Wikipedia:United States Education Program/Courses/JHU MolBio Ogg 2012/Section 81/Group 81B

Group 81B

This is the Wikipedia page for 410.602 Molecular Biology, 2012, group 81B. This group will be editing the Helicase article.

Use the talk page here to collaborate as a group, when learning to use and navigate Wikipedia, assessing articles, or for any other topic.

Use this page (not the talk page) for article assessments (optional, see Unit 5); rationale for selecting an article (Unit 6); progress reports (Units 9 and 12); and the final report (Unit 14). Please create a new section here for each of those assignments.

Article Assessments (Unit 5)

Assessments for choosing topic

Telomeres assessment

• A few citations needed are present that could be resolved and elaborated on.

• A few sources from magazine/newspaper articles such as The Guardian and LA Times – which are OK as sources, but I would like to see more scientific-based sources, as these are not reviewed and approved by the scientific community prior to publishing, so aren’t as reliable as a scientific source.

• Entire Telomere shortening section requires citations (one citation is present but isn’t cited properly according to Wikipedia)

• Measurement of telomere length in laboratory requires Clean Up (one of the Quickfails: Wikipedia:Good article criteria)

• Human telomeres, cancer and ALT requires Clean Up (one of the Quickfails: Wikipedia:Good article criteria)

• Telomeres and Cancer requires elaboration

• It appears some of the organization (headings, for example Human telomeres, cancer, and ALT, could benefit from reorganization with better headings - the information in this heading doesn't seem to correlate completely with the heading, may be difficult for some readers to find what they're looking for.

• It has a higher quality rating, which could make elaboration more difficult

• Possible sections/information that could be added:
  • Telomeres and stem cells
  • Telomeres and aging
  • Telomeres as targets in therapy/medicine
  • Telomere testing
  • Telomere binding proteins

Helicase assessment

• Doesn’t have many sections, just a basic definition of helicases and function

• Superfamilies could be elaborated on

• No Wikipedia Quickfails

• Could benefit from more images showing helicase structure and function if available.

• Page ratings between 3.0 – 3.3 – not bad with room for improvement. The article does have basic info here, so introductory information is already here, however, there seems to be many other topics involving telomeres (as noted below) that could be included to add to the completeness of the article.

• Sections/information that could be added:
  • Translocation of helicases
  • Helicase disorders and human disease
  • Activation Barrier in helicase activity (ΔGbp ΔGf Gint, destabilization forces)
  • Active and Passive Helicases
  • Helicase Motifs
  • Annealing Helicases
  • Viral Helicases
  • Diagnostics for Measuring Helicase Activity

Segmentation gene assessment

• A web search on “segmentation gene” shows only short descriptions of the term, including the Wikipedia stub article. There is evidently a need of a well built reference article about segmentation gene in Wikipedia

• There are several published scientific articles that discuss segmentation gene in Drosophila. We can also expand on the different classifications of segmentation genes Biology online

• There is an evolutionary transcription regulatory relationship within segmentation gene networks that can be referenced as well as how segmentation genes act as transcription factors. [1]

2'O-methylation assessment

• Sections that can be added:

-Catalysis pathway of reaction

-Purpose

-Diagnostic uses

• Currently there is a picture of a methylated adenosine, a definition of what 2'O-methylation is, and two examples of functional importance of 2'O-methylation.
• Various articles speak of the importance of 2'O-methylation to RNA biogenesis.
• There is an article on 2'-O-methylated ribose providing molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5 that can be delved into.
• Reverse transcriptase pauses at 2'O-methylated sites. This is being used in the diagnostic field.
• REGRETABLY most of the articles dealing with this phenomenon are on pay sites and we would have to pay to read and pull information from these articles.

Transversion assessment

• Sections that can be added

-Types of mutations

-Transversion related diseases

-Causes or conditions that cause transversions

• There are various forms of cancer directly correlated to transversons
• Effect due to chemical structure change can be discussed.
• Mutation severity can be discussed

Article Choice Rationale Summary

The Helicase Wikipedia article is comprised of basic analysis of helicase type and function. Group 81B feels that this article is not only missing important aspects about helicase but there are areas in this article that can be expanded upon, therefore we wish to choose the Helicase Wikipedia page for our Molecular Biology group project. The first aspect of helicases that we wish to expand upon are the classes of helicase, active and passive, the similarities and differences between the two, and how to distinguish one from the other. In this expansion we will offer examples of each and the processes those examples are responsible for catalyzing. While there is already an area distinguishing types of helicases into “superfamilies”, we feel that this basic definition of some important helicases is insufficient and we would like to delve into the characteristics and functions of the different types of helicases. For example, helicases involved in viral function, annealing processes, DNA repair, and DNA replication are all references but there is no characterization or functional analysis of these types of helicase and why they are important. Adding these aspects to those sections would expand the scope and wealth of this article. Helicase disorders and diseases associated with such disorders would be a valuable addition to this article. Helicase disorders are associated with cancer predisposition and premature aging disorders. The discussion of such disorders would bring value to the helicase Wikipedia article. At the same time, we would like to include diagnostic analysis methods of helicase activity. Within this section we can discuss how these tools are used to measure helicase activity in various diseases such as hepatitis C, as well as referencing commercial diagnostic kits such as the “TruPoint Helicase System” from PerkinElmer which measures helicase activity by fluorescent labeling. The RNA helicase section offers only a short description that highlights some important facts but still leaves room for improvement. The history of helicase discovery is not found in this article. While this is a scientific project historical aspects of this protein is an important part which is not discussed in this Wikipedia page. Helicase is a vast, multibranching subject that is involved in many aspects of molecular biology. While the Wikipedia article on helicases does a good job of providing basic information on helicase function, structure, and grouping, more in depth discussions on the aspects provided above would add tremendous value to the article and encompass many aspects of this vast subject into one central article.

Unit 9 progress report

We have identified and assigned the different sections of the article.

Section	Author
Passive/Active Helicases	Jennifer
Helicases Disorders/Disease	Jennifer
Helicase Groups (w/Superfamily elaboration)	Gisela
Helicase Discovery	Hanna
Diagnostic Methods	Hanna
RNA helicase	Gisela

We have also established a preliminary structure of the article.

• 1. History (Discovery)

In this section we have identified various articles and reviews including the first published article on helicases which was found in E.coli. We have also found the article cronicling the discovery of the first eukaryotic helicase in lily. We have located a helicase discovery timeline that outlines major discoveries in the field of helicases such as the discovery of seven conserved amino acid domains that make up a helicase motif as well as articles that chronicle the discovery of new helicase motifs that were identified in DEAD box helicases. We have located an article that chronicles the discovery of human helicases in 1990. Finally we have so far located an article that chronicles the discovery of biochemically active helicases found in the malaria parasite.

• 2. Function

A section on passive and active helicases is being added to the Function section of the article. An outline of this section has been developed with the primary resource: Manosas M, Xi XG, Bensimon D, Croquette V (September 2010). "Active and passive mechanisms of helicases". Nucleic Acids Res. 38 (16): 5518–26. doi:10.1093/nar/gkq273. PMC 2938219. PMID 20423906. Still to do here is composition of section from outline before posting for group review.

• 3. Structural Features
• 4. Superfamilies

Compiled several scientific articles on superfamilies organizion of Helicases. Working on a better structure of the section that explains on what basis the helicases are classified besides showing some examples. Added references to previously cited examples of the different superfamilies.

• 5. Helicase disorders/disease

This is a new section being added to the article. The article currently only lists one disease associated with helicase mutations, without any explanation or references. Progress has been made on this chapter in the researching of various helicase mutations and the human disease they are associated with. The current proposal for the structure of this section is to group disorders by mutations (of a specific helicase). As research continues, this may change.

The proposed sections on mutations of the XPD helicase and RecQ family helicases are finished, and will be posted in the group's Talk section for review. Once these have undergone group revision, we'll be ready to post into the current Wikipedia article as the first published sections of the Helicase disorders/disease portion of the article, and it can then undergo review by other Wikipedia contributors and classmates.

Still to do for this piece of the article are sections on X-linked a-thalassemia mental retardation syndrome (ATR-X), adPEO, and Juberg-Marsidi syndrome (JMS), as well as the identification of possible other mutations to include. Also included in this section will be a brief table listing the pathology and associated helicase mutation.

• 6. Diagnostic methods

Various methods have been developed to measure or monitor helicase activity. Some methods use a fluorescence signal that will fluoresce with increased activity while other methods use a fluorescence tag and a "quencher" that when brought into close proximity will suppress fluorescence signalling. These increases or decreases in signalling is the measurement used to determine and quantify helicase activity.

Commercially available assays for detection/quantitation of helicase activities have been identified and will be displayed in this section, outlining their modes of action.

• 7. RNA helicases

Compiled several scientific articles to expand on the mechanism of RNA helicases.

Interactons with the Wikipedia editors (mostly Klortho) has been mostly use of the Klortho's talk page discussions which have been an excellent resource of frequently asked questions.

TO DO LIST FOR THE REMAINDER OF THE PROJECT

1. Completion of research of each group member's assigned section.

2. Submission of project sections for group review.

3. Implementation of project sections into the Wikipedia article.

4. Review and editing of assigned group's (Group 81E - Bacteriophage T12) wikipedia page.

81D Peer Review

Hi Gisela, Hanna & Jennifer! This is Monica from 81D Nucleic Acid Structure and can I just say WOW?! Your group definitely has its work cut out but you have also made some great progress! I have a few suggestions. For one, you might want to think of moving the DNA Helicase Discovery History to the top of the article. I think it flows better being at the beginning rather than near the end. I also think that more images could be added to Superfamilies, RNA Helicase (general picture of RNA Helicase) as well as Diagnostic Tools for Helicase Measurement(images of Perkin Elmer's products although I'm not sure if it would violate any copyright laws). In addition to adding a general image of an RNA Helicase, perhaps you could add images of canonical duplex unwinding and local strand separation. I think you could also expand on proteins of the Swi/Snf family in the RNA Helicase section. These are just a few thoughts for now but I will check back later. Monicamcoulter (talk) 15:09, 15 November 2012 (UTC)Monica

Hi Group 81B, this is Ravinder from group 81D. I was reading your group’s article and it looks very good. Most of the key concepts are discussed. I think as the helicases functions are mentioned, it would be good to add description on helicase mechanism. Adding the various models of helicase translocation would make it even more interesting. I think a paragraph on how helicase can be used as antiviral drug targets can be added. There is a review paper on it. Information on the RNA helicase database (www.rnahelicase.org) can also be added to the page. These are just a few suggestions, overall great job guys! Ravinder2012 (talk) 01:11, 25 November 2012 (UTC)

Hi Ravinder. Thank you for your feedback!. I'm already in the process of adding the rna database info. Gisela Gonzalez (talk) 15:32, 27 November 2012 (UTC)

Unit 12: Progress Report

• Added both the Helicase discovery history section and the Diagnostic Tools for Measuring Helicase Activity section

-Elected to change the Diagnostic tools for measuring helicase activity section" to "Diagnostic tools in Analysis/Characterization of Helicases" to include the assays that are used to not only monitor and determine helicase activity, but to also include assays that determine helicase polarity.

• Rewrote and restructured Superfamilies section due to the lack of references.
• Added links to molecular biology key terms in superfamilies section.
• Added Helicase disorders and diseases section covering three types of helicase mutations and the disorders associated with them.
• Added sub-section under Function: Helicase activation barriers.
• Added sub-section under Function: Acitve and passive helicases.
• Edited previous material in Function by adding references, taking out unreferenced material when no references could be found, and clarifying information
• Added all references to source material.
• Reviewed each other's sections and commented/edited accordingly.
• Submitted peer review comments on Group 81E's article.

We have interacted with editors that recommended the addition of figures and the expansion of RNA helicase which is already in our to-do list. We have also reviewed and added comments to the Bacteriophage T12 group page.

Issues to resolve before project completion

1. Implementation of relevant reviewer comments.

2. Possible rearrangement of article contents.

3. Addition of final aspects of our perspective sections.

4. Possible edits to pre-established sections in this article.

Final Progress Report

Through these last 14 units this group has:

• Added multiple sections to the helicase article
  • History of DNA helicase discovery
  • Helicase disorders and diseases
  • Diagnostic tools for helicase measurement
• Revised multiple pre-existing sections to the helicase article
  • Function: added information on activation barrier and active and passive helicases; added references and clarity to previous section; added image
  • Superfamilies
  • RNA helicases
• Restructured the content of the article for a better reading sequence
• Implemented revisions that were suggested by peer-reviewers
• Worked with other editors to maintain the correct formatting
• Added relevant images

These points have led to the successful enhancement of the Helicase article that can now serve as a point of reference for not only basic information on helicases, but on information involving helicase families, helicase functionality, the history of helicase discovery, diseases/disorders associated with helicase deficiencies/mutations, and methodology associated with the identification of helicase polarity and the measuring helicase activity.

We, as a group, would like to acknowledge Group 81D for their peer review suggestions, and Klortho for his constant and helpful instruction involving Wikipedia formating and processes.