Talk:WikiJournal of Science/Lysenin
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WikiJournal of Science
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WikiJournal of Science is an open-access, free-to-publish, Wikipedia-integrated academic journal for science, mathematics, engineering and technology topics.WJSWikiJSciWiki.J.Sci.WikiJSciWikiSciWikiScienceWikiscienceWikijournal of ScienceWikiversity Journal of ScienceWikiJournal ScienceWikipedia ScienceWikipedia science journalSTEMScienceMathematicsEngineeringTechnologyFree to publishOpen accessOpen-accessNon-profitonline journalPublic peer review
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It was adapted from theWikipedia pageLysenin and contains some or all ofthat page's content licensed under aCC BY-SA license. Post-publicationreview comments ordirect edits can be left at the version as itappears on Wikipedia.
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DOI:10.15347/wjs/2019.006
QID:Q76846397
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Ignacio L. B. Munguira (17 August 2019)."Lysenin".WikiJournal of Science2 (1): 6. doi:10.15347/WJS/2019.006.Wikidata Q76846397. ISSN 2470-6345.https://upload.wikimedia.org/wikiversity/en/1/12/Lysenin.pdf.
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Wikipedia: This work is adapted from the Wikipedia articleLysenin (CC BY-SA). Content has also subsequently been used to update that same Wikipedia articleLysenin.
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This is an open access article distributed under the Creative Commons Attribution ShareAlike License, which permits unrestricted use, distribution, and reproduction, provided the original author and source are credited.
Thomas Shafee
(handling editor)contact
Ian Alexander(proofreader)contact
Daniel Fologea
Milda Pleckaityte
Submitting author: Ignacio L. B. Munguira[a][i]
Additional contributors:Wikipedia community
Pass.WMF copyvio tool using TurnItIn. Fully unique content.T.Shafee(Evo﹠Evo)talk09:05, 6 February 2019 (UTC)Reply
Comments byThomas Shafee ,
These editorial comments were submitted on, and refer tothis previous version of the article
The article is almost ready for peer review, however the abstract is very short. Ideally it should summarise the key points of the subsequent sections of the article. I would suggest it to 100-200 words long for a short review article such as this. Could you therefore expand the abstract to cover the main topics.
Comments byIan Alexander ,
These editorial comments were submitted on, and refer tothis previous version of the article
The article needs copy-editing for use of English, and I'd suggest also for readability by non-specialists. I will make a brief pass on this but I would suggest a thorough checking-over.
Comments byMarshallsumter ,
These editorial comments were submitted on, and refer tothis previous version of the article
I made some minor copy-edits for use of English in the abstract as a non-specialist. Have a read to see if I've kept your meaning intact. --Marshallsumter (discuss •contribs)02:38, 12 February 2019 (UTC)Reply
Comments byJack Nunn ,
These editorial comments were submitted on, and refer tothis previous version of the article
Copyedits for language and readability and comments in attached PDF. See also edits inthis diff.
I will like to thank all the Editors for their comments. After them the article has improve a lot. I have accepted most of the changes, except those in which the meaning was different from the original one.
I wish to peer review the article Lysenin and dedicate myself for this journal's welfare. Also to gain an opportunity to develop myself further and brush my knowledge and research skills time by time. I completed my Post graduation and M.Phil in Biotechnology. I published 2 research papers in journals and 2 in conference proceedings. Now I am helping and motivating students to pursue in their research.--Sreenandhini (discuss •contribs)16:26, 6 February 2019 (UTC)Reply
WikiJSci.org.T.Shafee(Evo﹠Evo)talk03:08, 7 February 2019 (UTC)Reply
Review byDaniel Fologea , Boise State University, USA
These assessment comments were submitted on, and refer tothis previous version of the article
The review entitled “Lysenin” and intended for the WikiJournal of Science addresses recent advancements in relation to lysenin interaction with membranes, channel oligomerization and pore formation. The major focus of the review is on lysenin binding to sphingomyelin, oligomerization, and channel insertion. The intricate mechanism by which lysenin transition from a water soluble form to a fully-formed pore is supported by X-ray and Cryo-EM data, as well as AFM measurements.
The title of the review is too general to properly reflect what the author(s) chose to present. This review is chiefly limited to descriptions of the steps that lead to channel formation and structural data. In my opinion, this is far from sufficient. Lysenin is one of the most intriguing pore-forming toxins with respect to its biological activity and functionality yet the author(s) overlooked such features.
Lysenin is considered a pore-forming toxin owing to its cytolytic activity. However, lysenin shares multiple salient features specific to ion channels, and such important biophysical properties are not mentioned in this review.
The fact that the reviewer treat pore-forming toxins as channels for biotechnological purposes do not change its very nature as unspecific pores. Being unspecific pores its properties as channels are of none importance for the natural function of lysenin. However I included some studies about its biophysical properties as channels in a new section entitled “Applications” at the end of the review.
Lysenin forms a voltage gated channel when reconstituted in bilayers lipid membranes (1-4); interestingly, this feature is abrogated when the target membrane is composed of neutral lipids. In the presence of multivalent ions, lysenin channels present an intriguing ligand-induced gating (5, 6). While trivalent metals induce rapid and complete channel closing, divalent metal and multivalent organic ions elicit only partial closing of the channel (sub-conducting states), suggesting that charge density rather than net charge plays an important role in the gating mechanism. Notably, large polymeric cations induce irreversible blockage of the channels most probably through a trapping mechanism (7). Lysenin channels show a strong hysteresis in conductance (2), which may be linked to a gating mechanism that implies movement of the voltage sensor domain from the eater environment into the hydrophobic core of the membrane (8). Lysenin is a molecular tool useful for investigating the effects of surface crowding on the functionality of transmembrane transporters (9).
Its true that lysenin was used to study the effects of crowding and I include the following paragraph about that at the end of the section "Lysenin binding, oligomerization and insertion"
"The prepore to pore transition can be blocked in crowded conditions, a mechanism that could be general to all β-PFTs.. The first hint of crowding effect on prepore to pore transition was given by congestion effects in electrophysiology experiments.[1] High-Speed AFM studies incubating Lysenin on sphingomyelin/cholesterol membranes has shown that under crowded conditions the prepore to pore transition gets blocked by steric interactions.[2][3]"
Similar to other pore-forming proteins, lysenin may be used for single molecule detection and characterization by the resistive pulse technique (10) or to investigate interactions between protein channels and nanomaterials (11).
The reviewer rise and important point that I overlock. I have added a section about the biotechnological applications of lysenin after the section entitled "Biological role".
"Lysenin conductive properties have been studied for years.[1] As most pore-forming toxins lysenin forms an unspecific channel also permeable to small peptides.[2] 2 Behind all those studies along more than three decades underlie the interest of finding a sequencing system biocompatible and with tunable conductive properties by point mutation.[3] Owing its binding affinity for sphingomyelin, lysenin or lysenin receptor binding domain has been used as a fluorescence marker to detect sphingomyelin domain in membranes.[4]"
In my opinion, the current version of the review on lysenin does not address many of the channel’s salient features; such additions will make the review more palatable to a broader audience and enhance the scientific impact.
I add some references about the channel properties in a new section about the applications.
The current version also needs serious editing with regards to language, grammar, and English composition. A careful check of the references is needed; identical references appear multiple times and with different numbers in the list.
I have revised the references in order to remove those references that appear multiple times with different names. The article was checked by some native speakers, however, any additional specific comment is welcome.
I would not recommend including work referenced as “under submission” in a review article since the interested readers may not have immediate access to those references.
In my view the article entitled “lysenin” is good. But need some modifications and corrections. In my opinion,
a) Abstract: An ideal abstract should be the brief summary of the article (usually not exceeding 200 words) which helps to understand the key points of the article. I think it would be nice to have or expand the abstract with biological role of lysenin also.
b) The lysenin article only focused on the general idea of lysenin interaction, channel oligomerization and pore formation. And the biological information provided is not enough for a good scientific review. Due to these, the article is very far from adequate data. Could you please add more general and applied biological information about lysenin with suitable reference?
If the reviewer find more biological information about the biological role of lysenin I will be really interested in read and include it.
c) I think these links will be useful for the lysenin article (biological information).
There is no new biological information in those references.
d) Reference : Kindly provide links to the journals in the reference (that can be made more convenient by taking readers to a specific page and also helps to locate the source).
I have no idea of how to do it, feel welcome to do it if you consider that is important. However, be aware that not all journals are open access.
e) I have made some minor changes directly to the article (Corrected the identical reference appeared in multiple times and also provided the links). Kindly go through it. And one thing also, the article needs serious editing with regards to English composition.
I hope the comments will be helpful for the authors.--Sreenandhini (discuss •contribs)09:08, 15 May 2019 (UTC)Reply
Review byMilda Plečkaitytė , Institute of Biotechnology Vilnius University
These assessment comments were submitted on, and refer tothis previous version of the article
The article Lysenin needs more condensed, structured information on the object presented in a clearer way. Below, please, find my suggestions toimprove the article.
Abstract: the second sentence should be modified, as follows ‘Pore-forming toxins (PFTs) are proteinaceous virulence factors produced by manypathogenic bacteria. PFTs are produced also by archea, fungi, plants and animals’.
I have modified the sentence following reviewer advice, to include all kingdoms of nature in which PFTs can be found.
The sentences “After the membrane attachment, the oligomerization results in a nonamer on top of the membrane. This oligomer is known as aprepore” need revision. I propose ‘After the membrane attachment, oligomerization of lysenin takes place and results in a nonamer on the lipidbilayer forming prepore before membrane insertion’.
Abstract also needs information on biological significance of lysenin.
I have modified the sentence following reviewer advice and add two sentences at the end of the abstract in order to give some biological information.
I propose to rename the subchapter ‘Monomer’ to ‘Protein’ and present more structured information of lysenin as a protein in the following way
(starting from the 3rd sentence): ‘The topology of the lysenin structural fold specifies it to the aerolysin family of small β-pore-forming toxins (β-PFT) (Bokori-Brown et al., 2016). Structurally lysenin contains a receptor binding domain and a Pore Forming Module (PFM), which contributes
to β-barrel pore. Lysenin like other PFT’s is secreted as inactive, water-soluble monomer (33 kDa). Lysenin binds to sphingomyelin (SM) that is a
major lipid of the plasma membrane located mainly in its outer leaflet. Upon binding to SM, lysenin executes common assembly pathway for β-PFT: it forms oligomers, undergo structural rearrangements, inserts into membrane bilyer and form a pore.’
There were two important data that I forgot to include. First, that monomer are water soluble. Second, sphingomyelin is mostly found in the outer membrane leaflet. Both are now included. I keep the section almost in its aroginal form since I want to keep all the information contained in it.
Subchapter ‘Membrane receptors’ should be modified as information like “In lysenin, the detergent belt is 32 Å in height” is not clear for thereaders. I propose to combine this subchapter with the next one under the name like ‘Mechanism of oligomeric assembly and pore formation’.This subchapter needs revision presenting the described events of lysenin pore formation in a coherent and sequential way, e.g. nine monomersthat compose oligomeric lysenin is repeated twice.
I have tried to remove redundancies and clarify some concepts.