Talk:Viroid

Taxonomy

Viroid
Scientific classification
Superdomain:	Biota
Domain:	Aphanobionta
Superkingdom:	Acytota
Kingdom:	Virus

I find that there are references to domain virus, and aphanobionta to categorize these things (the domains covering the same content) ; and there's the superkingdom Acytota 132.205.15.43 20:20, 25 Nov 2004 (UTC)

WikiProject

• Wikipedia:WikiProject Viruses
• We need more people to join and help out, please consider having a look at our project page if you're interested in helping out -- Serephine ♠ talk - 12:16, 19 June 2006 (UTC)

detecting viroids

I reluctantly reverted the addition of To determine whether an infectious agent is a viroid, culture the substance by itself on a nutritive medium, away from plant cells.

While this would certainly distinguish viroids (which wouldn't grow) from bacteria (which would grow on the media), this does nothing to distinguish between (RNA) viroids and DNA viruses -- right?

So how does one determine whether an infectious agent is a viroid? Or, in practice, do we not bother -- we just use the "culture" test to decide whether to use an antibacterial treatment, or instead the other treatment that generically applies to virus, viroid, virusoid, etc. ?

The virus page mentions RNA viruses and DNA viruses. What is the difference between a "viroid" and a "RNA virus"? Or are they the same thing?

--DavidCary 14:08, 13 December 2005 (UTC)

The edit you reverted was really a nonsense. However, there is a big difference between viruses and viroids - viroids do not code their own proteins but are autocatalytic RNAs. RNA viruses code proteins. There are also virusoids, which do not code proteins, but are dependent (paraziting) on a virus. There is no general antivirus treatment (nor antiviroid etc.), there is even no general antibacterial treatment. --Kyknos 19:33, 13 December 2005 (UTC)

I'd even be cautious to suggest a close evolutionary relationship between viri and viroids. Viroids really seem to be "escaped introns" or more specifically, autocatalytic transgenes. While a virus during its lysogenic phase has something like a rudimentary sort of "life" (i.e., it causes proteins to be produced which otherwise wouldn't, and thus does have a non-autonomous metabolism - note that the infectious virus particle itself is definitely non-living), viroids seem to be "genome detritus" so to speak.

How to detect them? Tough, very tough. At first, somebody has to suspect that there is something odd going on, which is quite tough as these things are often enough symptomless. Then, you need to do RT-PCR, reversely transcribing the RNA prsent in a cell into DNA. Then, you have to note that there is a large quantity of RNA present in the original sample which does not come from the host (i.e. does not map onto the host genome in DNA sequence). And having thus determined the viroid sequence (hopefully), one could use molecular probes to fish for denaturated viroid DNA (heated, so that it does not align in double strands). IONO whether it is done that way, but it would work.

It might be added (ref?) that the mode how viroids cause pathogenic effects is unknown, but possibly has something to do with them interfering in host DNA directly (i.e., physically), compare Antisense DNA (which is single-strand however) - viroids might do it by "edging" their way into the DNA transcription/replication apparatus. Molecular monkeywrenching might be a quite appropriate expression - IF that hypothesis is correct. Dysmorodrepanis 18:26, 22 October 2006 (UTC)

List of currently existing viroids

This is a list of unique viroids including their assigned abbreviations (via ICTVdB Index of Viruses):

(ADFVd)		Apple dimple fruit viroid
(AFCVd)		Apple fruit crinkle viroids
(ASSVd)		Apple scar skin viroid
(AGVd)		Australian grapevine viroid
(ASBVd)		Avocado sunblotch viroid
(BluMVd-RNA)	Blueberry mosaic viroid
(BuSVd)		Burdock stunt viroid
(CChMVd)	Chrysanthemum chlorotic mottle viroid
(CSVd)		Chrysanthemum stunt viroid
(CBLVd)		Citrus bent leaf viroid
(CEVd)		Citrus exocortis viroid
(CbVd)		Citrus viroid III
(CVd-IV)	Citrus viroid IV
(CVd-OS)	Citrus viroid original source
(CCCVd)		Coconut cadang-cadang viroid
(CTiVd)		Coconut tinangaja viroid
(CbVd-1)	Coleus blumei viroid 1
(CbVd-2)	Coleus blumei viroid 2
(CbVd-3)	Coleus blumei viroid 3
(CLVd)		Columnea latent viroid
(ELVd)		Eggplant latent viroid
(GYSVd-1)	Grapevine yellow speckle viroid 1
(GYSVd-2)	Grapevine yellow speckle viroid 2
(HpLVd)		Hop latent viroid
(HpSVd)		Hop stunt viroid
(IrVd-1)	Iresine viroid 1
(MPVd)		Mexican papita viroid
(NGSVd)		Nicotiana glutinosa stunt viroid
(PLMVd)		Peach latent mosaic viroid
(PBCVd)		Pear blister canker viroid
(PPMMoVd)	Pigeon pea mosaic mottle viroid
(PSTVd)		Potato spindle tuber viroid
(TASVd)		Tomato apical stunt viroid
(ToBTVd)	Tomato bunchy top viroid
(TCDVd)/(TPMVd)	Tomato planta macho viroid

Van der Hoorn 15:43, 13 June 2007 (UTC)

Initial Explanation of Viroids

I realise this is a rather specialised article, but for a non-expert in biology it's relatively easy to find oneself here when looking at the most primitive forms of life/pseudo-life, as the article on virus links to this. However, on reading the intro, it's very difficult to discern what exactly a viroid is. If you assume that anyone getting here has a reasonable knowledge of what a virus is, and (roughly) what it does and how it is composed, then a short starter section comparing and contrasting viroids to traditional virii would be a lot of help to a passing reader.

Unfortunately, this is not a very active article, but if anyone reading this understands the basics of this subject, even if you don't consider yourself an expert, I urge you to take a few minutes to add some intro-level description to the opening paragraph. Every little change helps. Jovial Air (talk) 15:58, 7 March 2008 (UTC)

If the definition of Viroid changes, then I believe a section called "History" should be added or expanded, and reflect on the meaning and intent of the old term, and the new term. In most books I come across Viroid as a pathogen, specifically a small plant pathogen. And this definition seems simple enough. I mean, if you look at the big picture, it's all just a string of RNA. And RNA can do a lot of stuff, just look at "RNA Biology" for all functions of RNA inside of a living cell. 84.112.136.52 (talk) 00:16, 26 October 2013 (UTC)

Inconsistencies regarding inclusion of Hepatitis Delta

This article begins by saying, "Viroids are plant pathogens...", and then under "Pathology" it describes Hepatitis D, a human pathogen. In the ICTV (the virus database), Hepatitis D is listed as a ssRNA virus, though there are publications that list hepatitis delta in parallel with viroids. Clearly, this article needs work. I'm not a viroid expert, so I'm going to add a reference in the first paragraph to hepatitis delta having similar properties, link to the hepatitis D article, and delete the Pathology section. Perhaps there should be some content on Pathology of viroids, but I don't know what that would be.Scray (talk) 09:39, 10 March 2008 (UTC)

Isn't it a virusoid or satellite virus rather than a viroid?--Miguelferig (talk) 17:41, 26 May 2012 (UTC)

References

removal of "without the protein coat that is typical for viruses.[1]" sentense

The sentense "without the protein coat that is typical for viruses.[1]" is wrong, There are indeed at least three virus families that do not encode for any capsid or coat proteins: Hypoviridae, Endornaviridae and Narnaviridae. The fact that viroids do not encode a capsid is not linked to their non-classification in viruses. Reference: Capsid-Less RNA Viruses http://onlinelibrary.wiley.com/doi/10.1002/9780470015902.a0023269/abstract Philippe Le Mercier (talk) 11:29, 29 November 2012 (UTC)

I disagree, because exceptions do not invalidate "typical" characteristics. Humans typically have hair, teeth, 2 arms, and 2 legs. That not all humans have all of those characteristics does not invalidate my first statement. The material you removed was supposed by the reliable source you removed. Your source does NOT say that the material you removed was incorrect. Care to justify your removal further, or shall I just restore it? -- Scray (talk) 16:17, 29 November 2012 (UTC)

Pictures

Can we not get a few pictures from electron-microsopy? I figure it's nothing fancy, given that it has only about 2000 base pairs, and may look like a small plasmid (though it is ssRNA), but still - pictures folks! We want EM-pictures! 84.112.136.52 (talk) 00:14, 26 October 2013 (UTC)

To editor who wishes EM-pictures of the viroid: I am sorry for the delay in answering your pertinent request. Answer: If you look at my portrait on the Wikipedia "Theodor Diener" page, you will see to the right of my head an EM picture displaying a mixture of non-denatured, double-stranded viral DNA molecules (the long strands) and equally non-denatured viroid RNA (the short strands, with one located to the right of my face, where my finger touches ir. This picture comes from the first EM study of a viroid. It confirmed at the time the double-stranded nature of non-denatured viroid molecules, as well confirmed their length. As you predicted, aside from these features, the EM pictures doesn't show any details of the viroid structure I hope rhis answers your question. TOD

User:Dienerto Edits: ok - or not?

Seems User:Dienerto (contribs), without discussion, has been rewriting several articles (ie, Viroid; RNA world hypothesis; Potato spindle tuber viroid; Circular RNA; Non-cellular life) - in order to promote himself, his own studies and his own WP:POV - in addition - seems the editor is attempting to remove references to other studies, again without discussion, that may not agree with his own studies or WP:POV - the editor may (or may not) be correct in the contents - a closer look at the edits may be indicated - nonetheless - possible issues of WP:COI, WP:PROMO, WP:OWN, and WP:SPA may (or may not?) apply - comments welcome - in any case - Enjoy! :) Drbogdan (talk) 12:56, 16 November 2014 (UTC)

To Drbogdan: I am sorry for having made edits without discussion, which occurred because I am new to this and couldn't figure out how to discuss my suggested edits. To comment on your comments: You are quite correct that, without my input, there would be serious concerns about the objectivity of my proposed changes, which all concern Zimmer's New York Times article .

Last night, I have submitted a justification for my changes, but I don't know whether you have received it and therefore copy it here:

Reference No.10 is fatally flawed by omitting the very publication which originally introduced the “living relic” hypothesis, of which Flores et al.’s review paper---the source of Zimmer’s NYT piece---is, in Flores et al..’s own words, only a summary of Diener’s 1989 supporting evidence, with the addition of some additional data that further support its plausibility---not a new hypothesis. I quote Flores et al.: “Hereafter, we discuss the evidence that supports Diener’s claim, summarizing his arguments and supplying others.”

Zimmer’s failure to recognize my original 1989 publication is tantamount to a serious flaw in his willingness to adhere to basic rules of scientific ethics---an attitude further documented by his omission of a question mark in the title of his NYT piece, which is inexcusable, because it gives the reader the erroneous impression that the “new research" cited establishes the ancient age of viroids, when, in fact, it is still a hypothesis, not a scientific fact. Without reference to my 1989 paper, the reader of Zimmer's article must conclude that the "living relic" hypothesis was conceived by the Spanish group.

References to Zimmer’s NYT piece should be deleted from Wikipedia, not only in its Viroid page, but wherever else he has willy nilly added a reference to his flawed piece.

I may add that I contacted the Senior Author of the Spaniards' review paper, R Flores by e-mail (I have been on friendly terms with Ricardo for many years and consider him a topnotch scientist and the foremost viroid researcher today) and acquainted him with my concern. but also questioned some of his own wording in the review paper. I quote from his response:

"Dear Ted,

I am very pleased that this misunderstanding between us is gone, and that our long lasting friendship remains as ever.

Just some short comments to explain a couple of points of our review. With "provocative title" (perhaps should I have used "appealing title"?) I tried to convey to the reader the message that some ground-breaking hypothesis was put forward in your paper. Then, to reinforce this idea, the phrase went on to say " ... Diener gave a twist to previous perspectives and proposed that viroids and viroid-like satellite RNAs were ... living fossils of a precellular RNA world". With "twist" I tried to mean "a complete new view". I have checked an editorial dictionary (I always have one open in my computer screen) and found "Copernican twist". So, it seems that "twist" can be used in a scientific context to highlight something particularly novel. This, and only this, was my purpose.

One final remark. As a member of the Research Counclil, I do not have teaching obligations, but I teach every year voluntarily on "Viroids" for 10-12 h to graduate students. Instead of dealing with new developments (deep sequencong and so on) I start from the very beginning, trying to explain them how a new scientific concept (the viroid concept in this case) emerged and became consolidated, using for this aim illustrations taken from your 1979 book. I tell the students that you are certainly "the very beginning" and a good portion of the ensuing story.

With my warmest regards. Ricardo"

I also contacted Carl Zimmer and criticized his omission of my 1989 Paper. He responded that it was due to space limitations, but then quite arrogantly remarked that he stood by his paper. In view of his quoting at length and redundantly each author of the Spanish review, I cannot accept his justification.

I hope that this info. will help you to arrive at a fair decision regarding my editing of the Zimmr piece. Thank you.Dienerto (talk) 20:25, 16 November 2014 (UTC)

Thank you for your comments - (made several formatting adjs - to try and better read your post - please note - afaik => such a WP:WALLOFTEXT and/or WP:CHUNK are usually discouraged on Wikipedia discussions) - in any case - others are welcome to comment on all this of course - Thanks again for your post - and - Enjoy! :) Drbogdan (talk) 21:01, 16 November 2014 (UTC)

BRIEF Followup - my present position on one of the concerns => the "Carl Zimmer reference" should remain in the articles (per WP:NPOV & related) - this reference seems very relevant to the articles - readers can then sort out, based on cited references from other WP:Reliable Sources, the better understanding for themselves - hope this helps in some way - in any case - Enjoy! :) Drbogdan (talk) 23:27, 16 November 2014 (UTC)

Dienerto: I would agree with you, 1. had Zimmer recognized the correct originator of the “living relic” hypothesis, which he did not; and 2. had he presented the hypothesis as speculation, not as scientific fact, which he did not, certainly not in the title. Conclusion: Zimmer’s NYT piece, being objectively and demonstrably faulty, should not be referred to.Dienerto (talk) 15:31, 17 November 2014 (UTC)

Seems There Is No WP:CONSENSUS Regarding This Issue At This Time - Comments From Other Editors On This Issue And Others (such as possible WP:COI, WP:PROMO, WP:OWN and related noted above) Welcome Of Course - In Any Case - Enjoy! :) Drbogdan (talk) 16:04, 17 November 2014 (UTC)

Dienerto to Drbogdan: I disagree, I think we CAN achieve a consensus. You have identified the problem: the viroid page needs a better introduction. I suggest we use as such the first three paragraphs of Zimmer's NYT piece, which are excellent, quote Zimmer, together with what is now refs [3]and [4](but delete [5], which is redundant and not a real publication anyway) and follow with the description of viroids' properties, etc. If you agree with this general outline, I shall rewrite the page.Dienerto (talk) 09:54, 18 November 2014 (UTC)Dienerto (talk) 09:59, 18 November 2014 (UTC)

@Dienerto: Thank you for your comments - seems like an excellent idea - however - before posting on the Viroid article page - let's first look at your suggested updated introduction on this talk page - and then go from there - Thanks again for your comments - and - Enjoy! :) Drbogdan (talk) 14:15, 18 November 2014 (UTC)

Dienerto to Drbogdan: Thank you for your suggestion, which I was going to follow anyway. Here is my corrected intro to viroids: Dienerto o Drbogdan: Thank you for your suggestions, which, of course, are correct. Below I have broken up the text into Introduction, History, Molecular Properties, and Living Relics of the RNA World?

VIROIDS

"Viroids are the smallest infectious pathogens known, consisting solely of short strands of circular, single-stranded RNA without protein coats. They are mostly plant pathogens, some of which are of economical importance."

History

The viroid story starts early in the 20th century, when symptoms of a previously unknown potato disease were noticed in farmers’ New York and New Jersey fields. Because tubers on affected plants become elongated and miss-shaped, they named it the potato spindle tuber disease.

Scientists soon showed that symptoms appeared on plants onto which pieces from affected plants had been budded---that the disease therefore was caused by a transmissible pathogenic agent. However, they couldn’t identify a fungus or bacterium consistently associated with symptom-bearing plants and therefore, as was then the custom, placed the disease into a grab-bag type category called virus diseases.

Despite numerous attempts over the years, by a number of scientists, to isolate and purify the assumed virus, using increasingly sophisticated methods, these were uniformly unsuccessful when applied to extracts from potato spindle tuber disease-afflicted plants.

Until, that is, when Theodor O. Diener, a plant pathologist at the U.S. Department of Agriculture’s Pioneering Laboratory for Plant Virology at Beltsville, Maryland, showed in 1971 that the agent was not a virus, but a totally unexpected novel type of pathogen, one-80th the size of typical viruses, for which he proposed the term “Viroid.”[1][2]

In experiments stretching over ten years, Dr. Diener had obtained conclusive evidence that the potato spindle tuber viroid consists solely of a single-stranded, circular RNA thread without protein coat. He and other scientists have since identified 30-odd diseases of crop, ornamental, and wild plants, as viroid-, not virus-caused, as had been assumed.

Molecular Properties

Parallel to agriculture-directed studies, more basic scientific research has elucidated many of viroids’ physical, chemical, and macromolecular properties. Thus, viroids have been shown to consist of short stretches (a few hundred nucleobases) of single-stranded RNA. Unlike most viruses, viroids don’t have a protein coat. Compared with other infectious plant pathogens, viroids are extremely small in size, ranging from 246 to 467 nucleobases; they thus consist of fewer than 10,000 atoms. In comparison, the genome of the smallest known viruses capable of causing an infection by themselves are around 2,000 nucleobases long.

In 1976, Sänger et al[3] presented evidence that potato spindle tuber viroid is a “single-stranded, covalently closed, circular RNA molecule, existing as a highly base-paired rod-like structure"—--believed to be the first such molecule described. Circular RNA, unlike linear RNA, forms a covalently closed continuous loop, in which the 3' and 5' ends present in linear RNA molecules have been joined together. Sänger et al. also provided evidence for the true circularity of viroids by finding that the RNA could not be phosphorylated at the 5’ terminus. Then, in other tests, they failed to find even one free 3’ end, which ruled out the possibility of the molecule having two 3’ ends. Viroids thus are true circular RNAs.

The single-strandedness and circularity of viroids has been confirmed by electron microscopy[4] and the complete nucleotide sequence of potato spindle tuber viroid has been determined.[5] PSTV was the first pathogen of a eukaryotic organism for which the complete molecular structure has been established.

Viroid RNA does not code for any protein.[6] It is replicated by RNA polymerase II, a host cell enzyme normally associated with synthesis of messenger RNA from DNA, which instead catalyzes "rolling circle synthesis” of new RNA, using the viroid RNA as template. Some viroids are ribozymes, having catalytic properties which allow self-cleavage and ligation of unit-size genomes from larger replication intermediates.[7] .

Living relics of the RNA World?

With Diener’s 1989 hypothesis[8]---claiming that viroids are more plausible candidates than introns or other RNAs considered in the past as “living relics” of a hypothetical, non-cellular RNA world---viroids have attained potential significance far beyond plant plant pathology to evolutionary biology, by representing the most plausible macromolecules known capable of explaining crucial intermediate steps in the evolution of life from inanimate matter to life as we know it today.

While Diener’s hypothesis was dormant for 25 years, it has recently been resurrected in a review[9] and its plausibility as a living relic of the hypothetical RNA world further enhanced by additional characteristics of viroids and viroid-like satellite viruses. Flores et al. summarized Diener’s arguments supporting his hypothesis and combined these with two additional ones (2 and 4). These properties include: (1) viroid’s small size, imposed by error-prone replication; (2) their high G + C content, which increases stability and replication fidelity; (3) their circular structure, which assures complete replication without genomic tags; (4) existence of structural periodicity, which permits modular assembly into enlarged genomes; (5) their lack of protein-coding ability, consistent with a ribosome-free habitat; and (6) replication mediated in some by ribozymes—the fingerprint of the RNA world.[9][10]

References

1. Diener TO (1971). "Potato spindle tuber "virus". IV. A replicating, low molecular weight RNA". Virology 45 (2): 411–28. doi:10.1016/0042-6822(71)90342-4. PMID 5095900.

2. "ARS Research Timeline - Tracking the Elusive Viroid". 2006-03-02. Retrieved 2007-07-18.

3. Sänger, HL; Klotz, G; Riesner, D; Gross, HJ; Kleinschmidt, AK (1970). "Single-stranded covalently closed circular RNA molecules, existing as highly base-paired rod-like structures". Proc.Natl.Acad.Sci.USA 73 (11): 3852–56.

4. Sogo, JM, Koller T, Diener TO. (1973) “Potato spindle tuber viroid. X. Visualization and size determination by electron microscopy.” Virology.(1973) 55(1):70-80.

5. Gross HJ, Domdey H, Lossow C, Jank P, Raba M, Alberty H, Sänger HL .“(1978) “Nucleotide sequence and secondary structure of potato spindle tuber viroid.” Nature.273, :203-208. . 6. Tsagris EM, de Alba AE, Gozmanova M, Kalantidis K (2008). "Viroids". Cell. Microbiol. 10 (11): 2168–79. doi:10.1111/j.1462-5822.2008.01231.x. PMID 18764915.

7. Daròs JA, Elena SF, Flores R (2006). "Viroids: an Ariadne's thread into the RNA labyrinth". EMBO Rep. 7 (6): 593–8. doi:10.1038/sj.embor.7400706. PMC 1479586. PMID 16741503.

8. Diener, T.O. (1989). "Circular RNAs: Relics of precellular evolution?". Proc.Natl.Acad,Sci:86, 9370–9374, Retrieved November 1, 2014

9. Flores, R., Gago-Zachert, S., Serra, P., Sanjuan, R., Elena, S.F. (2014). "Viroids: Survivors from the RNA World?". Annual Review of Microbiology 68: 395–414. Retrieved November 1, 2014.

10. Zimmer, Carl (November 12, 2014). "A Tiny Emissary From the Ancient Past". New York Times. Retrieved September 26, 2014.

I look forward to your comments dienertoDienerto (talk) 16:46, 18 November 2014 (UTC)

Comments - This is too long for an introduction and much belongs in the body of the article, possibly under a History heading. And, it is the custom that the first sentence (or two) provides a definition of the subject. Graham Beards (talk) 17:03, 18 November 2014 (UTC)

Thanks for adding the definition. I think it would be better switched:

"Viroids are the smallest infectious pathogens known, consisting solely of short strands of circular, single-stranded RNA without protein coats. They are mostly plant pathogens, some of which are of economical importance."

And, "causing disease" is redundant as this is what pathogens do. The piped link to capsid would be useful. Graham Beards (talk) 17:43, 18 November 2014 (UTC)

The first three paragraphs above under History cannot be used in the article because they are taken directly from Zimmer's article. This would be copyright violation. Graham Beards (talk) 12:10, 20 November 2014 (UTC)

dienerto to Graham Beards: Thank you for pointing out what would obviously be a copyright infringement. How could I not see this myself?! No problem though. I'll work on it today.

This, of course, brings up again the Zimmer NYT piece, whose inclusion as a reference I opposef, because it is, demonstrably, deeply flawed. Already the title, by omitting a question mark, falsely claims that viroids ARE "living relics" of the RNA world, when this is still a hypothesis, not a scientific fact. Then, Zimmer commits an inexcusable disregard of scientific ethics, by not quoting, or even mentioning my 1989 PNAS paper, in which I introduced and substantiated, for the first time, the concept of viroids being "relics of the RNA world" , on which Flores et al.'s review paper is based, and which, as a review, properly contains almost no original, new information, but is almost exclusively based, and so recognized by the authors, as a repeat of the reasons given in my 1989 paper. Despite this, Zimmer saw fit to blatantly disregard or even quote my 1989 paper and, when so reminded, arrogantly excused it as the result of "a space problem," (Zimmer's e-mail message). He then falsely gives credit to Flores et al. to have originated the "living relic" hypothesis and claims that it is based on "new research," when, in fact, it is little more than a repeat of the reasons already stated by me in 1989. I quote Flores et al.: "Hereafter we discuss the evidence that supports Diener's claim, summarizing his arguments and supplying others."

In conclusion, the Zimmer paper, being deeply flawed, certainly doesn't deserve to be quoted---despite its superficial attractiveness---and all citations to it, which he willy nilly inserted in Wikipedia. should be deleted.Dienerto (talk) 12:00, 21 November 2014 (UTC)

I doubt that Zimmer added the citations. You are in danger of using Wikipedia to set the record straight, which we do not allow. (See WP:RGW). If Zimmer's article is erroneous, we have to wait for, or find, a reliable source to substantiate this. I suggest you publish a letter in a mainstream journal, rather than attempting to use Wikipedia to publicize your disagreements. Graham Beards (talk) 13:03, 21 November 2014 (UTC)

FWIW - yes - I *entirely* agree with the comments of User:Graham Beards above re the Carl Zimmer article - citing a WP:RS (and/or presenting the material in some WP:NPOV way) re possible errors in the Zimmer article may be helpful I would think - in any case - Enjoy! :) Drbogdan (talk) 14:12, 21 November 2014 (UTC)

Dienerto to Drbogdan and Graham Beards;L I didn't know of Wikipedia's WP:RGW policy and will follow your suggestions and requote the Zimmer piece. Thank you for all your help in this matter Dienerto (talk) 18:26, 21 November 2014 (UTC)

Thanks - I will incorporate your additions over the weekend, as you appear to need help with the stripped down version of HTML that we use here and the reference formatting does not follow our house style. But we have to mindful that the article is open to editing by other contributors. Nobody owns Wikipedia articles and we have to work collaboratively (hence the Talk Page). Thank you for taking the time to improve the article and as a fellow virologist, I feel it is an honor to be working with you on this. Graham Beards (talk) 18:49, 21 November 2014 (UTC)

Dienerto to Graham Beards: I am most grateful to you for helping me with the viroid page, but I also must express my embarrassment for requiring so much help with it, i.e., my unfamiliarity with Wikipedia's formatting house style. This is in several ways a new experience for me. I do agree, though, with Wikipedia's open, anti-elitist, editing policy and am, after some soul-searching, happy to conform to it. Thank you for your kind words.DienertoDienerto (talk) 11:46, 22 November 2014 (UTC)

You are very welcome. I have incorporated your text into the article, hopefully adhering to WP:NPOV. Please let me know if I have introduced any errors or omitted anything. Graham Beards (talk) 12:53, 22 November 2014 (UTC)

@Graham Beards: & @Dienerto: Thank you *very much* for the efforts - update of article seems *Excellent* - no problem whatsoever - if interested, several related articles (ie, Circular RNA; Non-cellular life; Potato spindle tuber viroid; RNA world hypothesis) may also need some possible updating of earlier User:Dienerto edits - in any case - Enjoy! :) Drbogdan (talk) 13:40, 22 November 2014 (UTC)

Dienerto to Graham Beards: Great job! I sugges7 only a few minor changes/corrections. as follows: Introduction Paragraph 2, line 2: changed to: “... at the U.S Department of Agriculture's Research Center in Beltsville, Maryland,,,” Transmission Line 1; “...following ... mechanical damage to plants as a result of horticultural or agricultural practices.” Note to Editor: I have mistakenly deleted the second sentence of “Transmission" and don’t find it any more to reinstate it. Could you please insert it again? Sorry Thank you so much for all your help, Dr.Beards.Dienerto (talk) 10:57, 23 November 2014 (UTC)

You are very welcome. With regards to transmission, are aphids a vector? There seems to be some doubt. If so, can you point me to a source? Best wishes, Graham Beards (talk) 11:11, 23 November 2014

Dienerto to Dr Beards: yes: De Bokx, J. A and P. G. M. Piron, “Transmission of potato spindle tuber viroid by aphids,” Netherlands Journal of Plant Pathology,1981, Volume 87, Issue 2, pp 31-34 "Abstract Aulacorthum solani (Kaltenbach),Macrosiphum euphorbiae (Thomas) andMyzus persicae (Sulzer) were used for transmission experiments in laboratory and glasshouse. As inoculum served PSTV-containing tomato foliage and artificial diets containing purified PSTV. It is concluded that M. euphorbiae can transmit PSTV in a non-persistent way." I believe this article is referred to in the lost second sentence of the "Transmission" section (which I did not write), but I cannot be sure. Best wishesDienerto (talk) 17:40, 23 November 2014 (UTC)

Pasted from my Talk Page Dr Beards, For unknown reasons, I have not been able to enter anything in my talk page for several days now. Above all, I wanted to thank you for your kind offer to help me reinsert the missing computer codes in the references, which I so ignorantly deleted. I tried to follow your instruction and ask for help with it on the viroid's Talk page. Trouble is, I couldn't write on that page either and was, therefore, stuck. I then found your talk page and described my problem, but I didn't hear from you, so, apparently you somehow didn't receive my comments there either.

Aside from the reinsertion of the computer codes, I have a problem with reference No. 1, Wolfram's book. I have read portions of it, after which I have no idea what possible connection its content could have with viroids, because it concerns exclusively matters of Particle Physics. While I am not a physicist, further investigation revealed that both the book and Wolfram himself (a self-pronounced genius) are most controversial. One atomic physicist summarized the book as follows: "What is new [in it] is not true and what is true, is not new."

In view of Wikipedia's expressed policy of tolerating demonstrably incorrect statements (such as the ones in Zimmer's New York Times piece), I wonder what can be done to delete the reference to Wolfram's book, which is obviously uncalled for. I don't know who or when this ref. was inserted, evidently without discussion, but whoever did so should be required to justify its inclusion. With kind regards and hope that we can now finalize the viroid page to everybody's satisfaction.96.26.126.134 (talk) 1:41 pm, Today (UTC+0)

Dr Diener,

I have replaced the reference in question with this one:

Lewin, Benjamin.; Krebs, Jocelyn E.; Kilpatrick, Stephen T.; Goldstein, Elliott S.; Lewin, Benjamin. Genes IX. (2011). Lewin's genes. Sudbury, Mass.: Jones and Bartlett. p. 23. ISBN 9780763766320.

As you probably know, this is a highly regarded textbook.

I cannot find a reliable source for the number of atoms, so I have deleted this statement.

I don't understand why you are having difficulties posting your comments. In any case, please remember to login with your username and password otherwise you posts will be anonymous and you will reveal you IP address to others. Graham Beards (talk) 15:07, 29 November 2014 (UTC)

New edits February 2015

Hi - I came to this page from the note at RNA world hypothesis. The information on viroids was 5 paragraphs inserted into the lead (WP:UNDUE), so I moved it into a separate section. I'll let you guys decide what should be done with it. :-) Sunrise (talk) 07:07, 24 February 2015 (UTC)

Added: I didn't realize this was from November. I'm moving this into a new section and pinging User:Graham Beards, User:Drbogdan, User:Dienerto. (Dr. Diener, if you want to get someone's attention as you intended with the note on your talk page, you can make sure they get a notification by linking their usernames like I have just done.) Thanks! Sunrise (talk) 08:29, 24 February 2015 (UTC)

@Sunrise, Graham Beards, and Dienerto: - FWIW - Yes - I *entirely* agree with the edit in the "RNA world hypothesis" article by User:Sunrise atm - also Yes - the moved text to the newly created "RNA world hypothesis#Viroids" section could use some trimming I would think - in any case - Thanks for the help with this - and - Enjoy! :) Drbogdan (talk) 13:01, 24 February 2015 (UTC)

Hi, it says "Diener's hypothesis was mostly forgotten until 2014". But on Google Scholar I found that the paper was being cited regularly after publication. --ImproveEverything (talk) 01:12, 14 January 2017 (UTC)

RNA World Hypothesis

I found the list given of the six arguments of Dr. Diener, that were summarized etc by Flores et al, a little confusing so would like to ask @Dienerto, Graham Beards, Drbogdan, and Sunrise: if the following, a precis of the Flores text which expands those given here slightly, would be acceptable in its place:

1. the intrinsic error-prone replication of primitive RNA systems led to limitation of the size of their master sequences to avoid the extinction of “error catastrophe”.

2. viroids increase replication fidelity of RNA systems through higher thermodynamic stability. Furthermore, ribozymes can be formed by the two strands and both function as templates.

3. reiterative copying of their circular genomes would avoid loss of genetic information. This rolling-circle replication would result in multiple copies of the genetic information, a condition likely favored in primitive replicons with a high mutation rate.

4. the sequence of some viroids exhibits a structural periodicity characterized by repeat units of different length. This periodicity points to a mechanism by which larger genomes could have evolved. The recombinant nature of some viroids, which are formed by fragments present in other viroids, is consistent with this view.

5. viroids are non-protein-coding RNAs which traces their origin back to the first age of the RNA World, wherein no ribosomes existed.

6. (and most important) viroids have the catalytic activity required for the three steps of viroid replication — cleavage, ligation, and RNA polymerization (in in vitro evolution studies) — via hammerhead ribozymes.

LookingGlass (talk) 17:32, 2 February 2018 (UTC)

Having consulted and (at least) Graham Beards having read my proposal) and having received no feedback I propose to now edit the article as detailed (no comment = approval). Thank you. LookingGlass (talk) 17:30, 9 February 2018 (UTC)

Your suggestions are not an improvement and contain inaccuracies. In particular, I do not like your use of the word "primative" as all extant RNA polymerases are error prone. By using the term "thermodynamics" instead of the high G-C content, you are dumbing down the article. Also, your suggestions are too long and contain many technical terms that would need linking. To be blunt, and please forgive me, I think you are out of your depth in this field. Graham Beards (talk) 07:25, 10 February 2018 (UTC)

Smallest infectious pathogens?

Hi! Just wondering; aren't infectious proteins, eg Prions, smaller than viroids? It seems to me that the introductory sentence is false; since I am new to editing Wikipedia, I didn't want to make an edit myself. — Preceding unsigned comment added by Dynexo (talk • contribs) 09:11, 27 August 2020 (UTC)

No, prions are large protein molecules and are bigger than (the RNA of) viroids. Graham Beards (talk) 09:59, 27 August 2020 (UTC)

Hmm in what sense are viroids smaller than prions? If we assume 1 nucleotide in RNA is 325 Da, the smallest viroid listed on this page (246 nucleotides) would weigh roughly 80 kDa. This article suggests that the human prion protein is only 36 kDa. This would suggest that prions are indeed smaller than viroids. Is there something I'm missing on this? Marcconnell95 (talk) 01:42, 10 March 2021 (UTC)

References

Prion vs viroid size

Just rehashing a question from the previous section. Going to repost the question:

In what sense are viroids smaller than prions? If we assume 1 nucleotide in RNA is 325 Da, the smallest viroid listed on this page (246 nucleotides) would weigh roughly 80 kDa. This article suggests that the human prion protein is only 36 kDa. This would suggest that prions are indeed smaller than viroids. Is there something I'm missing on this?

Marcconnell95 (talk) 15:35, 6 April 2021 (UTC)

Removed, because the source never mentions this, and even if it did it would probably be wrong. --Jules (Mrjulesd) 15:42, 6 April 2021 (UTC)

From the first linked article: "In humans, the newly synthesized and unprocessed PrPC is approximately 253 amino acids in length and has a molecular weight of 35–36 kDa ". Furthermore, here is the human protein atlas report for human prion protein. It shows human prion protein having a mass of ~27 kDa. Marcconnell95 (talk) 16:21, 6 April 2021 (UTC)

References

Recent edits and reversions

I worked on this article with Theodor Otto Diener and although this affords me no editorial privileges, I have an interest in it. In my humble opinion more recent edits have not been an improvement overall and my requests for changes to be discussed here, on the Talk Page, seem to have been ignored. Of course we need to keep the article up to date with tertiary sources, which should be presented well with a consistent citation style. Recent edits in this regard have not been an improvement. Why do we need page numbers and quotations from fairly short papers? If we do, there are better ways of citing them. I am always open to arguments but edit warring achieves nothing other than animosity. Graham Beards (talk) 22:15, 20 January 2022 (UTC)

4rr is the place to discuss this. Not this talk page. Invasive Spices (talk) 20 January 2022 (UTC)

On the contrary, this is the place to discuss edits to the article. I suggest you retract your comments elsewhere. You are in danger of appearing to be a novice and inexperienced. Graham Beards (talk) 23:00, 20 January 2022 (UTC)

In summary, I think we need to update the citations, some of which are quite old and we should do this taking WP:CITEVAR to account and stick to the established citation style. Sadly, we no have Dr Diener's guidance on more recent developments in the field, ribozyme activity for example, but these seems reasonably straight forward. The prose needs some work to eliminate redundancies and jargon. I have made a start on all these issues. Graham Beards (talk) 17:58, 22 January 2022 (UTC)

Contentious paragraph

My removal of this paragraph has been objected to. I am sorry for not seeking consensus on this.

""Discovery of new viroids has been difficult with methods available prior to ~2013. Ito et al 2013 uncovered one using next generation dsRNA sequencing more easily than previously possible... in part because plants do not produce dsRNAs, lessening noise..."

I removed it because I don't think the meaning is at all clear. Why was ds RNA sequencing needed? What is meant by "next generation"? Plants do produce dsRNA (see Morozov SY, Solovyev AG, Kalinina NO, Taliansky ME (2019). "Double-Stranded RNAs in Plant Protection Against Pathogenic Organisms and Viruses in Agriculture". Acta Naturae. 11 (4): 13–21. doi:10.32607/20758251-2019-11-4-13-21. PMC 6977960. PMID 31993231.. And noise is jargon which some readers might think it means noise, which it certainly does not. I have re-added the paragraph, but I am not happy with it. Comments please. Graham Beards (talk) 19:18, 22 January 2022 (UTC)

Is anyone concerned about retaining this? Graham Beards (talk) 14:07, 1 February 2022 (UTC)

Invasive Spices? Graham Beards (talk) 14:40, 3 February 2022 (UTC)

As there are no objections, I will delete the paragraph for the reasons I have given above. Graham Beards (talk) 12:16, 4 February 2022 (UTC)

Hello GB.

I have deliberately taken time to reply. I had hoped the 4RR would deescalate and defuse this entire thing. That is its purpose and yet here we are again just a few days later. The 4RR process failed due to shocking admin conduct. I needed time to consider how to avoid being shrieked (... not by you ...) at again for noticing things that were in front of me.

I am saying: The dsRNA text should not be removed from this page on behalf of another editor who is not here; nor because it is written by a particular editor; nor as a continuance here of an edit war elsewhere. This is what produced the 4RR situation (+ 3 = 5? + 3 = 4? I don't want more shrieking but this record keeping is esoteric to me).

Replies to your objections:

• Why was ds RNA sequencing needed? – !? Wu 2015 is provided. If you want more explanatory text then you could have added it.
• What is meant by "next generation"? – !? There is [[next generation dsRNA sequencing]] and Wu to answer that. If the page number is needed it is {{rp|434}}.
• Morozov Can you quote where Morozov says there are truly endogenous dsRNAs? I find only exogenous if we note that they use endogenous to mean transexpressed. More importantly I am suspicious of this journal and the citations are not wonderful although there is Amari & Niehl 2020. However A&N cites Morozov only in passing and explicitly only for exogenous application of dsRNAs.
• And noise is jargon which some readers might think it means noise, which it certainly does not. Some readers will mistake many things. That is not a reason to remove instead of improve. We certainly could make that [[statistical noise|noise]]. I did not do so because the readership for this page would understand that and I was working quickly. You understood well enough to know it certainly does not after all. Invasive Spices (talk) 4 February 2022 (UTC)

Is there a more recent reference than Wu (2015)? The technique is not novel now. There is: Pecman A, Kutnjak D, Gutiérrez-Aguirre I, Adams I, Fox A, Boonham N, Ravnikar M (2017). "Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches". Frontiers in Microbiology. 8: 1998. doi:10.3389/fmicb.2017.01998. PMC 5645528. PMID 29081770.{{cite journal}}: CS1 maint: unflagged free DOI (link), a review and Bester R, Cook G, Breytenbach J, Steyn C, De Bruyn R, Maree HJ (March 2021). "Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids". Virology Journal. 18 (1): 61. doi:10.1186/s12985-021-01523-1. PMC 7986492. PMID 33752714. {{cite journal}}: Vancouver style error: initials in name 3 (help)CS1 maint: unflagged free DOI (link). If we are going to included this, we need more than a couple of sentences sourced to a 2015 paper. Graham Beards (talk) 11:51, 5 February 2022 (UTC)

Pecman and Bester are both investigations while Wu is an AR. I feel good about basing this text entirely upon a well regarded AR from 2015. There is Villamor 2019 for HTS+viroids however it does not include dsRNAs or "how has the search been going?" For this specific question we may only have Wu. Is there a better source? If no editor here knows of one then it is desirable to have something more recent for such a fast moving field but Wu is the best we have. Invasive Spices (talk) 5 February 2022 (UTC)

You have lost me, what is an "AR" and why do you not add the timestamp to your sig? Why aren't you using four tildes? Graham Beards (talk)

Wu is from Annual Review of Phytopathology. Invasive Spices (talk) 6 February 2022 (UTC)

Graham Beards? While newer information would be good I don't have any. You've said this is no longer new (if you're objected to the name, yes "new" or next is always a bad name for anything but that is the title of our WP article about it) and that you are familiar with recent developments. Do you have newer reviews we could add? Invasive Spices (talk) 22 February 2022 (UTC)

Formatting

While reading through this article, I found the taxonomy section difficult to decipher, would it be a good idea to add the first species in each genera to the bullet point list to make it easier to read. Yirch (talk) 05:34, 22 September 2023 (UTC)

References

References

Obelisk - merger(s) would help?

Main page: Talk:Obelisk (life form)

Currently - seems there's several wikilinks to the purportedly newly discovered life form "obelisk" - "Obelisk (virology)" and "Obelisk (life form)" and "Obelisk (viroid)" - perhaps some merger(s) would help? - Comments Welcome - iac - Stay Safe and Healthy !! - Drbogdan (talk) 13:29, 31 January 2024 (UTC)

All merged. Naming can be discussed on the talk page of the resultant article. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 22:01, 31 January 2024 (UTC)

Move discussion in progress

There is a move discussion in progress on Talk:Obelisk (life form) which affects this page. Please participate on that page and not in this talk page section. Thank you. —RMCD bot 01:52, 1 February 2024 (UTC)