User talk:Dbb5012/sandbox

MICB 301 – Wikipedia Assignment

Name: Junbo (Bryan) Wang

Article Name: Peptidoglycan

1. Citations

Generally speaking, most of the presented facts are supported by appropriate and reliable references. For example, the comment about MreB proteins is supported by one academic journal and two papers that place MreB as the centerpiece of discussion. Very few facts are supported by less reliable sources as in the case of the comment made on NAM and NAG sugars, which was based on a blog post. The article shows little signs of plagiarism and closed paraphrasing. While some references can be looked up in literature databases, not all of them are assigned working hyperlinks.

2. Content

The article discusses the structure and biosynthesis of peptidoglycan in great depths while placing a lighter emphasis on inhibition and pseudopeptidoglycan.

The article excels at providing a good overview of Peptidoglycan without expressing any biases towards a particular position. Viewpoints presented were generally neutral and equally represented. The subjects of antibiotic (i.e. Penicillin) and antibiotic resistance (i.e. transpeptidase mutations) are brought up very briefly near the end of “Inhibition”. A potential revision could extend the discussion of peptidoglycan structure to the role of peptidoglycan in bacterial virulence and its susceptibility to antibiotic treatments.

3. Revisions

One Wikipedia contributor pointed out that gram-staining was overlooked in one of the earlier versions of the article. There was also a comment about whether or not it was necessary to supplement the discussion of peptidoglycan structure and sugar cross-linking with diagrams. Both of these issues were adequately addressed shortly after being brought to attention.

Dbb5012 (talk) 21:04, 16 September 2017 (UTC)

MICB 301 – Wikipedia Article Critique for Methanogen (Assignment #2)

Submitted by: Bryan Wang (10486158)

Methanogens are organisms of the domain Archaea whose role in ecological and industrial processes such as methane emission and waste water treatment, respectively, is just beginning to materialize. It was during the discussion of global warming when the organism’s relevance was fully realized. Before we are able harness the machineries of methanogens and utilize them for human purposes, it is necessary to obtain an adequate understanding of the lifestyle of methanogens. And at the core of methanogen lifestyle, like that of any other organism, is metabolism, the collective chemical reactions that sustain life.

The current ratings of the Wikipedia article reflect the level of work that is needed to be put into revising the piece. As many Talk users have mentioned, the article needs significant re-organization and can be perhaps formatted in a way that is similar to “Achaea”, a featured Wikipedia article with excellent structure. Most importantly, previous Talk users have pointed out that details relevant to methanogen lifestyle lack depth. Metabolism is one of those details that requires further explanation.

Two important aspects of metabolism in methanogens that the current article does not discuss in depth are the methanogenic reactions associated with different substrates and the role of coenzymes in the anaerobic oxidation of methane. For example, the article does not elaborate on the current literature finding that while methanogens are capable of using H2/CO2, formate, methanol, methylamines and acetate as sources of energy, they do so using different enzymes, coenzymes, via different reaction mechanisms, and producing different intermediates with varying thermodynamic stabilities.

For instance, the very first step of H2/CO2 methanogenesis is catalyzed by formylmethanofuran dehydrogenase, producing the stable intermediate CO2-methanofuran. The complexity of this reaction arises due to the dependency of formylmethanofuran dehydrogenase to H2 reduction as well as its endergonic nature – the enzyme cannot directly use the elections of H2 without some kind of hydrogenase “mediator” where elections from H2 are first transferred to the hydrogenase and then donated to the formylmethanofuran-dehydrogenase-catalyzed reaction. A potential revision to the Wikipedia article would include a detailed biochemical description like the one I had provided for CO2-methanofuran formation.

Dbb5012 (talk) 00:58, 26 September 2017 (UTC)

Original- "Methanogens"

Fermentative metabolism

The understanding of methanogen metabolism has progressed steadily since the 1930s.

Although most marine biogenic methane is the result of carbon dioxide (CO₂) reduction, a small amount is derived from acetate (CH₃COO⁻) fermentation.

In the fermentation pathway, acetic acid undergoes a dismutation reaction to produce methane and carbon dioxide:

CH₃COO⁻ + H⁺ → CH₄ + CO₂       ΔG° = -36 kJ/reaction

This disproportionation reaction is enzymatically catalysed. One electron is transferred from the carbonyl function (e⁻ donor) of the carboxylic group to the methyl group (e⁻ acceptor) of acetic acid to respectively produce CO₂ and methane gas.

Archaea that catabolize acetate for energy are referred to as acetotrophic or aceticlastic. Methylotrophic archaea utilize methylated compounds such as methylamines, methanol, and methanethiol as well.

Dbb5012 (talk) 16:18, 8 October 2017 (UTC)

Dbb5012's peer review

The edit consists of a new section on methane production. The placement of the new section is logical since it follows the fermentative metabolism section and is about another type of metabolism. The content describes the main points of methane production without veering off-topic and contains relevant details on the reactions (eg. free-energy change, coenzymes involved). However, the "H2/CO2 Methanogenesis" section starts by delving into dense information about the reaction mechanism. Adding a brief overview on H2/CO2 methanogenesis - a mention of its ecological impact, abundance in the methanogen community, or a list of some methanogens that use H2/CO2 methanogenesis - and adding another subheading for the mechanism would aid in creating a clearer lead and structure for the section, making it easier for readers to understand.

The writing is concise and neutral, with no identifiable instances of close paraphrasing. Many terms are linked to other Wikipedia articles - this makes it easier to understand the content and access related information if needed. The reaction mechanism descriptions contain relevant information, however, the language is dense and the steps are difficult to follow, especially since the topic is complex. Since the paragraphs are already written in a step-wise manner, the addition of the chemical equation of each step before the step’s explanation (or a picture of all the steps in the beginning of the section) would aid in making the reaction details more clear and understandable for more readers, thus making it easier to read.

There are sentences about the reaction mechanism in the first three paragraphs under the subheading without citations, even though the articles used to write these are cited later. Citations should be added after each sentence that contains information from other sources in order to give credit and avoid plagiarism. Also, adding the links for the journals used in the citations would make the citations more complete and accessible. The nine sources that are used are peer-reviewed (which means the edits are more reliable), are from a variety of different journals, and are not reused multiple times in close proximity - they're well balanced. -A hashimi (talk) 01:38, 6 November 2017 (UTC)