User:Ssue123/sandbox

Article Evaluation

Article: Chromosome Abnormality

After reading this article, everything on this page is relevant to the topic chromosome abnormality, however there were some distractions making it hard to read. Some of the ideas don't completely finish before jumping onto the next point. For example, in the introduction, the article was talking about the definition of chromosome abnormality and then jumped right to the definition of a karyotype, which wasn't necessarily even needed in the introduction. All of the claims or facts were neutral with none being heavily biased towards a particular position. Since this was a fairly short article, nothing was overrepresent, however I felt that there was a lot of information underrepresented. For example, the method of actually getting an aneuploidy either through mitosis or meiosis could have been covered as this is known (what leads to trisomies and monosomies). Another example is when the article talks about acquired chromosomal abnormalities, this section was very brief and more information could have been added such as what sparks these abnormalities and can you get them from other mutations. Furthermore, a heavily underrepresented topic was that chromosome abnormalities can cause diseases, although it was mentioned I think that the result of chromosomal abnormalities should have a larger impact on this article. In terms of citations, all the links work, however I found that a lot of the cited information was copied word for word from the source, for example with cite 11. In addition, not all of the facts were cited, whole subsections of the topic such as how to detect abnormalities and inheritance were not cited. Furthermore, some of the information doesn't seem to come from a credible source, a lot was taken from the same source which was a website seemingly made by some professors, however this information on this website should have been cited from somewhere. Not a lot of information seems to be out of date, however I think new technology or ways to detect chromosomal abnormalities have recently been discovered or used which could be added. I think there should also be more information about the many types of popular chromosomal diseases resulting from chromosomal abnormalities added to this article. On this article's Talk page there are conversations or suggestions about adding more recently discovered types of chromosomal abnormalities and a proposition about adding more tables to the article. This article was rated as a start and Wikipedia discusses this article very generically covering the very basics of chromosome abnormality. In class and previous courses, we've talked more in depth about chromosomal abnormality again showing how it occurs and the results of these abnormalities.

Possible topics

Article : https://en.wikipedia.org/w/index.php?title=Caspase%2D%39 Caspase-9

I can add a lot more information such as what it's purpose is, etc. I can also add the damaging effects that might occur if this doesn't work or get activated.

Article: Wild type

I can improve this article by using the correct terms to explain what wild type is and include more examples of wild types commonly used in research.

Draft Article

Caspase-9
Caspase-9 is an enzyme encoded by the CASP9 gene in humans. It is an initiator caspase, responsible for initiating the intrinsic apoptosis pathway (mitochondrial apoptosis). Caspase-9 belongs to the family of caspases, cysteine-aspartic acid proteases involved in apoptosis & cytokine signalling.

Correct caspase-9 function is required for apoptosis, leading to the normal development of the central nervous system. Without correct function, abnormal development of tissues can occur leading to diseases and premature death. Certain diseases involving caspase-9 are treated with therapy by targeting this enzyme.

Different protein isoforms of caspase-9 are produced due alternative splicing.

Structure
Similar with other caspases, caspase-9 has 3 domains: N-terminal pro-domain, large subunit, and small subunit. The N-terminal pro-domain is also called the long pro-domain and this contains the caspase activation domain (CARD) motif.

The caspase-9 monomer consists of one large and one small subunit, both comprising the catalytic domain. Differing from the normally conserved active site motif QACRG in other caspases, caspase-9 has the motif QACGG.

When dimerized, caspase-9 has two different active site conformations within each dimer. One site closely resembles the catalytic sites of other caspases, whereas in the second, there is no present "activation loop", disrupting the catalytic machinery in that particular active site. The active catalytic site has broad substrate specificity because of a wide substrate-binding cleft.

The caspase-9 dimer is asymmetrical

Localization
Caspase-9 is found in the mitochondria, cytosol, and nucleus.

Expression
Caspase-9 in humans is expressed in fetus and adult tissues. Tissue expression of caspase-9 is ubiquitous with the highest expression in the heart, specifically in its muscle cells. The liver, pancreas, and skeletal muscle express this enzyme at moderate levels, and all other tissues express caspase-9 at lower levels.

Mechanism
Active caspase-9 acts as an executioner pathway, initiating apoptosis When inactive, caspase-9 is in the cytosol of a cell as a monomer (zymogen)
 * Activated caspase-9 then cleaves further caspases, initiating the caspase cascade (thus initiating apoptosis)
 * It is recruited and activated by the CARDs (caspase recruitment domain motif) in the APAF1 oligomeric complex



Processing

 * Before activation, caspase-9 has to be processed
 * It has to be processed because caspase-9 is first made as single-chain zymogens which are inactive
 * Further processed into its large & small subunits
 * In order to start apoptosis, Apaf-1 helps the autoproteolytic processing of the single-chain caspsase-9 zymogen
 * Processing occurs when the apoptosome binds to caspase-9 zymogen the processed caspase-9 stays bound to the apoptosome forming a holoenzyme

Activation
Two different ways for activation: 2. Activated by proteolytic cleavage by a previously activated caspase, which then dimerizes caspase-9
 * 1) Activated when binding to APAF1 (through apoptotic signal), it dimerizes - activated by the apoptosome
 * Apaf1 oligomerizes pro-caspase-9's precursor molecules for auto activation of caspase-9

Catalytic Activity

 * Asp at position P1 (strict) & marked preference for His at position P2
 * Preferred cleavage sequence of Leu-Gly-His-Asp-(cut) Xaa

Regulation

 * Regulation of caspase-9 occurs through phosphorylation
 * Negative regulation
 * Through Akt, a serine-threonine kinase phosphorylates caspase-9 on serine-196 which inhibits its activation and protease activity, thus suppressing caspase-9 & further apoptosis
 * Akt can phosphorylate both processed & unprocessed caspase-9 in-vitro
 * On processed, it phosphorylates on large subunit in vitro
 * Since the phosphorylated serine is far from the substrate-binding site of caspase-9, this means that caspase-9 is allosterically inhibited
 * Inhibition may affect the way caspase-9 dimerizes and it may alter the substrate-cleft/active site of caspase-9 through conformational changes

Mutations/Deficiency

 * When you have a deficiency in caspase-9 it can affect the development of the brain
 * Ex. Caspase-9 deficient mice have large brains as a result of decreased apoptosis and an increase in extra neurons
 * Also, when homozygous for no caspase-9, in mice, they usually die perinatally due to a an abnormally developed cerebrum
 * The effects of being caspase-9 deficient or a mutant is detrimental compared to mutants of other caspase
 * This may demonstrate that caspase-9 plays a very important role in apoptosis as it is responsible for further activation of other caspases
 * Caspase-9 deficient mice have a main phenotype showing an impact on the brain
 * This could mean that caspase-9 could play a role in the pathway of many disease that are associated with the brain such as a stroke, hypoxia, or neurodevelopment disorders

Clinical Significance

 * Expression of caspase-9 is found at different levels among different tissues in the human body
 * Different levels of caspase-9 have a physiological role
 * Too low amount of caspase-9 results in neurodegenerative diseases & malignancies
 * Alzheimer's disease is a result of low expression of caspase-9
 * Mutations in the caspase-9 gene can also cause diseases
 * Germline variation is linked to non-Hodgkin's lymphoma
 * Alteration at both gene & SNP levels of caspase-9 have been associated with this disease risk
 * Caspase-9 can also affect a person's risk of lung cancer
 * Certain polymorphisms in the caspase-9 promoter give rise to a higher chance of lung cancer due to an increase promoter activity which enhances caspase-9 activity/expression
 * However, the induction of caspases may have medical benefits
 * It can be used to eliminate lymphocytes in graft versus host disease by having a modified version of a caspase-9 that you can turn on & off where in the presence of a small molecule it will dimerize & activate its hydrolyzing domain which will trigger apoptosis

Alternative Transcripts
Through alternative splicing, four different caspase-9 variants are produced.

Caspase-9α (9L)
This variant is used as the reference sequence, and it has full cysteine protease activity. (insert picture of reference sequence)

Caspase-9β (9S)
This variant doesn't include exons 3, 4, 5, and 6; it is missing amino acids 140-289. Caspase-9S doesn't have central catalytic domain, therefore it functions as an inhibitor of caspase-9α by attaching to the apoptosome, suppressing the caspase enzyme cascade and apoptosis. Caspase-9β is referred to as the endogenous dominant-negative isoform.

Caspase-9γ
This variant is missing amino acids 155-416, and for amino acids 152-154, the sequence AYI is changed to TVL.

Isoform 4
In comparison with the reference sequence, it is missing amino acids 1-83.