BIO 3

In partial completion of the requirements in Biology 3A

[bio3project-blog]

[bio3project-blog]

INTRODUCTION

Background on Bioinformatics

a. Combination of different sciences like mathematics, computer science, informatics, statistics, chemistry.

b. Application of biological tools on molecular data.

c. Gives improvements on storing, retrieving, organizing, and analyzing biological data.

Importance of Bioinformatics

a. Plays important role in gene analysis and protein expression.

b.  Allows scientists to make accurate deductions on the pattern of descent.

c. Gives scientists and researchers a proper venue to store data which enables them to have the same data to work on, limiting inaccuracies and discrepancies.

Objectives

What are our objectives?

a. The objective of this video is to discuss how bioinformatics works

b. To discuss the similarities of PD gene and PD protein

c. It is important to create a phylogenetic tree to identify which organism will be closely related to the reference sequence (human).

d. To identify what organism can be used as a substitute for studying PD in humans

Phylogeny being addressed

To find a certain organism that could be used in order to conduct tests to find a cure for Parkinson’s disease

PARKINSON’S DISEASE

What is it?

a. It is one of the most common diseases that affects the nervous system

b. This disease targets the dopamine-producing cells found in the brain

Symptoms:

·         Tremor

·         Stiffness

·         Slowness

·         Impaired balance

·         Dementia

c. Specific genes associated with Alzheimer’s:

·         SNCA – makes protein alpha-synuclein

·         PARK2 – makes protein parkin

·         PARK7 – makes protein DJ-1

·         PINK1 – makes protein with no known function

·         LRRK2 – makes protein dardarin

[bio3project-blog]

a. Open the software to be used, in this case, MEGA b. Click “Align” then “Edit/Build Alignment” c. Select “Create a new alignment” and click “OK” d. If you are building a DNA sequence alignment, click “DNA” or click “Protein” if you are building a protein sequence alignment e. On the new window, click “Insert sequences from MEGA/FASTA/Text/Sequencer files” or simply press Ctrl+I 

[bio3project-blog]

f.   Press Ctrl+A then click “Alignment” and “Align by ClustalW” g. Based on the reference sequence, delete the excess bases on both ends h.  Click “Data,” “Phylogenetic Analysis,” then “Export Alignment” in FASTA format i. On the first window, click “Models” then “Find Best DNA/Protein Models” and click “Yes” and “Compute”

[bio3project-blog]

j. After the analysis, a new window will appear showing the results. Check the BIC column and the model to be used is the one with the lowest value. k. Back on the first window, click “Phylogeny” then “Construct/Test Maximum Likelihood Tree” and click “Yes” l. Another window will appear and set some options based on the following: Test of Phylogeny: Bootstrap method No. of Bootstrap Replications: 1000 Substitution Types: Nucleotides (DNA) or Amino Acid (Protein) Model/Method: Use the model from the result of the earlier analysis Rates among Sites: Use the result from the result of the earlier analysis m.   Click “Compute” then the analysis will begin n.   After some time (based on the “No. of Bootstrap Replications” and number of sequences), the constructed tree will appear and it will show two versions: Original and Bootstrap

[bio3project-blog]

ANALYSIS

Based on the phylogenetic tree, it can be said that Pan troglodytes, or chimpanzee, is closely related to the reference sequence, Homo sapiens. Between the chimpanzee and human, the bootstrap value that was obtained from the analysis is 98% . The result that shows the close relationship between the two is reliable since the value is greater than 75% and is also near 100%.

With those results, Pan troglodytes can be used as a substitute for Homo sapiens for conducting studies regarding Parkinson’s disease. Humans cannot be used as test subjects since doing it is considered unethical. With the close relationship between the chimpanzee and human, chimpanzees can be used for such experiments.  

[bio3project-blog]

REFERENCES

Adnan, A. (2010, July 5). Importance and Applications of Bioinformatics in Molecular Medicine. Retrieved November 25, 2017, from https://www.biotecharticles.com/Bioinformatics-Article/Importance-and-Applications-of-Bioinformatics-in-Molecular-Medicine-214.html

Biological and Medical Informatics Research Center . (n.d.). Bioinformatics. Retrieved November 25, 2017, from http://informatics.sdsu.edu/bioinformatics/

Heyn, S. N. (n.d.). Parkinson's Disease: 17 Early Signs, Symptoms & Treatment. Retrieved December 1, 2017, from https://www.medicinenet.com/parkinsons_disease/article.htm

Kapetanovic, I. M., Rosenfeld, S., & Izmirlian, G. (2004). Overview of Commonly Used Bioinformatics Methods and Their Applications. Annals of the New York Academy of Sciences, 1020(1), 10-21. doi:10.1196/annals.1310.003

Saeys, Y., Inza, I., Larranaga, P. (2007). A review of feature selection techniques in bioinformatics. Bioinformatics, 23(19), 2507-2517. doi:10.1093/bioinformatics/btm344

ScienceDaily. (n.d.). Bioinformatics. Retrieved November 25, 2017, from https://www.sciencedaily.com/terms/bioinformatics.htm

WebMD. (n.d.). Parkinson's Disease. Retrieved November 25, 2017, from https://www.webmd.com/parkinsons-disease/default.htm