Search Results - "Wichman, Holly"
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Epistasis between beneficial mutations and the phenotype-to-fitness Map for a ssDNA virus
Published in PLoS genetics (01-06-2011)“…Epistatic interactions between genes and individual mutations are major determinants of the evolutionary properties of genetic systems and have therefore been…”
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Mutational effects and population dynamics during viral adaptation challenge current models
Published in Genetics (Austin) (01-01-2011)“…Adaptation in haploid organisms has been extensively modeled but little tested. Using a microvirid bacteriophage (ID11), we conducted serial passage…”
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Genetic and functional basis of the reduction effect in bacteriophage ΦX174
Published in Virology (New York, N.Y.) (01-11-2023)“…The ΦX174 reduction effect describes a plasmid-based inhibitory phenomenon that mimics the superinfection inhibition found in wild phage populations. In this…”
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Experimental evolution of viruses: Microviridae as a model system
Published in Philosophical transactions of the Royal Society of London. Series B. Biological sciences (27-08-2010)“…φX174 was developed as a model system for experimental studies of evolution because of its small genome size and ease of cultivation. It has been used…”
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Tracing the history of LINE and SINE extinction in sigmodontine rodents
Published in Mobile DNA (21-05-2019)“…L1 retrotransposons have co-evolved with their mammalian hosts for the entire history of mammals and currently compose ~ 20% of a mammalian genome. B1…”
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Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development
Published in BMC genomics (11-03-2014)“…Chromatin diminution is the programmed deletion of DNA from presomatic cell or nuclear lineages during development, producing single organisms that contain two…”
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Modeling the Directed Evolution of Broad Host Range Phages
Published in Antibiotics (Basel) (27-11-2022)“…The host ranges of individual phages tend to be narrow, yet many applications of phages would benefit from expanded host ranges. Empirical methods have been…”
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Positive selection and multiple losses of the LINE-1-derived L1TD1 gene in mammals suggest a dual role in genome defense and pluripotency
Published in PLoS genetics (01-09-2014)“…Mammalian genomes comprise many active and fossilized retroelements. The obligate requirement for retroelement integration affords host genomes an opportunity…”
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Ecological Approach to Understanding Superinfection Inhibition in Bacteriophage
Published in Viruses (17-07-2021)“…In microbial communities, viruses compete with each other for host cells to infect. As a consequence of competition for hosts, viruses evolve inhibitory…”
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Controlling Recombination to Evolve Bacteriophages
Published in Cells (Basel, Switzerland) (01-04-2024)“…Recombination among different phages sometimes facilitates their ability to grow on new hosts. Protocols to direct the evolution of phage host range, as might…”
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Changing folding and binding stability in a viral coat protein: a comparison between substitutions accessible through mutation and those fixed by natural selection
Published in PloS one (18-11-2014)“…Previous studies have shown that most random amino acid substitutions destabilize protein folding (i.e. increase the folding free energy). No analogous studies…”
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New Perspectives on Ebola Virus Evolution
Published in PloS one (01-08-2016)“…Since the recent devastating outbreak of Ebola virus disease in western Africa, there has been significant effort to understand the evolution of the deadly…”
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13
Selecting among three basic fitness landscape models: Additive, multiplicative and stickbreaking
Published in Theoretical population biology (01-07-2018)“…Fitness landscapes map genotypes to organismal fitness. Their topographies depend on how mutational effects interact – epistasis – andare important for…”
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The Genetics of Adaptation for Eight Microvirid Bacteriophages
Published in Journal of molecular evolution (01-09-2009)“…Theories of adaptive molecular evolution have recently experienced significant expansion, and their predictions and assumptions have begun to be subjected to…”
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Selection affects genes involved in replication during long-term evolution in experimental populations of the bacteriophage φX174
Published in PloS one (22-03-2013)“…Observing organisms that evolve in response to strong selection over very short time scales allows the determination of the molecular mechanisms underlying…”
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Reviving the dead: history and reactivation of an extinct l1
Published in PLoS genetics (01-06-2014)“…Although L1 sequences are present in the genomes of all placental mammals and marsupials examined to date, their activity was lost in the megabat family,…”
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First-step mutations for adaptation at elevated temperature increase capsid stability in a virus
Published in PloS one (29-09-2011)“…The relationship between mutation, protein stability and protein function plays a central role in molecular evolution. Mutations tend to be destabilizing,…”
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18
ΦX174 Attenuation by Whole-Genome Codon Deoptimization
Published in Genome biology and evolution (03-02-2021)“…Abstract Natural selection acting on synonymous mutations in protein-coding genes influences genome composition and evolution. In viruses, introducing…”
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The impact of spatial structure on viral genomic diversity generated during adaptation to thermal stress
Published in PloS one (12-02-2014)“…Most clinical and natural microbial communities live and evolve in spatially structured environments. When changes in environmental conditions trigger…”
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Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage φX174
Published in BMC evolutionary biology (17-03-2008)“…BACKGROUND: In large asexual populations where beneficial mutations may co-occur and recombination is absent, the fate of beneficial mutations can be…”
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