User:Rmiller587/sandbox

  • miRNA formation using Dicer from mRNA. Could be used for RISC
    miRNA formation using Dicer from mRNA. Could be used for RISC
  • Overall process of formation of miRNA. We can choose either this one or the previous file (or both) in the article
    Overall process of formation of miRNA. We can choose either this one or the previous file (or both) in the article
  • RNAi/gene silencing diagram for both plants and animals
    RNAi/gene silencing diagram for both plants and animals
  • Drosophila (fly)
    Drosophila (fly)
  • C.elegans (worm)
    C.elegans (worm)
  • Arabidopsis thaliana
    Arabidopsis thaliana
  • RNAi in mammalian cells
    RNAi in mammalian cells

Article 1 - "Structural Basis for dsRNA Processing..."[1]

Key Notes
- Includes great variety of detail into the actual structure and functions of the dicer.
- They go into the crystallography of dicer with specific interactions (amino acids, metals) within the structure.
- It covers the basis of the whole function in the introduction that is known up to 2006.

Article 2 - "Dicey Role of Dicer..."[2]

Key Notes
- This article goes over the technology of cancer therapy using RNAi.
- It shows that lower dicer amounts or expression usually with more advanced tumor stages. Also showed that tumor cells usually had lower dicer amounts as well.
- Has a good picture explaining the methodology behind external RNAi therapy.

Article 3 - Dissecting Human Dicer [3]

Key Notes
- Short but broad basic overview of dicer.
- Has concise explanations of catalytic site.
- Good for writing the intro and has some info for other paragraphs but doesn't go too in depth.

Article 4 - Gene silencing in human embryonic stem cells by RNA interference. [4]

Key Notes
- Dicer is not the focus of this article but it is important for functional implications.
- This article is good for explaining a use of dicer as a molecular biology or therapeutic tool.
- Information from this article could be condensed into a small paragraph that allows linking the dicer article to articles about stem cells, pluripotence and siRNA.

Article 5 - Partners in dicing [5]

Key Notes
- Focuses on dicers interactions with other proteins.
- The main idea is to explore how a single enzyme without functional variants can accomplish different tasks (siRNA, miRNA etc.)
- There's a small, basic picture that may or may not be useful.
- Reporting protein-protein interactions will be important for linking dicer with other molecular biology articles.

Article 6 - Dicing and slicing: The core machinery of the RNA interference pathway [6]

Key Notes
- Great for pictures
- Discusses domains of functional dicer and has picture
- Pictures of mechanism of action
- Good article for discussing the biochemistry and functional actions of dicer

References from previous weeks:

References used talk about the function of dicer in different organisms such as Arabidopsis, in mice, and roundworm. [7] [8] More information about gene regulation can be explored too. [9]


Dicer as an anti-viral [10]

Dicer in immune cell development and function [11]

Dicer in DNA damage and repair. [12]

Concise Intro

Key Points

Related References

1. Dissecting Human Dicer [13]

History

Key Points

Related References

Function

Key Points

Related References

1. "Structural Basis for dsRNA Processing..."[1]
2. "Dicing and slicing: The core machinery of the RNA interference pathway" [14]
3. "The Role of dicer in DNA damage repair" [12]

Catalytic Domains/Mechanism of Action

Key Points

Related References

1. Partners in dicing [15]
2. Dicing and slicing: The core machinery of the RNA interference pathway [16]

Implications in RNAi therapy

Key Points

Related References

1. Gene silencing in human embryonic stem cells by RNA interference. [17]
2. "Dicey Role of Dicer..."[2]

Role in Immune System Function

Key Points

Related References

1. "Dicer as an anti-viral" [10]
2. "Dicer in immune cell development and function" [11]

Arabidopsis, Drosophilia, C. Elegans, Filamentous Fungi

Key Points

Related References

1. "Dissecting Arabidopsis thaliana DICER function..." [7]
2. "Dicer function is essential for lung epithelium morphogenesis" [8]


References

  1. ^ a b MacRae, I. J. (13 January 2006). "Structural Basis for Double-Stranded RNA Processing by Dicer". Science. 311 (5758): 195–198. doi:10.1126/science.1121638. PMID 16410517. S2CID 23785494.
  2. ^ a b Merritt, William M.; Bar-Eli, Menashe; Sood, Anil K. (23 February 2010). "The Dicey Role of Dicer: Implications for RNAi Therapy". Cancer Research. 70 (7): 2571–2574. doi:10.1158/0008-5472.CAN-09-2536. PMC 3170915. PMID 20179193.
  3. ^ Nicholson, AW (2012 Sep 28). "Dissecting human dicer: some assembly required". Journal of Molecular Biology. 422 (4): 464–5. doi:10.1016/j.jmb.2012.07.001. PMID 22771361. {{cite journal}}: Check date values in: |date= (help)
  4. ^ Rassouli, F. B.; Matin, M. M. (2009 Dec 25). "Gene silencing in human embryonic stem cells by RNA interference". Biochemical and Biophysical Research Communications. 390 (4): 1106–10. doi:10.1016/j.bbrc.2009.10.038. PMID 19833094. {{cite journal}}: Check date values in: |date= (help)
  5. ^ Ketting, RF (2006). "Partners in dicing". Genome Biology. 7 (3): 210. doi:10.1186/gb-2006-7-3-210. PMC 1557742. PMID 16584538.
  6. ^ Hammond, SM (2005 Oct 31). "Dicing and slicing: the core machinery of the RNA interference pathway". FEBS Letters. 579 (26): 5822–9. doi:10.1016/j.febslet.2005.08.079. PMID 16214139. S2CID 14495726. {{cite journal}}: Check date values in: |date= (help)
  7. ^ a b Henderson, Ian R.; Zhang, Xiaoyu; Lu, Cheng; Johnson, Lianna; Meyers, Blake C.; Green, Pamela J.; Jacobsen, Steven E. (14 May 2006). "Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning". Nature Genetics. 38 (6): 721–725. doi:10.1038/ng1804. PMID 16699516. S2CID 10261689.
  8. ^ a b Harris, Kelley S.; Zhang, Zhen; McManus, Michael T.; Harfe, Brian D.; Sun, Xin (1 February 2006). "Dicer function is essential for lung epithelium morphogenesis". Proceedings of the National Academy of Sciences. 103 (7): 2208–2213. doi:10.1073/pnas.0510839103. PMC 1413733. PMID 16452165.
  9. ^ He, Lin; Hannon, Gregory J. (July 2004). "MicroRNAs: small RNAs with a big role in gene regulation". Nature Reviews Genetics. 5 (7): 522–531. doi:10.1038/nrg1379. PMID 15211354. S2CID 5270062.
  10. ^ a b Mackay CR, Wang JP, Kurt-Jones EA (2014). "Dicer's role as an antiviral: still an enigma". Curr Opin Immunol. 26C: 49–55. doi:10.1016/j.coi.2013.10.015. PMC 3932008. PMID 24556400.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  11. ^ a b Devasthanam AS, Tomasi TB (2014). "Dicer in immune cell development and function". Immunol Invest. 43 (2): 182–95. doi:10.3109/08820139.2013.863557. PMC 4751989. PMID 24303839.
  12. ^ a b Tang KF, Ren H (2012). "The role of dicer in DNA damage repair". Int J Mol Sci. 13 (12): 16769–78. doi:10.3390/ijms131216769. PMC 3546719. PMID 23222681.
  13. ^ Nicholson, AW (2012 Sep 28). "Dissecting human dicer: some assembly required". Journal of Molecular Biology. 422 (4): 464–5. doi:10.1016/j.jmb.2012.07.001. PMID 22771361. {{cite journal}}: Check date values in: |date= (help)
  14. ^ Hammond, SM (2005 Oct 31). "Dicing and slicing: the core machinery of the RNA interference pathway". FEBS Letters. 579 (26): 5822–9. doi:10.1016/j.febslet.2005.08.079. PMID 16214139. S2CID 14495726. {{cite journal}}: Check date values in: |date= (help)
  15. ^ Ketting, RF (2006). "Partners in dicing". Genome Biology. 7 (3): 210. doi:10.1186/gb-2006-7-3-210. PMC 1557742. PMID 16584538.
  16. ^ Hammond, SM (2005 Oct 31). "Dicing and slicing: the core machinery of the RNA interference pathway". FEBS Letters. 579 (26): 5822–9. doi:10.1016/j.febslet.2005.08.079. PMID 16214139. S2CID 14495726. {{cite journal}}: Check date values in: |date= (help)
  17. ^ Rassouli, F. B.; Matin, M. M. (2009 Dec 25). "Gene silencing in human embryonic stem cells by RNA interference". Biochemical and Biophysical Research Communications. 390 (4): 1106–10. doi:10.1016/j.bbrc.2009.10.038. PMID 19833094. {{cite journal}}: Check date values in: |date= (help)
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