User:Agulati4/sandbox

Introduction to Sandbox Page
This is my sandbox page. On my sandbox page, I can practice editing and formatting articles. I can make letters bold and italic.

The Five Pillars of Wikipedia
1. Wikipedia is an encyclopedia.
 * Wikipedia is a reference for information. It contains a summary of information on all subjects.

2. Wikipedia is written from a neutral point of view.
 * Articles and information posted on Wikipedia should be unbiased. As such, editors who post or revise articles on Wikipedia should refrain from incorporating their own opinions or personal experiences into the information that they present. All information should be written as accurately as possible and every point of view should be presented equally and precisely.

3. Wikipedia is free content that anyone can edit, use, modify, and distribute.
 * All of the articles and information presented on Wikipedia can be edited by other fellow Wikipedians and viewed by the public.

4. Editors should treat each other with respect and civility.
 * Everyone has a varying viewpoint on several subjects and so will your fellow editors. Treat everyone's opinion with respect and calmly discuss any differences in the talk pages.

5. Wikipedia does not have firm rules.
 * Wikipedia rules are not set in stone. Editors should use their judgement when revising articles and remember that the ultimate goal is to improve Wikipedia and the information presented on it.

Summary of Characteristics of our Target Article
The goal of any Wikipedian editor is to get an article to the FA class. However, this is very difficult to achieve! For our course, we will be working on taking an article from the stub class to a B or GA class.


 * B Class
 * An article under the B class should have several references and include in-line citations when needed. In addition, the article should flow well, contain images and diagrams to support the context, and be well developed for the most part. However, the article still needs to be further developed to be listed under the GA class.


 * GA Class
 * An article under the good article class would have passed an official review to achieve such a status. A good article is written to include all aspects of a topic without presenting any bias or personal opinions. It is written clearly with many references, contains images to enhance the understanding of the content, and abides by the Wikipedia laws and guidelines. In addition, the information in a good article should be consistent and not be changed drastically every day.

Adeno-Associated Viral Vectors used in Gene Therapy

 * Adeno-associated viral (AAV) vectors are a class of viral vectors used in gene therapy. Numerous AAV serotypes and more than 100 variants have been isolated from various animal species and are currently being used to further study the use of AAV vectors in gene therapy. The specificity of each AAV vector is thought to be associated with the unique topology of their capsids. Researchers use this specificity to target certain regions throughout the body. However, AAV vectors are not equally successful in delivering genes to all target regions. For instance, AAV vectors used to deliver genes to areas affected by retinal disorders were found to be successful, whereas AAV vectors used to deliver genes to the liver and muscle to combat diseases, such as hemophilia B and muscular dystrophy, were not. This is due to the immune response elicited by the introduction of AAV vectors in areas, such as the liver, that are not immune privileged. Other AAV vectors are being studied and utilized to address this issue in gene therapy.

Preliminary Outline for Gene Silencing Article
1. Introduction
 * a. Definition of gene silencing
 * b. Use of gene silencing in cells and research experiments

2. Gene silencing in cells
 * a. Transcriptional gene silencing (TGS)
 * b. Post-Transcriptional gene silencing (PTGS)
 * c. Meiotic gene silencing

3. Gene silencing in research
 * a. Gene silencing research techniques
 * i. RNAi
 * 1. Virus-Induced gene silencing
 * ii. Antisense oligonucleotides
 * iii. Ribozymes
 * b. Uses in medical research
 * i. Cancer
 * ii. Infections
 * 1. Viruses
 * 2. Bacteria
 * 3. Parasites
 * iii. Respiratory diseases
 * iv. Neurodegenerative disorders
 * 1. ALS
 * 2. Huntington’s Disease
 * c. Challenges to gene silencing therapeutics

References:

1. Wilson, RC and Doudna, JA. Molecular mechanisms of RNA interference. Annual review of biophysics. 2013. 42: 217-39. PMID 23654304
 * Discusses the process of RNAi and the molecules involved

2. Fukushige, S. and Horii, A. DNA methylation in cancer: a gene silencing mechanism and the clinical potential of its biomarkers. The Tohoku journal of experimental medicine. 2013. 229(3): 173-85. PMID 23419314
 * Discusses the role of DNA methylation in gene silencing and how it can lead to cancer

3. Lee, HJ. Exceptional stories of microRNAs. Experimental biology and medicine (Maywood, N.J.). 2013 Apr. 238(4): 339-43. PMID 23759998
 * Discusses the ability of microRNAs to regulate gene expression
 * Looks at the function of microRNAs in post-transcriptional gene regulation

4. Moss, T and Wallrath, L. Connections between Epigenetic Gene Silencing and Human Disease. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis. 2007. 618(1-2): 163-74.
 * Discusses DNA methylation and histone methylation
 * Relates methylation to gene silencing and explores when defects in these processes can lead to disorders

5. Vaucheret, H and Fagard, M. Transcriptional Gene Silencing in Plants: Targets, Inducers and Regulators. Trends in Genetics. 2001. 17(1): 29-35.
 * Discusses post-transcriptional gene silencing (PTGS) and transcriptional gene silencing in plants
 * Provides definitions for PTGS, TGS, paramutation, and other words associated with gene silencing

6. Leung, R and Whittaker, P. RNA Interference: From Gene Silencing to Gene-specific Therapeutics. Pharmacology & Therapeutics. 2005. 107(2): 222-39.
 * Discusses the use of RNAi in producing gene-specific therapeutics
 * Discusses how RNAi can be used to study disease-associated genes in cancer, infectious diseases, and respiratory diseases

7. Unver, T and Budak, H. Virus-Induced Gene Silencing, a Post Transcriptional Gene Silencing Method. International Journal of Plant Genomics. 2009. (2009): 1-8.
 * Discusses virus-induced gene silencing and its use in research

8. Guo, D. and Wu, B., et al. A possible gene silencing mechanism: Hypermethylation of the Keap1 promoter abrogates binding of the transcription factor Sp1 in lung cancer cells. Biochemical and Biophysical Research Communications. 2012. 428: 80-85.
 * Discusses hypermethylation in regards to Keap1, a tumor suppressor gene. It is found that hypermethylation may be a gene silencing mechanism that could play a vital role in cancer treatment.

9. Felippes, F. and Wang, J, et al. MIGS: miRNA-induced gene silencing. The Plant Journal. 2012. 70:541-547.
 * Discusses microRNA gene-silencing (MIGS) as applied to Arabidopsis thaliana. It is found that MIGS can be used for gene silencing.
 * Discusses history behind VIGS, amiRNA, and hpRNAi in gene silencing.

10. Aly, M and Sham, A. MicroRNA: A powerful tool for post-transcriptional gene silencing in plants. Plant Knowledge Journal. 2013. 2(3):8-19.
 * Discusses miRNA-induced post-transcriptional gene silencing in plants. It is a great review article that provides insight into how bioinformatics and computational methods helped determine the roles of miRNA in gene silencing.

11. Schumann, U and Smith, N, et al. Analysis of hairpin RNA transgene-induced gene silencing in Fusarium oxysporum. Silence: A Journal of RNA regulation. 2013. 4(3).
 * Discusses the role of hairpin RNAs in RNA silencing in a plant fungus.

12. Pooggin, M. How can plant DNA viruses evade siRNA-Directed DNA methylation and silencing? International Journal of Molecular Sciences. 2013. 14:15244-15259.
 * Discusses what mechanisms plant viruses employ in order to evade silencing. Informative review! I wonder if there are reviews like this for other kinds of viruses? This paper only discusses geminiviruses and pararetoviruses. Worth a look.

13. Llorens, F, and Banez-Coronel, M, et al. A highly expressed miR-101 isomiR is a functional silencing small RNA. BMC Genomics. 2013. 14(104).
 * Discusses IsomiRs as potential "fine-tuners" of gene expression. Although they are sequence variants of miRNAs, it was found that they may still play a role in gene silencing.

14. Malek, A and Catapano, CV, et al. Selection of optimal combinations of target genes for therapeutic multi-gene silencing based on miRNA co-regulation. Cancer Gene Therapy. 2013. 20:326-329.
 * Discusses the potential of employing multiple types of gene silencing at once for personalized cancer therapies.

15. Guo, X and Li, WX, et al. Silencing of host genes directed by virus-derived short interfering RNAs in Caenorhabditis elegans. Journal of Virology. 2012 86(21):116545-11653.
 * Discusses the effect of virus-induced gene silencing in C. elegans through viRNAs.

Unit 12 Writing/Editing Area
RNAi Interference

RNA interference (RNAi) is a natural process used by cells to regulate gene expression. It was discovered in 1998 by Andrew Fire and Craig Mello, who won the Nobel Prize for their discovery in 2006. The process to silence genes first begins with the entrance of a double-stranded RNA (dsRNA) molecule into the cell, which triggers the RNAi pathway. The double-stranded molecule is then cut into small double-stranded fragments by an enzyme called Dicer. These small fragments, which include small interfering RNAs (siRNA) and microRNA (miRNA), are approximately 21-23 nucleotides in length. The fragments integrate into a multi-subunit protein called the RNAi induced silencing complex (RISC), which contains Argonaute proteins that are essential components of the RNAi pathway. One strand of the molecule, called the "guide" strand, binds to RISC, while the other strand, known as the "passenger" strand is degraded. The guide or antisense strand of the fragment that remains bound to RISC directs the sequence-specific silencing of the target mRNA molecule. The genes can be silenced by siRNA molecules that cause the endonucleatic cleavage of the target mRNA molecules or by miRNA molecules that suppress translation of the mRNA molecule. With the cleavage or translational repression of the mRNA molecules, the genes that form them are essentially inactive. RNAi is thought to have evolved as a cellular defense mechanism against invaders, such as RNA viruses, or to combat the proliferation of transposons within a cell’s DNA. Both RNA viruses and transposons can exist as double-stranded RNA and lead to the activation of RNAi. Currently, siRNAs are being widely used to suppress specific gene expression and to assess the function of genes.

Respiratory Diseases
Ribozymes, antisense oligonucleotides, and more recently RNAi have been used to target mRNA molecules involved in asthma (Popescu). These experiments have suggested that siRNA may be used to combat other respiratory diseases, such as chronic obstructure pulmonary disease (COPD) and cystic fibrosis. COPD is characterized by goblet cell hyperplasia and mucus hypersecretion (Pistelli). The mucus secretion was found to be reduced when the transforming growth factor (TGF)-a by siRNA in NCI-H292 human airway epithelial cells (Shao).