Talk:Okazaki fragments/Archive 1

opposite of the text description
Is it me, or in the picture the ends (3' and 5') are exactly the opposite of the text description ? —Preceding unsigned comment added by 195.141.71.130 (talk) 13:37, 31 January 2008 (UTC)


 * The picture is somewhat misleading. It reads like a puzzle. Sentriclecub (talk) 11:58, 29 April 2008 (UTC)

The diagram currently in use is wrong. Okazaki fragments are formed with DNA polymerase delta, not episilon. Polymerase episilon has been assigned to leading strand synthesis. Read: McElhinny, S. et al, “Division of Labor at the Eukaryotic Replication Fork.” Mol Cell. 2008 May 9;30(3):259-60. Before the paper, it wasn't even clear which polymerases were involved in which processes. The diagram needs to be revised. —Preceding unsigned comment added by 143.48.48.239 (talk) 16:32, 11 August 2008 (UTC)
 * For sake of accurate archives: The current image has no known errors. 87.155.85.82 (talk) 20:35, 23 January 2010 (UTC)

=Team 14 Peer Review of Team 12=

Summary:
Okazaki fragments are short pieces of DNA that are formed on the lagging strand of DNA during replication. Because the replicating enzymes only operates in one direction, 5’ to 3’, discontinuities occur on the 3’ to 5’ strand; these fragments of DNA are later filled in by other enzymes. Although most of the same enzymes are used on both strands, the entire process of DNA replication is different on the lagging strand than on the leading strand, causing differences in mutations that occur during replication. The differences in these two processes has led to a variety of experiments to explore the opportunities that these Okazaki fragments create in both the medical field and in different engineering aspects.

Major Corrections:
The last paragraph of the opening section seems to be unrelated to the rest of the information contained in that section. This paragraph also does not contain citations, and the sentences do not really have much of a flow. The information seems similar to the description of the experiment in the “History” section, and should be combined together.

Specify the pronoun “this” in the Primase paragraph so that it is easier for the a reader to follow along in the section.

The “History” section should be renamed to “Experiments”. Two experiments were discussed in this paragraph, and the paragraph should be split, and there should be more clarification of the transition between these two experiments.

In the “Pathway” paragraph, the nucleases FEN1, etc. are described as doing various things; however, the reader does not know what these are yet. Consider moving the enzyme section to before this section or at least provide more background information - the reader’s knowledge is assumed to exist here when it doesn’t exist.

In the “Biological Function” section, the first paragraph seems irrelevant to the title of the section. It may be better served being moved to the beginning of the article. The second paragraph of this section jumps around various topics until it finally arrives to the point in the last part of the last sentence. This section should be either taken out, or reorganized so that it really explains why the fragments “maintain our evolutionary development.”

The section titled “Okazaki Fragments in Prokaryotes and Eukaryotes” contains a lot of information about the differences between the two types of organisms, but not a lot of information about the significance of these differences. Maybe the point of the section was just to highlight the information, but if the significance could be pointed out, it would strengthen the section.

The “Alternate Pathway” section doesn’t contain a lot of information about the proposed new pathway that can form the fragments. If the amount of information is to remain the same, then the section should just be combined with the “Pathways” section. Otherwise, try to find more sources to adequately explain this new pathway.

Minor Corrections:
Second paragraph in Engineering Concepts

-Change “incite” to “insight”.

-Change “stains” to “strains”?

Section title “Okazaki fragments in Prokaryotes and Eurkaryotes”; Eukaryotes is misspelled.

Section “Alternate Pathway”

-Capitalize “Okazaki”

“Pathways”

-Explain what FEN1 and Pif1 are

Citations:
Random articles were checked, and citations are accurate.

Dmikulis (talk) 00:35, 13 April 2011 (UTC)

=Team 4 Review of Team 12=

Brief Summary:
The Okazaki fragment is a small portion of a DNA strand. Specificially, it is the fragment that is created during DNA replication that is formed by the lagging strand. The 5’-3’ pattern must be used when the lagging strand of an Okazaki fragment is being replicated on the original strand. As the two antiparallel strands are separated, the lagging strand produces these fragments that are complimentary to the original strand. Once the fragments are attached, DNA polymerase, an enzyme for replication, extends the strand to match the length of the original strand. The main pathways that the Okazaki fragments take place in are the FEN1 nuclease and Dna2 nuclease pathways. Additional enzymes also take place during the replication in order to aid and speed up the process.

Major Concerns:
A major concern for the article is that there seems to be a lot of repetition. For example the introduction talks about how “the nascent lagging strand reads from 5' to 3” as does the history section and various other sections. An introduction is helpful but don’t give away all your information in the introduction and then repeat yourself in the sub sections. Also, in the medical concepts sections it says, “As previously stated, Okazaki fragments are the source of genetic information for the lagging strand of DNA during DNA replication.” If it has been previously stated-which it has been many times in the article- try not to state it again. Make the sentences flow with one another and move the topic along so that the reader won’t get lost. There are also some parts of the article that could be clearer. Try to be concise so as to not confuse your reader, while still appearing to be an expert on the subject.

The group has done a good job collecting a lot of information and creating this draft. As the students go back and write the next draft, my overarching suggestion is to make each section clearer so uninformed readers can follow more easily. The introduction rapidly gets into detail without explaining (or linking) to some of the important concepts. After the first paragraph, the rest of the introduction should be part of the body of the article. I think instead, it would be helpful in the introduction to briefly discuss (or just link to) the process of DNA replication, to introduce the importance of the Okazaki fragment. I think it would be helpful to expand the section discussing the significance of the Okazaki fragments as they pertain to organisms. The importance as a tool of evolution was interesting and I would be interested to know more specifics (ex, the frequency of mutations in the Okazaki fragment)

Minor Concerns:
Minor concerns for the article include length and citation issues. The article seems to be very lengthy. Going over the word limit is not a problem, but you are repeating a lot of information and at times including unnecessary information. Try to condense the article so that the material will be more comprehensible. There seems to minor citation problems within the article. The citations are in order and included throughout the article, but the citations themselves, under the references section do not seem to be consistent. The first citation has unnecessary information and some citations do not include the web address correctly. For example some say “Retrieved from”, while others have <> enclosing the address. Double check to be sure all references are cited correctly.

I think the word choice and grammar was very good overall. My main concerns involve the links to other articles. I would like to see more. The introduction has a large number of links, but there are very few through the rest of the article. I think these links would help with the article’s clarity. Also the first picture was very helpful as a summary of the first half of the article. I think more pictures and diagrams could be included through the rest of the article. Diagrams corresponding to the engineering studies mentioned would go a long way towards clarifying and reducing monotony.

Sources & Citations:
The reference list is correctly formatted and they are all hyperlinked from their respective cite-note from within the article. The randomly selected references that were previewed all originated from scholarly journals and were deemed to be trustworthy sources of accurate information. These respectable journals include Nature Publishing Group, Journal of Biological Chemistry, and the Journal of Molecular Cell Biology. Most of the information gathered for this article came from works published within the last 10 years. This indicates that much of the info is up to date and there is little chance of the group overlooking any new research that may antiquate the info included in their article. Overall this article, from a quality of research standpoint, can be considered Wikipedia worthy.

Ascrimge (talk) 20:21, 13 April 2011 (UTC) Group 4

Some suggestions
--Smokefoot (talk) 16:25, 17 April 2011 (UTC)
 * The references should mainly be to reviews and books. See WP:SECONDARY.
 * References require DOI's.
 * The article seems too specialized and too long for Wikipedia.
 * De-emphasize who and where experiments were done. This article is not a beauty contest.

References formating
I agree with Smokefoot's observations above. Meanwhile, I have formatted the current references. This tool saves a lot of time with formatting (there are other tools, but this is one I use). Also notice how references can be named, which saves having to reproduce the full citation when it is used more than once. Graham Colm (talk) 08:19, 25 April 2011 (UTC)

A quick review
There are a couple of initial reviews on your article's my talk page:

http://en.wikipedia.org/wiki/Talk:Okazaki_fragment http://en.wikipedia.org/wiki/User_talk:UM_BIOE120_Instructor

Change the tone of your article to match that of a typical Wikipedia featured article on a science/engineering topic. Some style suggestions:
 * Titles of sections should be in sentence case and not title case
 * "Further information" -> *Main article"
 * "scientists genetically altered" -> "researchers genetically altered"
 * "Another study concerning Okazaki fragments was published in volume 74 of PNAS" -> "A study by [corresponding author] and co-workers inferred/found/observed/determined that ..." Find out who the corresponding author is by looking at the article.
 * "One last study that is interesting to mention was ..." -> "In another interesting study, ..."
 * "and is now recorded on PubMed.gov, sponsored by the U.S National Library of Medicine and the National Institute of Health" -> simply replace with the in-text citation -- pretty much any biological work is recorded on PubMed.gov and your article does not need to provide info on who hosts the PubMed website.

There are a good number of stylistic changes, but you get the idea. Once you do a revamp, I will be glad to look at it again. Let me know if you have questions. UM BIOE120 Instructor (talk) 11:50, 25 April 2011 (UTC)

Team 14 review of Team 12: Round Two
In general, many sentences require revision to improve overall clarity and general readability. Consider restructuring unclear or awkward phrases and using active voice when sentences become a overly jumbled and fragmented.

In particular,
 * In the introduction, the phrase 'It was' could be replaced with 'the fragment' for clarity
 * The first sentence in the 'experiments' section seems awkwardly constructed. Perhaps you could use the active voice here.
 * Under the 'experiments' section, consider changing 'to distinguish the experimentally the method' to 'to distinguish the method of replication experimentally'
 * The 'Pathways' section contains many short sentences in a row that limit the flow of the whole paragraph. Consider combining some sentences or removing those containing unnecessary information
 * In the 'Medical concepts' and 'Use in technology' sections, rather than use parenthesis, use links to other articles or work these ideas into the actual sentences themselves.
 * In the final section, the statement 'One last study that is interesting to mention' sounds opinion based and somewhat unprofessional.
 * The use of the semicolon in the second paragraph of 'Engineering concepts' is incorrect

Also, citations seem to be missing in several paragraphs that include information that is not clearly common knowledge. Specifically, add additional citations to the 'experiments' and 'Biological function' sections.

Many sections have an appropriate number of links to other articles, though the 'Use in technology' and 'Process' sections are lacking necessary links. This will also help eliminate the need to further explain sub-ideas contained in these sections.

Despite these fairly minor issues, the article as a whole seems complete and relatively well written and will be of general Wikipedia quality once some sentence structure and citation issues are corrected.WatALE7 (talk) 14:32, 3 May 2011 (UTC)

This article should be renamed Okazaki fragments
There are always more than one formed during DNA replication. This is more accurate and will also help with the prose. At the moment the opening sentence reads, "An Okazaki fragment is a relatively short fragment of DNA created on the lagging strand during DNA replication." It would be more precise to write, "Okazaki fragments are relatively short fragments of DNA created on the lagging strand during DNA replication".Graham Colm (talk) 17:32, 3 May 2011 (UTC)
 * Since there have been no objections, I have renamed the article. Graham Colm (talk) 21:29, 7 May 2011 (UTC)

=Team 4 Review of Team 12: Round Two=

Brief Summary
The Okazaki fragment is a small portion of DNA that is used during the replication process produced by the lagging strand. The 5’-3’ pattern must be used when the Okazaki fragment is being replicated on the original strand so that the carbons on the deoxyribose sugars may attach together. As the two antiparallel strands are separated, the DNA and RNA primers are removed, and the lagging strand produces these fragments that are complimentary to the original strand. Once the fragments are attached, DNA polymerase, an enzyme for replication, extends the strand to match the length of the original strand. Due to the replication process being extremely repetitive, the probability of error also increases. This may include fragment maturation to cause chromosomal abnormalities. In result, as replication continues, the genetics of these strands of DNA will cause further mutations in the genome. Scientists have experimented with various organisms to determine which chromosomal irregularities cause certain mutations. This research can be applied medically to treat genetic diseases and cancers. —Preceding unsigned comment added by Sshakeel18 (talk • contribs) 22:48, 3 May 2011 (UTC)

Major Concerns

 * In the Experiments heading, it is unclear what the 3'5' and 5'3' directions are. I understand that they represent the carbon atoms, but can a link elsewhere be provided that clarifies what this means? A picture or diagram would be even better
 * In general, the Experiments section is confusing without links. I suggest adding more links to topics like "pulse-labeling," and the mentioned enzymes.
 * In the pathways section, I am unclear what "flaps" are. Can this be clarified.
 * In general, I think there should be more links. The topic is covered very thoroughly, but there are many terms that are unclear that can be easily clarified with links to other articles
 * All types of people use Wikipedia. Make sure you sound professional, but clarify everything you say, whether it be with explanation or additional links to separate Wikipedia pages.

Minor Concerns

 * The first sentence in the "medical concepts" section could be removed
 * In the medical concepts section, there is a good amount of detail about a specific study. Can the name of the study and researchers involved be mentioned? It reads strangely to explain the study without mentioning its title (The next section, on engineering concepts, does a good job introducing studies)
 * The intro sentence to the third study in the engineering section is awkward. "One last study that is interesting to mention was...". This could simply be changed to "Another study of interest was..." —Preceding unsigned comment added by Jrapp99 (talk • contribs) 21:39, 3 May 2011 (UTC)
 * Be clear and concise. Don't overwhelm your reader with unnecessary information.

Assessment comment
Substituted at 15:30, 1 May 2016 (UTC)