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User:Rmiller587/sandbox

< User:Rmiller587

Potential pictures

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

Citations and Summary

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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]

Dicer Outline

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Concise Intro

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Key Points

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1. Dissecting Human Dicer [13]

History

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Key Points

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Function

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Key Points

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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

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Key Points

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

Implications in RNAi therapy

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Key Points

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

Role in Immune System Function

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Key Points

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

Arabidopsis, Drosophilia, C. Elegans, Filamentous Fungi

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Key Points

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


References

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  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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