User talk:Mabelz97/sandbox

Overall, the "Phototroph" article has good, peer-reviewed scholarly sources, such as journal articles and textbooks, but is very poor at referencing each fact. For instance, under the "photoautotroph" heading, the vast majority of information is not common knowledge and there should be a reference after almost every sentence, such as the sentence "… chemotrophs that obtain their energy by the oxidation of electron donors in their environments." As well, the word “many” in the fourth sentence of the article should be avoided since it adds no context and is too arbitrary. There are also terms and ideas in the article that a general audience would not understand well, such as "photon" and "photosynthesize" that should have been linked to their respective Wikipedia pages. Simple words like "light" and "energy" did not need to be linked. When clicking the citation for “organelle,” it leads to the Wikipedia page for “chloroplast” which was not mentioned in the original article. The article did a very poor job at remaining neutral. There was far too much focus on photoautotrophs, including an unnecessarily detailed paragraph about cyanobacteria, compared to photoheterotrophs, which had no examples at all. The history section was also very lacking and should have went into greater detail of the origin of the word. Subcategories of phototroph should have also been mentioned; photolithoautotrophs was mentioned once, but other categories, like photoorganoheterotrophs, were left out. The “talk” page calls some facts in the article into question, such as the mention of fungi as phototrophs, and plagiarism within the first sentence of the article but those issues have been resolved since. --Mabelz97 (talk) 06:28, 18 September 2017 (UTC)

Assignment 2

Heterocysts are notable because they are an ingenious adaptation that some cyanobacteria form in response to a lack of fixed nitrogen. The ability of cyanobacteria to divide itself into two different cell types- heterocysts and vegetative cells- is exceedingly beneficial to the organism because the heterocysts can provide fixed nitrogen for anabolism and the vegetative cells provide electrons and energy to fuel this process, allowing the cyanobacteria to survive in harsh, oligotrophic environments. This supports the vast abundance of cyanobacteria in the world which is important for global cycling of Nitrogen, Oxygen, and Carbon. While the Wikipedia article addresses the necessity of cyanobacteria to form heterocysts to protect the nitrogenases, which fix gaseous nitrogen into forms plants can use, from degradation in the presence of oxygen, as well as talking about what kind of physical changes the vegetative cells need to undergo to transform into a heterocyst, it does not go into detail which key players are involved in the process and why specific structures, such as the additional cell wall layers of the heterocyst, are formed. For example, the first sentence of the article mentions that heterocysts are “formed during nitrogen starvation” but doesn’t mention how the cell knows this or what transpires afterwards. This will be the part that I will focus on. I will be adding content regarding the gene expression, signalling molecules, enzymes, and any other microscopic factors that are crucial in the process of changing vegetative cells into heterocysts. For instance, the first indication for the organism to form heterocysts is the lack of environmental nitrate or ammonium which is detected by 2-oxoglutarate, an intermediate in the Krebs cycle which halts that process (Laurent et al. 2005). The article also describes how “heterocysts develop about every 9-15 cells” but doesn’t say mention how this is controlled by inhibitory proteins, patS and hetN so that the cyanobacteria will have maximal metabolic cooperation between vegetative cells and heterocysts (Khudyakov and Golden 2004). It is fine details like this, the “how it happens” to complement Wikipedia’s “what happens,” that I will be focusing on editing. Mabelz97 (talk) 06:43, 28 September 2017 (UTC) Mabelz97

Assignment 3 - Editing your article

Original - "Heterocyst"

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.

The cyanobacteria that form heterocysts are divided into the orders Nostocales and Stigonematales, which form simple and branching filaments respectively. Together they form a monophyletic group, with very low genetic variability.

References

Category:Nitrogen cycle Category:Cyanobacteria

Edits - "Heterocyst"

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:

• A lack of fixed environmental nitrogen, such as ammonium or nitrate, leads to decreased amounts of 2-oxoglutarate, an intermediate in the Krebs cycle, in vegetative cells.
• NtcA, a transcriptional regulator detects the changes in 2-oxoglutarate. The Krebs cycle becomes halted and heterocyst formation initializes.
• Heterocyst formation is controlled by the patS and hetR genes. HetR expression promotes heterocyst formation whereas patS inhibits heterocyst formation. Vegetative cells that express patS at high levels will not differentiate into heterocysts and cells that express patS at low levels will become heterocysts. This results in a heterocyst cell found every 9-15 vegetative cells. Expressions of patS and hetR are carefully controlled.
• The cell gradually enlarges and becomes rounder in shape.
• Granular inclusions decrease.
• Photosynthetic lammele reorients.
• Phycobilisomes, light-harvesting protein complexes that are associated with Photosystem II begin to degrade. Chlorophyll levels also drop. This leads to the degradation and eventual disappearance of Photosystem II from the differentiating cells whereas the concentration of Photosystem I remains approximately the same in developing heterocysts compared to vegetative cells.
• The wall finally becomes triple-layered for additional protection from the external environment. These three layers develop outside the cell's outer layer.
  • The middle layer is homogeneous.
  • The inner layer is laminated.
• Nitrogenases are produced upon the expression of nitrogen-fixation genes.
• The senescent heterocyst undergoes vacuolation and finally breaks off from the filament causing fragmentation. These fragments are called hormogonia and undergo asexual reproduction.
• Heterocyst formation is complete after 20-30 hours.

The cyanobacteria that form heterocysts are divided into the orders Nostocales and Stigonematales, which form simple and branching filaments respectively. Together they form a monophyletic group, with very low genetic variability.

References

Category:Nitrogen cycle Category:Cyanobacteria Mabelz97 (talk) 06:53, 9 October 2017 (UTC)Mabelz97

Mabel Zhang's Peer Review

Mable edited the article Heterocyst, providing more detail on the sequences that occur during the formation of these specialized cells. The structure is well balanced, as she extends on key concepts by adding bullet points intermittently between those already established in chronological order.

Her content is also appropriate for the original article. Mabel draws on the introductory paragraph in that section, referring back to the patS enzyme previously mentioned. The new content appears to have no bias and is stated factually.

Mabel’s writing is fairly concise (bullet points) and flows well. She uses simple language to explain several terms, such as 2-oxoglutarate and phycobilisomes, making her edits very easy to comprehend. This does add length to her points, but I believe this is valuable in context for understanding the terminology. One explanation that may not be necessary is in the third bullet point, where Mabel describes the function of the hetR and patS enzymes and then provides an example of this. The example may not be necessary if readers can extrapolate how different levels of these enzymes would lead to changes in heterocyst differentiation.

Mabel uses all reliable sources (journal articles) and cites all her edits accordingly. There are quite a few points from one particular source, (7/13 bullet points cite reference 2) so perhaps it would be most important to broaden her sources of information to ensure all viewpoints are accurately represented. The second bullet point describing NtcA is also on the borderline of close-paraphrasing, as the verbs are modified, but the sentence structure is similar to the original article in reference 2. Rewording this bullet point would be important to avoid any potential plagiarism. In general, Mabel’s edits significantly increase the understanding of heterocyst formation to the reader, without being bogged down in jargon and complicated sentence structure.Celina Sewlochan (talk) 01:19, 9 November 2017 (UTC)

Symbiotic Relationships

Anabaena-Azolla

A notable symbiotic relationship is that of Anabaena cyanobacteria with Azolla plants. Anabaena reside on the stems and within leaves of Azolla plants. The Azolla plant undergoes photosynthesis and provides fixed carbon for the Anabaena to use as an energy source for dinitrogenases in the heterocyst cells.. In return, the heterocysts are able to provide the vegetative cells and the Azolla plant with fixed nitrogen in the form of ammonia which supports growth of both organisms.

This symbiotic relationship is exploited by humans in agriculture. In Asia, Azolla plants containing Anabaena species are used as biofertilizer where nitrogen is limiting as well as in animal feed. Different strains of Azolla-Anabaena are suited for different environments and may lead to differences in crop production. Rice crops grown with Azolla-Anabaena as biofertilizer have been shown to result in a much greater quantity and quality of produce compared to crops without the cyanobacteria. Azolla-Anabaena plants are grown before and after rice crops are planted. As the Azolla-Anabaena plants grow, they accumulate fixed nitrogen due to the actions of the nitrogenase enzymes and organic carbon from photosynthesis by the Azolla plants and Anabaena vegetative cells. When the Azolla-Anabaena plants die and decompose, they release high amounts of fixed nitrogen, phosphorus, organic carbon, and many other nutrients into the soil, providing a rich environment ideal for the growth of rice crops.

The Anabaena-Azolla relationship has also been explored as a possible method of removing pollutants from the environment, a process known as phytoremediation. Anabaena sp. together with Azolla caroliniana has been shown to be successful in removing uranium, a toxic pollutant caused by mining, as well as the heavy metals mercury (II), chromium(III), and chromium(VI) from contaminated waste water. 

Category:Nitrogen cycle Category:Cyanobacteria

Category:Nitrogen cycle Category:Cyanobacteria

References

Mabelz97 (talk) 07:37, 20 November 2017 (UTC)

Final Revision

Original - "Heterocyst"

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.

Edits - "Heterocyst"

Symbiotic Relationships

Anabaena-Azolla

A notable symbiotic relationship is that of Anabaena cyanobacteria with Azolla plants. Anabaena reside on the stems and within leaves of Azolla plants. The Azolla plant undergoes photosynthesis and provides fixed carbon for the Anabaena to use as an energy source for dinitrogenases in the heterocyst cells.. In return, the heterocysts are able to provide the vegetative cells and the Azolla plant with fixed nitrogen in the form of ammonia which supports growth of both organisms.

This symbiotic relationship is exploited by humans in agriculture. In Asia, Azolla plants containing Anabaena species are used as biofertilizer where nitrogen is limiting as well as in animal feed. Different strains of Azolla-Anabaena are suited for different environments and may lead to differences in crop production. Rice crops grown with Azolla-Anabaena as biofertilizer have been shown to result in a much greater quantity and quality of produce compared to crops without the cyanobacteria. Azolla-Anabaena plants are grown before and after rice crops are planted. As the Azolla-Anabaena plants grow, they accumulate fixed nitrogen due to the actions of the nitrogenase enzymes and organic carbon from photosynthesis by the Azolla plants and Anabaena vegetative cells. When the Azolla-Anabaena plants die and decompose, they release high amounts of fixed nitrogen, phosphorus, organic carbon, and many other nutrients into the soil, providing a rich environment ideal for the growth of rice crops.

The Anabaena-Azolla relationship has also been explored as a possible method of removing pollutants from the environment, a process known as phytoremediation. Anabaena sp. together with Azolla caroliniana has been shown to be successful in removing uranium, a toxic pollutant caused by mining, as well as the heavy metals mercury (II), chromium(III), and chromium(VI) from contaminated waste water. 

Category:Nitrogen cycle Category:Cyanobacteria

Category:Nitrogen cycle Category:Cyanobacteria

References

Mabelz97 (talk) 07:42, 20 November 2017 (UTC)