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GMU:Life in an aquatic ecosystem/Dahye Seo (view source)
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''Dead Life Live Life'' | {{#ev:youtube|bGzmhJ9kQi4}} | ||
=== '''Dead Life Live Life (working title)''' === | |||
'''Dead Life Live Life''' is a poetic exploration of the interconnectedness of life and death through the sonification of the DNA movement.� It sonifies the DNA movement of a persimmon tree planted at my grandmother's house, who passed away in 2018. The tree serves as a living memory of her, still enduring in the now-empty house. The project visualizes the movement of the tree’s DNA through electrophoresis experiments, converting this movement into sound in real time. | |||
[[File:Diagram Dead LifeLiveLife.jpg|center|thumb|800x800px]] | |||
[[File:Dlll 1.001.jpg|center|frameless|800x800px]] | [[File:Dlll 1.001.jpg|center|frameless|800x800px]] | ||
[[File:Dlll 2..jpg|center|frameless|800x800px]] | [[File:Dlll 2..jpg|center|frameless|800x800px]] | ||
| Line 10: | Line 16: | ||
==== Technical solution ==== | ====Technical solution==== | ||
===== 1. Biological part ===== | =====1. Biological part===== | ||
Instruction of DNA analysis<gallery> | Instruction of DNA analysis<gallery> | ||
File:Instruction1 DNAworkshop.jpg | File:Instruction1 DNAworkshop.jpg | ||
| Line 37: | Line 42: | ||
</gallery>DNA of the persimmon is amplified through a PCR experiment. The amplified DNA is visualized in a gel electrophoresis experiment. DNA molecules dyed to respond to UV light glow and flow electromagnetically in an agar-gel chamber | </gallery>DNA of the persimmon is amplified through a PCR experiment. The amplified DNA is visualized in a gel electrophoresis experiment. DNA molecules dyed to respond to UV light glow and flow electromagnetically in an agar-gel chamber | ||
* �Extra Guide of Electrophoresis https://blog.naver.com/kmkae52/222804356219<br /> | |||
=====2. Sound part===== | |||
===== 2. Sound part ===== | |||
1) Sonification of DNA movementMax/Msp patch | 1) Sonification of DNA movementMax/Msp patch | ||
| Line 46: | Line 50: | ||
2) Sound Design | 2) Sound Design | ||
===== | ===== *reference : Paul '''''Latent Figure Protocol'', Paul Vanouse, 2007-09''' https://www.paulvanouse.com/lfp.html ===== | ||
<u> | ====Work in Biolab==== | ||
====='''2024.11.16. Sat'''===== | |||
<u>Introduction</u> | |||
Gel Electrophoresis Exercise | |||
I started by relearning how to use a micropipette to pick up where I left off a year ago. I tested two DNA ladders and a green stain that I had stored in the freezer to see if they were still functional. | I started by relearning how to use a micropipette to pick up where I left off a year ago. I tested two DNA ladders and a green stain that I had stored in the freezer to see if they were still functional. | ||
<u>Procedure</u> | |||
''recipe'' | |||
Agarosegel : 0.5g Agarose, 50 ml TBE Buffer, 2.5 µl DNA Stein green | |||
TBE Buffer for cover gel : 50 ml TBE Buffer, 1.25 µl DNA Stein green | |||
Gel Electrophoresis : 5V - 40 min -> 5V - 40 min -> 6V - 60 min (current 400 in every process) | |||
The instructions say to electrophoresis at 5v for 40 min. Due to the short distance of DNA migration, I did 2 additional cycles. | The instructions say to electrophoresis at 5v for 40 min. Due to the short distance of DNA migration, I did 2 additional cycles. | ||
<gallery> | |||
File:DNA ladder1.jpg | |||
File:DNA Ladder2.jpg | |||
File:Prepare GelElectrophoresis.jpg | |||
File:Gel electrophoresis1.jpg | |||
File:GelElectrophoresis.jpg | |||
File:Note.jpg | |||
</gallery> | |||
<u>Result</u> | |||
First Column: 1 kb DNA ladder | |||
Last to first and second Columns: 100 bp DNA ladder <gallery> | |||
File:First round 5V-40min.jpg | File:First round 5V-40min.jpg | ||
File:2round 5v-40min.jpg | File:2round 5v-40min.jpg | ||
File:3round 6v-60min.jpg | File:3round 6v-60min.jpg | ||
</gallery>*DNA moves slow. Next time, reduce the percentage of agarose gel. | </gallery> | ||
<nowiki>*</nowiki>DNA moves slow. Next time, reduce the percentage of agarose gel ? | |||
How to set up the current for the gel electrophoresis? Does it impact the value of current for the movement of DNA? | |||
<small>ps. after around 50 hours. Still there remains the trace of the DNA movement.</small> | |||
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery> | |||
=====''' 2024.11.18. Mon'''===== | |||
<u>Introduction</u> | |||
The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process. | |||
<u>Procedure</u> | |||
A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes. | |||
<small>* Note</small> | |||
<small>1. Reused the gel from 2 days ago.</small> | |||
<small>2. Did not put stain green in the TBE buffer covering the gel.</small> | |||
<u>Result</u> | |||
When the UV was shined throughout the experiment, the DNA movement is very blurry compared to when it was not. | |||
However, I am not sure if this is due to the UV light or the reuse of the gel or the lack of stain green. | |||
<gallery> File:DNALadder UV lighting.jpg </gallery> | |||
====='''2024.11.19. Tue'''===== | |||
<u>Introduction</u> | |||
DNA Extraction Exercise_ Kaki,Blueberry | |||
<u>Procedure</u> | |||
I followed the guide from Julian's workshop (see photo above) | |||
<gallery> | |||
File:Kaki ex.jpg | |||
File:Kaki ex1.jpg | |||
File:Blueberry dna.jpg | |||
File:Dna Ex.jpg | |||
File:Dna Ex1.jpg | |||
File:Dna Ex2.jpg | |||
File:Dna Ex3.jpg | |||
</gallery> | |||
<u>Result</u> | |||
Blueberries were successful in extracting DNA, but kaki failed again. | |||
<gallery> | |||
File:Dna Ex5.jpg | |||
File:Dna Ex6.jpg | |||
</gallery> | |||
====='''2024.11.20. Wed'''===== | |||
<u>Introduction</u> | |||
DNA Extraction Exercise_ Kaki, Leaf | |||
- I failed to extract Kaki's DNA in my experiment yesterday. This time i followed the guide from the result of research by Alessandro to extract Kaki's DNA. | |||
- Alessandro's research results show that DNA is mainly extracted from the leaves of the persimmon. Since I can't get the leaves of the persimmon right now, I tried the experiment with the weeds on the roadside. | |||
<u>Procedure</u> | |||
-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf. | |||
<small>To extract DNA from kaki (persimmon) fruit, you'll need about '''3-4 fruits''' to get a sufficient amount of DNA for analysis. Here's a step-by-step procedure:</small> | |||
<small>### Materials Needed:</small> | |||
<small>- 3-4 kaki fruits</small> | |||
<small>- 5g washing up liquid or hand soap</small> | |||
<small>- 2g salt</small> | |||
<small>- 100ml tap water</small> | |||
<small>- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)</small> | |||
<small>- Knife and fork for cutting and mashing</small> | |||
<small>- Beaker or large bowl</small> | |||
<small>- Coffee filter or fine sieve</small> | |||
<small>- Saucepan for hot water bath</small> | |||
<small>- Ice water bath</small> | |||
<small>### Procedure:</small> | |||
<small>1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.</small> | |||
<small>2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.</small> | |||
<small>3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.</small> | |||
<small>4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.</small> | |||
<small>5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.</small> | |||
<small>6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.</small> | |||
<small>7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.</small> | |||
<small>8. '''DNA Precipitation''': Slowly pour ice-cold alcohol down the side of the container to form a layer on top of the filtered mixture. DNA will precipitate out as a white, jelly-like substance at the interface.</small> | |||
<small>9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.</small> | |||
<gallery> | |||
File:Leaaaaf.jpg | |||
File:Leaaaaf1.jpg | |||
File:Dh1.jpg | |||
File:Dh2.jpg | |||
File:Dh3.jpg | |||
File:Dh4.jpg | |||
File:Dh5.jpg | |||
File:Dh6.jpg | |||
File:Dh7.jpg | |||
File:Dh8.jpg | |||
</gallery> | |||
<u>Result</u> | |||
Both the leaves and the persimmon failed to extract DNA. I was a little frustrated. | |||
It seems like I need to extract DNA from the leaves persimmon tree. | |||
But where do I get the leaves?<gallery> | |||
File:Dh9.jpg | |||
File:Dh10.jpg | |||
</gallery> | |||
====='''2024.11.21. Thu'''===== | |||
<u>Introduction</u> | |||
Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry. | |||
<u>Procedure</u> | |||
I followed the guide from Julian's workshop as usual<gallery> | |||
File:DNA Extraction Banana-blueberry.jpg | |||
File:DNA Extraction Banana-blueberry1.jpg | |||
File:DNA Extraction Banana-blueberry2.jpg | |||
</gallery><u>Result</u> | |||
DNA extraction was successful for both bananas and blueberries. DNA extraction is particularly easy for bananas. Blueberries, like strawberries and raspberries, do not have a high DNA extraction rate compared to other berry types.<gallery> | |||
File:DNA from BANANA.jpg | |||
File:DNA from Blueberry.jpg | |||
File:DNA from blueberry in tube.jpg | |||
File:DNA from Banana in tube.jpg | |||
</gallery> | |||
====='''2024.11.23. Sat'''===== | |||
<u>Introduction</u> | |||
Exercise for DNA centrifugation and PCR Experiment | |||
<u>Procedure</u> | |||
I followed the instruction in Julian's workshop for setting up the centrifugation of DNA sample and PCR. | |||
#Centrifuge setting: 8kg, 60 seconds | |||
#PCR: see instructional photo above. | |||
A total of five DNA samples were subjected to DNA amplification by PCR | |||
*Label information | |||
*#B11: DNA of Blueberries (from 19.Nov) | |||
*#B12: DNA of Blueberries (from 19.Nov) | |||
*#B2: DNA of Blueberries (from 21.Nov) | |||
*#BA: DNA of Banana (from 21.Nov) | |||
*# K: Kaki pulp with soap, salt, hot water (from 20.Nov) | |||
<small>*sample B11, B12 are dirtier than B2</small> | |||
<small>*So far no success to extract Kaki DNA. I used this time kaki pulp instead of DNA. It seems like there are no DNA in pulp, but at least I wanted experiment with pulp until Gel-electrophoresis just for double checking. </small> | |||
<gallery> | |||
File:Centrifugation1.jpg | |||
File:Material for pcr.jpg | |||
File:Pcr1.jpg | |||
File:Pcr2.jpg | |||
File:Pcr setting bento machine.jpg | |||
<nowiki></gallery> | |||
====='''2024.11.26. Tue'''===== | |||
<u>Introduction</u> | |||
Extracting DNA from leaves using DNeasy Kit with supervising by Alessandro Volpato_ Since there are no leaves from persimmon trees, I experimented with leaves from other trees in Ilm park. | |||
<u>Procedure</u> | |||
The protocol below was followed. | |||
[[File:DNeasy protocol.pdf|left|thumb]] | |||
<nowiki>https://youtu.be/c1WOBy5vSg8?si=ksFltpYkG1ytvugT</nowiki> | |||
<gallery> | |||
File:Dneasy kit1.jpg | |||
File:Dneasy kit.jpg | |||
File:Dneasy kit2.jpg | |||
File:Dneasy kit3.jpg | |||
File:Dneasy kit4.jpg | |||
File:Dneasy kit5.jpg | |||
File:Dneasy kit6.jpg | |||
</gallery> | |||
<u>Result</u> | |||
I followed the protocol to extract DNA from the leaves, but I could not visually check if the DNA was extracted correctly. After the gel electrophoresis, i I will know if the DNA was extracted. �I will start electrophoresis as soon as the Stein green arrives. | |||
===== '''2024.12.11''' ===== | |||
[[File:Pcr 29241211.jpg|thumb]] | |||
<u>Introduction</u> | |||
PCR / Gel electrophoresis | |||
I did PCR 3 samples which are DNA of leaves extracted by DNA EXTRACT KIT, Banana, Blueberry. | |||
<u>Result</u> | |||
During the PCR experiment, I successfully amplified all the sample DNA and proceeded with gel electrophoresis. However, I encountered an error message indicating that no electricity was flowing through the gel, which prevented me from continuing the experiment. | |||
===== '''2024.12.17. Tue''' ===== | |||
<u>Introduction</u> | |||
Electrophoresis was performed under constant UV light and the movement of the dna was filmed live. Experiments with DNA Ladder. | |||
<u>Result</u> | |||
<nowiki>https://youtu.be/OsDsI0Ecbg4?si=UxQGSdfn7OdSeWgl</nowiki> | |||
Under constant UV light, the DNA becomes increasingly blurry. I feel that it is not against the artistic message of this work that the DNA gradually disappears as an inherent property during the experiment. | |||