User:Tkwon22/sandbox

Week 3: Article Evaluation
Some guidelines for evaluating an article related to genetics/molecular biology: Evaluating ChIP-sequencing:
 * Is everything in the article relevant to the article topic? Is there anything that distracted you?
 * Is the article neutral? Are there any claims, or frames, that appear heavily biased toward a particular position?
 * Are there viewpoints that are overrepresented, or underrepresented?
 * Check a few citations. Do the links work? Does the source support the claims in the article?
 * Is each fact referenced with an appropriate, reliable reference? Where does the information come from? Are these neutral sources? If biased, is that bias noted?
 * Is any information out of date? Is anything missing that could be added?
 * Check out the Talk page of the article. What kinds of conversations, if any, are going on behind the scenes about how to represent this topic?
 * How is the article rated? Is it a part of any WikiProjects?
 * How does the way Wikipedia discusses this topic differ from the way we've talked about it in class?
 * Article evaluation is a C, and it is a part of WikiProject Genetics
 * It is classified as a mid-importance article
 * No citations were used in the overview paragraph, despite claims being made within the paragraph
 * In fact, many claims are made in the article that are not always cited; there are two instances of [citation needed]
 * Words like "is thought to" are used - who are the people who "think" a statement to be true?
 * Qualifying words such as "enormously high" and "most popular" are used
 * Article is not neutral; there is a bias towards advocating for ChIP-sequencing
 * In the Current Research heading, "transcription factors" is shortened to "TFs" without any prior designation of creating an acronym for it
 * Some citations lead to a bad gateway or a dead page, causing a 503 Error
 * One citation (citation 2) leads directly a PDF of a scientific journal article; other such cited articles are linked to the PubMed page
 * Lack of consistency for citations
 * Some citations have no link to the original source, period
 * More than half of the citations are prior to 2010; some information may be outdated
 * Article makes a considerable effort to show how the genetics technique differs from alternative methods
 * Some relevant information is missing: what is the history of ChIP-sequencing? What are the explicit advantages and disadvantages of the technique?
 * The Current Research heading is not well-organized; no subheadings are used, and no links are given to the things ChIP-sequencing is being used for
 * Flow of the article is disjointed, with many sentences in the article reading as a list of statements rather than expanding upon the previous sentence
 * The talk page is quite outdated; the last edit was made in 24 May 2013, and the second last edit was made in 5 April 2010
 * Previous edits demonstrate that the article used to read like an advertisement and, to a degree, still does
 * Compared with the talk pages on featured articles of top importance such as acetic acid, the ChIP-sequencing talk page is lacking

Week 4: Add to an Article
Familiarize yourself with editing Wikipedia by adding a citation to an article. There are two ways you can do this : What I will do: add a cited sentence (or two) to the LGR6 page, and add a citation to an uncited statement.
 * Add 1-2 sentences to a course-related article, and cite that statement to a reliable source, as you learned in the online training.
 * The Citation Hunt tool shows unreferenced statements from articles. First, evaluate whether the statement in question is true! An uncited statement could just be lacking a reference or it could be inaccurate or misleading. Reliable sources on the subject will help you choose whether to add it or correct the statement.

Added cited sentence
I am adding this cited sentence to the article:"Along with the other G-protein coupled receptors LGR4 and LGR5, LGR6 is a Wnt signaling pathway mediator. LGR6 also acts as an epithelial stem cell marker in squamous cell carcinoma in mice in vivo"Using this reliable source:

https://www.nature.com/ng/journal/v49/n11/full/ng.3957.html

Huang, P. Y., Kandyba, E., Jabouille, A., Sjolund, J., Kumar, A., Halliwill, K.,. . . Balmain, A. (2017). Lgr6 is a stem cell marker in mouse skin squamous cell carcinoma. Nature Genetics,49(11), 1624-1632. doi:10.1038/ng.3957

Week 5: Selecting Potential Topics
All the candidate topic genes are underdeveloped, and have nothing on their talk pages. Essentially, no other Wikipedians have done much to contribute to the base articles, two of which were written in or before 2008. PLD3 conversely was last updated on September 2, 2017.

LGR6

 * Current article page is missing what LGR6 even does as a GPCR and its role in the cell and overall function
 * Also missing its clinical significance; current information on page may be outdated (most information seems to be from the early 2000s)
 * This was the gene that I added additional information to, so I could build upon that
 * Add information on its role in diseases like squamous cell carcinoma and its use as an epithelial stem cell marker

PICALM

 * Information, citations, and further readings are all outdated information dating back to the early 2000s --> get more recent information on it, which there should be considering PICALM's implications in Alzheimer's Disease (AD)
 * Article discusses how different alleles of PICALM are associated with increased risk of late-onset AD, but doesn't really elaborate which alleles
 * Article also doesn't really mention the function of PICALM beyond its name, phosphatidylinositol binding clathrin assembly protein
 * Need to expand on function, role in the normal cell, clinical significance, and interactions with other proteins like CLTC

PLD3

 * Need to expand on normal function of PLD3 in cells, its clinical significance, and interactions with other molecules like amyloid-beta precursor protein
 * Also need to elaborate on how its mutant forms contribute to AD risk and its role in the disease
 * May have to clarify what differentiates PLD3 from the other phospholipases in the same family (phospholipase D)
 * Would be best to try looking for more contemporary and current information --> most information on the page is from 2009 or earlier

Week 7: Finalizing topic and finding sources
Finalized Topic: PLD3

Ideas for improving the article
November 21 Edit: PLD3 article lifts the content from the Function subheading directly from the NCBI gene summary!! Need to paraphrase!!
 * As a stub-class article, the PLD3 article is lacking a cohesive structure such as a proper lead section, an organized body, and sections explaining its function, interactions with other proteins, and its relevance to the larger scope of human genetics
 * The InfoBox could also be expanded, such as including its amino acid sequence, its CAS number, and EC (Enzyme Commission) number --> the article as of November 7, 2017 has none of those things
 * GO code may be missing, but some Gene Ontology information is included in the article's InfoBox already, like its Molecular function, Cellular component, and Biological process
 * Opening sentence for lead section needs the UniProt Name of the protein as well Human Genome Organization (HUGO) gene symbol that encodes the protein
 * The article already has this, but that's all there is to the lead section
 * Need to also include a summary of PLD3's function, what it mainly interacts with, and its clinical significance (i.e., its role in Alzheimer's Disease)
 * That is to say, I would need to read through all my source articles first and generate a paragraph of what I think summarizes the most important aspects of the PLD3 protein and gene for my article --> lead section should stand on its own as a concise version of the article
 * Lead article should not contain no more than four well-composed paragraphs
 * Referencing the style guide for gene and protein articles from the Molecular and Cell Biology WikiProject for guiding the organizational structure of my article
 * Examine endoplasmic reticulum protein interactions that PLD3 may have for the interaction section
 * Look at UniProt publications and review articles

Sources (so far)

 * https://link.springer.com/article/10.1007/s12035-015-9353-5
 * https://link.springer.com/article/10.1007/s12035-014-8779-5
 * https://www.nature.com/articles/hgv201428
 * https://alzres.biomedcentral.com/articles/10.1186/s13195-014-0070-5
 * https://content.iospress.com/articles/journal-of-alzheimers-disease/jad150110
 * https://www.nature.com/articles/nature14039
 * https://www.nature.com/articles/nature14040
 * https://www.nature.com/articles/nature14036
 * https://www.nature.com/articles/nature12825
 * http://www.sciencedirect.com/science/article/pii/S0006322314003394
 * List of publications from UniProt: http://www.uniprot.org/uniprot/Q8IV08/publications
 * OMIM database entry --> use for references to history and structure descriptions of PLD3

Infobox
EC number: EC 3.1.4.4

CAS number: Not Available (?)

Other aliases for PLD3 (from human and murine UniProt):
 * schwannoma-associated protein 9, or SAM-9, in mice
 * choline phosphatase 3
 * phosphatidylcholine-hydrolyzing phospholipase D3
 * HindIII K4L homolog

Source article notes

 * Initial impressions:
 * Only a few articles are really claiming that there is clinical significance between a rare coding variant of PLD3 and late-onset Alzheimer's Disease
 * Many articles from the source list look to a study by Cruchaga et al. in 2013 which claimed that rare coding variants of PLD3 confer risk for AD
 * These same articles claim that they could not replicate the same results as Cruchaga et al. --> relation between PLD3 and AD is tenuous
 * Focus on finding sources for protein interactions and actual cellular functions of PLD3
 * PLD3 is a member of the phospholipase D protein family, however, it has no known catalytic activity unlike PLD1 and PLD2.
 * Mutations in PLD3 have been studied for their potential role in the pathogenesis of late-onset Alzheimer's disease (LOAD).
 * In 2013, Cruchaga et al. found that a particular rare coding variant or missense mutation in PLD3 (Val232Met) doubled the risk for Alzheimer's disease among cases and controls of European descent.
 * Results from the same study also indicated that PLD3 is involved in amyloid precursor protein (APP) processing, and that PLD3 loss-of-function increases risk for Alzheimer's disease by affecting APP processing.
 * PLD3 mRNA and protein expression was also reduced in AD brains, a finding corroborated by Satoh et al. who also found that PLD3 accumulates on neuritic plaques in AD brains.
 * Another study found that PLD3 mRNA and protein levels were modestly reduced in AD brains compared with non-AD brains
 * However, the same findings could not be replicated in follow-up studies on the role of PLD3 in both familial and non-familial, sporadic Alzheimer's disease in Western population samples.
 * The Val232Met PLD3 mutant was also not identified in a sample of AD patients and healthy control subjects from mainland China, suggesting that this particular PLD3 mutant may not significantly affect AD risk in the mainland Chinese population.
 * Moreover, a study by Schulte et al. showed that while there is an excess of PLD3 variants in LOAD, none of the variants described in Cruchaga et al. drive the association between PLD3 and LOAD in a European cohort, including the Val232Met variant.
 * Schulte et al. and another study also demonstrated that these rare coding variants of PLD3 were not observed in early-onset AD (EOAD) in a European cohort, suggesting that PLD3 may not have a role in EOAD.
 * The involvement of PLD3 in APP metabolism was challenged in a study by Fazzari et al., which showed that a PLD3 loss-of-function does not significantly affect amyloid plaque burden in mice, contradictory to what Cruchaga et al. found.
 * PLD3 loss-of-function in this study did, however, change the morphology of the lysosomal system in neurons, indicating that PLD3 loss-of-function may be involved in the pathophysiology of AD by contributing to the impairment of the endosomal-lysosomal system that occurs during AD.
 * In 2017, Nibbeling et al. identified PLD3 as one of the novel genes linked to spinocerebellar ataxia, another neurodegenerative genetic disease.

= PLD3 =

Lead section
Phospholipase D3, also known as PLD3, is a protein that in humans is encoded by the PLD3 gene. PLD3 belongs to the phospholipase D superfamily because it contains the two HKD motifs common to members of the phospholipase D family, however, it has no known catalytic function similar to PLD1 or PLD2. PLD3 is highly expressed in the brain in both humans and mice, and is mainly localized in the endoplasmic reticulum (ER) and the lysosome.

PLD3 may play a role in regulating the lysosomal system, myogenesis, late-stage neurogenesis, inhibiting insulin signal transduction, and amyloid precursor protein (APP) processing. The involvement in PLD3 in the lysosomal system and in APP processing and the loss-of-function mutations in PLD3 are thought to be linked to late-onset Alzheimer's disease (LOAD). However, there are also studies that challenge the finding that PLD3 and Alzheimer's disease (AD) are linked.

How APP processing by PLD3 during AD still remains unclear, and its role in the pathogenesis of AD is ambiguous. PLD3 may contribute to the onset of AD by a mechanism other than by influencing APP metabolism, with one proposed mechanism suggesting that PLD3 contributes to the onset of AD by impairing the endosomal-lysosomal system. In 2017, PLD3 was shown to have an association with another neurodegenerative disease, spinocerebellar ataxia.

Genetics
PLD3 was first characterized as a human homolog of the HindIII K4L protein in the vaccinia virus, having a DNA sequence 48.1% similar to the viral gene. The PLD3 gene in humans is located at chromosome 19q13.2, with a sequence comprising at least 15 exons and is alternatively spliced at the low GC 5' UTR into 25 predicted transcripts. Translation of the 490 amino acid-long PLD3 protein is initiated around exons 5 to 7, and ends at the stop codon in exon 15.

Structure
PLD3 is a 490 amino acid-long type 2 transmembrane protein, unlike PLD1 and PLD2 which do not contain a transmembrane protein domain in their protein structure.

The cytosolic N-terminal of the protein faces towards the cytoplasm of the cell, and lacks consensus sites for N-glycosylation. The N-terminus is also predicted to contain a transmembrane domain.

The bulk of the protein is located in the ER lumen, containing the C-termina l domain. The C-terminal domain contains seven glycosylation sites along with a prenylation motif and two HXKXXXXD/E (HKD) motifs. In PLD1 and PLD2, this is the catalytic domain or active site of the protein, which is why PLD3 was assigned to the phospholipase D superfamily. However, PLD3 has no known catalytic activity and aside from presence of the HKD motifs, PLD3 has no structural commonalities with PLD1 or PLD2.



Tissue and Subcellular Distribution
Expression of PLD3 in tissues differs with the transcript size of its mRNA. The longer 2200 base pair transcript is ubiquitously expressed in the body, exhibiting higher expression levels in the heart, skeletal muscle, and the brain. Meanwhile, the shorter 1700 base pair transcript is found in abundance in the brain, but at low expression in non-nervous tissue. PLD3 expression is especially pronounced in mature neurons in the mammalian forebrain. High expression of PLD3 is specifically seen in the hippocampus and the frontal, temporal, and occipital lobes in the cerebral cortex. The PLD3 gene is also found with high expression in the cerebellum.

Subcellular localization of PLD3 is thought to primarily be in the endoplasmic reticulum (ER), as it has been shown to co-localize with protein disulfide-isomerase, a protein known to be a marker for the ER. PLD3 may also be localized in lysosomes, co-localizing with lysosomal markers LAMP1 and LAMP2 in lysosomes in separate studies. PLD3 was identified as a protein in insulin secretory granules derived from pancreatic beta cells.

Function
PLD3 is a member of the phospholipase D protein family, however, it has no known catalytic activity like that of PLD1 and PLD2.

PLD3 may play some role in influencing protein processing through the lysosome as well as a regulatory role in lysosomal morphology. Some studies suggest that PLD3 is involved in amyloid precursor protein (APP) processing and regulating amyloid beta (Aβ) levels. Overexpression of wildtype PLD3 is linked to a decrease in intracellular APP and extracellular amyloid beta isoforms Aβ40 and Aβ42, while a knockdown of PLD3 is linked to an increase in extracellular Aβ40 and Aβ42. PLD3 was implied to be involved in sensing oxidative stress, such that suppressing the PLD3 gene with short hairpin RNA increased the viability of cells exposed to oxidative stress.

Increased PLD3 expression was shown to increase myotube formation in differentiated mouse myoblasts in vitro, and ER stress which also increases myotube formation was also shown to increase PLD3 expression. Decreasing PLD3 expression meanwhile decreases myotube formation. These findings suggest a possible role of PLD3 in myogenesis, although its exact mechanism of action remains unknown. Overexpression of PLD3 in mouse myoblasts in vitro may inhibit Akt phosphorylation and block signal transduction during insulin signalling. PLD3 may be involved in the later stages of neurogenesis, contributing to processes associated with neurotransmission, target cell innervation, and neuronal survival.

Elevated expression of PLD3 was found to be one of the consistent factors that contribute to the self-renewal activity of hematopoietic stem cell populations, suggesting a possible role of PLD3 in the mechanism behind the maintenance of durable, long-term self-renewing cell populations.

Interactions
The human progranulin protein (PGRN), encoded by the human granulin gene (GRN), is co-expressed with and interacts with PLD3 accumulated on neuritic plaques in AD brains. PLD3 may interact with APP and amyloid beta, as some studies indicate that PLD3 is involved with APP processing and regulating Aβ levels. PLD3 may also interact with Akt and insulin in myoblasts in vitro.

Alzheimer's disease
Mutations in PLD3 have been studied for their potential role in the pathogenesis of late-onset Alzheimer's disease (LOAD).

In 2013, Cruchaga et al. found that a particular rare coding variant or missense mutation in PLD3 (Val232Met) doubled the risk for Alzheimer's disease among cases and controls of European and African-American descent. PLD3 mRNA and protein expression was reduced in AD brains compared with non-AD brains in regions that PLD3 is normally found with high expression, and another study also found that PLD3 accumulates on neuritic plaques in AD brains. Another study found that the Val232Met PLD3 rare coding variant may increase risk for LOAD, finding an association between PLD3 and brain atrophy in the regions vulnerable to neurodegeneration in LOAD. A common PLD3 single nucleotide polymorphism (SNP) was also found to have an association with Aβ pathology among normal, healthy individuals, suggesting that common PLD3 variants may also be involved in the pathogenesis of AD. A meta-analysis conducted in 2015 concluded that the Val232Met PLD3 variant has a modest effect on increasing AD risk.

However, the findings from Cruchaga et al. could not be replicated in follow-up studies on the role of PLD3 in both familial and non-familial, sporadic Alzheimer's disease in Western population samples. The Val232Met PLD3 mutant was also not identified in a sample of AD patients and healthy control subjects from mainland China, suggesting that this particular PLD3 mutant may not significantly affect AD risk in the mainland Chinese population. A study showed that while there is an excess of PLD3 variants in LOAD, none of the variants described by Cruchaga et al. drive the association between PLD3 and LOAD in a European cohort, including the Val232Met variant. This study along with an additional study also demonstrated that these rare coding variants of PLD3 were not observed in early-onset AD (EOAD) in a European cohort, suggesting that PLD3 may not have a role in EOAD.

The underlying mechanisms on how mutations in PLD3 affects APP processing in AD remains unclear. Results from the study by Cruchaga et al. indicated that PLD3 loss-of-function increases risk for Alzheimer's disease by affecting APP processing. How mutations in PLD3 affect APP processing along with Aβ levels was suggested to be due to alterations in its function in the lysosome. The involvement of PLD3 in APP processing was challenged in a recent study which showed that a PLD3 loss-of-function does not significantly affect the burden of amyloid plaques on AD development in mice. PLD3 loss-of-function in this study did, however, change the morphology of the lysosomal system in neurons, indicating that PLD3 loss-of-function may still be involved in the pathophysiology of AD through some other mechanism such as by contributing to the impairment of the endosomal-lysosomal system that occurs during AD.

Spinocerebellar ataxia
In 2017, the PLD3 gene was identified as one of the novel genes linked to spinocerebellar ataxia, another neurodegenerative genetic disease.