Talk:Arabidopsis thaliana

I was wondering what the reasoning was behind the latest revert? Adenosine | Talk 18:45, July 15, 2005 (UTC)

The current version:

• It plays the role for agronomy that mouse and fruit fly (Drosophila) play in human biology.

The version I reverted:

• It plays the role in botany that the mouse and the fruit fly (Drosophila) play in zoology.

The idea of a model system is to use a simple system to get clues as to how the complex (however you define this) system works. My reasoning is that Drosophila is a model system as is mouse, but for zoology? This is technically correct but, in my view too broad. The real reason that NIH is pouring money into these model system research programs is because it helps us understand disease and development with regard to human biology. Using that rationale then the equivalent of human biology in botany is agronomy.

I believe that the same argument for agronomy can be made as above for human biology. Arabidopsis research is heavily funded by USDA as well as NSF. There is no doubt that this has huge implications for botany but again I think that is too broad. The fact is that this model system is being used as a starting point to understand crop plants. Consequently it is a model system to understand plant biology with regard to having a better understanding agronomic crops.

So in essence, I think that human biology/agronomy is more relevent to the actual research goals of these model systems. As an aside the broad goals of zoology and botany are to sequence as many genomes as possible. To understand ecosystems and diversity. I don't think the model systems of Arabidopsis and Drosophila are useful from this regard. I hope this makes sense. David D. 19:46, 15 July 2005 (UTC)Reply

Wierd, i don't know what to say about it, but its an interesting read. [1]

This stuff is really exciting, this just came out (today! wedneday the 23rd/05) so it is really new, but if correct, there could be completly new forms of inheritance than DNA. Our genomes may no longer be completely explained by the human genome project. I'm excited about this and actually plan to to some work on this for my plant genetics class this semester, but after i do some work I will be sure to update the page(s). Anyone else work with arabidopsis thaliana know anything else about this? Adenosine | Talk 09:22, Mar 23, 2005 (UTC)

As I write this (JS Hoyer (talk) 13:42, 20 October 2016 (UTC)), essentially no one believes the original hothead paper except the authors.Reply

Several other parts of this article need judicious editing. Examples:

• "In 2016, it was named as one of the organisms that would be involved in CRISPR-based genetic engineering." What does this even mean? CRISPR mutagenesis was described back in 2013 (Li et al.), and has been used by many labs since then.
• The word 'ecotype' is not used according to its proper ecological meaning. The outdated usage of the word persists in the A. thaliana community, unfortunately. This page should uniformly use the more neutral word 'accession' instead.
• The phrase 'agronomically performant line' does not make sense for a non-crop. The NASC page cited (which is not such a great reference...) just says that Col-0 gives a good seed yield.
• (See further discussion below on improving referencing for this page)

---

I think the HOTHEAD section should be removed, but for a different reason than you. We shouldn't present fringe theories as fact, but they should be included in Wikipedia if they have enough notability. The most "recent" paper cited is from 2006, and the section doesn't address whether it's currently accepted or not. I would take this as evidence that the theory is not notable and should be removed, unless someone can find more recent sources. Clarinetguy097 (talk) 05:30, 22 October 2016 (UTC)Reply

I think that the controversy is notable, but that it does not merit more than a brief mention on this particular page. I see now that the stand-alone HOTHEAD_(gene) page is pretty good: it cites another paper from 2008. Another pro-RNA-cache-theory paper was published in 2013: https://f1000research.com/articles/2-5/v2. JS Hoyer (talk) 23:55, 22 October 2016 (UTC)Reply

Those are valid points. How much acceptance does the 2013 paper have? Clarinetguy097 (talk) 20:57, 23 October 2016 (UTC)Reply

The 2013 paper has attracted little attention; the backlash against the original paper continues, but I can only cite my personal experience talking with people on that point. The 2013 paper seems to have attracted eight citations: https://scholar.google.com/scholar?cites=8434230634355466927

I will try to continue improving the HOTHEAD_(gene) page, but leave it to others to trim down the HOTHEAD section on this page (or not), because I am more interested in the three other points I raised above. JS Hoyer (talk) 13:30, 26 October 2016 (UTC)Reply

Update: I trimmed down the section, but it could still be shortened further and/or moved/removed. I added more detail to the other page. JS Hoyer (talk) 18:49, 9 April 2017 (UTC)Reply

I think we need to be cautious about jumping to conclusions regarding the above research. Although the researchers showed very strong evidence for a "molecular cache" of genetic information, there are some major assumptions in the research. Most importantly, the researchers suggest that this process is RNA mediated. However, in their study they had no proof of the fact, only that DNA was not. Regardless, I think that in five years, the way we study inheritence will be much different.--Doucher 08:42, 18 Apr 2005 (UTC)

I agree with Doucher that this research is in it's infancy. I made a change to make their conclusions more speculative. In general, is it appropriate to have research on this page? It seems that the research should be on the appropriate topic page. For example, phototropism should probably be moved to the phototropism page. Like wise the RNA cache should probably have it's own page, although, I think it is premature to create one at present. David D. 15:49, 12 May 2005 (UTC)Reply

Original research doesn't belong in Wikipedia. But once research has been published in scientific literature, it is recommended that Wikipedians mention it (with the necessary caution). This way, Wikipedia can lead the way and be taken seriously. JoJan 16:40, 12 May 2005 (UTC)Reply

I was not suggesting that the research does not belong in Wikipedia. It just seems that the body of significant research results from Arabidopsis is huge and that trying to document it on this page is a bad precident to set. It would seem to be more appropriate to link a new article to this page. i think this page should be reserved for information about the model plant Arabidopsis. Possibly a section about the history of Arabidopisis as a model system.David D. 16:47, 12 May 2005 (UTC)Reply

No kidding, in the entire universe of Arabidopsis research, (of which I am just one small planet) someone seeks to put their own speculative work in an article that is only a few paragraphs long? I'm yanking it.--Aufidius 23:47, 20 July 2005 (UTC)Reply

Do you think that the primary researchers on this project are the ones that put this on wikipedia? You're right this is new research, it did though get the cover of one particular back-water journal (Nature!! (http://www.nature.com)). Wikipedia is supposed to be a vibrant, current source of all the world's information (at least in my eyes). Your (Aufidius) last revert erased what was very unbias, and well cited material that could end up being one of the greatest discoveries in genetics, molecular biology and botany in the last decade. I believe that we need to present all information, this is not speculative work, this work has data to back it up. Arabidopsis thaliana is our model orgainism for genetics in plants, this is the very information that belongs here because this is the very information we hope to discover from Arabidopsis. I wish not to create a revert war, so please anyone respond here with your views/opinions. This is just my honest (and perhaps not so humble) opinion. Adenosine | Talk 02:23, July 21, 2005 (UTC)

I agree with Adenosine, there is no way that the paragraph was written by the original authors. Many have contributed to clean it up to the unbiased summary that Aufidius deleted. My initial response was also to yank it, but then i considered tha fact that this research was on the front page of many national newspapers, it was on TV and radio too. It is rare that science gets so much air time (let alone plant science) and, therefore, despite it's controversial nature, it is the one research paragraph I would keep on this page. It is certainly more appropriate than a paragraph on phototropism. At the end of the day this whole page needs to be rewritten. When that day comes i can see this paragraph having a it's rightful place. If nothing else this research has madfe Arabidopsis notorious. David D. 04:22, 21 July 2005 (UTC)Reply

I noticed that there is significant overlap between the Arabidopsis page and this (Arabidopsis thaliana) page. I think this might lead to confusion with people coming into wikipedia to edit the Arabidopsis page or linking to the incorrect page. I propose we strip out the thaliana specific info on the Arabidopsis page or merge the two together. If we keep them separate the Arabidopsis page should be discussing the whole genus and redirect to the Arabidopsis thaliana page for specific infomation about the genetic model system.David D. 16:36, 12 May 2005 (UTC)Reply

Many journals use Arabidopsis to refer to the species Arabidopsis thaliana. In other words, they are taking the common name from the generic (ie, the genus) name. This is quite typical, common names for lots of plants are taken from their genus (iris, camelia, rhododendron, to name just three). It is so common that the Council of Biology Editors established a rule for this practice: Common names taken from the genus are neither capitalized nor italicized, and form plurals as in English. This rule makes a lot of sense. Scientific names (binomials) are set in italic to recognize the fact that they are Latin, by definition (Linneus decreed that all binomials be Latin so they would be Universal), and English printing recognizes words that are in a foreign language by setting them in italic font. Common names are common, that is they are in the common language and so equally by definition must be taken as no longer foreign, whatever their origin. Likewise, Linneus also established the convention that the generic name is capitalized. This is useful, it makes there be no ambiguity when writing about a genus. For some reason, modern journal editors ignore this sensible rule and capitalize Arabidopsis even when it is used as a common name. Indeed, some journals even capitalize AND italicize Arabidopsis when it is used as the common name. In matters of regular usage, something that starts out as a mistake, with enough repetition, becomes correct. However, in matters of nomenclature, a mistake is always a mistake. Please use arabidopsis (small a, Roman font) to refer to Arabidopsis thaliana (a usage that is far far more widespread than using thale or mouse-ear cress). Strike a blow for the wisdom of Linneus.

This person knows what they're talking about. My dad is a botanist, and he is always complaining about this. Amphion 21:15, 24 December 2005 (UTC)Reply

How is arabidopsis pronounced and which syllable gets the stress?

Something like this A (as in had)-ra (a as in had)-bid-op-sis I'm not sure how to use the offical nomenclature. David D. (Talk) 23:13, 8 May 2006 (UTC)Reply

I came to the article specificatelly to see what is the correct pronunciation, namely the th group (th like this, dh like that or t like thyme?), but I did not find what I was looking for... Could an IPA pronunciation be given? --Squidonius (talk) 06:10, 12 August 2011 (UTC)Reply

Found out that it is a "th" in thale from thale-cress (so /θeɪl/), so I think it should be /ə.rɑ.bɪ.'dɒp.siːs θeɪ.'lɪɑ.nə/, but I am not that good at IPA vowels. --Squidonius (talk) 21:32, 24 September 2011 (UTC)Reply

I'm a student in both Plant Science and Linguistics, and I am new to having a Wikipedia account, but I think I can help here. The IPA would be: /əˌræbɨ'dapsɪs ˌθeiliˈanə/ (the ei is a diphthong) or, as I am familiar with it, /ˌθæliˈanə/. In conveyance to English speakers, I'd write it as uh-Rab-uh-DOP-sis Thal-ee-AH-nuh where the 'a' in Thal is like the 'a' in at and the syllables in all caps are primary stress and the syllables in initial caps are secondary stressed. Josiah (Talk) 04:45, 18 March 2015 (UTC)Reply

"A collaboration between researchers at the Salk Institute for Biological Studies and the University of California at Los Angeles captured the genome-wide DNA methylation pattern of the plant Arabidopsis thaliana - the "laboratory rat" of the plant world - in one big sweep..."[2]69.6.162.160 01:42, 1 September 2006 (UTC)Brian PearsonReply

http://www.bioedonline.org/news/news.cfm?art=2821 89.58.168.184 23:45, 5 April 2007 (UTC)Reply

Maybe it's not a big deal but I wonder if it might make more sense to rate this topic high importance rather than top importance in the plants wikiproject. This is the only plant species in Category:Top-importance plant articles; pretty much everything else in there covers a very broad botany topic (e.g. tree, leaf, pollen, etc.)--Eloil 21:58, 3 May 2007 (UTC)Reply

It is the first plant genome to be sequenced. That alone should classify it as top importance. David D. (Talk) 06:37, 19 June 2007 (UTC)Reply

It feels like this article is missing an important section on Arabidopsis t. biology in general: life cycle, growing reqirements, and other related bits of information. Also, there is a whole bunch of reasons it was selected to be a model organism to beging with, which are not discussed here. Some of this can be easily googled up:

http://www.bio.davidson.edu/people/kabernd/seminar/2004/GMevents/MT/MTArabidopsis.html

http://www.arabidopsis.org/info/growth.jsp

-- User:Denger 9 Sept. 2007 —Preceding unsigned comment added by Denger (talk • contribs) 13:19, 9 September 2007 (UTC)Reply

Yes, the article needs a lot of work in these areas. Since you see the omission so clearly, why not fix the article? KP Botany 18:06, 9 September 2007 (UTC)Reply

I've added a description of the plant and its distribution - MPF 21:00, 19 September 2007 (UTC)Reply

Good job, that helps a lot. I wish I had noticed how poorly this article was done earlier, considering how important the plant is. KP Botany 01:01, 20 September 2007 (UTC)Reply

If we are to describe the a plant, we should talk about the whole flower, has four white petals is not enough. I could do it, but I think we should instead make a good description of flowers on the article Brassicaceae about its family. Their structure is very consistent within the family. Then we could list what makes them peculiar on this page the pages of the single species. The fruit is not a capsule, but a siliqua, which is a particular kind of capsule. Aelwyn 09:56, 20 September 2007 (UTC)Reply

Good idea! Agreed - MPF 10:18, 20 September 2007 (UTC)Reply

Ok, Brassicaceae will be my 'next victim'. You can watch my edits if you want, or we can fix it together or ask for collaboration. This evening I'll start (you are English, so 'this evening' has the same meaning for us!). We should work more this way. Aelwyn 11:21, 20 September 2007 (UTC)Reply

Yes, I agree to this idea. Would work for a number of families, and seems obvious and important for this article. KP Botany 22:29, 20 September 2007 (UTC)Reply

Sure. This is not the first time we say family articles need more attention, but there have been only few major improvements since then. Little interest on this point, perhaps. I'd like to see articles like Asteraceae, Fabaceae, Lamiaceae, Poaceae reach a decent level, but more cooperation is needed, I can't write all myself (after the simple-English wikipedia, the awkward-English wikipedia!). Revamping the most important articles is more difficult than posting a comment now and then, but much more useful. Aelwyn 08:47, 22 September 2007 (UTC) PS: Don't get me wrong, this means: Come on, let's do it together, and not Why haven't you already done it?Reply

I know our family level article are dreadful--I can't even bear to look at the Fabaceae article. I just don't have any time right now. Brassicaceae, however, would be a great place to start--thanks. KP Botany 16:18, 22 September 2007 (UTC) —Preceding unsigned comment added by Aelwyn (talk • contribs)

For those who have taken park at this conversation: I have worked on Brassicaceae and it is more satisfactory now, the description of the flower is fairly detailed and could be 'recycled' here. I'd be very glad if you could have a look at it (and to its discussion) and give some feedback (on that page, of course). Thank you very much. Next victim: Fabaceae, maybe. Aelwyn 23:08, 25 September 2007 (UTC)Reply

Should clearyl be 135 Mbp, who came up with 157? https://www.arabidopsis.org/portals/genAnnotation/gene_structural_annotation/agicomplete.jsp

I believe it should be 125 Mbp Nature 408, 796-815 (14 December 2000) | doi:10.1038/35048692; Received 20 October 2000; Accepted 15 November 2000 http://www.nature.com/nature/journal/v408/n6814/full/408796a0.html — Preceding unsigned comment added by 68.119.35.243 (talk) 07:35, 2 October 2014 (UTC)Reply

There is some disagreement concerning the leaves. Webb, Parnell and Doogue 1996. note: "...Leaves mostly basal, stalkless, oblong,..." and Clapham, Tutin and Warburg 1968. note "..."Basal lvs in a rosette, elliptical or spathulate, distantly tooth, stalked,...". The specimens I have looked at have are shortly stalked basal leaves. Those on the stem are "sessile" as noted in Clapham et al.

Leaves are covered with small, unicellular hairs (called trichomes).

Is this unusual, if so to what extent, and what are the hairs there for? — Preceding unsigned comment added by 82.139.81.0 (talk) 15:58, 28 May 2014 (UTC)Reply

... needs to be replaced or updated. Macdonald-ross (talk) 08:41, 6 November 2014 (UTC)Reply

There appears to be a typo in the last sentence under the Distribution section:

"It is frequently be found in Belfast."

Rather it should be "It is frequently found in Belfast." Brainbowboy (talk) 15:04, 26 March 2015 (UTC)Reply

Fixed Plantdrew (talk) 16:01, 26 March 2015 (UTC)Reply

I was wondering if these references would be a good study on the Arabidopsis Thailana resistance to plant pathogens

1. Zipfel, C., Robatzek, S., Navarro, L. 2004. Bacterial disease resitance in Arabidopsis through flagellin perception. Nature. 428: 764-767.

2. Delaney, T., Uknes, S., Vernooij, B. 1994. A Central Role of Salicylic Acid in Plant Disease Resistance. Science. 266: 1247-1252.

3. Bent, AF., Kunkel, BN., Dahlbeck, D. 1994. RPS2 of Arabidopsis thaliana: a leucine-rich repeat class of plant disease resistance genes. Science. 265: 1856-1860.

4. Lawton, K., Friedrich, L., Hunt, M. 1996. Benzothiadizaole induces disease resistance by a citation of the systemic acquired resistance signal transduction pathway. The Plant Journal. 10: 71-82. — Preceding unsigned comment added by Fireblade7869 (talk • contribs) 23:06, 24 September 2015 (UTC)Reply

Mainly, this sections talks about the impact of environmental forces on plant pathogen resistance evolution, as it allowed plants to develop ways to counteract the pathogens that may have come up while living in their dynamic environments. Two of the variations of plant pathogen resistance include those that go through the signal transduction pathway as well as that of the systemic acquired resistance. Fireblade7869Fireblade7869 (talk) —Preceding undated comment added 21:46, 21 October 2015 (UTC)Reply

It would be helpful to clarify in your first paragraph whether Arabidopsis Thaliana has any unique forms of pathogen resistance. I understood the paragraph as a general overview of plant pathogen resistance, rather than a discussion that is specific to Arabidopsis Thaliana. I liked that you clearly connect plant pathogen resistance to its significance and use. Evolution43 (talk) —Preceding undated comment added 04:35, 26 October 2015 (UTC)Reply

Hello I am thinking of adding something to your page about Arabidopsis thaliana. Hello Fireblade7869,

I really enjoy your article. This definitely goes in great depth for readers, especially when you are mentioning the specific defense mechanisms. Your research is also in very effective in this article and it does a great job of tying everything together in the article. From here I just have a few quick suggestions. My first suggestion would be to explain a little more about the different environments the plants could be found in. You mention that there could be a difference in the resistance based on the different environments, and then you talk about dynamic environments. What kind of dynamic environments do you mean here? This could be an area where there could be just a little bit more information specifically explaining what types of dynamic environments. Also, just in general, especially for the first paragraph, possibly explain a few of your word choices. For example, apoptosis would be a term that we would understand, but possibly people who do not have a science background might not understand this. Once again this could further the understanding of the article for the readers. Overall, this article seems very well researched and very well put together. Nice job, looking forward to reading more! Slu 2018 (talk) 05:40, 26 October 2015 (UTC) Slu 2018 (talk) 05:40, 26 October 2015 (UTC)SLU_2018 25 October 2015Slu 2018 (talk) 05:40, 26 October 2015 (UTC)Reply

Thank you for the helpful comments! I have changed the first paragraph to better illustrate the fact that Arabidopsis Thaliana does not actually have any unique forms of pathogen resistance, but was just used as model for plant life in general, because the plant-pathogen resistance pathway that is present in the Arabidopsis is present in most other plant populations. I have also tried to explain dynamic environments as well as some other words readers may have a hard time understanding. I've changed around the organization of the entire document to allow for a smoother introduction into plant-pathogen resistance and then moving onto how Arabidopsis Thaliana was used as a model organism in many studies to show the two main types of plant-pathogen resistance that is present in most plant populations. At the end of the document, I added a little bit about the evolutionary mechanisms for the arrival of plant-pathogen resistance. There were a few grammar mistakes that I have also cleared up. Fireblade7869 (talk) 23:20, 8 November 2015 (UTC)Fireblade7869Reply

Hello, I'm 2015evolution7 (talk) 22:03, 15 November 2015 (UTC) I found the distribution section lacking so added some information that I had found . I think as far a bettering the article as a whole, all of the research information should be condensed to just the truly relevant information, so it's not so overwhelming. Feel free to change any edits I made and use my advice in any way you would like 2015evolution7 (talk) 22:03, 15 November 2015 (UTC).Reply

Hello Fireblade7869, I made a few edits to the first paragraph in your Plant Pathogen Resistance section to make some of the sentences more concise and easier to understand. Some of the sentences include a lot of information/jump between ideas and should be broken down into smaller sentences that can be more easily followed by an individual outside of the field. I found your explanations of certain terms helpful, and would suggest that you use some of the explanations for terms such as "rapidly changing" in place of the actual term you use (dynamic environments). You should also add references after every sentence to ensure that any contributions made in the future do not interrupt the sources for your ideas. Overall this section contains a lot of relevant information and provides just enough for a good understanding of the concepts applied to A. thaliana. Further contributions could expand on variation across populations because you mention it briefly but do not go much into detail about it. Anon2831 (talk) 05:53, 16 November 2015 (UTC)Reply

I appreciate all of the comments! I've changed the sentences into shorter, clearer thoughts for the reader to follow. The paragraphs have been moved around a little to allow for a more logical progression of thoughts. In addition, I have changed the studies around to include more general information rather than focusing on the specific studies. Citations have been added to the necessary sentences. Finally, links have been added to the following pages: pathogens, plant disease resistance, and systemic acquired resistance. Also, the following pages have been linked to my section: necrosis and signal transduction pathway. Fireblade7869 (talk) 03:54, 10 December 2015 (UTC)Fireblade7869Fireblade7869 (talk) 03:54, 10 December 2015 (UTC)Reply

This page has had a note on it since February 2016 indicating that the article relies too much on primary sources. This is a shame, given the very large number of review articles and historical perspective pieces on A. thaliana, including an entire special issue of The Plant Journal in 2010. A long review by Provart et al. (2015), a recent eLife review by Krämer, and an older perspective piece by Koornneef and Somerville (2002) also come to mind.

I think there should be separate page on the history of A. thaliana as a reference plant and perhaps a separate page on its use as a model for plant-microbe interactions, given how much current text the page currently has on (evolution of) disease resistance.

The current section entitled 'Light emitting' seems trivial and out-of-date to me. A single Kickstarter campaign (out of a number of different efforts to develop commercially viable luminescent plants) does not seem notable, especially given that luciferase reporter genes are now routine tools than have yielded many fundamental insights, particularly in studies of the A. thaliana circadian clock.

I will try to add some references alluded to above, but the current structure of the page has inhibited work on this. JS Hoyer (talk) 16:09, 7 March 2017 (UTC)Reply

Be bold. This article has accumulated a lot of cruft during the years, as the plant is a common target for primary research. As far as I can tell, this article has no "core" editors curating its contents, so a lot of passers-by just came along and inserted the material about the research that they or somebody close to them was working on, with variable levels of quality and scientific weight. The article should be based on review articles indeed. I have done some formatting and structuring on the article, but evaluating the research is out of my league. I agree that the article should be split, with large chunks of material moved to e.g. Research on Arabidopsis thaliana, briefly summarized in this article per Wikipedia:Summary style. Consider placing a notice at WT:WikiProject Plants, which is pretty active – somebody might be interested in helping out and reviewing. No such user (talk) 10:18, 9 March 2017 (UTC)Reply

Thanks for the feedback. I started a Draft:History of research on Arabidopsis thaliana, and included some of the citations mentioned above. Some of it is currently patchy, uneven, and under-referenced. JS Hoyer (talk) 00:04, 21 April 2017 (UTC)Reply

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