User talk:Tsoroski/sandbox

Bacterial Circadian Rhythms Article Critique
The Wikipedia article "Bacterial circadian rhythms" is well-structured and relevant, however it could improve on citing sources, writing style, and close paraphrasing.

The Wikipedia training library recommends "citing at least once per paragraph". However, the two introductory paragraphs of the article did not cite any sources. This is problematic as the article begins by clearly defining a bacterial circadian rhythm, but does not cite any source to verify this definition.

The article also employs a persuasive tone throughout. The author uses the phrase, "ground-breaking study", to describe research relevant to the article. According to the Wiki Education training module, value statements such as "the best" or "the most important" should be avoided. The article should be as neutral as possible, so "ground-breaking study", should be replaced with "new research shows".

The article also draws its own conclusions. This is evident in the sentence; "Apparently cyanobacteria are able to simultaneously and accurately keep track of two timing processes that express significantly different periods," especially since the author does not cite any source. The second pillar of Wikipedia is that "[it] has a neutral point of view", and to avoid "sharing your own analysis of the information you find". This article is clearly analyzing information, which undermines the credibility of the article as a whole.

Furthermore, the author closely paraphrases. The article says,

"circadian clocks are usually assumed to enhance the fitness of organisms by improving their ability to adapt to daily cycles".

Comparing that to the first sentence of the cited journal article,

"Circadian clocks are thought to enhance the fitness of organisms by improving their ability to adapt to extrinsic influences, specifically daily changes in environmental factors".

It is immediately obvious that the author of the Wikipedia article plagiarized the journal article.

In conclusion, adding citations, utilizing neutrality, and avoiding plagiarism would allow for this article to go from mediocre to excellent.

Tsoroski (talk) 21:03, 16 September 2017 (UTC)

Article Critique Reflection
The main take-away from critiquing the article was that Wikipedia does not condone authors from drawing their own conclusions or interpreting data themselves, as Wikipedia serves to provide facts in a neutral manner. I will keep this in mind when using Wikipedia from now on, so that I can decide where scientists draw conclusions and to not confuse that with Wikipedia authors drawing conclusions.

Tsoroski (talk) 21:03, 16 September 2017 (UTC)

Assignment 2: Porin (protein)
The Wikipedia article "Porin (protein)" is coherent, however it needs to be expanded upon in some sections. As well, it is lacking proper referencing.

This article is an excellent candidate for improvement, as it is rated as "High-Importance". The article has notability, with over 45,000 references appearing in an online UBC library search, a 300+ page book focusing only on porins, and hundreds of journal articles on the subject, many of which have been published recently.

The first section of the article is about porin structure. The section gives a good overview of the general structure of porins, however it fails to mention the defining aspects of porin structure. Information about the basic parameters of porins, (e.g. tilting angle (a), shear number (S), strand number (n), and barrel radius (R)), would be a valuable addition. These parameters have widespread use, and there have even been formulas developed that relate these parameters together. Furthermore, upon examination of a quote from the article:

"The porin channel is partially blocked by a loop, called the eyelet, which projects into the cavity. In general, it is found between strands 5 and 6 of each barrel, and it defines the size of solute that can traverse the channel. It is lined almost exclusively with charged amino acids arranged on opposite sides of the channel, creating a transversal electric field across the pore."

Comparing the Wikipedia article to the cited source:

"The channel is, however, partially blocked by a long loop region between β strands 5 and 6 that projects into the channel. This arrangement [...] defines the size of solute molecules that can traverse the channel. The eyelet is lined almost exclusively with positively and negatively charged groups that are arranged on opposite sides of the channel, causing a transversal electric field across the pore."

It is clear that the Wikipedia article is not just closely paraphrasing, it is plagiarizing. As well, the source cited was published in 1999. There have been significant research advances relating to porins and their structure in the last eighteen years. The information in the section is also incorrect. Current research shows that the individual amino acids in a porin can have a high amount of variation. The Wikipedia article discusses how the porin is negatively charged due to having "four glutamic acid and seven aspartic acid residues". It is now known that not all amino acids have eyelets, and if they do have eyelets, there is no guarantee that there will be four glutamic acid and seven aspartic acid residues.

Furthermore, the "Cellular Roles" section of the article needs citations. There are three "citation needed" markers in the section. To improve this section, numerous literature sources will be added. A section on the role that porins play in terms of antibiotics would be a valuable addition to this article, as there is extensive research into porins and antibiotics.

Tsoroski (talk) 23:56, 24 September 2017 (UTC)

Assignment 3
Original- Porin (protein)

Structure
Porins are composed of β strands, which are, in general, linked together by beta turns on the cytoplasmic side and long loops of amino acids on the other. The β strands lie in an antiparallel fashion and form a cylindrical tube, called a β barrel. The amino acid composition of the porin β strands are unique in that polar and nonpolar residues alternate along them. This means that the nonpolar residues face outward so as to interact with the nonpolar lipids of outer membrane, whereas the polar residues face inwards into the center of the beta barrel to create the aqueous channel.

The porin channel is partially blocked by a loop, called the eyelet, which projects into the cavity. In general, it is found between strands 5 and 6 of each barrel, and it defines the size of solute that can traverse the channel. It is lined almost exclusively with charged amino acids arranged on opposite sides of the channel, creating a transversal electric field across the pore. The eyelet has a local surplus of negative charges from four glutamic acid and seven aspartic acid residues (in contrast to one histidine, two lysine and three arginine residues) is partially compensated for by two bound calcium atoms, and this asymmetric arrangement of molecules is thought to have an influence in the selection of molecules that can pass through the channel.

Edits- Porin (protein)

Structure
Porins are composed of β strands, which are linked together by beta turns on the cytoplasmic side and long loops of amino acids on the other. The β strands lie in an antiparallel fashion and form a cylindrical tube, called a β barrel. The amino acid composition of the porin β strands are unique in that polar and nonpolar residues alternate along them. This means that the nonpolar residues face outward so as to interact with the nonpolar lipids of outer membrane, whereas the polar residues face inwards into the center of the beta barrel to create the aqueous channel. The specific amino acids in the channel determine the specificity of the porin to different molecules.

The β barrels that make up a porin are composed of as few as eight β strands to as many as twenty-two β strands. The individual strands are joined together by loops and turns. The majority of porins are monomers, however some dimeric porins have been discovered, as well as an octameric porin. Depending on the size of the porin, the interior of the protein may either be filled with water, have up to two β strands folded back into the interior, or contain a "stopper" segment composed of β strands.

All porins form homotrimers in the outer membrane, meaning that three identical porin subunits associate together to form a porin super-structure with three channels. Hydrogen bonding and dipole-dipole interactions between each monomer in the homotrimer ensure that they do not dissociate, and remain together in the outer membrane.

Several parameters have been used to describe the structure of a porin protein. They include the tilting angle (α), shear number (S), strand number (n), and barrel radius (R). The tilting angle refers to the angle relative to the membrane. The shear number (S) is the number of amino acid residues found in each β strands. Strand number (n) is the amount of β strands in the porin, and barrel radius (R) refers to the radius of the opening of the porin. These parameters are related via the following formulas:

$$ 2 \pi R=\frac{nb}{2cos( \alpha )} $$

and,

$$tan(\alpha)= \frac{S a}{nb}$$

Using these formulas, the structure of a porin can be determined by knowing only a few of the available parameters. While the structure of many porins have been determined using X-ray crystallography, the alternative method of sequencing protein primary structure may also be used instead.

Tsoroski (talk) 01:18, 10 October 2017 (UTC)

Tsoroski Peer Review of Article: Porin (Protein)
This wiki article on Porin (protein) was already structured with different categories explaining porins, but was out of date and is rated as “high-importance” and requires improvements, so this was good choice of article to edit.

The author did a good job staying unbiased with their tone and style. The article is easy to read and flows well, and draws from additional sources. They bring the original articles’ content up more to date and into this century, since some of the original article’s references are from 1991, 1999, etc.. One might notice that some of the sources are still old (2004, 2006, etc.), but this information is still relevant and is what additional detailed/in-depth experiments are based off of today. (1)

Overall, my main critique is that it is possible to add even more information to this article. The author did draw from numerous sources, but could expand more on those ideas, possibly even creating sub-sections of the article’s “structure” section, ie., expanding on the different types of porins (monomers/dimers/octamers), or adding a category/table discussing the different porins and relating them to which organisms they are present in. There could also be a new section dedicated to signaling pathways and porins, or a section added on diseases and problems if an organisms’ porins do not function properly, or a section on possibilities for the future and porins.

This is all a lot to consider and can get highly specific, and since the author has already done a good job in the “structure” section, maybe they could focus on picking one other section to add to the article with detailed information, rather than adding all the sections I’ve suggested, to be efficient with time and accurate with the presentation of information.

Some articles the author may want to look at to help (mostly involving signaling): 1.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706956/ 2.	https://www.ncbi.nlm.nih.gov/pubmed/13129608/ 3.	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC97875/ 4.	https://www.ncbi.nlm.nih.gov/pubmed/16455995

(1)	: http://jb.asm.org/content/187/24/8232

KaileeWark (talk) 06:55, 9 November 2017 (UTC)

Structure
Porins are composed of β strands, which are linked together by beta turns on the cytoplasmic side and long loops of amino acids on the other. The β strands lie in an antiparallel fashion and form a cylindrical tube, called a β barrel. The amino acid composition of the porin β strands are unique in that polar and nonpolar residues alternate along them. This means that the nonpolar residues face outward so as to interact with the nonpolar lipids of outer membrane, whereas the polar residues face inwards into the center of the beta barrel to create the aqueous channel. The specific amino acids in the channel determine the specificity of the porin to different molecules.

The β barrels that make up a porin are composed of as few as eight β strands to as many as twenty-two β strands. The individual strands are joined together by loops and turns. The majority of porins are monomers, however some dimeric porins have been discovered, as well as an octameric porin. Depending on the size of the porin, the interior of the protein may either be filled with water, have up to two β strands folded back into the interior, or contain a "stopper" segment composed of β strands.

All porins form homotrimers in the outer membrane, meaning that three identical porin subunits associate together to form a porin super-structure with three channels. Hydrogen bonding and dipole-dipole interactions between each monomer in the homotrimer ensure that they do not dissociate, and remain together in the outer membrane.

Several parameters have been used to describe the structure of a porin protein. They include the tilting angle (α), shear number (S), strand number (n), and barrel radius (R). The tilting angle refers to the angle relative to the membrane. The shear number (S) is the number of amino acid residues found in each β strands. Strand number (n) is the amount of β strands in the porin, and barrel radius (R) refers to the radius of the opening of the porin. These parameters are related via the following formulas:

$$ 2 \pi R=\frac{nb}{2cos( \alpha )} $$

and,

$$tan(\alpha)= \frac{S a}{nb}$$

Using these formulas, the structure of a porin can be determined by knowing only a few of the available parameters. While the structure of many porins have been determined using X-ray crystallography, the alternative method of sequencing protein primary structure may also be used instead.

Tsoroski (talk) 22:32, 18 November 2017 (UTC)