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At least 883 records · Page 49Linked to original sources
PubMed2001

Ancestral divergence, genome diversification, and phylogeographic variation in subpopulations of sorbitol-negative, beta-glucuronidase-negative enterohemorrhagic Escherichia coli O157.

The O157:H7 lineage of enterohemorrhagic Escherichia coli is a geographically disseminated complex of highly related genotypes that share common ancestry. The common clone that is found worldwide carries several markers of events in its evolution, including markers for acquisition of virulence genes and loss of physiological characteristics, such as sorbitol fermentation ability and beta-glucuronidase production. Populations of variants that are distinct with respect to motility and the sorbitol and beta-glucuronidase markers appear to have diverged at several points along the inferred evolutionary pathway. In addition to these variants, distinct subpopulations of the contemporary non-sorbitol-fermenting, beta-glucuronidase-negative O157:H7 clone were recently detected among bovine and human clinical isolates in the United States by using high-resolution genome comparison. In order to determine if these recently described subpopulations were derived from a regional or ancestral divergence event, we used octamer-based genome scanning, marker sorting, and DNA sequence analysis to examine their phylogenetic relationship to populations of non-sorbitol-fermenting, beta-glucuronidase negative O157:H7 and O157:H- strains from Australia. The inferred phylogeny is consistent with the hypothesis that subpopulations on each continent resulted from geographic spread of an ancestral divergence event and subsequent expansion of distinct subpopulations. Marker sorting and DNA sequence analyses identified sets of monophyletic markers consistent with the pattern of divergence and demonstrated that phylogeographic variation occurred through emergence of regional subclones and concentration of regional polymorphisms among distinct subpopulations. DNA sequence analysis of representative polyphyletic markers showed that genome diversity accrued through random drift and bacteriophage-mediated events.

Animals↗
PubMed2003

Genome diversification in phylogenetic lineages I and II of Listeria monocytogenes: identification of segments unique to lineage II populations.

Thirteen different serotypes of Listeria monocytogenes can be distinguished on the basis of variation in somatic and flagellar antigens. Although the known virulence genes are present in all serotypes, greater than 90% of human cases of listeriosis are caused by serotypes 1/2a, 1/2b, and 4b and nearly all outbreaks of food-borne listeriosis have been caused by serotype 4b strains. Phylogenetic analysis of these three common clinical serotypes places them into two different lineages, with serotypes 1/2b and 4b belonging to lineage I and 1/2a belonging to lineage II. To begin examining evolution of the genome in these serotypes, DNA microarray analysis was used to identify lineage-specific and serotype-specific differences in genome content. A set of 44 strains representing serotypes 1/2a, 1/2b, and 4b was probed with a shotgun DNA microarray constructed from the serotype 1/2a strain 10403s. Clones spanning 47 different genes in 16 different contiguous segments relative to the lineage II 1/2a genome were found to be absent in all lineage I strains tested (serotype 4b and 1/2b) and an additional nine were altered exclusively in 4b strains. Southern hybridization confirmed that conserved alterations were, in all but two loci, due to absence of the segments from the genome. Genes within these contiguous segments comprise five functional categories, including genes involved in synthesis of cell surface molecules and regulation of virulence gene expression. Phylogenetic reconstruction and examination of compositional bias in the regions of difference are consistent with a model in which the ancestor of the two lineages had the 1/2 somatic serotype and the regions absent in the lineage I genome arose by loss of ancestral sequences.

Biological Transport↗
PubMed2004

Comparative analysis of agr locus diversification and overall genetic variability among bovine and human Staphylococcus aureus isolates.

The accessory gene regulator (agr) is a central system that controls the expression of Staphylococcus aureus virulence factors. In this study, the distribution of agr alleles, defined by agr restriction fragment length polymorphism within agr interference groups, among S. aureus isolates from bovine and human origin was measured with PCR-based techniques. Statistically highly significant associations of some agr alleles with the infection of a specific host were found. The genetic difference between the two S. aureus populations was further stressed after analysis of their genetic background by binary typing.

Animals↗
PubMed2004

Continuing diversification of Neisseria meningitidis W135 as a primary cause of meningococcal disease after emergence of the serogroup in 2000.

The occurrence of a clonal outbreak of serogroup W135 (of the electrophoretic type 37 [ET-37] clonal complex) meningococcal disease among Hajj pilgrims in 2000 has led to enhanced surveillance of the evolution of this particular serogroup, formerly considered rare, in invasive infections. Since the first case of meningococcal disease due to a serogroup W135 strain was detected in France in 1994, all isolates were characterized phenotypically. We further used phenotypic and genotypic approaches to type the 101 serogroup W135 strains isolated from patients with invasive meningococcal diseases in France in 2001 and 2002. Overall, 55% of these isolates had Hajj strain-related phenotypes (60 and 52% in 2001 and 2002, respectively), although only 45% belonged to the ET-37 clonal complex. Moreover, pulsed-field gel electrophoresis of the ET-37 clonal complex isolates showed that only 32% of the serogroup W135 isolates were indistinguishable from the 2000 Hajj-related strain. Our results suggest the continuous emergence of new genetic lineages of serogroup W135 independently of the 2000 global outbreak.

Bacterial Typing Techniques↗
PubMed2006

Expansion and diversification of virus-specific T cells following immunization of human immunodeficiency virus type 1 (HIV-1)-infected individuals with a recombinant modified vaccinia virus Ankara/HIV-1 Gag vaccine.

Affordable therapeutic strategies that induce sustained control of human immunodeficiency virus type 1 (HIV-1) replication and are tailored to the developing world are urgently needed. Since CD8(+) and CD4(+) T cells are crucial to HIV-1 control, stimulation of potent cellular responses by therapeutic vaccination might be exploited to reduce antiretroviral drug exposure. However, therapeutic vaccines tested to date have shown modest immunogenicity. In this study, we performed a comprehensive analysis of the changes in virus-specific CD8(+) and CD4(+) T-cell responses occurring after vaccination of 16 HIV-1-infected individuals with a recombinant modified vaccinia virus Ankara-vectored vaccine expressing the consensus HIV-1 clade A Gag p24/p17 sequences and multiple CD8(+) T-cell epitopes during highly active antiretroviral therapy. We observed significant amplification and broadening of CD8(+) and CD4(+) gamma interferon responses to vaccine-derived epitopes in the vaccinees, without rebound viremia, but not in two unvaccinated controls followed simultaneously. Vaccine-driven CD8(+) T-cell expansions were also detected by tetramer reactivity, predominantly in the CD45RA(-) CCR7(+) or CD45RA(-) CCR7(-) compartments, and persisted for at least 1 year. Expansion was associated with a marked but transient up-regulation of CD38 and perforin within days of vaccination. Gag-specific CD8(+) and CD4(+) T-cell proliferation also increased postvaccination. These data suggest that immunization with MVA.HIVA is a feasible strategy to enhance potentially protective T-cell responses in individuals with chronic HIV-1 infection.

AIDS Vaccines↗
PubMed1981

Linkage and evolutionary diversification of developmentally regulated multigene families: tandem arrays of the 401/18 chorion gene pair in silkmoths.

The coordinately expressed silkmoth chorion genes, 401 and 18, are closely linked as a pair, in divergent orientation. Analysis of overlapping clones (chromosomal "walk") demonstrated that each of the multiple copies of this gene pair is embedded within a larger deoxyribonucleic acid unit, which is tandemly repeated in a few arrays or possibly a single array. Southern analysis and examination of clones from a single individual moth demonstrated that the repeat units are extensively polymorphic in restriction sites, length, and possibly number, no differential amplification was evident during choriogenesis. Intron and 5'-flanking sequences were shown to be specific for the 401/18 gene pair and not to be present elsewhere in the genome. The spatial distribution of variations in the genes and their flanking sequences were examined.

Animals↗
PubMed1996

The receptor-DNA complex determines the retinoid response: a mechanism for the diversification of the ligand signal.

To obtain insights into the principles governing the complex biological responses to retinoids, we have analyzed the ligand sensitivities of various retinoid receptor-DNA complexes. We find that different retinoid receptor heterodimers show distinct activation patterns with various response elements while a given heterodimer can be activated at different retinoic acid concentrations on different response elements. In vitro binding experiments suggest that the same retinoic acid receptor-retinoid X receptor (RAR-RXR) heterodimer can have different ligand affinities, depending on the response element it is bound to. The differential responses of a particular receptor heterodimer with various retinoic acid responsive elements can be enhanced through the use of conformationally restricted retinoids. RAR- and RXR-selective retinoids can also synergistically activate the receptor heterodimers, indicating that both partners in the heterodimer can contribute to ligand-induced transcriptional activation. However, the relative influence of the RAR or RXR partner is specific for each response element. Together, our data demonstrate that it is the receptor-DNA complex and not the receptor alone that determines the ligand response. This flexibility allows for a highly pleiotropic retinoid response. Furthermore, conformationally restricted retinoids can accentuate the differential responses and exhibit a certain degree of gene selectivity by differentially activating the RAR or RXR component in the context of a given response element.

Animals↗
PubMed2000

Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily.

This review summarizes the recent discovery of the cupin superfamily (from the Latin term "cupa," a small barrel) of functionally diverse proteins that initially were limited to several higher plant proteins such as seed storage proteins, germin (an oxalate oxidase), germin-like proteins, and auxin-binding protein. Knowledge of the three-dimensional structure of two vicilins, seed proteins with a characteristic beta-barrel core, led to the identification of a small number of conserved residues and thence to the discovery of several microbial proteins which share these key amino acids. In particular, there is a highly conserved pattern of two histidine-containing motifs with a varied intermotif spacing. This cupin signature is found as a central component of many microbial proteins including certain types of phosphomannose isomerase, polyketide synthase, epimerase, and dioxygenase. In addition, the signature has been identified within the N-terminal effector domain in a subgroup of bacterial AraC transcription factors. As well as these single-domain cupins, this survey has identified other classes of two-domain bicupins including bacterial gentisate 1, 2-dioxygenases and 1-hydroxy-2-naphthoate dioxygenases, fungal oxalate decarboxylases, and legume sucrose-binding proteins. Cupin evolution is discussed from the perspective of the structure-function relationships, using data from the genomes of several prokaryotes, especially Bacillus subtilis. Many of these functions involve aspects of sugar metabolism and cell wall synthesis and are concerned with responses to abiotic stress such as heat, desiccation, or starvation. Particular emphasis is also given to the oxalate-degrading enzymes from microbes, their biological significance, and their value in a range of medical and other applications.

Amino Acid Motifs↗
PubMed2026

Genomic and phenotypic diversification of Pseudomonas aeruginosa during sustained exposure to a ciliate predator.

UNLABELLED: Predator-mediated selection is an important ecological force shaping bacterial evolution, but its effects on genomic adaptation and virulence in opportunistic pathogens are not fully understood. Here, we used experimental evolution to study how exposure to the ciliate predator Tetrahymena thermophila affects Pseudomonas aeruginosa. Replicate populations were evolved for 60 days with or without the predator, followed by whole-genome shotgun metagenomic sequencing and phenotypic analyses. Both treatments showed strong selection and evidence of parallel evolution at gene and nucleotide levels, indicating constrained adaptation. However, predator exposure altered evolutionary dynamics. Predator-evolved populations showed a wider distribution of mutation frequencies, with many mutations persisting at intermediate frequencies, consistent with increased clonal interference and ongoing competition among lineages. In contrast, populations evolved without predators showed more high-frequency mutations, consistent with selective sweeps, although some low-frequency variants remained. Despite substantial genomic change, phenotypic outcomes were variable. Virulence in an invertebrate host model did not consistently increase. Instead, evolved isolates showed context-dependent changes, including modest decreases or occasional increases. Competition assays also showed no consistent fitness advantage for predator-evolved isolates, suggesting trade-offs between predator resistance and growth in other environments. Overall, predator-mediated selection reshaped evolutionary dynamics by maintaining diversity and altering the balance of lineages rather than producing uniform increases in virulence. These results highlight how ecological complexity influences adaptive evolution and the context-dependent nature of pathogen traits. IMPORTANCE: Opportunistic pathogens such as Pseudomonas aeruginosa often evolve in environmental settings before infecting hosts, raising questions about how ecological interactions influence virulence. Predator-mediated selection has been suggested to increase virulence via coincidental evolution, but evidence is inconsistent. Here, we show that exposure to a eukaryotic predator does not consistently elevate virulence but does reshape evolutionary dynamics by altering how mutations spread in populations. Predator-exposed populations retained more intermediate-frequency mutations, consistent with increased clonal interference and ongoing competition among lineages, whereas non-predator populations were dominated by selective sweeps. These differences were also reflected in functional targets of adaptation, with predator exposure favoring mutations in genes involved in environmental sensing and interaction. Together, these findings suggest that ecological complexity shapes the dynamics of adaptation rather than driving a single evolutionary outcome, highlighting that virulence is an emergent property influenced by underlying evolutionary processes.

Pseudomonas aeruginosa↗
PubMed1999

Diversification of Pseudomonas corrugata 2140 produces new phenotypes altered in GC-FAME, BIOLOG, and in vitro inhibition profiles and taxonomic identification.

Bacteria are known to rapidly produce new phenotypes, but it is unclear how phenotype "plasticity" relates to studies on the population ecology of bacteria in complex environments. We characterised a collection of 14 spontaneous phenotype variants, derived from in vitro and in vivo cultures (wheat roots) of Pseudomonas corrugata 2140, using fatty acid methyl ester profiles (GC-FAME), carbon substrate utilisation (BIOLOG), and in vitro inhibition against seven soil microorganisms. All three phenotype profiles indicated marked differences between some variants and the parent isolate. Some variant types were classified taxonomically by GC-FAME as different species to their wild-type parent, and up to a Euclidian distance of 11 from their parent. Taxonomic identification by the BIOLOG assay was more consistent; however, use of 22 carbon sources were altered (lost or gained) in one or more variants. All variant types had a reduced ability to inhibit one or more test organisms, depending on the variant and test organism. Hierarchical cluster analysis of variants using GC-FAME, BIOLOG, and inhibition profiles produced different groupings. The ability of variants to cross taxonomic boundaries specified by the GC-FAME and BIOLOG libraries at the species level has implications for both taxonomy and the ecological study of bacterial communities.

Antibiosis↗
PubMed2003

Flower development: initiation, differentiation, and diversification.

Flowering is one of the most intensively studied processes in plant development. Despite the wide diversity in floral forms, flowers have a simple stereotypical architecture. Flowers develop from florally determined meristems. These small populations of cells proliferate to form the floral organs, including the sterile outer organs, the sepals and petals, and the inner reproductive organs, the stamens and carpels. In the past decade, analyses of key flowering genes have been carried out primarily in Arabidopsis and have provided a foundation for understanding the underlying molecular genetic mechanisms controlling different aspects of floral development. Such studies have illuminated the transcriptional cascades responsible for the regulation of these key genes, as well as how these genes effect their functions. In turn, these studies have resulted in the refinement of the original ideas of how flowers develop and have indicated the gaps in our knowledge that need to be addressed.

Arabidopsis↗
PubMed2001

Diversification of cardiac insulin signaling involves the p85 alpha/beta subunits of phosphatidylinositol 3-kinase.

Ventricular cardiomyocytes and cardiac tissue of lean and genetically obese (fa/fa) Zucker rats were used 1) to study the role of the p85 regulatory subunit isoforms p85 alpha and p85 beta for insulin signaling through the phosphatidylinositol (PI) 3-kinase pathway, and 2) to elucidate the implications of these mechanisms for cardiac insulin resistance. Western blot analysis of cardiomyocyte lysates revealed expression of p85 alpha and p85 beta but no detectable amounts of the splice variants of p85 alpha. Essentially no p85 alpha subunit of PI 3-kinase was found to be associated with insulin receptor substrate (IRS)-1 or IRS-2 in basal and insulin-stimulated (5 min) cardiomyocytes. Instead, insulin produced a twofold increase in p85 beta associated with IRS-1, leading to a three- to fourfold increase in p85 beta-associated PI 3-kinase activity. This response was significantly reduced in obese animals. Comparable results were obtained in the intact heart after in vivo stimulation. In GLUT-4-containing vesicles, an increased abundance (3.7 +/- 0.7-fold over basal) of p85 alpha was observed after insulin stimulation of lean animals, with no significant effect in the obese group. No p85 beta could be detected in GLUT-4-containing vesicles. Recruitment of the p110 catalytic subunit of PI 3-kinase and a twofold increase in enzyme activity in GLUT-4-containing vesicles by insulin was observed only in lean rats. We conclude that, in the heart, p85 alpha recruits PI 3-kinase activity to GLUT-4 vesicles, whereas p85 beta represents the main regulator of IRS-1- and IRS-2-mediated PI 3-kinase activation. Furthermore, multiple defects of PI 3-kinase activation, involving both the p85 alpha and the p85 beta adaptor subunits, may contribute to cardiac insulin resistance.

Animals↗
PubMed2004

Rapid evolution and diversification of mammalian alpha-defensins as revealed by comparative analysis of rodent and primate genes.

Mammalian alpha-defensins constitute a family of cysteine-rich, cationic antimicrobial peptides produced by phagocytes and intestinal Paneth cells, playing an important role in innate host defense. Following comprehensive computational searches, here we report the discovery of complete repertoires of the alpha-defensin gene family in the human, chimpanzee, rat, and mouse with new genes identified in each species. The human genome was found to encode a cluster of 10 distinct alpha-defensin genes and pseudogenes expanding 132 kb continuously on chromosome 8p23. Such alpha-defensin loci are also conserved in the syntenic chromosomal regions of chimpanzee, rat, and mouse. Phylogenetic analyses showed formation of two distinct clusters with primate alpha-defensins forming one cluster and rodent enteric alpha-defensins forming the other cluster. Species-specific clustering of genes is evident in nonprimate species but not in the primates. Phylogenetically distinct subsets of alpha-defensins also exist in each species, with most subsets containing multiple members. In addition, natural selection appears to have acted to diversify the functionally active mature defensin region but not signal or prosegment sequences. We concluded that mammalian alpha-defensin genes may have evolved from two separate ancestors originated from beta-defensins. The current repertoires of the alpha-defensin gene family in each species are primarily a result of repeated gene duplication and positive diversifying selection after divergence of mammalian species from each other, except for the primate genes, which were evolved prior to the separation of the primate species. We argue that the presence of multiple, divergent subsets of alpha-defensins in each species may help animals to better cope with different microbial challenges in the ecological niches which they inhabit.

Amino Acid Sequence↗
PubMed2002

Karyologic evidence of diversification of the genus Thrichomys (Rodentia, Echimyidae).

Karyologic analysis of Thrichomys specimens from different Brazilian localities, in Pantanal, Cerrado and Caatinga biomes, shows different chromosome complements. The 2n = 34, FN = 64 karyotype is found in Mato Grosso do Sul state; the 2n = 30, FN = 54 karyotype in Bahia, Pernambuco, Piauí and Ceará states; the 2n = 30, FN = 56 karyotype in Goiás and Tocantins states, the 2n = 28, FN = 50 karyotype in Minas Gerais state, the 2n = 28, FN = 52 and 2n = 26, FN = 48 karyotypes in Bahia state. Comparisons of G-band patterns allowed the identification of homologies shared by all karyotypes and show that the two karyotypes with the lowest diploid number (2n = 26 and 2n = 28) belong to two different evolutionary lineages. The most proper names for each karyomorphic population are: Thrichomys pachyurus for 2n = 34; Thrichomys apereoides apereoides for 2n = 28, FN = 50; Thrichomys apereoides laurentius for 2n = 30, FN = 54 and Thrichomys inermis for 2n = 26. Two karyotypes (2n = 28, FN = 52 and 2n = 30, FN = 56) could not be attributed to any subspecies. These different karyomorphotypes are allopatric and/or parapatric.

Animals↗
PubMed2005

The genome organization and diversification of maize and its allied species revisited: evidences from classical and FISH-GISH cytogenetic analysis.

The present review summarizes our classical and molecular cytogenetic investigations in the genus Zea. The results obtained from the meiotic behavior analysis of Zea species and hybrids, confirm the amphiploid nature of all species in the genus, with a basic number of x = 5 chromosomes. All species with 2n = 20 are diploidized allotetraploids, whereas Z. perennis (2n = 40) is an allooctoploid with four genomes somewhat divergent from one another. These analyses also revealed the existence of postzygotic reproductive isolation among Zea species. Our studies using genomic in situ hybridization (GISH) provide evidence about the evolutionary relationships among maize and its allied species, and reveal remarkable genomic divergences. Particularly, knob sequences were not completely shared between taxa previously considered to be closely related. Our data strongly suggest that the teosinte Z. mays parviglumis is not the only progenitor of cultivated maize. Introgression of Tripsacum into cultivated maize cannot be discarded.

DNA, Plant↗
PubMed2005

Diversification in indigenous and ethnic food culture.

A diversified food supply is contingent on underlying biodiversity in the locality where one lives or at a distance from it, if trade routes are established. Indigenous people generally settled at the water's edge so that aquatic foods made up part of their diversified diet, with the rest of the diversity dependent on how much they hunted and gathered, on herded animals, engagement in subsistence agriculture, the ability to process and preserve food and/or food commodities traded. The rapid urbanization of much of the world's population distances people from the origin of their food, the understanding of the required commodities in the human diet (e.g., aquatic food, plant foods, lean animal foods, what animals are fed, basics of freshness). At the same time, adequacy of food intake may be more reliably achieved when the food supply can continue irrespective of season, climate or distant conflict. Urban gardens partly rectify this discord between urbanization and a genuinely varied diet, replaced by purported variety where the same basic commodity is presented in many different forms (e.g., wheat grains such as bread, breakfast cereal of various kinds, pasta and baked goods). However, diversified processing may 'dilute out' health adverse techniques. The health benefits of a diversified diet relate in part to the environmental integrity, which the required biodiversity provides, in part to minimizing adverse factors, which may exceed acceptable thresholds in a narrow diet, and to the need for the wide spectrum of food components, macronutrients, micronutrients and phytochemicals, which Homo sapiens' physiology requires. Whilst most food diversity is attributable to plant sources, animal sources often provide significant nutritional security (e.g., fish and eggs for vitamin D, fish for n-3 fatty acids, lean meat for iron and zinc and in readily assimilable forms). Food diversity assumes greater importance with aging populations as their physical activity usually (if not necessarily) declines and the required food component diversity of the diet increases correspondingly. There are ways in which the required food diversity (probably 20-30 biologically different distinct foods over the course of a week) can be reduced. This is by the inclusion of more food component dense foods--like fish, lean meat, eggs, seeds and nuts. Not only does food diversity have relevance in a public health and food policy sense, but also in individual counseling in clinical practice. Assessment of a patient's food variety can be rapid and semi-quantitative, encouraging small and consequential changes in diet. When ethnicity is taken into account, in the clinical setting, this process can be even more rewarding for the practitioner and patient.

Aging↗