Acknowledgements
- Thanks to Nicholas Adams, Research Assistant Professor of Biomedical Engineering at Vanderbilt University, for further explaining the process of PCR and the limitations of current day PCR technology.
- Thanks to Andrea Dickstein, director of eBuisness and Marketing Communications at Eppendorf North America, for explaining the processes of amplifying DNA and PCR.
- Thanks to Ryan Duffe, fellow classmate, for providing us with a 3D printer to print out parts of the prototype of the ScatScan.
- Thanks to Zachary Kurtz, scientist at Lodo Therapeutics, for pushing us in the right direction, and for providing extra information about the microbiome.
- Thanks to John Murray, technology teacher and engineer at Commack Middle School, for providing us with a 3D printer to print out parts of the prototype of the ScatScan.
- Thanks to Ya'ir Preiss, Mechanical Engineering student at the City College of New York, for giving invaluable insight and advice on engineering and 3D printing.
Selected References
1. Adams, J. U. (2008). DNA Sequencing Technologies. Nature Education, 1(1), 193. Retrieved from http://www.nature.com/scitable/topicpage/dna-sequencing-technologies-690
2. American Gut. (2016, February 17). How It Works. Retrieved from http://americangut.org/how-it-works/
3. Anthony, S. (2013, July 26). 7nm, 5nm, 3nm: The new materials and transistors that will take us to the limits of Moore’s law. Retrieved from https://www.extremetech.com/computing/162376-7nm-5nm-3nm-the-new-materials-and-transistors-that-will-take-us-to-the-limits-of-moores-law
4. Blaser, M. J. (2014). Missing Microbes: How the Overuse of Antibiotics is Fueling Our Modern Plagues. New York: Henry Holt and Company.
5. Blaser, M. J., & Falkow, S. (2009). What are the consequences of the disappearing human microbiota? Nature Reviews Microbiology, 7(12), 887-894. Retrieved from https://www.scribd.com/document/36381738/Disappearing-Human-Microbiota.
6. Cho, I., & Blaser, M. J. (2012, March 13). The Human Microbiome: at the interface of health and disease. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418802/
7. Fishbein, P. G. (2016, June 28). The Importance of Our Microbiome. Retrieved from https://www.gastrohealth.com/physician/importance-microbiome/
8. Gartenberg, C. (2016, October 06). The world's smallest transistor is 1nm long, physics be damned. Retrieved from http://www.theverge.com/circuitbreaker/2016/10/6/13187820/one-nanometer-transistor-berkeley-lab-moores-law
9. Gill, S. R., Pop, M., DeBoy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., . . . Nelson, K. E. (2006, June 02). Metagenomic Analysis of the Human Distal Gut Microbiome. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3027896/
10. Janda, J. M., & Abbott, S. L. (2007, July 11). 16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls. Journal of Clinical Microbiology, 45(9), 2761-2764.
11. Oblath, E. A., Henley, W. H., Alarie, J., & Ramsey, J. M. (2013). A microfluidic chip integrating DNA extraction and real-time PCR for the detection of bacteria in saliva. Lab on a Chip, 13(7), 1325-1332. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617581/.
12. Proctor, L. M. (2013, September). The Human Microbiome: A True Story about You and Trillions of Your Closest (Microscopic) Friends. Retrieved from http://www.actionbioscience.org/genomics/the_human_microbiome.html
13. Rogers, K. (2011, December 5). Human Microbiome. In Encyclopedia Britannica. Retrieved from https://www.britannica.com/science/human-microbiome
14. Shah, N., Tang, H., Doak, T. G., & Ye, Y. (2010, September 20). Comparing Bacterial Communities Inferred From 16S rRNA Gene Sequencing and Shotgun Metagenomics [Scholarly project]. Retrieved from http://psb.stanford.edu/psb-online/proceedings/psb11/shah.pdf
15. UBiome. (2017). Actionable Insights to Improve Your Gut Health. Retrieved from https://ubiome.com/
16. University of Washington Health Sciences/UW Medicine. (2017, January 19). 'FishTaco' sorts out who is doing what in your microbiome: A new method reveals roles different bacteria play in microbiome imbalances linked to disease. ScienceDaily. Retrieved from https://www.sciencedaily.com/releases/2017/01/170119134530.htm
17. Wesolowska-Andersen, A., Bahl, M. I., Carvalho, V., Kristiansen, K., Sicheritz-Pontén, T., Gupta, R., & Licht, T. R. (2014, June 5). Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4063427/
2. American Gut. (2016, February 17). How It Works. Retrieved from http://americangut.org/how-it-works/
3. Anthony, S. (2013, July 26). 7nm, 5nm, 3nm: The new materials and transistors that will take us to the limits of Moore’s law. Retrieved from https://www.extremetech.com/computing/162376-7nm-5nm-3nm-the-new-materials-and-transistors-that-will-take-us-to-the-limits-of-moores-law
4. Blaser, M. J. (2014). Missing Microbes: How the Overuse of Antibiotics is Fueling Our Modern Plagues. New York: Henry Holt and Company.
5. Blaser, M. J., & Falkow, S. (2009). What are the consequences of the disappearing human microbiota? Nature Reviews Microbiology, 7(12), 887-894. Retrieved from https://www.scribd.com/document/36381738/Disappearing-Human-Microbiota.
6. Cho, I., & Blaser, M. J. (2012, March 13). The Human Microbiome: at the interface of health and disease. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418802/
7. Fishbein, P. G. (2016, June 28). The Importance of Our Microbiome. Retrieved from https://www.gastrohealth.com/physician/importance-microbiome/
8. Gartenberg, C. (2016, October 06). The world's smallest transistor is 1nm long, physics be damned. Retrieved from http://www.theverge.com/circuitbreaker/2016/10/6/13187820/one-nanometer-transistor-berkeley-lab-moores-law
9. Gill, S. R., Pop, M., DeBoy, R. T., Eckburg, P. B., Turnbaugh, P. J., Samuel, B. S., . . . Nelson, K. E. (2006, June 02). Metagenomic Analysis of the Human Distal Gut Microbiome. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3027896/
10. Janda, J. M., & Abbott, S. L. (2007, July 11). 16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls. Journal of Clinical Microbiology, 45(9), 2761-2764.
11. Oblath, E. A., Henley, W. H., Alarie, J., & Ramsey, J. M. (2013). A microfluidic chip integrating DNA extraction and real-time PCR for the detection of bacteria in saliva. Lab on a Chip, 13(7), 1325-1332. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617581/.
12. Proctor, L. M. (2013, September). The Human Microbiome: A True Story about You and Trillions of Your Closest (Microscopic) Friends. Retrieved from http://www.actionbioscience.org/genomics/the_human_microbiome.html
13. Rogers, K. (2011, December 5). Human Microbiome. In Encyclopedia Britannica. Retrieved from https://www.britannica.com/science/human-microbiome
14. Shah, N., Tang, H., Doak, T. G., & Ye, Y. (2010, September 20). Comparing Bacterial Communities Inferred From 16S rRNA Gene Sequencing and Shotgun Metagenomics [Scholarly project]. Retrieved from http://psb.stanford.edu/psb-online/proceedings/psb11/shah.pdf
15. UBiome. (2017). Actionable Insights to Improve Your Gut Health. Retrieved from https://ubiome.com/
16. University of Washington Health Sciences/UW Medicine. (2017, January 19). 'FishTaco' sorts out who is doing what in your microbiome: A new method reveals roles different bacteria play in microbiome imbalances linked to disease. ScienceDaily. Retrieved from https://www.sciencedaily.com/releases/2017/01/170119134530.htm
17. Wesolowska-Andersen, A., Bahl, M. I., Carvalho, V., Kristiansen, K., Sicheritz-Pontén, T., Gupta, R., & Licht, T. R. (2014, June 5). Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. Retrieved from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4063427/
Figures
1. [American Gut ]. (n.d.). Retrieved from https://www.indiegogo.com/projects/american-gut-what-s-in-your-gut--7#/
2. [Bacteria]. (n.d.). Retrieved from http://hdwallpaperdaily.com/wp-content/uploads/2013/05/microscopic-blue-bacteria-wallpaper.jpg
3. [Chart on phone]. (n.d.). Retrieved from http://www.beaconlearningcenter.com/weblessons/InterpretingLineGraphs/default.htm
4. [DNA ]. (n.d.). Retrieved from https://media1.britannica.com/eb-media/73/151873-004-E4641720.jpg
5. [Doctors]. (n.d). Retrieved from https://3.bp.blogspot.com/-
TASeSyMtdug/VwIJmJ7qnuI/AAAAAAAAABE/cp9heUfUCjs2L9WHnqdd5bOWRYuaeeMwQ/s640/Happy-Doctors-Diverse.jpg
6. [Environment]. (n.d.). Retrieved from http://asiarisingtv.com/wp-content/uploads/2016/03/air-800x515.jpg
7.[Food Plate]. (n.d.). Retrieved from http://1.bp.blogspot.com/-g1BqohVALgM/TeElpUxwZMI/AAAAAAAABdY/Tu22O79Nmv4/s1600/Plate -- pizza chart.jpg
8. [Gut Microbiome]. (n.d.). Retrieved from http://www.malaghan.org.nz/assets/Microbiota-intestinal.jpg
9. [Hygiene]. (n.d.). Retrieved from http://en-uk.ecolab.com/solutions/food-plant-personal-hygiene/~/media/ecolab/ecolab%20home/images/solutions/foodandbeverage/a%20person%20washing%20their%20hands%20show%20personal%20hand%20hygiene.jpg?as=1&w=550
10. [Overhead View of a Toilet]. (2013, February 6). Retrieved from http://www.langleytoday.ca/issue-canadas-ei-surplus-now-you-see-it-now-you-dont/
11. [Phone Diagram]. (n.d.). Retrieved from http://www.phonearena.com/news/The-Apple-iPhone-turns-10-today-a-decade-of-redefining-the-smart-in-smartphone_id89746
12. [Processed foods]. (n.d.). Retrieved from https://www.daystofitness.com/wp-content/uploads/2015/11/processed-food-graphic.png
13. [Stomach]. (n.d). Retrieved from http://img.tfd.com/dorland/stomach_hourglass.jpg
14. [Toilet Diagram]. (n.d.). Retrieved from http://www.homerepairforum.com/forum/plumbing/3001-toilet-parts.html
15. [Toilet for Logo]. (n.d.). Retrieved from http://images.clipartpanda.com/toilet-clipart-71434f79f883930ded6927b8138046c7.jpg
16. [UBiome Kit]. (n.d.). Retrieved from http://blogs.discovermagazine.com/crux/2015/10/07/poop-sample-ubiome/#.WIuH-FMrId
17. [UBiome Logo]. (n.d.). Retrieved from https://pbs.twimg.com/profile_images/793381419342897152/Kb41gpKu.jpg
2. [Bacteria]. (n.d.). Retrieved from http://hdwallpaperdaily.com/wp-content/uploads/2013/05/microscopic-blue-bacteria-wallpaper.jpg
3. [Chart on phone]. (n.d.). Retrieved from http://www.beaconlearningcenter.com/weblessons/InterpretingLineGraphs/default.htm
4. [DNA ]. (n.d.). Retrieved from https://media1.britannica.com/eb-media/73/151873-004-E4641720.jpg
5. [Doctors]. (n.d). Retrieved from https://3.bp.blogspot.com/-
TASeSyMtdug/VwIJmJ7qnuI/AAAAAAAAABE/cp9heUfUCjs2L9WHnqdd5bOWRYuaeeMwQ/s640/Happy-Doctors-Diverse.jpg
6. [Environment]. (n.d.). Retrieved from http://asiarisingtv.com/wp-content/uploads/2016/03/air-800x515.jpg
7.[Food Plate]. (n.d.). Retrieved from http://1.bp.blogspot.com/-g1BqohVALgM/TeElpUxwZMI/AAAAAAAABdY/Tu22O79Nmv4/s1600/Plate -- pizza chart.jpg
8. [Gut Microbiome]. (n.d.). Retrieved from http://www.malaghan.org.nz/assets/Microbiota-intestinal.jpg
9. [Hygiene]. (n.d.). Retrieved from http://en-uk.ecolab.com/solutions/food-plant-personal-hygiene/~/media/ecolab/ecolab%20home/images/solutions/foodandbeverage/a%20person%20washing%20their%20hands%20show%20personal%20hand%20hygiene.jpg?as=1&w=550
10. [Overhead View of a Toilet]. (2013, February 6). Retrieved from http://www.langleytoday.ca/issue-canadas-ei-surplus-now-you-see-it-now-you-dont/
11. [Phone Diagram]. (n.d.). Retrieved from http://www.phonearena.com/news/The-Apple-iPhone-turns-10-today-a-decade-of-redefining-the-smart-in-smartphone_id89746
12. [Processed foods]. (n.d.). Retrieved from https://www.daystofitness.com/wp-content/uploads/2015/11/processed-food-graphic.png
13. [Stomach]. (n.d). Retrieved from http://img.tfd.com/dorland/stomach_hourglass.jpg
14. [Toilet Diagram]. (n.d.). Retrieved from http://www.homerepairforum.com/forum/plumbing/3001-toilet-parts.html
15. [Toilet for Logo]. (n.d.). Retrieved from http://images.clipartpanda.com/toilet-clipart-71434f79f883930ded6927b8138046c7.jpg
16. [UBiome Kit]. (n.d.). Retrieved from http://blogs.discovermagazine.com/crux/2015/10/07/poop-sample-ubiome/#.WIuH-FMrId
17. [UBiome Logo]. (n.d.). Retrieved from https://pbs.twimg.com/profile_images/793381419342897152/Kb41gpKu.jpg