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PubMed2006

Evolutionary dynamics of Ralstonia solanacearum.

We investigated the genetic diversity, extent of recombination, natural selection, and population divergence of Ralstonia solanacearum samples obtained from sources worldwide. This plant pathogen causes bacterial wilt in many crops and constitutes a serious threat to agricultural production due to its very wide host range and aggressiveness. Five housekeeping genes, dispersed around the chromosome, and three virulence-related genes, located on the megaplasmid, were sequenced from 58 strains belonging to the four major phylogenetic clusters (phylotypes). Whereas genetic variation is high and consistent for all housekeeping loci studied, virulence-related gene sequences are more diverse. Phylogenetic and statistical analyses suggest that this organism is a highly diverse bacterial species containing four major, deeply separated evolutionary lineages (phylotypes I to IV) and a weaker subdivision of phylotype II into two subgroups. Analysis of molecular variations showed that the geographic isolation and spatial distance have been the significant determinants of genetic variation between phylotypes. R. solanacearum displays high clonality for housekeeping genes in all phylotypes (except phylotype III) and significant levels of recombination for the virulence-related egl and hrpB genes, which are limited mainly to phylotype strains III and IV. Finally, genes essential for species survival are under purifying selection, and those directly involved in pathogenesis might be under diversifying selection.

Evolution, Molecular↗
PubMed2005

Genotype x environment interactions, stoichiometric food quality effects, and clonal coexistence in Daphnia pulex.

The role of stoichiometric food quality in influencing genotype coexistence and competitive interactions between clones of the freshwater microcrustacean, Daphnia pulex, was examined in controlled laboratory microcosm experiments. Two genetically distinct clones of D. pulex, which show variation in their ribosomal rDNA structure, as well as differences in a number of previously characterized growth-rate-related features (i.e., life-history features), were allowed to compete in two different arenas: (1) batch cultures differing in algal food quality (i.e., high vs. low carbon:phosphorus (C:P ratio) in the green alga, Scenedesmus acutus); (2) continuous flow microcosms receiving different light levels (i.e., photosynthetically active radiation) that affected algal C:P ratios. In experiment 1, a clear genotype x environment interaction was determined with clone 1 out-competing clone 2 under high nutrient (i.e., low food C:P) conditions, while the exact opposite pattern was observed under low nutrient (i.e., high C:P) conditions. In experiment 2, clone 1 dominated over clone 2 under high light (higher C:P) conditions, but clonal coexistence was observed under low light (low C:P) conditions. These results indicate that food (nutrient) quality effects (hitherto an often overlooked factor) may play a role in microevolutionary (genotypic) responses to changing stoichiometric conditions in natural populations.

Analysis of Variance↗
PubMed2004

Evidence for gene flow and local clonal selection in field populations of the grain aphid (Sitobion avenae) in Britain revealed using microsatellites.

Samples of the grain aphid, Sitobion avenae (F.), a major European pest of cereals, were collected in June and July 1997 from fields sown with winter wheat in a rough transect south-west of Rothamsted, UK. These aphids were genotyped at four microsatellite loci known from previous studies to be highly polymorphic. Allelic frequencies were similar between samples collected in the fields and in the 12.2 m high suction trap at Rothamsted, and there were many widespread genotypes (clones), providing evidence that the species is highly migratory. However, field samples were found to display a high level of genotypic heterogeneity (= variable clonal composition), most probably the result of clonal selection. The suction trap genotypes sample were slightly different from the field samples, indicative of the inclusion of genotypes from plant hosts (cereals and grasses, Poaceae) other than winter wheat and/or genotype-biased emigration from the field. The relevance of these data to modelling of aphid outbreaks is briefly discussed.

Animals↗
PubMed2005

Exploitative and hierarchical antagonism in a cooperative bacterium.

Social organisms that cooperate with some members of their own species, such as close relatives, may fail to cooperate with other genotypes of the same species. Such noncooperation may take the form of outright antagonism or social exploitation. Myxococcus xanthus is a highly social prokaryote that cooperatively develops into spore-bearing, multicellular fruiting bodies in response to starvation. Here we have characterized the nature of social interactions among nine developmentally proficient strains of M. xanthus isolated from spatially distant locations. Strains were competed against one another in all possible pairwise combinations during starvation-induced development. In most pairings, at least one competitor exhibited strong antagonism toward its partner and a majority of mixes showed bidirectional antagonism that decreased total spore production, even to the point of driving whole populations to extinction. Differential response to mixing was the primary determinant of competitive superiority rather than the sporulation efficiencies of unmixed populations. In some competitive pairings, the dominant partner sporulated more efficiently in mixed populations than in clonal isolation. This finding represents a novel form of exploitation in bacteria carried out by socially competent genotypes and is the first documentation of social exploitation among natural bacterial isolates. Patterns of antagonistic superiority among these strains form a highly linear dominance hierarchy. At least some competition pairs construct chimeric, rather than segregated, fruiting bodies. The cooperative prokaryote M. xanthus has diverged into a large number of distinct social types that cooperate with clone-mates but exhibit intense antagonism toward distinct social types of the same species. Most lengthy migration events in nature may thus result in strong antagonism between migratory and resident populations, and this antagonism may have large effects on local population sizes and dynamics. Intense mutual antagonism appears to be more prevalent in this prokaryotic social species than has been observed in the eukaryotic social slime mold Dictyostelium discoideum, which also exhibits multicellular development. The finding of several cases of facultative social exploitation among these natural isolates suggests that such exploitation may occur frequently in nature in many prokaryotes with cooperative traits.

Animals↗
PubMed1990

Environmental health: flow cytometric methods to assess our water world.

Flow cytometry/cell sorting in aquatic sciences has been driven in two directions. The frontier directions are on shipboard and shore-based. On the one hand, the rapid analytical technique has been taken on shipboard to provide a real-time assessment of the particles and phytoplankton in water masses. These data also give information on the amount of vertical mixing and advection, and denote fronts between two or more water masses. There is an optical characterization (based on sizes, numbers, and pigment groups) of the individual primary producers, as well as detritus and suspended sediments. An optical-closure question is being addressed: "Does the total optical signal equal the sum of the parts?" Additionally, associations with chemical and physical oceanographic features are readily accomplished. A "census" of thousands of phytoplankton cells is obtained and can be mapped. Scientists are able to identify "who is where?" Such data are critical to understand the optical-feedback loop or the so-called photon-budget-in-the-sea, which in turn controls the rates at which growth processes occur in nature. On the other hand, an in-depth understanding is sought as to how particle size, shape, refractive index, nutritional status (nutrient and/or light limitation), growth dynamics, and cell cycle combine to control the optics (light scatter and fluorescence at the moment, and ideally absorption as well) or the photon-budget-of-the-cell. For this purpose, a shore-based facility associated with a diverse collection of phytoplankton is ideal. The development at Bigelow Laboratory of the Jane J. MacIsaac Facility is to provide services for the oceanographic community. Association and co-location with the Provasoli-Guillard Center for Culture of Marine Phytoplankton is key. Visitors are trained and given access to state-of-the-art instrumentation. Visiting investigators have available "the tropical, temperate, and polar seas" in concentrated form, as marine phytoplankton isolated worldwide and maintained as living clonal cultures. In this way, frontline cell biology questions can be addressed. The relentless exploration of standards and controls appropriate for the aquatic community must be continued. An intercalibration effort is a vital step. It is only with the widespread acceptance of particular reference materials and uniform optical filters among research groups utilizing FCM that comparable data sets describing aquatic particle distributions will be possible. For a global science, this strategy is imperative.

Colorimetry↗
PubMed2006

Minimal selfing, few clones, and no among-host genetic structure in a hermaphroditic parasite with asexual larval propagation.

Little is known about actual mating systems in natural populations of parasites or about what constitutes the limits of a parasite deme. These parameters are interesting because they affect levels of genetic diversity, opportunities for local adaptation, and other evolutionary processes. We expect that transmission dynamics and the distribution of parasites among hosts should have a large effect on mating systems and demic structure, but currently we have mostly speculation and very few data. For example, infrapopulations (all the parasites in a single host) should behave as demes if parasite offspring are transmitted as a clump from host to host over several generations. However, if offspring are well mixed, then the parasite component population (all the parasites among a host population) would function as the deme. Similarly, low mean intensities or a high proportion of worms in single infections should increase the selfing rate. For species having an asexual amplification stage, transmission between intermediate and definitive (final) hosts will control the variance in clonal reproductive success, which in turn could have a large influence on effective sizes and rates of inbreeding. We examined demic structure, selfing rates, and the variance in clonal reproductive success in natural populations of Plagioporus shawi, a hermaphroditic trematode that parasitizes salmon. Overall levels of genetic diversity were very high. An a posteriori inference of population structure overwhelmingly supports the component population as the deme, rather than individual infrapopulations. Only a single pair of 597 adult individuals was identified as clones. Thus, the variance in clonal reproductive success was almost zero. Despite being hermaphroditic, P. shawi appears to be almost entirely outcrossing. Genetic estimates of selfing (<5%) were in accordance with the proportion of parasites from single infections. Thus, it appears that individual flukes outcross whenever possible and only resort to selfing when alone. Finally, our data support the hypothesis that aquatic transmission and the use of several intermediate hosts promotes high genetic diversity and well-mixed infrapopulations.

Animals↗
PubMedDate not supplied

The development of humoral immunological memory to a T-cell-dependent antigen requires thymic emigrant cells.

Immunological memory is embodied in the rapid and enhanced immune responsiveness to previously encountered antigens. Classically, memory would depend on the presence of small resting long-lived specific lymphocytes which, through clonal expansion after priming with antigen, would be present at higher frequencies than in naive animals. Here we report that T-cell-reconstituted athymic mice, which lack recent thymic emigrants, mount a primary response to a T-cell-dependent antigen, but do not develop memory or the capacity to produce specific anti-TNP IgG1 antibodies during the secondary immune response. On the other hand, if thymocytes are continuously provided during the secondary response, a typical secondary immune response is achieved with high levels of specific IgG1. These results lead us to propose that the development of humoral immunological memory cannot be explained solely by the long life span of primed T lymphocytes, but is rather a dynamic state dependent on the continuous presence of recent thymic emigrants and qualitative functional differences in responder T cells.

Animals↗
PubMed1993

Do deleterious mutations act synergistically? Metabolic control theory provides a partial answer.

Metabolic control theory is used to derive conditions under which two deleterious mutations affecting the dynamics of a metabolic pathway act synergistically. It is found that two mutations tend to act mostly synergistically when they reduce the activity of the same enzyme. If the two mutations affect different enzymes, the conclusion depends on the way that fitness is determined by aspects of the pathway. The cases analyzed are: selection for (1) maximal flux, (2) maximal equilibrium concentration (pool size) of an intermediate, (3) optimal flux, (4) optimal pool size. The respective types of epistasis found are: (1) antagonistic, (2) partly synergistic, (3-4) synergism is likely to predominate over antagonism. This results in somewhat different predictions concerning the effect of metabolic mutations on fitness in prokaryotes and eukaryotes. The fact that bacteria are largely clonal but have often a mosaic gene structure is consistent with expectations from the model.

Enzymes↗
PubMed2003

Population structures and the role of genetic exchange in the zoonotic pathogen Cryptosporidium parvum.

Apicomplexan protozoan parasites include some of the most globally important human and animal pathogens, all of which have obligatory sexual cycles in their definitive hosts. Despite their importance and the relevance of understanding the population genetic structure and role of genetic exchange in generating diversity, population genetic analysis has largely been restricted to Plasmodium spp. and Toxoplasma gondii. These species show a considerable diversity of population structure suggesting different strategies for transmission and survival in mammalian hosts. We have undertaken a population genetic analysis of a further apicomplexan species (Cryptosporidium parvum) to extend our understanding of the diversity of genetic structures and test whether it has a clonal population structure. Nothing is known about the population structure of this parasite. We have analyzed 180 parasite isolates from both humans and cattle derived from a single discrete geographical area, using three minisatellite and four microsatellite markers that define 38 multilocus genotypes. Analysis of linkage disequilibria between pairs of loci combined with measures of genetic distance and similarity provides evidence that the sample comprises four genetically isolated populations. One group of human isolates consists primarily of two closely related multilocus genotypes (clonal), while the major subtypes of a second group, common to both humans and animals, show a panmictic population structure. The data provide an important step in understanding the role of genetic exchange in these parasites, which is an essential prerequisite for determining the value of multilocus genotyping for the analysis of sources of human infection as well as future molecular epidemiological studies.

Animals↗
PubMedDate not supplied

[An analysis of the viability of clonal plants based on a morphometric approach (exemplified by Calamagrostis langsdorffii)].

Clonal plants viability has been studied on the basis of morphostructure variability of clone modules. The research has been carried out on the Calamagrostis langsdorffii (Poaceae) in the flood-lands of the Amur River Basin (Khabarovsk Territory). Plants vitality has been evaluated by 26 morphometric parameters, characterizing their growth, productivity and reproduction. Clone ramets differed from each other by considerable variability and plasticity. Significant changes of all morphometric parameters according to humidity and alluvion gradients were very specific. Reproductive parameters were the most stable ones. Parameters of growth and dimension were characterised by increased variability. Wide reaction of morphometric parameters of C. langsdorffii to the changes in ecological conditions can be considered as an adaptation to the existence in dynamical environment of the flood-land.

Cloning, Organism↗
PubMed2006

Unintended consequences of plant transformation: a molecular insight.

Plant genomes are dynamic structures having both the system to maintain and accurately reproduce the information encoded therein and the ability to accept more or less random changes, which is one of the foundations of evolution. Crop improvement and various uncontrolled stress factors can induce unintended genetic and epigenetic variations. In this review it is attempted to summarize factors causing such changes and the molecular nature of these variations in transgenic plants. Unintended effects in transgenic plants can be divided into three main groups: first, pleiotropic effects of integrated DNA on the host plant genome; second, the influence of the integration site and transgene architecture on transgene expression level and stability; and third, the effect of various stresses related to tissue handling, regeneration and clonal propagation. Many of these factors are recently being redefined due to new researches, which apply modern highly sensitive analytical techniques and sequenced model organisms. The ability to inspect large portions of genomes clearly shows that tissue culture contributes to a vast majority of observed genetic and epigenetic changes. Nevertheless, monitoring of thousands transcripts, proteins and metabolites reveals that unintended variation most often falls in the range of natural differences between landraces or varieties. We expect that an increasing amount of evidence on many important crop species will support these observations in the nearest future.

Epigenesis, Genetic↗
PubMed2001

Drosophila par-1 is required for oocyte differentiation and microtubule organization.

BACKGROUND: Drosophila oocyte determination involves a complex process by which a single cell within an interconnected cyst of 16 germline cells differentiates into an oocyte. This process requires the asymmetric accumulation of both specific messenger RNAs and proteins within the future oocyte as well as the proper organization of the microtubule cytoskeleton, which together with the fusome provides polarity within the developing germline cyst. RESULTS: In addition to its previously described late oogenic role in the establishment of anterior-posterior polarity and subsequent embryonic axis formation, the Drosophila par-1 gene is required very early in the germline for establishing cyst polarity and for oocyte specification. Germline clonal analyses, for which we used a protein null mutation, reveal that Drosophila par-1 (par-1) is required for the asymmetric accumulation of oocyte-specific factors as well as the proper organization of the microtubule cytoskeleton. Similarly, somatic clonal analyses indicate that par-1 is required for microtubule stabilization in follicle cells. The PAR-1 protein is localized to the fusome and ring canals within the developing germline cyst in direct contact with microtubules. Likewise, in the follicular epithelium, PAR-1 colocalizes with microtubules along the basolateral membrane. However, in either case PAR-1 localization is independent of microtubules. CONCLUSIONS: The Drosophila par-1 gene plays at least two essential roles during oogenesis; it is required early in the germline for organization of the microtubule cytoskeleton and subsequent oocyte determination, and it has a second, previously described role late in oogenesis in axis formation. In both cases, par-1 appears to exert its effects through the regulation of microtubule dynamics and/or stability, and this finding is consistent with the defined role of the mammalian PAR-1 homologs.

Animals↗
PubMedDate not supplied

[The population genetics of nodule bacteria].

The data are reviewed on the population structure and evolutionary dynamics of the nodule bacteria (rhizobia) which are among the most intensively studied microorganisms. High level of the population polymorphism was demonstrated for the rhizobia populations using the enzyme electrophoresis (MLEE profiles). The average value of Nei's coefficient of heterogeneity (H = 1 - sigma pi2 [n/(n - 1)]) were: 0.590 for rhizobia (Rhizobium, Bradyrhizobium), 0.368 for enterobacteria (Escherichia, Salmonella, Shigella) and 0.452 for pathogenic bacteria (Bordetella, Borrelia, Erysipelothrix, Haemophilus, Helicobacter, Listeria, Mycobacterium, Neisseria, Staphylococcus) populations. In spite of being devoid of the effective systems for the gene conjugative transfer, many rhizobia populations possess an essentially panmictic structure. However, the enterobacteria populations in which the gene transfer may be facilitated due to the conjugative F- and R-factors, usually display the clonal population structure. The legume host plant is proved to be a key factor that determines the high levels of polymorphism and of panmixis as well as high evolutionary rates of the symbiotic bacteria populations. The host may ensure: a) an increase in mutation and gene transfer frequencies; b) stimulation of the competitive (selective) processes in both symbiotic and free-living rhizobia populations. A "cyclic" model of the rhizobia microevolution is presented which allows to assess the inputs the interstrain competition for the saprophytic growth and for the host nodulation into evolution of a plant-associated rhizobia population. The nodulation competitiveness in the rhizobia populations is responsible for the frequency-dependent selection of the rare genotypes which may arise in the soil bacterial communities as a result of the transfer of symbiotic (sym) genes from virulent rhizobia strains to either avirulent rhizobia or to the other (saprophytic, phytopathogenic) bacteria. Therefore, the nodulation competitiveness may ensure: a) panmictic structure of the natural rhizobia populations; b) high taxonomic diversity of rhizobia which was apparently caused by a broad sym gene expansion in the soil bacterial communities. The kin selection models are presented which explain evolution of the "altruistic" (essential for the host plant, but not for the bacteria themselves) symbiotic traits (e.g., the ability for symbiotic nitrogen fixation and for differentiation into non-viable bacteroids) in the rhizobia populations. These models are based on preferential multiplication of the nitrogen-fixing clones either in planta (due to an elevated supply of the nitrogen-fixing nodules with photosynthates) or ex planta (due to a release of the rhizopines from the nitrogen-fixing nodules). Speaking generally, interactions with the host plants provide a range of mechanisms increasing a genetic heterogeneity and an evolutionary potential in the associated rhizobia populations.

Altruism↗
PubMedDate not supplied

Information transfer at the immunological synapse.

Antigen-specific activation of T lymphocytes requires the interaction of their clonally distributed T-cell receptors with plasma membrane ligands composed of foreign peptide antigens bound to major histocompatibility complex molecules. For proliferation and differentiation to ensue, a variety of other adhesive and accessory proteins must also interact with their counter-receptors on the antigen-presenting cell to facilitate and complement the T-cell receptor-antigen recognition event. Recent studies have revealed that these various proteins show an unexpected degree of spatial organization in the zone of cell-cell contact. This region of membrane approximation is now referred to as the "immunological synapse" because of its functional analogy to the site of intercellular information transfer between neurons. Here, we review the evidence for signaling-dependent control of the dynamic changes in protein distribution that gives rise to the synapse and try to relate the emerging spatio-temporal information on synapse formation to T-cell biology.

Animals↗
PubMed2025

Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories.

Tumor evolution is driven by various mutational processes, ranging from single-nucleotide variants (SNVs) to large structural variants (SVs) to dynamic shifts in DNA methylation. Current short-read sequencing methods struggle to accurately capture the full spectrum of these genomic and epigenomic alterations due to inherent technical limitations. To overcome that, here we introduce an approach for long-read sequencing of single-cell derived subclones, and use it to profile 23 subclones of a mouse melanoma cell line, characterized with distinct growth phenotypes and treatment responses. We develop a computational framework for harmonization and joint analysis of different variant types in the evolutionary context. Uniquely, our framework enables detection of recurrent amplifications of putative driver genes, generated by independent SVs across different lineages, suggesting parallel evolution. In addition, our approach revealed gradual and lineage-specific methylation changes associated with aggressive clonal phenotypes. We also show our set of phylogeny-constrained variant calls along with openly released sequencing data can be a valuable resource for the development of new computational methods.

Journal Article↗
PubMed2003

Clonal diversity in the Japanese silver crucian carp, Carassius langsdorfii inferred from genetic markers.

The Japanese silver crucian carp, Carassius langsdorfii, is a naturally polyploid fish that reproduces by gynogenesis, resulting in a geographically clustered clonal population. To determine the amount of clonal diversity in this species, we used genetic markers to compare fish from several Japanese locations. Samples were collected from Lake Kasumigaura (Ibaraki Pref.), Lake Imba (Chiba Pref.), Lake Fukushimagata (Niigata Pref.), Lake Biwa (Shiga Pref.), Lake Koyama (Tottori Pref.), and the Niyodo and Monobe Rivers (Kochi Pref.). The genetic markers used were the microsatellite loci GF1(*), GF17(*), and GF29(*), as well as isozyme (creatinekinase CK(*)) and mtDNA (D-loop region) RFLP. In the seven locations sampled, 61 clonal lines were identified by combining the genotypes of the three microsatellite loci. Populations at all locations consisted of six to 28 clonal lines. Fourteen common clonal lines were detected in two or more locations, and 13 of these were observed in Lake Biwa. We suggest that these clonal lines have been widely distributed in Japanese freshwaters through the intentional stocking of fish species such as "gengorobuna" (C. cuvieri) and "ayu" (Plecoglossus altivelis altivelis) obtained from Lake Biwa and its adjacent waters. The CK(*) genotypes and mtDNA haplotypes of fish from Lake Kasumigaura differed from those of other locations.

Animals↗
PubMedDate not supplied

[The multinucleate cells of the spermatogenic layer in rats as a criterion of hypoxic damage to the testis].

The formation and dynamics of transformations of multinucleated cells in the spermatogenic layer was studied in mature male albino rats in a model experiment with 10-12 min. long clinical death followed by revivification at different periods of the postreanimation period. The maximum formation of multinucleated cells is observed on the 2nd-3rd days after revivification, and further their occurrence becomes less. With an increase of degenerative alterations in the nuclei and cytoplasm of multinucleated cells, the latter become isolated from the spermatogenic layer causing disturbances of its structure. A variant with the multiple formation of multinucleated cells is described resulting in an injury of the spermatogenic layer at a considerable distance. A supposition is put forward of the relationship of the formation of multinucleated cells with the clonal syncytial principle of organization of the developing sex cells and the cycle of spermatogenesis. The appearance of multinucleated cells is an undoubtable indicator of degenerative alterations of the spermatogenic layer under conditions of hypoxia.

Animals↗
PubMed2003

Effects of triclosan-containing rinse on the dynamics and antimicrobial susceptibility of in vitro plaque ecosystems.

Dental plaque microcosms were established under a feast-famine regimen within constant-depth film fermentors and exposed four times daily postfeeding to a triclosan (TR)-containing rinse (dentifrice) (TRD). This was diluted so that the antimicrobial content was 0.6 mg/ml. Microcosms were characterized by heterotrophic plate counts and PCR-denaturing gradient gel electrophoresis (DGGE) with primers specific for the V2-V3 region of the eubacterial 16S rRNA gene (rDNA). Dominant isolates and PCR amplicons were identified by partial sequencing of 16S rDNA. TRD caused considerable decreases in the counts of both gram-negative organisms and total anaerobic cells, transiently lowered the numbers of streptococci and actinomycetes, and markedly increased the proportion of lactobacilli. DGGE indicated the presence of putatively unculturable bacteria and showed that a Porphyromonas sp. and Selenomonas infelix had been inhibited by TRD. Pure culture studies of 10 oral bacteria (eight genera) showed that Neisseria subflava, Prevotella nigrescens, and Porphyromonas gingivalis were highly susceptible to TR, while the lactobacilli and streptococci were the least susceptible. Clonal expansion of the lactobacilli in the pulsed microcosm could be explained on the basis of TR activity. The mean MICs of TR, chlorhexidine, erythromycin, penicillin V, and vancomycin for the population before and after 5 days of exposure to TRD showed few significant changes. In conclusion, changes in plaque microcosm populations following repeated exposure to TRD showed inhibition of the most susceptible flora and clonal expansion of less susceptible species.

Anti-Bacterial Agents↗