User talk:Deelye/sandbox

Assignment 1 - Peptidoglycan
When reviewing the contents of the peptidoglycan article, there are numerous citation-related errors that results in the article having potentially unreliable and biased information. With that being said there are incorrect hyperlinks leading to undesired page links, taking citations 5 and 9 as an example. As such, there creates difficulties in attempting to verify the information referenced, and almost facilitates the need to remove some of the content found within the article. In addition, when stating that peptidoglycan as one of the most important D-amino acids, there is a lack of proper referencing to support that argument, and should be revised with reliable sources to back up the claim to avoid persuasive tones within the article. Furthermore, given that biosynthesis section is largely emphasized throughout the article, there is only one source utilized to reference the bulk of the material, and therefore subject to bias. To emphasize, the biosynthesis section may contain non-neutral, unbalanced arguments over the manner in which peptidoglycan is synthesized, even if from a reputable source. Additionally, given that the functions of peptidoglycan are noted within the lead of the article, there lacks any relevant section dedicated towards explaining the importance of how and why these functions are essential for bacterial survivability. As a suggestion, there should be a new subsection introduced primarily for this reason, as the information can help provide further insight upon the importance of the biosynthesis and inhibition processes of peptidoglycan in bacterial species, which are already found in the article. --Deelye (talk) 06:32, 18 September 2017 (UTC)

Assignment 2 - Dehalococcoides
Given that dehalococcoides plays a vital part in various bioremediation processes, in addition to our relatively uncertain understanding of the metabolic pathways involved, extensive research has generated high notability for this article. In many cases, analysis of various metabolic pathways involving carbon metabolites, dehydrogenases, and the reductive dehalogenases have been the target of many research studies involving dehalococcoides. In general, dehalococcoides have generated large publicity due to their bioremediation potential against common anthropogenic halogenated compounds, which often act as pollutants. As such, various research results have been compiled through reliable journal sources, each presenting results independent of the subject.

However, within the “Activities” and “Application” sections of the article, although there are some references that encompasses key developments extrapolated from research results, there is a lack of context behind the statements proposed. In this sense, the article emphasizes the unique capacity of dehalococcoides to perform reductive dehalogenation on specific recalcitrant compounds, in comparison to other bacterial species. Nonetheless, the article lists specific components (i.e. H2 electron donors) that are related towards the metabolic functions of dehalococcoides, yet fails to provide an appropriate rationale for why or how these selective components are to be utilized. Admittedly, many of the metabolic pathways involved with dehalococcoides are still unbeknownst to us. However, additional research conducted should be referenced within the article, in order to provide further insight upon metabolic relationships by examining localization patterns of hydrogenase and reductive dehalogenases, as well as carbon metabolism pathways. Furthermore, the article builds upon the transformation of halogenated compounds, and strictly praises the potential applications of dehalococcoides for bioremediation tactics utilized in contaminated soil and groundwater. However, there is insufficient detail about the dangers associated with applications of dehalococcoides haphazardly without understanding the metabolic mechanisms behind them. Rather, content should be included that discusses the importance of understanding the ecophysiology of dehalococcoides, as the presence of varying environmental factors (i.e. nutrient availability) can and will affect the quality of bioremediation tactics. For example, dechlorinating activities can have altered results in the presence of multiple dechlorinating microorganisms. Additionally, various strains of dehalococcoides have shown to have different dechlorination tendencies. --Deelye (talk) 23:48, 27 September 2017 (UTC)

Original - Dehalococcoides
Dehalococcoides are obligately organohalide-respiring bacteria, which means that they can only grow by using halogenated compounds as electron acceptor. They use hydrogen as an electron donor. Energy is generated by transferring electrons from hydrogen to the halogenated electron acceptor. To synthesize cell material Dehalococcoides strains additionally need actate.

Dehalococcoides can transform many highly toxic and/or persistent compounds that are not transformed by any other known bacteria. This included tetrachloroethene (PCE) and trichloroethene (TCE) which is transformed to the non-toxic ethene, chlorinated dioxins, benzenes, PCBs, phenols and many other aromatic substrates.

Activities
Dehalococcoides are obligately organohalide-respiring bacteria, which means that they can only grow by using halogenated compounds as electron acceptors. Currently, hydrogen (H2) is often regarded as the only known electron donor to support growth of dehalococcoides bacteria. However, studies have shown that utilizing various electron donors such as formate, and methyl viologen , have also been effective in promoting growth for various species of dehalococcoides. In order to perform reductive dehalogenation processes, electrons are transferred from electron donors through dehydrogenases, and ultimately utilized to reduce halogenated compounds, many of which are human-synthesized chemicals acting as pollutants. Furthermore, it has been shown that a majority of reductive dehalogenase activities lie within the extracellular and membranous components of D. ethenogenes, indicating that dechlorination processes may function semi-independently from intracellular systems. Currently, all known dehalococcoides strains require acetate for producing cellular material, however, the underlying mechanisms are not well understood as they appear to lack fundamental enzymes that complete biosynthesis cycles found in other organisms.

Applications
Dehalococcoides can uniquely transform many highly toxic and/or persistent compounds that are not transformed by any other known bacteria, in addition to halogenated compounds that other common organohalide respirers utilize. For example, common compounds such as chlorinated dioxins, benzenes, PCBs, phenols and many other aromatic substrates can be reduced into less harmful chemical forms. However, dehalococcoides are currently the only known dechlorinating bacteria with the unique ability to degrade the highly recalcitrant, tetrachloroethene (PCE) and tricholoroethene (TCE) compounds into less-toxic forms that are more suitable for environmental conditions, and thus utilized in bioremediation.

Although dehalococcoides have shown to reduce contaminants such as PCE and TCE, it appears that individual species have various dechlorinating capabilities which contributes to the degree of which these compounds are reduced to, which have implications on the effects of bioremediation tactics. For example, particular strains of dehalococcoides has shown preference to producing more soluble, carcinogenic intermediates such as 1,2–dichloroethene isomers and vinyl chloride that contrasts against bioremediation goals, primarily due to their harmful nature. Therefore, an important aspect of current bioremediation tactics involves the utilization of multiple dechlorinating organisms to promote symbiotic relationships within a mixed culture to ensure complete reduction to less-toxic ethene. As a result, studies have focused upon metabolic pathways and environmental factors that regulate reductive dehalogenative processes in order to better implement dehalococcoides for bioremediation tactics. --Deelye (talk) 02:07, 20 November 2017 (UTC)

References