User talk:Negarrezqi/sandbox

Peptidoglycan
The overall tone of the Wikipedia article regarding peptidoglycan represents information in an unbiased form. Therefore, it is fair to say that the article has a neutral tone. However, there are some flaws in the article which can be improved upon. For example, comparing the first three sentences of the Wikipedia article with the cited reference, it’s evident that it has been copied directly with minor changes both text and structure vise. Moreover, the first cited reference isn’t reliable because it’s just a website for educational purposes, and it is not peer-reviewed. Moving on, the first paragraph of the structure section lacks citations which violates the Wikipedia rules that each paragraph must contain at least one source. Furthermore, reference number five doesn’t take us to the cited material, and reference number nine doesn’t work. Looking at the overall flow of the article, the inhibition section is shorter compared to the first three sections despite having significance. To improve this section, information regarding B-lactamase antibiotics and how they disturb the peptidoglycan synthesis can be added. The article titled, “Induction of b-lactamase production in Aeromonas hydrophila is responsive to b-lactam-mediated changes in peptidoglycan composition” can be used to explain this. Further improvement includes talking about gram staining procedures as mentioned in the talk section. The difference between gram positive and negative is explained in the second paragraph of the article. Therefore, it’s fair to include the gram staining procedure which is important in identifying gram positive and negative bacteria.

Heterocyst
The topic of heterocyst has a high notability as it has been covered by reliable sources. As a matter of fact, 3380 journals were found on Google Scholar since 2013, and by checking some, it was evident that they were independent of the subject and were peer-reviewed. The subject itself is important as the heterocyst allows Cyanobacteria to fix nitrogen which in turn can be used in agriculture. The Nitrogen fixation of cyanobacteria can be used in flooded rice fields to provide natural bio fertilizer.

Looking at the article as a whole it is evident that it is missing subtopics and the information provided is not organized and is very difficult to follow. The fifth paragraph briefly touched upon the gene regulation involved in heterocyst formation, but it can be improved upon. This can be done by adding in a new subtopic called “gene expression”. Under this subtopic heterocyst differentiation will be discussed. The article mentions inhibitor PatS, which is the enzyme used for controlling heterocyst differentiation, but does not discuss how the differentiation is initiated. After reviewing scholarly articles, it has been shown that heterocyst differentiation is triggered by transcriptional regulator nctA. NctA in turn controls the expression of several genes including HetR which is crucial for heterocyst differentiation. It is also worthy to note that the expression of nctA, and HetR are dependent on each other and their presence promotes heterocyst differentiation even in the presence of nitrogen. It has also been recently found that other genes such as PatA, hetP regulate heterocyst differentiation. This added content will improve the article as gene expression is the basis for understanding how heterocyst differentiates. This can have an important application in promoting or inhibiting heterocyst in a lab setting by up or down regulating nctA, and HetR genes. Negarrezqi (talk) 05:48, 28 September 2017 (UTC)

Original- "Heterocyst"
Single heterocysts develop about every 9-15 cells, producing a one-dimensional pattern along the filament. The interval between heterocysts remains approximately constant even though the cells in the filament are dividing. The bacterial filament can be seen as a multicellular organism with two distinct yet interdependent cell types. Such behavior is highly unusual in prokaryotes and may have been the first example of multicellular patterning in evolution. Once a heterocyst has formed it cannot revert to a vegetative cell. Certain heterocyst-forming bacteria can differentiate into spore-like cells called akinetes or motile cells called hormogonia, making them the most phenotyptically versatile of all prokaryotes.

The mechanism of controlling heterocysts is thought to involve the diffusion of an inhibitor of differentiation called patS. Heterocyst formation is inhibited in the presence of a fixed nitrogen source, such as ammonium or nitrate. Heterocyst maintenance is dependent on an enzyme called hetN. The bacteria may also enter a symbiotic relationship with certain plants. In such a relationship, the bacteria do not respond to the availability of nitrogen, but to signals produced by the plant. Up to 60% of the cells can become heterocysts, providing fixed nitrogen to the plant in return for fixed carbon.

The following sequences take place in formation of heterocysts from a vegetative cell:

The cell enlarges. Granular inclusions decrease. Photosynthetic lammele reorients. The wall finally becomes triple-layered. These three layers develop outside the cell's outer layer. The middle layer is homogeneous. The inner layer is laminated. The senescent heterocyst undergoes vacuolation and finally breaks off from the filament causing fragmentation. These fragments are called hormogonia and undergo asexual reproduction. Negarrez (talk) 02:04, 9 October 2017 (UTC) References — Preceding unsigned comment added by Negarrez (talk • contribs) 07:03, 9 October 2017 (UTC)

Edit-"heterocyst"
Single heterocysts develop about every 9-15 cells, producing a one-dimensional pattern along the filament. The interval between heterocysts remains approximately constant even though the cells in the filament are dividing. The bacterial filament can be seen as a multicellular organism with two distinct yet interdependent cell types. Such behavior is highly unusual in prokaryotes and may have been the first example of multicellular patterning in evolution. Once a heterocyst has formed it cannot revert to a vegetative cell. Certain heterocyst-forming bacteria can differentiate into spore-like cells called akinetes or motile cells called hormogonia, making them the most phenotyptically versatile of all prokaryotes.

Gene Expression

In low nitrogen environment, heterocyst differentiation is triggered by transcriptional regulator NctA. NctA influences heterocyst differentiation by signaling to proteins involved in the process. For instance, NctA controls the expression of several genes including HetR which is crucial for heterocyst differentiation. It is crucial in that it up regulates other genes such as hetR, patS, hepA by binding to their promoter thus acting as a transcription factor. It is also worthy to note that the expression of nctA, and HetR are dependent on each other and their presence promotes heterocyst differentiation even in the presence of nitrogen. It has also been recently found that other genes such as PatA, hetP regulate heterocyst differentiation. PatA patterns the heterocysts along the filaments, and it is also important for cell division. PatS influences the heterocyst patterning by inhibiting heterocyst differentiation when a group differentiating cells come together to form a proheterocyst (immature heterocyst). Heterocyst formation is inhibited in the presence of a fixed nitrogen source, such as ammonium or nitrate. Heterocyst maintenance is dependent on an enzyme called hetN. The bacteria may also enter a symbiotic relationship with certain plants. In such a relationship, the bacteria do not respond to the availability of nitrogen, but to signals produced by the plant. Up to 60% of the cells can become heterocysts, providing fixed nitrogen to the plant in return for fixed carbon.

The following sequences take place in formation of heterocysts from a vegetative cell: Negarrez (talk) 07:02, 9 October 2017 (UTC)
 * The cell enlarges.
 * Granular inclusions decrease.
 * Photosynthetic lammele reorients.
 * The wall finally becomes triple-layered. These three layers develop outside the cell's outer layer.
 * The middle layer is homogeneous.
 * The inner layer is laminated.
 * The senescent heterocyst undergoes vacuolation and finally breaks off from the filament causing fragmentation. These fragments are called hormogonia and undergo asexual reproduction.

References

Negar's Peer Review
The edit of the “Heterocyst” Wikipedia article has reliable sources, neutral unbiased content and overall the new content is incorporated into the old article well. The references all link to the correct source, and the research is presented neutrally, with no bias. After reviewing the sources of the article, I can confirm that the researchers’ findings are accurately summarized in the edit. The overall structure and content order is presented in a logical and easy to follow manner. I suggest the following revisions to improve the article’s content and writing. Firstly, the article does not define what a heterocyst is, which would be an important thing for readers who do not know the function of a heterocyst, or where it is found. Another change I would suggest that would have a positive impact on the article would be to make the 3rd-8th sentences of the “Gene Expression” section more concise, perhaps by doing bullet or point form for each gene involved. I think that change would improve the article by making it clearer and easier for the reader to understand. Another small change I suggest is to move the 3 sentences on symbiotic bacteria and their heterocyst’s into a different section because I do not think that topic is related to gene expression, perhaps it could be moved to the intro or into its own section. Also adding hyperlinks of key words (like transcriptional regulator, for example) that link to their appropriate Wikipedia pages would allow the audience to learn or review what certain words or phrases are referring to. Overall the edit has good structure and is well-sourced so making the changes described would improve reader comprehension even more. Spflueger (talk) 02:29, 9 November 2017 (UTC)