User:AbdulazizBholat/sandbox

= Week 3 Article Evaluation = Article evaluated: BLAST

The article is properly formatted, with subheadings, and diagrams. All information in the article pertains to BLAST and the processes of BLAST, except the section pertaining to the alternatives which while relevant did not need to take up that much space. The information requires citations for the whole process and part of the background section of the article. A few of the reference links do not work properly but they are all from reliable sources (scientific articles). The article is not part of any Wiki-project but requires new citations. There is discussion going on in the talk page as well. The information on the Wikipedia page is a lot more in-depth than how BLAST is taught in class.

All in all its a decent article with a lot of information present, but some of the information needs to have credible sources in order to be a good Wikipedia article.

= Week 4 Add to an Article = I edited Protein moonlighting and added a citation to Dr. Kohlami's paper. adding the statement "ADT2 and ADT5 are another example of moonlighting proteins found in plants. Both of these proteins have roles in phenylalanine biosynthesis like all other ADTs. However ADT2, together with FtsZ is necessary in chloroplast division and ADT5 is transported by stromules into the nucleus. " to the Functions section of the article and properly cited the article.

= Week 7 = What I plan to contribute to the topic of SLITRK1 is to build upon the information that is already present in the article. The sources are from 2005-2007 and there has been new studies done on the gene since then so I would include those discoveries. Mutations in the gene have also been linked to a few other disorders so I would add information on those. I would also build upon the part it plays in Trichotillomania since there is only one sentence there. I would reformat the page as well to add sections and headings to better organize the information. Below are a few sources that I can use when editing the information.

https://www.nature.com/articles/srep27343

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3749144/pdf/pone.0070376.pdf

http://apps.webofknowledge.com/full_record.do?product=WOS&search_mode=GeneralSearch&qid=6&SID=3B9JN5tnYtqfLuQWoAM&page=1&doc=6&cacheurlFromRightClick=no

= SLITRK1 (Draft) =

SLITRK1 ("SLIT and NTRK-like family, member 1")  is a human gene that codes for a transmembrane and signalling protein that is part of the SLITRK gene family, which is responsible for synapse regulation and presynaptic differentiation in the brain. Expression of the gene has been linked to early formation of excitatory synapses through binding with receptor tyrosine phosphatase PTP (LAR-RPTP). Various studies over the years have linked mutations in the gene to conditions on the OCD spectrum, Tourette Syndrome and Trichotillomania, however the mutations in the genome itself vary greatly between individuals, with most mutations observed being hard to find in repeat studies.

Gene Information
The gene for SLITRK1 is located on chromosome 13q31.1. The gene is expressed only in the brain of humans. The mRNA can differ from alternative splicing, and contains domains for the extracellular matrix as well as for the LRRs. Mice contain an ortholog of the gene called Slitrk1.

Protein Structure
SLITRK1 contains 2 horseshoe shaped leucine rich repeat domains (LRRs) in its extracellular domain which are vital to its function. The LRRs have 6 modules each and are connected by a 70-90 amino acid loops. LRR1 is a more conserved sequence and is present as a dimer while LRR2 is a monomer and has a more variable sequence. The conserved sequence of LRR1 contains critical binding pockets and specific charged residues that are important for it to carry out its function of binding to LAR-RPTPs on the N-terminus. Both LRR sequences are randomly positioned on the protein and contain variable linker regions. The protein also contains a short intracellular domain, but lacks a tyrosine phosphorylation motif which is present in other SLITRK genes.

Function
SLITKR1 is highly expressed in the central nervous system. It plays a critical part in regulating synapse formation between hippocampal neurons and in differentiation of synapses, helping in neuronal outgrowth. It is expressed during embryonic stages and postnatally but expression decreases over time and is localized to the postsynaptic membrane.

Overexpression of SLITKR1 promotes postsynaptic differentiation for excitatory and inhibitory synapses, but because of the localization only excitatory synapses are affected. Inhibition of SLITKR1 only reduces differentiation of excitatory synapses because of this.

Interaction with LAR-RPTP
Since they lack tyrosine phosphorylation motifs, SLITKR1 binds to LAR-RPTP through its LRR1 region in order to differentiate synapses. The LRR2 domain's function is not clearly understood yet but it is hypothesised that it is for dimerization to the cell surface.

LAR-RPTP binds to the LRR1 region through its PTPδ Ig region, with 3 separate binding sites in a 1:1 binding ratio. Ig1 binds through electrostatic and hydrophobic interactions, Ig2 binds through ionic and hydrogen bonds, and Ig2 binds through hydrogen bonding. The unique properties on the concave surface are what determine which LAR-RPTP binds to it. If the proper LAR-RPTP is not bound to the LRR1 then synapse formation cannot occur, but bonding can still occur. Once they are bound properly, the complex is sufficient for synapse differentiation. Point mutations in the LRR1 region impaired differentiation as well but not binding.

Tourette Syndrome
In 2005, medical researchers observed a de novo translocation on 13q in a patient with Tourette syndrome (TS) which broke the patient's chromosome near the SLITRK1 genome. In screening of additional patients, the authors observed a frameshift mutation in SLITRK1 in a patient with TS and the same rare non-coding variant (called var321 and varCDfs) in two patients with TS. These variants were not found in several thousand controls supporting an association of the variants with TS. It is hypothesized that this mutation in SLITRK1 may be a direct or indirect cause of Tourette syndrome in this small subset (1–2%) of Tourette's patients.

A subsequent examination of the region of the SLITRK1 gene found the mutation in none of 82 patients with Tourette syndrome. The authors concluded that tests to detect variant(s) in the gene probably would have little diagnostic utility. An experiment in the effects of a microdeletion in chromosome 13q31.1 was done in a fetus, the mother had passed the microdeletion to the child and both did not have tourettes or any other OCD symptoms, showing that it may not be a direct cause of tourettes. Further attempts to replicate the study were done in multiple studies. In a Japanese study, next-gen sequencing was used to screen 92 TS patients and 361 healthy controls, none of TS patients were found to have mutations at either variant or any new mutations in the gene. In a European study it was found that the 2 original variations were not found in any of the 222 trios that were studied. However, tests were also done on SNPs in the groups and 3 were found to have variations. Two of the three variations were found to be associated with the formation of tourette syndrome. In a different study of 381 Caucasians with with some form of OCD with 356 non-OCD control patients, 3 genetic changes were found after genetic screening. Of the 3, 2 were identified only once each and the third was found in 4 OCD patients but also in a non-OCD patient. The non-OCD patient did have compulsive nail biting, but these studies show that a genetic link between SLITRK1 and patients with tourette syndrome may exist they are more complex in nature than previously understood.

The impact of the research findings to the population of Tourette Syndrome patients as a whole is unclear. SLITRK1, while it may not be a major gene implicated in the cause of tourette syndrome, can help contribute to our understanding of tourettes. Rare variants in SLITRK1 may lead to tourettes, and mutations in non-coding regions of SLITRK1 may also play a part, but further research needs to be done before any conclusions can be drawn.

Trichotillomania
The SLITRK1 gene has also been implicated in a small percentage of cases of trichotillomania, an impulse disorder where the patients compulsively pull their own hair. In one of the previously mentioned studies the mother of the child who had a de novo translocation on 13q had trichotillomania, this would suggest that there could be a genetic link between SLITRK1 and trichotillomania as well.

A study was done where 44 families with individuals who had trichotillomania had their SLITRK1 gene sequenced. 2 new non-synonymous mutations were discovered about 9 base pairs apart from each other, in an area separate from the one the tourettes mutations were found. These results were compared to a controls and none had the mutation, suggesting that these mutations, while rare were associated with trichotillomania.