User:Littorina littorea/Codon reassignment/Bibliography

You will be compiling your bibliography and creating an outline of the changes you will make in this sandbox.

Bibliography As you gather the sources for your Wikipedia contribution, think about the following: Is the source from a reliable publication? Reliable publications include established newspapers, academic journals and books, textbooks, and other published sources with reputations for accuracy and fact-checking. Unreliable sources include blog posts and other self-published works, press releases, and social media posts. Is the source verifiable? In order for a source to be considered verifiable, other editors should be able to consult the source. Is the source independent of the subject? Is the source connected in any way to the subject? This is especially important when writing biographies or about organizations. For example, if you were writing a biography, sources like the person's webpage or personal blog would not be considered independent. Is the source primary or secondary? Primary sources include first-hand accounts, autobiographies, and other original content. Wikipedia allows limited use of primary sources, but typically only for straightforward, descriptive statements of facts, and only if they are published and verifiable without requiring specialized knowledge. Secondary sources should be the main basis for a biography on Wikipedia. If you're working on a topic related to medicine or psychology, ensure that your sources follow these special guidelines. If you're creating a new article, consider the following: Ensure that your topic meets Wikipedia's notability guidelines. In order for a topic to meet the notability requirement, you must be able to identify 2-3 sources that are reliable, verifiable, and independent of the subject you're writing about. Finding sufficient sources to establish notability can be especially hard when writing about people or organizations. Sources that are not independent of the subject might be useful additions, but don't count towards the notability requirement. Wikipedia has developed special guidelines for writing about living persons. Please follow these carefully. Wikipedia has a series of guidelines for writing about different categories of people, such as academics and artists. If you're trying to create a new entry about a living person, please look at these carefully. If you're not sure whether a source is reliable, ask a librarian! If you have questions about Wikipedia's sourcing rules, you can use the Get Help button below to contact your Wikipedia Expert. Get Help

Bibliography

Edit this section to compile the bibliography for your Wikipedia assignment. Add the name and/or notes about what each source covers, then use the "Cite" button to generate the citation for that source.

https://www.sciencedirect.com/science/article/pii/S0168952500021442 codon assignment is not as universal as it seems, and this has implications for the continuing evolution of genetic code. ^[1]

https://pubs.rsc.org/en/content/articlelanding/2015/sc/c4sc01534g unnatural amino acids are common in protein research, and is usually done with blank amino acids. Codon reassignment can allow even more unnatural amino acids to be invented and present new ways to use existing amino acids. ^[2]

https://academic.oup.com/nar/article/50/19/11374/6775395 synthetic tRNA background information and how they relate to codon reassignment. ^[3]

 

Amino acid Table

https://commons.wikimedia.org/wiki/File:Aminoacids_table.svg Wikimedia codon wheel to demonstrate that many codons code for the same amino acid. (Not sure how to cite yet)

https://www.ncbi.nlm.nih.gov/books/NBK26829/ Great general overview for transcription, background information. Look at the "There Are Minor Variations in the Standard Genetic Code" section. Though there are 64 codon combinations, only 20 amino acids are used by our cells.^[4]

https://academic.oup.com/ismecommun/article/4/1/ycae079/7696150#468717066 Viral stop codon reassignment in bacteriophages. ^[5]

Examples: Luke, Learie. 2007. Identity and secession in the Caribbean: Tobago versus Trinidad, 1889–1980 Kingston, Jamaica: University of the West Indies Press. This is a book published by a university press, so it should be a reliable source. It also covers the topic in some depth, so it's helpful in establishing notability. Galeano, Gloria; Bernal, Rodrigo (2013-11-08). "Sabinaria , a new genus of palms (Cryosophileae, Coryphoideae, Arecaceae) from the Colombia-Panama border". Phytotaxa. This is a peer-reviewed scientific journal, so it should be a reliable source. It covers the topic in some depth, so it's helpful in establishing notability. Baker, William J.; Dransfield, John (2016). "Beyond Genera Palmarum: progress and prospects in palm systematics". Botanical Journal of the Linnean Society. This is a peer-reviewed scientific journal, so it should be a reliable source for a specific fact. Since it only dedicates a few sentences to the topic, it can't be used to establish notability.

References

1. O'Sullivan, Justin M; Bernard Davenport, J; Tuite, Mick F (2001-01-01). "Codon reassignment and the evolving genetic code: problems and pitfalls in post-genome analysis". Trends in Genetics. 17 (1): 20–22. doi:10.1016/S0168-9525(00)02144-2. ISSN 0168-9525.
2. Dumas, Anaëlle; Lercher, Lukas; Spicer, Christopher D.; Davis, Benjamin G. (2014-12-01). "Designing logical codon reassignment – Expanding the chemistry in biology". Chemical Science. 6 (1): 50–69. doi:10.1039/C4SC01534G. ISSN 2041-6539.
3. McFeely, Clinton A L; Dods, Kara K; Patel, Shivam S; Hartman, Matthew C T (2022-10-28). "Expansion of the genetic code through reassignment of redundant sense codons using fully modified tRNA". Nucleic Acids Research. 50 (19): 11374–11386. doi:10.1093/nar/gkac846. ISSN 0305-1048.
4. Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Raff, Martin; Roberts, Keith; Walter, Peter (2002), "From RNA to Protein", Molecular Biology of the Cell. 4th edition, Garland Science, retrieved 2025-02-10
5. Cook, Ryan; Telatin, Andrea; Bouras, George; Camargo, Antonio Pedro; Larralde, Martin; Edwards, Robert A; Adriaenssens, Evelien M (2024-01-01). "Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages". ISME Communications. 4 (1): ycae079. doi:10.1093/ismeco/ycae079. ISSN 2730-6151.

Outline of proposed changes

Click on the edit button to draft your outline.

• Create a proper lead section
• Description of what codon reassignment is
  • Normal codon behavior
  • How a tRNA can code for a different amino acid
  • What this means for the proteins
• Examples of codon reassignment
  • Human cancer cells, expand on present example
  • Bacteria
• Uses for codon reassignment
  • Artificial amino acids

Now that you have compiled a bibliography, it's time to plan out how you'll improve your assigned article. In this section, write up a concise outline of how the sources you've identified will add relevant information to your chosen article. Be sure to discuss what content gap your additions tackle and how these additions will improve the article's quality. Consider other changes you'll make to the article, including possible deletions of irrelevant, outdated, or incorrect information, restructuring of the article to improve its readability or any other change you plan on making. This is your chance to really think about how your proposed additions will improve your chosen article and to vet your sources even further. Note: This is not a draft. This is an outline/plan where you can think about how the sources you've identified will fill in a content gap. Get Help