338 research outputs found
Data and Code for "Universal Constraints on Protein Evolution in the Long-Term Evolution Experiment with Escherichia coli"
No full textinput data files are located in the data/ directory.
source code is located in the src/ directory.
code and data for the LTEE 60,000 generation metagenomics dataset are located in the LTEE-metagenomic-repo/ directory.
results from running the source code are located in the results/ directory.
for all inquiries: contact the author at rohan dot maddamsetti at duke dot ed
DRYAD-STLE-analysis
No full textData files and scripts for all analyses and figures in Maddamsetti and Lenski (2018)
In Defence of "the Lesser Cousin of History": An Interview with Rohan Wilson
No full textFew branches of postcolonial literature are as contested \ud
as the historical fiction of settler societies. This interview with the Australian historical novelist Rohan Wilson, author of The Roving Party (2011) and To Name Those Lost (2014), explores the intersections between truth, accuracy, and existential authenticity in his fictional accounts of nineteenth-century Tasmania. Wilson offers \ud
a nuanced yet robust defence of fiction’s role in narrating colonial history. He explains his intentions in writing two linked yet distinctive novels of the frontier—one that focuses on the “Black War” of the 1820s and 1830s, and another that explores how racial violence is refracted by capitalism in subsequent decades
Shape optimization of channels for incompressible flows
No full textNázev práce: Optimalizace tvaru kanálu v úlohách nestlačitelného proudění Autor: Zuzana Záhorová Katedra: Katedra numerické matematiky Vedoucí diplomové práce: Doc. Dr. Ing. Eduard Rohan e-mail vedoucího: [email protected] Abstrakt: V předložené práci studujeme problém tvarové optimalizace pro úlohy vnitřního proudění ve 3D. Uvažováno je laminární, nestlačitelné, stacionární proudění popsané Navier- Stokesovými rovnicemi. Jsou popsány stabilizace Navier-Stokesových rovnic potřebné pro řešení úloh s nízkou viskozitou. Předloženy jsou teoretické poznatky týkající se problému tvarové optimalizace včetně důkazu existence řešení. Je popsána adjungovaná metoda pro řešení optimalizační úlohy. Odvozena je analytická analýza citlivosti. Představujeme postupy využité při výpočtech a numerický software pro řešení optimalizačních úloh. Jsou prezentovány výsledky pro stabilizované i nestabilizované řešení Navier-Stokesových rovnic. Představíme výsledky zahrnující lineární omezení geometrie oblasti. Klíčová slova: Nestlačitelné Navier-Stokesovy rovnice, SUPG/PSPG stabilizace, Adjun- govaná metoda, Analýza citlivosti Title: Shape optimization of channels for incompressible flows Author: Zuzana Záhorová Department:..
Evolution of laboratory and natural populations of Escherichia coli
No full textMy dissertation spans two dichotomies: evolution in the laboratory versus evolution in nature, and asexual versus sexual evolutionary dynamics. In Chapter 1 I describe asexual evolutionary dynamics in one population of Lenski\u2019s long-term evolution experiment with Escherichia coli. I describe cohorts of mutations that sweep to fixation together as characteristic of clonal interference dynamics. I also describe an ecological interaction that evolved and then went extinct after thousands of generations, and discuss how such interactions affect cohorts of mutations. In Chapter 2 I report that conserved core genes tend to be targets of selection in the long-term experiment. In Chapter 3, I investigate the surprising observation that synonymous genetic diversity is not uniform across the genomes of natural E. coli isolates. This observation is surprising because in clonal organisms with a constant point mutation rate, synonymous diversity should be constant across the genome. I use patterns of synonymous mutations in the long-term experiment to argue that genome-wide variation in the mutation rate does not adequately explain patterns of synonymous genetic diversity. In Chapter 4, I propose that recombination and gene flow could account for genome-wide variation in synonymous genetic diversity. In Chapter 5, I analyze E. coli genomes isolated from an evolution experiment with recombination in which E. coli K-12 with known growth defects could donate genetic material to recipient populations founded by long-term experiment clones. The degree of recombination varied dramatically across sequenced clones. The strongest predictor of successful transfer was proximity to the oriT origin of transfer in the K-12 donors. Donor alleles close to oriT replaced their recipient counterparts at a high rate, and in many of those cases, known beneficial mutations in the recipients were replaced by donor alleles.Thesis (Ph. D.)--Michigan State University. Zoology, 2016Includes bibliographical reference
Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection
No full textFew experimental studies have examined the role that sexual recombination plays in bacterial evolution, including the effects of horizontal gene transfer on genome structure. To address this limitation, we analyzed genomes from an experiment in which Escherichia coli K-12 Hfr (high frequency recombination) donors were periodically introduced into 12 evolving populations of E. coli B and allowed to conjugate repeatedly over the course of 1000 generations. Previous analyses of the evolved strains from this experiment showed that recombination did not accelerate adaptation, despite increasing genetic variation relative to asexual controls. However, the resolution in that previous work was limited to only a few genetic markers. We sought to clarify and understand these puzzling results by sequencing complete genomes from each population. The effects of recombination were highly variable: one lineage was mostly derived from the donors, while another acquired almost no donor DNA. In most lineages, some regions showed repeated introgression and others almost none. Regions with high introgression tended to be near the donors’ origin of transfer sites. To determine whether introgressed alleles imposed a genetic load, we extended the experiment for 200 generations without recombination and sequenced whole-population samples. Beneficial alleles in the recipient populations were occasionally driven extinct by maladaptive donor-derived alleles. On balance, our analyses indicate that the plasmid-mediated recombination was sufficiently frequent to drive donor alleles to fixation without providing much, if any, selective advantage.Version of Recor
KŌDA ROHAN\nTsuyu Dandan and Nineteenth Century English Literature
No full textpdfKōda Rohan recorded explanatory notes for Tsuyu Dandan (1889) as follows. "One: The ineptitude of the writing aside, to say that my literary devices are quite something and that Edward George Bulwer Lytton and William Makepeace Thackeray are really nothing is a big lie, for in fact I indulge in mere magic tricks. The discerning reader will quickly penetrate them."
Here with the coyness of a neophyte author, a self-assertive attitude which emphasizes the use of as a narrative technique can be seen. This study will deal with four questions.
① What function did Kōda Rohan think that narrative technique had in Edo popular fiction? I will first investigate the topology of , clarifying this technique which overflows the boundaries of , , in connection with Lytton and Thackeray. Naturally, this will result in ③ an investigation as to whether or not Lytton and Thackeray were borrowed from Tsubouchi Shōyō's Shōsetsu shinzui, Tō sei shosei katagi, or translations. If so,④ the question of why it was not George Eliot or Charles Dickens naturally arises. Through questions ② to④ I would like to clarify the relationship between Koda Rohan and nineteenth century English literature and to capture anew the stratifications of Rohan's literature.conference pape
Gene level selection is a conceptually complete theory of evolution
No full text<p>Recent workers have argued that evolutionary theory is<br>incomplete, due to several unsolved problems in the<br>field. These problems include the evolution of sex, the<br>evolution of complexity, and speciation. Theoretical<br>ideas such as modularity, robustness, and evolvability<br>have been proposed as part of an “Extended Synthesis,” necessary to solve these problems (Pigliucci 2009).</p>
<p>Further, recent empirical work in microbes has<br>challenged key ideas of the Modern Synthesis. In<br>particular, workers have argued that the mutation rate<br>might be an adaptive trait in microbes (Martincorena<br>2012, Paul 2013). Other workers have questioned the<br>role of natural selection in the evolution of complex<br>genomes and organisms (Lynch 2007). Here, I argue<br>that the Modern Synthesis is conceptually complete<br>(Williams 1966, Dawkins 1976, Lynch 2007). Considering evolution as an adaptive process working on genes, with organisms as higher-level, but temporary coalitions made of genes, is sufficient to turn these theoretical problems into mere “puzzles.” Higher levels of selection might largely serve to change the genetic, somatic, and ecological environments to which genes adapt (Williams 1966). I propose some hypotheses for future exploration in microbial and digital evolution experiments.</p>
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Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection
No full textAbstractWe analyzed genomes from an experiment in whichEscherichia coliK-12 Hfr donors were periodically introduced into 12 evolving populations ofE. coliB. Previous work showed that recombination did not increase adaptation, despite increasing variation relative to asexual controls. The effects of recombination were highly variable: one lineage was mostly derived from the donors, while another acquired almost no donor DNA. In most lineages, some regions showed repeated introgression and others almost none. Regions with high introgression tended to be near the donors origin of transfer sites. To determine whether introgressed alleles imposed a genetic load, we extended the experiment for 200 generations without recombination and sequenced whole-population samples. Beneficial alleles in the recipient populations were occasionally driven extinct by maladaptive donor-derived alleles. On balance, our analyses indicate that the plasmid-mediated recombination was sufficiently frequent to drive donor alleles to fixation without providing much, if any, selective advantage.</jats:p
Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection
No full text- …
