Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genetic Structures”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,405 records · Page 78Linked to original sources
PubMed1994

Contrasting the distribution of chloroplast DNA and allozyme polymorphism among local populations of Silene alba: implications for studies of gene flow in plants.

The distribution of chloroplast DNA (cp-DNA) length variants was analyzed within and among 10 local populations of Silene alba, a dioecious angiosperm. The populations displayed considerable allele frequency variation, resulting in an estimate of Wright's Fst of 0.67 over a 25 x 25 km portion of the species' range. By contrast, a concurrent analysis of the genetic structure of these same populations based on seven polymorphic allozyme loci yielded an estimate of Fst of 0.13. The two Fst estimates are significantly different from one another when their respective confidence limits are estimated by jackknifing. The results of a breeding study were consistent with maternal inheritance of the cpDNA variants. With maternal inheritance the genetic structure of the cpDNA should reflect seed movement, whereas the genetic structure of the nuclear-encoded allozyme loci should reflect the movement of both seeds and pollen. Comparison of the two markedly different Fst estimates in the context of recent models of the population genetics of organelles suggests that the movement of both seeds and pollen contributes significantly to gene flow.

Journal Article↗
PubMed2006

Differential population structuring and demographic history of two closely related fish species, Japanese sea bass (Lateolabrax japonicus) and spotted sea bass (Lateolabrax maculatus) in Northwestern Pacific.

The Quaternary cold periods in the Northwestern Pacific are thought to have heavily influenced the amount and distribution of intraspecific genetic variation in marine fishes. To estimate the demographic history and genetic structure of Lateolabrax maculatus and L. japonicus in the Northwestern Pacific, 256 individuals were sampled from 19 localities throughout the distribution range of the two species. Mitochondrial DNA variation was analyzed using DNA sequence data from the cytochrome b gene and control region. Nucleotide diversity was much higher in L. japonicus (0.030) than in L. maculatus (0.012). The demographic history of the two species was examined using neutrality tests and mismatch distribution analyses and results indicated Pleistocene population expansion in both species. Estimates of population expansion time suggested earlier population expansion in L. japonicus than in L. maculatus. Molecular variance analyses showed differential genetic structuring for these two closely related species. The results indicated that L. japonicus is panmictic throughout its range. In contrast, populations of L. maculatus showed statistically significant levels of genetic structuring. Pattern of isolation by distance was observed in L. maculatus, suggesting that L. maculatus is in genetic equilibrium. In contrast, L. japonicus did not exhibit isolation by distance.

Animals↗
PubMed2003

The role of environment in shaping the genetic diversity of the subalpine mosquito, Aedes rusticus (Diptera, Culicidae).

The relative involvement of larval dietary tolerance to the leaf-litter toxic polyphenols in shaping population genetic structure of the subalpine mosquito Aedes rusticus was examined. This was compared with other parameters such as geographical range, type of vegetation surrounding the breeding site, and occurrence of annual larvicidal treatments. Population genetic structure was analysed at 10 presumed neutral polymorphic isoenzyme loci. Toxicological comparisons involved standard bioassays performed on larvae fed on toxic decomposed leaf litter. Significant overall genetic differentiation was observed among the 22 studied populations and within the five defined geographical groups. Analysis of molecular variance revealed an absence of relation between genetic and environmental parameters, genetic variance being essentially found within populations. This suggested that the larval dietary tolerance to the toxic leaf litter and the other studied parameters poorly influence population genetic structure. The local adaptation of subalpine mosquito populations to the surrounding vegetation thus appears as a labile trait. Such a dynamic adaptation is also suggested by the correlation between geographical and toxicological distances and the correlation between dietary tolerance to the leaf-litter toxic polyphenols and annual larvicidal treatments.

Aedes↗
PubMed2006

Non-B DNA structure-induced genetic instability.

Repetitive DNA sequences are abundant in eukaryotic genomes, and many of these sequences have the potential to adopt non-B DNA conformations. Genes harboring non-B DNA structure-forming sequences increase the risk of genetic instability and thus are associated with human diseases. In this review, we discuss putative mechanisms responsible for genetic instability events occurring at these non-B DNA structures, with a focus on hairpins, left-handed Z-DNA, and intramolecular triplexes or H-DNA. Slippage and misalignment are the most common events leading to DNA structure-induced mutagenesis. However, a number of other mechanisms of genetic instability have been proposed based on the finding that these structures not only induce expansions and deletions, but can also induce DNA strand breaks and rearrangements. The available data implicate a variety of proteins, such as mismatch repair proteins, nucleotide excision repair proteins, topoisomerases, and structure specific-nucleases in the processing of these mutagenic DNA structures. The potential mechanisms of genetic instability induced by these structures and their contribution to human diseases are discussed.

Base Sequence↗
PubMed1999

Temporal and spatial genetic variation within and among populations of the mosquito Culex tarsalis (Diptera: Culicidae) from California.

The genetic structure of 11 populations of Culex tarsalis Coquillett from California and 1 population from Nevada was examined at 18 loci using polyacrylamide gel electrophoresis. Six populations from northern and southern California were sampled repeatedly to determine if the genetic structure of Cx. tarsalis changes seasonally. Significant differences in allele frequencies at 13 different loci were seen in 3 populations over time as determined by contingency chi-square tests. Nei's genetic distance coefficients among different sampling dates was consistently < 0.025. The number of alleles per locus in these populations ranged from 1.6 to 2.7, whereas the average heterozygosity ranged from 0.086 to 0.228. No single locus was found to vary in a consistent pattern within all populations that were sampled repeatedly. These results indicate that Cx. tarsalis populations are genetically stable over time and that temporal variation is due to fluctuations in population size or immigration of genetically distinct individuals. In contrast, Cx. tarsalis did exhibit some differences in genetic structure that were related to geographical features including the Sierra Nevada and the Tehachapi Mountains of southern California. Genetically differentiated populations occurred in Nevada, southern and northeastern California, and the Central Valley of California. Little differentiation was observed among populations located in the Central Valley of California and those located at high elevations in the Sierra Nevada. Thus, in the populations examined, mountain ranges or arid conditions that limit the number of larval development sites appeared to be important barriers to the dispersal of Cx. tarsalis.

Animals↗
PubMedDate not supplied

Some genetic considerations for the design of better mammalian assay systems for the detection of chemical mutagens and carcinogens.

Fuller utilization of the potential for genetic manipulation of the laboratory animal populations producing test animals should aid in the development of more sensitive, relevant, and economic toxicologic assay systems for the generation of dose response data at environmental exposure levels. One example of such genetic manipulation is the incorporation, in laboratory mouse populations of any desired genetic structure, of dominant visible mutations which enhance tumor formation. Thus, two different levels of inherent susceptibility to tumor formation can be incorporated and visually identified in the same test population. Another example is the manipulation of the genetic structure of a laboratory animal population in order to generate F-1 hybrids, hybrid crosses, or minimally inbred stocks from the same gene pool. Which of these genetic structures is most suitable in any particular case depends on the purpose for which the assay data are to be used. In making a choice, the desired degree of genetic heterogeneity of the population and the phenotypic variability of the toxicologic responses to be assayed must be considered.

Animals↗
PubMed2005

An inquiry into protein structure and genetic disease: introducing undergraduates to bioinformatics in a large introductory course.

This inquiry-based lab is designed around genetic diseases with a focus on protein structure and function. To allow students to work on their own investigatory projects, 10 projects on 10 different proteins were developed. Students are grouped in sections of 20 and work in pairs on each of the projects. To begin their investigation, students are given a cDNA sequence that translates into a human protein with a single mutation. Each case results in a genetic disease that has been studied and recorded in the Online Mendelian Inheritance in Man (OMIM) database. Students use bioinformatics tools to investigate their proteins and form a hypothesis for the effect of the mutation on protein function. They are also asked to predict the impact of the mutation on human physiology and present their findings in the form of an oral report. Over five laboratory sessions, students use tools on the National Center for Biotechnology Information (NCBI) Web site (BLAST, LocusLink, OMIM, GenBank, and PubMed) as well as ExPasy, Protein Data Bank, ClustalW, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and the structure-viewing program DeepView. Assessment results showed that students gained an understanding of the Web-based databases and tools and enjoyed the investigatory nature of the lab.

Algorithms↗
PubMed2001

Spatial patterns of genetic diversity in Posidonia oceanica, an endemic Mediterranean seagrass.

Posidonia oceanica is an endemic seagrass species in the Mediterranean Sea. In order to assess levels of genetic structure in this species, the microsatellite polymorphism was analysed from meadows collected in several localities, along the coasts of the Tyrrhenian Sea (Mediterranean Sea). The existence of single population units and the recruitment of seedlings collected in some localities were investigated. Moreover, genetic structure at different spatial scales and biogeographic relationships among populations were also assessed. Our analysis showed the existence of clear patterns of genetic structure in P. oceanica in the area considered in the analysis. P. oceanica, in fact, is present in separate meadows that represent discrete populations, characterized by low genetic diversity. Comparable levels of genetic variability between mature meadows and seedlings were found. Patterns of genetic relatedness among populations seem to be in accord with direction of dominant current flux in the whole area, separating South Tyrrhenian from North Tyrrhenian populations. Moderate levels of gene flow between populations and genetic substructure within populations, together with the finding of the limited role of sexual reproduction in increasing genetic variability, should be a cause for concern for the persistence of this essential resource in the Mediterranean basin.

Genetic Variation↗
PubMed1998

Influence of plant genotype on the selection of nodulating Sinorhizobium meliloti strains by Medicago sativa.

We analysed the genetic diversity of 270 Sinorhizobium meliloti strains isolated from nodules of three different Medicago sativa varieties, planted in three different Italian soils, combining the Analysis of Molecular Variance (AMOVA) with the Random Amplified Polymorphic DNA (RAPD) technique to estimate variance among RAPD patterns with the aim to draw an objective description of the population genetic structure. Results indicated that a general intraspecific genetic diversity was globally distributed among all the population, however a very high level of diversity was found among strains nodulating different Medicago sativa varieties. Moreover the distribution of the RAPD haplotypes among the plant varieties also showed to be non-random. The overall data indicated that the plant genotype is a major factor in shaping the genetic structure of this natural Rhizobium population.

Analysis of Variance↗
PubMed2006

Restricted gene flow in the Caribbean staghorn coral Acropora cervicornis: implications for the recovery of endangered reefs.

Coral reef conservation requires information about the distance over which healthy reefs can rescue damaged reefs through input of coral larvae. This information is desperately needed in the Caribbean where the 2 dominant shallow water corals Acropora cervicornis and Acropora palmata have suffered unprecedented declines. Here we compare the population genetic structure in the staghorn coral A. cervicornis across the greater Caribbean using DNA sequence data from 1 mitochondrial and 3 nuclear genes. Data from 160 individuals from 22 populations and 9 regions show that A. cervicornis exhibits significant population genetic structure across the greater Caribbean in both the mitochondrial (Phi(st) = 0.130) and nuclear data (Phi(st) = 0.067). The highest population structure was observed in the species' own, native mtDNA haplotypes (Phi(st) = 0.235). Introgressed alleles from A. palmata tempered higher population structure in A. cervicornis over regional scales but in some cases generated highly localized "introgression hot spots" and fine-scale genetic structure among reefs separated by as few as 2 km. These data show that larval dispersal over moderate or long distances (>500 km) is limited for this threatened species and in some cases locally limited as well. Thus, the endangered Caribbean staghorn corals require local source populations for their recovery and targeted conservation efforts over spatial scales much smaller than the hundreds to thousands of kilometers usually proposed for marine reserves.

Animal Migration↗
PubMed1983

Surnames in Sardinia. I. Fit of frequency distributions for neutral alleles and genetic population structure.

Distributions of surnames were examined using data from about 40 000 individuals from consanguineous marriages (1930-59) in the island of Sardinia. They fit the Karlin-McGregor (1967) distribution for neutral alleles. The logarithmic distribution by Fisher (1943) and the Karlin-McGregor (1967) distribution give practically indistinguishable fits to these data. The two parameters underlying the Fisher distribution, alpha and nu, are fully interdependent, given the sample size N. From the latter and from the number of surnames S, they can be easily and satisfactorily estimated. The quantity nu measures immigration to the area and can be taken as a measure of the richness of the gene pool, being closely related to the quantity theta = Nemu (Ne = effective population size, mu = mutation rate) after the necessary corrections have been taken care of. Surnames behave like genes transmitted by the male line. Differences of female and male migrations require correction for comparison with data from autosomal gene frequencies but there seem to be no important differences between female and male migration in this area, as judged by analysis of pedigrees of consanguineous marriages. It is probable that the migration estimates obtained in this material are lower than real ones, mostly because of a bias characteristic of the particular source of surnames here employed. The distribution of surnames from areas which have very recently undergone economic development is not at equilibrium and is not fitted as well as that of areas which have had less important recent changes. As might be expected, the disturbance is particularly marked in the class most sensitive to effects of recent increases in migration, that of rarest surnames (represented by only one individual). In fact in this material it is noticeable only in this class and correction can be made for it. At equilibrium of migration and drift, the number of surnames in a population sample of given size can give a complete description of the population structure for that sample, in the same sense that the number of alleles is a sufficient statistic for the study of neutral evolution. The study of surnames, given their nature of 'neutral' alleles, the large number of alleles and the ease with which large numbers of individual data can be collected, can be a valuable help in the study of genetic population structure.

Alleles↗
PubMed2004

Microsatellite variation and population structure in a declining Australian Hylid Litoria aurea.

The green and golden bell frog (Litoria aurea) was once a common Australian Hylid. Today, many populations are small and fragmented as a result of dramatic declines in distribution and abundance. We undertook a large-scale assessment of genetic structure and diversity in L. aurea using four species-specific microsatellite markers. Twenty-one locations were sampled from throughout the species range covering 1000 km of the east coast of Australia. Levels of allelic diversity and heterozygosity were high (uncorrected mean alleles/locus and H(E) were 4.8-8.8 and 0.43-0.8, respectively) compared to other amphibian species and significant differences among sampled sites were recorded. Despite recent population declines, no sites displayed a genetic signature indicative of a population bottleneck. Significant genetic structuring (overall F(ST) 0.172) was detected throughout the species range, but was relatively low compared to previous amphibian studies employing microsatellites. In addition we found that some areas sampled within continuous habitat showed evidence of weak genetic structuring (data subset F(ST) 0.034). We conclude that maintaining areas of continuous habitat is critical to the conservation of the species and argue that population recovery and/or persistence in all areas sampled is possible if appropriate protection and management are afforded.

Animals↗
PubMed2004

A comprehensive in vitro characterization of pancreatic ductal carcinoma cell line biological behavior and its correlation with the structural and genetic profile.

There are a large number of stable pancreatic ductal carcinoma cell lines (PDCL) that are used by researchers worldwide. Detailed data about their differentiation status and genetic alterations are present in the literature, but a systematic correlation with cell biological behavior is often lacking. PDCL ( n=12) were clustered by source of tumor cell (ascites, primary tumor, metastasis), and the data of functional cell biology were correlated with the reported structural and genetic profiles. Major histocompatibility complex expression, chemosensitivity and aneuploidia appeared to be related to the source of PDCL, and proliferative capacity appeared to be related to the grade of differentiation. No correlation between genetic/structural features of PDCL and biological behavior was found. All the cell lines appeared generally insensitive to in vitro treatment with 5-fluorouracil and showed variable degrees of susceptibility to gemcitabine, raltitrexed and oxaliplatin. All the PDCL showed resistance to Fas-mediated apoptosis but were significantly sensitive to the pro-apoptotic effect of inflammatory cytokines [interleukin (IL)-1beta, tumor necrosis factor (TNF)alpha and interferon gamma]. PDCL were characterized for the secretion of several factors relevant to the tumor-immune cross talk. Vascular endothelial growth factor, CCL2, CCL5 and transforming growth factor beta were the factors most frequently released; less frequent was the secretion of CXCL8, CCL22, IL-6 and sporadically CXCL12, IL-10 and hepatocyte growth factor. The cytokines IL-1beta and TNFalpha were always undetectable. In conclusion, a clear correlation between structural/genetic features and function could not be detected, suggesting the weakness of a "morphological" classification for the in vitro studies of pancreatic cancer.

Antineoplastic Agents↗
PubMed2004

Structural and genetic characterization of the Shigella boydii type 13 O antigen.

Shigella is an important human pathogen. It is generally agreed that Shigella and Escherichia coli constitute a single species; the only exception is Shigella boydii type 13, which is more distantly related to E. coli and other Shigella forms and seems to represent another species. This gives S. boydii type 13 an important status in evolution. O antigen is the polysaccharide part of the lipopolysaccharide in the outer membrane of gram-negative bacteria and plays an important role in pathogenicity. The chemical structure and genetic organization of the S. boydii type 13 O antigen were investigated. The O polysaccharide was found to be acid labile owing to the presence of a glycosyl phosphate linkage in the main chain. The structure of the linear pentasaccharide phosphate repeating unit (O unit) was established by nuclear magnetic resonance spectroscopy, including two-dimensional COSY, TOCSY, ROESY, and H-detected 1H, 13C and 1H, 31P HMQC experiments, along with chemical methods. The O antigen gene cluster of S. boydii type 13 was located and sequenced. Genes for synthesis of UDP-2-acetamido-2,6-dideoxy-L-glucose and genes that encode putative sugar transferases, O unit flippase, and O antigen polymerase were identified. Seven genes were found to be specific to S. boydii type 13. The S. boydii type 13 O antigen gene cluster has higher levels of sequence similarity with Vibrio cholerae gene clusters and may be evolutionarily related to these gene clusters.

Carbohydrates↗
PubMed2002

Evidence of low gene flow in a neotropical clustered tree species in two rainforest stands of French Guiana.

The spatial genetic structure of the neotropical, clustered tree species Vouacapoua americana (Aublet) was studied in two natural forest stands (Paracou and Nouragues) in French Guiana. Using eight microsatellite loci, V. americana is characterized by a marked genetic structure at small spatial distances (under 30-60 m), in agreement with the limited seed dispersal by rodent species. Gene flow through pollen is also shown to be mainly restricted to less than 100 m. This result suggests that most pollination events (mediated through small insects) are probably limited to within-patches of individuals, which might explain the high genetic differentiation among patches (F(ST) = 0.11) separated by less than 2 km. We also assume that stronger genetic structure in Paracou is likely to be due to lower seed dispersal by rodents, large spatial distances separating patches, or a recent recolonization event.

DNA, Plant↗
PubMed1990

Genetic latent structure analysis of dysmorphology in attention deficit disorder.

Dysmorphology--in the form of minor physical anomalies--has been frequently reported in children with attention deficit disorder (ADD). The authors report an overrepresentation of minor physical anomalies in both ADD probands and their first-degree relatives. Further, ADD probands who are not dysmorphic have non-ADD relatives who are dysmorphic; this familial pattern suggests that a single underlying factor may influence transmission of both traits. A genetic latent structure model was fit to these data to describe the factor's mode of transmission. In this analysis, an autosomal dominant model emerged. Successfully fitting this model is not equivalent to testing the validity of the model itself. Meaningful tests of the model will require larger samples than available at present, and would benefit from diagnostic refinement of the ADD and dysmorphic phenotypes.

Attention Deficit Disorder with Hyperactivity↗
PubMed1988

Idiotypic and subgroup analysis of human monoclonal rheumatoid factors. Implications for structural and genetic basis of autoantibodies in humans.

Rheumatoid factors (RFs) in humans have been studied intensively because of their association with autoimmune and lymphoproliferative diseases. Many human IgM-RFs express cross-reactive idiotypes (CRIs) and have homologous light chains, some of which are encoded by a single V kappa gene, termed V kappa 325. However, although antibody activity generally requires the interaction between heavy and light chain variable regions, much less is known about structural relationships among RF heavy chains. To delineate further the structural and genetic basis of RF autoantibody synthesis, we generated "sequence-dependent" reagents specific for the human heavy and kappa light chain subgroups, and used them to analyze a panel of 27 monoclonal RFs. In addition, these proteins were tested for the expression of a heavy chain-associated CRI (G6), and a light chain-associated CRI (17.109). The results showed that most 17.109-reactive RFs contain heavy chains of the VHI subgroup, which bear the G6 idiotypic marker. However, among the 14 17.109-reactive RFs, two have heavy chains of the VHII subgroup, and another two contain heavy chains of the VHIII subgroup. Previously, we have shown that 17.109 is a phenotypic marker of the human V kappa 325 gene. Accordingly, these results demonstrate that the same human V kappa gene can combine with several VH genes from different VH gene subgroups to generate RF activity.

Amino Acid Sequence↗
PubMed1983

[Polymorphic biochemical systems in the population of immigrant inhabitants of the northeastern USSR. II. Genotypic distances between groups of persons with a varying duration of living under extreme environmental conditions].

Analysis of the differences in the groups examined for phenotypes and genes has shown that the longer dwelling in the regions of the extreme conditions, the greater changes are in the genetic structure of separate selections with "retreating" from middle latitudes'population and "approaching" the aboriginal one of the North-East. This "dynamics" is mostly pronounced in men and groups characterized by very long dwelling in the region; the differences between representatives of both sexes are maximal. A slightly more isolated position is occupied by the genetic structure of individuals living in the North from the birth. The data obtained allow to assume that the genetic structure of the man's population being formed in the extreme conditions, tends to the ecological fit on account of the selectivity of migratory behaviour. The ecological fit of separate genotypes may well be assumed to be different for representatives of both sexes and on different stages of ontogenesis.

Adolescent↗