User:Emillyjones/sandbox

I am a student at the University of Western Ontario taking part in the 3595 Ad Gen Wikipedia Project. I am intending to improve the article Daf-16, and this sandbox contains my draft.

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The article is pretty focused on the topic, there is not much unnecessary distracting information - although on the talk page there are comments that information about histones are unnecessary because only people who have been educated in biology would be familiar with the term.

There is a citation needed in the first paragraph, where it says the core DNA sequence is normally followed by 3 or more adenine bases

It describes the scientific process using the words 'normally' and 'usually' - is this correct?

The second to last paragraph does not include the name of the study even though it is referenced

It is a stub rated, high class importance article and a project on WikiProject Genetics

Possible articles to edit
genetic viability wild type - grammar needs fixed chromosomal deletion syndrome. could add definition of a deletion = loss of parts of chromosomes, generally visible on karyotyping because they are larger deletions definition of karyotyping = looking at the appearance of chromosomes

My article to edit
Daf-16 I will add: the gene is daf 16 - FOXO transcription factor it 65% is similar to the protein FOXO in humans - homologous to four FOXOs http://www.sciencedirect.com/science/article/pii/S0531556515300498 FOXO 3 increases lifespan

its structure located downstream of IIS kinase cascade https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4361755/

its function needed for longevity - activates proteins involved in stress resistance and longevity such as MnSOD, CuZnSOD, catalase,heat shock proteins, chaperones, stress response proteins is also involved in regulating epidermis damage https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3798571/

clinical relevance this gene can be targeted in ageing studies

Daf 16 draft
DAF-16 is the sole ortholog of the FOXO family of transcription factors in the nematode Caenorhabditis elegans. DAF-16 is notable for being the primary transcription factor required for the profound lifespan extension observed upon mutation of the insulin-like receptor daf-2. Moreover, the tractability of C. elegans as a model and interest in teasing out this conserved aging-associated genetic pathway allowed the intricacies of Insulin and Insulin-like growth factor (IGF) Signaling (IIS) to be thoroughly characterized primarily through studies using this model organism. Daf -16 is responsible for the protection of C. elegans during food deprivation, causing it to transform into a hibernation - like state, known as a Dauer.

DAF-16 is the sole ortholog of the FOXO family of transcription factors in the nematode Caenorhabditis elegans. It is responsible for activating genes involved in longevity, lipogenesis, heat shock survival and oxidative stress responses. It also protects C.elegans during food deprivation, causing it to transform into a hibernation - like state, known as a Dauer. DAF-16 is notable for being the primary transcription factor required for the profound lifespan extension observed upon mutation of the insulin-like receptor daf-2. The gene has played a large role in research into longevity and the insulin signalling pathway as it is located in C. elegans, a successful ageing model organism.

Genetics
DAF-16 is a gene conserved across species, with homologs being found in C. elegans, humans, mice, and Drosophila (fruit flies). In C. elegans, DAF-16 is located on Chromosome 1, at position 175-268. It is made up of 15 exons. DAF-16 is also located downstream of Daf-2, which signals in the IIS pathway. Mutants in this pathway age slower and have a lifespan up to twice as long as normal. The lifespan extension is dependent on DAF-16. Other consequences of mutations in the Daf-16 gene is the inability to form dauers.

FOXO (Forkhead box protein O)
DAF-16 encodes FOXO (Forkhead box protein O), which binds to gene promoters that contain the sequence TTGTTTAC in their regulatory region – this is the DAF-16 binding element (DBE). FOXO is involved in the Insulin / IGF1 signalling pathway (IIS) which affects longevity, lipogenesis,  dauer formation, heat shock and oxidative stress responses, by activating proteins such as MnSOD and Catalase. Expression of FOXO in the intestine normally leads to longevity signalling. It is inhibited by the protein AKT in the IIS pathway, as DAF-16 is inactivated when phosphorylated, which is why a reduction in insulin signalling generally leads to longevity in C. elegans and across species. FOXO has been shown to have a protective role against cancer, as it regulates and suppresses genes involved in tumour formation. It also has a protective role against muscular dystrophy.

FOXO is also important in embryonic development, as it promotes apoptosis.

For the carbon dioxide avoidance response, inhibition of Daf-16 is needed. When inhibition is lost, Daf-16 translocates to the nucleus and regulates genes that delay growth and reproduction but increase stress resistance and longevity Daf-16 mutants fail to arrest cell division in L1 arrest as it is dependent for transcription of the cyclin-dependent kinase inhibitor cki-1 in response to starvation in stem cells.

Insulin Signalling Insulin is the primary hormone dictating energy functions such as glucose and lipid metabolism. The signalling pathway is evolutionary conserved and found across species. Insulin activates an insulin receptor molecule (in C. elegans, this is DAF-2), which in turn activates a kinase and AKT. However AKT inhibits DAF-16 and FOXO, so a reduction in insulin signalling corresponds to an increase in FOXO and the longevity proteins it activates.

Insulin and IGF1 are peptide hormones dictating energy functions such as glucose and lipid metabolism. The signalling pathway is evolutionary conserved and found across species. Signalling occurs through kinases such as PI3K to produce phospholipid products such as AKT. This causes downstream phosphorylation of targets such as DAF-16 by a phosphorylation cascade, blocking nuclear entry. Therefore a reduction in insulin signalling generally leads to an increase in FOXO expression. When not phosphorylated, DAF-16 is active and present in the nucleus, so FOXO can be transcribed and can up-regulate production of about 100 beneficial proteins that increase longevity.

Species, tissue, subcellular distribution
C. elegans is the only known species to contain the DAF-16 gene, although orthologs are conserved across species. DAF-16 may localise to the nucleus or cytoplasm, depending on resources. In nutrient rich conditions, Daf-2 and Akt-1/Akt-2 in the insulin pathway inhibits entry of DAF-16 to the nucleus as it is phosphorylated. However starvation, heat and oxidative stress inhibit phosphorylation by AKT and allow the localisation of DAF-16 to the nucleus. DAF-16 is sequestered in the cytoplasm when associated with ftt-2. Translocation to the nucleus and translation of longevity genes occurs after DAF-16 associates with prmpt-1 Translocation to the nucleus is also promoted by jnk-1 in heat stress and sek-1 in oxidative stress

Expression

Isoform b and Isoform c are expressed in muscles, ectoderm, the intestine and neurones. Isoform b is additionally expressed in the pharynx. Expression can be induced by quinic acid.

Clinical Significance
Implication in Aging

DAF-16 is necessary for dauer formation and the protection of C. elegans during periods of starvation, as DAF-16, DAF-18 and DAF-12 loss - of - function mutants lose the ability to form dauers. A 2003 study by Murphy et. al showed the significance of DAF-16 for longevity, as it up-regulates genes involved in lifespan extension such as stress response genes and down regulates specific life-shortening genes. It has been proven that telomeres have an implication in the aging process, and in C. elegans the lifespan - extending effect of long telomeres is dependent on DAF-16. DAF-2 mutations more than double the lifespan of C. elegans, and this effect is dependent on the activity of DAF-16 as it encodes a member of the hepatocyte nuclear family 3 (HNF3)/ Forkhead family of transcription factors.

C. elegans has long been used in aging research. Although DAF-16 increases longevity, treating C.elegans with resvatrol extends lifespan in a method independent of Daf-16 and fully dependent on SIR2.1.

Interactions
Daf-16 is known to interact with:
 * RLE-1
 * PRMT-1
 * UNC-43
 * TAX-6
 * JNK-1
 * FTT-2

History
In 1963 Sydney Brenner realised the success of biology was due to model organisms, and C. elegans has been widely used in research laboratories since. In 1998 the genome of C. elegans was completely sequenced and found to be a 97 megabase genomic sequence consisting of 19,000 genes, with 40% protein products having significant matches in other organisms. The DAF genes DAF-2 and DAF-16 were discovered in the Thomas and Ruvkun labs, after isolating dauer-consituative (DAF-c) mutants and dauer - defective mutants (DAF-d). Mutations in Daf-2 and DAF-23 caused the dauer - constitutive phenotype, through activation of the dauer - defective genes DAF-16 and DAF-18. This showed that DAF-2 and DAF-23 prevent dauer arrest by antagonising DAF-16 and DAF-18

Notable scientists involved in the initial and continued characterization of DAF-16-associated aging pathways:
 * Cynthia Kenyon
 * Gary Ruvkun