It final presentation
-
Upload
chris-thompson -
Category
Documents
-
view
85 -
download
0
Transcript of It final presentation
![Page 1: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/1.jpg)
IT Final PresentationChris ThompsonApril 18th, 2013
CNIT 227
![Page 2: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/2.jpg)
Introduction
Materials
Methods
Results and Conclusion
Table of Contents
![Page 3: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/3.jpg)
INTRODUCTION
![Page 4: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/4.jpg)
Biotechnology
Biotechnology - Any technological application that uses biological systems, living organisms or derivatives thereof, to make or modify products or processes for specific use.
Biotechnology is important because without biotechnology, many of the advancements in the latter half of the 20th century would not have been possible, like the Green Revolution
![Page 5: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/5.jpg)
IT
IT is the biotechnology course at Purdue, focused on researching and characterizing the properties of mycobacteriophages.
This semester our overall goal was to develop a system for schools without a DNA sequencer to determine the cluster assignments of phages.
![Page 6: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/6.jpg)
Bacteriophages• A virus that infects and replicates in bacteria• One of the most common and populous
organism in existence • Many have a mosaic genome• Unlimited potential usage• Mycobacteriophages infect M.smegmatis
![Page 7: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/7.jpg)
Clusters
• System to organize bacteriophages• Phages sorted by factors such as genome
length, presence of certain genes, organization of genome, GC content, and plaque size and characteristics
• A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, Singleton, and T
![Page 8: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/8.jpg)
MATERIALS
![Page 9: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/9.jpg)
Materials
• Unknown phage• M.smegmatis• Qiagen miniprep kit• Pressure Cycler• Mass spectrophotometer• BBC Proteomics Pipeline
![Page 10: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/10.jpg)
METHODS
![Page 11: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/11.jpg)
Organization
• HHMI gave us 15 unknown phages to work with• Each student performed assays on their own phage
to determine its cluster assignment• HHMI knows the cluster assignment, and will tell us if
we’re correct
![Page 12: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/12.jpg)
Plaque Assays• Created serial dilutions of phages from 10-1 to 10-10
• Let the bacteriophages infect plates of M.smegmatis• Observed plaque sizes and characteristics• Compared observations to known trends of clusters
![Page 13: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/13.jpg)
DNA Extraction
• Used a pressure cycling machine to destroy cell membrane and organelles
• Did a standard DNA extraction of the phage genome using buffers and centrifuges
• Used a NanoDrop machine to analyze the concentration of nucleotides in the sample
![Page 14: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/14.jpg)
Bradford Dye
• Used Bradford Dye as a qualitative measure of whether or not we had proteins in our sample
• My solution turned blue, so I had proteins
![Page 15: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/15.jpg)
Protein Indicator Paper
• Darkness of spots shows how much protein is present
• Darker the spot, more protein there is
![Page 16: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/16.jpg)
Mass Spectrometry
• Used mass spectrometry to analyze protein products• Went through the BBC Proteomics Discovery Pipeline• Compared results with negative control and positive
control• Phages that showed up the most:– Bxz2 (13)– EpicPhail (3)– Rockstar (4)– Dori (15)
![Page 17: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/17.jpg)
RESULTS AND CONCLUSION
![Page 18: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/18.jpg)
Final Guess
• Cluster: A• Subcluster: A3
• Reasons:– Plaque size and shape looks like cluster A plaques– Most related phages were mostly related from cluster A
and subcluster A3. EpicPhail, Rockstar, Bxz2.
![Page 19: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/19.jpg)
Accomplishments
• Used complex lab procedures to analyze phage properties
• Used mass spectrometry to discover protein products of phage
• Were able to compare cluster properties of certain phages to our unknown and make a prediction
![Page 20: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/20.jpg)
Significance
• Cluster assignment method can be used by schools that don’t have the funds to do full genome sequencing
• Proves validity of undergraduate research• Learned about biotechnology, bacteriophages,
genomes, plaques, and clusters
![Page 21: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/21.jpg)
Future Work and Questions
• Was the phage novel or a common phage?• How close was my guess?• Is there a better method to assign clusters without
sequencing the genome?
![Page 22: It final presentation](https://reader031.fdocuments.us/reader031/viewer/2022013013/589fbbd81a28abf9038b6bab/html5/thumbnails/22.jpg)
The End