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Research Article

Exploiting Nucleotide Composition to Engineer Promoters

  • Manfred G. Grabherr equal contributor,

    equal contributor Contributed equally to this work with: Manfred G. Grabherr, Jens Pontiller

    Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America

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  • Jens Pontiller equal contributor,

    equal contributor Contributed equally to this work with: Manfred G. Grabherr, Jens Pontiller

    Affiliation: Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria

    X
  • Evan Mauceli mail,

    evan@broadinstitute.org

    Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America

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  • Wolfgang Ernst,

    Affiliation: Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria

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  • Martina Baumann,

    Affiliation: Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria

    X
  • Tara Biagi,

    Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America

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  • Ross Swofford,

    Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America

    X
  • Pamela Russell,

    Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America

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  • Michael C. Zody,

    Affiliations: Broad Institute, Cambridge, Massachusetts, United States of America, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

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  • Federica Di Palma,

    Affiliation: Broad Institute, Cambridge, Massachusetts, United States of America

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  • Kerstin Lindblad-Toh,

    Affiliations: Broad Institute, Cambridge, Massachusetts, United States of America, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

    X
  • Reingard M. Grabherr

    Affiliation: Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria

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  • Published: May 18, 2011
  • DOI: 10.1371/journal.pone.0020136
  • Published in PLOS ONE

Reader Comments (1)

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In vitro typo

Posted by MichaelC on 01 Jun 2011 at 20:52 GMT

In reading this paper, I noticed that the authors claimed to have performed in vitro experiments. Upon reading the materials and methods, it appears that all of the promoter activity assays were performed in vivo using luciferase as the experimental readout. Please make sure to update this error as the interpretations are different depending on in vitro or in vivo experiments.

No competing interests declared.

RE: In vitro typo

Vertebrate replied to MichaelC on 03 Jun 2011 at 01:12 GMT

Dear MichaelC,

Thank you for your comment. However, there might be a semantical problem: cell culture experiments are generally regarded as "in vitro", since "in vivo" refers to whole organisms, e. g. immunization studies in mice are so-called "in vivo" studies. Although the results reported here were performed in whole cells, the experiments were performed in a "reaction tube", along the lines of "in vitro fertilization - "and that is all what "in vitro" means: "vitro" (vitrum, n., n.), in Latin, is the "glass tube" or "reaction tube".

Besides all that, the experiments are described accurately and in detail, including the correct use of terminology (and semantics).

No competing interests declared.

RE: RE: In vitro typo

MichaelC replied to Vertebrate on 09 Jun 2011 at 19:15 GMT

Dear Vertebrate,

Thank you for the clarification. I approached the paper as a biochemist, not used to thinking about isolated cells as 'in vitro.'

I understand the etymology of in vitro, but perhaps there should be different terms to communicate the differences between transcription initiation within whole, intact cells vs. purified, reconstituted transcription factors. Each would be labeled as 'in vitro transcription' even though they correspond to dramatically different techniques and interpretations.

No competing interests declared.