User:Pierrj/sandbox

Reflection

 * Critiquing articles:    The article evaluation taught me     that there is a lot of missing or not very useful sources that are cited     in the articles and that some articles aren’t fully polished and still     need plenty of work to be complete. The article I was given was the     Rhizobia article. I quickly noticed that a lot of sources were missing and     some of the information was outdated, especially in the formation of the     symbiosis and the information on other similar symbioses. Given the fact     that I know a pretty good amount about these two topics and I know some     good sources I decided to focus on those things.
 * Summarizing your contributions: My edits were to the “establishing    the symbiosis” and “other diazatrophs” sections of the Rhizobia page. I     made major edits and rewritings to the “establishing symbiosis” section     since it was pretty poorly worded and organized and a lot of specific     details and hyperlinks were missing. Some of the information was wrong as     well, such as the fact that Rhizobia give N to their host in the form of     ammonia. I think the edits I made had the effect of making the page     stronger as a whole, especially for the first section since I think a lot     of people will come to this page expecting this kind of information.
 * Peer Review: I read over two other peers’ articles, one for    Glomeromycota (AM fungi) and one for endophytes. The first edits were a     bit lacking and too informal so I pointed out a couple of areas that they     could expand on, such as how the symbiosis is established. In the     endophyte article, there wasn’t much to add as the editor had already made     very significant progress, so I only had a couple of grammatical and     phrasing errors to point out. These peers told me to change one of my     sources since it was too old, which I did, and pointed out a couple of     missing hyperlinks and grammar mistakes which I fixed.
 * Feedback:    No I did not receive any feedback     from other Wikipedia editors. This page is pretty low traffic so that isn’t     very surprising.
 * Wikipedia generally:    Through this project I learned a     lot about Wikipedia as a source. Specifically, Wikipedia is really great     for basic research but any specific article tends to be lacking, especially     in biology. This isn’t really because of misinformation but rather the     outdated or misleading nature of some of the information that is posted on     pages. Additionally, I learned how to write in a formal, neutral,     explanatory tone and how to properly cite articles and books using the DOI     numbers and ISBNs. I further learned how to do my own research through     Google scholar and piece together that research into a full, strong few     paragraphs. This was a very interesting progress since it felt like I was     actually contributing to scientific knowledge even if it was in an     incredibly small way. This is something that a lot of people don’t get to do in their college course work. Wikipedia is very useful because it boils     down very complex topics to simple and approachable explanations including     a number of tools to fully understand a topic. This includes the citations     and hyperlinks provided in each of the articles. This is extremely     important because people need to be able to educate themselves and learn     more when they want to so we can be more educated and knowledgeable as a     species and make more educated decisions. This is especially true for     topics like plant behavior where certain beliefs are not widely accepted     and educating the public is one of the ways to help public acceptance of     the point of view that plants have behavior and are intelligent.

First paragraph/Intro (added citation where citation was needed)
In order to express genes for nitrogen fixation, rhizobia require a plant host; they cannot independently fix nitrogen.

Infection and signal exchange (major edits)

Original:

The symbiotic relationship implies a signal exchange between both partners that leads to mutual recognition and development of symbiotic structures. Rhizobia live in the soil where they are able to sense flavonoids secreted by the roots of their host legume plant. Flavonoids trigger the secretion of nod factors, which in turn are recognized by the host plant and can lead to root hair deformation and several cellular responses, such as ion fluxes. The best-known infection mechanism is called intracellular infection, in this case the rhizobia enter through a deformed root hair in a similar way to endocytosis, forming an intracellular tube called the infection thread. A second mechanism is called "crack entry"; in this case, no root hair deformation is observed and the bacteria penetrate between cells, through cracks produced by lateral root emergence. Later on, the bacteria become intracellular and an infection thread is formed like in intracellular infections.

.

Infection threads grow to the nodule, infect its central tissue and release the rhizobia in these cells, where they differentiate morphologically into bacteroids and fix nitrogen from the atmospheric, elemental N2 into a plant-usable form, ammonium (NH3 + H+ → NH4+), using the enzyme nitrogenase. The reaction for all nitrogen-fixing bacteria is:
 * N2 + 8 H+ + 8 e− → 2 NH3 + H2

In return, the plant supplies the bacteria with carbohydrates, proteins, and sufficient oxygen so as not to interfere with the fixation process. Leghaemoglobins, plant proteins similar to human hemoglobins, help to provide oxygen for respiration while keeping the free oxygen concentration low enough so as not to inhibit nitrogenase activity. Recently, a Bradyrhizobium strain was discovered to form nodules in Aeschynomene without producing nod factors, suggesting the existence of alternative communication signals other than nod factors.

New:

The formation of the symbiotic relationship involves a signal exchange between both partners that leads to mutual recognition and development of symbiotic structures. The most well understood mechanism for the establishment of this symbiosis is through intracellular infection. Rhizobia are free living in the soil until they are able to sense flavonoids, derivatives of 2-phenyl-1.4-benzopyrone, which are secreted by the roots of their host plant triggering the accumulation of a large population of cells and eventual attachment to root hairs. These flavonoids then promote the DNA binding activity of NodD which belongs to the LysR family of transcriptional regulators and triggers the secretion of nod factors after the bacteria have entered the root hair. Nod factors trigger a series of complex developmental changes inside the root hair, beginning with root hair curling and followed by the formation of the infection thread, a cellulose lined tube that the bacteria use to travel down through the root hair into the root cells. The bacteria then infect several other adjacent root cells. This is followed by continuous cell proliferation resulting in the formation of the root nodule. A second mechanism, used especially by rhizobia which infect aquatic hosts, is called crack entry. In this case, no root hair deformation is observed. Instead the bacteria penetrate between cells, through cracks produced by lateral root emergence.

Inside the nodule, the bacteria differentiate morphologically into bacteroids and fix atmospheric nitrogen into ammonium, using the enzyme nitrogenase. Ammonium is then converted into amino acids like glutamine and asparagine before it is exported to the plant. In return, the plant supplies the bacteria with carbohydrates in the form of organic acids. The plant also provides the bacteroid oxygen for cellular respiration, tightly bound by leghaemoglobins, plant proteins similar to human hemoglobins. This process keeps the nodule oxygen poor in order to prevent the inhibition of nitrogenase activity.

Recently, a Bradyrhizobium strain was discovered to form nodules in Aeschynomene without producing nod factors, suggesting the existence of alternative communication signals other than nod factors, possibly involving the secretion of the plant hormone cytokinin.

Interestingly, it has been observed that root nodules can be formed spontaneously in Medicago without the presence of rhizobia. This implies that the development of the nodule is controlled entirely by the plant and simply triggered by the secretion of nod factors.

Other diazotrophs subheading
Original:

Many other species of bacteria are able to fix nitrogen (diazotrophs), but few are able to associate intimately with plants and colonize specific structures like Legume nodules. Bacteria that do associate with plants include the actinobacteria Frankia, which form symbiotic root nodules in actinorhizal plants, and several cyanobacteria (Nostoc) associated with aquatic ferns, Cycas and Gunneras. Free-living diazotrophs are often found in the rhizosphere and in the intercellular spaces of several plants including rice and sugarcane, but in this case the lack of a specialized structure results in poor nutrient transfer efficiency compared to legume or actinorhizal nodules.

New (added citations, changed wording, commented on symbioses)

Many other species of bacteria are able to fix nitrogen (diazotrophs), but few are able to associate intimately with plants and colonize specific structures like legume nodules. Bacteria that do associate with plants include the actinobacteria Frankia, which form symbiotic root nodules in actinorhizal plants, although these bacteria have a much broader host range implying the association is less specific than in legumes. Additionally, several cyanobacteria like Nostoc are associated with aquatic ferns, Cycas and Gunneras, although they do not form nodules.

New (added short paragraph on endophytes)

Additionally, loosely associated plant bacteria, termed endophytes, have been reported to fix nitrogen in planta. These bacteria colonize the intercellular spaces of leaves, stems and roots in plants but do not form specialized structures unlike rhizobia and Frankia. Diazotrophic bacterial endophytes have very broad host ranges, in some cases colonizing both monocots and dicots.

First paragraph/Intro (added citation where citation was needed)
In order to express genes for nitrogen fixation, rhizobia require a plant host; they cannot independently fix nitrogen.

Infection and signal exchange (added sentence on flavonoids)

Original:

Rhizobia live in the soil where they are able to sense flavonoids secreted by the roots of their host legume plant. Flavonoids trigger the secretion of nod factors, which in turn are recognized by the host plant and can lead to root hair deformation and several cellular responses, such as ion fluxes.

New:

Rhizobia live in the soil where they are able to sense flavonoids secreted by the roots of their host legume plant. Flavonoids, which are derivatives of 2-phenyl-1.4-benzopyrone, promote the DNA binding activity of nod factors like NodD which belong to the LysR family of transcriptional regulators. These nod factors are in turn recognized by the host plant and can lead to root hair deformation and several cellular responses, such as ion fluxes.

Other diazotrophs subheading
Original:

Many other species of bacteria are able to fix nitrogen (diazotrophs), but few are able to associate intimately with plants and colonize specific structures like Legume nodules. Bacteria that do associate with plants include the actinobacteria Frankia, which form symbiotic root nodules in actinorhizal plants, and several cyanobacteria (Nostoc) associated with aquatic ferns, Cycas and Gunneras. Free-living diazotrophs are often found in the rhizosphere and in the intercellular spaces of several plants including rice and sugarcane, but in this case the lack of a specialized structure results in poor nutrient transfer efficiency compared to legume or actinorhizal nodules.

New (added citations, changed wording, commented on symbioses)

Many other species of bacteria are able to fix nitrogen (diazotrophs), but few are able to associate intimately with plants and colonize specific structures like Legume nodules. Bacteria that do associate with plants include the actinobacteria Frankia, which form symbiotic root nodules in actinorhizal plants, although these bacteria have a much broader host range implying the association is less specific than in legumes. Additionally, several cyanobacteria (Nostoc) are associated with aquatic ferns, Cycas and Gunneras, although they do not form nodules. Free-living diazotrophs are often found in the rhizosphere and in the intercellular spaces of several plants including rice and sugarcane, but in this case the lack of a specialized structure results in poor nutrient transfer efficiency compared to legume or actinorhizal nodules.

New (added short paragraph on endophytes)

Addtionally, loosely associated plant bacteria, termed endophytes, have been reported to fix nitrogen in planta. These bacteria colonize the intercellular spaces of leaves, stems and roots in plants and do not form specialized structures unlike rhizobia and Frankia. Diazotrophic bacterial endophytes have very broad host ranges, colonizing both monocots and dicots.

Potential topics
Buzz polination

-nothing on plant mechanisms/function of buzz pollination

-a couple of citations missing

Endophytes

-lots of very outdated information

-way too many sources, a few reviews would be sufficient

-specifically: we now know most endophytes are intercellular rather than intracellular

Rhizobia

-nothing on molecular biology of establishing the symbiosis

-could focus on chemicals produced by plants (flavonoids, etc.)

Hypersensitive response

-could expand pathogen evasion subheader

Secondary metabolites

-not much on how they are produced in response to pathogens, could add more to that

Plant physiology

-this might be a lot of work but fix a lot of typos and missing or old citations

-restructure article? exclude biochemistry?

Specific topics
Rhizobia

-very little on plant interactions

-"research" subheader could be renamed to something like "plant response" or establishing the symbiosis

-some citations missing (history)

-could add list of symbionts to go with species

-could suggest deletion/redirection of "rhizobium" article

-could add a lot of info on the molecular mechanisms of the interaction, especially the plant secreted flavonoids

-maybe add a blurb about endophytes to the "other diazotrophs" subheader?

To add to article:
Add citation: In order to express genes for nitrogen fixation, rhizobia require a plant host; they cannot independently fix nitrogen.

Added more info on flavonoids: Flavonoids, which are derivatives of 2-phenyl-1.4-benzopyrone, promote the DNA binding activity of nod factors like NodD which belong to the LysR family of transcriptional regulators.

Buzz pollination

-a few citations needed, "8% of flowers..."

-"physics of buzz pollination"

-any molecular work done on the mechanism of the interaction? or is it purely physical?

-one of the cited articles is a newspaper article which isn't too great of a source...

To add to article:
Add citation: "About 8% of the flowers of the world are primarily pollinated using buzz pollination"

"Techniques for agricultural pollination of species normally requiring buzz pollination" is very wordy and could use rewording maybe to something like "Buzz pollination in agriculture"

Botany
-the picture used at the top doesn't make a lot of sense, I think it would make more sense to have a broader representation of botany rather than cooking/medicine

-paragraph 2 through 4 of the intro don't have any citations (??) there might be something that I am not getting here, is it that all of the citations are contained in the body of the article so they don't need to be cited in the intro?

-it seems like the subheader "systemic botany" should be renamed/reworded to something regarding phylogeny or evolutionary biology, it seems like it could be moved to the plant evolution section

-overall did not notice any biases in the article (as expected of such a heavily screened and editted article). However, the scope/importance section seems to be a bit biased, that is a bit difficult to argue though since that is the purpose of the section, but it seems to downplay the role of algae and cyanobacteria in terms of C fixation and O2 production. essentially, that is an example of an over represented view point

-the links seem to be working for the couple of citations that I checked

-scanning the list of sources it seems like most are pulled from books/textbooks which tend to be a good source of reliable, information that is not directly scientific research, more of a review of the scientific landscape, which is appropriate for a wikipedia article

-the footnote seems very informal ("a bunch of")

-some of these sources are very old (as old as 1940) but overall all of the information is up to date (2000s+)

-non of the sources seem biased at a glance (all textbooks, books, papers) if any of them are biased there is not statement about them

-some of this info/categorization is a bit overly generalized, the example being the "five key areas of plant physiology" which a lot of scientists would disagree with. I would definitely place phytochemistry and molecular/cell biology in there own categories apart

-current status: good article, it is part of the biology, plants, horticulture/gardening and rated top importance in two of them

-talk: it looks like the article has been overall decided to be fairly complete, a lot of the more recent edits are changing external links. Additionally, I have to disagree with the most recent comment saying that the article doesn't contain any concise definitions, the intro section does a great job of introducing the topic and making a clear and concise definition. of course, this is an encyclopedia article so it makes sense for it to be extensive and in depth

-as for class, this seems to take a much less behavior focused approach to the topic as a whole (duh, this is a plant behavior class.) Notably though, there are a lot less comparisons to animals in the wikipedia article, whereas in class we have talked a lot about comparing plants to animals and talking about how terminology apply to each of them

-overall very great and complete article (especially when compared to the plant physiology one...) a lot of sources that are appropriately cited, these sources are all very strong and unbiased, the article is very in depth and well balanced, it would be difficult to make more than very small edits to this article through this class

Plant Physiology
-again, not a fan of the opening picture but I am not totally sure what you could put instead of that, maybe a map of hormones or something like that?

-not sure about that "closely related fields" sentence, if you're going to include molecular/cell biology you could also include microbiology and animal physiology, the related fields listed are extremely broad

-title should have two capitals no?

-what are the two parts of plant water relations?

-again, really don't like the "five key areas" of physiology that they use

-no citations at all in the "Aims" paragraph, this really gives no merit to what the author is talking about. as a reader of an article like this, I am not interested in what the author thinks the goals of plant physiology are, especially if those goals are misinterpreted and include plant biochemistry which I would definitely put in a different category/article from plant physiology

-again and again, it irks me that biochemistry is included in this article at all, but of course, that is according to my purely subjective definition of physiology

-additionally, that section is structured extremely weirdly, I really feel like pigments should deserve its own category or that it should be taken out completely, it is very strange to me to talk about plant biochemistry without talking about metabolism

-lots of typos through the article, example : "Plant hormones are often not transported to other parts of the plant and production is not limited to specific locations." the sentence losing meaning because of the typo

-the history subsection is very incomplete, why start with early history if that is all that is going to be described? there is lots to work on here

-"drug companies spend billions of dollars" how do we know this? is there an actual number? shouldn't this be cited?

-the "current research" subheading could be very easily and greatly expanded

-I don't think there are nearly enough citations/sources cited overall

-none of the sources are older than 1994 (!!!) I think that shows how outdated and how much work needs to be put into this article

-there is a book that is cited as a website (??), that link clearly doesn't work

-otherwise the sources are okay but there aren't nearly enough of them and they are very outdated, they do come from fairly reliable sources without bias

-"Paradoxically, the subdiscipline of environmental physiology is on the one hand a recent field of study in plant ecology and on the other hand one of the oldest" the first line of the environmental physiology paragraph is likely close paraphrasing, this should be quoted from the source most likely. Very weird that a citation was included here but not at some of the other places (obviously though, this was written by quite a few different people)

-no citations at all in many sections (photoperiodism, plant hormones, many others)

-when cited, usually the first citation is used over and over again

-this is a B-class article, it is of top importance in the plants project

-this article seems to have been fairly forgotten about, the last post (besides what I assume is from this class) is from 2007. weird since this seems like it would be a higher priority/interest article

-overall, this article has a much, much broader view of plant physiology than the one that we use in class, since it includes "biochemistry"

-overall this article is really poor quality, lots of missing information, lots of weirdly placed/distracting details and extra topics that shouldn't be there, very "unbalanced" definitely needs a lot of work, it might be a great article to work on for this class!