Talk:Polyclonal B cell response/Archive 1

Refs
Kindly provide inline references! Ketan Panchal, MBBS (talk) 16:57, 30 April 2008 (UTC)


 * Is there something in particular that you'd like to have a separate ref for? Or do you just want an easy way to link the main ref to particular statements taken from it?  WhatamIdoing (talk) 00:45, 1 May 2008 (UTC)

Quick review
I made some (mostly minor) changes to the article you drafted. Overall, I think this is a terrific start and hope you'll continue contributing at this level. I have questions for you about two bits:

1) So, when an antigen is recognized by an antigen presenting cell (APC) like the macrophage or the B lymphocyte, it is broken down into various peptides in the lysosome of that cell following phagocytosis.

This doesn't seem quite right to me. Do you mean when an antigen is internalized instead of recognized? Macrophages are non-specific, so they don't really "recognize" anything.

2) that have the same paratope as that present on the B and the T cells that had got stimulated initially.

This is true, but perhaps misleading. Given an antigen of CTHGIRPVVSTQLLLNGSLAE (for example), the B cell might have a paratope that binds to CTHGIRP, but the T cell might have responded to QLLLNG. The B cell, in its role as an APC, is going to display chopped-up bits of the entire antigen, not just the particular epitope that it can bind. WhatamIdoing (talk) 00:45, 1 May 2008 (UTC)

Lead
Thanks for your recent changes. That's exactly what I was hoping for, but couldn't quite figure out how to say it. WhatamIdoing (talk) 14:51, 1 May 2008 (UTC)

Review
Here's a brief review that i've conducted after no sleep in 48 hours, so forgive me if it's a little vague or beyond comprehension.
 * WP:MEDMOS needs to be applied to the article.
 * An infobox would be a good idea, i'll get down to that at some point for you.
 * Significance needs to be expanded upon and written in continuous prose rather than bullet pointed.
 * Polyclonal response needs to be added to the immune system template at the bottom of the page. ::Regards, CycloneNimrod Talk? 22:43, 3 May 2008 (UTC)

My two cents: I think the article's recent expansion qualifies it for B class, so I've updated the status above. The next step is "GA", which requires successful completion of the WP:GA process. WhatamIdoing (talk) 19:39, 5 May 2008 (UTC)
 * WP:MEDMOS's suggested section orders do not apply: this is not a disease, a drug, or a notable case.  Other parts of it may be useful here.
 * I'd like to see some mention of the difference between antibodies against conformational epitopes vs non-conformational (aa sequence) epitopes. The schematic, of course, ignores conformational epitopes (which is okay:  drawing that would not significantly add to comprehension).
 * The image is beautiful, but large. Could it (easily, quickly, without a lot of extra effort) be made smaller by reducing the number of epitopes (say, delete a pair of reactive clones from the middle), or by re-arranging it to display vertically?


 * Hi! Thanks for your attention to this article.


 * I'll try to include a mention of conformational epitopes. May be I can also include a figure explaining the concept, but the issue is if doing so would be within the scope of this article? On second thoughts, I believe it would be. The unfortunate aspect has been that articles devoted to the concepts of antigen-recognition and B cell response haven't been effective enough in conveying the related concepts.


 * Even I'd thought of making the figure smaller, but couldn't succeed as there were 9 domains in the original protein (antigen). I've tried to project each domain as an antigen, which of course is inaccurate, but thought alright in a schematic. If I'd have omitted any of the domains from the promary structure, it might have created confusion in the minds of those less aware of this subject (I suppose who are also the targeted audience according to "Wikipedia policies"). Moreover I'd to resort to showing so many clones to emphasize on the overlapping pattern of epitope recognition. In retrospect, I did think that a vertical image would have been accommodated  into smaller space. But, of course all this would be pretty cumbersome. The image in the article was created using Microsoft Paint and Microsoft PowerPoint(!). Doing that all over again would be very agonizing. I'd be glad if you, or someone you know who has better idea of "graphic designing" could do it. Now, it would be easier to do as the basic concept has been made quite clear in the existing image.


 * Regards.


 * Ketan Panchal, MBBS (talk) 07:15, 6 May 2008 (UTC)


 * I'm impressed! It's quite a nice little article, although I'm itching to have a go through the language and making it more "layman's terms" if at all possible. However, I'm hesitant just at this stage given the previous comment ->GA (and given my own efforts to date have been much more modest). Well done KC Panchal! Orinoco-w (talk) 23:39, 5 May 2008 (UTC)

Image
KC, I fully take your meaning about working with MS being agonizing. Can you export the graphics as something sensible and e-mail them to me? If it's easier, sending the individual pieces is fine with me; I can re-type the information boxes. I'd love to have something vector-based (.svg file format, for example), but I don't think that Paint supports that. You'll find a link to my e-mail address on (the side of) my talk page, a few lines under the search box. I have Adobe Photoshop and Adobe Illustrator, which are much better suited to this than anything by Microsoft, and I can have a go at it this coming weekend. (No guarantees that it will improve matters, but I'll at least provide some options.) WhatamIdoing (talk) 21:21, 6 May 2008 (UTC)

Inexpert review
I hope a review from someone completley outside the field might help you clarify the article a little. Re. previous comments - I'm sure it is a well written article, so please forgive my 'aggressive-sounding' notes below. The article as it stands may be great for folk within the field, but wouldn't help the laymen much.

My initial thoughts;

Polyclonal response

Lead paragraph is not clear enough for non-expert readers, and left me wondering "yeah, but what IS it?". Would it be possible to describe the gist of the topic, as though explaining it to a 10-year-old? The lead could easily be longer.

Perhaps lead should mention B-cell response specifically, as that features so much in the body.

I hate the diagram. It's too small to be of use within the article, the dark colour doesn't help.

Ref 2 leads me to a dictionary definition of the single word "Polyclonal" - I don't see the relevence of this reference in the lead. Perhaps it's unnecessary to have this reference there, if the book (ref1) provides sufficient citation?

In B cell response,

"As the proteins are relatively large," - relative to what?

" portions on it--the epitopes—-are recognized." - remove excess dashes and I think it might be better to say "...portions of them" rather than "portions on it" because "it" is a little ambiguous.

Instead of "when an antigen is phagocytosed" could you say "when an antigen is engulfed by phagocytosis" - because that would give me the idea without having to look at the linked article.

"broken down into various peptides in its lysosomes." - is this correct, or should it be "by its lysosomes."? ie are they broken down WITHIN the lysosomes, or do these 'suicide bag' things perform the breaking down?

"The individual peptides are then complexed with..." - I don't know what 'complexed with' means, please define it, reference an article or clarify it within the sentence

"...and is elaborated..." - I don't know what 'elaborated' means in this context

I hate the diagram. It's too small to be of use within the article, the dark colour doesn't help. If it's too small to read anyway, it might as well be smaller - as users will have to click it to expand it. But personally I don't like the style of the diagram itself - too much text on it, font not clear.

There's a typo on the diagram too. "Indeed" is one word.

don't say "(see the schematic above)" because it might not be above, depending on the users browser. Just 'see diagram' would do.

In "Greatest probability of recognizing antigen",

It begins, "This is because, " - WHAT is because? If you're referring to the text in the previous section, I think you need to clarify that, because it's now a new section.

I don't like the word "unlikelier" - even though it is in the dictionary. I'd strongly prefer "less likely".

In "Increased chances of autoimmune reactions",

"mistaking certain native molecules in the body to be foreign," - maybe better "mistakely identifying certain native molecules in the body as foreign,"

"eliminated in course..." should be "eliminated in the course..."

Sentence starting with "Moreover" is very long - consider splitting it

Last para - should 'avidity' be a link? avidity - I think there's a bracket missing?

Hope this helps,

Chzz (talk) 11:02, 6 May 2008 (UTC)

Hi!

 * I hope a review from someone completley outside the field might help you clarify the article a little. Re. previous comments - I'm sure it is a well written article, so please forgive my 'aggressive-sounding' notes below. The article as it stands may be great for folk within the field, but wouldn't help the laymen much.


 * Well, it wasn’t pleasurable to get the article negatively criticized, but I completely appreciate the effort you took to review the article so thoroughly, and also write such a detailed review (almost approaching the length of the article!). And after all, that’s what is the purpose of a review. I knew that I must have overlooked certain aspects of the article like its simplicity. But, then it can’t be really helped that some of the concepts dealt with in the article cannot really be understood by a ten-year-old child in all their subtleties.


 * Here I’m trying to address all your concerns. Some by making the changes that you’ve suggested, some by making the modifications I think fit, and others, by clarifying your concepts, which might be wrong (in my opinion)


 * My initial thoughts;


 * Polyclonal response


 * Lead paragraph is not clear enough for non-expert readers, and left me wondering "yeah, but what IS it?". Would it be possible to describe the gist of the topic, as though explaining it to a 10-year-old? The lead could easily be longer.


 * I have made some changes. Do let me know if they are satisfactory. But, a problem is a working compromise between simplicity and length of the lead; leads are supposed to be introductions and not very long.


 * Perhaps lead should mention B-cell response specifically, as that features so much in the body.


 * I have made a mention of B cells now.


 * I hate the diagram. It's too small to be of use within the article, the dark colour doesn't help.


 * Well, I have had differing reviews about the diagram. You might be hating the black color, but believe me, it would be difficult to make ‘’’nine’’’ different colors appear distinct from each other on a white background. Also, the text in the diagram is essential to sufficiently explain the concept attempted.


 * Ref 2 leads me to a dictionary definition of the single word "Polyclonal" - I don't see the relevence of this reference in the lead. Perhaps it's unnecessary to have this reference there, if the book (ref1) provides sufficient citation?


 * Firstly, hardly any readers would have access to the book cited, though it’s a well known book on the subject of immunology. The purpose of reference to the dictionary is instant access for the readers as well as to provide greater authenticity to the definition given in the article as it is a very renowned (Webster’s) dictionary that has been cited.


 * In B cell response,

"As the proteins are relatively large," - relative to what?


 * In the original edit I’d submitted “large” was followed by “(of course, at the molecular scale)” that was removed by a user, which I didn’t change thinking it wasn’t required. Again, I have made a mention of molecular scale.

and I think it might be better to say "...portions of them" rather than "portions on it" because "it" is a little ambiguous.
 * " portions on it--the epitopes—-are recognized." - remove excess dashes


 * I have made some change.


 * Instead of "when an antigen is phagocytosed" could you say "when an antigen is engulfed by phagocytosis" - because that would give me the idea without having to look at the linked article.


 * I liked your suggestion. So, made changes accordingly.


 * "broken down into various peptides in its lysosomes." - is this correct, or should it be "by its lysosomes."? ie are they broken down WITHIN the lysosomes, or do these 'suicide bag' things perform the breaking down?


 * Well, I am afraid, here your concept needs correction. Even though lysosomes are called “suicide bags”, they do not function only during apoptosis (programmed cell death), but in digestion of any molecule entering from outside the cell (not necessarily from outside the body). Lysosomes are large cavities that contain proteins (enzymes) called proteases that break down proteins. So, indeed, more specifically, it is the proteases that break down proteins INSIDE the lysosomes.


 * "The individual peptides are then complexed with..." - I don't know what 'complexed with' means, please define it, reference an article or clarify it within the sentence


 * Added “(attached loosely)” following “complexed”


 * "...and is elaborated..." - I don't know what 'elaborated' means in this context


 * “Elaborated” is used in molecular biology to mean “show prominently” especially at the surface of the cell. I had seriously overlooked that persons not attached to the field would be unaware of this usage.


 * I hate the diagram. It's too small to be of use within the article, the dark colour doesn't help. If it's too small to read anyway, it might as well be smaller - as users will have to click it to expand it. But personally I don't like the style of the diagram itself - too much text on it, font not clear.


 * I have addressed the issue above. If I’d have submitted a smaller image, the text would have been unclear even upon enlarging the diagram.


 * There's a typo on the diagram too. "Indeed" is one word.

“Indeed” is not necessarily a typographic error. http://dictionary.reference.com/browse/indeed


 * don't say "(see the schematic above)" because it might not be above, depending on the users browser. Just 'see diagram' would do.


 * Corrected the error.


 * In "Greatest probability of recognizing antigen", it begins, "This is because, " - WHAT is because? If you're referring to the text in the previous section, I think you need to clarify that, because it's now a new section.


 * I have changed the heading, as well as omitted “This is because”, but personally, I never thought that should have created confusion as it was in continuation with the heading immediately above it.


 * I don't like the word "unlikelier" - even though it is in the dictionary. I'd strongly prefer "less likely".


 * In "Increased chances of autoimmune reactions", "mistaking certain native molecules in the body to be foreign," - maybe better "mistakely identifying certain native molecules in the body as foreign,"


 * Made changes somewhat as suggested by you. But the original expression made sure that emphasis was on body making a mistake because of RESEMBLANCE with foreign antigens.


 * "eliminated in course..." should be "eliminated in the course..."


 * Well, I am not sure about the usage of “the” here. As it is, it is a tricky word. “The” would have sounded more appropriate had the sentence begun with the “In the course”. I believe, this should be one of the minor aspects of the article. But, I’d like views of other people, too in this regard.


 * Sentence starting with "Moreover" is very long - consider splitting it


 * Yes, you were right. I have split the sentence, and also tried to simplify the sentence.


 * Last para - should 'avidity' be a link? avidity - I think there's a bracket missing?


 * No, “avidity” wasn’t supposed to be linked. It is supposed to serve as a synonym for “strength of binding”, and since the phrase “(all of them bind with the same epitope with same strength {avidity})” was itself in brackets, I couldn’t have added “” kind of parentheses again, so had added “[ ]”—square brackets, which I have now changed to “{ }”—curly brackets.


 * Hope this helps,


 * Of course, your comments were most useful. I have tried to address all issues brought forth by you as completely as possible. You are most welcome to bring more issues to my attention, or areas already pointed out by you which you think I haven’t sufficiently addressed.


 * Regards.


 * Ketan Panchal, MBBS (talk) 14:33, 6 May 2008 (UTC)

Second look
2nd look by Chzz (talk) 18:12, 6 May 2008 (UTC)

I think that the edits have vastly improved the article. Even I can *almost* follow it now :-) Definitely it's more readable now.

A few thoughts;


 * As an aside - in trying to follow, I also read 'Polyclonal antibodies' and I think the first line of that article should link to [B-cell] rather than [cell]. But this is out of my area, so I wouldn't change it...perhaps you could?


 * Is it worth perhaps explaining (early on) the difference between monoclonal and polyclonal? I have heard of the former (through cancer treatments and suchlike), so I suspect it's a more common term, and might help laypersons to relate a bit more


 * I think "In the immune system, these are the T (TCR) and the B (BCR) cell receptors." should read "...the T-cell receptors (TCR) and the B-cell receptors (BCR)." - for the same reason the phrase "ATM Machine" or "ROM Memory" annoys me.


 * same para - perhaps [ligand] could be a link? (I had to look it up)


 * IL2 should link to Interleukin-2 (to avoid the disambiguation page). Ditto 4,5,6.


 * Paracrine signalling (the article name) is spelt with 2 'l's, to avoid a redirect. Even though the body text f said article spells it with one 'l'.


 * Would one of those very pretty pictures of interleukin be relevent enough to add into this article? 'coz they're very pretty :-) would brighten it up a bit?


 * I'd rather it said "Immunoglobulin M" than IgM  - but maybe anyone else reading this would know the abbrev, so feel free to ignore that one (& IgG)


 * I still don't like the double-bracket business in somatic hypermutation...is there not a way to write it avoiding the nested brackets? It looks a bit odd

Maybe this could be something to improve 'one day'...but in the interests of making a good article great, I think it's worth mentioning here.
 * Re. diagram - I now understand why it's black...however, the text could be made much clearer. I've made a little sample with same size text but antialiased to show that it can be readable.


 * re. the remainder...is OK, I think. It's pretty hard goin g for me, but as you say, there is a fine balance between understandability for the masses, and conveying detailed technical info without sounding condescending to more expert readers.

I hope I've been able to help a little,

Good look with going for GA,

Chzz (talk) 18:12, 6 May 2008 (UTC)

Thanks for the second look!
Thanks for your “second look”. Well, firstly excuse me for adding that heading “Second look” before your reply. I did as the leads had become pretty long and confusing without a heading in between. Second look


 * 2nd look by Chzz (talk) 18:12, 6 May 2008 (UTC)


 * I think that the edits have vastly improved the article. Even I can *almost* follow it now :-) Definitely it's more readable now.

A few thoughts;

As an aside - in trying to     follow, I also read 'Polyclonal antibodies' and I think the first line of      that article should link to [B-cell] rather than [cell]. But this is out     of my area, so I wouldn't change it...perhaps you could?
 * You were right. I made that     change. I too had read the article a few times. I think that change must      have been made pretty recently.

Is it worth perhaps     explaining (early on) the difference between monoclonal and polyclonal? I     have heard of the former (through cancer treatments and suchlike), so I      suspect it's a more common term, and might help laypersons to relate a bit      more
 * Well, the article is about     polyclonal response—a NATURAL mechanism of immune response. The thrust is      over the “process” part of it and not its product, i.e., polyclonal      antibodies or their monoclonal counterpart the monoclonal antibodies. The      article of polyclonal antibodies deals so much with the “artificial”      aspect of their production, unlike the article on polyclonal response. I      don’t know if I have expressed myself with sufficient clarity.

I think "In the immune     system, these are the T (TCR) and the B (BCR) cell receptors." should     read "...the T-cell receptors (TCR) and the B-cell receptors      (BCR)." - for the same reason the phrase "ATM Machine" or     "ROM Memory" annoys me.
 * There’s a difference between     the example you cited: here the two abbreviations are in brackets. It’s a      common technique employed in writing to avoid repetition (of “cell      receptor” in this case).

same para - perhaps [ligand]     could be a link? (I had to look it up)
 * Added a short explanation in     the text itself apart from wikilinking it to appropriate article.

IL2 should link to     Interleukin-2 (to avoid the disambiguation page). Ditto 4,5,6.
 * That was very careless on my     part. I’d blindly wikilinked them, and since all those words turned out in      blue, I didn’t suspect that they weren’t specifically linking to the      intended articles. Thanks a lot for pointing this out.

Paracrine signalling (the     article name) is spelt with 2 'l's, to avoid a redirect. Even though the     body text f said article spells it with one 'l'.
 * Corrected this too.

Would one of those very     pretty pictures of interleukin be relevent enough to add into this      article? 'coz they're very pretty :-) would brighten it up a bit?
 * I have added another     picture. Don’t know if it qualifies to be pretty, but definitely more      relevant than the images of any of the interleukins

I'd rather it said     "Immunoglobulin M" than IgM - but maybe anyone else reading this      would know the abbrev, so feel free to ignore that one (& IgG)
 * No, you were right. Any     first mention of any entity should not be in abbreviated form. I have      corrected the folly.

I still don't like the     double-bracket business in somatic hypermutation...is there not a way to      write it avoiding the nested brackets? It looks a bit odd
 * That’s the established     convention. Can’t really help it. It’s grammatically correct to do do.

Re. diagram - I now     understand why it's black...however, the text could be made much clearer. I've made a little sample with same size text but antialiased to show that     it can be readable.
 * I really don’t know how you     managed that. I’d be very grateful if you could liven up all the text in      the diagram with the border intact for the note. Well, I don’t have much      idea of drawing and editing with PC. What I had used were pretty      primitive—Microsoft PowerPoint and Microsoft Paint. And, it had taken a      lot of effort to get those images. The current one explaining the linear      epitopes has already taken more than 8 hours. Need I mention that I’m a      student and have to study myself in this very competitive world.

Maybe this could be something to improve 'one day'...but in the interests of making a good article great, I think it's worth mentioning here.

re. the remainder...is OK, I     think. It's pretty hard goin g for me, but as you say, there is a fine     balance between understandability for the masses, and conveying detailed      technical info without sounding condescending to more expert readers.

I hope I've been able to help a little,

Good look with going for GA,

Chzz (talk) 18:12, 6 May 2008 (UTC)


 * Thanks again. That was very nice for an article I created to get showered by so much attention. Well, if it is not inappropriate, can I know something about you? I mean we’ve communicated quite a bit (and hopefully will communicate a bit more), so was just curious as your user page does not reveal anything about you.


 * Thanks for your good wishes with GA nomination.

Ketan Panchal, MBBS (talk) 19:25, 6 May 2008 (UTC)

Thoughts
Very nice work on the part I read. My biggest trouble was understanding the technical language (however I'm very tired, so that could be contributing :P ). Here are some specific thoughts: I'm just at the beginning of the article, but I'll have to finish later :(  delldot on a public computer   talk  05:51, 8 May 2008 (UTC)
 * I think the first sentences in the lead should be even clearer for the completely oblivious lay person. For example, maybe in addition to wikilinking 'B lymphocytes', have a parenthetical thing explaining what it is. I see that you do this a bit later on, but incorporating explanatory stuff into the first couple sentences can prevent the reader from starting out lost.  I see that you've done a good job adding explanations for technical terms throughout the article.
 * "Schematic diagram to explain how a secondary immune response is stronger, quicker and more specific" -- stronger... than what?
 * Expand the references that are just URLs: Find author, date, publisher, title, and access date. You can use cite web or cite journal for this.
 * Passive voice should be avoided where possible :P
 * No tags in headers, that ref should be moved down to within the text
 * I don't get this sentence: "The individual peptides are then complexed (attached loosely) with major histocompatibility class II (MHC class II) molecules located in the lysosome—exogenous pathway of antigen processing." MHC is probably another concept that needs a parenthetical explanation.  Similarly, "lysosome—exogenous pathway of antigen processing" is a little much to wrap your mind around.

Hi Delldot!
Firstly, thanks a lot for your helpful review. I believe I have resolved all the issues pointed out by you (hopefully to your satisfaction), except for the usage of passive voice. I don't know if it's my linguistic trait to use passive voice, but here for instance use it because it gives a sense of a story being told with a certain focus (e.g., the antigen in case of this article). This focus on "protagonist" would be lost in using active voice. I hope you get my point. But, still if it makes the matter sound complicated, I'd try changing the concerned sentences to active voice. But, as food for some thought try comparing "the MHC molecule complexes with the peptide, and then the complex migrates to the cell surface, where the T helper cells recognize and bind with it to stimulate the B cell" with "the peptide gets complexed with the MHC molecule, migrates to the cell surface, where it is recognized by the T helper cells, which in turn leads to the stimulation of the B cell". The events in the preceding sentence may not be factually very accurate, but that was just an attempt to reason out my inclination in using the passive voice.

Well, I've uploaded the second image again with some improvements. Just out of the way, how well versed are you with immunology? Just asking so that I can understand if I should take your views as that of some one from outside the field, or some one from within, or may be somewhere in between(!) Well, if you'd consider yourself fairly from outside the field (I think that consideration would be wrong), how would you rate the article in terms of its intelligibility to those uninitiated to this field?

I've to appear for an exam, so would not be able to reply to your messages for next three days, which is not to mean don't send them (messages)!

Thanks a lot for your effort.

Have a good day. Take care.

Ketan Panchal, MBBS (talk) 19:54, 8 May 2008 (UTC)


 * Ah, thanks for the passive voice explanation, that's fine then (my suggestions should in no way be considered mandates from heaven, they're just vague ideas. If there's some reason not to take them, that's fine).


 * I have a bachelor's in "natural sciences" (a little biology, a little chemistry, etc.) but didn't do anything more advanced with immunology than your basic cell bio and microbio, so I should probably be considered a lay reader for this article. Unfortunately, I had a bit of a hard time following it, but I was also extremely tired last night.  I'll give it another read in the next couple days, hopefully before your exam's over (on which, good luck!).   delldot on a public computer   talk  07:03, 9 May 2008 (UTC)