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 1,045 records · Page 58Linked to original sources

Gravity, weightlessness and the genetic structures of organisms.

The whole evolution of life on earth has proceeded under the action of earth's gravity which must have influenced the structure and function of organisms. During space flights organisms are exposed to the entirely new condition of weightlessness, and to variations in gravity that produce various changes. Current flight data suggest that organisms most often respond to weightlessness by disturbances in physiological function, which are reversible after the brief exposures that have at present been possible. Only longer space flights will show whether these changes will be compensated, or will lead to alterations in the more important systems of organisms including their hereditary properties. There is evidence that weightlessness has a direct effect on genetic properties. Thus, in microspores of Tradescantia abnormal mitoses (that were not observed in the ground-based control) were recorded to an extent of 3%. The numerous changes in various vital systems suggest that for terrestrial organisms weightlessness is a factor which, if administered for a long time, may bring about serious disturbances in their activities and heredity. The higher the evolutionary position of the organism, the more pronounced the effect is likely to be.

Adaptation, Physiological↗

Genetic structure and history of populations of the deep-sea fish Helicolenus dactylopterus (Delaroche, 1809) inferred from mtDNA sequence analysis.

Helicolenus dactylopterus is an Atlantic benthopelagic fish species inhabiting high-energy habitats on continental slopes, seamounts and islands. Partial sequences of the mitochondrial control region (D-loop) and cytochrome b (cyt b) were used to test the hypothesis that H. dactylopterus disperses between continental margin, island and seamount habitats on intraregional, regional and oceanic scales in the North Atlantic. Individuals were collected from five different geographical areas: Azores, Madeira, Portugal (Peniche), Cape Verde and the northwest Atlantic. D-loop (415 bp) and cyt b (423 bp) regions were partially sequenced for 208 and 212 individuals, respectively. Analysis of variation among mitochondrial DNA sequences based on pairwise F-statistics and AMOVA demonstrated marked genetic differentiation between populations in different geographical regions specifically the Mid-Atlantic Ridge (Azores)/northeast Atlantic (Portugal, Madeira) compared to populations around the Cape Verde Islands and in the northwest Atlantic. Some evidence of intraregional genetic differentiation between populations was found. Minimum-spanning network analysis revealed star-shaped patterns suggesting that populations had undergone expansion following bottlenecks and/or they have been colonized by jump dispersal events across large geographical distances along pathways of major ocean currents. Mismatch distribution analysis indicated that Azores and northwest Atlantic populations fitted a model of historical population expansion following a bottleneck/founder event estimated to be between 0.64 and 1.2 million years ago (Ma).

Analysis of Variance↗

Occurrence and genetic structure of the systemic grass endophyte Epichloë festucae in fine fescue populations.

Epichloë species are systemic fungal endophytes that usually specialize in a certain group of related grass species. We examined the infection frequency of Epichloë festucae in populations of two fine fescue species (Festuca rubra and F. ovina) in natural and seminatural habitats at 86 study sites (total=2514 plants) across Finland and northern Norway. Infection incidence varied significantly among grass species and populations. A substantial number of the F. rubra and F. ovina populations (53 out of 77 and 25 out of 30, respectively) were either endophyte-free or had very low (<20%) infection frequencies. The highest infection frequencies were found in subarctic areas. Moreover, infection incidence differed between habitats. In the area with the highest infection frequencies, we used microsatellite markers to study genetic diversity and the rates of gene flow of E. festucae among 12 F. rubra populations. Twenty out of the 25 fungal genotypes detected with four microsatellite markers were carrying multiple alleles in at least one locus, indicating multiple infections or vegetative hybridization of the fungus. One dominant genotype occurred in all 12 populations, representing 63.5% of all isolates. We found a moderate level of average genotypic variation and a low level of genetic differentiation (Fst=0.0814). There was no correlation between infection frequency and genotypic diversity. Although the existence of a dominant genotype and the detected linkage disequilibrium suggest that the fungus is mainly asexual and vertically transmitted, the multiallelic loci and variation of genetic diversity among populations indicate occasional contagious spread and sexual or parasexual recombination of the fungus in some populations. Furthermore, the genotypes carrying multiallelic loci suggest the possibility of multiple infections or hybridization of the endophyte.

DNA, Fungal↗

Analysis of mitochondrial DNA variability and genetic structure in populations of New World screwworm flies (Diptera: Calliphoridae) from Uruguay.

The New Word screwworm, Cochliomyia hominivorax (Coquerel 1858) (Diptera: Calliphoridae), is one of the most important insect pests of livestock in the Neotropical region. In this work, polymerase chain reaction-restriction fragment length polymorphism of mitochondrial DNA (mtDNA) was used to study the diversity and population structure of seven geographically distinct populations of C. hominivorax from most of the important livestock areas in Uruguay. The control region (A+T/12S) and subunits 1 and 2 of cytochrome oxidase (cox1/cox2) were amplified and digested with restriction endonucleases. Nine haplotypes were observed among the populations sampled. The mean nucleotide diversity and the haplotype diversity indicated high mtDNA variability in this species. The similarity index, average nucleotide divergence, and analysis of molecular variance results showed no evidence of subpopulation differentiation, indicating that the C. hominivorax populations of Uruguay form a single panmitic population. The distribution pattern of the genetic variation in natural populations of C. hominivorax and the implications of these results for establishing control program are discussed.

Animals↗

Structural, genetic and functional characterization of the flagellin glycosylation process in Helicobacter pylori.

Mass spectrometry analyses of the complex polar flagella from Helicobacter pylori demonstrated that both FlaA and FlaB proteins are post-translationally modified with pseudaminic acid (Pse5Ac7Ac, 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno -n o n-ulosonic acid). Unlike Campylobacter, flagellar glycosylation in Helicobacter displays little heterogeneity in isoform or glycoform distribution, although all glycosylation sites are located in the central core region of the protein monomer in a manner similar to that found in Campylobacter. Bioinformatic analysis revealed five genes (HP0840, HP0178, HP0326A, HP0326B, HP0114) homologous to other prokaryote genes previously reported to be involved in motility, flagellar glycosylation or polysaccharide biosynthesis. Insertional mutagenesis of four of these homologues in Helicobacter (HP0178, HP0326A, HP0326B, HP0114) resulted in a non-motile phenotype, no structural flagella filament and only minor amounts of flagellin protein detectable by Western immunoblot. However, mRNA levels for the flagellin structural genes remained unaffected by each mutation. In view of the combined bioinformatic and structural evidence indicating a role for these gene products in glycan biosynthesis, subsequent investigations focused on the functional characterization of the respective gene products. A novel approach was devised to identify biosynthetic sugar nucleotide precursors from intracellular metabolic pools of parent and isogenic mutants using capillary electrophoresis-electrospray mass spectrometry (CE-ESMS) and precursor ion scanning. HP0326A, HP0326B and the HP0178 gene products are directly involved in the biosynthesis of the nucleotide-activated form of Pse, CMP-Pse. Mass spectral analyses of the cytosolic extract from the HP0326A and HP0326B isogenic mutants revealed the accumulation of a mono- and a diacetamido trideoxyhexose UDP sugar nucleotide precursor.

Amino Acid Sequence↗

The genetic structure of a tribal population, the Yanomama Indians. VI. Analysis by F-statistics (including a comparison with the Makiritare and Xavante).

The infra-structure of three relatively undisturbed tribes of American Indians (Yanomama, Makiritare, Xavante) has been investigated by means of the F-statistics of Wright, using 8, 9 and 6 codominant systems respectively. The data for the first two mentioned tribes are much more extensive (37 and 7 villages) than for the third (3 villages), and much of the argument is based on the first two. An additive model partitioning F(IS) into an average effect (F(A)) and deviations due to deme size, systems effects, village effects, and random error has been employed. The Cannings-Edwards formulation suggests that the small size of the demes alone would result in an F(IS) of -0.008 for the Yanomama and -0.007 for the Makiritare. There is no evidence for significant village or systems effects. Despite considerable scatter, F(A) values are not significantly heterogeneous and tend to be negative (-0.012 to -0.023). On the basis of a computer simulation model, it appears that there is an excess of consanguineous marriage over random expectation, i.e. the negative F(A) values are probably not due to avoidance of close inbreeding in a subdivided population in which demes are small. Aspects of population structure which could contribute to negative F(A) values are identified. These include unequal gene frequencies in the sexes and occasional marked differential fertility. It is at this point unnecessary to introduce overdominance as a cause of the negative F(A) values, since a computer simulation program which does not incorporate selection satisfactorily reproduces the observed F(IS) values. If population breeding structure alone can result in negative F(IS) values, then this may constitute a mechanism for retarding random fixation.-Mean F(ST) values are 0.063 for the Yanomama and 0.036 for the Makiritare. While truly comparable data are lacking, it seems likely these will be found to be relatively high values for human populations. F(IT) values have been calculated by both direct and indirect approaches. The direct approach yields a value of 0.045 for the Yanomama and -0.009 for the Makiritare; the respective indirect values are 0.085 and 0.017. The primary identifiable reason for this difference between tribes is the greater genetic heterogeneity among Yanomama villages. The assumptions underlying the indirect approach to the calculation of F(IT) do not appear to be met in these populations.

Analysis of Variance↗

Genetic structure of the mating-type locus of Chlamydomonas reinhardtii.

Portions of the cloned mating-type (MT) loci (mt(+) and mt(-)) of Chlamydomonas reinhardtii, defined as the approximately 1-Mb domains of linkage group VI that are under recombinational suppression, were subjected to Northern analysis to elucidate their coding capacity. The four central rearranged segments of the loci were found to contain both housekeeping genes (expressed during several life-cycle stages) and mating-related genes, while the sequences unique to mt(+) or mt(-) carried genes expressed only in the gametic or zygotic phases of the life cycle. One of these genes, Mtd1, is a candidate participant in gametic cell fusion; two others, Mta1 and Ezy2, are candidate participants in the uniparental inheritance of chloroplast DNA. The identified housekeeping genes include Pdk, encoding pyruvate dehydrogenase kinase, and GdcH, encoding glycine decarboxylase complex subunit H. Unusual genetic configurations include three genes whose sequences overlap, one gene that has inserted into the coding region of another, several genes that have been inactivated by rearrangements in the region, and genes that have undergone tandem duplication. This report extends our original conclusion that the MT locus has incurred high levels of mutational change.

Amino Acid Oxidoreductases↗

Differences in the genetic structure of Bacillus subitilis strains carrying the trpE26 mutation and strain 168.

It was previously shown that in strains of Bacillus subtilis bearing the trpE26 mutation a chromosome segment (from trpD to ilvA) is translocated to a position near the thr region. Further PBS1-mediated transduction data have now revealed that these strains also possess an inversion of part of the chromosome from the origin of replication, down to the tre locus on one side and the cysB locus on the other. These data concern evidence of linkage of tre-12- to markers in the translocation (hisH2, tyrA1, and metB3) as well as linkage of the cysB3 marker to thi-86, gly-133, and catA. They explain the previously observed absence of linkage of markers in the translocated segment to cysB3. The model proposed for the formation of merodiploids in trpE26 strains, which calls for the fusion of two genetic elements, is not incompatible with this new finding.

Bacillus subtilis↗

Genetic structure of the abd-A gene of Drosophila.

We report the embryonic and adult phenotypes of a number of mutations of the abd-A gene of the bithorax complex. Some of them result in loss of abd-A function in the whole abd-A domain and are usually lethal. These probably eliminate or inactivate abd-A protein products. Other mutations affect only part of the abd-A domain. These are viable, appear to map outside the abd-A transcription unit, and presumably alter the normal spatial regulation of abd-A products. We propose a model of abd-A structure based on a protein-coding region and two cis-regulatory regions. Regulatory region 1, 3' to the transcription unit, contains positive and negative regulatory elements. Regulatory region 2, 5' to the transcription unit, establishes the correct level of abd-A activity in the abdominal metameres.

Animals↗

[Genetic structure of the native populations of the northeastern USSR. I. Distribution of phenotype and gene frequencies in subpopulations of the coast Chukchi].

An analysis of the genotypic structure of three subpopulations of coast chuckchies for 11 polymorphic loci is presented. 1245 individuals were surveyed in total. It is shown that, in spite of variability of phenotypes and gene frequencies in subpopulations, the genotypic structure maintains specific features. In the total sample of coast, a deviation from equilibrium was found for GPT and Gc loci. It is noted that this disequilibrium is maintained for GPT locus in some subpopulations. Such a deviation is probably due to the influence of some systematic factor.

ABO Blood-Group System↗

Population genetic structure and phylogeographical pattern of a relict tree fern, Alsophila spinulosa (Cyatheaceae), inferred from cpDNA atpB- rbcL intergenic spacers.

Sequences of chloroplast DNA (cpDNA) atpB- rbcL intergenic spacers of individuals of a tree fern species, Alsophila spinulosa, collected from ten relict populations distributed in the Hainan and Guangdong provinces, and the Guangxi Zhuang region in southern China, were determined. Sequence length varied from 724 bp to 731 bp, showing length polymorphism, and base composition was with high A+T content between 63.17% and 63.95%. Sequences were neutral in terms of evolution (Tajima's criterion D=-1.01899, P>0.10 and Fu and Li's test D*=-1.39008, P>0.10; F*=-1.49775, P>0.10). A total of 19 haplotypes were identified based on nucleotide variation. High levels of haplotype diversity (h=0.744) and nucleotide diversity (Dij=0.01130) were detected in A. spinulosa, probably associated with its long evolutionary history, which has allowed the accumulation of genetic variation within lineages. Both the minimum spanning network and neighbor-joining trees generated for haplotypes demonstrated that current populations of A. spinulosa existing in Hainan, Guangdong, and Guangxi were subdivided into two geographical groups. An analysis of molecular variance indicated that most of the genetic variation (93.49%, P<0.001) was partitioned among regions. Wright's isolation by distance model was not supported across extant populations. Reduced gene flow by the Qiongzhou Strait and inbreeding may result in the geographical subdivision between the Hainan and Guangdong + Guangxi populations (FST=0.95, Nm=0.03). Within each region, the star-like pattern of phylogeography of haplotypes implied a population expansion process during evolutionary history. Gene genealogies together with coalescent theory provided significant information for uncovering phylogeography of A. spinulosa.

Biological Evolution↗

[Population genetic structure of the char species of the Northern Kuril Islands and the rank of the Dolly Varden Char in the system of the genus Salvelinus (Salmonidae: Teleostei)].

Analysis of the taxonomic position of most species and forms of the char (genus Salvelinus, Salmonidae: Teleostei) was made based on RAPD-PCR. The material was represented by samples from 29 populations from the Kuril Islands, coast of the Sea of Okhotsk, Kamchatka, Chukotka, Taymyr, Transbaikalia, the Kola Peninsula, Svalbard, Finland, and North America. It was shown that the genus Salvelinus splits into three well-justified clusters: (1) all the forms assigned to the Salvelinus alpinus--S. malma complex; (2) two samples of the White-Spotted Char from the Southern Kuril Islands and from Kamchatka; (3) two North American species, S. fontinalis and S. namaycush (samples of the North American species S. confluentis were absent from the collection). Analysis of the absolute values of genetic disctances of the S. alpinus--S. malma forms relative to S. leucomaenis, S. fontinalis, and S. namaycush revealed distances approaching the species rank between the following isolates: Frolikh Char, Mountain Char, Black Lake Char, Goggle-Eyed Char, and Neyva Char. Samples of Dolly Varden currently considered as "S. malma", do not constitute a separate cluster, falling within the group of the Arctic char S. alpinus. This conclusion is supported by the analysis of the results of three series of experiments by R. Phillips on ITS1 ribosome genes (Pleute et al., 1992; Phillips et al., 1995; Phillips et al., 1999). This indicates the infraspecific rank of malma within S. alpinus. Isolated populations of "Salvethymus svetovidovi" from the lake Elgygytgyn (Chukotka Peninsula) and of the char from the lake Chyornoye (Onekotan Island), recently described as S. gritzenkoi (Vasil'eva, Stygar, 2000), fell withing the S. alpinus--S. malma complex, the Onekotan char grouped together with another isolate from the same island. Comparison of genetic distances between the samples showed that the differences between the two isolated of Onekotan and migratory forms of the Kuril Islands are approximately equal, yet the homogeneity of the Chyornoye sample is higher than that of the other samples. The revealed 330-nucleotide diagnostic sequence of the Onekotan lake isolate showed identity of part of the fragment with a section of expressed DNA from the library of EST clones derived from the gills of Salmo salar, this possibly indicates the adaptive character of the evolution.

Animals↗

The hierarchical genetic structure of an urban town, Kidlington, Oxfordshire, examined by the coefficient of relationship by isonymy.

The surnames of the 3443 males registered to vote in Kidlington in 1977 yield a Coefficient of Relationship by Isonymy of 0.000564 {Ri = sigma(n(n-1))/2 N(N-1), in which n = the number of men of each surname and N = sigma n}. Those of the four wards separately average 0.000722. However, if one includes only one male of any one surname in each residence, the values are, respectively, 0.000534 and 0.000535. That is, the only structure seen between the two levels is in the influence of men of the same surname resident in the same house. An analysis of relationship by residence on the same street yields a value of Ri somewhat higher than that for the ward as a whole, however, suggesting that even within a ward there may be a tendency for the house of relatives occasionally to lie close together.

England↗

Physical and genetic structure of the glpD-malT interval of the Escherichia coli K-12 chromosome. Identification of two new structural genes of the glp-regulon.

A transducing lambda phage carrying glpD''lacZ, glpR, and malT was isolated from a strain harboring a glpD''lacZ fusion. Comparison of restriction endonuclease cleavage patterns of DNA isolated from this phage with that of the previously cloned malT region (Raibaud and Schwartz 1980) facilitated the construction of recombinant plasmids carrying different portions of the glpD-malT region. Results of minicell analysis and complementation studies showed that this region of the chromosome encodes at least five polypeptides. These included the previously identified glpD, glpR, and malT gene products. In addition, two new structural genes of the glp regulon (glpE and glpG) located between the glpD and glpR genes were identified. Hybrid plasmids carrying glpD''lacZ and glpR''lacZ fusions were constructed. Restriction endonuclease cleavage analysis of these two plasmids demonstrated that glpD and glpR are divergently transcribed.

Bacteriophage lambda↗

The genetic structure of Escherichia coli populations in primary and secondary habitats.

Escherichia coli were recovered from the members of two two-person households and their associated septic tanks. The E. coli were isolated using selective and non-selective isolation techniques, characterized using the method of multi-locus enzyme electrophoresis and screened for the presence of virulence factors associated with extra-intestinal disease by using PCR. The growth rate-temperature relationships of strains from the two habitats were also determined. Temporal variation explained 25% of the observed electrophoretic type (ET) diversity in the humans. Among-host variation accounted for 29% of the observed allelic diversity. In one household, ET diversity of the E. coli population in the septic tank was significantly lower than ET diversity in the humans providing the inputs to the septic tank. Molecular analysis of variance revealed that, on average, strains recovered from the septic tank of this household were genetically distinct from strains recovered from the humans providing the faecal inputs to the septic tank. Further, the growth rate-temperature response of strains differed between strains isolated from the septic tank and strains isolated from the humans. Septic tank isolates grew better at low temperatures than strains isolated from humans, but more slowly at high temperatures compared to the human isolates. By contrast, no real differences in ET diversity, allelic diversity, or the growth characteristics of strains could be detected between strains from the humans and strains from the septic tank of the other household. The results of this study suggest there are strains of E. coli that are better "adapted" to conditions found in the external environment compared to strains isolated from the gastrointestinal habitat. Further, the finding that the numerically dominant clones and clonal diversity in secondary habitats can differ substantially from those found in the source populations will confound efforts to identify the sources of faecal pollution in the environment.

Environment↗

Genetic structure of the deep-sea coral Lophelia pertusa in the northeast Atlantic revealed by microsatellites and internal transcribed spacer sequences.

The azooxanthellate scleractinian coral Lophelia pertusa has a near-cosmopolitan distribution, with a main depth distribution between 200 and 1000 m. In the northeast Atlantic it is the main framework-building species, forming deep-sea reefs in the bathyal zone on the continental margin, offshore banks and in Scandinavian fjords. Recent studies have shown that deep-sea reefs are associated with a highly diverse fauna. Such deep-sea communities are subject to increasing impact from deep-water fisheries, against a background of poor knowledge concerning these ecosystems, including the biology and population structure of L. pertusa. To resolve the population structure and to assess the dispersal potential of this deep-sea coral, specific microsatellites markers and ribosomal internal transcribed spacer (ITS) sequences ITS1 and ITS2 were used to investigate 10 different sampling sites, distributed along the European margin and in Scandinavian fjords. Both microsatellite and gene sequence data showed that L. pertusa should not be considered as one panmictic population in the northeast Atlantic but instead forms distinct, offshore and fjord populations. Results also suggest that, if some gene flow is occurring along the continental slope, the recruitment of sexually produced larvae is likely to be strongly local. The microsatellites showed significant levels of inbreeding and revealed that the level of genetic diversity and the contribution of asexual reproduction to the maintenance of the subpopulations were highly variable from site to site. These results are of major importance in the generation of a sustainable management strategy for these diversity-rich deep-sea ecosystems.

Animals↗

The pathogenicity island-associated K15 capsule determinant exhibits a novel genetic structure and correlates with virulence in uropathogenic Escherichia coli strain 536.

The K15 capsule determinant of uropathogenic Escherichia coli strain 536 (O6:K15:H31) is part of a novel 79.6-kb pathogenicity island (PAI) designated PAI V536 that is absent from the genome of nonpathogenic E. coli K-12 strain MG1655. PAI V536 shows typical characteristics of a composite PAI that is associated with the pheV tRNA gene and contains the pix fimbriae determinant as well as genes coding for a putative phosphoglycerate transport system, an autotransporter protein, and hypothetical open reading frames. A gene cluster coding for a putative general secretion pathway system, together with a kps(K15) determinant, is localized downstream of a truncated pheV gene ('pheV) also present in this chromosomal region. The distribution of genes present on PAI V536 was studied by PCR in different pathogenic and nonpathogenic E. coli isolates of various sources. Analysis of the 20-kb kps locus revealed a so far unknown genetic organization. Generally, the kps(K15) gene cluster resembles that of group 2 and 3 capsules, where two conserved regions (regions 1 and 3) are located up- or downstream of a highly variable serotype-specific region (region 2). Interestingly, recombination of a group 2 and 3 determinant may have been involved in the evolution of the K15 capsule-encoding gene cluster. Expression of the K15 capsule is important for virulence in a murine model of ascending urinary tract infection but not for serum resistance of E. coli strain 536.

Animals↗

Comparative microsatellite linkage analysis and genetic structure of two populations of F6 lines derived from Lycopersicon pimpinellifolium and L. cheesmanii.

A population of recombinant inbred lines (RILs) has several advantages over its F2 population counterpart with respect to quantitative trait loci (QTLs) and genomic studies. The objective of the investigation reported here was the comparative characterization by simple sequence repeat (SSR) and sequence characterized amplified region (SCAR) markers of two populations of F6 lines derived from Lycopersicon pimpinellifolium (P population, consisting of 142 lines) and L. cheesmanii (C population, consisting of 115 lines) and sharing the female parent, L. esculentum var. cerasiforme. Almost the same percentage of polymorphic markers was found for each population although a different set of markers was involved. The proportion of SSR primer pairs (93 in total) that resulted in polymorphism for the main band was larger (55-56%) than for SCAR ones (13-16%). The C population showed the largest proportion of markers with zygotic and gametic segregation distortion, which is in agreement with the larger genetic distance reported between L. esculentum and L. cheesmanii than with the former and L. pimpinellifolium. Zygotic distortion corresponded primarily to an excess of heterozygotes in both populations, suggesting that the increment of homozygosity was the main factor limiting viability/self-fertility of the lines. Despite both populations sharing the female parent, P alleles were slightly favored in the P population while E alleles were the most frequently fixed in the C population. A linkage map for each population was obtained, with the average distances between consecutive markers being 3.8 cM or 3.4 cM depending on the population. Discrepancy between the maps for the location of only four markers on chromosomes 3, 6 and 10 was observed. Two possible causes of this discrepancy were investigated and can not be discarded: (1) the presence of duplicated markers and (2) segregation distortion caused by the selective advantage of gametes carrying one of the two alleles. This marker characterization of both populations will continue and will enable the comparative QTLs and candidate gene analysis of complex traits towards a more efficient utilization of genetic resources and breeding strategies.

Chromosome Mapping↗