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Introduction to Bioinformatics Final Project and Term Paper The final project is an individual project! Topic: Conduct a phylogenetic study

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Introduction to Bioinformatics Final Project and Term Paper The final project is an individual project! Topic: Conduct a phylogenetic study. First do a literature (PubMed search) and select a gene or protein which is of interest to you. Then analyze it using the tools we talked about in class (find homologs, build an MSA and phylogenetic tree and discuss your findings). In your paper talk about the importance of this gene\protein and why you picked it (more on the paper below). In your project you have to use at least one tool to do MSA\Tree building that was NOT discussed in class\lab! Write up: For any of the topics above you will have to write up a scientific paper that will have the following sections to it: Use single space; times new roman font, size 12. 1. Abstract: Half a page summary of the paper. 2. Introduction: Provide background on your selected gene or protein (what disease it plays a role in…etc.), or if analyzing an experiment provide background on the experiment. Discuss the significance of your gene, protein or experiment that you chose and justify its selection as the topic for this project. Put your objective and any hypothesis here. Two to three pages. 3. Materials and Methods: Provide details on how data was generated or gathered, including any databases used. Include the tools and parameters used in your analysis. One to two pages. 4. Results: Include tables and figures summarizing your results. For instance a multiple sequence alignment, phylogenetic tree (snap shots if fine) or protein structure would go here. The length of this section will vary depending on what you do and how much data you have to show. 5. Discussion and conclusion: Discuss your results and talk about any difficulties you had. The discussion usually should address the objective and/or hypothesis posed in the introduction. About one to two pages. 6. References: At least 5 references (minimum of 3 peer reviewed journal publications), arranged alphabetically based on author last name. Make sure references are cited in the paper. 7. Supplemental material: Include ALL sequences in FASTA format that were used in your project. If your MSA is big you can also include that here instead of the materials and methods section. Grading: The project and associated presentation and paper are worth 20% of your total grade. THE F8 GENE By: Obumneme Nnah History of the F8 gene ? The f8 gene was discovered in 1937 ? It was alter on purified in the year 1937 by Edward Tuddeham and his collegues workers . This therefore enabled the F8 gene to be molecularly identified. ? In 190s, this gene experienced a contamination scandal where some pharmaceutical companies sold contaminated factor VIII ? In 1990s, pharmaceutical companies begun producing recombinant synthesized factor product. Introduction The f8 gene has so many other names which can be used to refer to it. The names include DXS1253E, the FVII, HEMA, Coagulation factor VII, pro-coagulant factor among many other names. >the gene is referred to as a coagulation factor because together with other proteins, they coagulate to form blood clots. ? It is located on the X chromosome and specifically at the q28th position. ? It is made up of six domains that is the A1-A2-B-A3-C1-C2 Information about the f8 gene ? The primary site of release of this gene is human is so ambiguous ? It synthesis and release occurs in the vascular, gromelular and tubular ? While in the blood, it circulates but in a noncovalent complex form. ? It is activated by thrombin form the noncovalent complex form to allow it interact with other factors such as IXa to allow coagulation to take place ? It has a half-life of about 12 hours in the bloodstream on a condition that it has been stabilized by the von Wilebrand factor. ? It is never affected by the liver disease on the contrary , when the liver is affected by any diseases, it performs better and its level is increased. Importance of the F8 gene ? It provides instructions for making coagulation factor ? It also participates in the coagulation of blood itself considering the fact that it is a cofactor for factor IXa. ? When it has been concentrated in the plasma, it can help haemophiliacs to restore their homeostasis back to normal. ? It can help the patients who are undergoing therapy to avoid any incidences of bleeding. Diseases in which the F8 gene is present ? Mutation of the f8 gene causes Haemophilia which is one of the most tragic and common form of bleeding disorder ? When the genetic material of the f8 gene are inverted, they cause haemophilia Homologs of the F8 gene MSA of the f8 gene Tree Discussion ? A blood test called factor VIII essay is carried out to measure the activity of factor VIII ? The F8 gene contains 26 exons which are spread over-16kb. ? Factor VII is not produced in the hepatocytes in the liver. The genes are biosynthesized in the endothelial cells of the liver