DNA. The results of this study have shown that the cryptic prophage CP-1639 is associated with an integrative element at a particular site in the E. coli chromosome that possesses high genetic variability.

Chromosome Mapping↗
PubMed1997

Population genetic structure of Ixodes pacificus (Acari:Ixodidae) using allozymes.

Genetic analysis of the population structure of the western blacklegged tick, Ixodes pacificus Cooley & Kohls, was conducted using allozymes. This vector tick transmits the Lyme disease spirochete, Borrelia burgdorferi Johnson, Schmid, Hyde, Steigerwalt & Brenner, in the far-western United States. It ranges from British Columbia to Baja California and disjunct populations are present in Oregon, Nevada, Utah, and Arizona. Host-seeking adult ticks were collected from vegetation across the range of the species and were partially fed on rabbits prior to analysis. Twelve putative loci were resolved using starch gel electrophoresis. One locus, glucose-6-phosphate isomerase, formed an apparent north/south latitudinal cline and showed significant geographic structure. None of the remaining loci exhibited much genetic differentiation. Estimates of gene flow were high relative to other arthropods. Isolation-by-distance analysis suggests a recent and rapid range expansion. We conclude that the overall lack of differentiation is due high rates of gene flow.

Alleles↗
PubMed1988

Genetic structure of the Saguenay, 1852-1911: evidence from migration and isonymy matrices.

The Saguenay is a region in northeastern Québec populated in the second half of the 19th century through migration from other parts of Québec. The present-day population of nearly 300,000 is the result of both immigration and high rates of intrinsic growth. This population has been of interest to geneticists because of the high incidence of certain hereditary diseases, notably spastic ataxia, tyrosinemia, agenesis of the corpus callosum, vitamin D-dependent rickets, and myotonic dystrophy. Parent-offspring migration and isonymy matrices were used to estimate random kinship using the Malécot model for six 10-year time periods from 1852-1911. Comparisons between two estimates of kinship--one from parent-offspring migration matrices (phi) and the other from isonymy (R)--and geographic distance were made using both product-moment and Mantel correlation. Comparisons of within- and between-subdivision kinship were made using nonparametric and Mantel correlation. Within-subdivision kinship from the phi matrix was also compared with kinship estimated from marriage dispensations for endogamous marriages. The estimates of random kinship from the parent-offspring matrices showed a good fit with geography. However, isonymy did not correlate well with geographic distance; and phi and R showed no correlation until the last two time periods, and the diagonal of phi did not correlate with the marriage dispensations. Examination of scatterplots of phi vs. R suggests that nonrandom migration during the process of settlement formation is responsible for the lack of correlation. While movement across space seems to be highly dependent on distance, nonrandom selection of migrants means that between-subdivision estimates of kinship based on migration are not congruent with those obtained by other methods. On the whole, genetic differentiation seems to have been low due to the high levels of movement between subdivisions and immigration. The weak dependence of genetic structure on geographic distances in the present population is demonstrated by mapping the geographic distribution of cases of three recessively inherited diseases.

Emigration and Immigration↗
PubMed1998

Genetic structure of five susceptibility gene regions for coronary artery disease: disequilibria within and among regions.

We analyzed two-locus disequilibria for 16 polymorphic loci of seven susceptibility genes for coronary artery disease located in five chromosomal regions distributed across four chromosomes. Included were the genes coding for apolipoprotein B (ApoB, chromosome 2, four marker loci), lipoprotein lipase (LPL, chromosome 8, three marker loci), apolipoproteins AI, CIII AIV (ApoAI-CIII-AIV, chromosome 11, three marker loci), apolipoprotein E (ApoE, chromosome 19, two marker loci), and the low density lipoprotein receptor (LDLR, chromosome 19, four marker loci). Our sample included 540 unrelated individuals from the Rochester, Minn. population. There were no statistically significant deviations of single-locus genotypes from Hardy-Weinberg equilibrium. The strongest associations within genes were for composite diallelic disequilibria; 17/19 were significant (13 at Pr <0.001, 1 at Pr <0.01, 3 at Pr <0.05). These observations suggest marker alleles within genes have a shared evolutionary history reflected by disequilibria that have not been dissipated by recombination. Disequilibrium was not generally concordant with the physical orderings of markers. Only two significant higher-order disequilibria were observed although 12 triallelic disequilibria were at maximum possible values. We observed 19 statistically significant disequilibria (Pr <0.05; 4 composite diallelic, 13 triallelic, and 2 quadriallelic) between 101 pairs of marker loci, where each locus in a pair was from a different unlinked region. These unexpected results are most likely explained by recent historical factors, including worldwide population expansion and amalgamation with continuous admixture, that influence the genetic structure (organization of alleles and non-alleles into genotypes) of a population. We conclude that disequilibria between loci from unlinked regions may be more extensive than is commonly assumed. Our findings also suggest that it is, on average, at least 15 times more likely to not detect significant disequilibrium among unlinked loci when it is really present than to make a false positive inference. Disequilibria between functional loci within or between regions will impact estimates of genetic variance associated with particular functional mutations within a susceptibility gene region.

Apolipoproteins↗
PubMed2002

Spawning times, reproductive compatibilities and genetic structuring in the Acropora aspera group: evidence for natural hybridization and semi-permeable species boundaries in corals.

Species boundaries among five sympatric coral species of the Indo-Pacific Acropora aspera group were examined by a combination of in vitro breeding trials, comparisons of spawning times and DNA sequence analysis of ribosomal DNA internal transcribed spacer (rDNA ITS) and 5.8S regions. The breeding trials showed that reproductive compatibility exists between at least some colonies of all the species pairs tested, suggesting a large potential for natural hybridization and introgression. The Acropora ITS regions exhibited extremely high levels of variability (up to approximately 62% for ITS1, approximately 11% for 5.8S and approximately 43% for ITS2), but most of the variation was shared among four of the five species, A. millepora, A. papillare, A. pulchra and A. spathulata, consistent with extensive introgression. Phylogenetic analyses did not resolve these four species as distinct clusters across a wide biogeographic region stretching from the southern Great Barrier Reef to Papua New Guinea. However, most colonies of the fifth species, A. aspera, constituted a distinct clade in phylogenetic analyses. This is consistent with our observations of a semi-permeable temporal barrier involving differences in spawning times between this and the other four species. Although the majority of colonies of all five species generally spawned within 90 min of each other, in two out of four years, gametes were absent prior to mass spawning episodes from at least some A. aspera colonies. Hence, our data suggest that transient reproductive barriers may be the result of year-to-year variation in the date of spawning and that this difference in spawning time contributes to the genetic structure detected among Acropora species in this group. Occasional leakage through the reproductive barrier was confirmed by the observation of A. aspera xA. pulchra F1 hybrids, identified based on additivity of ITS sequences.

Animals↗
PubMed2006

Genetic structure of sibling butterfly species affected by Wolbachia infection sweep: evolutionary and biogeographical implications.

It was recently recognized that in Japan, the common yellow butterfly, Eurema hecabe, consists of two sibling species, which have been unnamed yet and tentatively called yellow (Y) type and brown (B) type. We investigated the diversity of nuclear and mitochondrial genes in Japanese populations of Y type and B type of E. hecabe. The phylogeny based on nuclear genes agreed with the distinction between Y type and B type, which had been also supported by a wide array of biological data. However, the phylogeny based on mitochondrial genes did not reflect the distinction. PCR survey of Wolbachia revealed that B-type populations were all infected while Y-type populations contained both infected and uninfected individuals. A single genotype of Wolbachia, which was inferred to be a CI-inducing strain from their wsp gene sequence, was prevalent in these populations. Notably, the mitochondrial phylogeny was in perfect agreement with the pattern of Wolbachia infection, suggesting that the Wolbachia infection had affected the mitochondrial genetic structure of the host insects. Probably, the Wolbachia strain and the associated mitochondrial genomes have been occasionally introduced from B-type populations to Y-type populations through migration and subsequent interspecific hybridization, and CI-driven population sweep has been spreading the Wolbachia strain and the particular mitochondrial haplotypes, which originated from B-type populations, into Y-type populations. On the basis of these results together with the geological and biogeographical knowledge of the Japanese Archipelago, we proposed an evolutionary hypothesis on the invasion and spread of Wolbachia infection in B-type and Y-type of E. hecabe.

Animals↗
PubMed1986

Fine structure genetic analysis of a beta-globin promoter.

A novel procedure for saturation mutagenesis of cloned DNA was used to obtain more than 100 single base substitutions within the promoter of the mouse beta-major globin gene. The effects of these promoter substitutions on transcription were determined by transfecting the cloned mutant genes into HeLa cells on plasmids containing an SV40 transcription enhancer, and measuring the levels of correctly initiated beta-globin transcripts after 2 days. Mutations in three regions of the promoter resulted in a significant decrease in the level of transcription: (i) the CACCC box, located between -87 and -95, (ii) the CCAAT box, located between -72 and -77, and (iii) the TATA box, located between -26 and -30 relative to the start site of transcription. In contrast, two different mutations in nucleotides immediately upstream from the CCAAT box resulted in a 3- to 3.5-fold increase in transcription. With two minor exceptions, single base substitutions in all other regions of the promoter had no effect on transcription. These results precisely delineate the cis-acting sequences required for accurate and efficient initiation of beta-globin transcription, and they establish a general approach for the fine structure genetic analysis of eukaryotic regulatory sequences.

Animals↗
PubMed1985

Molecular basis of mutations at the waxy locus of maize: correlation with the fine structure genetic map.

More than 40 mutant alleles of the waxy (Wx) locus of maize are available for molecular analysis. Previous studies have examined the nature of phenotypically unstable Wx mutant alleles caused by insertion of the maize transposable activator (Ac) and dissociation (Ds) elements. In this study we have used Southern blot analysis to characterize the locus in 22 strains harboring wx alleles with stable mutant phenotypes. Of these mutations, 17 are of spontaneous origin, 4 were induced by gamma rays, and 1 was induced by ethyl methanesulfonate. Of these 22 alleles, we find that 13 have either insertions or deletions within the Wx transcription unit. The insertions range in size from 150 base pairs to 6.1 kilobases. For 4 of the 6 deletions identified, the two breakpoints are within the Wx gene. For 9 other alleles we can detect no obvious lesions within or around the transcription unit. Evidence is presented that the insertions and deletions result in the mutant phenotype and are not polymorphisms. This conclusion is based on two findings: (i) a survey of inbred lines revealed only a single instance of polymorphism within the transcription unit, whereas all of the lesions described alter the transcription unit; and (ii) there is an excellent correlation between the position of these lesions on the physical map and their relative position on a fine structure genetic map of the locus.

Alleles↗
PubMed1999

The genetic structure of enteric bacteria from Australian mammals.

A total of 246 isolates representing five species of the family Enterobacteriaceae, taken from a variety of Australian mammal species, were characterized using multi-locus enzyme electrophoresis. Genome diversity estimates varied significantly among species, with the Klebsiella pneumoniae sample exhibiting the lowest diversity and the Citrobacter freundii sample the highest. Multi-locus linkage disequilibrium estimates revealed that alleles were non-randomly associated in all five species samples, but the magnitude of the estimates differed significantly among species. Escherichia coli had the lowest linkage disequilibrium estimate and Klebisella oxytoca the largest. Molecular analyis of variance was used to determine the extent to which population structure explained the observed genetic variation in a species. Two population levels were defined: the taxonomic family of the host from which the isolate was collected and the geographical locality where the host was collected. The amount of explained variation varied from 0% for K. oxytoca to 22% for K. pneumoniae. Host locality explained a significant amount of the genetic variation in the C. freundii (12%), E. coli (5%), Hafnia alvei (17%) and K. pneumoniae (22%) samples. Host family explained a significant fraction of the variation in E. coli (6%) H. alvei (7%) and K. pneumoniae (20%). Estimates of effective population size for all five species, based on the probability that two randomly chosen isolates will be identical, failed to reveal any relationship between the effective population size and the genetic diversity of a species.

Alleles↗
PubMed1995

Genetic Structure of Acetobacter diazotrophicus Populations and Identification of a New Genetically Distant Group.

A total of 55 isolates of Acetobacter diazotrophicus recovered from diverse sucrose-rich host plants and from mealybugs associated with sugarcane plants were characterized by the electrophoretic mobilities of 12 metabolic enzymes. We identified seven different electrophoretic types (ETs), six of which are closely related within a genetic distance of 0.195 and exhibit high DNA-DNA homology. The seventh ET was largely divergent, separated at a genetic distance of 0.53, and had only 54% DNA homology to the reference strain. Strains corresponding to ET 7 could represent a distinct nitrogen-fixing species of the genus Acetobacter. More genetic diversity was found in isolates from Brazil than in those from Mexico, probably due to the very different crop nitrogen fertilization levels used.

Journal Article↗