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Title: A minimum information standard for reproducing bench-scale bacterial cell growth and productivity

Abstract

Reproducing, exchanging, comparing, and building on each other’s work is foundational to technology advances. Advancing biotechnology calls for reliable reuse of engineered organisms. Reliable reuse of engineered organisms requires reproducible growth and productivity. Here, we identify the experimental factors that have the greatest effect on the growth and productivity of our engineered organisms in order to demonstrate reproducibility for biotechnology. Here, we present a draft of a Minimum Information Standard for Engineered Organism Experiments based on this method. We evaluate the effect of 22 factors on Escherichia coli engineered to produce the small molecule lycopene, and 18 factors on E. coli engineered to produce red fluorescent protein. Container geometry and shaking have the greatest effect on product titer and yield. We reproduce our results under two different conditions of reproducibility: conditions of use (different fractional factorial experiments), and time (48 biological replicates performed on 12 different days over four months).

Authors:
 [1];  [2];  [3];  [4]
  1. Joint Initiative for Metrology in Biology, Stanford, CA (United States); National Inst. of Standards and Technology, Stanford, CA (United States); Stanford Univ., Stanford, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)
  2. Joint Initiative for Metrology in Biology, Stanford, CA (United States); National Inst. of Standards and Technology, Stanford, CA (United States); Stanford Univ., Stanford, CA (United States)
  3. Joint Initiative for Metrology in Biology, Stanford, CA (United States); National Inst. of Standards and Technology, Stanford, CA (United States); Stanford Univ., Stanford, CA (United States); Univ. of Minnesota, Minneapolis, MN (United States)
  4. National Inst. of Standards and Technology (NIST), Gaithersburg, MD (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1480469
Grant/Contract Number:  
AC02-76SF00515
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Communications Biology
Additional Journal Information:
Journal Volume: 1; Journal Issue: 1; Journal ID: ISSN 2399-3642
Publisher:
Springer Nature
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Salit, Marc, Hecht, Ariel, Munro, Sarah A., and Filliben, James. A minimum information standard for reproducing bench-scale bacterial cell growth and productivity. United States: N. p., 2018. Web. doi:10.1038/s42003-018-0220-6.
Salit, Marc, Hecht, Ariel, Munro, Sarah A., & Filliben, James. A minimum information standard for reproducing bench-scale bacterial cell growth and productivity. United States. doi:10.1038/s42003-018-0220-6.
Salit, Marc, Hecht, Ariel, Munro, Sarah A., and Filliben, James. Sat . "A minimum information standard for reproducing bench-scale bacterial cell growth and productivity". United States. doi:10.1038/s42003-018-0220-6. https://www.osti.gov/servlets/purl/1480469.
@article{osti_1480469,
title = {A minimum information standard for reproducing bench-scale bacterial cell growth and productivity},
author = {Salit, Marc and Hecht, Ariel and Munro, Sarah A. and Filliben, James},
abstractNote = {Reproducing, exchanging, comparing, and building on each other’s work is foundational to technology advances. Advancing biotechnology calls for reliable reuse of engineered organisms. Reliable reuse of engineered organisms requires reproducible growth and productivity. Here, we identify the experimental factors that have the greatest effect on the growth and productivity of our engineered organisms in order to demonstrate reproducibility for biotechnology. Here, we present a draft of a Minimum Information Standard for Engineered Organism Experiments based on this method. We evaluate the effect of 22 factors on Escherichia coli engineered to produce the small molecule lycopene, and 18 factors on E. coli engineered to produce red fluorescent protein. Container geometry and shaking have the greatest effect on product titer and yield. We reproduce our results under two different conditions of reproducibility: conditions of use (different fractional factorial experiments), and time (48 biological replicates performed on 12 different days over four months).},
doi = {10.1038/s42003-018-0220-6},
journal = {Communications Biology},
number = 1,
volume = 1,
place = {United States},
year = {Sat Dec 01 00:00:00 EST 2018},
month = {Sat Dec 01 00:00:00 EST 2018}
}

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Works referenced in this record:

Measuring the activity of BioBrick promoters using an in vivo reference standard
journal, January 2009

  • Kelly, Jason R.; Rubin, Adam J.; Davis, Joseph H.
  • Journal of Biological Engineering, Vol. 3, Issue 1, Article No. 4
  • DOI: 10.1186/1754-1611-3-4

Protein production by auto-induction in high-density shaking cultures
journal, May 2005