title: Experimental design to evaluate directed adaptive mutation in Mammalian cells.
abstract: BACKGROUND
  We describe the experimental design for a methodological approach to determine whether directed adaptive mutation occurs in mammalian cells. Identification of directed adaptive mutation would have profound practical significance for a wide variety of biomedical problems, including disease development and resistance to treatment. In adaptive mutation, the genetic or epigenetic change is not random; instead, the presence and type of selection influences the frequency and character of the mutation event. Adaptive mutation can contribute to the evolution of microbial pathogenesis, cancer, and drug resistance, and may become a focus of novel therapeutic interventions.
  
  
  OBJECTIVE
  Our experimental approach was designed to distinguish between 3 types of mutation: (1) random mutations that are independent of selective pressure, (2) undirected adaptive mutations that arise when selective pressure induces a general increase in the mutation rate, and (3) directed adaptive mutations that arise when selective pressure induces targeted mutations that specifically influence the adaptive response. The purpose of this report is to introduce an experimental design and describe limited pilot experiment data (not to describe a complete set of experiments); hence, it is an early report.
  
  
  METHODS
  An experimental design based on immortalization of mouse embryonic fibroblast cells is presented that links clonal cell growth to reversal of an inactivating polyadenylation site mutation. Thus, cells exhibit growth only in the presence of both the countermutation and an inducing agent (doxycycline). The type and frequency of mutation in the presence or absence of doxycycline will be evaluated. Additional experimental approaches would determine whether the cells exhibit a generalized increase in mutation rate and/or whether the cells show altered expression of error-prone DNA polymerases or of mismatch repair proteins.
  
  
  RESULTS
  We performed the initial stages of characterizing our system and have limited preliminary data from several pilot experiments. Cell growth and DNA sequence data indicate that we have identified a cell clone that exhibits several suitable characteristics, although further study is required to identify a more optimal cell clone.
  
  
  CONCLUSIONS
  The experimental approach is based on a quantum biological model of basis-dependent selection describing a novel mechanism of adaptive mutation. This project is currently inactive due to lack of funding. However, consistent with the objective of early reports, we describe a proposed study that has not produced publishable results, but is worthy of report because of the hypothesis, experimental design, and protocols. We outline the project's rationale and experimental design, with its strengths and weaknesses, to stimulate discussion and analysis, and lay the foundation for future studies in this field.
authors.affiliation: Department of Basic Sciences, The Commonwealth Medical College, Scranton, PA, United States. mbordonaro@tcmedc.org.
authors.forename: Michael
authors.identifier: http://orcid.org/0000-0002-6667-0096
authors.initials: M
authors.lastname: Bordonaro
authors.forename: Christopher R
authors.identifier: http://orcid.org/0000-0002-4705-0529
authors.initials: CR
authors.lastname: Chiaro
authors.forename: Tobias
authors.identifier: http://orcid.org/0000-0002-4042-4815
authors.initials: T
authors.lastname: May
keywords: adaptive mutation; mouse embryo fibroblast; quantum