Talk:Fluorescent tag

message: This article has been selected for improvement to complete a class project for the Johns Hopkins University 410.602 Molecular Biology Course. Main topics for construction include the following:
* History of Fluorescent tagging
* Methods and types of tagging
* Fluorescent labeling techniques and chemistry
* Latest discoveries utilizing fluorescent tags
* Advantages and disadvantages of fluorescent tagging over other methods
These topics will be expanded upon based on reliable sources, and images will also be utilized to improve the quality of this article.
Tisquestra (talk) 17:24, 13 March 2013 (UTC)
thread_title: Untitled

message: Concerning the images in this article, some may be redundant or unnecessary.  I have reduced the size and it looks better than before.  Suggestions? Jberendt (talk) 01:58, 5 April 2013 (UTC)
replies: text: The images now fit next to their respective paragraphs and topics nicely. If further images are brought on in smaller size, it can remain well integrated as well. Tisquestra (talk) 02:32, 5 April 2013 (UTC)
replies: text: Note for clarity purposes that initial contributions have been made and will continue to be ongoing.  Due to the multiple sections that we intend to add to this article, subheadings have been added even without content (so far) for organizational purposes.  These sub-sections will be contributed to within the next few weeks. Jberendt (talk) 03:21, 11 April 2013 (UTC)
thread_title: Article Contributions

message: ===Does the lead section follow Style Guidelines?===
My only comment is that since there are so many acronyms and abbreviations, a consistent approach should be used. The Style Guidelines state that "[i]f the subject of the page has a common abbreviation or more than one name, the abbreviation (in parentheses) and each additional name should be in boldface on its first appearance." The example cited is: Sodium hydroxide (NaOH), also known as lye and caustic soda, is ...
:Thank you for the suggestions here. The lead section has been edited to follow a more consistent approach.Jberendt (talk) 02:38, 23 April 2013 (UTC)
replies: text: Looks great! I feel like Wikipedia is great for figuring out what acronyms mean because they have this guideline. Acronyms are so abundant in the sciences, using this format is a very valuable and systematic way of categorizing terminology by subject. It is no small undertaking but worth the effort. Ppelletier (talk) 14:18, 23 April 2013 (UTC)

text: I agree that the sections do overlap.  Perhaps we can reorganize and make "Fluorescent Labeling Techniques" a subhead to a more general header such as "Methods" or "Types".  Suggestions?  Jberendt (talk) 02:52, 23 April 2013 (UTC)
replies: text:  Not to add confusion, but the more I look at it, the more it makes sense the way you have it. Maybe all you need is an explanatory sentence or two underneath the major header "Methods and Various Types of Tags" (e.g., there are various types of tags that can be used ... some are more appropriate for some experiments than others"). Then for "Fluorescent Labeling Techniques" you could preface with saying that "the major techniques used are the following" or something. In brief, a little context may go a long way and avoid having to chop it up into more headers than necessary. Ppelletier (talk) 14:29, 23 April 2013 (UTC)
replies: text: Added something to see how it flows.  A little better I think.Jberendt (talk) 03:49, 24 April 2013 (UTC)
replies: text:  Agreed. Think it sounds great. Ppelletier (talk) 02:39, 7 May 2013 (UTC)

text: Perhaps the lead section could contain more detail on the general process.  Thank you for this suggestion. Jberendt (talk) 02:52, 23 April 2013 (UTC)

text: I edited this section to not include the term "biotech" to avoid confusion.Jberendt (talk) 02:52, 23 April 2013 (UTC)

text: See above on my comment about overlap.  We should probably reorganize.  I will also suggest possibly taking away the sections under "Fluorescent labeling techniques" and making it series of paragraphs.  Jberendt (talk) 02:52, 23 April 2013 (UTC)
replies: text:  The organization looks great with "Methods and various types of tags" and "Fluorescent tagging techniques." I think it is very clearly organized now. Great work. Ppelletier (talk) 02:35, 7 May 2013 (UTC)

text: This information is intended to be added.  Thank you again!Jberendt (talk) 02:52, 23 April 2013 (UTC)
replies: text: I decided to modify the Advantages and Disadvantages header to just Advantages after adding the content suggested above.  I believe this was the best section to add it to, but needed modification of the header to clarify.Jberendt (talk) 03:52, 24 April 2013 (UTC)
replies: text:  Looks great! I think that is really good way to set the right tone. Ppelletier (talk) 02:30, 7 May 2013 (UTC)
thread_title: Comments from Ppelletier

message: My only comment is that since there are so many acronyms and abbreviations, a consistent approach should be used. The Style Guidelines state that "[i]f the subject of the page has a common abbreviation or more than one name, the abbreviation (in parentheses) and each additional name should be in boldface on its first appearance." The example cited is: Sodium hydroxide (NaOH), also known as lye and caustic soda, is ...
:Thank you for the suggestions here. The lead section has been edited to follow a more consistent approach.Jberendt (talk) 02:38, 23 April 2013 (UTC)
replies: text: Looks great! I feel like Wikipedia is great for figuring out what acronyms mean because they have this guideline. Acronyms are so abundant in the sciences, using this format is a very valuable and systematic way of categorizing terminology by subject. It is no small undertaking but worth the effort. Ppelletier (talk) 14:18, 23 April 2013 (UTC)
thread_title: Does the lead section follow Style Guidelines?

message: The contents of each section all appear to belong in that section. There are many headers that have not been completed as of this review and perhaps instead of separate headers they could be incorporated into each other. For example, it may be better to clarify the distinction between "Methods and Various Types of Tags" and "Fluorescent Labeling Techniques" as separate headers. To the extent there is overlap, maybe this could all be one section.
:I agree that the sections do overlap.  Perhaps we can reorganize and make "Fluorescent Labeling Techniques" a subhead to a more general header such as "Methods" or "Types".  Suggestions?  Jberendt (talk) 02:52, 23 April 2013 (UTC)
replies: text:  Not to add confusion, but the more I look at it, the more it makes sense the way you have it. Maybe all you need is an explanatory sentence or two underneath the major header "Methods and Various Types of Tags" (e.g., there are various types of tags that can be used ... some are more appropriate for some experiments than others"). Then for "Fluorescent Labeling Techniques" you could preface with saying that "the major techniques used are the following" or something. In brief, a little context may go a long way and avoid having to chop it up into more headers than necessary. Ppelletier (talk) 14:29, 23 April 2013 (UTC)
replies: text: Added something to see how it flows.  A little better I think.Jberendt (talk) 03:49, 24 April 2013 (UTC)
replies: text:  Agreed. Think it sounds great. Ppelletier (talk) 02:39, 7 May 2013 (UTC)
thread_title: Do the contents of each section belong in that section?

message: If there is a way to explain plainly upfront the general process of how a fluorescent tag is attached, i.e., chemically, that may be helpful as a segue into the more technical discussion of the different types and techniques. That is only out of consideration of the fact that if you did not know anything about this subject, that may make it more accessible right off the bat before drilling down into the nuts and bolts of the individual techniques.
:Perhaps the lead section could contain more detail on the general process.  Thank you for this suggestion. Jberendt (talk) 02:52, 23 April 2013 (UTC)
thread_title: Are there gaps in the content?

message: I did not observe anything in particular that looks ambiguous. There are some very good primers on the history and the development of the techniques. Generally, when referring to "biotech" it is unclear what that means. So I would suggest removing reference to that term, at least in abbreviated form. To the extent these techniques have been widely adopted by researches and developers of biochemical assays, you may want to be more specific or else cite to something that refers to biotechnology as a sector. That is not inaccuracy but may need clarification.
:I edited this section to not include the term "biotech" to avoid confusion.Jberendt (talk) 02:52, 23 April 2013 (UTC)
thread_title: Is there ambiguity or inaccuracy over sources?

message: As mentioned, it may be helpful to clarify the distinction between "Methods and Various Types of Tags" and "Fluorescent Labeling Techniques" as separate headers. To the extent there is overlap, maybe this could all be one section. Overall my recommendation is that the headers should correspond to discrete concepts. Currently there are different headers for chemicals used, methods used to attach them, different types of sensing, but they all seem to be somewhat related. It may be worth rethinking the organization and removing some of the headers.
:See above on my comment about overlap.  We should probably reorganize.  I will also suggest possibly taking away the sections under "Fluorescent labeling techniques" and making it series of paragraphs.  Jberendt (talk) 02:52, 23 April 2013 (UTC)
replies: text:  The organization looks great with "Methods and various types of tags" and "Fluorescent tagging techniques." I think it is very clearly organized now. Great work. Ppelletier (talk) 02:35, 7 May 2013 (UTC)
thread_title: Could the content be structured differently?

message: One thought is that since labeling is a technique, it easily turns into a more specialized and technical or niche topic. It is something scientists use rather than study. So to the extent that people have developed labeling to help identify, measure, or otherwise detect something at the molecular level maybe providing a few concrete examples of what the research applications are, e.g., why would you want to detect and/or determine a quantity of protein, would be helpful.
:This information is intended to be added.  Thank you again!Jberendt (talk) 02:52, 23 April 2013 (UTC)
replies: text: I decided to modify the Advantages and Disadvantages header to just Advantages after adding the content suggested above.  I believe this was the best section to add it to, but needed modification of the header to clarify.Jberendt (talk) 03:52, 24 April 2013 (UTC)
replies: text:  Looks great! I think that is really good way to set the right tone. Ppelletier (talk) 02:30, 7 May 2013 (UTC)
thread_title: Are there parts of the article that are not clearly explained

message: Yes! Great job so far. Keep up the good work.
Ppelletier (talk) 21:31, 12 April 2013 (UTC)
thread_title: Is the content within Wikipedia's guidelines

message: * Keep in mind that my comments are just suggestions -- don't feel compelled to take my advice if you disagree with it.
* In the lead, I'd change "researchers have attached" to something like "can be attached".
* The second mention of "flourescent" (not the bolded one) could be linked to flourescence
* It is not clear what is meant by "labeling techniques".  This term comes out of the blue, without any explanation.
* In the last sentence, you say those three are "common tags".  Do you mean they are common fluorescent tags?  The way I read it, it was confusing, because I thought maybe a "tag" was a part of a flourescent tag; i.e. that those three were components of a flourescent tag, rather than the tags themselves.  (Maybe it's just because it's late and I'm sleepy.)
* Ah, in "History", you mention again "fluorescent labelling".  So, are tagging and labeling the same thing?  I think it would be worthwhile to make this clear.
* If it is true that a f. tag and an f. label are the same, then ping me on my talk page, because I think we need to do some work (outside the scope of this class project) on the way the various redirects are done.  (C.f  fluorescent tagging and fluorescent labeling.)
* You have a subsection of "fluorescent labels", under "Methods and various types of tags".  But if tags and labels are the same, how does this make sense?  I admit to being very confused.  
* This "tag" vs. "label" confusion seems to permeate this article completely, since the next section is, "Fluorescent labeling techniques".  Maybe it is just that I didn't read carefully enough, but I kind of feel that if I'm this confused, then other readers probably will be, too.
* Under "Protein labeling" and a few other places, don't use bold for emphasis.
* The body of the article could use some more wiki-links.  But be careful not to overdo them -- check WP:Link for guidance.
* On the whole, there are lots of good contributions here.  Best of luck in the final couple of weeks of the class!
Klortho (talk) 02:56, 26 April 2013 (UTC)
replies: text: Klortho, thank you for your suggestions.  I see where our terms of tagging vs labeling are confusing and seems to be our main issue.  We will work on clarifying this in the article. Jberendt (talk) 03:45, 26 April 2013 (UTC)
replies: text: I agree, it is a bit confusing. In terms of my understanding, fluorescent tagging would be terminology for the specific fluorescent probes (ie, GFP) that are used. Fluorescent labelling is the method that is described in the respectively named section. Is this indeed the correct way of thinking about it? Or could it be even further clarified, given that we mention throughout our article the use of fluorescent probes in 'tagging' methods.Tisquestra (talk) 03:51, 26 April 2013 (UTC)

text:  Given what I just said above, I changed the section "Fluorescent labeling techniques" to "Fluorescent tagging techniques" (although now that sounds weird to me. If we stuck with consistent terminology with the method vs the topic throughout our article in a similar manner, do you think that would help clarify?Tisquestra (talk) 03:58, 26 April 2013 (UTC)
replies: text: I believe your description of "tagging" and "labeling" is accurate and maybe we should state this in the lead.  I agree that the section for "Fluorescent tagging techniques" sounds off and may not be necessary if we clarify these terms.  Klortho, I believe these two topics are almost identical since we refer to tagging as applying a "tag" or "probe."  Labeling as Tisquestra puts it, is the method of identifying and marking biomolecules for detection and is done so with a tag.  So essentially, I fail to see much difference.  Am I wrong?Jberendt (talk) 03:13, 8 May 2013 (UTC)
replies: text: I tried to do some research to see if there was a difference in how these two terms were used (fluorescent labeling vs tagging) and I couldn't really find any. So yes, I guess we should clarify that these terms are interchangeable. To that effect I added a teensy clarification in the introductory paragraph. Chris, we can talk on your talk page since I think these two terms are the same (for a possible redirect as you mentioned). Tisquestra (talk) 23:52, 8 May 2013 (UTC)
thread_title:  Comments from Klortho 

message: This is a good article with a lot of relative information in it.  I think it is structured properly but I do agree with some of the threads already on this page that the inconsistent switching between label and tag can be a little confusing.  I would suggest changing everything to tag to match the article.  The other issue that was somewhat confusing was the 'Methods' section followed by the 'Techniques' section.  It seemed like there should be a marked difference between the sections, but that difference was a bit ambiguous.  If you concentrated on the physical tags in the 'Types of tags' section and moved what methods material there was to the techniques section I think it might improve the flow.  It's mostly there, the 'Fluorescent labels can be hybridized to mRNA...' is a pretty good example.  Some other points:
* the photochromic compounds paragraph is a little awkward, it could with a re-write.
::Thanks for the perspective. I have attempted a slight re-organization and re-write. I will also try to add a little more information or example if possible to that paragraph. Hopefully it is clearer now.  — Preceding unsigned comment added by Tisquestra (talk • contribs) 18:43, 9 May 2013 (UTC)
replies: text: Thank you for the suggesions, especially on the flow.  Sometimes another look from someone else's perspective makes all the difference.  We will be continuing to make changes and improvements in the next week to sort out our areas of confusion such as tag vs label.Jberendt (talk) 02:08, 2 May 2013 (UTC)
replies: text: Looks like there have been some changes and it has made a positive difference.  One suggestion I have is in the overview you could have a sentence that states tags, labels, probes all refer to basically the same thing.  Dugalmaguire (talk) 17:56, 8 May 2013 (UTC)
replies: text: Done!  Thanks for the input.  I hope these slight modifications have helped with the confusion.Jberendt (talk) 18:08, 8 May 2013 (UTC)
replies: text: Nice one! Dugalmaguire (talk) 20:14, 8 May 2013 (UTC)
replies: text: Ah, I added a little more to the first paragraph before I saw that this terminology had been sufficiently cleared up. I think mentioning that labeling and tagging are the same can still be kept however =). Thanks for the suggestion! Tisquestra (talk) 00:45, 9 May 2013 (UTC)
thread_title:  Comments from dugalmaguire 

message: The lead section is a great overview of the article topic which includes frequently used techniques and common tags.  Without going into too much detail, this section conveys the notability of fluorescent tagging so I don’t think much if anything needs to be added to it.  The image is also a great addition!
I think one of the main issues, as has been discussed, is distinguishing or remaining consistent with the terms “tagging” and “labeling”.  If they are synonymous, then I think that it should be mentioned in the lead section (i.e. In molecular biology and biotechnology, a fluorescent tag or label….).  If they aren’t synonymous then I think it would help the reader greatly if this distinction was made in this section.  Either label(ing) or tag(ging) should then be used throughout the remainder of the article.  For example, the third section is titled “Fluorescent tagging techniques” but is followed by a paragraph that starts with “Fluorescent labeling is known for…..”.  
I agree with dugalmaguire that the difference between “Methods and various types of tags” and “Fluorescent tagging techniques” is a bit unclear.  It seems as if the former section is about ways in which tagged biomolecules can be visualized, while the latter is about how these biomolecules are tagged.  If I have a correct understanding about the nature of the two sections, then I think it would be helpful if the section titled “Methods and various types of tags” is changed to “Methods of visualizing biomolecules”, alleviating some confusion between the two sections.   In addition, it would be helpful to include a short summary (1 or 2 sentences) in the “Methods and various types of tags” section to give a general overview/brief summary of the range of biomolecule tracking.  
:I have reworded the headers for these sections.  Not sure if they sound too wordy now, but are a bit more clear.Jberendt (talk) 03:36, 8 May 2013 (UTC)
replies: text: I think the section title edit adds a lot of clarity to those sections.  "Fluorescent labeling techniques with the use of tags" could be worded differently.  It could possibly be modified to "The use of tags in fluorescent labeling"; not much of a change but I think it flows better. Nguych01 (talk) 16:42, 9 May 2013 (UTC)
replies: text: Agreed, and changed. Tisquestra (talk) 16:53, 9 May 2013 (UTC)

text: Agreed!  I added a few lines of content based on your sources.  Thanks! Jberendt (talk) 03:13, 8 May 2013 (UTC)
replies: text: Added content based on this article as well.Jberendt (talk) 17:46, 8 May 2013 (UTC)
thread_title:  Comments from Nguych01 

message: According to the descriptions here, they are the same, and the two terms can be used interchangeably.  The description of the process on that page backs this up; it says, "Fluorescent labelling is the process of covalently attaching a fluorophore to another molecule ...".  So, let's merge them.  Any discussion? Klortho (talk) 11:45, 13 May 2013 (UTC)
replies: text: No opposes, so merged now. Brandmeistertalk   09:14, 10 May 2015 (UTC)
thread_title:  Propose merging Fluorescent labelling into this article 

message: Overall I think that the improvements to the initial article are good.  Most of the statements had good references.  There were a few places where a general statement about the subject was made with no supporting information, but then that statement was referenced in a later paragraph.  An example of this is the area where the beginnings and "firsts" of fluorescence were mentioned.  There is a paragraph with references, but the last sentence of the paragraph before that was not cited in anyway. 
The contributors did a good job of trying to not make the article too technical which can be difficult with a topic such as this.  There were a few areas where technical words were used without any explanation, but again this may have been necessary due to the subject matter.  
The organization of the article works well with separate sections and subsections for each of the topics.  There was also decent amount of information for each of the subsections.  A few of the pictures that went with the subsections may not have been necessary.  Although they are interesting to look at, without more explanation as to their significance, they don't add to the understanding of the subject matter. Jbmcgregor (talk) 21:12, 8 July 2013 (UTC)
thread_title:  Comments by Jbmcgregor