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User:ZRamey/sandbox

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Part I - Objectives graded as 'credit/no credit'

edit

Critique an article

A few comments about the page:

Some of the citations are a bit out of date. The updated Office of Financial Management's "Population change and rank" spreadsheet has Auburn listed as the 15th most populated city in Washington state. [1] Additionally, the top employers currently cited on the page shows data from 2011. An updated employer list is needed. I have found one for 2015. [2]

The education section is in need of citation after the sentence "Currently the Auburn School District has fourteen elementary schools, four middle schools and three high schools, making twenty-two schools in all." Maybe a citation that leads to the Auburn School District website?

Add to an article

I updated the citation concerning the top employers of Auburn and the associated table with the information. I also added the citation for the information about the school districts.

Draft your article

DNA sequencing within droplets is quantized by the fluorescence of the drop after it is activated by a laser. FRET probes within the drop align complementary to the DNA strand and fluoresce at an intensity relative to their distance from each other. [3]

Part II - Graded objectives

edit

My peer reviews

Respond to your peer reviews

My article before peer reviews

Information such as sequence heterogeneity and mutations of healthy and diseased tissue is highly valuable in the medical field. Mutations that lead to diseases can be identified, individualized medical care can be properly implemented, and organisms can be quickly identified and catalogued with adequate sequence reading. [1] [2] [3] Droplet-based microfluidics has become an important, cost effective approach to DNA sequencing as it provides a high throughput with high accuracy characterized by its small-scale nature. [4] DNA sequencing with droplet-based microfluidics gained popularity with the implementation of fluorescent probes within single molecules; these probes are ideal for their high measurement sensitivity and region specificity.[4] [5] [6]

Most DNA sequencing done today focuses on single base reading, steering away from PCR amplification characteristic of older sequencing methods for more accurate readings. [7] [8] Single-molecule sequencing holds high accuracy as immediate attachment of fluorescent labels to nucleotides during DNA synthesis within the droplets creates a low threshold for error. [9] Commercially available devices utilizing cyclic-array sequencing of DNA synthesis with fluorophore attachment provide sample throughput that is ideal. [10] [11] Real-time DNA sequencing provides the means of single-molecule processing within even smaller environments.[11] This method uses various fluorophores which can attach to all four base types and essentially eliminating the need for cyclic-assay sequencing. [12] With more than one type of fluorophore for detection, reading speeds are decreased and accuracy is increased. [4]

My article after peer reviews

Information gathered from healthy and diseased tissue is highly valuable in the medical field as mutations can be identified, individualized medical care can be administered, and organisms identified and catalogued. [4][5] First demonstrated on an integrated microchip by Mathies et. al.[6], droplet-based microfluidics has become an important, cost effective approach to DNA sequencing that provides high throughput and high accuracy.[7] DNA sequencing via droplets gained popularity with the utilization of fluorescent probes for high sensitivity and region specificity. [8][9]

Most DNA sequencing done today focuses on single nucleobase reading. [10][11] Commercially available devices utilizing cyclic-array sequencing of DNA with immediate fluorophore attachment provide adequate sample throughput, but suffer from photobleaching and complications with multi-component biomolecules.[12][13] Real-time DNA sequencing provides the means of single-molecule processing within even smaller environments.[13] This method uses various fluorophores which can attach to specific nucleobase types and essentially eliminate the need for cyclic-array sequencing. [14] Multi-dye methods produce an increased accuracy at a decreased throughput. However, this method can be hindered by proximity limitations, biased detection, and labeling efficiencies. [7]

Reflective Essay

I worked on the Drolet-based Microfluidics article. It is a pre-existing subsection of the Microfludics article, but the information has been transferred to its own, new Droplet-based Microfluidics page. In this article I focused mainly on the section about DNA sequencing. For this section, I provided details about the importance of DNA sequencing overall, not specifically with sequencing via microfluidics. In order for a smoother transition, I discussed the advantages of using droplet-microfluidics for sequencing and discussed the various ways scientists achieve accurate methods, including their advantages and disadvantages. Both in-class reviewers agreed in saying my word choice needed to be a bit more scientific; to fix this I read and re-read my article to find instances of non-scientific wording. In most instances, such as the last sentence in the first paragraph, I removed the wording entirely rather than changing it as it helped the flow of the article. My paper also felt very one-side towards the advantages of droplet-microfluidics. After reviewing I went back to my sources and found disadvantages and challenges to be included in the article near the end. This assignment was very helpful in critically reading journal articles and referencing them for review. I hope that this portion of the article serves as a jumping off point for people interested in droplet-based DNA sequencing and I hope that someone finds the information useful enough. Overall, the assignment was a nice substitute for a term paper; it was not a lot of work when taken in small chunks and the concise nature of the article helps in gathering the important information from numerous articles.

  1. ^ Management, Office of Financial. "Washington State April 1 official population estimates". www.ofm.wa.gov. Retrieved 2017-04-18.
  2. ^ "City of Auburn CAFR 2015".
  3. ^ Abate, Adam (2013). "DNA sequence analysis with droplet-based microfluidics". Lab on a Chip. 13 (24): 4864–4869. doi:10.1039/c3lc50905b. PMC 4090915. PMID 24185402.
  4. ^ Abate, Adam R.; Hung, Tony; Sperling, Ralph A.; Mary, Pascaline; Rotem, Assaf; Agresti, Jeremy J.; Weiner, Michael A.; Weitz, David A. (2013-11-12). "DNA sequence analysis with droplet-based microfluidics". Lab on a Chip. 13 (24): 4864–4869. doi:10.1039/c3lc50905b. ISSN 1473-0189. PMC 4090915. PMID 24185402.
  5. ^ Shendure, Jay; Mitra, Robi D.; Varma, Chris; Church, George M. (2004). "Advanced sequencing technologies: methods and goals". Nature Reviews Genetics. 5 (5): 335–344. doi:10.1038/nrg1325. PMID 15143316. S2CID 205483006.
  6. ^ Woolley, Adam T.; Mathies, Richard A. (1995-10-01). "Ultra-High-Speed DNA Sequencing Using Capillary Electrophoresis Chips". Analytical Chemistry. 67 (20): 3676–3680. doi:10.1021/ac00116a010. ISSN 0003-2700. PMID 8644919.
  7. ^ a b Hohlbein, Johannes; Gryte, Kristofer; Heilemann, Mike; Kapanidis, Achillefs N (2010). "Surfing on a new wave of single-molecule fluorescence methods". Physical Biology. 7 (3): 031001. doi:10.1088/1478-3975/7/3/031001. PMID 20686191.
  8. ^ Harriman, O L J; Leake, M C (2011). "Single molecule experimentation in biological physics: exploring the living component of soft condensed matter one molecule at a time". Journal of Physics: Condensed Matter. 23 (50): 503101. doi:10.1088/0953-8984/23/50/503101. PMID 22067659.
  9. ^ Shendure, Jay; Ji, Hanlee (2008-10-01). "Next-generation DNA sequencing". Nature Biotechnology. 26 (10): 1135–1145. doi:10.1038/nbt1486. ISSN 1087-0156. PMID 18846087. S2CID 6384349.
  10. ^ Margulies, Marcel; Egholm, Michael; Altman, William E.; Attiya, Said; Bader, Joel S.; Bemben, Lisa A.; Berka, Jan; Braverman, Michael S.; Chen, Yi-Ju (2005-09-15). "Genome sequencing in microfabricated high-density picolitre reactors". Nature. 437 (7057): 376–380. doi:10.1038/nature03959. ISSN 0028-0836. PMC 1464427. PMID 16056220.
  11. ^ Harris, Timothy D.; Buzby, Phillip R.; Babcock, Hazen; Beer, Eric; Bowers, Jayson; Braslavsky, Ido; Causey, Marie; Colonell, Jennifer; DiMeo, James (2008-04-04). "Single-Molecule DNA Sequencing of a Viral Genome". Science. 320 (5872): 106–109. doi:10.1126/science.1150427. ISSN 0036-8075. PMID 18388294. S2CID 16725564.
  12. ^ Braslavsky, Ido; Hebert, Benedict; Kartalov, Emil; Quake, Stephen R. (2003-04-01). "Sequence information can be obtained from single DNA molecules". Proceedings of the National Academy of Sciences. 100 (7): 3960–3964. doi:10.1073/pnas.0230489100. ISSN 0027-8424. PMC 153030. PMID 12651960.
  13. ^ a b Levene, M. J.; Korlach, J.; Turner, S. W.; Foquet, M.; Craighead, H. G.; Webb, W. W. (2003-01-31). "Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations". Science. 299 (5607): 682–686. doi:10.1126/science.1079700. ISSN 0036-8075. PMID 12560545. S2CID 6060239.
  14. ^ Korlach, Jonas; Bibillo, Arek; Wegener, Jeffrey; Peluso, Paul; Pham, Thang T.; Park, Insil; Clark, Sonya; Otto, Geoff A.; Turner, Stephen W. (2008-08-28). "Long, Processive Enzymatic DNA Synthesis Using 100% Dye-Labeled Terminal Phosphate-Linked Nucleotides". Nucleosides, Nucleotides and Nucleic Acids. 27 (9): 1072–1082. doi:10.1080/15257770802260741. ISSN 1525-7770. PMC 2582155. PMID 18711669.
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