User:Rhuynh/sandbox

Article Evaluation
The following is my evaluation of the article titled DNA Clamp.

This particular article is part of the Molecular and Cell Biology WikiProject, rated as a B-Class article with low importance. All the information presented in the article was relevant to understanding what exactly a DNA clamp is. The author(s) included a very easy to understand overview that explained broadly what a DNA clamp is, how it works and what it's involved in before going more in depth with the subsections below it.

The structure section was where I started feeling a bit overwhelmed and lost. While the descriptions under each sub-heating conveyed how these DNA clamps functioned in the various kingdoms, the authors also included boxes with information about the specific domains of its structure which I did not find very helpful since they were not accompanied by any graphics/figures. They seemed out of place because they did not add to the understanding of the actual function of the DNA clamp. I did however, find the figures associated with each of the clamp types helpful in terms of identifying and comparing the similarities/differences among the types listed.

One thing that I would have liked to see is a sub-heading showing the mechanism by which this structure functions. While I have heard of DNA clamps in previous coursework, it is not something that is covered in depth when discussing DNA replication. As such, a visual representation in the form of a figure or animated diagram would greatly enhance a reader's ability to understand how such a structure works in tandem with the basic knowledge they already have on DNA replication.

The citations provided in the article were functional and mostly linked to primary articles that supported the claims in the article. Further inspection indicates that the citations redirected users to the source paper on the NCBI website, indicating that the author(s) indeed used reliable references and cited the information they found appropriately.

While limited, the talk page of this article does have discussions on how to expand the scope of the page, corrections to claims and identification of claims that either do not have references or are not true. It seems that the current version of this article is actually the result of the merging of two similar pages: DNA clamp and beta clamp. The users that contributed to this article discussed the similarities between the two pages and agreed that to reduce redundancy, it would be best to merge the two pages. Moreover, similar to other talk pages, the users are meticulously going through the validity of the facts presented to ensure accuracy.

Wikipedia Project Topic Selection

 * A-site - Binding site on ribosomes for incoming tRNAs during protein synthesis
 * Anaphase Lag - Contributes to mosaicism
 * Aspects to expand on: how it occurs, the mechanisms that lead to anaphase lag, associated diseases/disorders
 * Clonal Interference
 * DmX gene
 * MAP4K4 - Emerging therapeutic target for cancer

= MAP4K4 = Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) – also known as hepatocyte progenitor kinase-like/germinal center kinase-like kinase (HGK) and Nck-interacting kinase (NIK) – is an enzyme, specifically a serine/threonine (S/T) kinase encoded by the MAP4K4 gene in humans.

MAP4K4 is involved in a wide array of biological and physiological processes and its activity has been implicated in systemic inflammation, immune response, metabolic disorders, cardiovascular disease and cancer.

While MAP4K4 has been found to be upregulated in a wide array of cancers, there is currently limited information regarding its specific involvement. However, there is increasing evidence that suggests MAP4K4 has an important role in the development and progression of cancer, and may serve as a novel target for cancer therapeutics.

Discovery and Classification
MAP4K4 is categorized under the mammalian sterile 20 protein (Ste20p) kinase family due to its shared homology with the Ste20p kinase found in budding yeast. MAP4K4 is well conserved and orthologues are found across a wide range of species. Mammalian MAP4K4 was initially identified in mice as a kinase activator for a protein called Nck followed shortly by identification and cloning of the human orthologue encoded by the MAP4K4 gene. It is categorized under the mammalian Ste20 protein kinase family and is a member of the GCK-IV subfamily.

Structure and Expression
In humans, MAP4K4 is encoded by the MAP4K4 gene located on chromosome 2, position q11.2 and consists of 33 exons responsible for its synthesis. It contains approximately 1200 amino acids, has a molecular mass of ~140 KDa. and its orthologues across various species share molecular and structural similarities.

Structurally MAP4K4 contains the following domains : Alternative splicing of the MAP4K4 gene yields five functional isoforms, all of which display fully homologous kinase and CNH domains but differences in the interdomain domain. While the biological significance of these isoforms remains to be determined, it can be speculated that such variations alter and determine MAP4K4's interactions with other proteins and factors, ultimately leading to the activation/inhibition of different biochemical and physiological cascades.
 * N-Terminal Kinase Domain
 * Coiled-coil domain
 * C-Terminal Hydrophobic Leucine-Rich Citron Homology Domain (CNH)
 * Two Putative Caspase Cleavage Sites
 * Interdomain - Connects the kinase and CNH domains, facilitates protein-protein interactions. Although it has been identified, its structural components and functionality are currently poorly understood

The mammalian class of Ste20 kinases require phosphorylation at specific sites for full activity. Primary phosphorylation at the activation site in their kinase domain is believed to cause a conformational change in the protein, stabilizing the structure of its activation segment to allow suitable substrate binding. Secondary sites also require phosphorylation for the enzyme to assume full activation and is achieved via autophosphorylation or by upstream kinases.

To date, MAP4K4 has been found to be expressed in all tissue types with a relatively more pronounced expression in the brain and testes. Multiple isoforms of MAP4K4 can be present at any given time in the same cell but the abundance of each isoform in the cell differs depending on the cell-type or tissue-type.
 * E.g. In humans, the shorter isoform of MAP4K4 is predominantly expressed in organs including the liver, placenta, skeletal muscles while a longer isoform is expressed in the brain

TNF-α
Evidence from mammalian and fly studies indicate that MAP4K4 is involved with tumour necrosis factor alpha (TNF-α) and its c-jun N-terminal kinase (JNK) signaling pathway. MAP4K4 not only mediates TNF-α signaling but also promotes its expression ; moreover, TNF-α can elevate MAP4K4 expression using transcription factors. This positive feedback interaction between TNF-α and MAP4K4 is observed in cellular processes involved with development as well as tissue homeostasis.

The JNK pathway is implicated in a number of physiological processes and involves JNK s – kinases responsible for the phosphorylation of a downstream protein called c-Jun. This further leads to the increase in expression and activity of specific transcription factors that respond to a variety of cellular stressors, growth factors and cytokines. The activation of the JNK signal transduction pathway by MAP4K4 has been implicated in apoptotic regulation of many different cell types, tumorigenesis and/or inflammation.

p53
p53 is a tumour suppressor gene and is involved with cellular response to stress. When expressed, the cell cycle is halted in the G1 phase and can induce senescence or apoptosis. Mutations to the p53 gene are often found in many types of cancers.

The MAP4K4 gene contains four binding sites for p53. Upon binding, p53 up-regulates MAP4K4 expression leading to the activation of the JNK signaling pathway. siRNA knockdown experiments have also shown a reduction of p53 induced apoptosis. Current evidence therefore suggests that MAP4K4 has a modulating effect on p53 induced apoptosis in the JNK signaling pathway.

Metabolic Disease
MAP4K4 has been identified to be involved in the negative regulation of insulin-dependent glucose transport. Increasing evidence suggests cytokines such as TNF-α mediate biological effects antagonistic to insulin action. TNF-α specifically

suggesting it may play a role in signaling by TNF-α, specifically as an upstream element in the TNF-α signaling cascade. Increasing evidence indicates cytokines such as TNF-α mediate biological effects antagonist to insulin action

. Based on the association of MAP4K4 with inflammatory response pathways

A recent siRNA screen identified involvement of MAP4K4 in the regulation of the glucose transporter GLUT4.

Studies have identified involvement of MAP4K4 in the negative regulation of insulin-dependent glucose transport; suggesting MAP4K4 has a signaling role for TNF-α, specifically as an upstream element in the TNF-α signaling cascade.

TNF-α is a cytokine associated with the inflammation response and there has been increasing evidence indicating that cytokines mediate certain biological effects antagonistic to insulin action. Specifically, TNF-α attenuates the signaling pathway initiated by insulin receptors, ultimately reducing the amount of glucose transport and uptake.

A recent siRNA screen identified involvement of MAP4K4 in the regulation of the glucose transporter GLUT4. siRNA silencing of MAP4K4 caused an elevated expression of peroxisome proliferator-activated receptor y (PPARy) – a nuclear hormone receptor responsible for the regulation of genes associated with adipocyte differentiation, including GLUT4. Furthermore, MAP4K4 silencing appears to prevent insulin resistance, restoring insulin sensitivity in human skeletal muscles by down-regulating the TNF-α signaling cascade.

Additionally, miRNA silencing of MAP4K4 in pancreatic beta-cells protected them against TNF-α repression of insulin transcription and secretion, suggesting that MAP4K4 targeting is a potential strategy for diabetes prevention and treatment.

Cancer
The biggest causes of death for patients with cancer are tumour invasion and metastasis, processes that are highly correlated with cell migration and motility. There is limited information regarding how MAP4K4 is involved in cancer but studies have shown that MAP4K4 is overexpressed in a number of cancer types including lung, prostate, pancreatic and ovarian cancer where such up-regulation is associated with increased cell migration, adhesion and invasiveness.