---
res:
  bibo_abstract:
  - "The lac operon is a classic model system for bacterial gene regulation, and has
    been studied extensively in E. coli, a classic model organism. However, not much
    is known about E. coli’s ecology and life outside the laboratory, in particular
    in soil and water environments. The natural diversity of the lac operon outside
    the laboratory, its role in the ecology of E. coli and the selection pressures
    it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore
    the genetic diversity, phylogenetic history and signatures of selection of the
    lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia.
    I found that complete lac operons were present in all isolates examined, which
    in all but one case were functional. The lac operon phylogeny conformed to the
    whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal
    gene transfer as an explanation for the presence of functional lac operons in
    these clades. All lac operon genes showed a signature of purifying selection;
    this signature was strongest for the lacY gene. Lac operon genes of human and
    environmental isolates showed similar signatures of selection, except the lacZ
    gene, which showed a stronger signature of selection in environmental isolates.\r\nIn
    Chapter Three, I try to identify the natural genetic variation relevant for phenotype
    and fitness in the lac operon, comparing growth rate on lactose and LacZ activity
    of the lac operons of these wild isolates in a common genetic background. Sequence
    variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase
    binding motif, predicted variation in LacZ activity at full induction, using a
    thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation
    in LacZ activity, nor RNA polymerase binding predicted by the model correlated
    with variation in growth rate. Lac operons of human and environmental isolates
    did not differ systematically in either growth rate on lactose or LacZ protein
    activity, suggesting that these lac operons have been exposed to similar selection
    pressures. We thus have no evidence that the phenotypic variation we measured
    is relevant for fitness.\r\nTo start assessing the effect of genomic background
    on the growth phenotype conferred by the lac operon, I compared growth on minimal
    medium with lactose between lac operon constructs and the corresponding original
    isolates, I found that maximal growth rate was determined by genomic background,
    with almost all backgrounds conferring higher growth rates than lab strain K12
    MG1655. However, I found no evidence that the lactose concentration at which growth
    was half maximal depended on genomic background.@eng"
  bibo_authorlist:
  - foaf_Person:
      foaf_givenName: Fabienne
      foaf_name: Jesse, Fabienne
      foaf_surname: Jesse
      foaf_workInfoHomepage: http://www.librecat.org/personId=4C8C26A4-F248-11E8-B48F-1D18A9856A87
  bibo_doi: 10.15479/AT:ISTA:th_857
  dct_date: 2017^xs_gYear
  dct_isPartOf:
  - http://id.crossref.org/issn/2663-337X
  dct_language: eng
  dct_publisher: Institute of Science and Technology Austria@
  dct_title: The lac operon in the wild@
...