User talk:Miaoran Li/sandbox

Critique for Response Regulator

Eight scientific papers are used as references in this article. But two of the references in this article are not appropriate. The picture of the crystal structure of yeast proteins from the reference is different from the one on the website. Even though the descriptions of both pictures are similar, the colors of proteins and positions of certain ions do not match each other. A reference with the same picture should be given.

A sentence in Function section is " there is very little cross-talk between different two-component signaling systems in the same cell". , and the original sentence from the reference is "Unlike eukaryotic signaling networks, there is very little crosstalk between bacterial TCS(two component signaling) pathways". The sentence from Wikipedia is not paraphrased well, and the content now is not the same as the reference's. For instance, "the same cell" is not accurate, which could make the sentence confusing.

The article is relatively neutral, but there is one reference that has been used six times. This may affect the reliability of the article. The information for the function and classification of the response regulator is underrepresented. The functions should be described in the perspective of response regulator not histidine kinase, and there should be more functions about functions of effector domains.

For classification, the one based on domain architecture should be mentioned with more details. The reference article provides details about different types of response regulator based on the domains, such as response regulator with DNA-binding, RNA-binding, and enzymatic output domains. It is better to show how these two systems separate various response regulators.

Miaoran Li (talk) 23:01, 17 September 2017 (UTC)

Critique for Green Sulfur Bacteria
This article gives general information about the classification, metabolism, genomes, and distributions of green sulfur bacteria. For the metabolism part, more details should be obtained to describe photosynthesis pathway in the bacterial cells, and the roles of the bacteria in sulfur cycle. The article also talks about the locations of two species, GSB1 and Chlorobium ferrooxidans. This may help people to have an understanding of bacterial distributions, but these two examples are extreme, and not many details have been provided to explain why they also exist in these areas. The demonstration of these species may not be necessary for this topic.

The eight sources for citations in the article are both scientific and reliable. But there are some sentences that are not related to the cited sources. In the first paragraph, it says "Together with the non-photosynthetic Ignavibacteriaceae, they form the phylum Chlorobi." There is no information about Ignavibacteriaceae in the original article of citation. The description of phylum chlorobi is also controversial. LPSN (List of prokaryotic names with standing in nomenclature shows that phylum Chlorobi includes class Chlorobea, Dehalococcoida and Ignavibacteria. This means that not just Ignavibacteria and Chorobea in the phylum Chlorobi. A source with evidence that can prove this sentence is required. Another sentence in the first paragraph "Most closely related to the distant Bacteroidetes, they are accordingly assigned their own phylum." is not interpreted in the same way as the source. The source says "In contrast to the extraordinary richness of cyanobacterial diversity, the phylum Chlorobi (comprising the green sulfur bacteria) is a metabolically limited, physiologically well-defined and genetically closely related bacterial group, which shares a common root with the Bacteroidetes." Even though both sentences demonstrate closed connection between green sulfur bacteria and Bacteroidetes, the source does not provide any information about bacterial phylum. This is considered to be a bias caused by editors' own understanding of the source material. Another source with evidence that green sulfur bacteria form their own phylum even though they are highly related to Bacteroidetes is required in this case. The taxonomy section uses NCBI as reference, but the website of NCBI claims that "the NCBI taxonomy database is not an authoritative source of nomenclature or classification." NCBI cannot be considered as a very reliable source for classification. A scientific literature about taxonomy should be used as reference in this case.

This article is not very notable because few deficiencies exists in significant coverage and reliable sources, and no assumption is created in the article. But the article is quite independent of the subject since all the information is related to the topic.Miaoran Li (talk) 06:04, 28 September 2017 (UTC)

Editing "Green sulfur bacteria"
Original "Green sulfur bacteria"

The green sulfur bacteria (Chlorobiaceae) are a family of obligately anaerobic photoautotrophic bacteria. Together with the non-photosynthetic Ignavibacteriaceae, they form the phylum Chlorobi. Most closely related to the distant Bacteroidetes, they are accordingly assigned their own phylum.

Edit "Green sulfur bacteria"

Together with the non-photosynthetic Ignavibacteriaceae and Dehalococcoida, they form the phylum Chlorobi. The phylum Chlorobi (comprising the green sulfur bacteria) is related to the Bacteriodetes which shares a common ancestor with the Chlorobi.

Original "Green sulfur bacteria"

Photosynthesis is achieved using a Type 1 reaction centre using bacteriochlorophyll (BChl) a and in chlorosomes which employ BChl c, d, or e; in addition chlorophyll a is also present.

Edit "Green sulfur bacteria"

Photosynthesis is achieved by several steps. BCHl c, d and e of the cells absorb light at 720-750 nm, and the light energy is transferred to BChl a-795 and a-808 before being transferred to Fenna-Matthews-Olson (FMO)-proteins which are connected to reaction centers (RC). The FMO complex then transfers the energy to RC in the plasma membrane where BChl a-840 and Chl a-670 work as the primary electron donor and the primary electron acceptor respectively.

Original "Green sulfur bacteria"

A species of green sulfur bacteria has been found living near a black smoker off the coast of Mexico at a depth of 2,500 m in the Pacific Ocean. At this depth, the bacterium, designated GSB1, lives off the dim glow of the thermal vent since no sunlight can penetrate to that depth.

Green sulfur bacteria appear in Lake Matano, Indonesia, at a depth of about 110–120 m. The population may include the species Chlorobium ferrooxidans.

Edit "Green sulfur bacteria"

Green sulfur bacteria can be found in many shallow freshwater, marine sedimentary environments and many meromictic lakes. For example: A species of green sulfur......

Green sulfur bacteria appear in Lake Matano,......

Original "Green sulfur bacteria"

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)

Edit "Green sulfur bacteria"

Delete the source of NCBI because it is not reliable. The information for the taxonomy is all from LSPN. Miaoran Li (talk) 02:37, 9 October 2017 (UTC)

Miaoran's Peer Review
For the most part, the edited material is appropriately placed within the lead. Good changes were made to the second sentence, correcting which families belong to the Chlorobi phylum. However, I would suggest that the additional details added on the steps of photosynthesis and the specific components involved could be added in a new section named Mechanism of Phototrophy instead of the lead. These details can make the lead a bit more difficult to understand especially without an image of the phototrophic apparatus. Also, the edit about the habitats of GSB is a good addition of content to the article. I suggest that instead of adding this information to the end of the lead, to add it in the beginning, near the sentence describing the motility of GSB. This will allow reader to get more general info about GSB in the beginning. Overall, the content added is relevant to the article. However, I feel like more information could have been added to the lead such as the fact that they use reverse TCA cycle to fix CO2, some general characteristics about structure and its significance. This could allow the reader to get a good grasp of what GSB are just by reading the lead. The edited content is concise and neutral since it does not try to convince the reader. However, in the original article, it is stated that “although only 10 genomes have been sequenced, these are quite comprehensive…”. This statement can be changed as it tries to persuade the reader about the significance of the 10 sequenced genes and thus is not neutral. The sources used are reliable. Most sources are journal articles and one of them is the LSPN website which also reliable. Also, many sources are used, contributing to the article’s reliability. Overall, more general information can be added in the lead for better understanding of GSB. Prabhreet Sekhon (talk) 22:39, 7 November 2017 (UTC)

final editing
Introduction

Together with the non-photosynthetic Ignavibacteriaceae and Dehalococcoida, they form the phylum Chlorobi. The phylum Chlorobi (comprising the green sulfur bacteria) is related to the Bacteriodetes which shares a common ancestor with the Chlorobi.

The green sulfur bacteria are also autotrophic. They fix CO2 through reverse TCA cycle which is driven in the reductive direction by using ATP. There are several enzymes involved in this process to allow the reversal of the oxidative TCA cycle.

The habitats of green sulfur bacteria are shallow freshwater, marine sedimentary enviroments and many meromictic lakes. For examples:

Photosynthesis in the Green Sulfur Bacteria

The green sulfur bacteria use PS I for photosynthesis. Thousands of bacteriochlorophyll(BCHl) c, d and e of the cells absorb light at 720-750 nm, and the light energy is transferred to BChl a-795 and a-808 before being transferred to Fenna-Matthews-Olson (FMO)-proteins which are connected to reaction centers (RC). The FMO complex then transfers the excitemnet to the RC with its special pair which absorbs at 840 nm in the plasma membrane.

After the reaction centers receive the energy, electrons are ejected and transferred through electron transport chains (ETCs). Some electrons form Fe-S proteins in electron transport chains are accepted by ferredoxins (Fd) which can be involved in NAD(P) reduction and other metabolic reactions.

Carbon Fixation of Green Sulfur Bacteria

The reactions of reversal of the osixative tricarboxylic acid cycle are catalyzed by four enzymes :

1. pyruvate:ferredoxin (Fd) oxidoreductase: acetyl-CoA + CO2 + 2Fdred + 2H+ ⇌ pyruvate + CoA + 2Fdox 2.ATP citrate lyase: ACL, acetyl-CoA + oxaloacetate + ADP + Pi ⇌ citrate + CoA + ATP 3.α-keto-glutarate:ferredoxin oxidoreductase: succinyl-CoA + CO2 + 2Fdred + 2H+ ⇌ α-ketoglutartate + CoA + 2Fdox 4.fumarare reductase succinate + acceptor ⇌ fumarate + reduced acceptor --Miaoran Li (talk) 22:32, 19 November 2017 (UTC)