User:Ashley Young/sandbox

Week 3: Article Evaluation

Article: Complementary DNA

• Everything in the article was relevant to the topic of Complementary DNA
• The article does in fact, appear to be neutral, it does not appear to be biased towards a particular position
• Yes there are viewpoints that are underrepresented! The heading titled "Viruses" only gives a single sentence explanation and shows no sign of any citation making it impossible for the reader to know where this information was obtained from
• There are a lot of citations that need to be added as there are very few. However, the few that are present do work and support claims in the article and seem to be from reliable sources.
• More information needs to be added to this page for sure as it is very brief
• The Talk page of the article is very outdated posts from 2006 and there is dispute on a sorting out similar pages
• This article is rated as a Start-Class on the project's quality scale with mid-importance as part of the WikiProject Genetics and is rated Start-Class with high importance as part of the WikiProject Molecular and Cell Biology
• Different then how it was talked about in class due to the fact it wasn't as descriptive

Week 4: Add to an article

Added a few sentences under "Viruses" section in the article on Complementary DNA and backed it up by adding a citation reference [3].

Week 5: Potential Articles

• ESR1 gene - the article for ERα states it is encoded by the gene ESR1 but ESR1 itself doesn't have it's own article so I could add in a function, structure, clinical significance, etc. as sections about the gene
• FITM2 gene - add to the function, add it's clinical significance **I THINK THIS IS MY #1 choice.
• OPN1LW gene - add structure and it's clinical significance
• Ubiquitin C

Week 7: Fidnalizing Topic and Finding Sources

Topic: FIT2/FITM2 gene FITM2

• Only one line for function
• Add in "What it codes for"
• Add in "Structure"
• Add in "Function"
• Add in "Clinical Uses or Diseases a lack of it can result in"

Sources:

• https://www.ncbi.nlm.nih.gov/gene/128486
• https://www.ncbi.nlm.nih.gov/pubmed/21396481
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975007/
• https://www.ncbi.nlm.nih.gov/pubmed/26304121
• https://www.ncbi.nlm.nih.gov/pubmed/18160536
• https://www.ncbi.nlm.nih.gov/pubmed/22106267
• https://www.ncbi.nlm.nih.gov/pubmed/20520733
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5312003/

Week 8: Article Draft AND Peer Review

Article Draft

What it codes for / Evolutionary history

• From NCBI: FITM2 also known as FIT2, stands for fat storage inducing transmembrane protein 2, protein coding, belongs to evolutionary conserved family of proteins involved in fat storage
• From Evolutionarily conserved gene family important for fat storage: ability to store fat in form of cytoplasmic triglyceride droplets is conserved from Saccharomyces cerevisiae to humans, FIT1 and FIT2 DR resident membrane proteins inducing lipid droplet accumulation, Ex: of shRNA silencing of FIT2 and results to highlight important role for FIT2 in lipid droplet formation in vivo, Triglycerides stored in cytoplasm surrounded by monolayer of phospholipid in distinct structures/organelles such as lipid droplets and provides other names for lipid droplets
• Direct binding of triglyceride to fat storage-inducing transmembrane proteins 1 and 2 is important for lipid droplet formation: evolutionary conserved family ER resident transmembrane proteins important for LD formation, FITM1/FIT1 and FITM2/FIT2, FIT1 292-aa and FIT2 262-aa long, 6 transmembrane domains, both N and C termini facing the cytosol, FIT1 and FIT2 share similarity of 50% at the amino acid level, do not share homology to known protein domains or other protein families, FIT2 ancient orthologue of the FIT family and has orthologues found in Saccharomyces cerevisiae, expression of FIT1 and FIT2 in cells lead to triglyceride droplet formation

Structure

• Fat Storage-inducing Transmembrane Protein 2 is required for Normal Fat Storage in Adipose Tissue: FIT2 functions downstream of DGAT enzymes, purified FIT2 binds directly to triacylglycerol that is essential for FIT2 mediated lipid droplet formation in cells, triglyceride lens forms between leaflets of the ER FIT2 through ability to bind triacylglycerol might increase solubility of triacylglycerol in the ER leading to accumulation of sufficient triacylglycerol to facilitate the process of lipid droplet formation, gatekeeper or regulator downstream of triacylglycerol biosynthesis that determines the number of nascent LDs that will form, triacylglycerol in adipose tissue is the major energy storage form in higher eukaryotes
• Postnatal Deletion of Fat storage-inducing Transmembrane Protein 2 (FIT2/FITM2) Causes Lethal Enteropathy: part of a two gene family, FIT2 35% identity with FIT1, FIT1 expressed, where FIT2 expressed, FIT2 262 amino acid protein in mammals, 6 transmembrane domains, both N and C termini facing the cytoplasm,

Function

• From Evolutionarily conserved gene family important for fat storage: recent discoveries of aspects to lipid droplets from S. cerevisiae, drosophila, and mammalian cells, highly regulated process, lipid droplet formation, and association with cytoplasmic face of the ER, importance in accumulation of lipid droplets, four major lines of evidence that FIT proteins are important for the accumulation of lipid droplets,
• Fat Storage-inducing Transmembrane Protein 2 is required for Normal Fat Storage in Adipose Tissue: FIT2 required for normal triacylglycerol storage in adipose tissue, not essential for LD formation but required for normal storage of triacylglycerol and maintenance for metabolic homeostasis,
• Postnatal Deletion of Fat storage-inducing Transmembrane Protein 2 (FIT2/FITM2) Causes Lethal Enteropathy: Cytosolic lipid droplets are organelles made up of hydrophobic core of neutral lipids such as triglycerides and cholesteryl esters surrounded by phospholipid monolayer, common view on LD formation, two pools of LDs have been identified, FIT2 essential for adipose tissue triglyceride storage and survival,
• Direct binding of triglyceride to fat storage-inducing transmembrane proteins 1 and 2 is important for lipid droplet formation: unique function mediate partitioning of de novo synthesized triglyceride into LD without meditating triglyceride biosynthesis, lacking in adipocytes lead to reduced size and number LDs per cell, FIT proteins bind directly to triglyceride and this binding important for LD formation, distinction between FIT1 and FIT2, FIT2 long term TAG storage, FIT1 rapidly turning over LDs in skeletal,

Clinical Uses/Disease

• From Evolutionarily conserved gene family important for fat storage: under normal physiological conditions, lipid droplets involved in vs under rapid lipid droplet formation and its role in causing obesity, as well as increased risk for diseases like type 2 diabetes and cardiovascular diseases as well

Peer Review

I have left a review on the "talk" page of User:Achild2/sandbox.

Week 10: Full Written Draft

FITM2 (fat storage inducing transmembrane protein 2) also known as FIT2, is a protein coding gene. FITM2 plays a role in fat storage and is also a part of a protein family that has been evolutionarily conserved. Conserved from Saccharomyces cerevisiae to humans is the capability to take fat and store it as cytoplasmic triglyceride droplets. Both FIT2 and FIT1 from the same family are present in the endoplasmic reticulum (ER). FIT proteins facilitate the segregation of triglycerides into cytosolic lipid droplets but at the same time do not facilitate the biosynthesis of triglycerides.  FITM2 is a protein in the ER membrane which aids in instigating the regulation of lipid droplet formation in the cytosol in mammals and in the yeast Saccharomyces cerevisiae, it plays a role in the metabolism of phospholipids. These triglycerides (TGs) are kept and stored fenced in by a phospholipid monolayer in the cytoplasm in configurations or organelles that have been given many different names including lipid particles, oil bodies, adiposomes, eicosasomes, and most prevalent in scientific research – lipid droplets. 

FITM2 one of two genes in its family. The other being FITM1 also known as FIT1 in which it shares 35% identity with. However, FITM1 and FITM2 have a similarity score of 50% at the amino acid level but it is important to not that they do not have overlapping homology to families of other proteins or any additional notorious protein domains. Of the two protein coding genes, FITM2 is the ancient orthologue of this family of FIT proteins with orthologues also found in Saccharomyces cerevisiae. FITM1 is seen in humans also but is conserved from fish and it is not seen in adipose tissue or adipocytes but it is however, displayed mostly in muscles both skeletal and cardiac in nature. FITM2 is seen most frequently and in increased expression in adipose tissue and is regulated by receptor γ (peroxisome proliferator activated) directly. This γ is the principal transcription factor for the differentiation of adipocytes.

Cytosolic lipid droplets are classified as organelles that are composed of a core that is hydrophobic is nature and which contains neutral lipids (like triglycerides) as well as cholesteryl esters that have a phospholipid monolayer in addition to a distinctive proteome that surrounds them. The most generally accepted view on the formation of lipid droplets is that the neutral lipids build up between the ER leaflets due to de novo synthesizing enzymes for both triglyceride phospholipids and cholesteryl esters which as a result, leads to the budding lipid droplets growing into the cytoplasm space. There are two different groups of lipid droplets that are known. One being characterized by its phospholipid leaflet in continuity with the membrane of the ER and the other classified as definitively cytosolic without a connection to the ER.

A generally acknowledged model of the biogenesis of a lipid droplet includes the construction of a center or lens of triglycerides that are produced new, flanked by the leaflets of the membrane in the ER that sprouts off with the leaflet in the cytoplasm of the ER that surrounds the core of the lipid (neutral) and obtains interchangeable proteins that are associated with lipid droplets in the cytoplasm. However, this model has been tested by observations that make it seem as though lipid droplets actually form on the cytosolic leaflet of the ER membrane.

Studies done have suggested that FITM2 works downstream of DGAT enzymes and binds to triacylglycerides (TAG), which is crucial for a cell’s FITM2 facilitated lipid droplet formation after being purified. When looking at the most recent view of lipid droplet formation as described above, where a TAG lens is established between ER leaflets, FITM2’s capacity to bind TAG may aid in the increase of TAG’s solubility in the ER which can then instigate the gathering of amounts of TAG necessary to mediate the progression of lipid droplet formation. This is why FITM2 has been referred to as a “gatekeeper” or regulator that is situated downstream of TAG biosynthesis that can as a result, control the number of lipid droplets formed.

In mammals, FITM2 protein is made up of 262 amino acids (while FIT1 part of the same family is 292 amino acids long) and has six transmembrane domains in which the N and C termini are both geared to face the cytoplasm. When FIT2 is found overexpressed in cells it has unfailingly caused the buildup of TG rich lipid droplets that contain in their fourth transmembrane domain, a mutation that happens to be a gain-of-function. This mutation has been described as having a significant effect on increasing both the amount and size and lipid droplets. When comparative sequence analysis was done in a study by Gross et al. (2010) there was a tract of residues that were deemed as extensively conserved located in this transmembrane 4 that was later named the “FIT signature sequence”.

In the cells of mammals, the putting together of lipid droplets is a process that is strictly regulated and involves many signals that are hormone induced, droplet-associated proteins, and include the work of lipases as well. There are four concepts that have been used as evidence to support the statement outlining the importance of FIT proteins in the build up and mediation of lipid droplets. First, they are evolutionarily conserved and solely found in the ER which is the primary site for TG biosynthesis. Second, when FIT proteins are overexpressed in either the liver of a mouse of even in cells that have been cultured in vivo, there has been observable build up of lipid droplets that are rich in triglycerides as an outcome. Third, it has been known that FIT proteins are not DGATs. DGATs facilitate the biosynthesis of the TGs. FIT proteins strictly aid in the conversion of the TGs (made by DGATs) into lipid droplets. Therefore knowing the function of these FIT proteins helps us to make sense of why they are placed downstream of the DGATs. Lastly, a shRNA-facilitated reduction in FITM2 in adipocytes (3T3-L1) or even a knockdown of it in the embryos of zebrafish resulted in great reductions in the build-up of lipid droplets.

FITM2 is notorious for being overexpressed throughout the time 3T2-L1 is being differentiated which shows resemblance to PPAR γ at a specific period when lipid droplets are known to build up which results in the adipocyte phenotype that is seen in the 3T2-L1 cells. It was also discovered that the overexpression of FITM2 when the 3T2-L1 cells were combined with rosiglitazone (a PPAR γ agonist) which as a result, serves as evidence for the idea FITM2 is functionally regulated by PPAR γ).

The specificity of the tissue dispersal of FITM1 and FITM2 and the realization that FITM2 binds TAG more intensely than FITM1 which forms a weak bond presents separate functions for the proteins in the FIT family in regards to the metabolism of lipids. Lipid droplet development induced by FITM2 may function in TAG storage for long-term purposes in adipose. Whereas FITM1 may function to make the smaller lipid droplets that are seen in skeletal muscle where there is a fast turnover of LDs.

Under pretenses where physiological circumstances were normal, lipid droplets are depended on to keep energy balanced at not only at the cellular level, but for the sake of the whole organism’s sustainability. However, under circumstances where the situation that presents itself shows excessive acquirement of lipid droplets such as in obesity, the risk for obtaining disease including type 2 diabetes, atherosclerosis, and heart disease rises. The documentation of the FIT proteins should help in evolving substances to revert FIT expression or activity back to a normal regulatory state as treatment for diseases linked to extreme accumulation of lipid droplets.

Week 12: Revised Written Draft

Introduction

FITM2 (fat storage inducing transmembrane protein 2) also known as FIT2, is a protein coding gene in humans that plays a role in fat storage. Its location is 20q13.12 and it contains 2 exons. it is also a member of the FIT protein family that has been evolutionarily conserved. Conserved from Saccharomyces cerevisiae to humans is the capability to take fat and store it as cytoplasmic triglyceride droplets. While FIT proteins facilitate the segregation of triglycerides (TGs) into cytosolic lipid droplets, they are not involved in triglyceride biosynthesis. In mammals, both FIT2 and FIT1 from the same family are present, embedded in the wall of the endoplasmic reticulum (ER) where they regulate lipid droplet formation in the cytosol. In S. cerevisiae, it plays a role in the metabolism of phospholipids. These TGs are in the cytoplasm, encapsulated by a phospholipid monolayer in configurations or organelles that have been given many different names including lipid particles, oil bodies, adiposomes, eicosasomes, and most prevalent in scientific research – lipid droplets. 

FIT Protein Family

FITM2 one of two genes in its family. The other being FITM1 also known as FIT1 in which it shares 35% identity with. However, FITM1 and FITM2 have a similarity score of 50% at the amino acid level. Of the two protein coding genes, FITM2 is the ancient orthologue of this family of FIT proteins with orthologues also found in S. cerevisiae. FITM1 is also found in humans but is conserved from fish. FITM1 is not seen in adipose tissue or adipocytes but it is however, displayed mostly in muscles both skeletal and cardiac in nature. FITM2 is seen most frequently and in increased expression in adipose tissue and is regulated by receptor γ (peroxisome proliferator activated) directly. This γ is the principal transcription factor for the differentiation of adipocytes.

Lipid Droplets (LDs)

Cytosolic lipid droplets are organelles that are composed of a core that is hydrophobic is nature containing neutral lipids (like triglycerides) as well as cholesteryl esters that have a phospholipid monolayer in addition to a distinctive set of expressed proteins that surrounds them. The most generally accepted view on the formation of lipid droplets is that the neutral lipids build up between the ER leaflets due to de novo synthesizing enzymes for both triglyceride phospholipids and cholesteryl esters. This leads to the budding lipid droplets growing into the cytoplasm space. There are two different groups of lipid droplets that are known: the first is characterized by its phospholipid leaflet in continuity with the membrane of the ER and the second is classified as definitively cytosolic without a connection to the ER.

Structure

A generally acknowledged model of the creation of a lipid droplet includes the construction of a center or lens of TGs that are produced new. This TG center is flanked by the leaflets of the membrane in the ER that sprouts off with the leaflet in the cytoplasm of the ER that surrounds the core of the lipid (neutral). It is then able to obtain interchangeable proteins that are associated with lipid droplets in the cytoplasm.

Studies done have suggested that FITM2 works downstream of diglyceride acyltransferase (DGAT) enzymes and binds to TGs, which is crucial for a cell’s FITM2 facilitated lipid droplet formation after being purified. When looking at the most recent view of lipid droplet formation as described above, where a TG lens is established between ER leaflets, FITM2’s capacity to bind TG may aid in the increase of TAG’s solubility in the ER. This can then instigate the gathering of amounts of TG necessary to mediate the progression of lipid droplet formation. Consequently, FITM2 has been referred to as a “gatekeeper” because it is situated downstream of TG biosynthesis and controls the number of lipid droplets formed.

In mammals, FITM2 protein is made up of 262 amino acids (while FIT1 part of the same family is 292 amino acids long) and has six transmembrane domains in which the N and C termini are both geared to face the cytoplasm. When FITM2 has a mutation in its fourth transmembrane domain that happens to be a gain-of-function one, is found overexpressed in cells, it has unfailingly caused the buildup of TG rich lipid droplets. A comparative sequence analysis of FITM2 showed a tract of residues that were deemed as extensively conserved located in this transmembrane 4 that was later named the “FIT signature sequence”.

Function

In the cells of mammals, the construction of lipid droplets is a process that is strictly regulated involving hormone induced signals, droplet-associated proteins, and lipases as well. Four observations support the role of FIT proteins in the build up and mediation of lipid droplets. First, they are evolutionarily conserved and solely found in the ER which is the primary site for TG biosynthesis. Second, when FIT proteins are overexpressed in either the liver of a mouse of even in cells that have been cultured in vivo, there has been observable build up of lipid droplets that are rich in triglycerides as an outcome. Third, FIT proteins are not DGATs. DGATs facilitate the biosynthesis of the TGs. FIT proteins strictly aid in the conversion of the TGs (made by DGATs) into lipid droplets. Therefore knowing the function of these FIT proteins helps us to make sense of why they are placed downstream of the DGATs. Lastly, a shRNA-facilitated reduction in FITM2 in adipocytes (3T3-L1) or even a knockdown of it in the embryos of zebrafish resulted in great reductions in the build-up of lipid droplets.

FITM2 has been identified as being overexpressed throughout the time 3T3-L1 (from the adipocyte cell line) is being differentiated which shows resemblance to the peroxisome proliferator-activated receptor gamma (PPAR γ) at a specific period when lipid droplets are known to build up which results in the adipocyte phenotype that is seen in the 3T2-L1 cells. The overexpression of FITM2 when the 3T3-L1 cells were combined with rosiglitazone (a PPAR γ agonist). This serves as evidence for the idea FITM2 is functionally regulated by PPAR γ.

The specificity of the tissue dispersal of FITM1 and FITM2 and the fact that FITM2 binds TG more intensely than FITM1 (which forms a weak bond) presents separate functions for the proteins in the FIT family in regards to the metabolism of lipids. Lipid droplet development induced by FITM2 may function in TG storage for long-term purposes in adipose whereas FITM1 may function to make the smaller lipid droplets that are seen in skeletal muscle where there is a fast turnover of LDs.

Clinical Uses

When physiological circumstances are normal, lipid droplets are depended on to keep energy balanced at not only at the cellular level, but for the sake of the whole organism’s sustainability. However, excessive acquirement of lipid droplets can result in obesity, and increased risk for obtaining disease including type 2 diabetes, atherosclerosis, and heart disease. The documentation of the FIT proteins should help in evolving substances to revert FIT expression or activity back to a normal regulatory state as treatment for these diseases.

In addition, a recent study done on a family with a new homozygous mutation in FITM2 that results in a truncated protein. The individuals in the family that are affected by this mutation exhibit Siddiqi syndrome. Siddiqi syndrome is identified by gradual development of hearing loss, late motor development, decreased BMI, ichthyosis-like changes to the skin, and minor fiber neuropathy. In this family, the collection of symptoms presented for this syndrome is new. However, they also overlap with several recognized monogenic conditions that are neurological in nature including Troyer syndrome, Mohr-Tranebjaerg syndrome, and Megdel syndrome.

Week 13: Upload to the FITM2 Page for Grading

I have uploaded my final draft to the FITM2 page for grading.

Good job. Keep it up! AdamCF87 (talk) 17:37, 5 October 2017 (UTC)

Peer Review

Hi, I'm Andrew and I am assigned to peer review your draft article. After reading it through it is a good start but I found some initial easy fixes right away. To begin with, siting your information and resources is a good way to organize and help you and your readers know where the information is coming from. I also think that putting links in for other proteins, genes, organs etc. would be beneficial for you and the readers as well. Now more into the grammar of the article, I found most paragraphs consisted of run-on sentences and multiple comma splices per sentence. I recommend reading these sentences out loud and seeing how they sounds and if they are easy to follow. It is better to have more smaller sentences than longer choppy ones. Also I was confused on what DR and LD were and if I did not have a more so science background ER would be confusing too. I recommend that specifying what these are by having the word written once then in brackets what the abbreviation is, for example: Acute Myeloid Leukemia (AML). Also something else to check on is checking for capitalization in sentences and words that need capitals. A specific to add would a location of the gene within the genome and where on the chromosome it lies, a photo could also be found and added to help visualize this on the article.

Good start, looking forward to seeing what comes next! -Andrew Elliott