User:Kmeehan0214/Complementarity-determining region/Judgementkazzy822 Peer Review

General info
Kmeehan0214
 * Whose work are you reviewing?


 * Link to draft you're reviewing:User:Kmeehan0214/Complementarity-determining region - Wikipedia
 * Link to the current version of the article (if it exists):Complementarity-determining region - Wikipedia

Lead
" Complementarity-determining regions (CDRs) are polypeptide segments of the variable chains in immunoglobulins (antibodies) and T cell receptors, generated by B-cells and T-cells respectively. CDRs are where these molecules bind to their specific antigen and their structure/sequence determines the binding activity of their respective antibody. A set of CDRs constitutes a paratope, or the antigen-binding site. Antigen-antibody interactions are highly specific and have high-affinity. The strength of the bond between the epitope of the antigen and the paratope of the antibody will determine the affinity of the interaction. As the most variable parts of the molecules, CDRs are crucial to the diversity of antigen specificities generated by lymphocytes."

The changes to the first three sentences of this lead section are an improvement compared to the original, however, the fourth and fifth sentence you added are problematic. When compared to the introduction of the work you cited, this sentence is still too close the original in composition and could be flagged for plagiarism. I would advise you to alter the sentences, perhaps simplifying the process to the importance of affinity when it comes to antigen bonding strength. For reference, the sections I'm mentioning that could be hit for plagiarism are this section in the first paragraph of the introduction of the cited source "The most remarkable feature of the antigen–antibody interaction is the high specificity and high affinity [6–9]. A binding strength between an antigenic determinant in an antigen (epitope) and an antigen-binding site in an antibody (paratope) is regarded as affinity."

Your additions also feels as though they were meant to be a separate section of this Wikipedia page. For instance, you could include a short first section about binding affinity before you get into the location and structure section. You could make it so that this section details the variables that are involved with CDR binding affinity.

With that said, you have maintained a neutral tone in this section, and the minor edits to preexisting sections are an improvement. Although, it has come at the cost of concision for this section which is a negative, though that could be corrected if you alter the "plagiarized" section. Additionally, you have helped introduce the idea of binding affinity before your added section at the end of the Wikipedia page.

Content
Regarding the additions you've made to other sections of the Wikipedia article, some of them need alteration. For instance, in the added section "It has been found with X-ray crystallography that all CDRs, except for H3, have similar or identical framework", the phrase "The framework sequences between CDRs can be similar or identical" is dangerously similar, and can trigger plagiarism. Furthermore, the article in question doesn't appear to mention "X-ray crystallography". Furthermore, this begins a continual use of citations that are inappropriate for Wikipedia, articles must be from either a medical text or be a review, and both the previous citations added, Osajima et al. 2014 and Polonelli et al. 2008, are primary literature detailing their own research. Different articles need to be chosen for reference, or they will be removed by the page moderator eventually. Moving to the sentence, "There is a wide variety in the length and amino acid sequence of H3, as well as no distinguishable canonical structures that have been identified for it", again the citation isn't appropriate as Gabrielli et al. 2009 is primary literature. Again, the original text is practically lifted directly from the source material " The third CDR of the heavy chain (H3) displays wide variety in its length and amino acid sequence, and no canonical structures have ever been established for it.". This needs to be altered extensively and another article needs to be chosen to reference. For the sentence, "There are three CDR loops per variable domain in antibodies. Sixty CDRs can be found on a pentameric IgM molecule, which is composed of five antibodies.", where is the information that the lgM molecule is composed of 5 antibodies sourced from? Did you discover this? If not, then the source should be cited, even if it's referenced in the linked lgM page you should source their citation for that sentence in this sentence.

Moving to the next paragraph, the sentence "This rearrangement of the V-region is where the CDR-L3 and CDR-H3 are encoded and diversified, whereas the other four CDRs are generated in the germ-line", compared to this sentence in the source material " Variety of CDR1 and CDR2 is encoded by the germline and furtherly diversified by somatic mutation while the one of CDR L3 and CDR H3 is somatically generated by rearrangement of the variable (V) segment with the joining (J) L or diversity (D) H and JH segments, respectively", it's altered but may still trigger plagiarism. Again, this is also sourced from primary literature, Gabrielli et al. 2009. This needs to change because of that too. The follow up sentence doesn't appear to lift heavily from the source material; however, it wouldn't require a citation if it uses the same source as the previous sentence. But it would require a new citation regardless due to the use of primary literature, which is inappropriate for Wikipedia. Continuing with sentence "CDR-H3 often undergoes conformational changes when an antibody is bound to its antigen, such as an induced-fit change, which is important for the high-specificity and high-affinity interaction", while it doesn't appear to lift material directly from the source it is referencing, it is using primary literature as a reference so that needs to be changed. Continuing to the following sentence, "Antibodies with different antigen specificities can develop identical V-regions of the light chain and different V-regions on the heavy chain, so although they are very similar in sequence/structure, they are only specific to one antigen", it doesn't appear to lift directly, but it also requires a new reference.

Moving on to the next paragraph, the sentences "The structure and sequence of all six CDRs combined will determine the binding activity of the antigen receptor on an antibody or T-cell Receptor. CDRs have been separated into canonical classes based on their varying loop lengths, which are commonly used to differentiate the CDRs from each other . The structural relationship between different length CDRS is based on length-independent components, such as their sequence, and can further characterize CDRs" are different enough from the source material that they don't need to be reworded for plagiarism, however, there may be a more concise way of wording them. The issue lies in the article reference, which for me personally, is right on the edge of what Wikipedia would accept. It is a report and not a review article, and it does mention a method they came up with for the research detailed beyond the introduction, which may be grounds for the reference being rejected. On the other hand, the following sentence while not your work, sets off some red flags. I would ask that you investigate the validity of the claims that Chothia et al, is the pioneer paper for that field of research/finding or why North et al needed to be included at all. The modeling sentences make sense, however there is no clear connection between the previous sentences and them so that could use improvement as well.

Finally, your last section that you added. The second sentence is dangerously close to the source material, and I would consider rewording it if you opt to keep the original article you referenced. Your final few sentences need rewording as well due to the similarity to source material, remember your paraphrase needs to be transformative compared to the original. That said, the article seems to be a solid review article on the subject, so it is worth keeping.

Tone
Regardless of the edits recommended above, you did a commendable job in maintaining a neutral tone consistent with the content presented prior to your additions and edits. The only thing that requires further investigation is the claims related to Chothia and North made by the previous editors, as these claims seem to heavily imply that this study was the hallmark study for CDR classification, which could run counterintuitive Wikipedia's standard for writing.

Sources and references
Osajima et al. 2014 and Polonelli et al. 2008, are primary literature detailing their own research and as such should be removed and swapped for literature reviews instead. Nowak et al. 2016 is borderline for me as a layman, it could be considered ok for Wikipedia, it may be required to be replaced. If you do opt to keep it, the publication time is reasonable for currency, and the use in your writing is done in an alright manner, though the citations don't need to be after consecutive sentences referencing the same article. I would recommend re-examining how often you double reference a paper in consecutive sentences and consider how you would do so in your own research publication. Finally, I would investigate the validity of the claims for Chothia and North and their inclusion in this Wikipedia page.

Organization
Your organization is reasonable in the location and structure sections, however, there is room for improvement. First, I think you can move part of your lead into a section of its own and be expanded. Then, the final paragraph you added in the content section could be positioned earlier in the article, so it is more relevant to the previously covered material such as after the second paragraph in location and structure, so that after you go over antibody affinity interactions, you're following it up with the idea of amino acid residue interactions. Additionally, if modeling is this important to the subjects previously discussed then this section should be expanded, and if not, then it should consider being removed.

Images
I would recommend adding an image of either the different CDRs and their classes, or the antibody CDR affinity and specificity. Otherwise, I'm unsure whether you'll need to add an image to be honest.

Finishing thoughts
Overall, I think you have an alright start to your edits! However, I think you have much to fix as explained above. You desperately need to fix some of your edits for plagiarism and swap some references, so they are Wikipedia compliant. Some sections could be more concise and positioned more coherently. That said, you did an excellent job conveying the information in an accessible manner and with a neutral tone, so hopefully after these next edits your work will be faultless!