User talk:Sophiaszy/sandbox

Assignment 1
The article I am critiquing is Response Regulator

Although most facts have references from academic journals, sources such as Stock et al’s study from 2000 may contain out-dated information. For the first paragraph, matching facts with corresponding references may be difficult as all citations occur at the end of the paragraph. Overall, only eight sources are cited, with some acting as references for multiple facts, and this limited number of sources make the article less reliable. The article contain excessive details on histidine kinase that can be moved to the page for two component signaling system; only information on its interaction with response regulator should be kept. Under ‘Function’, since the mechanisms by which response receptor (RR) gets activated is important, this information should have more than one reference for accuracy. Also, the second last paragraph simply points to the fact that phosphoaspartate is unstable but does not elaborate on its significance and its effect on RR functions. The last paragraph discussing the high specificity of RR should not be placed under ‘Function’; one possible fix is to include an additional section named ‘Specificity’. Under ‘Classification’, one example should be provided for each of the three classes to provide evidence that each class contains at least one RR. Information on RR variations (over 4000 RRs have been identified) and examples of common RRs (“regulators of the OmpR, MarL, and MtrC families”) can be provided (Galperin 2006). The fact that RR is defined by “the presence of a receiver domain” should also be mentioned in the article (Bourret 2011).

Sophiaszy (talk) 07:22, 17 September 2017 (UTC)

Assignment 2
Assignment #2: the article I am critiquing is Betaproteobacteria

Betaproteobacteria is a diverse class of bacteria that belongs to the largest phylum of the domain Bacteria – Proteobacteria (Marin 2011). This class contains over 200 species (Dworkin et al 2006) and interacts with human due to both its pathogenicity and economic importance, giving this topic high notability. Since betaproteobacteria cause disease in humans, knowledge of their mode of metabolism will enable scientists to better understand how betaproteobacteria interact with humans, and possibly, ways to prevent betaproteobacteria-caused diseases. Betaproteobacteria are also economically important for processes such as biodegradation through nitrification (Prasad et al 2015). One section I am critiquing is ‘Role in diseases’, because the section is poorly cited and requires more details. Although five different diseases are mentioned in this section, there is only one source provided (Dworkin et al 2006), making this section less reliable. It is also unclear which diseases the source provides direct evidence for. I will add references for each example to increase the reliability. Furthermore, although specific diseases are mentioned, there is no information on how this group of bacteria generally cause disease in humans. This section can be improved by listing the characteristics of some betaproteobacteria that enable them to cause diseases, such as N. meningitidis’s capsule (Spinosa et al 2006) and N. gonorrhoeae’s pili (Craig et al 2004). This will allow readers to see some types of virulence factors present in betaproteobacteria without reading more about specific bacteria. Additionally, the first paragraph mentions that betaproteobacteria participate in soil nitrification and wastewater treatment, but there is no further elaboration on the processes. I will add a section named ‘Economic Importance’ to provide further evidence. This section will briefly list several species of Betaproteobacteria, such as Nitrosomonas and Nitrobacter (ECOS), that participate in wastewater nitrification. This will back up the claim that some bacteria in this class participate in these processes. Also, the processes will be briefly described, such as how Nitrosomonas is used to degrade ammoniacal nitrogen in the first stage of nitrification (Prasad et al 2015). The addition of this section will allow readers to better understand how betaproteobacteria provide economic benefits.

Sophiaszy (talk) 06:35, 28 September 2017 (UTC)

Assignment 3
Original - Betaproteobacteria

Did not contain a section on economic importance

Edit - Betaproteobacteria

Economic Importance
Ammonia buildup in aquatic environments due to heavy industrialization could lead to eutrophication, and biological methods to remove excessive ammonia is dependent on microorganisms that undergo nitrification and denitrification. Wastewater treatment plants can utilize two species in Betaproteobacteria - Nitrosospira sp. and Nitrosomonas sp. - to remove ammonia from waste water through ammonia oxidation. After ammonia is oxidized to nitrite by Nitrosomonas sp., another species in Betaproteobacteria - Nitrobacter sp. - can further oxidize nitrite into nitrogen through denitrification.

Sophiaszy (talk) 22:50, 8 October 2017 (UTC)

Peer Review Assignment
A noteworthy point: edits for the article were made under the “Talk Page” instead of the “User Page”. With that out of the way, the first point of concern becomes immediately obvious as Sophia never indicated where her “Economic Importance” section would be situated in the original article. Would it be the last section, or would it fall somewhere in between? Not knowing that it is hard to critique the overall structure of the article with the new edits in mind. Nonetheless, I do agree with the addition of this section to the article. Assignment 2 goes into detail regarding this addition. While on the topic of assignment 2, it is important to mention that none of the improvements outlined in that assignment actualized except the addition of “Economic Importance” section.

When looking at the content under “Economic Importance”, the main idea is the use of different species of Betaproteobacteria to treat waste water and avoid eutrophication. This is well supported by the literature, and is presented in a balance and neutral way. However, given the title of the section and the scale of this problem, it would have been advisable to dedicate more time to explain the processes in more detail, present examples of where Nitrosospira sp. and Nitrosomonas sp. have been implemented, and most importantly the economical outcomes of such applications.

The writing for the most part is concise and flows smoothly. There are however some issues with respect to the grammar and punctuation. For instance, “is” after “excesses ammonia” in the first sentence has to be “are”. In the second sentence, the dashes used to separate “Nitrosospira sp. and Nitrosomonas sp.” are hyphens. They instead have to be changed to either en or em dashes. One last point, in the aforementioned sentence it is not indicated whether “Nitrosospira sp. and Nitrosomonas sp.” are the only Betaproteobacteria species in charge of waste water treatment, or simply an example of a wider range of species. One reader might assume that they are the only ones; which if that is the case it is good to indicate it.

The citations for this edit are quite good. The statements are sourced often with accuracy, and show no signs of plagiarism or close paraphrasing. It is a shame however, that only a superficial level of information was drawn from the reliable and wide gamut sources that were presented.

Farshad.F (talk) 07:50, 9 November 2017 (UTC)

Economic Importance
Various human activities, such as fertilizer production and chemical plant usage, release significant amounts of ammonia into the freshwaters and the seas. Ammonia buildup in aquatic environments due to heavy industrialization is potentially dangerous because high aquatic ammonia content could lead to eutrophication. Biological wastewater treatment systems, as well as other biological ammonia-removing methods, depend on the metabolism of certain groups of Betaproteobacteria that undergo nitrification and denitrification to remove excessive ammonia from wastewater. For example, Betaproteobacteria is predominant in the microbial community of a membrane bioreactor for wastewater treatment, with 13 genera in the class identified in the bioreactor. These processes decrease the ammonia content in the wastewater to tolerable limits before the treated wastewater is released into the environment.

Wastewater treatment plants (WWTPs) utilize different species of Betaproteobacteria to remove ammonia from wastewater by converting ammonia to nitrogen gas. Nitrobacter sp. is an example of the Betaproteobacteria that are used in a wastewater treatment plant at Thizy. WWTPs often rely on ammonia-oxidizing bacteria to collaboratively oxidize ammonia to nitrate via nitrification. For example, Nitrosomonas sp. is an autotrophic betaproteobacterium that is commonly used in the WWTPs in Tokyo to oxidize ammonia to nitrite. Nitrite-oxidizing Betaproteobacteria such as Nitrosospira sp. and Nitrobacter sp. can subsequently oxidize nitrite to nitrate. The final step after ammonia have been fully oxidized to nitrate is denitrification. Nitrate-reducing bacteria in WWTPs can reduce nitrate to nitrogen gas, which is able to diffuse out of wastewater. Rhodocyclales is a betaproteobacterial denitrifier found in multiple WWTPs in China.

Sophiaszy (talk) 08:17, 19 November 2017 (UTC)