12 results on '"Cooper, Vaughn S"'
Search Results
2. Breaking the language barrier: experimental evolution of non-native Vibrio fischeri in squid tailors luminescence to the host
- Author
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Schuster, Brian M., Perry, Lauren A., Cooper, Vaughn S., and Whistler, Cheryl A.
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- 2010
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3. Polygenic Adaptation and Clonal Interference Enable Sustained Diversity in Experimental Pseudomonas aeruginosa Populations.
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Harris, Katrina B, Flynn, Kenneth M, and Cooper, Vaughn S
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PSEUDOMONAS aeruginosa ,BACTERIAL adaptation ,CONVERGENT evolution ,GENOTYPES ,BIODIVERSITY - Abstract
How biodiversity arises and can be maintained in asexual microbial populations growing on a single resource remains unclear. Many models presume that beneficial genotypes will outgrow others and purge variation via selective sweeps. Environmental structure like that found in biofilms, which are associated with persistence during infection and other stressful conditions, may oppose this process and preserve variation. We tested this hypothesis by evolving Pseudomonas aeruginosa populations in biofilm-promoting arginine media for 3 months, using both a bead model of the biofilm life cycle and planktonic serial transfer. Surprisingly, adaptation and diversification were mostly uninterrupted by fixation events that eliminate diversity, with hundreds of mutations maintained at intermediate frequencies. The exceptions included genotypes with mutator alleles that also accelerated genetic diversification. Despite the rarity of hard sweeps, a remarkable 40 genes acquired parallel mutations in both treatments and often among competing genotypes within a population. These incomplete soft sweeps include several transporters (including pitA, pntB, nosD , and pchF) suggesting adaptation to the growth media that becomes highly alkaline during growth. Further, genes involved in signal transduction (including gacS , aer2, bdlA , and PA14_71750) reflect likely adaptations to biofilm-inducing conditions. Contrary to evolution experiments that select mutations in a few genes, these results suggest that some environments may expose a larger fraction of the genome and select for many adaptations at once. Thus, even growth on a sole carbon source can lead to persistent genetic and phenotypic variation despite strong selection that would normally purge diversity. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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4. One gene, multiple ecological strategies: A biofilm regulator is a capacitor for sustainable diversity.
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Mhatre, Eisha, Snyder, Daniel J., Sileo, Emily, Turner, Caroline B., Buskirk, Sean W., Fernandez, Nicolas L., Neiditchf, Matthew B., Waters, Christopher M., and Cooper, Vaughn S.
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BURKHOLDERIA cenocepacia ,QUORUM sensing ,CAPACITORS ,BACTERIAL population ,GENES - Abstract
Many bacteria cycle between sessile and motile forms in which they must sense and respond to internal and external signals to coordinate appropriate physiology. Maintaining fitness requires genetic networks that have been honed in variable environments to integrate these signals. The identity of the major regulators and how their control mechanisms evolved remain largely unknown in most organisms. During four different evolution experiments with the opportunist betaproteobacterium Burkholderia cenocepacia in a biofilm model, mutations were most frequently selected in the conserved gene rpfR. RpfR uniquely integrates two major signaling systems--quorum sensing and the motile-sessile switch mediated by cyclic-di-GMP--by two domains that sense, respond to, and control the synthesis of the autoinducer cis-2-dodecenoic acid (BDSF). The BDSF response in turn regulates the activity of diguanylate cyclase and phosphodiesterase domains acting on cyclic-di-GMP. Parallel adaptive substitutions evolved in each of these domains to produce unique life history strategies by regulating cyclic-di-GMP levels, global transcriptional responses, biofilm production, and polysaccharide composition. These phenotypes translated into distinct ecology and biofilm structures that enabled mutants to coexist and produce more biomass than expected from their constituents grown alone. This study shows that when bacterial populations are selected in environments challenging the limits of their plasticity, the evolved mutations not only alter genes at the nexus of signaling networks but also reveal the scope of their regulatory functions. [ABSTRACT FROM AUTHOR]
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- 2020
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5. Negative frequency‐dependent selection maintains coexisting genotypes during fluctuating selection.
- Author
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Turner, Caroline B., Buskirk, Sean W., Harris, Katrina B., and Cooper, Vaughn S.
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GENOTYPES ,BURKHOLDERIA cenocepacia ,POPULATION ecology ,POPULATION dynamics ,PSEUDOMONAS aeruginosa infections - Abstract
Natural environments are rarely static; rather selection can fluctuate on timescales ranging from hours to centuries. However, it is unclear how adaptation to fluctuating environments differs from adaptation to constant environments at the genetic level. For bacteria, one key axis of environmental variation is selection for planktonic or biofilm modes of growth. We conducted an evolution experiment with Burkholderia cenocepacia, comparing the evolutionary dynamics of populations evolving under constant selection for either biofilm formation or planktonic growth with populations in which selection fluctuated between the two environments on a weekly basis. Populations evolved in the fluctuating environment shared many of the same genetic targets of selection as those evolved in constant biofilm selection, but were genetically distinct from the constant planktonic populations. In the fluctuating environment, mutations in the biofilm‐regulating genes wspA and rpfR rose to high frequency in all replicate populations. A mutation in wspA first rose rapidly and nearly fixed during the initial biofilm phase but was subsequently displaced by a collection of rpfR mutants upon the shift to the planktonic phase. The wspA and rpfR genotypes coexisted via negative frequency‐dependent selection around an equilibrium frequency that shifted between the environments. The maintenance of coexisting genotypes in the fluctuating environment was unexpected. Under temporally fluctuating environments, coexistence of two genotypes is only predicted under a narrow range of conditions, but the frequency‐dependent interactions we observed provide a mechanism that can increase the likelihood of coexistence in fluctuating environments. [ABSTRACT FROM AUTHOR]
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- 2020
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6. Hidden resources in the Escherichia coli genome restore PLP synthesis and robust growth after deletion of the essential gene pdxB.
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Juhan Kim, Flood, Jake J., Kristofich, Michael R., Gidfar, Cyrus, Morgenthaler, Andrew B., Fuhrer, Tobias, Sauer, Uwe, Snyder, Daniel, Cooper, Vaughn S., Ebmeier, Christopher C., Old, William M., and Copley, Shelley D.
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DELETION mutation ,ESCHERICHIA coli ,GENOMES ,ENZYMES ,TURBIDITY - Abstract
PdxB (erythronate 4-phosphate dehydrogenase) is expected to be required for synthesis of the essential cofactor pyridoxal 5'-phosphate (PLP) in Escherichia coli. Surprisingly, incubation of the ΔpdxB strain in medium containing glucose as a sole carbon source for 10 d resulted in visible turbidity, suggesting that PLP is being produced by some alternative pathway. Continued evolution of parallel lineages for 110 to 150 generations produced several strains that grow robustly in glucose. We identified a 4-step bypass pathway patched together from promiscuous enzymes that restores PLP synthesis in strain JK1. None of the mutations in JK1 occurs in a gene encoding an enzyme in the new pathway. Two mutations indirectly enhance the ability of SerA (3-phosphoglycerate dehydrogenase) to perform a new function in the bypass pathway. Another disrupts a gene encoding a PLP phosphatase, thus preserving PLP levels. These results demonstrate that a functional pathway can be patched together from promiscuous enzymes in the proteome, even without mutations in the genes encoding those enzymes. [ABSTRACT FROM AUTHOR]
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- 2019
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7. Parallel genetic adaptation across environments differing in mode of growth or resource availability.
- Author
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Turner, Caroline B., Marshall, Christopher W., and Cooper, Vaughn S.
- Abstract
Abstract: Evolution experiments have demonstrated high levels of genetic parallelism between populations evolving in identical environments. However, natural populations evolve in complex environments that can vary in many ways, likely sharing some characteristics but not others. Here, we ask whether shared selection pressures drive parallel evolution across distinct environments. We addressed this question in experimentally evolved populations founded from a clone of the bacterium Burkholderia cenocepacia. These populations evolved for 90 days (approximately 600 generations) under all combinations of high or low carbon availability and selection for either planktonic or biofilm modes of growth. Populations that evolved in environments with shared selection pressures (either level of carbon availability or mode of growth) were more genetically similar to each other than populations from environments that shared neither characteristic. However, not all shared selection pressures led to parallel evolution. Genetic parallelism between low‐carbon biofilm and low‐carbon planktonic populations was very low despite shared selection for growth under low‐carbon conditions, suggesting that evolution in low‐carbon environments may generate stronger trade‐offs between biofilm and planktonic modes of growth. For all environments, a population's fitness in a particular environment was positively correlated with the genetic similarity between that population and the populations that evolved in that particular environment. Although genetic similarity was low between low‐carbon environments, overall, evolution in similar environments led to higher levels of genetic parallelism and that genetic parallelism, in turn, was correlated with fitness in a particular environment. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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8. Character displacement and the evolution of niche complementarity in a model biofilm community.
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Ellis, Crystal N., Traverse, Charles C., Mayo‐Smith, Leslie, Buskirk, Sean W., and Cooper, Vaughn S.
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BURKHOLDERIA cenocepacia ,BIOFILMS ,ECOLOGICAL niche ,BACTERIAL evolution ,BACTERIAL genetics - Abstract
Colonization of vacant environments may catalyze adaptive diversification and be followed by competition within the nascent community. How these interactions ultimately stabilize and affect productivity are central problems in evolutionary ecology. Diversity can emerge by character displacement, in which selection favors phenotypes that exploit an alternative resource and reduce competition, or by facilitation, in which organisms change the environment and enable different genotypes or species to become established. We previously developed a model of long-term experimental evolution in which bacteria attach to a plastic bead, form a biofilm, and disperse to a new bead. Here, we focus on the evolution of coexisting mutants within a population of Burkholderia cenocepacia and how their interactions affected productivity. Adaptive mutants initially competed for space, but later competition declined, consistent with character displacement and the predicted effects of the evolved mutations. The community reached a stable equilibrium as each ecotype evolved to inhabit distinct, complementary regions of the biofilm. Interactions among ecotypes ultimately became facilitative and enhanced mixed productivity. Observing the succession of genotypes within niches illuminated changing selective forces within the community, including a fundamental role for genotypes producing small colony variants that underpin chronic infections caused by B. cenocepacia. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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9. Parallel evolution of small colony variants in Burkholderia cenocepacia biofilms.
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Cooper, Vaughn S., Staples, Rachel K., Traverse, Charles C., and Ellis, Crystal N.
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EVOLUTIONARY theories , *BURKHOLDERIA cenocepacia , *BIOFILMS , *BIOLOGICAL variation , *PHENOTYPES , *GENETIC mutation - Abstract
A common phenotype within bacterial biofilms is the small, “wrinkly” colony, which may associate with worse prognoses from biofilm-associated infections. The mechanisms that produce these variants in Burkholderia are undefined. Here we report the mutational and ecological causes of wrinkly (W) colonies that evolved during experimental biofilm evolution of Burkholderia cenocepacia . Mutations clustered in a homologous pathway to the Pseudomonas wsp operon but with a distinct terminal signaling mechanism, and their parallel evolution suggested that they inhabited an equivalent biofilm niche. We tested this hypothesis of niche complementarity by measuring effects of substituting different W variants in the same evolved biofilm community. Despite phenotypic differences among W mutants growing alone, fitness of reconstituted mixed biofilms did not differ significantly. In conclusion, the evolution of small-colony variants in Burkholderia biofilms appears to be driven by an ecological opportunity that generates strong selection for constitutive wsp mutants to inhabit a common niche. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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10. Antibiotic resistance correlates with transmission in plasmid evolution.
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Turner, Paul E., Williams, Elizabeth S. C. P., Okeke, Chijioke, Cooper, Vaughn S., Duffy, Siobain, and Wertz, John E.
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DRUG resistance in microorganisms ,PLASMIDS ,TETRACYCLINE ,BIOMARKERS ,ESCHERICHIA coli ,BIOLOGICAL evolution - Abstract
Conjugative (horizontally transmissible) plasmids are autonomous replicators, whose 'self-interests' do not necessarily overlap with those of their hosts. This situation causes plasmids and bacteria to sometimes experience differing selection pressures. Escherichia coli plasmid pB15 contains genes for resistance to several antibiotics, including tetracycline. When plasmid-bearing cells were experimentally evolved in the laboratory, changes in resistance level in the unselected tetracycline marker coincided with changes in plasmid rates of vertical versus horizontal transmission. Here, we used minimum inhibitory assays that measure resistance levels as quantitative traits to determine phenotypic correlations among plasmid characters and to estimate divergence among plasmid lineages. Results suggested that plasmid-level evolution led to formation of two phenotypically dissimilar groups: virulent (highly infectious) and avirulent (weakly infectious) plasmids. In contrast, measures of carbon-source utilization, and fitness assays relative to a common competitor revealed that bacterial hosts generally converged in phenotypic performance, despite divergence among their associated plasmids. Preliminary sequence analyses suggested that divergence in plasmid conjugation was due to altered configurations of a shufflon region (a site-specific recombination system), where genetic rearrangements affect conjugative ability. Furthermore, we proposed that correlated resistance and transmission in pB15 derivatives were caused by a tetracycline-resistance transposon inserted into a transfer operon, allowing transcription from its promoter to simultaneously affect both plasmid resistance and transmission. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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11. Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature
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David A. Stahl, Judy D. Wall, Bo Wu, Adam P. Arkin, Megan L. Kempher, Jizhong Zhou, Rong Song, Xuanyu Tao, Aifen Zhou, Rosenzweig, Raphael F, and Cooper, Vaughn S
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0106 biological sciences ,Physiological ,Population ,Biology ,Bacterial Physiological Phenomena ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,Divergence ,03 medical and health sciences ,temperature stress ,Virology ,Genetics ,Desulfovibrio vulgaris ,Adaptation ,education ,Gene ,030304 developmental biology ,0303 health sciences ,education.field_of_study ,Experimental evolution ,Natural selection ,Sulfates ,fungi ,evolutionary biology ,Temperature ,food and beverages ,Genetic Variation ,Replicate ,QR1-502 ,stress adaptation ,Genetic divergence ,Evolutionary biology ,Mutation ,Genetic Fitness ,Directed Molecular Evolution ,Oxidation-Reduction - Abstract
Adaptation via natural selection is an important driver of evolution, and repeatable adaptations of replicate populations, under conditions of a constant environment, have been extensively reported. However, isolated groups of populations in nature tend to harbor both genetic and physiological divergence due to multiple selective pressures that they have encountered. How this divergence affects adaptation of these populations to a new common environment remains unclear. To determine the impact of prior genetic and physiological divergence in shaping adaptive evolution to accommodate a new common environment, an experimental evolution study with the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) was conducted. Two groups of replicate populations with genetic and physiological divergence, derived from a previous evolution study, were propagated in an elevated-temperature environment for 1,000 generations. Ancestor populations without prior experimental evolution were also propagated in the same environment as a control. After 1,000 generations, all the populations had increased growth rates and all but one had greater fitness in the new environment than the ancestor population. Moreover, improvements in growth rate were moderately affected by the divergence in the starting populations, while changes in fitness were not significantly affected. The mutations acquired at the gene level in each group of populations were quite different, indicating that the observed phenotypic changes were achieved by evolutionary responses that differed between the groups. Overall, our work demonstrated that the initial differences in fitness between the starting populations were eliminated by adaptation and that phenotypic convergence was achieved by acquisition of mutations in different genes. IMPORTANCE Improving our understanding of how previous adaptation influences evolution has been a long-standing goal in evolutionary biology. Natural selection tends to drive populations to find similar adaptive solutions for the same selective conditions. However, variations in historical environments can lead to both physiological and genetic divergence that can make evolution unpredictable. Here, we assessed the influence of divergence on the evolution of a model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, in response to elevated temperature and found a significant effect at the genetic but not the phenotypic level. Understanding how these influences drive evolution will allow us to better predict how bacteria will adapt to various ecological constraints.
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- 2020
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12. Experimental Evolution In Vivo To Identify Selective Pressures during Pneumococcal Colonization
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Stephanie L. Neville, Hannah M. Rowe, Amy R. Iverson, Christopher A. McDevitt, Christopher Deitrick, Vaughn S. Cooper, Colin C. Kietzman, Erin S. Honsa, Jason W. Rosch, Jonathan J. Whittall, Cooper, Vaughn S, Honsa, Erin, Rowe, Hannah, Deitrick, Christopher, Iverson, Amy R, Whittall, Jonathan J, Neville, Stephanie L, McDevitt, Christopher A, Kietzman, Colin, and Rosch, Jason W
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Physiology ,Niche ,Antimicrobial peptides ,Population ,lcsh:QR1-502 ,respiratory pathogens ,Biology ,Biochemistry ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,Genetics ,Colonization ,education ,Molecular Biology ,Gene ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,streptococcus pneumoniae ,Ecological niche ,0303 health sciences ,Experimental evolution ,education.field_of_study ,030306 microbiology ,Mechanism (biology) ,pathogenesis ,evolutionary biology ,QR1-502 ,Computer Science Applications ,Streptococcus pneumoniae ,Modeling and Simulation - Abstract
Experimental evolution is a powerful technique to understand how populations evolve from selective pressures imparted by the surrounding environment. With the advancement of whole-population genomic sequencing it is possible to identify and track multiple contending genotypes associated with adaptations to specific selective pressures. This approach has been used repeatedly with model species in vitro, but only rarely in vivo. Herein we report results of replicate experimentally evolved populations of Streptococcus pneumoniae propagated by repeated murine nasal colonization with the aim of identifying gene products under strong selection as well as the population-genetic dynamics of infection cycles. Frameshift mutations in one gene, dltB, responsible for incorporation of D-alanine into teichoic acids on the bacterial surface, evolved repeatedly and swept to high frequency. Targeted deletions of dltB produced a fitness advantage during initial nasal colonization coupled with a corresponding fitness disadvantage in the lungs during pulmonary infection. The underlying mechanism behind the fitness tradeoff between these two niches was found to be enhanced adherence to respiratory cells balanced by increased sensitivity to host-derived antimicrobial peptides, a finding recapitulated in the murine model. Additional mutations were also selected that are predicted to affect trace metal transport, central metabolism and regulation of biofilm production and competence. These data indicate that experimental evolution can be applied to murine models of pathogenesis to gain insight into organism-specific tissue tropisms.ImportanceEvolution is a powerful force that can be experimentally harnessed to gain insight into how populations evolve in response to selective pressures. Herein we tested the applicability of experimental evolutionary approaches to gain insight into how the major human pathogen Streptococcus pneumoniae responds to repeated colonization events using a murine model. These studies revealed the population dynamics of repeated colonization events and demonstrated that in vivo experimental evolution resulted in highly reproducible trajectories that reflect the environmental niche encountered during nasal colonization. Mutations impacting the surface charge of the bacteria were repeatedly selected during colonization and provided a fitness benefit in this niche that was counterbalanced by a corresponding fitness defect during lung infection. These data indicate that experimental evolution can be applied to models of pathogenesis to gain insight into organism-specific tissue tropisms.
- Published
- 2020
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