Genetic latent structure models: implication for research on schizophrenia.
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Diseases in Twins↗
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Structural and genetic organization of IS232, a new insertion sequence of Bacillus thuringiensis.
In the Bacillus thuringiensis strains toxic for the lepidopteran larvae, the delta-endotoxin genes cryIA are frequently found within a composite transposonlike structure flanked by two inverted repeat sequences. We report that these elements are true insertion sequences and designate them IS232. IS232 is a 2,184-bp element and is delimited by two imperfect inverted repeats (28 of 37 bp are identical). Two adjacent open reading frames, overlapping for three codons, span almost the entire sequence of IS232. The potential encoded polypeptides of 50 and 30-kDa are homologous to the IstA and IstB proteins of the gram-negative insertion sequence IS21. The N-terminal part of the 50-kDa polypeptide contains a helix-turn-helix DNA-binding motif. The junctions at the insertion sites of three IS232 elements were analyzed. Each case was different, with 0, 4, or 6 bp of the target DNA being duplicated. Transposition of IS232 in Escherichia coli was demonstrated by using a genetic marker inserted upstream of the two open reading frames.
Amino Acid Sequence↗
Hereditary 'white nails': a genetic and structural study.
BACKGROUND: Hereditary subtotal leuconychia is a rare nail disease. The gene(s) underlying this phenotype is (are) not known. Immunohistochemical and ultrastructural studies of nails are performed infrequently. OBJECTIVES: To perform genetic linkage analysis and to assess ultrastructure and soft/hard keratin expression in hereditary white nails. METHODS: We have analysed microscopically and ultrastructurally the white nails of a patient from a family in which the trait is inherited in an autosomal dominant manner as an isolated symptom. No skin lesions or hair abnormalities could be detected. Genetic linkage studies were performed on DNA samples obtained from several members of the affected family. A longitudinal surgical biopsy of the nail from a great toe was split in two parts. One part was fixed in formalin and processed for histopathology. Another part was further subdivided and embedded either in Epon, following fixation in 2% glutaraldehyde, or in Lowicryl K4M, after fixation in 3% paraformaldehyde. Dewaxed nail sections and Lowicryl ultrathin sections were also stained with various antikeratin antibodies. RESULTS: Genetic linkage studies of the family pointed to the disease gene mapping to the chromosomal 12q13 region. Genes mapping within this chromosomal region include the genes coding for type II (basic) cytokeratins and hard keratins. The nail matrix presented an abnormal hypergranulosis. The upper part of the nail plate, originating from the proximal nail matrix, had a nonhomogeneous lamellar appearance, with numerous intracellular 'lipidic' vacuoles and 'empty' spaces separating keratin filament bundles. These cells were progressively shed at the nail surface. The cell loss was compensated by hyperproliferation of the distal matrix and of the nail bed keratinocytes, with persistent marked parakeratosis and loose arrangement of keratin bundles. The distal matrix and the nail bed contributed equally to formation of the lower plate. This presented the characteristics of a tissue composed of soft keratins. Accordingly, there was virtually no labelling with the Hb1 antibody to a basic hard keratin in the white nail, whereas the labelling with AE3 antibody to all type II keratins and with KL1 recognizing suprabasal soft keratins was normal or even enhanced. CONCLUSIONS: Genetic linkage indicates that the gene defect underlying the leuconychia in the family studied resides on chromosome 12q13. As the type II keratins map within this chromosomal interval, it is possible that a mutation in one of these keratin genes may be a cause of the hereditary leuconychia. The white appearance of nails in this disease seems to be due to an abnormal keratinization of cells originating from the proximal nail matrix, leading to the presence of abundant intracellular vacuoles and to a lesser compactness of keratins.
Chromosome Mapping↗
Genetic fine structure of the pyrE region containing the genes for ribosomal proteins L28 and L33 in Escherichia coli.
Temperature-sensitive mutants harbouring alterations in ribosomal proteins L28 and L33 have been isolated and used in mapping the genes coding for the two proteins. It was found that they mapped very close to each other and near pyrE at 80.7 min on the E. coli genetic map. The genes affected by the mutations have been concluded to be the structural genes for proteins L28 (rpmB) and L33 (rpmG) by constructing merodiploids heterozygous for pyrE and for the two ribosomal proteins. Various transduction studies with P1kc phages indicate the gene order in this region to be (rpmB, rpmG)-pyrE-spoT-gltC.
Bacterial Proteins↗
Habitat barriers limit gene flow and illuminate historical events in a wide-ranging carnivore, the American puma.
We examined the effects of habitat discontinuities on gene flow among puma (Puma concolor) populations across the southwestern USA. Using 16 microsatellite loci, we genotyped 540 pumas sampled throughout the states of Utah, Colorado, Arizona, and New Mexico, where a high degree of habitat heterogeneity provides for a wide range of connective habitat configurations between subpopulations. We investigated genetic structuring using complementary individual- and population-based analyses, the latter employing a novel technique to geographically cluster individuals without introducing investigator bias. The analyses revealed genetic structuring at two distinct scales. First, strikingly strong differentiation between northern and southern regions within the study area suggests little migration between them. Second, within each region, gene flow appears to be strongly limited by distance, particularly in the presence of habitat barriers such as open desert and grasslands. Northern pumas showed both reduced genetic diversity and greater divergence from a hypothetical ancestral population based on Bayesian clustering analyses, possibly reflecting a post-Pleistocene range expansion. Bayesian clustering results were sensitive to sampling density, which may complicate inference of numbers of populations when using this method. The results presented here build on those of previous studies, and begin to complete a picture of how different habitat types facilitate or impede gene flow among puma populations.
Animals↗
Multilocus sequence typing as an approach for population analysis of Medicago-nodulating rhizobia.
Multilocus sequence typing (MLST), a sequence-based method to characterize bacterial genomes, was used to examine the genetic structure in a large collection of Medicago-nodulating rhizobial strains. This is the first study where MLST has been applied in conjunction with eBURST analysis to determine the population genetic structure of nonpathogenic bacteria recovered from the soil environment. Sequence variation was determined in 10 chromosomal loci of 231 strains that predominantly originated from southwest Asia. Genetic diversity for each locus ranged from 0.351 to 0.819, and the strains examined were allocated to 91 different allelic profiles or sequence types (STs). The genus Medicago is nodulated by at least two groups of rhizobia with divergent chromosomes that have been classified as Sinorhizobium meliloti and Sinorhizobium medicae. Evidence was obtained that the degree of genetic exchange among the chromosomes across these groups is limited. The symbiosis with Medicago polymorpha of nine strains placed in one of these groups, previously identified as S. medicae, ranged from ineffective to fully effective, indicating that there was no strong relationship between symbiotic phenotype and chromosomal genotype.
Alleles↗
An analysis of selection on a colour polymorphism in the northern leopard frog.
In this study, we investigated the role of selection in the maintenance of a dorsal colour polymorphism in natural populations of the northern leopard frog, Rana pipiens. We determined genetic structure both spatially and temporally from a suite of putatively neutral molecular markers and tested whether or not the colour locus exhibited patterns of genetic variation that differed from those of the neutral loci. Spatial genetic structure at the colour locus was indistinguishable from structure at neutral loci [95% confidence intervals of F(ST) (neutral) = (0.07, 0.35), F(ST) (colour locus) = 0.114]. In the temporal analysis, we found that the variance among populations in the change in allele frequency at the colour locus (equal to 0.004) lies within the 95% confidence intervals for the variance among populations in changes in allele frequencies at neutral loci. In light of our inability to show evidence for the selective maintenance of the colour polymorphism, we used computer simulations to infer the power of our spatial and temporal techniques to detect selection. The computer simulations showed that although the strength of selection (s) would need to be relatively strong to have been detected by the temporal approach (s = 0.1-0.4, depending on the model tested), the spatial analysis would have detected all but weak selection (s = 0.01-0.04, depending on the model tested). This study illustrates the importance of using a locus comparison approach to detect evidence for selective maintenance before conducting studies to measure the selective mechanisms maintaining a polymorphism.
Alleles↗
Susceptibility to lung tuberculosis--a population-genetic study.
The aim of this study was to compare the genetic structure of lung tuberculosis (LTB) patients (Pts) to healthy controls i.e. to evaluate dependency of LTB occurrence and course of the disease in regard to subject's genetic constitution. The study group consisted of 100 LTB Pts, while the same number of healthy non-sibling individuals served as controls. The groups were analyzed with respect to homozygous recessive characteristics (HRC) that served as genetic markers, which were studied in each subject. Twenty-three HRCs were chosen according to HRC-test rules. The results show significant difference in average HRC number between two samples, a decreased number in Pts group, total cumulative chi2 difference (p<0.001) and frequency distribution (p = 0.0027). We conclude that the analyzed groups make two different samples in regard to their population-genetic structure. It means that they may give a different response to similar environmental agents. A significantly decreased HRC number in the Pts group may be a manifestation of their decreased degree of homozygosity and indicate a dominant factor inluence in predisposition to LTB. It is possible that individuals with such genetic and physiological constitution are more liable to infection/disease caused by M. tuberculosis. Deviation from optimal degree of homozygosity appoints to possibility of altered genetic-physiological organism homeostasis and its altered reaction norm that leads to illness. Particular phenotype distribution analysis of significantly decreased frequency of HRC and characteristic expression (eye and hair colour) suggest that there is a possibility of related gene alleles association with genetic basis for susceptibility to TB in humans.
Gene Frequency↗
Genetic and structural characterization of the avirulence gene avrBs3 from Xanthomonas campestris pv. vesicatoria.
The avirulence gene avrBs3 from Xanthomonas campestris pv. vesicatoria was cloned and found to be localized on a self-transmissable plasmid. Genetic analysis of an avrBs3 insertion mutation revealed that avrBs3 constitutes a single locus, specifying the resistant phenotype on pepper plants. Southern blot experiments showed that no DNA sequences homologous to avrBs3 were present in other races of X. c. pv. vesicatoria, which are unable to induce a hypersensitive reaction on ECW-30R. However, the DNA of several different pathovars of X. campestris hybridized to the avrBs3 probe. A deletion analysis defined a region of 3.6-3.7 kb essential for avrBs3 activity. The nucleotide sequence of this region was determined. A 3561 nucleotide open reading frame (ORF1), encoding a 125,000 dalton protein, was found in the 3.7 kb region that was sufficient for avrBs3 activity. A second long ORF (2351 nucleotides) was identified on the other strand. A remarkable feature of both ORFs is the presence of 17 direct repeats of 102 bp which share 91%-100% homology with each other.
Amino Acid Sequence↗
Structural and genetic analysis of protein stability.
One very encouraging development has been the freedom with which amino acid replacements can be introduced in a protein of interest. This has made it possible to obtain detailed structural and thermodynamic data on a wide variety of mutants that modify protein stability. Substitutions of solvent-exposed amino acids on the surfaces of proteins are seen to have little if any effect on protein stability or structure, leading to the view that it is the rigid parts of proteins that are critical for folding and stability. There is every reason to expect that it will be possible to rationalize the stabilities of mutant proteins from accurate knowledge of their structures. Substantial progress is being made in quantitating the interactions that determine and stabilize protein structures. Although not specifically the subject of this review, substantial progress is also being made in developing methods to engineer proteins of enhanced stability.
Drug Stability↗
The effect of alternative economic and genetic covariation structures on the relative economic gain from selection using stayability traits.
Three alternative cost ratios and the ratio of annual fixed cost for cows to net replacement cost for three populations that differed in genetic (co)variances were investigated. We studied their effect on the value of longevity records to supplement production records to achieve genetic gains for reducing the nonfeed cost of producing a unit of milk. Data files were constructed from stochastically generated production records and culling variant records; the later records represented the relative value for cow survival of all nonproduction traits. The use of one stayability trait instead of none increased gain by 1 to 9% across the populations and cost ratios. Only 2% additional gain occurred with two stayability traits instead of one. Populations that differed in genetic correlation between production and the survival value of nonproduction traits and in survival heritabilities contributed 2 to 5% toward the greater gains. The different cost ratios contributed 1 to 3%. The effect of increasing the length of herd life independent of production is inherently secondary to the effect of increasing the production during lactation. If genetic antagonism between production and the survival of nonproduction traits is found and if the net replacement costs are high, the use of production and longevity records for selection can enhance gain by up to 10%.
Animals↗
Phylogeography of Ophioblennius: the role of ocean currents and geography in reef fish evolution.
Many tropical reef fishes are divided into Atlantic and East Pacific taxa, placing similar species in two very different biogeographic regimes. The tropical Atlantic is a closed ocean basin with relatively stable currents, whereas the East Pacific is an open basin with unstable oceanic circulation. To assess how evolutionary processes are influenced by these differences in oceanography and geography, we analyze a 630-bp region of mitochondrial cytochrome b from 171 individuals in the blenniid genus Ophioblennius. Our results demonstrate deep genetic structuring in the Atlantic species, O. atlanticus, corresponding to recognized biogeographic provinces, with divergences of d = 5.2-12.7% among the Caribbean, Brazilian, St. Helena/Ascension Island, Gulf of Guinea, and Azores/Cape Verde regions. The Atlantic phylogeny is consistent with Pliocene dispersal from the western to eastern Atlantic, and the depth of these separations (along with prior morphological comparisons) may indicate previously unrecognized species. The eastern Pacific species, O. steindachneri, is characterized by markedly less structure than O. atlanticus, with shallow mitochondrial DNA lineages (dmax = 2.7%) and haplotype frequency shifts between locations in the Sea of Cortez, Pacific Panama, Clipperton Island, and the Galapagos Islands. No concordance between genetic structure and biogeographic provinces was found for O. steincdachneri. We attribute the phylogeographic pattern in O. atlanticus to dispersal during the reorganization of Atlantic circulation patterns that accompanied the shoaling of the Isthmus of Panama. The low degree of structure in the eastern Pacific is probably due to unstable circulation and linkage to the larger Pacific Ocean basin. The contrast in genetic signatures between Atlantic and eastern Pacific blennies demonstrates how differences in geology and oceanography have influenced evolutionary radiations within each region.
Animals↗
Genetic fine structure and polarized negative inteference at the lys-51(FL) locus of Aspergillus nidulans.
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Aspergillus↗
Evidence of altered gene flow, mutation rate, and genetic diversity in redbreast sunfish from a pulp-mill-contaminated river.
To determine effects of pulp mill effluent on population genetic structure, redbreast sunfish (Lepomis auritus) were collected from several sites along the Pigeon River, NC, as well as from reference sites. Previous studies found effects on molecular, biochemical, physiological, population, and community level endpoints in these populations. The population genetic structure of these fish was determined using the randomly amplified polymorphic DNA (RAPD) technique. The level of genetic diversity was higher in the Pigeon River populations than in the reference populations. Genetic distances among populations could not be explained by drainage patterns and may have been altered by contaminant exposure. Phylogeographic analysis, maximum likelihood analysis, and assignment tests suggested that there were fewer emigrants and more immigrants in the contaminated sites than in the reference sites, suggesting that the contaminated sites may harbor "sinklike" populations. Finally, a "terminal branch amplitype" analysis (neighbor-joining and minimum-spanning trees) and maximum likelihood analysis indicated that there may be an elevated mutation rate in the polluted sites. Thus, the genetic diversity (within and among populations) in the Pigeon River populations may have been affected by altered gene flow and mutational processes as a result of pulp mill effluent discharge.
Animals↗
Contrasting patterns of genetic variation in the two sympatric geckos Gekko tawaensis and G. japonicus (Reptilia: Squamata) from western Japan, as revealed by allozyme analyses.
Allozyme variation in two congeneric sympatric geckos, Gekko tawaensis and G. japonicus, from western Japan was examined. These species show similar densities and spatial arrangements of populations in this region, and their genetic structures are thus expected to have been formed under the influences of comparable geohistorical, environmental, and demographic factors. Results of the analyses, however, revealed strikingly different genetic patterns in the two species. Populations of G. tawaensis invariably showed a remarkably lowered heterozygosity (0-0.017) compared to G. japonicus (0.089-0.124). On the other hand, the genetic heterogeneity among populations is much greater in G. tawaensis (F(ST)=0.726) than in G. japonicus (F(ST)=0.101). The Mantel test failed to detect any significant correlations between log (estimated migration rate) and log (geographic distance) in either species, or between matrices of interpopulation pairwise F(ST) for the two species. These results suggest that, in each species, formation of the current genetic structure in western Japan has been chiefly influenced by stochastic factors, rather than the geohistorical architecture of this region. The high F(ST) and low heterozygosity in G. tawaensis suggest the effects of severe local fragmentation. On the other hand, the relatively low F(ST) and high heterozygosity in G. japonicus imply extensive gene flow among populations. Absence of significant correlations between the estimated migration rate and geographic distance in G. japonicus may suggest that such gene flow is promoted by human-mediated transport of this primarily house-dwelling lizard.
Animals↗
Genome-wide SNP data support species boundaries in sympatric Polylepis Ruiz & Pav. (Rosaceae) species from Bolivia and Ecuador.
Species delimitation in the South American genus Polylepis is notoriously challenging due to high morphological similarity and phenotypic plasticity, likely driven by hybridization and gene flow. Previous phylogenetic studies suggested that genetic structure aligns more strongly with geography than with taxonomy, questioning existing species concepts and hampering conservation efforts. We used double-digest RAD sequencing (ddRADseq) to generate genome-wide SNP data for 11 Polylepis species sampled across multiple localities in Bolivia and Ecuador. Population genetic analyses, phylogenetic inference, and network approaches were combined to assess whether genetic structure aligns more closely with taxonomy or geography. Morphologically defined species formed largely cohesive genetic lineages across regions, with species identity explaining substantially more genetic variation than locality. While localized admixture and reticulation were detected among closely related taxa, widespread species showed strong genetic cohesion and clear separation from congeners. Our results indicate that the sampled Polylepis species from Bolivia and Ecuador maintain distinct genetic identities despite localized signals consistent with gene flow. This genome-wide support for current taxonomy highlights Polylepis as a valuable model for studying speciation under gene flow and indicates that multiple geographic sampling will be essential in reconstructing a robust phylogeny of the genus, with important implications for conservation planning in Andean montane forests.
Bolivia↗
Structural and genetic characterization of the Shigella boydii type 10 and type 6 O antigens.
Comparison of the O antigens of Shigella boydii types 10 and 6 by chemical analysis and nuclear magnetic resonance spectroscopy showed that their structures are similar, with the only difference being the presence or absence of d-ribofuranose, which is the immunodominant sugar in S. boydii type 10. In S. boydii type 6, a residue previously reported as alpha-d-GlcpA, was shown to be beta-d-GlcpA as in S. boydii type 10. S. boydii types 10 and 6 are reported not to cross-react serologically, and the role of d-ribofuranose in the specificity of S. boydii was confirmed by making a mutant of type 10 that lacked d-ribofuranose. However, S. boydii type 11, which has a d-ribofuranose but with different linkage does show cross-reaction with type 10. The O-antigen gene loci of S. boydii types 10 and 6 were shown to be virtually identical except that orf8 (wbaM), which was confirmed as the ribofuranosyltransferase gene, is interrupted by IS629 in type 6. Therefore, it is proposed that the O-antigen gene cluster of S. boydii type 6 was derived from type 10 by an IS element insertion.
Amino Acid Sequence↗
The structural and genetic basis for expression of normal and latent VHa allotypes of the rabbit.
The immunoglobulin heavy chain variable regions of the rabbit are unusual in having genetically controlled, serologically detectable alternative forms, the VHa allotypes, as well as minor VH allotypes of the x, y and w groups. New insights into the probable structural basis for the VHa allotypes have come from re-examination of earlier protein sequence data in the light of newly deduced protein sequences derived from sequencing cloned cDNAs and genomic DNAs encoding VH regions. Here we review this sequence information, and define the allotype-correlated differences at seven positions in framework region 1 and 10 positions in framework region 3 that may lead to the serologically detectable allotypic determinants (allotopes). Most alternative amino acids at allotype-correlated positions can be derived from each other by single-base changes. Thus somatic mutations and/or gene conversion-like events must be considered along with other serological and genetic explanations for various reported observations of the production of latent VHa allotypes. The proximity of rabbit VH genes (approximately 3 kb apart) might enhance the likelihood of conversion-like events in both germline and somatic cells.
Amino Acid Sequence↗