Talk:Dictyostelium discoideum

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Dictyostelium discoideum was a Natural sciences good article nominee, but did not meet the good article criteria at the time. There are suggestions below for improving the article. Once these are addressed, the article can be renominated. Editors may also seek a reassessment of the decision if they believe there was a mistake. Reviewed version: May 17, 2008

	Biology Portal Dictyostelium discoideum is part of WikiProject Microbiology, which aims to improve Wikipedia's coverage of microbiology and microbiology-related topics. Please work to improve this article, or visit our project page to find other ways of helping.
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This article is currently or was the subject of an 2008-01-16 educational assignment.

Thanks to Touchstone42 for providing content on the importance of D. discoideum as a model for studying Legionella infection. I was not aware of that aspect of the topic. I edited the section to try to provide context (i.e., mention of Legionnaire's disease). Also, I reorganized the content to try to make it flow a little better.Bruno in Columbus (talk) 03:15, 12 March 2008 (UTC)

Contents 1 Jobs 2 Question about section on apoptosis 3 More Jobs 4 Classification and Phylogeny Edit 5 Model Organism Edit...and Question 6 GA review 7 Earlier work

[edit] Jobs

Now that the content has been compiled and posted, we need to start revising and reformatting.

Note that species names should be in italics. That did not come through from the Word documents, so those need to be spotted and corrected quickly. Also, after first use, Dictyostelium discoideum should be referred to as D. discoideum.

Also, we need to make sure that all of the citations use the format that has been started in the article. The easiest way is copy and paste one that has already been created and then fill in the information for the new citation.

The section on laboratory culture has a lot of good information, but it has the feel of a lab manual procedure. It needs to be revised to read like an encyclopedia. Step-by-step procedures should not be included, but a reference to the lab manual would be helpful to someone who might want to culture it. Rather than step-by-step procedures, the section should just indicate generally how they are cultured. It's good to note the two ways they are cultured, but some discussion of the purposes of the two ways would be nice.

I would like to see the section on the genome expanded. I posted in CougarVIEW an article that summarizes what is known about the genome. There's some pretty interesting material in the paper that could be included.

The section on classification and phylogeny starts a little abruptly. I think it needs an opening topic sentence that indicates that there is some disagreement on exactly how the organism should be classified.

I have posted some pictures in the WikiMedia Commons. Those should be incorporated into the article to illustrate the life cycle. Also, there is a life cycle diagram in the article on Dictystelids that we could use if you all want to.Bruno in Columbus (talk) 02:48, 20 March 2008 (UTC)

I added a link at the bottom of the article to a gallery of pictures at Wikimedia Commons. It connects directly to a page that has pictures that you can download and incorporate into the article.Bruno in Columbus (talk) 03:30, 21 March 2008 (UTC)

Hey everyone, I edited the first sentence in the Genome section by removing the number 1 after the word institutes. —Preceding unsigned comment added by EuniceYu (talk • contribs) 19:56, 26 March 2008 (UTC)

Hey. Its Meredith! I went ahead and pulled out all the unnecessary information in the lab cultivation section but it still needs to be expanded a bit. —Preceding unsigned comment added by ChrlisHalo (talk • contribs) 19:52, 2 April 2008 (UTC)

Hey I added some info to the lab cultivation. I think we should expand on the second method for cultivating the Dictyostelium. Megan

I found a typo with a period in the middle of a sentence in the lab cultulvation section and removed it. ~ Meredith ChrlisHalo (talk) 00:01, 21 April 2008 (UTC)

I changed the format of some of the references. I added the Gilbert 2006 reference to the notes section. The references for the "use as a model organism" section that are still in (Author Year) format should be changed to the [#] format but I don't have the full references for Wordnet 2008, Tyler 2006, Kay et.al 1978, or the American Heritage reference. ~Mandy —Preceding unsigned comment added by Mandy4885 (talk • contribs) 23:08, 27 April 2008 (UTC)

I added in the DictyBase link that has some really useful resources!~ Meredith ChrlisHalo (talk) 00:37, 28 April 2008 (UTC)

Ok- i have been looking and looking for more information on the second form of lab cultivation but cant find a thing! Sorry! I did italicize E.coli in the natural habitat and diet section where it was miscoded. - Meredith ChrlisHalo (talk) 19:29, 28 April 2008 (UTC)

[edit] Question about section on apoptosis

Under the "Use as a Model Organism" section, in the paragraph on programmed cell death, I don't think the specific examples of structures formed via apoptosis in humans are really necessary. Saying that it is a normal part of development in many species would suffice, yes? Cmcwell (talk) 22:15, 24 March 2008 (UTC)

I agree. Mentioning the importance of programmed cell death and apoptosis to sculpting tissues in a variety of higher organisms might be enough. If editors want to retain specific examples of apoptosis in humans, it would be good to begin the sentence with "For example, in humans, apoptosis is used in..." Then discuss apoptosis in D. dictyostelium as a model.Bruno in Columbus (talk) 02:28, 25 March 2008 (UTC)

I edited the model oranism and apoptosis section a little. —Preceding unsigned comment added by RAMrod2001 (talk • contribs) 15:34, 27 March 2008 (UTC)

[edit] More Jobs

We need references in the reference list for each citation in Model Organisms and Classification.Bruno in Columbus (talk) 20:59, 12 April 2008 (UTC)

I will finish the internal links sometime in the near future if someone doesn't beat me to it. Also, I expect to do a fairly major edit of the life cycle and reproduction section. No content changes, but I noticed during my hyperlinking marathon that it seems like the sentence patterns don't mesh well internally or externally to the rest of the article. Once I run through the second half, I might do the same for it too, for consistency's sake, unless anyone has any issues with this or would prefer to do it themself. Neoteny84 (talk) 15:34, 16 April 2008 (UTC)

[edit] Classification and Phylogeny Edit

I changed the first sentence from "The aggregation of a single amoebae into a multicellular fruiting body..." to "The aggregation of individual amoebae into a multicellular fruiting body..." 68.153.156.168 (talk) 01:58, 21 April 2008 (UTC)

[edit] Model Organism Edit...and Question

I changed the sentences on fruiting body formation in the apoptosis paragraph from future verb tense to present tense. 68.153.156.168 (talk) 02:19, 21 April 2008 (UTC)

After I edited that, I realized that this paragraph repeats the same information about fruiting body formation that is found in the life cycle section. I suggest shortening this paragraph to include only the specific example of apoptosis in fruiting body formation. Any objections? 74.165.58.168 (talk) 02:33, 21 April 2008 (UTC)

[edit] GA review

Thanks for the opportunity to read this, it's very well done, and a fascinating article. Very cool little organisms! Most of these points are are just suggestions, so they can be disregarded if there's reason to; however the citation and lay-friendliness do need to be addressed before I can pass this as a GA. On the whole, though, the article is close!

• The lead should mention the fact that it's a slime mold. Something from the Genome section might be good too.
• You can probably do et. al after three or six authors in a ref (at least that's what it is in WP:MEDMOS, I assume it's similar here).
• Don't forget to italicize journal article titles.
• Choose a single format for references: Full first name vs. initial, et. al vs. listing all the names, semicolons vs. commas for separating names. Also, the template adds periods, so you have double periods in some refs.
• The habitat section is kind of skimpy, is that really all there is to say?
• "D. discoideum has a simple life cycle that includes vegetative, aggregation, migration, and culmination stages" means nothing to me. You might try describing what goes on in those actions: "...a stage in which it migrates, one in which..."
• Define unusual words like "Uninucleate". If defininitions would make the text too bulky or complex, you can get away with wikilinking, but having it in the article so people don't have to leave your page.
• "Uninucleate amoebae of D. discoideum consumes bacteria contiguous to its natural habitat, which includes deciduous forest soil and decaying leaves"—Singular or plural? Also, what does "contiguous to its natural habitat" mean? "...that exist in its natural habitat"?
• Also define "Myxamoebae". "[whatevers] called myxamoebae hatch..." would work.
• I'd recommend combining some of the choppy sentences under life cycle.
• "As the amoebas move, they bump into each other and stick together as glycoprotein adhesion molecules." amoebas -> amoebae, right? And what does "stick together as glycoprotein adhesion molecules" mean? Maybe "with adhesion molecules"?
• "an elongated mound that tips over to form the pseudoplasmodium, or slug" It 'tips over'? What does that mean? What significance does tipping over have in the development of the organism?
• Use en dashes (–) rather than hyphens (-) for number ranges per WP:DASH.
• Numbers and units should be separated with a non-breaking space (&nbsp;) so the units don't show up by themselves on the next line. See WP:NBSP.
• "It has an anterior and posterior end and moves only in a forward direction"—This sentence is introductory but comes after another use of 'anterior'. This whole paragraph is a little hard to follow, anything that could be done to simplify it would be good (e.g. referring to the image, expanding explanations, introducing each new term, as you do with "...made up of a type of cell called prestalk cells").
• "prestalk cells move down to where they need to be"—Where is that and why?
• "they can fuse during aggregation to form a giant cell." is 'giant cell' a technical term? If so, it should be something like "they can fuse during aggregation to form a new type of cell called a giant cell." Otherwise, I don't know about the use of 'giant', isn't that a kind of funny word?
• "This is known as a macrocyst." What is known as a macrocyst, the cell wall, or the whole cell thing? That's the problem with use of 'this', especially at the beginning of a sentence: the antecedent is frequently unclear.
• Under "Use as a model organism" you should turn the Harvard refs into the cite.php format that the rest of the article uses. Some of the refs aren't provided: Who is The American Heritage? “Cellular Differentiation"? Kay? Tyler 2006? Wordnet? You'll need to either provide full citations for these refs or find others (the cell differentiation and chemotaxis ones are so basic it probably doesn't need a cite).
• "Cell differentiation is the process that occurs when a cell becomes more specialized to become a multicellular organism" the article discusses differentiation further up, maybe this should be moved up.
• "In D. discoideum, the amoeba secretes the signal, cAMP, out of the cell attracting other amoebas to migrate toward the source" —awkward.
• It's not clear why the chemotaxis paragraph belongs in the "Use as a model organism" section. Maybe a topic sentence such as "The organism has also proven useful in the study of chemotaxis, the passage of an organism..." would help clarify, if that's the case.
• What is a "comprehensible example"?
• The next paragraph also needs a lead sentence explaining why you're reading it in the Use as a model organism section. The last sentence in that paragraph might work higher up in that section, e.g. in the first paragraph.
• I'm not sure about whether the detail about apoptosis and the biology of the organism belongs in the Use as a model organism section, but I'm not sure where else to put it. This will probably be OK once these paragraphs are properly introduced.
• The behavioral responses paragraph in "Use as a model organism" is completely unreferenced, you'll need to find at least one reference for this info, especially the sentence with a number in it, per WP:WIAGA.
• "Over 100,000 individual amoebae are attracted to one another through chemotaxis."—The meaning of this sentence is not really clear, and it comes in between two sentences about light, interrupting flow. A lot of different topics are covered in this paragraph.
• "It is usually grown in Petri dishes containing nutrient agar and the surface of the dishes are kept moist." Awkward.
• "Check the dish often and make detailed observations of the development." The article should not address the reader or read like a how to manual. Same for "While cultivating in a lab it is important to take into account D. discoideum's behavioral responses."
• Some of the choppy sentences could be combined in the first paragraph under lab cultivation.
• In this paragraph, am I right in assuming that ref 3 is the reference for the whole thing? You can get away with that, but I'd make it explicit and use it for each sentence. That way, if someone comes along and adds a sentence from another source, it will be clear who said what.
• The second paragraph under "Lab cultivation" is completely unreferenced.
• I don't get why "Classification and phylogeny" is a subsection of "Use as a model organism" rather than a section on its own. It might be better at the end, since the "Genome" section is more closely related to the study of the organism and use as a model so maybe should be closer to that topic.
• "Dictyostelium has maintained more of their ancestral genome diversity than plants and animals, although proteome-based phylogeny confirms that amoebozoa diverged from the animal–fungal lineage after the plant–animal split." This sentence needs more clarification. Amoebozoa? Plant–animal split? Diverging? An introductory sentence might be good here. Introduce the reader to the concepts they're about to read about. Same with the next sentence, and the next two: too technical. Introduce non-basic concepts or at the very least link to their articles. Use as much laypeople-friendly wording as possible.
• "Elongation factor-1α (EF-1α) data analyses support Mycetozoa as a monophyletic group even though rRNA trees place it as a polyphyletic group. Further, these data support the idea that the dictyostelid and myxogastrid are more closely related to each other than they are the protostelid. EF-1α analysis also placed the Mycetozoa as the immediate outgroup for the “animal-fungal clade.”" These sentences are so technical sounding I'm wondering if they were lifted straight from a journal article. Can you check the source?
• What are "crown eukaryotes"?
• That paragraph might be easier to understand if the last part of it, beginning with "The multicellularity of the dictyostelid evidences its relationship to animals" were moved up: it's less technical and easier to understand. I also recommend expanding on the concept of divergence.
• Under "Genome", the first two sentences should have a citation.
• Link the first occurrence of an unusual abbreviation such as Mb.
• Introduce the terms "trinucleotides", "centromeres", and "nucleotide expansion".
• "generally leading to many diseases"—Awkward. Surely it's one disease per person, right? How about an example or two?
• "A phylogeny based on the proteome showed that the amoebozoa deviated from the animal-fungal lineage after the plant-animal split" probably belongs in the above section (although if you take my advice about moving that section to the bottom, it would be a great transition).
• Is there anything that can be said about the history of the organism? E.g. who was first to use it? What important discoveries have been made using it?
• No need to repeat the refs in the refs and notes section. In fact, since there are no notes, I'd call all of this "references".

On the whole, very well done. I'm putting this on hold for a week to deal with the citation issues and the readability for laypeople in the "Genome" section (readability could also be improved in the "Life cycle and reproduction" section and others, though). Let me know if you need any help or clarification of any of this, give me a heads up when you think these have been addressed and you're ready for another GA review! delldot talk 19:47, 14 May 2008 (UTC)

The GA nominator doesn't intend to follow up on the suggestions, so I'm failing this for now. If someone wants to make these improvements, feel free to nominate again! Gimme a poke on my talk page if you have any questions or need anything. delldot on a public computer talk 01:30, 17 May 2008 (UTC)

[edit] Earlier work

Before it becomes a good article, I think it would need a considerable discussion of the hstory of work on the organism. For examples, the p[ioneering work of John Tyler Bonner, who essentially developed the subject. Don;t just rely on an elementary textbook and a few recent articles. DGG (talk) 13:41, 24 May 2008 (UTC)