Talk:Morpholino

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The status of this article should be changed to GA, as it has passed Good Article review.

JonMoulton 14:46, 8 June 2007 (UTC)


Contents

[edit] Jon

Good day, Wikipedians and Morpholino users;

This is a stub to invite discussion of the Morpholino article.

The Morpholino-RNA heteroduplex image was generated by me at Gene Tools LLC, may be freely copied, and is licensed by the owner under the terms of the Wikipedia copyright.

Regards,

 - Jon
     Jon D. Moulton, Ph.D.
     GENE TOOLS, LLC
     jmoulton (at) gene-tools.com
     www.gene-tools.com

[edit] 30 Aug 05

Nice editing, Daycd, the flow of the article has improved. However, I removed your assertion that Morpholinos are in Phase III clinical trials. While the AVI website may give that impression, there are currently no ongoing phase III trials. Jon

Hi Jon, I'm glad you approve. I got the phase three from the web site but obviously you should know better. David D. (Talk) 22:00, 30 August 2005 (UTC)

[edit] 23 Jan 06

I removed a long parenthetical description defining "oligo" from the first sentence of the article. As the work "oligo" is already linked, the definition within this page was not needed. Jon

[edit] 20 July 06

I removed the {{ChemicalSources}} tag from external links since all of the promises made in the text associated with that link are false: Morpholinos are not available from the listed suppliers, the MSDSs are not available from that page, there is no spectroscopic data available there, etc. As Morpholinos are custom-synthesized compounds the spectroscopic data are only available from the manufacturer (Gene Tools or AVI Biopharma) and vary with the sequence of the oligo. —Preceding unsigned comment added by JonMoulton (talk • contribs) (and added nowiki by Dirk Beetstra T C 15:56, 20 July 2006 (UTC))

I saw the edit, I think it is right to delete the ChemicalSources template here, though now the only link there is one to a company that you are working for. I would call that a commercial link. Could you please think that over? Maybe the complete external links section should go, or you should put your link into the Wikipedia:Chemical sources page (and reinstate the chemicalsources template) to avoid any commercial bias on the page. --Dirk Beetstra T C 15:56, 20 July 2006 (UTC)

Fair enough, I'll remove the external links section. As Gene Tools is the only commercial source of Morpholinos it seemed convenient to provide the link, but a search engine can find the company quickly enough. JonMoulton 19:06, 21 July 2006 (UTC)

[edit] 19 Sept 06

A lead sentance had been added saying "In biochemistry, a morpholino is a kind of molecule used for genetic engineering. " Because Morpholinos do not modify DNA, I do not think it is appropriate to say they are used for genetic engineering, which is a field generally involving artificial genetic recombination. Further, as Morpholinos have their direct effect at the gene expression level instead of the metabolic level, they are more closely related to molecular biology than to biochemistry. I have changed the first sentance to: "In molecular biology, a Morpholino is a kind of molecule used to modify gene expression. " Overall, I think that the addition of an introductory sentance is an improvement in the article and that the general form of the sentance was very good. These changes fine-tune the focus to the actual uses of Morpholino oligos. JonMoulton 15:28, 19 September 2006 (UTC)

[edit] 19 Oct 06

A statement that "Claim for absence of non-specific effects has been contested" has been added to the top of the Morpholino page. As far as I can tell the page does not claim that Morpholinos have no non-specific effects. Certainly the sequence-specificity of Morpholinos is not perfect, and targets with several mismatched bases can be knocked down. However, the sequence specificity is better than available from other antisense types, such as phosphorothioate oligo or siRNA, due to the longer complementarity required for Morpholino activity. I would be happy to discuss this further. NPOV has also been challenged; I would welcome the input of experienced Morpholino users in editing this page. I have tried to maintain NPOV but I think it would be better to have strong editorial input from independent Morpholino users. JonMoulton 16:47, 19 October 2006 (UTC)

The user who attached the NPOV tag is not registered, but I have requested clarification on the IP address' talk page. Shultzc 09:49, 26 October 2006 (UTC)

I noticed one phrase which could be interpreted as a strong claim of perfect specificity. This is the claim that Morpholinos do not have "off target effects". A narrower claim is that they do not have non-antisense effects (such as the physiological effects caused by interaction of the phosphorothioate backbone with proteins). I think it is reasonable to narrow that claim; as I point out above, Morpholiinos can interact with targets bearing a few mismatches, which would fall under "off-target effects". Therefore, I am changing that phrase to "non-antisense effects".JonMoulton 16:52, 19 October 2006 (UTC)

As the original user who flagged this as biased, I have now included a referenced paragraph outlining these issues so that concerned readers can access primary research papers backing the basis for the original claim. As a member of the morpholino-user community, I hope that this will encourage discussion about these very important issues that effect the research life of many scientists around the world.


[edit] 19 Feb 07

I accidentally edited the main page without signing in as JonMoulton: 00:45, 20 February 2007 65.249.23.4 (Talk) (Move Talk Board link to top level)

The last reference pointed to the siRNA vs. Morpholino discussion on the Morpholino talk board. I did not see how this was germane to the comment on intellectual property claims, where the outside talk board was referenced within the Wikipedia article text. I modified the link to point at the top level of the Morpholino talk board, so that a user can scan through the upper-level catagories and find a path into the discussion most useful for their needs. JonMoulton 00:50, 20 February 2007 (UTC)

[edit] 12 April 07

I removed this text from the section on specificity: or the comparison with alternative antisense (for example GripNAs[1][2])

The new paper on p53 knockdowns by Steve Ekker showed that gripNA oligos caused the same "Morpholino phenotype" as the Morpholinos, and this phenotype (small head, shortened body axis, specific neurodegeneration) is caused by p53-mediated apoptosis. Therefore it appears that the phenotype comes not from the antisense backbone, but from the knockdown of the targeted gene, implying the apoptotic effect is independant of knockdown technology.

JonMoulton 17:00, 12 April 2007 (UTC)

[edit] 29 May 07

The article was changed to claim that Morpholinos are in clinical trials as anticancer therapies: They have been used in mammals ranging from mice[11] to humans and some are currently being tested in clinical trials as anticancer therapies.[12]

They are not; current clinical trials include West Nile virus, Hepatitis C, Duchenne's muscular dystrophy and a coronary artery bypass graft anti-stenosis trial. Therefore I removed the claim regarding anticancer therapies.

JonMoulton 15:01, 29 May 2007 (UTC)


[edit] Good article nomination on hold

This article's Good Article promotion has been put on hold. During review, some issues were discovered that can be resolved without a major re-write. This is how the article, as of June 15, 2008, compares against the six good article criteria:

1. Well written?: On the whole, not too bad, but my main critisism of this article would be the excessive use of jargon. For example, the article talks about "U" this and "U" that without ever explaining what "U" is. There are many other scientific items that appear in the same way, that could be linked to help with their explaination. This really needs to be fixed before morpholino can be considered a GA.
2. Factually accurate?: Seems pretty accurate
3. Broad in coverage?: Could benefit from some additional sentences or sections to give the overall picture (i.e. why knockdown genes, how does it relate to the processes of translation) or to explain delivery methods and method of action a little better (a simple diagram would help here). And the Specificity, stability and non-antisense effects section - is this the same as saying the pros and cons??
4. Neutral point of view?: seems neutral
5. Article stability? no edit wars are occuring
6. Images?: as mentioned above, would benefit from a diagram to two to help visualize the activity of morpholinos. Current image meets copyright criteria

Please address these matters soon and then leave a note here showing how they have been resolved. After 48 hours the article should be reviewed again. If these issues are not addressed within 7 days, the article may be failed without further notice. Thank you for your work so far Ciar 18:22, 31 May 2007 (UTC)

[edit] Response to Good Article hold

My apologies for the delay -- I have been out of town for a meeting of the RNA society.

1. I have added links to clarify jargon. I can add more links as needed; I am concerned about adding so many links that I obfuscate the useful background links. However, I agree that some terms, such as the U1 and U2 (etc.) snRNPs, were needed for clarity. My familiarity with Morpholinos often blinds me to those gaps in the link structure; your input has been helpful.

3. I have several diagrams that might be useful, one illustrating translation blocking and another illustrating splice blocking. I will add those tomorrow. Specificity, stability and non-antisense effects could be considered as pros and cons, though really each section is a continuum from pro to con. Lousy specificity makes for bad oligos, good specificity makes an oligo more experimentally useful, and similarly for stability (more stable is better) and non-antisense effects (less non-antisense effects is better). I will consider how to compose a section on the overall picture. I can add a section on delivery techniques in the next day or two.

JonMoulton 23:55, 4 June 2007 (UTC)

I have added images cartooning normal gene expression, Morpholino translation blocking and Morpholino splice blocking. I have written a brief description of the steps of normal gene expression to support the interpretation of the images. I have added more links to pages explaining the jargon.

JonMoulton 15:37, 5 June 2007 (UTC)

I have added a section addressing delivery of Morpholinos into cells. I am still in the process of adding the references.

JonMoulton 22:42, 5 June 2007 (UTC)

I have linked and referenced the Delivery section and added more links throughout the article to address the problem of unexplained jargon.

JonMoulton 17:40, 6 June 2007 (UTC)

This is much better Jon. You're going a great job! A couple of paragraphs look a little awkward (or hard for me ;-)) - the section on structure, and the last paragraph in Specificity, stability and non-antisense effects. Ciar 18:05, 6 June 2007 (UTC)

The Structure section is tough. I've written many variants of that description and they are never easy going. I removed a reference to chimeric oligos (in order to link a description, I would have to add a new page for chimeric oligos) and I added a suggestion to look at the first figure. I would be delighted by recommendations. The difference in structure between Morpholinos and nucleic acids should be defined (simply writing "see figure for structure" seems a cop-out) but precisely describing the difference in prose involves some difficult language.

Regarding the Specificity, stability and non-antisense effects section:

The first paragraph (on specificity) is suffering from a lack of direct published data so I have had to construct the somewhat lengthy argument. A paper has been submitted using human splice arrays to test the specificity of a splice-blocking Morpholino (I saw the data at a meeting late last week). When the paper is published I can simplify that section.
The second paragraph, describing stability, innate immune responses and DNA-level effects, is admittedly fairly information dense. Unfortunately, the statements on innate immune responses are based on unpublished data, so I cannot reference the literature. If someone versed in the field were referring to this article, that paragraph would provide important information so I am loathe to cut it out, though that might improve the overall clarity for the lay reader.
The third paragraph grew out of comments posted by another editor whom I am unfamiliar with (edited from an IP rather than a Wikkipedia account). I have been hesitant to cut away the important and legitimate point of view presented there (that is, his argument for "off target" effects of Morpholinos). The discovery that these effects are mostly due to p53 activity is very new and I added a description of the discovery and a reference. However, I am hesitant to completely rearrange this section because I want to maintain NPOV and accept input from other editors. This is a case where I have felt constrained from rearranging this section further in order to give the other editor a voice.

Regardless of the outcome of the "good article" application, I am pleased by the improvement to this article as a consequence of going though this review process. Thanks to all who have been contributing!

JonMoulton 21:57, 6 June 2007 (UTC)

I tackled the specificity section, splitting off the description of the mRNA rescue experiment and expanding it; I'm afraid the concise description only made sense if the reader already knew how the experiment is supposed to work.

JonMoulton 14:03, 7 June 2007 (UTC)

I overcame my reticence and tackled the section on off-target effects. I hope it has become clearer without obscuring the point of view of the editor who originally contributed that section.

JonMoulton 14:21, 7 June 2007 (UTC)

[edit] Introduction

The following recent addition seems to have a few flaws:

Knocking down gene expression is a powerful method for learning about the function of a particular protein; similarly, causing a specific exon to be spliced out of a protein can help to determine the function of the protein domain encoded by that exon.

While it is possible that an exon MAY contain a domain this is not always the case. I think this might be a bit misleading. David D. (Talk) 18:16, 6 June 2007 (UTC)

Good point. I have changed "domain" to "moiety".

JonMoulton 21:30, 6 June 2007 (UTC)

[edit] Successful good article nomination

I am glad to say that this article which was nominated for good article status has succeeded. This is how the article, as of June 8, 2007, compares against the six good article criteria:

1. Well written?: The quality of writing is pretty good, and has improved a lot since initial review. This can still be made better though, so keep up the good work!
2. Factually accurate?: To my knowledge, the information seems highly accurate.
3. Broad in coverage?: Aspects of morpholino's are covered from structure, to function, to delivery - what else could there be?
4. Neutral point of view?: This is a neutral article
5. Article stability? No edit wars are occurring - it's very stable.
6. Images?: Now several images are in place, instead of just one, that helps explain the activity of these little molecules. Much better!

If you feel that this review is in error, feel free to take it to a GA review. Thank you to all of the editors who worked hard to bring it to this status. Ciar 05:36, 8 June 2007 (UTC)

[edit] Argument to revert to capitalized "Morpholino"

Morpholino is used as a trade name to describe morpholino phosphorodiamidate oligomers. Therefore it is appropriate to capitalize Morpholino, as you would capitalize Kleenex or Aspirin (http://en.wikipedia.org/wiki/Trade_name). The word "morpholino" is also used to describe chemical structures having morpholine rings as substituants; therefore the use of the uncapitalized "morpholino" to describe the morpholino phosphorodiamidate oligomers can be confusing. As the capitalization is appropriate for a trade name and the uncapitalized usage can be confusing, I strongly urge reversion to the capitalized usage.

JonMoulton (talk) 16:00, 23 May 2008 (UTC)