---
res:
  bibo_abstract:
  - "Horizontal gene transfer (HGT), the lateral acquisition of genes across existing
    species\r\nboundaries, is a major evolutionary force shaping microbial genomes
    that facilitates\r\nadaptation to new environments as well as resistance to antimicrobial
    drugs. As such,\r\nunderstanding the mechanisms and constraints that determine
    the outcomes of HGT\r\nevents is crucial to understand the dynamics of HGT and
    to design better strategies to\r\novercome the challenges that originate from
    it.\r\nFollowing the insertion and expression of a newly transferred gene, the
    success of an\r\nHGT event will depend on the fitness effect it has on the recipient
    (host) cell. Therefore,\r\npredicting the impact of HGT on the genetic composition
    of a population critically\r\ndepends on the distribution of fitness effects (DFE)
    of horizontally transferred genes.\r\nHowever, to date, we have little knowledge
    of the DFE of newly transferred genes, and\r\nhence little is known about the
    shape and scale of this distribution.\r\nIt is particularly important to better
    understand the selective barriers that determine\r\nthe fitness effects of newly
    transferred genes. In spite of substantial bioinformatics\r\nefforts to identify
    horizontally transferred genes and selective barriers, a systematic\r\nexperimental
    approach to elucidate the roles of different selective barriers in defining\r\nthe
    fate of a transfer event has largely been absent. Similarly, although the fact
    that\r\nenvironment might alter the fitness effect of a horizontally transferred
    gene may seem\r\nobvious, little attention has been given to it in a systematic
    experimental manner.\r\nIn this study, we developed a systematic experimental
    approach that consists of\r\ntransferring 44 arbitrarily selected Salmonella typhimurium
    orthologous genes into an\r\nEscherichia coli host, and estimating the fitness
    effects of these transferred genes at a\r\nconstant expression level by performing
    competition assays against the wild type.\r\nIn chapter 2, we performed one-to-one
    competition assays between a mutant strain\r\ncarrying a transferred gene and
    the wild type strain. By using flow cytometry we\r\nestimated selection coefficients
    for the transferred genes with a precision level of 10-3,and obtained the DFE
    of horizontally transferred genes. We then investigated if these\r\nfitness effects
    could be predicted by any of the intrinsic properties of the genes, namely,\r\nfunctional
    category, degree of complexity (protein-protein interactions), GC content,\r\ncodon
    usage and length. Our analyses revealed that the functional category and length\r\nof
    the genes act as potential selective barriers. Finally, using the same procedure
    with\r\nthe endogenous E. coli orthologs of these 44 genes, we demonstrated that
    gene dosage is\r\nthe most prominent selective barrier to HGT.\r\nIn chapter 3,
    using the same set of genes we investigated the role of environment on the\r\nsuccess
    of HGT events. Under six different environments with different levels of stress\r\nwe
    performed more complex competition assays, where we mixed all 44 mutant strains\r\ncarrying
    transferred genes with the wild type strain. To estimate the fitness effects of\r\ngenes
    relative to wild type we used next generation sequencing. We found that the DFEs\r\nof
    horizontally transferred genes are highly dependent on the environment, with\r\nabundant
    gene–by-environment interactions. Furthermore, we demonstrated a\r\nrelationship
    between average fitness effect of a gene across all environments and its\r\nenvironmental
    variance, and thus its predictability. Finally, in spite of the fitness effects\r\nof
    genes being highly environment-dependent, we still observed a common shape of\r\nDFEs
    across all tested environments.@eng"
  bibo_authorlist:
  - foaf_Person:
      foaf_givenName: Hande
      foaf_name: Acar, Hande
      foaf_surname: Acar
      foaf_workInfoHomepage: http://www.librecat.org/personId=2DDF136A-F248-11E8-B48F-1D18A9856A87
    orcid: 0000-0003-1986-9753
  dct_date: 2016^xs_gYear
  dct_isPartOf:
  - http://id.crossref.org/issn/2663-337X
  dct_language: eng
  dct_publisher: Institute of Science and Technology Austria@
  dct_title: Selective barriers to horizontal gene transfer@
...