User talk:Ben willox/sandbox

Assignment 3

Since the article I am editing does not have any sub sections, I will be creating a sub section on Industry Applications

Original- "Lignin-modifying enzymes"

Lignin-modifying enzymes (LMEs) are various types of enzymes produced by fungi that catalyze the breakdown of lignin, a biopolymer commonly found in the cell walls of plants. The terms ligninases and lignases are older names for the same class, but the name "lignin-modifying enzymes" is now preferred, given that these enzymes are not hydrolytic but rather oxidative (electron withdrawing) by their enzymatic mechanisms. LMEs include peroxidases, such as lignin peroxidase (EC 1.11.1.14), manganese peroxidase (EC 1.11.1.13), versatile peroxidase (EC 1.11.1.16), and many phenoloxidases of the laccase type.

LMEs have been known to be produced by many species of so-called white rot basidiomycetous fungi, including: Phanerochaete chrysosporium, Ceriporiopsis subvermispora, Trametes versicolor, Phlebia radiata, Pleurotus ostreatus and Pleurotus eryngii.

LMEs are produced not only by wood-white rotting fungi but also by litter-decomposing basidiomycetous fungi such as Agaricus bisporus (common button mushroom), and many Coprinus and Agrocybe species. The brown-rot fungi, which are able to colonize wood by degrading cellulose, are not able to produce LMEs.

Some results on LME-type of peroxidases have also been reported for some species of filamentous bacteria such as Streptomyces viridosporus T7A, Streptomyces lavendulae REN-7 and Clostridium stercorarium.

However, efficient lignin and lignin-like polymer degradation is only achieved by fungal LME peroxidases, and laccases in combinations with organic charge transfer mediator compounds. Laccases are more widely distributed enzymes belonging to the multicopper oxidase (MCO) superfamily encompassing all three domains of life (bacteria, archaea, eukarya).

LMEs and cellulases are crucial to ecologic cycles (for example, growth/death/decay/regrowth, the carbon cycle, and soil health) because they allow plant tissue to be decomposed quickly, releasing the matter therein for reuse by new generations of life.

Edit- "Lignin-modifying enzymes"

Lignin-modifying enzymes (LMEs) are various types of enzymes produced by fungi that catalyze the breakdown of lignin, a biopolymer commonly found in the cell walls of plants. The terms ligninases and lignases are older names for the same class, but the name "lignin-modifying enzymes" is now preferred, given that these enzymes are not hydrolytic but rather oxidative (electron withdrawing) by their enzymatic mechanisms. LMEs include peroxidases, such as lignin peroxidase (EC 1.11.1.14), manganese peroxidase (EC 1.11.1.13), versatile peroxidase (EC 1.11.1.16), and many phenoloxidases of the laccase type.

LMEs have been known to be produced by many species of so-called white rot basidiomycetous fungi, including: Phanerochaete chrysosporium, Ceriporiopsis subvermispora, Trametes versicolor, Phlebia radiata, Pleurotus ostreatus and Pleurotus eryngii.

LMEs are produced not only by wood-white rotting fungi but also by litter-decomposing basidiomycetous fungi such as Agaricus bisporus (common button mushroom), and many Coprinus and Agrocybe species. The brown-rot fungi, which are able to colonize wood by degrading cellulose, are not able to produce LMEs.

Some results on LME-type of peroxidases have also been reported for some species of filamentous bacteria such as Streptomyces viridosporus T7A, Streptomyces lavendulae REN-7 and Clostridium stercorarium.

However, efficient lignin and lignin-like polymer degradation is only achieved by fungal LME peroxidases, and laccases in combinations with organic charge transfer mediator compounds. Laccases are more widely distributed enzymes belonging to the multicopper oxidase (MCO) superfamily encompassing all three domains of life (bacteria, archaea, eukarya).

LMEs and cellulases are crucial to ecologic cycles (for example, growth/death/decay/regrowth, the carbon cycle, and soil health) because they allow plant tissue to be decomposed quickly, releasing the matter therein for reuse by new generations of life.

Industry Application

Lignin-modifying enzymes have been actively used in the paper and pulp industry for the last decade. They were first used in this industry after they were discovered to have both detoxifying and decolorizing properties. Although these enzymes have been applied to industry for the last ten years, optimal and robust fermentative processes have not been established. There is an area of active research as scientists believe that, the lack of optimal conditions for these enzymes are limiting industrial exploitation.

Lignin-modifying enzymes benefit industry as they can break down lignin; a common waste product of the paper and pulp industry. These enzymes have been used in the refinement of poplar. Lignin inhibits the enzymatic hydrolysis of treated poplar and Lignin-modifying enzymes can efficiently degrade the lignin thus fixing this problem. Another use of lignin modifying enzymes is the optimization of plant biomass use. Lignin is relatively inert towards degradation yet Lignin-modifying enzymes can effectively break it down into other aromatic compounds. The lack of these enzymes would result in the accumulation of huge amounts of waste products. Lignin-modifying enzymes were initially used for the bleaching of waste effluent. With regards to pulp bleaching there are now several patented processes that make use of these enzymes, many of which are still under development.

Ben willox (talk) 01:05, 9 October 2017 (UTC)

Assignment 2

Lignin-modifying enzymes - Article improvement

Lignin-modifying enzymes are an area of high notability that have poor coverage on Wikipedia. There are numerous ongoing studies into the topic, among them is the prevalence of these enzymes in bacteria and even their applications to industry. A study by Gonzalo et al. from 2016 details the applications of lignin-modifying enzymes to the paper and pulp industry, an actively growing area of manufacturing that has an estimated revenue of 317 Billion USD annually. It is likely that a great deal of research funding will continue to come out of this industry.

The page is short and does not contains sections, however there are multiple problems with the content. Firstly is the lack of citations; there is not a single citation in the entire page. When editing the page, citations will have to be filled in and sources will have to determined.

The Lignin-modifying enzyme page is missing information on much of the current active research topics in the field. This includes the details of lignin-modifying enzymes being found in bacteria and the subsequent genes encoding them. While the original article only states that lignin-modifying enzymes are present and less efficient in bacteria, this article clearly details the differences in lignin-modifying enzymes in bacteria and fungi and gives the different binding sensitivities as well as mechanistic differences; both of which would be an excellent addition to the original page.

The original article on lignin-modifying enzymes has no information on industry applications. Considering this may be the source of funding for much of the research into these enzymes, this section is highly relevant. Research from 1994 shows that lignin-modifying enzymes have applications in breaking down the major waste products of paper and pulp mills. The mechanism in which it does this will also be relevant to the section. Lignin-modifying peroxidases also have applications in the bleaching of paper.

Ben willox (talk) 16:46, 27 September 2017 (UTC)

References

Assignment 1

Peptidoglycan Article Critique

Although the majority of facts in this article are supported by an appropriate reference, the section on peptidoglycan structure is lacking many citations. The opening paragraph detailing the connectivity of the peptidoglycan structure has no citations. This section could be improved by adding references to reliable sources such as academic publishers in order to verify the information.

The first source cited in this article is a website called pharmaxchange.info. The information on the cited page has references, although upon trying to follow them, it appears that they do not exist (the webpage is down or invalid). This website is ad supported, blog style, and it is not clear if it actively checks facts. Also, the article almost directly copies a sentence from pharmaxchange.info with only a slight change, visible below:

"The peptide chain of one strand can be cross-linked with the peptide chain of another strand forming a mesh like network." The original.

"The peptide chain can be cross-linked to the peptide chain of another strand forming the 3D mesh-like layer." The nearly identical copy.

Plagiarism is an issue here; Paraphrasing from a more reputable source could improve the strength of this article. As well, citation 5 and 9 should be updated with a hyperlink that leads to the respective article.

The page also contains a section titled "Similarity to pseudopeptidoglycan". This section contains mainly information on pseudopeptidoglycan including how it is insensitive to lysozyme and the mechanism behind this resistance, all of which do not apply to peptidoglycan. This material could be on a separate wikipedia page.

Ben willox (talk) 02:12, 16 September 2017 (UTC)

What I learned - Article Critique

Through the evaluation of the article on peptidoglycan I learned how to analyze article sources for bias. Before this assignment, when I would check an article for bias, I would not check the actual cited sources for bias as well.

I also learned the basic questions I should ask myself when I go through the process of editing an article. Starting with checking if each fact is sourced and going trough each individual source to check for bias as well as validity.

Ben willox (talk) 02:17, 16 September 2017 (UTC)

Ben's Peer Review

The edited content reflects valuable and relevant information regarding the applications of lignin-modifying enzymes not previously covered in the article. Its placement is appropriate, as the rest of the article focuses solely on the enzymes themselves. Applications should follow general description for proper understanding.

The references are mostly from scientific journals with each idea from a different article, suggesting reliability and balance. Statements are sourced and can be found within the sources provided, though are not closely paraphrased. (Source [3] mentions “…the lignin component still inhibited enzymatic hydrolysis…”. The edited content phrases this differently). One could add more sources for credibility, though it is not necessary. All content is neutral with no attempt to persuade.

The flow of the edited content is good, though there are some areas for improvement: Most of the applications have an explanation regarding their importance; however, a description or link to the significance of detoxifying and decolorizing properties in the paper and pulp industry could be provided. It is currently unclear why one would need these properties. This was done well for fermentative processes, the breaking down of lignin, and plant biomass use optimization.

The content is well-structured and contains appropriate explanations; however, the content within the second paragraph could be broken into smaller sections. Paper and pulp, optimization of plant biomass use, and bleaching all seem to be separate ideas and could be separate paragraphs, each with a few descriptive sentences. This would provide clearer distinctions between the each of the enzyme applications and their contributing properties. If one property contributes to several applications, consider making the property its own paragraph.

Reading may flow more easily with a rarer use of “lignin” in the second paragraph. If the word can be removed in certain sentences (LME), try doing so. Otherwise, the language is straightforward.

Word Count: 300

Alexandra.Roine (talk) 06:51, 9 November 2017 (UTC)