User talk:David.Throop

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[edit] ALA Conversion

Hi David, I noticed that you have done a lot of EFA research. I would be interested in anything that you can cite that talks about the factors that limit ALA conversion to DHA. Apparently it is much more of a problem for men.

--Rjms 11:38, 14 April 2006 (UTC)

[edit] EFA

I saw your note on the essential fatty acids talk page. I'd be happy to create chemical structure images for you. Just let me know specifically what you'd like and I'll do it. Edgar181 18:37, 3 February 2006 (UTC)

OK. I created an image for stearidonic acid and a stub article for it too. Hope this helps. If you would like others, just ask and I'd be happy to do more. Edgar181 14:18, 4 February 2006 (UTC)

Thanks for your valuable contributions to the EFA topics on Wikipedia! It's often hard to find information on the Web about the details of EFAs that's understandable to a non-chemist. Frankg 16:57, 1 March 2006 (UTC)

[edit] Thanks for contributing to nutrition!

You contributed to the Science Collaboration of the Month that has just ended its run:

Natural selection - See improvements

Thanks, and let's keep improving it so it may become a Featured Article!

- Samsara contrib talk 12:08, 20 February 2006 (UTC)

[edit] Atherosclerosis

Hello David, I changed an edit you did in the atherosclerosis page about hyaline. The hyaline in arteriolosclerosis is amorphous proteins, not cartilage. Keep editing! Emmanuelm 20:55, 1 March 2006 (UTC)

[edit] New fatty acid images

I created a couple of new images for the essential fatty acid and omega-3 fatty acid pages. I hope these images will allow a better understanding of the numbering and naming conventions. Can you please look at them and let me know what you think of them? If you have any suggestions for improvement, please just let me know - it will only take a minute to make any changes you prefer. Thanks. --Ed (Edgar181) 18:05, 15 March 2006 (UTC)

[edit] Your link to the quackwatch article made me smile

Well, unfortunately Quackpotwatch will wipe it off. Then again, i might have time next week to decimate it down to something that will put the smile back. --Espoo 02:10, 17 March 2006 (UTC)

[edit] eicosane/icosane

I see you have reverted the rest of changes made by User:LucioP. I reverted some of the changes he made, but left the ones relating to systematic names because the IUPAC preferred name is icosane. See the note I left on his talk page. Please let me know what you think. Thanks. --Ed (Edgar181) 14:20, 17 May 2006 (UTC)

[edit] Adduct

Hi David

I tweaked your source, and looked at it more closely. Then I noticed that:

At http://www.chem.qmul.ac.uk/iupac/gtpoc/index.html

The definitions used in this glossary are identical to those in the published document, see P. Müller, Pure Appl. Chem., 66, 1077-1184 (1994) [Copyright IUPAC; reproduced with the permission of IUPAC]. If you use any of these definitions please cite this reference as their source.

and at http://goldbook.iupac.org/src_PAC1994661077.html

Entries from: PAC, 1994, 66, 1077. Glossary of terms used in physical organic chemistry.

It appears to me that the sources for both are one and the same; it doesn't add any value to cite them twice. What do you think? --Rifleman 82 20:13, 4 January 2007 (UTC)

[edit] Bringing Eicosanoid up to A level

This page sure has come a long way in the last year. I was pleased to see the Molecular and Cellular Biology WikiProject gave it a B grade. What would it take to get it up to A level?

  • The eicosanoids have such a bewildering set of functions and interactions in the body that they are very difficult to summarize well. What unifies them is their chemical structure. Even that is a little fuzzy - much of the literature claims that all eicosanoids derive from AA. But the interactions with the EPA-derived eicosanoids are very important, and the DGLA-derived ones merit mentioning too.
  • Even so, there needs to be a listing of all the major physiological functions affected by the eicosanoids. Maybe this should be a table.
    • [1] Table 1 would be a good place to start. But even there, he's too focused on the prostaglandins and completely misses the actions in the CNS.
  • The term 'eicosanoid' is somewhat context dependent. Pretty much all the review articles include only the prostanoids and the leukotrienes. But when I go to the literature for the other AA-derived molecules (the lipoxiins, hepoxilins, resolvins, EETs...) they all state that they are eicosanoids too. Since the academic literature disagrees, we probably need to get some expert opinion on how to treat those other groups.
  • The introduction: needs to be longer, and to summarize the other sections better.
  • Missing sections: There are some important issues that the article doesn't address at all:
    • Formation of eicosanoids involves oxygen, and this generates Reactive oxygen species (ROS). Some of the eicosanoids are themselves highly reactive, even mutagenic.
    • The location within the cell of eicosanoid generation, and where and how the eicosanoids travel either into the nucleus or out to the plasma.
    • The evolutionary history of eicosanoids, the suggestion that their signalling function evolved from the function of detoxifying peroxides and other ROS.
    • The article covers eicosanoids in inflammation and immunology. It says almost nothing about the Arachadonic Acid Cascade in neurology and the CNS.
    • Overview or prominent examples of how excesses and deficiencies of eicosanoids result in disease states
    • Use of eicosanoids (and their analogs) as medicines. E.g. alprostadil.
    • How eicosanoids are measured and assayed.
  • The relationship of omega 3/6 fats in the diet to the inflammation balance between the AA and EFA derived eicosanoids is of great general interest. I tried to lay that out in Essential fatty acid interactions but it needs to be at least summarized better here.
  • The high points in eicosanoid research history need to be covered better.
    • Who coined the term eicosanoid, anyhow?
    • Didn't somebody get a Nobel prize?
  • Need a lot more references
  • Most of the material in the section on Receptors needs to be in a table. The section needs an overview. The receptors all are in the same family of receptor proteins, (aren't they)? Discuss where they reside within the cell. The eicosanoids are plietropic - repeatedly, one molecule/receptor pair has been reused to signal vary different things in different tissues.
  • The chemical and physiological distintions between the subclasses of eicosanoid are needed.


[edit] Eicosanoids

Glad to help with the pictures. I found a bunch of them on Wikipedia commons so figured they would help out with that article. You should take a look and see if you prefer some of the others - I just searched for 'eicosanoid' and got to them. As for the acronym query, that was a suggestion for the main eicosanoid page, but looks like you're already working away to fix that! Great improvements already from what I can see!! Ciar 17:27, 8 January 2007 (UTC)

[edit] Eicosanoid refs

Hey David, I noticed your doing the references on Eicosanoid long-hand. Would you like a hand to do the inline references? I'd be happy to help you...or you could check out the wiki page for inline citations? Page is looking great by the way, and you're doing it pretty much by yourself...great work!! Ciar 04:50, 9 January 2007 (UTC)

Wikipedia:Wikiproject_Metabolic_Pathways/requested_pictures

[edit] Prostanoid synthesis

Hi there David. I've finished work on the diagram you requested on Wikipedia:WikiProject Chemistry/Image Request. Please follow this link to view the image; I've put relevant information in the Description box. If you have any comments or if there are any inaccuracies, please don't hesitate to contact me on my Talk page. Regards, Fvasconcellos 00:22, 12 January 2007 (UTC)

Hey, glad I could help. Fvasconcellos 15:47, 12 January 2007 (UTC)
I'd also like to extend a quick thank you for your edits to metformin, especially for providing citations for your additions—not everyone cares about verifiability. Fvasconcellos 14:21, 14 January 2007 (UTC)
So sorry about that. It should be fixed soon, meanwhile I'm removing the diagram from the prostanoid page. Fvasconcellos 15:02, 23 January 2007 (UTC)
David, the diagram should be fixed now. I've changed the layout a bit, let me know what you think. Sorry again, and thanks for pointing it out to me. Fvasconcellos 21:27, 23 January 2007 (UTC)

[edit] This month's MCB Collaboration of the Month article is Peripheral membrane protein!

Peripheral membrane protein
This month's MCB Collaboration of the Month article is Peripheral membrane protein.
Please help to improve this article to featured article status.
Last month's collaboration was RNA interference

– ClockworkSoul 18:51, 14 January 2007 (UTC)

[edit] Pucinic acid

Hi again David. I was wondering, is it pucinic acid or punicic acid? The binomial name of pomegranate is Punica granatum, so "pucinic" sounded a little strange to me. Fvasconcellos 22:07, 23 January 2007 (UTC)

In your sandbox, on the Chemical infobox (I went there to get the SMILES). Thanks, I thought it was punicic. Fvasconcellos 22:48, 23 January 2007 (UTC)
No thanks needed after my prostanoid synthesis screwup :) The structure's here, feel free to add it to the page when it's ready. Fvasconcellos 23:03, 23 January 2007 (UTC)

[edit] Essential fatty acid definition

The definition is given in the article Essential fatty acid : "they must be obtained from food as human cells have no biochemical pathways capable of producing them internally."

As far as I understand, this is not the case of arachidonic acid for the adult human since it is stated in Essential fatty acid interactions that "Most AA in the human body derives from dietary linoleic acid".

Following most assumptions, AA is an essential fatty acid for many mammals, the cat for example and perhaps also for infants but it is never considered to be an EFA for adult human. See also the Example section in Essential fatty acid where it is not cited.

Of course the fact that AA is not an EFA for adult human according to the definition does not mean that this acid is not essential for the human body metabolism.

I did not find any convincing information in the obscure Cunnane paper except that AA is probably an EFA for infants. Johner 21:22, 26 January 2007 (UTC)

The essential fatty acids were described by Burr and Burr in 1930 as those fatty acids which cured the deficiency disease brought on by a lack of fat in the diet. Arachidonic acid was one of the fatty acids which they tested and found to be effective. Further work has shown that any of the methylene-interrupted ω-3 or-6 fatty acids will work. And the common usage in the field is that the term essential fatty acid comprises all the ω-3 or-6 fatty acids (or at least the polyunsaturated methylene-interrupted ones; there are some conjugated oddities like calendic acid that aren't.) Authorative sources include the whole families, without qualification. So you have:
  • Heather Hutchins, MS, RD (10/19/2005). Symposium Highlights -- Omega-3 Fatty Acids: Recommendations for Therapeutics and Prevention.
    • "Omega-3 fatty acids and their counterparts, n-6 fatty acids, are essential polyunsaturated fatty acids (PUFA) because they cannot be synthesized de novo in the body."
  • Nugent K, Spigelman A, Phillips R (1996). "Tissue prostaglandin levels in familial adenomatous polyposis patients treated with sulindac". Dis Colon Rectum 39 (6): 659-62. PMID 8646953. 
    • "Arachidonic acid is an essential fatty acid..."
  • Carlstedt-Duke J, Brönnegård M, Strandvik B (1986). "Pathological regulation of arachidonic acid release in cystic fibrosis: the putative basic defect". Proc Natl Acad Sci U S A 83 (23): 9202-6. PMID 3097647. 
    • "[T]he turnover of essential fatty acids is increased (7). Arachidonic acid is one of the essential fatty acids affected."
You can certainly make a case that arachidonic acid (and eicosapentaenoic and DHA) aren't really essential because the body can make them, in some quantity, from lineolate or lineolinate. But that isn't how the field has generally used the term.
David.Throop 22:14, 26 January 2007 (UTC)

OK. The problem is that there are two different definitions for EFA which are used by Wiki contributors, the more restrictive one (sometimes referred to as "truly essential" or "really essential") and the one that you cite.

It is confusing for Wiki readers because only one definition (the restrictive one) is clearly given at the head of Essential fatty acid. It would be useful for the coherence of Wikipedia to give the two definitions at that place and explain that both are used in Wiki articles. Perhaps the new (enlarged) definition will subplant the restrictive one in the future but it must be recognized that the restrictive definition is still used by most authors.Johner 11:14, 27 January 2007 (UTC)

Fair enough. I'll try to work what we've discussed into a subsection under Nomenclature.David.Throop 14:11, 27 January 2007 (UTC)

That would be nice. Thank you, David, for your patience and efforts on this subject.Johner 18:13, 27 January 2007 (UTC)

[edit] Eicosanoids Peer Review

Hello DT. Im happy to look at the Eicosanoid article - thanks for asking. At first glance, two things jump out: 1. You have done a tremendous amount of work - kudos! indicating more than casual interest, and 2. Research on eicosanoids, etc. is running quickly - by the time you can achieve a tight, accurate description in encyclopedic form, something profound changes...in this case, the real-world body of knowledge is truly a WIP. I will look more closely as time allows and offer a more considered opinion on the review page. Are you looking to take it to FA? István 05:44, 27 January 2007 (UTC)

Hi David. I've left some comments on Wikipedia:Peer review/Eicosanoid. I'm not at all familiar with the peer review process, so I hope they can be useful. Congratulations on all you've done with the article, by the way—it shouldn't be far from GA status or that far from FAC. Fvasconcellos 14:32, 27 January 2007 (UTC)
Hi DT, I can give FAC advice based on only one instance[2] - enough to teach me to first go through at least one peer review to take it to a level at which you are comfortable and then another one to iron out the wrinkles. I would expect the definition point to be a lightening rod, as well as every point along the muddled fringe of what we as yet know. In the a.m. 1956 article, we contended with not only extreme POV and nationalism (which you won't have) but also spent far too much time discussing whether, despite overwhelming consensus, the "event" was a "revolution" or not (wikipedia can be a very pedantic place) so certainly fix the definition straightaway. Could any C20 metabolite of n3 or n6 qualify as eicosanoid (general) or are they defined by their activity (which we dont yet fully understand)? either by origin, action or both is fair play. Also, be prepared for heated commentary from those (self included) who know less on the subject than you do - keeping one's cool before hitting the "save page" key is tough sometimes, but will pay off in the end, as most silent observers see the discussion for what it truly is, and I believe the current FA director is a good one - well, that's the end of FAC advice. Good Luck! István 18:07, 27 January 2007 (UTC)
Hi David. Thank you, but my contribution was very modest, adding a interwiki link to the French version. Good luck Eras-mus 20:20, 27 January 2007 (UTC)

Re yct me on my talk page: Why, thank you for the compliment. I've started to look at the article and have made some very minor changes. --Coppertwig 02:48, 28 January 2007 (UTC)

I'm still working my way through the article. There's a lot of detailed information there! You've done a lot of work. I'm enjoying nitpicking it for little errors and hope my comments are useful in a small way to contribute to continuing improvement of an already impressive article. --Coppertwig 01:48, 31 January 2007 (UTC)

[edit] Images of the leukotriene molecules

It would be nice to include images of leukotriene molecules in the leukotriene article as has been done for prostaglandins and prostacyclins.Johner 22:34, 27 January 2007 (UTC)

[edit] Eicosanoid diagram

You're welcome. Thank Jfdwolff—he converted the file, I just got rid of the extra whitespace. If you'd like me to convert Image:EFA to Eicosanoid.JPG to SVG, I'd be happy to (unless you'd like someone else to do it, of course). Fvasconcellos 01:00, 31 January 2007 (UTC)

I don't think that's necessary, but you can send it to me anyway; I can compare it against the image and see what I can do :) Fvasconcellos 12:01, 31 January 2007 (UTC)
Hi David—Check your inbox. Best, Fvasconcellos 12:56, 1 February 2007 (UTC)
OK, David: Image:EFA to Eicosanoids.svg done. It's been done since yesterday evening but I'd been inexplicably unable to upload files to Commons, so sorry for the delay. I hope it's accurate and to your liking; I'd go ahead and add it to the article, but I thought you might like to check it first. Fvasconcellos 10:27, 3 February 2007 (UTC)
Great, then! I'll see what I can do. I can't promise quick service though—I'm both swamped with work and having ISP trouble, so I'll have to work on it over the weekend. Fvasconcellos 16:19, 3 February 2007 (UTC)

[edit] Barnstar

The E=mc² Barnstar
Thanks for all your wonderful contributions to fatty acids and related articles! --Ed (Edgar181) 15:34, 1 February 2007 (UTC)

[edit] re: lipid signaling

[edit] Re: Lipid signaling

i left a response on my user talk page. i'm not really sure how these threads are supposed to go... i'm still learning. Roadnottaken 15:16, 20 February 2007 (UTC) also i looked through your user page and wanted to thank you for what you're doing in the Eicosanoid section, its much more-well done than a lot of other lipid pages out there. i work in a lipid lab (i work on endocannabinoids, but others in my lab work on PAF and LPA and others at my institute focus quite heavily on S1P) and i'd be happy to help the general lipid effort if i can... i'm pretty good with chemdraw etc... anyway lemme know if i can be of assistance.

[edit] Visual cycle

Hi David, I was just poking around and couldn't find a good Wiki page on the visual cycle (involving all the different stages of cis/trans retinol/retinal regeneration etc). Seems like a very high-interest topic with lots of current research and recent developments that would be perfect for Wiki. There are lots of reviews on this topic, i'll dig some up. What do you think? Roadnottaken 00:25, 23 February 2007 (UTC)

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