User talk:Yousefmalnajjar/G-quadruplex

Natalie Gierat peer reviewing Yousef Alnajjar

• In regards to lead: I don't see a lead here or any edits that will be added to the current lead. This may be due to the fact that the lead already mentions this topic and Yousef is just further elaborating. If not, make sure to add some introductory information that is pertinent to your edits so the article can flow. :)
• this sentence: "This Genome-wide mapping sequencing method along with ChIP-sequencing, which maps both damage in AP sites and the enzyme responsible for its repair, AP endonuclease 1 (APE1), have indicated that AP site damage is nonrandom and is more prevalent in certain regions of the genome that contain specific active promoter and enhancer markers, some of which were linked to regions responsible for lung adenocarcinoma and colon cancer." this sentence was a little hard to read/understand because it was a little wordy. I might reword it so it flows more smoothly or just try splitting it into two separate sentences.
• Overall, the first paragraph is really good. Like the bullet point above, I would make sure to go through and ensure that the sentences aren't have a good flow to them and that the grammar is all good. Other than the bullet point above that points out a sort of major change, *I think any other changes you make to this paragraph will need to be minor tweaks.

• this sentence: "AP endonuclease 1 is an enzyme which is responsible for the promotion and the formation of G-quadruplex structures in the BER pathway, which is in charge of repairing damage caused to AP sites." i think i would find a way to make this sentence flow a little smoother. "Which" is used a lot and I think the sentence could be reworded to sound a little smoother.
• "forms oxidized forms of nucleotides" i think here you should just say "forms oxidized nucleotides"
• "indicates oxidative stress and damage" i would change indicates to something like "senses"
• "It does so by cleaving the oxidized base and thus creating an AP site" instead of "it" i would say the "ogg1" because i think its a little unclear if you dont.
• once again, this paragraph looks super good. the stuff i wrote above is really just some tweaks that i think might make your paragraphs flow better. in addition to what i wrote above, i'd just go through and see where you need to add some commas, fix grammar, and/or possibly split some sentences into two.

• from what i can tell even though i don't have a ton of g-quadruplex knowledge, everything you wrote seems very neutral and unbiased.
• all the references work for me and are in good format, a lot of them are very recently published.
  • • i think there is something wrong with the way your reference 4 is inserted, there is a note written in red on your page so I'd check that out.
• everything you wrote flows super well, there aren't any sentences thrown in that seem irrelevant. great organization.

good job! It was hard to find stuff wrong with your writing, super good.

Endogenous Oxidize DNA Bases Damage and G4 formation(BI) edits by LR // 8-oxo-2'-deoxyguanosine or (8-oxo-dG) is an oxidized derivative of ]8-oxo-2'-deoxyguanosine or (8-oxo-dG) is an oxidized derivative of deoxyguanosine. and the major products of DNA oxidation. deoxyguanosine.--> either delete the parentheses or delete the or.There is an uneseccary period in the middle of the sentence. // This is because guanine has a lower one-electron reduction potential than the other nucleotides bases in DNA. This means that the two of the most frequently oxidized bases in DNA, after ionizing radiation (causing oxidative stress) were the two oxidation products of guanine--> I like the content of this sentence but the structure could be fixed. You start both sentences with "This", consider combining the sentences. This also needs a citation. // One of the products being an enol form 8-OH-Gua, formed through a tautomeric shift from the original damage guanine, 8-oxo-Gua. --> Maybe say something like " An enol.... formed through.. " it was hard to read at first. // A chemically changed base such as 8-OHdG, represents DNA damage and can cause changes in the structure of the genetic material and prevent the replication mechanism from functioning and performing properly. --> needs a citation // AP sites, a location in DNA that has neither a purine or a pyrimidine base due to DNA damage are the most prevalent type of endogenous DNA damage in cells. AP sites are generated spontaneously or even after cleavage of modified bases, including oxidation of guanine. --> the flow to this is very good. It needs a citation //

With genome-wide ChIP-Seq analyses, cell-based assays, and in vitro biochemical analyses, a mechanistic framework has been provided linking oxidized DNA base-derived AP sites,  to G-quadruplex formation/stability, and the control of gene expression. --> delete the comma before to, it is not needed there. This will also need a citation

// It is believed that increased levels of 8-oxo-dG in a tissue can serve as a biomarker to determine the level of oxidative stress produce--> make this more affirmative. State why it is believed this, did some studies support this? needs a citation // When produced, 8-oxo-dG in the promoter of a gene, may also inactivate OGG1, an enzyme that targets 8-oxo-dG and normally initiates repair of 8-oxo-dG damage. The inactivation allows for un-repaired DNA damages to accumulate in non-replicating cells, such as cells in the brains or muscles of adult mammals, and can cause aging. Moreover, the increased levels of 8-oxo-dG are frequently found associated with carcinogenesis and disease. --> need a citation for this. Flows very well and great content // This type of oxidative DNA damage, such as 8-oxo-dG, likely contributes to carcinogenesis. by two mechanisms.--? There's a period there that needs to be deleted. Reconsider the sentence structure, posssibly delete the phrase "such as.." // The first- modulation of gene expression, and the second-induction of mutations. Since AP sites are the most prevalent type of endogenous DNA damage in cells, a map of these AP sites (AP-seq) in the genome using a biotin-labeled aldehyde reactive probe that reacts explicitly with an AP site in DNA, can signal oxidative stress and the formation of 8-oxoG and AP sites. This flows very well and presents valuable information to the page. It needs a citation // The edits has very content. The structure and the flow improves as you read down the article. More citations are needed. This has great potential but it needs be refine a bit. Overall good job picking the important facts that contribute to the page. — Preceding unsigned comment added by RamirezGLuis (talk • contribs) 01:18, 12 December 2020 (UTC)