Talk:Cofactor engineering

Untitled
This article is part of an educational assignment for BioE120, taught by proffessor Sriram of the University of Maryland. Please do not make any edits to this article until after May 10, 2011 unless of course you are one of the team members assigned to this particular page.

Thank you.


 * FYI, everything in Wikipedia is a work in progress, and you cannot prevent anyone from editing, their is no WP:Ownership. Fortunately, most of your content is a little to complex for the average reader, so you won't get content changes. However, I will be doing some formatting and style changes, Sadads (talk) 12:19, 17 April 2011 (UTC)

Comments
Group 15 chose to write their Wikipedia article on Cofactor Engineering. Cofactor Engineering is a branch of metabolic engineering in which the organism's metabolic pathways are engineered to enact changes in enzymes that utilize cofactors to catalyze chemical reactions. They start with a brief history of cofactor engineering that mostly details how the cofactors were discovered. Then they go over the tools and processes of Cofactor Engineering, talking about how the enzymes are engineered through the use of recombinant DNA technology to work in a particular fashion with their respective cofactors. Then, they explain what cofactors themselves are. They explain the difference between the inorganic cofactors and organic coenzymes and describe the properties of prosthetic groups. An example of a coenzyme given is vitamin B12 which effects the synthesis and regulation of cellular DNA in addition to the synthesis of fatty acids. The ion Zn2+ is a cofactor that assists carbonic anhydrase in converting carbon dioxide and water into bicarbonate and protons. The majority of the article then focuses on uses and potential applications of cofactor engineering. A yeast modified to use NADH instead of the more expensive NADPH could be used in the wine and beer industry, the citric acid cycle could be modified to increase lycopene, which has been proven to decrease the risk of prostate cancer, cofactor engineering could be used to convert biomass into biofuel, and chemicals could be mass produced by creating cellular “factories”. The team concludes with the “future of cofactor engineering” in which they say the technology could eventually be used to create unique cells that can mass produce specific chemicals from cheaper, more available ones. Thearn182 (talk) 21:48, 11 April 2011 (UTC) (Agrahn1 (talk) 23:26, 11 April 2011 (UTC)). Benlee92 (talk) 00:11, 12 April 2011 (UTC) (Ad kh2 (talk) 03:35, 12 April 2011 (UTC)) (Rakman813 (talk) 21:41, 12 April 2011 (UTC)).

Summary
Group 2: In this article they focus on the processes of cofactor engineering and its uses. The first three sections dealt with the history of cofactor engineering and how it is carried out, while the rest of the article was mainly devoted to the applications in various industries. Cofactor engineering deals with the manipulation of cofactors, non-protein chemical compounds, to alter enzymes which in turn alter metabolic pathways. They conclude with insight into the future of cofactor engineering. Mstamm1 (talk) 23:24, 12 April 2011 (UTC) Mayukoori (talk) 15:01, 13 April 2011 (UTC)

Major Concerns
Group 11: Tools and Processes of Cofactor Engineering section needs to be edited thoroughly for grammar mistakes so the English wording does not take away from the meaning of the article. An extension on the summary would be advised because a little more information is needed to provide the reader with enough information to grasp the entirety of the article. This will help to set-up the article and explain the premise of Cofactor Engineering to the reader and allow the reader to follow the article easier. Zwaisel (talk) 11:14, 12 April 2011 (UTC)

Group 2: - Wikipedia is a database used by "ordinary" people. The article sounded like something more out of a scientific journal rather than an informative article. We suggest explaining concepts more clearly and defining key scientific terms. For example, succinate and lycopene were mentioned but not defined or elaborated. -The Tools and Processes of Cofactor Engineering section seems to be a very important concept but we feel that it did not clearly relay information. -For example, you go through all the steps involved in the process of cofactor engineering such as putting the pre-cultures in the shaker etc, but that information did not seem to actually address how engineers actually alter cofactors to alter enzymes. This point ties in with the next point about differentiating important and not important information because while you provided many details about the actual steps of cofactor engineering, it was not actually helpful in understanding the overall process of cofactor engineering. Also, you mentioned a medium for cofactor engineering to take place in, but never actually described what this medium entails. Again, this goes back to our point of defining terms/elaborating on terms when you first introduce them. -We suggest differentiating between what information is necessary for the understanding of the article and what isn't. There was a lot of information which was mentioned but did not seem to pertain to the main topic. -In the Biofuels subsection, you did not really relate the subject of cofactor engineering to biofuels enough for that section to be relavent to the main topic. It's a good section to have but you need to elaborate more on how exactly cofactors play a role in biofuels. -The Changing an enzymes cofactor from NADPH to NADH section brought up great points it made sense yet it was not explained thoroughly. It is made clear that NADH is capable of being used in stead of NADPH yet we feel it would add to the content if Group 15 talked more on how effective it is. Is it less effective? Nelbehei (talk) 22:07, 12 April 2011 (UTC) Mstamm1 (talk) 23:24, 12 April 2011 (UTC) Mayukoori (talk) 15:00, 13 April 2011 (UTC)

Minor Concerns
Group 11: Most title contain the term "Cofactor Engineering," which causes the article to seem redundant. Perhaps new and more specific titles would be helpful to convey to the readers the exact section. A few diagrams illustrating the uses of Cofactor Engineering would help to aid the understanding as well. Zwaisel (talk) 11:14, 12 April 2011 (UTC)

Group 2: -There were a few minor grammar errors throughout the text. We suggest that the group re-reads the article to eliminate these errors. -The structure of some of the sentences also needs improvement. The wording of sentences seemed unclear in certain sections of the article. -To improve the overall structure of the article, some of the sections need to be reorganized. For example, the section which defines what a cofactor is was not mentioned until later in the article, even though the term cofactor was mentioned numerous times in the text that came previous. We suggest that the Cofactor section be placed directly after the Summary of Cofactor Engineering section. Nelbehei (talk) 22:23, 12 April 2011 (UTC) Mstamm1 (talk) 23:24, 12 April 2011 (UTC) Mayukoori (talk) 15:01, 13 April 2011 (UTC)

Peer Review 2
Group 2: Improvements: Group 15 better defined crucial terms which made the article easier to read and follow. They also went over what sections they really needed in their article and took out some parts completely that did not fit well with their topic. They organized their work into an chronological order. One improved section is the Significance section. This section defines the main topic and summarizes what cofactor engineering is all about. Anyone who finds this article will be able to get a better understanding about cofactor engineering. The Tools and Processes also improved significantly and they took most of our suggestions into account. They decided to keep this section which was a good choice and they improved it by better explaining how engineers use cofactors to alter enzymes. Added more pictures which aid the audience in visualizing the cofactor engineering process. Minimal grammatical errors.

A new section all together they added was Other Examples. We like the chart they included except we would suggest to put some information underneath it better explaining its purpose for being included. Also, they could possibly put the common names of the organisms somewhere, instead of just having the scientific names of them.

Overall, Group 15 took into account most of our considerations and improved their article based upon what we had to say. 128.8.238.165 (talk) 21:16, 3 May 2011 (UTC)

Group 15 response to group 2: Added a caption explaining the purpose of the table, which was to provide more examples of cofactor engineering, in an abbreviated form. It was deemed unnecessary to include the common names of the two organisms in the table. The first organism is hyperlinked to its corresponding wikipedia article, which includes the common name of the organism and a whole lot more. The other organism is simply a new strand of an ethanol producing thermophile, the name included is the name suggested by the cited article. It has yet to be formally adopted, and the organism has no common name. —Preceding unsigned comment added by Glennbeatty (talk • contribs) 23:13, 8 May 2011 (UTC)

Group 11: Group 15 did a great job addressing the comments made in the first peer review. "Tools for Cofactor Engineering" has been thoroughly edited for grammar and is much stronger as a result. Their introduction section is very helpful. It gives potential readers a brief overview of the topic and excellently sums up the article. The picture they added to the "Significance" section also gives readers another way to view the information. It breaks up the article in a positive sense because now it is not all text. It allows the readers to follow the text with the pathways picture as a supplement. The picture clearly illustrates the various pathways that affect this process which allows the reader to better follow the associated text. The table in the "Other examples" section is also very helpful. I would even go so far as to say they should make a table with all engineered organisms at the bottom of the page. All things considered, this is a great article that will definitely help anyone interested in learning about cofactor engineering. Thearn182 (talk) 22:12, 3 May 2011 (UTC) Zwaisel (talk) 22:17, 3 May 2011 (UTC) (Ad kh2 (talk) 22:54, 3 May 2011 (UTC))

Group 15 Response to Group 11: We looked into adding the table of all the organisms that cofactor engineering has been applied to. The field is relatively new and most of the time cofactor engineering is applied to the same model organisms, so the list would be short. We believe the importance is in the metabolic pathways that cofactor engineering alters, not the different organisms it is used in. Zrom (talk) 22:52, 8 May 2011 (UTC)

Instructor review
This article has begun well, but can be made significantly more informative. UM BIOE120 Instructor (talk) 02:23, 25 April 2011 (UTC)
 * What is primarily missing in the article is the significance of cofactor engineering. Metabolic engineering is often utilized to enhance the performance of a metabolic process by engineering segments of metabolic pathways important to the process. However, cofactor engineering is the branch of metabolic engineering that focuses on making crucial molecules (cofactors) to available to the metabolic pathways important to a metabolic process. Because a cofactor molecule can participate in several apparently disconnected regions of an organism's metabolic network, cofactor engineering requires the (nontrivial) amplification of flux in a far-off pathway to alter the flux in the pathway of interest. You might want to think of a geographical analogy for this.
 * Currently this seems as if it wants to stand by itself, which is not a good thing for a Wikipedia article. You have to link to Wikipedia articles on close topics.
 * For instance, you don't even provide a link to the cofactor article! You don't have to provide such a long introduction to cofactors when the cofactor article already does that. I would suggest shortening this introduction (not even making it a separate heading) and linking to cofactor.
 * Similarly "glycolysis (another metabolic pathway)" is unwarranted. Simply write "glycolysis" and link to its Wikipedia article.
 * Applications of cofactor engineering
 * I liked your three applications -- one dealing with NADH, one with CoA and the third on changing enzyme preference from NADH to NADPH.
 * Can you find a review article on this subject and use it to obtain several more examples? Review articles comprehensively review the literature on a subject, and one way to find biological review articles is to search on PubMed and check the review button. (Google Scholar also must have a mechanism to search for reviews.) Adding multiple examples of cofactor engineering (ideally, in a table) will make the article significantly more informative. You can still retain your original three examples -- these will be the ones you elaborate on.
 * Your original three examples need to be more fleshed out in terms of biochemistry.
 * A figure on one of your three applications would add to the value of your article.
 * Organism names (e.g. Saccharomyces cerevisiae) should be in italics. It is OK to abbreviate them (S. cerevisiae) after first mention.
 * Your article is improving already -- good job. The NAD+/NADH figure is somewhat appropriate for the article (keep it unless you get a majority of reviews that say otherwise), but the S. cerevisiae one is not (please remove). You might want to create a schematic figure to explain the first example (changing enzyme preference from NADPH to NADH). The figure could consist of simple lines and blocks, but if it serves to elucidate the corresponding text, it will be worth the effort. UM BIOE120 Instructor (talk) 13:12, 26 April 2011 (UTC)