User talk:Brendil Sabatino/sandbox

I came across three main issues present throughout Peptidoglycan (PG): plagiarism from the cited source material, inadequate sourcing of information, and missing depth for some topics. The Issue regarding the plagiarism is present as direct word for word copying of the entirety of the section up until the first cited source, from said source. This section needs to be either deleted or reworded and restructured as to not violate Wikipedia’s guidelines.

More present throughout the article are the sourcing issues. They’re encountered as missing sources for the claims of a structural role for PG, differing dry weight percentages and thickness of PG in different bacteria types, and all of paragraphs 1 of “Structure”, 2 of “Inhibition”, and 3 of “Biosynthesis”. Additionally, for several of the sources it is unclear where the cited information came from or the source does not direct you to the proper resource. For example, the source listed “5” redirects to the world encyclopedia website but does not take you to any article with relevant information, and upon searching for the cited “bacteria” entry there is no information regarding PG.

Lastly there are the issues regarding the depth of content Primarily in “Biosynthesis” and “Inhibition”. In the former, there is a lot of detail regarding cytoplasmic synthesis but very little about formation outside the cell. Also, “Inhibition” would benefit from a more detailed list of inhibitory substances and mechanisms. These two subjects are important to expand on because they provide information regarding PG targeting by inhibitory compounds. Brendil Sabatino (talk) 23:45, 17 September 2017 (UTC)

Osmoprotectants

Osmoprotectants are organic molecules primarily involved in stress resistance present in all organisms throughout the 3 domains of life. They play a key role in the persistence of soil microbes in dry environments, protection of plants against salinity and drought, and even control of certain virulence factors. They are also potential biosynthetic products that could combat drought and high salinity which has significant economic impacts in agriculture. However, despite this importance their Wikipedia article dosen't contain much information consisting of only two sections with little depth.

For example, in the introduction section the definition of an osmoprotectant is incomplete mentioning nothing about their collective properties such as neutral charge, organic nature, and non-toxicity at high concentrations. This section is also lacking mention of the three different chemical types of osmoprotectant. Also, while mentioning the secondary functions of these molecules in heat and frost resistance there is no detail added about the primary functions of maintaining osmotic pressure and protecting cytosolic contents from denaturation by salts. I am planning to address all the mentioned deficiencies in this first section. I will be adding information about the chemical classes of osmoprotectants, how they perform their role in resisting osmotic stress and how, they are regulated by stress conditions.

Most of the edits however will be to the second section of this article titled “Role of Osmoprotectants”. This section currently covers a vary narrow range of the functions carried out by osmoprotectants. All the information it provides regards drought and salinity resistance in crops. This is likely due to it being directly copy and pasted from the abstract of M. Singh’s paper. As this violates Wikipedia’s policy I plan to delete and reform the entirety of this section. In the revision, there will be a rewording as well as additions on the discovered regulatory role of these molecules in pseudomonas aeruginosa, the function they play in soil environments with Bacillus subtilis as an example, and its possible future role as a synthetic additive in plants to make them more versatile. Brendil Sabatino (talk) 06:51, 28 September 2017 (UTC)

Osmoprotectants or compatible solutes are small organic molecules with neutral charge and low toxicity at high concentrations that act as osmolytes and help organisms survive extreme osmotic stress. In plants, their accumulation can increase survival during stresses such as drought. Osmoprotectants can be placed in three chemical classes: betaines and associated molecues, sugars and polyols,and amino acids. These molecules accumulate in cells and balance the osmotic difference between the cell's surroundings and the cytosol. In extreme cases, such as in bdelloid rotifers, tardigrades, brine shrimp, and nematodes, these molecules can allow cells to survive being completely dried out and let them enter a state of suspended animation called cryptobiosis. In this state the cytosol and osmoprotectants become a glass-like solid that helps stabilize proteins and cell membranes from the damaging effects of desiccation.

Intercellular osmoprotectant concentrations are regulated in response to environmental conditions such as osmolarity and temperature via regulation of specific transcription factors and transporters. They have been shown to play a protective role by maintaining enzyme activity through freeze-thaw cycles and at higher temperatures. It is currently believed that they function by stabilizing protein structures through preferential exclusion from the water layers on the surface of hydrated proteins which favors the native conformation and displaces inorganic salts which cause misfolding.

Role of Osmoprotectants

Compatible solutes have a functional role in agriculture. In high stress conditions such as drought or high salinity plants that naturally create or take up osmoprotectants show increased survival rates. By inducing expression or uptake of these molecules in crops in which they are naturally not present there is an increase in the areas in which they are able to be grown. For this reason, introduction of biosynthetic pathways which result in the creation of osmoprotectants in crops is a current area of research, but inducing expression at significant amounts is currently posing a barrier in this area of research.

Osmoprotectants are also important for the maintenance of top soil bacteria populations. Desiccation of top soils results in increased salinity of the soils. In these situations, the soil microbes increase the concentration of these molecule in their cytoplasm in to the molar range allowing them to persist until conditions approve.

In addition to their role in stress resistance osmoprotectants have been shown to regulate the expression of some genes such as Phospholipase C in Pseudomonas aeruginosa.

Peer Review by Kelly
The original article only had three paragraphs, but the edits were placed appropriately within the limited material. Background information of the osmoprotectants was described first, followed by cellular roles. This organization made logical sense, but there were placements that could change; the sentence regarding chemical classes should occur after the first sentence, or in a new paragraph altogether. This would avoid breaking the background information flow.

The removal of many convoluted sentences brought out the most important and relevant material, especially in the “Roles” section. However, some exclusions could be elaborated on instead, such as the role of osmoprotectants in regulating reactive oxygen species (ROS). There should be an explanation of how osmoprotectants reduce the concentration of ROS, and prevent physiological damage in plants. Cryptobiosis’ stabilization and survival functions should be expanded on in the “Roles” section, or have the description from the first paragraph moved there. The last sentence about Phospholipase C only briefly describes the regulatory functions of osmoprotectants; there should be more on the enzyme’s natural role, and the osmoprotectant-mediated effects. This would create a more encompassing view of both the regulatory aspects and relevance of osmoprotectants. Overall, the edits are on-topic, and have also eliminated redundancies regarding drought and salinity stresses from the original article.

There does not appear to be close-paraphrasing, but the second citation’s hyperlink is broken. Generally, the article's statements are neutral, concise, and connected to reliable and independent sources. The viewpoints of these scientific journals and reviews are balanced, with every few sentences in the article having their own, separate citation. More details could be garnered from the 6th and 8th citations, on the topics listed above, to improve the content. The cryptobiosis information also has multiple citations, adding further depth. Simplifying certain run-on sentences and fixing the hyperlink would just add more clarity.

Grammar (not part of peer review)

There are two run-on sentences that make the respective concepts harder to understand: “It is currently believed that they function by stabilizing protein structures through preferential exclusion from the water layers on the surface of hydrated proteins which favors the native conformation and displaces inorganic salts which cause misfolding” and “ By inducing expression or uptake of these molecules in crops in which they are naturally not present there is an increase in the areas in which they are able to be grown”. Adding commas, or breaking the sentences down, would greatly aid in understanding.

Kwei3 (talk) 05:38, 9 November 2017 (UTC)