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Title: BioBits™ Bright: A fluorescent synthetic biology education kit

Abstract

Synthetic biology offers opportunities for experiential educational activities at the intersection of the life sciences, engineering, and design. However, implementation of hands-on biology activities in classrooms is challenging because of the need for specialized equipment and expertise to grow living cells. We present BioBits™ Bright, a shelf-stable, just-add-water synthetic biology education kit with easy visual outputs enabled by expression of fluorescent proteins in freeze-dried, cell-free reactions. We introduce activities and supporting curricula for teaching the central dogma, tunable protein expression, and design-build-test cycles and report data generated by K-12 teachers and students. We also develop inexpensive incubators and imagers, resulting in a comprehensive kit costing

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [1];  [4];  [4];  [5]; ORCiD logo [6];  [5];  [6];  [5];  [5];  [5];  [5]; ORCiD logo [7];  [5];  [8];  [9]; ORCiD logo [10];  [11] more »; ORCiD logo [12]; ORCiD logo [13]; ORCiD logo [14]; ORCiD logo [15];  [16];  [17];  [18];  [8];  [8];  [19]; ORCiD logo [20];  [21];  [22];  [8]; ORCiD logo [8];  [8]; ORCiD logo [4]; ORCiD logo [23]; ORCiD logo [24]; ORCiD logo [25] « less
+ Show Author Affiliations
  1. Northwestern Univ., Evanston, IL (United States)
  2. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Harvard Univ., Boston, MA (United States)
  3. Harvard Univ., Boston, MA (United States); Harvard Univ., Cambridge, MA (United States)
  4. Harvard Univ., Boston, MA (United States)
  5. Glenbard East High School, Lombard, IL (United States)
  6. Amos Alonzo Stagg High School, Palos Hills, IL (United States)
  7. Grover Cleveland Elementary School, Chicago, IL (United States)
  8. Evanston Township High School, Evanston, IL (United States)
  9. Glenbrook South High School, Glenview, IL (United States)
  10. Jones College Prep High School, Chicago, IL (United States)
  11. Gwendolyn Brooks College Preparatory Academy, Chicago, IL (United States)
  12. Delta High School, Muncie, IN (United States)
  13. ASPIRA Business and Finance High School, 2989 North Milwaukee Avenue, Chicago, IL (United States)
  14. Aptakisic-Tripp School District 102, Buffalo Grove, IL (United States)
  15. Oak Lawn Hometown Middle School, IL (United States)
  16. Hoffman Estates High School, Hoffman Estates, IL (United States)
  17. Vernon Hills High School, Vernon Hills, IL (United States)
  18. Morgan Park High School, Chicago, IL (United States)
  19. Northside College Prep High School, Chicago, IL (United States)
  20. Aqsa School, Bridgeview, IL (United States)
  21. Adlai E. Stevenson High School, Lincolnshire, IL (United States)
  22. Lyons Township High School, La Grange, IL (United States)
  23. Univ. of Toronto, ON (Canada)
  24. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Harvard Univ., Boston, MA (United States); Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA (United States); Broad Institute of MIT and Harvard, Cambridge, MA (United States)
  25. Northwestern Univ., Evanston, IL (United States); Northwestern University, Chicago, IL (United States)
Publication Date:
Research Org.:
Northwestern Univ., Evanston, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1499914
Grant/Contract Number:  
SC0018249
Resource Type:
Accepted Manuscript
Journal Name:
Science Advances
Additional Journal Information:
Journal Volume: 4; Journal Issue: 8; Journal ID: ISSN 2375-2548
Publisher:
AAAS
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Stark, Jessica C., Huang, Ally, Nguyen, Peter Q., Dubner, Rachel S., Hsu, Karen J., Ferrante, Thomas C., Anderson, Mary, Kanapskyte, Ada, Mucha, Quinn, Packett, Jessica S., Patel, Palak, Patel, Richa, Qaq, Deema, Zondor, Tyler, Burke, Julie, Martinez, Thomas, Miller-Berry, Ashlee, Puppala, Aparna, Reichert, Kara, Schmid, Miriam, Brand, Lance, Hill, Lander R., Chellaswamy, Jemima F., Faheem, Nuhie, Fetherling, Suzanne, Gong, Elissa, Gonzalzles, Eddie Marie, Granito, Teresa, Koritsaris, Jenna, Nguyen, Binh, Ottman, Sujud, Palffy, Christina, Patel, Angela, Skweres, Sheila, Slaton, Adriane, Woods, TaRhonda, Donghia, Nina, Pardee, Keith, Collins, James J., and Jewett, Michael C. BioBits™ Bright: A fluorescent synthetic biology education kit. United States: N. p., 2018. Web. doi:10.1126/sciadv.aat5107.
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Stark, Jessica C., Huang, Ally, Nguyen, Peter Q., Dubner, Rachel S., Hsu, Karen J., Ferrante, Thomas C., Anderson, Mary, Kanapskyte, Ada, Mucha, Quinn, Packett, Jessica S., Patel, Palak, Patel, Richa, Qaq, Deema, Zondor, Tyler, Burke, Julie, Martinez, Thomas, Miller-Berry, Ashlee, Puppala, Aparna, Reichert, Kara, Schmid, Miriam, Brand, Lance, Hill, Lander R., Chellaswamy, Jemima F., Faheem, Nuhie, Fetherling, Suzanne, Gong, Elissa, Gonzalzles, Eddie Marie, Granito, Teresa, Koritsaris, Jenna, Nguyen, Binh, Ottman, Sujud, Palffy, Christina, Patel, Angela, Skweres, Sheila, Slaton, Adriane, Woods, TaRhonda, Donghia, Nina, Pardee, Keith, Collins, James J., & Jewett, Michael C. BioBits™ Bright: A fluorescent synthetic biology education kit. United States. doi:10.1126/sciadv.aat5107.
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Stark, Jessica C., Huang, Ally, Nguyen, Peter Q., Dubner, Rachel S., Hsu, Karen J., Ferrante, Thomas C., Anderson, Mary, Kanapskyte, Ada, Mucha, Quinn, Packett, Jessica S., Patel, Palak, Patel, Richa, Qaq, Deema, Zondor, Tyler, Burke, Julie, Martinez, Thomas, Miller-Berry, Ashlee, Puppala, Aparna, Reichert, Kara, Schmid, Miriam, Brand, Lance, Hill, Lander R., Chellaswamy, Jemima F., Faheem, Nuhie, Fetherling, Suzanne, Gong, Elissa, Gonzalzles, Eddie Marie, Granito, Teresa, Koritsaris, Jenna, Nguyen, Binh, Ottman, Sujud, Palffy, Christina, Patel, Angela, Skweres, Sheila, Slaton, Adriane, Woods, TaRhonda, Donghia, Nina, Pardee, Keith, Collins, James J., and Jewett, Michael C. Wed . "BioBits™ Bright: A fluorescent synthetic biology education kit". United States. doi:10.1126/sciadv.aat5107. https://www.osti.gov/servlets/purl/1499914.
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@article{osti_1499914,
title = {BioBits™ Bright: A fluorescent synthetic biology education kit},
author = {Stark, Jessica C. and Huang, Ally and Nguyen, Peter Q. and Dubner, Rachel S. and Hsu, Karen J. and Ferrante, Thomas C. and Anderson, Mary and Kanapskyte, Ada and Mucha, Quinn and Packett, Jessica S. and Patel, Palak and Patel, Richa and Qaq, Deema and Zondor, Tyler and Burke, Julie and Martinez, Thomas and Miller-Berry, Ashlee and Puppala, Aparna and Reichert, Kara and Schmid, Miriam and Brand, Lance and Hill, Lander R. and Chellaswamy, Jemima F. and Faheem, Nuhie and Fetherling, Suzanne and Gong, Elissa and Gonzalzles, Eddie Marie and Granito, Teresa and Koritsaris, Jenna and Nguyen, Binh and Ottman, Sujud and Palffy, Christina and Patel, Angela and Skweres, Sheila and Slaton, Adriane and Woods, TaRhonda and Donghia, Nina and Pardee, Keith and Collins, James J. and Jewett, Michael C.},
abstractNote = {Synthetic biology offers opportunities for experiential educational activities at the intersection of the life sciences, engineering, and design. However, implementation of hands-on biology activities in classrooms is challenging because of the need for specialized equipment and expertise to grow living cells. We present BioBits™ Bright, a shelf-stable, just-add-water synthetic biology education kit with easy visual outputs enabled by expression of fluorescent proteins in freeze-dried, cell-free reactions. We introduce activities and supporting curricula for teaching the central dogma, tunable protein expression, and design-build-test cycles and report data generated by K-12 teachers and students. We also develop inexpensive incubators and imagers, resulting in a comprehensive kit costing},
doi = {10.1126/sciadv.aat5107},
journal = {Science Advances},
number = 8,
volume = 4,
place = {United States},
year = {2018},
month = {8}
}
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Journal Article:
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DOI:  10.1126/sciadv.aat5107
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Cited by: 13 works
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Figures / Tables:

Fig. 1 Fig. 1: BioBits™ Bright: A portable, cell-free synthesized fluorescent protein library for teaching the central dogma of molecular biology and synthetic biology. (A) We describe here the development of an educational kit containing two laboratory modules using FD-CF reactions and a library of in vitro–synthesized fluorescent proteins. (B) In modulemore » I, students investigate how biological systems can be engineered by adding varying amounts of DNA template to FD-CF reactions. Titrating the amount of DNA template results in varying levels of fluorescent protein production, which are visible to the naked eye and under a blue or black light. (C) In module II, users design their own in vitro program using DNA encoding the fluorescent protein library and any of the DNA template concentrations investigated in module I. This module offers the opportunity to go through a user-directed design-build-test (DBT) cycle. All reagents used in these activities (freeze-dried reactions and plasmids) can be stored and transported without refrigeration, making them highly portable for use outside of the laboratory.« less
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Works referenced in this record:

Programmable probiotics for detection of cancer in urine
journal, May 2015

Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components
journal, May 2016

Engineering and characterization of a superfolder green fluorescent protein
journal, December 2005

  • Pédelacq, Jean-Denis; Cabantous, Stéphanie; Tran, Timothy
  • Nature Biotechnology, Vol. 24, Issue 1, p. 79-88
  • DOI: 10.1038/nbt1172

Cell-free protein synthesis of a cytotoxic cancer therapeutic: Onconase production and a just-add-water cell-free system
journal, November 2015

  • Salehi, Amin S. M.; Smith, Mark Thomas; Bennett, Anthony M.
  • Biotechnology Journal, Vol. 11, Issue 2
  • DOI: 10.1002/biot.201500237

The new frontier of genome engineering with CRISPR-Cas9
journal, November 2014

Cell-free Protein Synthesis from a Release Factor 1 Deficient Escherichia coli Activates Efficient and Multiple Site-specific Nonstandard Amino Acid Incorporation
journal, January 2014

  • Hong, Seok Hoon; Ntai, Ioanna; Haimovich, Adrian D.
  • ACS Synthetic Biology, Vol. 3, Issue 6
  • DOI: 10.1021/sb400140t

Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein
journal, November 2004

  • Shaner, Nathan C.; Campbell, Robert E.; Steinbach, Paul A.
  • Nature Biotechnology, Vol. 22, Issue 12
  • DOI: 10.1038/nbt1037

An integrated cell-free metabolic platform for protein production and synthetic biology
journal, October 2008

  • Jewett, Michael C.; Calhoun, Kara A.; Voloshin, Alexei
  • Molecular Systems Biology, Vol. 4, Issue 1, Article No. 220
  • DOI: 10.1038/msb.2008.57

Cell-free protein synthesis: Applications come of age
journal, September 2012

Paper-Based Synthetic Gene Networks
journal, November 2014

Lyophilized Escherichia coli -based cell-free systems for robust, high-density, long-term storage
journal, April 2014

  • Smith, Mark Thomas; Berkheimer, Scott D.
  • BioTechniques, Vol. 56, Issue 4
  • DOI: 10.2144/000114158

High-throughput preparation methods of crude extract for robust cell-free protein synthesis
journal, March 2015

  • Kwon, Yong-Chan; Jewett, Michael C.
  • Scientific Reports, Vol. 5, Issue 1
  • DOI: 10.1038/srep08663

Broadening Horizons and Teaching Basic Biology Through Cell-Free Synthesis of Green Fluorescent Protein in a High School Laboratory Course
journal, July 2013

  • Albayrak, Cem; Jones, K. C.; Swartz, James R.
  • Journal of Science Education and Technology, Vol. 22, Issue 6
  • DOI: 10.1007/s10956-013-9442-z

TinkerCell: modular CAD tool for synthetic biology
journal, January 2009

  • Chandran, Deepak; Bergmann, Frank T.; Sauro, Herbert M.
  • Journal of Biological Engineering, Vol. 3, Issue 1
  • DOI: 10.1186/1754-1611-3-19

An Enhanced Monomeric Blue Fluorescent Protein with the High Chemical Stability of the Chromophore
journal, December 2011

Chimeric Antigen Receptor–Modified T Cells in Chronic Lymphoid Leukemia
journal, August 2011

  • Porter, David L.; Levine, Bruce L.; Kalos, Michael
  • New England Journal of Medicine, Vol. 365, Issue 8
  • DOI: 10.1056/NEJMoa1103849

Single-pot glycoprotein biosynthesis using a cell-free transcription-translation system enriched with glycosylation machinery
journal, July 2018

  • Jaroentomeechai, Thapakorn; Stark, Jessica C.; Natarajan, Aravind
  • Nature Communications, Vol. 9, Issue 1
  • DOI: 10.1038/s41467-018-05110-x

Site-Specific Incorporation of p -Propargyloxyphenylalanine in a Cell-Free Environment for Direct Protein−Protein Click Conjugation
journal, February 2010

  • Bundy, Bradley C.; Swartz, James R.
  • Bioconjugate Chemistry, Vol. 21, Issue 2
  • DOI: 10.1021/bc9002844

Authentic teaching and learning through synthetic biology
journal, January 2007

STEAM-Powered Computing Education: Using E-Textiles to Integrate the Arts and STEM
journal, September 2013

Engineering Escherichia coli to see light
journal, November 2005

  • Levskaya, Anselm; Chevalier, Aaron A.; Tabor, Jeffrey J.
  • Nature, Vol. 438, Issue 7067
  • DOI: 10.1038/nature04405

Evolutionary optimization of fluorescent proteins for intracellular FRET
journal, February 2005

  • Nguyen, Annalee W.; Daugherty, Patrick S.
  • Nature Biotechnology, Vol. 23, Issue 3
  • DOI: 10.1038/nbt1066

Meeting Report: Synthetic Biology Jamboree for Undergraduates
journal, March 2005

The Fluorescent Toolbox for Assessing Protein Location and Function
journal, April 2006

BioBits™ Explorer: A modular synthetic biology education kit
journal, August 2018

  • Huang, Ally; Nguyen, Peter Q.; Stark, Jessica C.
  • Science Advances, Vol. 4, Issue 8
  • DOI: 10.1126/sciadv.aat5105

Cell-Free Mixing of Escherichia coli Crude Extracts to Prototype and Rationally Engineer High-Titer Mevalonate Synthesis
journal, July 2016

  • Dudley, Quentin M.; Anderson, Kim C.; Jewett, Michael C.
  • ACS Synthetic Biology, Vol. 5, Issue 12
  • DOI: 10.1021/acssynbio.6b00154

Mimicking theEscherichia coli cytoplasmic environment activates long-lived and efficient cell-free protein synthesis
journal, January 2004

  • Jewett, Michael C.; Swartz, James R.
  • Biotechnology and Bioengineering, Vol. 86, Issue 1
  • DOI: 10.1002/bit.20026

Complete biosynthesis of opioids in yeast
journal, August 2015

Experiential Engineering Through iGEM—An Undergraduate Summer Competition in Synthetic Biology
journal, August 2010

  • Mitchell, Rudolph; Dori, Yehudit Judy; Kuldell, Natalie H.
  • Journal of Science Education and Technology, Vol. 20, Issue 2
  • DOI: 10.1007/s10956-010-9242-7

Water splitting–biosynthetic system with CO 2 reduction efficiencies exceeding photosynthesis
journal, June 2016

High-level semi-synthetic production of the potent antimalarial artemisinin
journal, April 2013

  • Paddon, C. J.; Westfall, P. J.; Pitera, D. J.
  • Nature, Vol. 496, Issue 7446
  • DOI: 10.1038/nature12051

Engineered bacteria can function in the mammalian gut long-term as live diagnostics of inflammation
journal, May 2017

  • Riglar, David T.; Giessen, Tobias W.; Baym, Michael
  • Nature Biotechnology, Vol. 35, Issue 7
  • DOI: 10.1038/nbt.3879

Nucleic acid detection with CRISPR-Cas13a/C2c2
journal, April 2017

  • Gootenberg, Jonathan S.; Abudayyeh, Omar O.; Lee, Jeong Wook
  • Science, Vol. 356, Issue 6336
  • DOI: 10.1126/science.aam9321

Directed evolution of a monomeric, bright and photostable version of Clavularia cyan fluorescent protein: structural characterization and applications in fluorescence imaging
journal, November 2006

  • Ai, Hui-wang; Henderson, J. Nathan; Remington, S. James
  • Biochemical Journal, Vol. 400, Issue 3
  • DOI: 10.1042/BJ20060874

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
journal, May 2011

  • Yim, Harry; Haselbeck, Robert; Niu, Wei
  • Nature Chemical Biology, Vol. 7, Issue 7
  • DOI: 10.1038/nchembio.580

Promoting microbiology education through the iGEM synthetic biology competition
journal, August 2015

  • Kelwick, Richard; Bowater, Laura; Yeoman, Kay H.
  • FEMS Microbiology Letters, Vol. 362, Issue 16
  • DOI: 10.1093/femsle/fnv129

Engineering Cellular Metabolism
journal, March 2016

Portable, On-Demand Biomolecular Manufacturing
journal, September 2016

Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors
journal, October 2016

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