User:Deacon C/sandbox

Minigene: This article addresses minigenes, their construction, differing types and usage. Minigenes provide a valuable tool to understand splicing patterns in both in vivo and biochemically assesed experiments. Specifically minigenes can act as a probe of which factors are important in spilcing outcomes; minigenes can be constructed to test the way both cis-regulatory elements (RNA effects) and trans-regulatory elements (associated proteins/splicing factors) affect splicing outcomes. Minigenes can also be used to test various factors found in different somatic cells, elements of which can also influence splicing.

=Minigene=

Suggested outline for Minigene article
Lead section to introduce the reader to the topic and provide a general description of minigenes, so they can decided whether they'd like to continue reading (organized above the sections box).

Definition of Minigene
"A minigene contains a genomic fragment including the alternative exon(s) and the surrounding introns as well as the flanking constitutively spliced cloned in a eukaryotic expression vector. Thus, the transfected minigenes should contain all RNA-elements necessary to show the same alternative splicing pattern as the corresponding endogenous alternatively spliced gene when compared in a specific cellular environment."

Construction of a Minigene
Minigenes can be constructed according to the protocol found in, "The in vivo minigene approach to analyze tissue-specific splicing", which provides a detailed recipe for construction of various minigenes. While the exact specifics are too detailed for this entry (the reader is referred to the cited article) a summation of the over all steps are as follows...

Types of Minigenes
Different minigenes can be constructed according to the basic information required.

Uses of Minigenes
Minigenes are used to elucidate cis-acting elements, trans-acting elements and other regulators of pre-mature RNA splicing that, when disrupted, can lead to disease. Using minigenes helps provide a better understanding of pathogenesis, which can then be used to identify potential targets of therapeutic intervention. Alternative splicing occurs in most human genes and can be carried out distinctly from cell to cell and between stages of development. Therefore, it is important that bioinformatic assumptions are confirmed in vivo. Minigenes provide the opportunity to do just that. Minigenes have been applied to the study of a diverse array of genetic diseases due to the aforementioned abundance of alternatively spliced genes and the specificity and variation observed in splicing regulation.



Images for minigene article
Until we move further into the minigene article construction this might be difficult. I don't want to fill out all the licensing information until we have a better of idea of the images we will use; so I will go through and put in the references, captions and page numbers where these images can be found for starters. We have three so far, but I really don't see this as being an image intensive article. Once again, I have to state that until we are further into the article, the exact images we will use are being decided.

Initial review article, Articles with Bullet Points TMO32
Bullet Points for Singh reference


 * Good explanation of the application of Minigenes in determining mutation affects on identification of splicing regulation elements
 * Describes how to design minigene plasmid vector for cis and trans acting factors
 * Great introduction on pre-mRNA and splicing processes
 * Image of plasmid vector (minigene)

Bullet Points for Faustino


 * Nice definition of splicing to help build background info for utility of minigenes
 * Provides splicing regulation breakdown

Bullet Points for Bonnet


 * Another application of minigenes, this time for BRCA analysis
 * Shows nice example of minigenes being good ways to screen splicing issues in precious sample types

Initial review article Deacon C
1. Cooper, T.A., *"Use of minigene systems to dissect alternative splicing elements" Departments of Pathology and Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA

Bulleted list for Cooper article


 * Provides an overview of how minigenes can be used to determine the effect of cis and trans-acting elements on alternative splicing scenarios.
 * Not only discusses what effect exon and intron differences can have on splicing, but also speaks to allelic variants and their effect on splicing.
 * Discusses what factor affect trans elements on splicing efficiencies.
 * Good diagram showing minigene construction in terms of exons and introns; would provide good images for the article.

2. Oliver Stoss, Peter Stoilov, Annette M. Hartmann, Oliver Nayler, Stefan Stamm, "The in vivo minigene approach to analyze tissue-specific splicing" Brain Research Protocols 1999. 383–394

Bullted list for Stamm article


 * ''Good description of minigene production and characterization, including PCR and minigene analysis references. This reference also gives the time it takes to produce the minigenes for in vivo experimentation. This really is more like a practical handbook than research paper.
 * Extended reference list for further research.
 * Speaks to the benefit of in-vivo analysis vs. biochemical analysis.
 * Provides a useful pictorial diagram of minigene generation from inception to transfection.

=This is the stop for the Minigene article except for references=

Two Articles for practice
My first article is, "Exocyclic DNA adducts as biomarkers of lipid oxidation and predictors of disease. Challenges in developing sensitive and specific methods for clinical studies". This is one of the articles I was looking at when exploring the "DNA adduct" topic in the list of articles we can improve. This is a review article from 2009 and talks about the role of oxidative-stress and its role in cancer etiology and risk. The use of these adducts as biomarkers for disease, as well as, individual genetic profiles, distribution in the body and rate of repair of DNA damage are also considered in assessing disease potential.

My second article is,"Single quantum dot imaging in living cells." This is another review article from 2013. I have been very interested in single molecule imaging as I used to work in this field when at Intel. This article talks about the unique photo-physical properties of quantum dots, as well as, how to attach them, the concepts involved in fluorescent microscopy and the necessary computer algorithms to perform tracking experiments. As I am looking at some of the references listed, I see a very interesting article, "Quantum dots and prion proteins: is this a new challenge for neurodegenerative diseases imaging?". This article discusses the benefits of how tagging prions and other nuerodegenerative agents with quantum dots can offer benefits in terms of early detection, disease assessment and tracking in difficult tissue types, especially in brain tissue.

Summary of Characteristics of a Target Article
The Stub:

Very basic description of topic, almost a dictionary description.

B class article:

''This article is basically complete, but still needs some work. This article may not'' satisfy a student or researcher and may be in need of expert knowledge input.

GA class article:

This article has been officially reviewed and is useful to almost everyone; it also has links to other current articles on the subject.

"The Five Pillars of Wisdom...from Wikipedia"
1. Wikipedia is an online encyclopedia: as such the articles should resemble an encyclopedia as much as possible; that is they should have meaningful content and comment on a relevant topic.

2. Wikipedia has a neutral point of view: Wikipedia is supposed to represent a "non-politicized" view point (this seldomly ever happens).

3. Wikipedia is free content: You cannot charge for use of a Wikipedia article and it will be used !

4. Wikipedians should interact in a respectful manner: follow the guideline for interacting with other members and be respectful.

5. Wikipedia has no firm rules: Wikipedia is a creative endeavor and as such, rules are not always adhered to.