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At least 541 records · Page 30Linked to original sources
PubMed2006

Characterization of the Legionella anisa population structure by pulsed-field gel electrophoresis.

We analysed 38 French isolates of Legionella anisa by means of pulsed-field gel electrophoresis (PFGE) with single or double digestion. Double digestion was more discriminatory than single digestion, and can thus be useful for epidemiological studies of L. anisa. Several isolates from different parts of France clustered together on the basis of their PFGE patterns (similarity cutoff of 80%), suggesting that the L. anisa population structure is homogenous or that a few clones of L. anisa strains have spread widely in France.

Electrophoresis, Gel, Pulsed-Field↗
PubMed2001

Gp63 gene polymorphism and population structure of Leishmania donovani complex: influence of the host selection pressure?

The gp63 encoding genes were characterized by PCR-RFLP in 35 isolates representative of the Leishmania donovani complex (L. infantum, L. donovani, L. archibaldi and L. chagasi), with special attention to Mediterranean L. infantum from different geographical origins, and in separate groups from Old World Leishmania (L. major, L. tropica and L. aethiopica). The aim was to evaluate how the possible selective pressure by the host on these important surface proteins would influence structuring of our sample. Comparison was carried out with the structure obtained (i) from reported isoenzyme data, characters supposed to vary neutrally, and (ii) from PCR-RFLP analysis of gp63 inter-genic regions, containing nontranslated spacers and regulatory genes. Polymorphism within the gp63-encoding region, was much higher than in gp63 inter-genic regions. In the gp63 intra-genic dendrogram, the 4 species of L. donovani complex were discriminated and quite distinct from outgroups. Within L. infantum, geographical structuring was observed and did not overlap with the structure built-up from isoenzymes and inter-genic data. These results support the idea of a strong host-selection on gp63, at vector level but most of all at vertebrate (human or dog) immunological level. Furthermore, they illustrate how the nature of genetic characters may influence the perception of population structuring.

Algeria↗
PubMed1999

The analysis of population structure based on morphometric dimensions of metacarpal bones (the Island of Krk, Croatia).

The aim of this study was to investigate: 1) a possibility of using the morphometric dimensions of metacarpal bones for approximation of biological distances, and 2) a relationship of biological matrices, based on the morphometric dimensions of metacarpal bones to other biological (dermatoglyphic, genetic), bio-cultural (migration) and geographic variables. The morphometry of the metacarpal bones was performed according to Barnett and Nordin procedure and biological distances were estimated using Mahalanobis D2 method. Population structure was assessed through Mantel's permutation test using E2 genetic distances for classical serogenetic markers, DA genetic distances for HLA, DSW genetic distances for STRs, geographic distances expressed in kilometres, and migration kinship matrix estimated according to the method proposed by Malécot and modified by Morton. This study clearly indicated the need for applying factorial analytical approach to study the factor structure of morphometric variables that may be measured on six metacarpal bones as well as the need for conducting complex family and segregation analyses to address not only the intriguing issue of genetic vs. ecological impact onto the bone mineral turnover, but also to test the hypothesis of major gene control in determining bone mineral density.

Adult↗
PubMed1977

Theories of quasi-linkage and "affinity": some implications for population structure.

"Quasi-linkage" refers to nonrandom assortment of genes located on different chromosomes. Although this phenomenon has been widely observed in many organisms since the early part of this century, it is barely known. Interest in it was recently rekindled by the report of an association between quasi-linkage and the expression of genes belonging to a group of cancer viruses whose genomes are integrated in mouse chromosomes. This prompted an examination of the question whether "sustained meiotic affinity," which is one of the explanations proposed for quasi-linkage, can influence population structure in a manner unattainable by other known modes of heredity. It is shown for a two-locus two-allele system that equilibrium is attained with the gametic phase disequilibrium D greater than 0, leading to a permanent excess of the preferred genotypes. The possible relationship of these concepts to the inheritance of susceptibility to cancer and other diseases is discussed.

Chromosomes↗
PubMed2001

Genetic population structure of coagulase-negative staphylococci associated with carriage and disease in preterm infants.

Coagulase-negative staphylococci (CoNS) are a leading cause of sepsis in the neonatal intensive care unit (NICU) setting. To evaluate the hypothesis that isolates of CoNS associated with disease belong to hypervirulent clones, as opposed to being drawn randomly from the neonatal unit carriage flora, we conducted a prospective, case-controlled study in a busy NICU. Using pulsed-field gel electrophoresis (PFGE), we compared the population structures of CoNS isolates associated with bacteremia with isolates from the skin of healthy and infected neonates and with blood culture contaminants. Endemic clones of CoNS were identified, but there was no difference in the distribution of the 6 species or 73 PFGE types between the carriage and disease isolate groups; this suggests that hypervirulent clones with an enhanced ability to cause disease were not present in this NICU setting.

Anti-Bacterial Agents↗
PubMedDate not supplied

Clonal population structure of Neisseria meningitidis serogroup A isolated from epidemics and pandemics between 1915 and 1983.

A bacterial strain collection has been established consisting of 423 strains of Neisseria meningitidis serogroup A isolated from 23 epidemics or outbreaks that have occurred since 1960 as well as from earlier epidemics and from numerous nonepidemic situations. A combination of starch gel electrophoresis of seven cytoplasmic enzymes and sodium dodecyl sulfate-polyacrylamide gel electrophoresis of two outer membrane proteins was used to resolve the clonal population structure of these bacteria. Fifty electrophoretic types were assigned to 21 clones on the basis of a cluster analysis. The clones were separated into four distinct serogroup A subgroups, all of which were isolated from cases as recently as 1983. Most epidemics or outbreaks were characterized by their association with a single or predominant clone, although some epidemics were apparently of mixed etiology and others yielded rare isolates belonging to other clones. Seven predominant clones were recognized that have caused sets of epidemics since 1915. At least two of these sets can be considered to represent mutually exclusive pandemics first detected in 1967 and 1973, respectively. The results define a new typing scheme, which can be used for a comprehensive description of former and future epidemics. A list of strains and their epidemiologic data is appended.

Bacterial Outer Membrane Proteins↗
PubMed1993

Genetic control of population structure in heterogeneous strains of methicillin resistant Staphylococcus aureus.

Cultures of heterogeneous strains of methicillin resistant Staphylococcus aureus are composed of several subpopulations of cells that differ in their level of antibiotic resistance and frequencies. Experimental evidence is presented indicating that the number of these subpopulations, their resistance level and the frequency with which they are represented in a culture are strain-specific and reproducible with a surprising degree of precision from one culture to another. This implies a genetic control of population structure in these bacteria.

Electrophoresis, Gel, Pulsed-Field↗
PubMed2003

Mutation rates: estimating phase variation rates when fitness differences are present and their impact on population structure.

Phase variation is a mechanism of ON-OFF switching that is widely utilized by bacterial pathogens. There is currently no standardization to how the rate of phase variation is determined experimentally, and traditional methods of mutation rate estimation may not be appropriate to this process. Here, the history of mutation rate estimation is reviewed, describing the existing methods available. A new mathematical model that can be applied to this problem is also presented. This model specifically includes the confounding factors of back-mutation and the influence of fitness differences between the alternate phenotypes. These are central features of phase variation but are rarely addressed, with the result that some previously estimated phase variation rates may have been significantly overestimated. It is shown that, conversely, the model can also be used to investigate fitness differences if mutation rates are approximately known. In addition, stochastic simulations of the model are used to explore the impact of 'jackpot cultures' on the mutation rate estimation. Using the model, the impact of realistic rates and selection on population structure is investigated. In the absence of fitness differences it is predicted that there will be phenotypic stability over many generations. The rate of phenotypic change within a population is likely, therefore, to be principally determined by selection. A greater insight into the population dynamics of mutation rate processes can be gained if populations are monitored over successive time points.

Bacteria↗
PubMed1997

Plasmodium falciparum antigenic diversity: evidence of clonal population structure.

Plasmodium falciparum, the agent of malignant malaria, is one of mankind's most severe scourges. Efforts to develop preventive vaccines or remedial drugs are handicapped by the parasite's rapid evolution of drug resistance and protective antigens. We examine 25 DNA sequences of the gene coding for the highly polymorphic antigenic circumsporozoite protein. We observe total absence of silent nucleotide variation in the two nonrepeated regions of the gene. We propose that this absence reflects a recent origin (within several thousand years) of the world populations of P. falciparum from a single individual; the amino acid polymorphisms observed in these nonrepeat regions would result from strong natural selection. Analysis of these polymorphisms indicates that: (i) the incidence of recombination events does not increase with nucleotide distance; (ii) the strength of linkage disequilibrium between nucleotides is also independent of distance; and (iii) haplotypes in the two nonrepeat regions are correlated with one another, but not with the central repeat region they span. We propose two hypotheses: (i) variation in the highly polymorphic central repeat region arises by mitotic intragenic recombination, and (ii) the population structure of P. falciparum is clonal--a state of affairs that persists in spite of the necessary stage of physiological sexuality that the parasite must sustain in the mosquito vector to complete its life cycle.

Amino Acid Sequence↗
PubMed1975

Fission-fusion and lineal effect: aspects of the population structure of the Semai Senoi of Malaysia.

Analysis of histories and genealogies from seven relatively unacculturated, swidden-farming Semai settlements shows that the composition of local groups fluctuates through time. This instability is similar to a pattern which Neel and his colleagues have suggested is typical of primitive society, the fission-fusion model. In addition, the individuals comprising Semai fission groups are kinsmen which implies that the number of independent genomes represented is markedly less than the number of individual migrants (the lineal effect). Fission groups may form new villages or fuse with an established settlement. In either case, the genetic effects of such migration are more pronounced than would be expected on the basis of founder effect or random migration. Despite several conspicuous differences in social organization between the Semai and the South American Indians (e.g., bilateral vs. unilineal descent) whose population structure provided the empirical basis for the fission-fusion, lineal effect model, the basic similarities are striking. The Semai case thus lends support to the proposition that this pattern may be of some generality in technologically primitive populations.

Family↗
PubMed2003

Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.).

To assess the usefulness of linkage disequilibrium mapping in an autogamous, domesticated species, we have characterized linkage disequilibrium in the candidate region for xa5, a recessive gene conferring race-specific resistance to bacterial blight in rice. This trait and locus have good mapping information, a tractable phenotype, and available sequence data, but no cloned gene. We sampled 13 short segments from the 70-kb candidate region in 114 accessions of Oryza sativa. Five additional segments were sequenced from the adjacent 45-kb region in resistant accessions to estimate the distance at which linkage disequilibrium decays. The data show significant linkage disequilibrium between sites 100 kb apart. The presence of the xa5 resistant reaction in two ecotypes and in accessions with different haplotypes in the candidate region may indicate multiple origins or genetic heterogeneity for resistance. In addition, genetic differentiation between ecotypes emphasizes the need for controlling for population structure in the design of linkage disequilibrium studies in rice.

Genetic Variation↗
PubMed1994

Epidemiological relationships of Trypanosoma brucei stocks from south east Uganda: evidence for different population structures in human infective and non-human infective isolates.

This study represents an analysis of trypanosome strains circulating within a confined location over a short period of time during a sleeping sickness epidemic in S.E. Uganda. A large number of Trypanosoma brucei isolates (88) were collected from a variety of hosts (man, cattle, pigs and tsetse) from villages within a 10 km radius and were analysed for variation in isoenzyme patterns, restriction fragment length polymorphism (RFLP) in repetitive DNA sequences and susceptibility to human serum. The human infective stocks form a clearly distinguishable population when compared with other stocks circulating in the domestic cattle reservoir. The data here support the occurrence of genetic exchange between the cattle stocks while an 'epidemic' population structure involving limited genetic exchange is a characteristic of the human infective stocks. Furthermore, it is shown that when both RFLP and isoenzyme analysis are carried out most stocks appear to have individual genotypes. Stocks which were formerly grouped as zymodemes are better considered as a collected of distinct individuals.

Animals↗
PubMed1999

Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments.

During the past few years Archaea have been recognized as a widespread and significant component of marine picoplankton assemblages and, more recently, the presence of novel archaeal phylogenetic lineages has been reported in coastal marine benthic environments. We investigated the relative abundance, vertical distribution, phylogenetic composition, and spatial variability of Archaea in deep-sea sediments collected from several stations in the Atlantic Ocean. Quantitative oligonucleotide hybridization experiments indicated that the relative abundance of archaeal 16S rRNA in deep-sea sediments (1500 m deep) ranged from about 2.5 to 8% of the total prokaryotic rRNA. Clone libraries of PCR-amplified archaeal rRNA genes (rDNA) were constructed from 10 depth intervals obtained from sediment cores collected at depths of 1,500, 2,600, and 4,500 m. Phylogenetic analysis of rDNA sequences revealed the presence of a complex archaeal population structure, whose members could be grouped into discrete phylogenetic lineages within the two kingdoms, Crenarchaeota and Euryarchaeota. Comparative denaturing gradient gel electrophoresis profile analysis of archaeal 16S rDNA V3 fragments revealed a significant depth-related variability in the composition of the archaeal population.

Archaea↗
PubMed2003

Population structure and dispersal of the freshwater mosquitoes Culex annulirostris and Culex palpalis (Diptera: Culicidae) in Papua New Guinea and northern Australia.

In 1995 and 1998, outbreaks of Japanese encephalitis (JE) virus occurred for the first time in Australia. Virus isolation from pools of mosquitoes indicated Culex annulirostris Skuse was the most likely vector. It was hypothesized that wind-blown mosquitoes introduced JE from Papua New Guinea to the Torres Strait and Cape York, northern Australia. This study used levels of genetic differentiation, as indirect evidence of dispersal of mosquitoes between the two continents. The results have demonstrated that in the region incorporating Western Province in PNG, the Torres Strait and Cape York Peninsula, Cx. annulirostris is represented by a panmictic population, indicating frequent widespread dispersal throughout the region of investigation. The closely related Cx. Palpalis Taylor was also present at some locations but the population structure of this species is uncertain. This supports the hypothesis that wind-blown Cx. annulirostris and possibly Cx. Palpalis could be a possible mechanism for introduction of JE virus into Australia.

Animals↗
PubMed2004

Geographic and within-population structure in variable resistance to parasite species and strains in a vertebrate host.

Host resistance to parasites and parasite infectivity may be subject to significant genetically determined variation within species. However, relatively little is known of how this variability is structured in natural vertebrate populations and their macroparasites. A laboratory experiment on host susceptibility-parasite infectivity variation in a wildlife host-parasite system (subspecies of the anuran X. laevis and their polystome flatworms), including 33 pairwise allopatric and sympatric host-parasite combinations (three parasite geographical isolates x 11 host full-sibling families, n=600), revealed a complex pattern of infection success. Results amongst host sibships from different localities suggested that infection success was subject to a highly significant locality x parasite isolate interaction. Within localities, a highly significant sibship x isolate interaction also occurred in one of two groups of sibships examined. The existence of such interactions suggests a potential for frequency-dependent, Red Queen-like selection. Interaction between locality and isolate was partly due to higher infection levels in sympatric combinations, consistent with a general pattern of host-specific adaptation. However, some allopatric combinations produced unpredictably high infection levels, resulting in very asymmetrical cross-infectivity patterns (where the reciprocal cross-infections produced negligible infection). This phylogeographically structured host-parasite system may, therefore, sometimes generate local parasite strains with high infectivity to allopatric hosts. Secondary contact between populations could thus result in significant, and unequal, transfer of parasites.

Animals↗
PubMed2002

Deammonification in biofilm systems: population structure and function.

For the development of alternative concepts for the cost effective treatment of wastewaters with high ammonium content and low C/N-ratio, autotrophic consortia of micro-organisms with the ability to convert ammonium directly into N2 are of particular interest. Several full-scale industrial biofilm plants eliminating nitrogen without carbon source for years in a stable process, are suspected for some time to harbor active anaerobic ammonium oxidizers in deeper, oxygen-limited biofilm layers. In order to identify the processes of the single-stage nitrogen elimination (deammonification) in biofilm systems and to allocate them to the responsible micro-organisms, a deammonifying moving-bed pilot plant was investigated in detail. 15N-labelled tracer compounds were used as well as 16S rDNA libraries and in situ identification of dominant organisms. The usage of rRNA-targeted oligonucleotide probes (FISH) was particularly emphasized on the ammonium oxidizers of the beta-subclass of Proteobacteria and on the members of the order Planctomycetales. The combined application of these methods led to a deeper insight into the population structure and function of a deammonifying biofilm.

Biofilms↗
PubMed1999

Mating pattern and population structure in Escazú, Costa Rica: a study using marriage records.

A primary focus of historical demographic research is to understand how a population's mating pattern can affect its genetic structure. By using surnames, researchers can reconstruct gene flow into a population as well as within it: the population structure. Indeed, Lasker (1988a) noted that the distribution of surnames reflects the effect of mate choice on a population's genetic structure. Here, we study the mating pattern of a small, clearly established breeding population in Costa Rica (Escazú) during 1800-1839 and 1850-1899. We found that a large proportion of marriages involved individuals who were members of long-standing or core families. Indeed, 27 families provided 56% of all consorts throughout the period under study. When new surnames appeared in the records (presumably as a result of immigration), they were introduced more frequently by males, indicating that more males than females migrated into the community. The core families did not mate preferentially among themselves but appear to have readily accepted the migrants. Indeed,the greatest preponderance of repeated-surname marriages was that expected by chance. However, nonrandom surname repetition is evident when marriages between nonillegitimate consorts are analyzed. That is, the frequency of repeated-pair surname marriages is statistically significant in marriages involving brides and grooms who carried 2 surnames. Interestingly, significant departures from random repetition of surnames occurred during the decade in which the great cholera epidemic affected Costa Rica and during the decade following it. This departure from panmixia supports the notion that mating patterns were altered as a result of the epidemic, a suggestion we made previously when we reported that inbreeding increased in these same decades (Madrigal and Ware 1997).

Catholicism↗
PubMed1995

Genetic diversity and population structure of Trypanosoma brucei: clonality versus sexuality.

Genomic fingerprinting by arbitrarily primed PCR was used to analyze the genetic variability among 59 Trypanosoma brucei stocks representing the three T. brucei subspecies isolated from various hosts and different countries in Africa. 14 oligonucleotide primers revealed 355 polymorphic binary characters which were used for phenetic and phylogenetic analysis and to perform recombination tests exploring the linkage disequilibrium in the sample. There was good concordance between arbitrarily primed PCR polymorphisms and isoenzyme data previously collected for many of the same strains [1]. However, the arbitrarily primed PCR typing was more discerning than multilocus enzyme electrophoresis typing. Phenetic and phylogenetic analysis using arbitrarily primed PCR markers did not confirm T. brucei brucei and T. brucei rhodesiense as separate subspecies, but T. brucei gambiense group I was monophyletic, confirming this group as suitable for the subspecies status. With this exception, there were no clear lineages among the sample, other than clustering of East African stocks and clustering of West African stocks. Some features of the phylogenetic analysis suggested that the population structure was not strictly clonal though recombination tests showed linkage disequilibrium, even in the absence of repeated genotypes. While genotypes appear stable enough for tracking in applied studies, sexuality will impact at the evolutionary time scale, and may be more frequent under some ecological conditions. The arbitrarily primed PCR approach should be an effective and simple approach to follow epidemics and to quantify the role of sexuality in T. brucei populations.

Africa↗