PHAR 5350 Assignment CYP2C9 Case Solution
Question1
Determine the phylogenetic relationships between members of the human CYP2 family. In your answer, you should indicate the overall strategy taken, and details of the bioinformatic tools used
Phylogenetics
Phylogenetics is the study based on DNA sequences and morphology to explore the evolutionary history and relationships among organisms. In this subject, phylogenetic treesare made which are compared and contrasted with the DNA sequences of other organisms to find historical relationship between organisms. This study is carried out with the help of mass spectrometry, which provides the data for the study. Proteins, which constitute an essential portion of organism’s body, investigated with the help of this.
Cytochrome P450
Cytochrome P450 (CYP 450) protein is investigated in detail with the help of this. As per the requirement of the study, CYP in human beings is discussed in the literature. There are eighteen families and forty-three subfamilies in human cytochrome. One of these eighteen families is CYP 2. The resource of obtaining CYP P450 is the liver cells and at intra cellular level, and they are found stuck with the walls of endoplasmic reticulum because of their involvement in protein processing.
CYP 2 Family in Human Beings
CYP2 family has thirteen subfamilies in it and equal number of sixteen genes and pseudogenes. CYP2 family is involved in toxicological and psychological processes in the human body. In the African region, malaria was identified being caused by lack of balance in the body chemicals and CYP2. For the collection of sample for carrying out the study, it was first obtained from human liver tissues. It was Gel Electrophorized to separate proteins and to color them. The proteins were then digested to disintegrate them for study. After which they are passed through the phosphopeptide enrichment and desalted to remove the salts present in the cells. After passing through all these stages, it is ready for identification. The observations plotted on the conserved sequence motif, pictorially given along.
There are three clades observed in the sequence obtained. Two of them had a similarity that they both contained arthropod CYP2 and the rest was different. An (H) denotes human sequence.
This chart depicts the entire map of Cytochrome P450 CYP2. The lines joined are for the help of extracting tree from the given chart.(Researchgate).
Question 2
- Compare the two following studies of gene expression profiles in normal human tissueson the NCBI GEO site:
- Series GSE7905
- Series GSE2361
Answer
There are various studies carried out in order to investigate the human genome. The purpose of these studies is to understand the genetic male-up of individuals and avoid the diseases and disorders, which are caused by genetic dysfunction. Other beneficial uses include making of chemical substances like human insulin for the treatment of diabetic patients. For such purposes, studies are carried out and following text explains the tests, which were carried.
Series GSE7905
With the sample size of 32 human tissues, expression profiling by array was carried out. Initially, tissue gene expression database was formed with thirty-one human tissues obtained from clontech and one from Strategene (UHR). There were three replicas made from each tissue using the Biosystems Chemiluminescent RT-IVT Labeling Kit and kit protocol. Other stages through which it went through includes, Microarray hybridization, chemiluminescence detection, picture taking and analyzing that picture. Therefore, with the use of 96 micro arrays, Human BodyMap was created in these tests.
Series GSE2361
This test was conducted in the year 2005. Sample size was 36 human beings and tissue specific genes to be tested were 2,503. This study was for identifying the importance of gene’s breadth of expression for cancers in terms of tumor differentiation, cell lineage and metastasis. In order to make the study cost effective, each samplehas been taken from different body organ.................
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