User:The Shabang/sandbox

To-do/consider (italics = completed; strikethrough = dropped)

 * 1) Edit the interactions section
 * 2) first learn how to edit double columns
 * 3) I hyperlinked the following words in the article copy below or my edits (34 total):
 * 4) *Phospholipase, choline, phospholipid, phosphatidylcholine, hydrolysis, phosphatidic acid, agonist
 * 5) *G protein-coupled receptor, receptor tyrosine kinase, signal transduction, membrane trafficking, coagulation
 * 6) *Mitosis, apoptosis, endocytosis, B cell, plasma membrane, endosome, Golgi apparatus, splice variant, Arf1
 * 7) *Calcium, Calphostin-c, magnesium, PIP2, PKC, Ribosomal S6 kinase, HeLa, cDNA, exocytosis
 * 8) *Alzheimer's Disease, cancer, type II diabetes, thrombosis
 * 9) Generate my own diagram of a phosphatidylcholine.
 * 10) I will add several new sections, including History, Structure, and Applications.
 * 11) Learn how to cite properly
 * 12) I will edit several other sections, including the sections on Function, Interactions, and Inhibitors.
 * 13) *I will add brief sub-sections to the Function section to expound on existing terms.
 * 14) Create oral presentation.
 * 15) Get online permission from the instructor to upload his image to Wikimedia Commons and then insert it into my draft

= Sources (used content in italics) =

Primary:

 * 1) Hanahan, D. J., & Chaikoff, I. L. (1947). The phosphorus-containing lipides of the carrot. Journal of Biological Chemistry, 168, 233-240.
 * 2) * "there exists in the raw carrot an enzyme ... capable of splitting choline from phospholipides"
 * 3) * Phospholipase D (PLD) was defined in 1947 by Hanahan and Chaikoff in carrot extracts as a phospholipid-specific phosphodiesterase that hydrolyzed phosphatidylcholine (PtdCho) to generate phosphatidic acid (PtdOH) and choline (Su, W., & Frohman, M. A. (2010). 3 Methods for Measuring the Activity and Expression of Phospholipase D. Lipid-Mediated Signaling, 55.)

Review articles:

 * 1) Jenkins, G. M., & Frohman, M. A. (2005). Phospholipase D: a lipid centric review. Cellular and Molecular Life Sciences CMLS, 62(19-20), 2305-2316.
 * 2) * "This review focuses on the lipid precursors and products of mammalian PLD metabolism, especially phosphatidic acid and the roles this lipid performs in the mediation of the functions of PLD"
 * 3) *"PLD activity was not demonstrated in a mammalian system until 1975, when Saito and Kanfer described a release of choline and ethanolamine from rat brain preparations"
 * 4) *"Mammalian PLD1 and PLD2 both contain two HKD motifs"
 * 5) *"Reports on PLD1 in numerous cell lines have described perinuclear localization suggestive of a Golgi, endoplasmic reticulum or late endosomal distribution" but this localization is still disputed.
 * 6) Selvy, P. E., Lavieri, R. R., Lindsley, C. W., & Brown, H. A. (2011). Phospholipase D: enzymology, functionality, and chemical modulation. Chemical reviews, 111(10), 6064-6119.
 * 7) * PLD1 subcellular localization. Also several organisms that contain PLD
 * 8) *"Because of the small headgroup, PA facilitates changes in lipid bilayer curvature that are important for membrane fusion events, such as vesicular trafficking and endocytosis"
 * 9) **It's thought that PA, a major product of PLD activity, is able to assist in membrane curvature due to its head group being smaller than in many other lipids.
 * 10) *"A large subset of enzymes with PLD activity share a conserved HxKxxxxDx6GSxN motif (HKD),18 or a variation thereof, which is responsible for catalytic activity"
 * 11) *History:
 * 12) **"While PLD was first identified in plants in 1947, PLD activity was not described in mammalian tissues until 1973 by Kanfer and colleagues."
 * 13) **"Cloning of plant and yeast PLD enzymes facilitated cloning of a full length PLD enzyme from HeLa cell cDNA205 and rat325 PLD1" in 1995 and 1997
 * 14) *early endosome, and the Golgi apparatus. Though there are two splice variants of the protein, PLD1a and PLD1b, they do not seem to localize any differently
 * 15) *implicated in platelet coagulation
 * 16) *potential therapeutic applications:
 * 17) **diabetes: "amino acids 762-801 of PLD1 interact with phosphoprotein enriched in diabetes (PED/PEA15)... . This protein is overexpressed in several tissues in individuals with type 2 diabetes, and its overexpression in cultured cells and transgenic animals impairs insulin regulation of glucose transport by a mechanism that is dependent on its physical interaction with PLD"
 * 18) **cancer: "They showed that PLD activity is necessary for the H-Ras induced transformation of Rat-2 fibroblasts. Wild-type Rat2 fibroblasts transfected with H-RasV12 grow in soft agar and form tumors in nude mice, but Rat-2 V25 cells (that overexpress a dominant-negative PLD) do not form colonies in soft agar and do not form tumors in nude mice when transfected with H-RasV12."
 * 19) **thrombosis: "Blood flow was monitored in two arterial thrombosis models triggered by chemical or mechanical perturbations and showed decreased occlusion in the PLD1-/- mice as compared to wild-type mice, thus showing protection against thrombosis."
 * 20) Donaldson, J. G. (2009). Phospholipase D in endocytosis and endosomal recycling pathways. Biochimica Et Biophysica Acta (BBA)-Molecular and Cell Biology of Lipids, 1791(9), 845-849.
 * 21) * I presented on this article.
 * 22) *"The localization of PLD2 and PLD1 to the PM could affect both endocytosis from the PM and fusion of recycled endosomes back to the PM."
 * 23) *Though biological activity of PLD1 is typically low, it has been shown to associate both at the plasma membrane and the late endosome.
 * 24) *one experiment in B cells showed that limiting PLD1 led to significantly reduced endocytosis of the B cell receptor

Other articles:

 * 1) Tanguy, E., de Bagneaux, P. C., Kassas, N., Ammar, M. R., Wang, Q., Haeberlé, A. M., ... & Chasserot-Golaz, S. (2020). "Mono-and Poly-unsaturated Phosphatidic Acid Regulate Distinct Steps of Regulated Exocytosis in Neuroendocrine Cells." Cell Reports, 32(7), 108026.
 * 2) * I presented on this article.
 * 3) *An experiment shows that "PLD1 knockout reduced catecholamine secretion in mice."
 * 4) *"Exocytosis Is Affected at Distinct Stages in Adrenal Chromaffin Cells," where PLD1 knockout reduced the number of exocytotic fusion events and lengthened the event average time.
 * 5) Andersson, L., Boström, P., Ericson, J., Rutberg, M., Magnusson, B., Marchesan, D., ... & Borén, J. (2006). PLD1 and ERK2 regulate cytosolic lipid droplet formation. Journal of cell science, 119(11), 2246-2257.
 * 6) *Just as the title says, PLD1 helps regulate the generation of lipid droplets in the cytoplasm.
 * 7) Zeniou-Meyer, M., Liu, Y., Béglé, A., Olanich, M. E., Hanauer, A., Becherer, U., ... & Vitale, N. (2008). The Coffin–Lowry syndrome-associated protein RSK2 is implicated in calcium-regulated exocytosis through the regulation of PLD1. Proceedings of the National Academy of Sciences, 105(24), 8434-8439.
 * 8) *RSK2 is a regulator of PLD1
 * 9) Siddiqi, A. R., Srajer, G. E., & Leslie, C. C. (2000). Regulation of human PLD1 and PLD2 by calcium and protein kinase C. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research, 1497(1), 103-114.
 * 10) *"PLD1 but not PLD2 activity was slightly enhanced by magnesium"
 * 11) *Calcium and PKC are activators
 * 12) Thakur, R., Naik, A., Panda, A., & Raghu, P. (2019). Regulation of membrane turnover by phosphatidic acid: cellular functions and disease implications. Frontiers in Cell and Developmental Biology, 7, 83.
 * 13) *"In cells undergoing phagocytosis, PLD1 is recruited to nascent and internalized phagosomes, whereas PLD2 is only observed on nascent phagosomes."
 * 14) *Alzheimer's Disease: "several studies have implicated PA produced by PLD1 and PLD2 in the intracellular trafficking of β-amyloid precursor protein (APP) and presenilin with important implications for amyloidogenesis"
 * 15) *"In genetically engineered mouse models, PLD1 can modulate tumor progression"
 * Yao, Y., Li, J., Lin, Y., Zhou, J., Zhang, P., & Xu, Y. (2020). Structural insights into phospholipase D function. Progress in Lipid Research, 101070.
 * 1) *"The messenger RNAs of some special PLD subtypes would generate alternative splicing variants, for instance, the full-length PLD1 is also named PLD1a and could be truncated into a smaller PLD1b"

= Excerpts from wiki article "Phospholipase D1" with my edits in italics = Phospholipase D1 (PLD1) is an enzyme that in humans is encoded by the PLD1 gene, though analogues are found in plants, fungi, prokaryotes, and even viruses [Selvy, 2011]. ...

History
''The possibility of PLD1 was first mentioned in 1947 [Frohman] by authors Hanahan and Chaikoff at Berkeley when describing a carrot enzyme that could "[split] choline from phospholipids" [Hanahan & Chaikoff]. PLD was first derived in mammals in 1975 by Saito and Kanfer, who noted its activity in rats [Jenkins]. PLD was first cloned from HeLa cell cDNA in 1995, while mammalian PLD1 was first cloned from a rat in 1997 [Selvy, 2011].''

Function
Phosphatidylcholine (PC)-specific phospholipases D (PLDs) EC 3.1.4.4 catalyze the hydrolysis of PC to produce phosphatidic acid (PA) and choline. A range of agonists acting through G protein-coupled receptors and receptor tyrosine kinases stimulate this hydrolysis. PC-specific PLD1 activity has been implicated in numerous cellular pathways, including membrane trafficking, signal transduction [swapped the two previous terms places], platelet coagulation, and the regulation of mitosis, apoptosis, and the creation of cytoplasmic lipid droplets [Andersson; Selvy] (Hammond et al., 1995).[supplied by OMIM]

Membrane trafficking
''PLD1 has been shown to associate at the plasma membrane, late endosome [Donaldson], early endosome, and the Golgi apparatus [Jenkins; Selvy]. There is evidence that PA is able to assist in negative membrane curvature due to its head group being smaller than in many other lipids [Selvy]. One experiment with PLD1 knockout showed a significant reduction in the number of exocytotic fusion events, implying a strong role in exocytosis [Tanguy].''

Signal transduction
''PLD1 may play a role in some cells in the endocytosis of signaling receptors or exocytosis of signaling molecules. For example, one experiment in B cells showed that limiting PLD1 led to significantly reduced endocytosis of the B cell receptor [Donaldson]. Another experiment showed that knocking out PLD1 may hinder the ability of mice to secrete catecholamines, molecules that are essential for vesicular communication across the body [Tanguy].''

Structure
''Mammalian PLD1 has several domains for activators, inhibitors, and catalysis, which it shares with PLD2. Domains for both activation and inhibition are referred to as the phox homology (PX) and pleckstrin homology (PH) domains. The catalytic domain consists of two HKD regions, so named for three of the amino acids that are key in catalysis. These domains are conserved across many organisms [Jenkins, 2005; Selvy, 2011]. There are two splice variants of the protein, PLD1a and PLD1b, but they do not seem to localize any differently [Selvy].''

Applications
Alzheimer's Disease: PA, which is produced in part by PLD1, seems to be involved in the movement of β-amyloid, which could precede amyloidogenesis [Thakur].

Cancer: certain rat tumors with dominant negative PLD do not appear to form new colonies or tumors [Selvy; Thakur]

Thrombosis: PLD knockout mice appear to have reduced occlusion, thus offsetting thrombosis [Selvy].

Type II Diabetes: the protein PED/PEA15 is often elevated in type II diabetic patients, thus enhancing PLD1 activity, and in turn impairing insulin [Selvy].

Interactions (changes have not been added to the article; did previous changes mess up these citations in the article?)
Phospholipase D1 has been shown to interact with:


 * Alpha-synuclein ,
 * Amphiphysin ,
 * Arf1, an activator [Selvy]
 * BIN1 ,
 * Calcium, an activator [Siddiqi]
 * CDC42, an activator [Jenkins]
 * Magnesium, an activator [Siddiqi]
 * PEA15 ,
 * PIP2, an activator [Donaldson]
 * PKC, an activator [Siddiqi]
 * Protein kinase N1 ,
 * Rac1, an activator
 * RALA, and
 * RHO GTPase family, as activators [Jenkins; Selvy]
 * RSK2, a regulator [Zeniou-Meyer]

Inhibitors

 * Calphostin-c, an inhibitor [Selvy]
 * VU-0359595: 1,700-fold selective versus phospholipase D2, IC50 = 3.7nM. [Selvy]

Rubric
(Instructor's description; on LS see also "Content/Final Project/Wiki Project")

"A minimum of one section must be added to the site. The quantity and quality of the added content will be evaluated based on:


 * 1) Readability - Is the web page suitable for first-time/general users as well as for those looking to understand the topic in more detail?
 * 2) Content – is the material an accurate representation of all current, available knowledge on the topic? Has the group enhanced the quality of the page?"

"A minimum of 1 figure or scheme must be added to the site.

"I will present a review of my topic (the content of the articles I read) and briefly show my contribution to the Wiki site."

"I must submit a 2 page written report containing a careful review of my topic referencing the articles read. In an appendix include: When reviewing, consider:
 * "will be given during class and will be based on the same literature as will be reviewed in the written report. Typically, oral reports will be 10-12 minutes and students are encouraged to use PowerPoint in preparing their presentations.  The maximum time of 12 minutes will be strictly enforced.
 * Oral reports should include...
 * background/overview
 * summaries of related research published in peer-reviewed journals (reviews and primary reports) and
 * written to general reader interested in the topic
 * Changes made to the article, and why (include screen shots of before and after)
 * Peer review suggestions made
 * Peer review suggestions incorporated ...
 * The professors will expect that the feedback you get from oral presentation will be fully incorporated into your final written report"

1. Is the web page suitable for first-time/general users as well as for those looking to understand the topic in more detail?

2. Is there a logical flow to the page?

3. Do the contents of each section justify its length?

4. Has a particular section been over-emphasized or under-emphasized compared to others?

5. Does the sandbox satisfy the aims/objectives listed in their outline?

6. Are all the important terms linked to their respective Wikipedia pages for further reference?

7. Do the images add to the educational value of the article?

8. Are the references relevant and integrated well into the article?

9. Rate the overall presentation of the webpage. Check for typos, hard-to-read images and equations or syntax errors.

10. Does the website satisfy all the assigned criteria (a minimum of one section, one figure, and three references)?