User:Ayun2/sandbox

Questions to consider evaluating article

This is my topic: Second messenger system

Choose at least 1 question relevant to the article you're evaluating and leave your evaluation on the article's Talk page. Be sure to sign your feedback with four tildes — ~~~~.

• What kinds of conversations, if any, are going on behind the scenes about how to represent this topic?
  • Nothing much, it is a project in the early stages and states that if possibly improved, to do so.
• How is the article rated? Is it a part of any WikiProjects?
  • Level 5 vital article in the start class
  • Its part of molecular biology, cell signaling, neuroscience.
• How does the way Wikipedia discusses this topic differ from the way we've talked about it in class?
  • It lacks lots of details, giving a general scope of second messengers and not how they work specifically.

• Check a few citations. Do the links work? Does the source support the claims in the article?
  • NONE of the sources work.
• Is each fact referenced with an appropriate, reliable reference? Where does the information come from? Are these neutral sources? If biased, is that bias noted?
  • CANT ANSWER, no sources work.

• Is the article neutral? Are there any claims that appear heavily biased toward a particular position?
  • neutral
• Are there viewpoints that are overrepresented, or underrepresented?
  • Gives the basic idea of second messengers, but fails to apply it.

• Is everything in the article relevant to the article topic? Is there anything that distracted you?
  • Yes
  • No
• Is any information out of date? Is anything missing that could be added?
  • Examples that can help it be better understood.
• What else could be improved?
  • a picture of a pathway
  • improve all citations.

Article Selection

Citations

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3504441/pdf/cshperspect-SIG-a011148.pdf

Sassone-Corsi, Paolo, The Cyclic AMP Pathway,Cold Spring Harb Perspect Biol 2012;4:a011148

https://www.jstage.jst.go.jp/article/jphs1951/74/2/74_2_125/_pdf/-char/en

Yoshida, Yutaka, Structure and Function of Inositol 1,4,5-Triphosphate Receptor, vol. 74, pp. 125–137

https://www.sciencedirect.com/science/article/pii/S2090123218300390

Hanna, Violette, Synopsis on arachidonic acid Metabolism: A review, vol. 11, pp. 23–32

Talk Page Post (article evaluation)

Hi all,

Many of the references for this page are not found anymore. Providing better references may also improve the content via expanding on the provided examples.

The following articles and reviews seem to encompass a majority of the provided information and much more:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3504441/pdf/cshperspect-SIG-a011148.pdf

Sassone-Corsi, Paolo, The Cyclic AMP Pathway,Cold Spring Harb Perspect Biol 2012;4:a011148

The above reference gives more information about the cAMP pathway that is used as an example. It is also a source that is published as an article, which "reviews" the pathway in general.

I would also like to talk about the epinephrine pathway. It is a good pathway that helps people understand how and where secondary messengers play a role, and it utilizes the stated examples.

Here is a paper that talks about the Inositol signaling pathway and how the other second messengers such as Ca2+ and DAG play a role, along with the end goal.

https://www.jstage.jst.go.jp/article/jphs1951/74/2/74_2_125/_pdf/-char/enYoshida, Yutaka, Structure and Function of Inositol 1,4,5-Triphosphate Receptor, vol. 74, pp. 125–137

And lastly, the last example which involves the Histimine Pathway, the following paper helps understand the contribution of the second messenger.

https://www.sciencedirect.com/science/article/pii/S2090123218300390 Hanna, Violette, Synopsis on arachidonic acid Metabolism: A review, vol. 11, pp. 23–32

The papers also provide descriptions of how each secondary messenger plays its role and provides a better understanding of a second messenger in general.

Now, I understand this may be stepping foot into other wiki pages, so I will try my best to cite other pages if need be, along with utilizing the information provided in these reviews and articles.

Please let me know what you think about the idea, the papers I plan on utilizing, and any ideas that come to mind that can support this endeavor.

Where I'd Like to Edit

Examples

	cAMP System	Phosphoinositol system	Arachidonic acid system	cGMP System	Tyrosine kinase system
First Messenger:Neurotransmitters(Receptor)	Epinephrine (α2, β1, β2) Acetylcholine (M2)	Epinephrine (α1) Acetylcholine (M1, M3)	Histamine (Histamine receptor)	-	-
First Messenger:Hormones	ACTH, ANP, CRH, CT, FSH, Glucagon, hCG, LH, MSH, PTH, TSH	AGT, GnRH, GHRH, Oxytocin, TRH	-	ANP, Nitric oxide	INS, IGF, PDGF
Signal Transducer	GPCR/Gs (β1, β2), Gi (α2, M2)	GPCR/Gq	Unknown G-protein	-	RTK
Primary effector	Adenylyl cyclase	Phospholipase C	Phospholipase A	guanylate cyclase	RasGEF (Grb2-Sos)
Second messenger	cAMP (cyclic adenosine monophosphate)	IP3; DAG; Ca2+	Arachidonic acid	cGMP	Ras.GTP (Small G Protein)
Secondary effector	protein kinase A	PKC; CaM	5-Lipoxygenase, 12-Lipoxygenase, cycloxygenase	protein kinase G	MAP3K (c-Raf)

Phosphoinositol system

-Provide more background information about the pathways involved, and how each second messenger is involved in the pathway

Utilize the first citation and a diagram to highlight where the second messenger is in the pathway, and simple details

Other fixes

All the references are outdated. The citations provided will be used and referenced, for all the information prior to edits. Also, references will be added for all the information. Relevant information will also be incorporated.

For Peer Review: What I Did

I found that the article does not really give a proper example portraying where second messengers play a role in the second messenger system pathway. So what I wanted to do was add a new section (4.1 of rubric), exhibiting the second messengers and their role in the pathway. As you can see from above, the article gives the table with examples, and states the second messengers without properly explaining them. So i chose one example from above, and gave a brief description of the pathway, where the second messengers come in, what they are signaled by, and what they eventually signal. Now, i felt that words would not complete the picture, so i added a picture (diagram that wouldnt properly post).

While going through my section, i noticed that some of my references can actually replace some references that were used in the article. I noticed that none of the references, when clicked, lead to an existing site anymore. So I, for now, found working links referring to the same source, and added them below. I know this is double dipping on the reference section of the rubric, but its something that I felt like I needed to do, even if im not graded it on it (seeing how poor the referencing on this article is). If you go below to the citations id like to update section, i added many citations for sentences that needed citations, along with updating broken (leading to page not found pages) links.

Citation 1 i used for the newly added section explains how epinephrine binds to the GPCR, or how the primary signal binds to the membrane receptor, causing the signaling pathway.

Citation 2 explains what we learned in class, GNRP (popularly referred to GEFS online), its functions, and the resulting activation.

Citation 3 continues the above citation, it gives more information on the resulting activation.

Citation 4,5,6 finally explain the second messengers involved, how they are introduced, and what they signal for.

Information i will be adding : Phosphoinositol system

IP3, DAG, and Ca2+ are second messengers in the phosphoinositol pathway. The pathway begins with the binding of extracellular primary messengers such as epinephrine, acetylcholine, and hormones AGT, GnRH, GHRH, oxytocin, and TRH, to their respective receptors. Epinephrine binds to the α1 GTPase Protein Coupled Receptor (GPCR) and acetylcholine binds to M1 and M2 GPCR.

Binding of a primary messenger to these receptors results in conformational change of the receptor. The α subunit, with the help of guanine nucleotide exchange factors (GEFS), releases GDP, and binds GTP, resulting in the dissociation of the subunit and subsequent activation. The activated α subunit activates phospholipase C, which hydrolyzes membrane bound phosphatidylinositol-4,4-biphosphate (PIP2), resulting in the formation of secondary messengers diacylglycerol (DAG) and inositol-1,4,5-triphosphate (IP3). IP3 binds to calcium pumps on endoplasmic reticula membrane, transporting Ca2+, another second messenger, into the cytoplasm. Ca2+ ultimately binds to many proteins, activating a cascade of enzymatic pathways.

The Phosphoinositol Signaling Pathway

^^So i made this image, its just not uploading like i want.

Citations i would like to update for the page

I will be replacing some of the references that they have stated with the following

Second messengers are intracellular signaling molecules released by the cell in response to exposure to extracellular signaling molecules—the first messengers. Second messengers trigger physiological changes such as proliferation, differentiation, migration, survival, and apoptosis. They are one of the triggers of intracellular signal transduction cascades.

Kodis, Erin J, Smindak, Richard J, Kefauver, Jennifer M, Heffner, Danielle L, Aschenbach, Krista L, Brennan, Elliot R, Chan, Kelvin, Gamage, Kanchana K, Lambeth, Philip S, Lawler, Jessica R, Sikora, Arthur K, Vercruysse, Nicholas R, and Deppmann, Christopher D(Oct 2012) First Messengers. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0024167]

Examples of second messenger molecules include cyclic AMP, cyclic GMP, inositol trisphosphate, diacylglycerol, and calcium.^1

[2]https://doi.org/10.1016/B978-0-323-34126-4.00026-8

http://www.biology-pages.info/S/Second_messengers.html <-- this one is the one by kimball that i have to update on the stuff.

The mechanisms were worked out in detail by Martin Rodbell and Alfred G. Gilman, who won the 1994 Nobel Prize.

https://www.nobelprize.org/prizes/medicine/1994/gilman/biographical/

https://www.nobelprize.org/prizes/medicine/1994/rodbell/biographical/

Secondary messenger systems can be synthesized and activated by enzymes, for example, the cyclases that synthesize cyclic nucleotides, or by opening of ion channels to allow influx of metal ions, for example Ca²⁺ signaling. These small molecules bind and activate protein kinases, ion channels, and other proteins, thus continuing the signaling cascade.

Purves D, Augustine GJ, Fitzpatrick D, et al., editors. Neuroscience. 2nd edition. Sunderland (MA): Sinauer Associates; 2001. Second Messengers.Available from: https://www.ncbi.nlm.nih.gov/books/NBK10794/

Second Messengers http://www.biology-pages.info/S/Second_messengers.html (accessed Nov 2, 2018). -- This is an updated citation for the first one in the article. Clicking the pages stated citation leads to an error saying page is not found. I noticed late that the whole page provides information without giving citations to which they based the stated information on. I will be working on providing citations for all the statements provided, but it will take some time. I will publish the citations i find as i go, but it will be a long process, and may go beyond the scope of this project. So, my primary agenda will be the information im providing about the phosphoinositol system. Overall the page is not in a great conditions. All previously added information is jeopardized due to poor references and improper citation.