Medien Wiki - User contributions [en]

GMU:Life in an aquatic ecosystem/Ecosystem of our pond

2025-01-28T11:35:56Z

Dahyeseo:

==Ecosystem of our pond==

=== '''Observation of the our pond's Ecology on January 22, 2025''' ===
It was a cold day, and the water and soil of the pond were completely frozen. Using a stone, I broke through approximately 5 cm of ice to collect a water sample from the pond. Under the microscope, the movement of a single species was particularly active. According to Alessandro Vopato, it is identified as ''Chlamydomonas''.

====== '''Chlamydomonas''' ======
Chlamydomonas is a genus of unicellular green algae comprising approximately 150 species. These microscopic organisms are predominantly found in freshwater environments, such as ponds and lakes, but can also inhabit damp soils and even snow. They are characterized by their spherical or oval shape and possess two anterior flagella, which facilitate movement. A notable feature is their cup-shaped chloroplast, essential for photosynthesis.

In scientific research, Chlamydomonas, particularly the species ''Chlamydomonas reinhardtii'', serves as a valuable model organism. It is extensively utilized to study various cellular processes, including photosynthesis, flagellar motility, and light perception. Research on this alga has significantly advanced our understanding of plant biology and cellular functions.

Under the microscope, Chlamydomonas exhibits active movement due to its flagella. Its adaptability allows it to thrive in diverse environments, making it a common subject of study in ecological and biological research.
<gallery mode="nolines">
File:Chalamydomonas.jpg
File:Chlamydomonas-reinhardtii-Agrisera-antibodies.png
File:Grunalge-chlamydomonas.jpg
</gallery>

====== Weather info on Jan 22, 2025 ======

[[File:Weather info on jan22-2025.png|thumb|600x600px|center]].

===VIDEO ESSAY===

[[File:Video essay still1.png|frameless|center|600x600px]]

====== '''Video Link : <nowiki>https://youtu.be/pK4iSMGivBQ?si=6y7W-pbcQaKUgvQc</nowiki>''' ======

===Still cut===
<gallery mode="nolines">
File:Video essay still1.png
File:Video essay still2.png
File:Video essay still3.png
File:Video essay still4.png
File:Video essay still7.png
File:Video essay still8.png
File:Video essay still9.png
File:Video essay still10.png
File:Video essay still11.png
File:Video essay still12.png
File:Video essay still13.png
File:Video essay still14.png
File:Video essay still15.png
</gallery>

GMU:Life in an aquatic ecosystem/Ecosystem of our pond

2025-01-28T11:35:31Z

Dahyeseo: /* Weather info on Jan 22, 2025 */

GMU:Life in an aquatic ecosystem/Ecosystem of our pond

2025-01-28T11:34:45Z

Dahyeseo:

==Ecosystem of our pond==

=== '''Observation of the our pond's Ecology on January 22, 2025''' ===
It was a cold day, and the water and soil of the pond were completely frozen. Using a stone, I broke through approximately 5 cm of ice to collect a water sample from the pond. Under the microscope, the movement of a single species was particularly active. According to Alessandro Vopato, it is identified as ''Chlamydomonas''.

====== '''Chlamydomonas''' ======
Chlamydomonas is a genus of unicellular green algae comprising approximately 150 species. These microscopic organisms are predominantly found in freshwater environments, such as ponds and lakes, but can also inhabit damp soils and even snow. They are characterized by their spherical or oval shape and possess two anterior flagella, which facilitate movement. A notable feature is their cup-shaped chloroplast, essential for photosynthesis.

In scientific research, Chlamydomonas, particularly the species ''Chlamydomonas reinhardtii'', serves as a valuable model organism. It is extensively utilized to study various cellular processes, including photosynthesis, flagellar motility, and light perception. Research on this alga has significantly advanced our understanding of plant biology and cellular functions.

Under the microscope, Chlamydomonas exhibits active movement due to its flagella. Its adaptability allows it to thrive in diverse environments, making it a common subject of study in ecological and biological research.
<gallery mode="nolines">
File:Chalamydomonas.jpg
File:Chlamydomonas-reinhardtii-Agrisera-antibodies.png
File:Grunalge-chlamydomonas.jpg
</gallery>

===VIDEO ESSAY===

[[File:Video essay still1.png|frameless|center|600x600px]]

====== '''Video Link : <nowiki>https://youtu.be/pK4iSMGivBQ?si=6y7W-pbcQaKUgvQc</nowiki>''' ======

====== Weather info on Jan 22, 2025 ======

[[File:Weather info on jan22-2025.png|left|thumb|600x600px]].

===Still cut===
<gallery mode="nolines">
File:Video essay still1.png
File:Video essay still2.png
File:Video essay still3.png
File:Video essay still4.png
File:Video essay still7.png
File:Video essay still8.png
File:Video essay still9.png
File:Video essay still10.png
File:Video essay still11.png
File:Video essay still12.png
File:Video essay still13.png
File:Video essay still14.png
File:Video essay still15.png
</gallery>

GMU:Life in an aquatic ecosystem/Ecosystem of our pond

2025-01-28T11:34:11Z

Dahyeseo:

==Ecosystem of our pond==

=== '''Observation of the our pond's Ecology on January 22, 2025''' ===
It was a cold day, and the water and soil of the pond were completely frozen. Using a stone, I broke through approximately 5 cm of ice to collect a water sample from the pond. Under the microscope, the movement of a single species was particularly active. According to Alessandro Vopato, it is identified as ''Chlamydomonas''.

====== '''Chlamydomonas''' ======
Chlamydomonas is a genus of unicellular green algae comprising approximately 150 species. These microscopic organisms are predominantly found in freshwater environments, such as ponds and lakes, but can also inhabit damp soils and even snow. They are characterized by their spherical or oval shape and possess two anterior flagella, which facilitate movement. A notable feature is their cup-shaped chloroplast, essential for photosynthesis.

In scientific research, Chlamydomonas, particularly the species ''Chlamydomonas reinhardtii'', serves as a valuable model organism. It is extensively utilized to study various cellular processes, including photosynthesis, flagellar motility, and light perception. Research on this alga has significantly advanced our understanding of plant biology and cellular functions.

Under the microscope, Chlamydomonas exhibits active movement due to its flagella. Its adaptability allows it to thrive in diverse environments, making it a common subject of study in ecological and biological research.
<gallery mode="nolines">
File:Chalamydomonas.jpg
File:Chlamydomonas-reinhardtii-Agrisera-antibodies.png
File:Grunalge-chlamydomonas.jpg
</gallery>

===VIDEO ESSAY===

[[File:Video essay still1.png|frameless|center|600x600px]]

====== '''Video Link : <nowiki>https://youtu.be/pK4iSMGivBQ?si=6y7W-pbcQaKUgvQc</nowiki>''' ======

====== Weather info on Jan 22, 2025 ======

[[File:Weather info on jan22-2025.png|left|thumb|600x600px]]

===Still cut===
<gallery mode="nolines">
File:Video essay still1.png
File:Video essay still2.png
File:Video essay still3.png
File:Video essay still4.png
File:Video essay still7.png
File:Video essay still8.png
File:Video essay still9.png
File:Video essay still10.png
File:Video essay still11.png
File:Video essay still12.png
File:Video essay still13.png
File:Video essay still14.png
File:Video essay still15.png
</gallery>

GMU:Life in an aquatic ecosystem/Ecosystem of our pond

2025-01-28T11:33:41Z

Dahyeseo:

==Ecosystem of our pond==

=== '''Observation of the our pond's Ecology on January 22, 2025''' ===
It was a cold day, and the water and soil of the pond were completely frozen. Using a stone, I broke through approximately 5 cm of ice to collect a water sample from the pond. Under the microscope, the movement of a single species was particularly active. According to Alessandro Vopato, it is identified as ''Chlamydomonas''.

====== '''Chlamydomonas''' ======
Chlamydomonas is a genus of unicellular green algae comprising approximately 150 species. These microscopic organisms are predominantly found in freshwater environments, such as ponds and lakes, but can also inhabit damp soils and even snow. They are characterized by their spherical or oval shape and possess two anterior flagella, which facilitate movement. A notable feature is their cup-shaped chloroplast, essential for photosynthesis.

In scientific research, Chlamydomonas, particularly the species ''Chlamydomonas reinhardtii'', serves as a valuable model organism. It is extensively utilized to study various cellular processes, including photosynthesis, flagellar motility, and light perception. Research on this alga has significantly advanced our understanding of plant biology and cellular functions.

Under the microscope, Chlamydomonas exhibits active movement due to its flagella. Its adaptability allows it to thrive in diverse environments, making it a common subject of study in ecological and biological research.
<gallery mode="nolines">
File:Chalamydomonas.jpg
File:Chlamydomonas-reinhardtii-Agrisera-antibodies.png
File:Grunalge-chlamydomonas.jpg
</gallery>

===VIDEO ESSAY===

[[File:Video essay still1.png|frameless|center|600x600px]]

====== '''Video Link : <nowiki>https://youtu.be/pK4iSMGivBQ?si=6y7W-pbcQaKUgvQc</nowiki>''' ======

====== �Weather info on Jan 22, 2025 ======
[[File:Weather info on jan22-2025.png|left|thumb|600x600px]]

===Still cut===
<gallery mode="nolines">
File:Video essay still1.png
File:Video essay still2.png
File:Video essay still3.png
File:Video essay still4.png
File:Video essay still7.png
File:Video essay still8.png
File:Video essay still9.png
File:Video essay still10.png
File:Video essay still11.png
File:Video essay still12.png
File:Video essay still13.png
File:Video essay still14.png
File:Video essay still15.png
</gallery>

File:Weather info on jan22-2025.png

2025-01-28T11:32:58Z

Dahyeseo:

weather info on jan22-2025

GMU:Life in an aquatic ecosystem/Ecosystem of our pond

2025-01-27T15:05:44Z

Dahyeseo:

==Ecosystem of our pond==

=== '''Observation of the our pond's Ecology on January 22, 2025''' ===
It was a cold day, and the water and soil of the pond were completely frozen. Using a stone, I broke through approximately 5 cm of ice to collect a water sample from the pond. Under the microscope, the movement of a single species was particularly active. According to Alessandro Vopato, it is identified as ''Chlamydomonas''.

====== '''Chlamydomonas''' ======
Chlamydomonas is a genus of unicellular green algae comprising approximately 150 species. These microscopic organisms are predominantly found in freshwater environments, such as ponds and lakes, but can also inhabit damp soils and even snow. They are characterized by their spherical or oval shape and possess two anterior flagella, which facilitate movement. A notable feature is their cup-shaped chloroplast, essential for photosynthesis.

In scientific research, Chlamydomonas, particularly the species ''Chlamydomonas reinhardtii'', serves as a valuable model organism. It is extensively utilized to study various cellular processes, including photosynthesis, flagellar motility, and light perception. Research on this alga has significantly advanced our understanding of plant biology and cellular functions.

Under the microscope, Chlamydomonas exhibits active movement due to its flagella. Its adaptability allows it to thrive in diverse environments, making it a common subject of study in ecological and biological research.
<gallery mode="nolines">
File:Chalamydomonas.jpg
File:Chlamydomonas-reinhardtii-Agrisera-antibodies.png
File:Grunalge-chlamydomonas.jpg
</gallery>

===VIDEO ESSAY===

[[File:Video essay still1.png|frameless|center|600x600px]]

====== '''Video Link : <nowiki>https://youtu.be/pK4iSMGivBQ?si=6y7W-pbcQaKUgvQc</nowiki>''' ======

===Still cut===
<gallery mode="nolines">
File:Video essay still1.png
File:Video essay still2.png
File:Video essay still3.png
File:Video essay still4.png
File:Video essay still7.png
File:Video essay still8.png
File:Video essay still9.png
File:Video essay still10.png
File:Video essay still11.png
File:Video essay still12.png
File:Video essay still13.png
File:Video essay still14.png
File:Video essay still15.png
</gallery>

GMU:Cybernetic Subjects - Ursula Damm (Georg Trogemann)/Dahye Seo

2025-01-27T13:38:19Z

Dahyeseo:

{{#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 2..jpg|center|frameless|800x800px]]

====Technical solution====

=====1. Biological part=====
Instruction of DNA analysis<gallery>
File:Instruction1 DNAworkshop.jpg
File:Instruction2 DNAworkshop.jpg
</gallery>1) DNA Extraction of Persimmons <gallery>
File:Kaki gelElectrophoresis 2.jpeg
File:Kaki gelElectrophoresis 3.jpeg
File:Kaki gelElectrophoresis 4.jpeg
File:Kaki gelElectrophoresis 5.jpeg
File:Kaki gelElectrophoresis 6.jpeg
File:Kaki gelElectrophoresis 7.jpeg
File:Kaki gelElectrophoresis 8.jpeg
</gallery>

2) PCR Experiment (DNA amplification) / Gel electrophoresis (DNA movement & visualization) . <gallery>
File:Kaki gelElectrophoresis 10.jpeg
File:Kaki gelElectrophoresis 9.jpeg
File:Kaki gelElectrophoresis 11.jpeg
File:Kaki gelElectrophoresis 12.jpeg
File:Kaki gelElectrophoresis 13.jpeg
File:Gelelectrophoresis workshop 20230428 Large.jpeg
</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 
=====2. Sound part=====
1) Sonification of DNA movementMax/Msp patch

Convert continuously changing number of RGB data (could be change to other data) of DNA movement animation to midi or frequency.{{#ev:youtube|bGzmhJ9kQi4}}

2) Sound Design

===== *reference : Paul '''''Latent Figure Protocol'', Paul Vanouse, 2007-09''' https://www.paulvanouse.com/lfp.html =====

====Work in Biolab====

====='''2024.11.16. Sat'''=====
Introduction

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.

Procedure

''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.

<gallery>
File:DNA ladder1.jpg
File:DNA Ladder2.jpg
File:Prepare GelElectrophoresis.jpg
File:Gel electrophoresis1.jpg
File:GelElectrophoresis.jpg
File:Note.jpg
</gallery>

Result

First Column: 1 kb DNA ladder

Last to first and second Columns: 100 bp DNA ladder <gallery>
File:First round 5V-40min.jpg
File:2round 5v-40min.jpg
File:3round 6v-60min.jpg
</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?

ps. after around 50 hours. Still there remains the trace of the DNA movement.
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>

=====''' 2024.11.18. Mon'''=====
Introduction

The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.

Procedure

A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.

* Note

1. Reused the gel from 2 days ago.

2. Did not put stain green in the TBE buffer covering the gel.

Result

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'''=====
Introduction

DNA Extraction Exercise_ Kaki,Blueberry

Procedure

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>
Result

Blueberries were successful in extracting DNA, but kaki failed again.
<gallery>
File:Dna Ex5.jpg
File:Dna Ex6.jpg
</gallery>

====='''2024.11.20. Wed'''=====
Introduction

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.

Procedure

-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.

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:

### Materials Needed:

- 3-4 kaki fruits

- 5g washing up liquid or hand soap

- 2g salt

- 100ml tap water

- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)

- Knife and fork for cutting and mashing

- Beaker or large bowl

- Coffee filter or fine sieve

- Saucepan for hot water bath

- Ice water bath

### Procedure:

1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.

2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.

3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.

4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.

5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.

6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.

7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.

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.

9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.
<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>

Result

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'''=====
Introduction

Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry.

Procedure

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>Result

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'''=====
Introduction

Exercise for DNA centrifugation and PCR Experiment

Procedure

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)

*sample B11, B12 are dirtier than B2

*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. 
<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'''=====
Introduction

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.

Procedure

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>

Result

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]]
Introduction

PCR / Gel electrophoresis

I did PCR 3 samples which are DNA of leaves extracted by DNA EXTRACT KIT, Banana, Blueberry.

Result

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''' =====
Introduction

Electrophoresis was performed under constant UV light and the movement of the dna was filmed live. Experiments with DNA Ladder.

Result

<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.

GMU:Life in an aquatic ecosystem/Ecosystem of our pond

2025-01-26T17:33:56Z

Dahyeseo:

==Ecosystem of our pond==

=== '''Observation of the our pond's Ecology on January 22, 2025''' ===
It was a cold day, and the water and soil of the pond were completely frozen. Using a stone, I broke through approximately 5 cm of ice to collect a water sample from the pond. Under the microscope, the movement of a single species was particularly active. According to Alessandro Vopato, it is identified as ''Chlamydomonas''.

====== '''Chlamydomonas''' ======
Chlamydomonas is a genus of unicellular green algae comprising approximately 150 species. These microscopic organisms are predominantly found in freshwater environments, such as ponds and lakes, but can also inhabit damp soils and even snow. They are characterized by their spherical or oval shape and possess two anterior flagella, which facilitate movement. A notable feature is their cup-shaped chloroplast, essential for photosynthesis.

In scientific research, Chlamydomonas, particularly the species ''Chlamydomonas reinhardtii'', serves as a valuable model organism. It is extensively utilized to study various cellular processes, including photosynthesis, flagellar motility, and light perception. Research on this alga has significantly advanced our understanding of plant biology and cellular functions.

Under the microscope, Chlamydomonas exhibits active movement due to its flagella. Its adaptability allows it to thrive in diverse environments, making it a common subject of study in ecological and biological research.
<gallery mode="nolines">
File:Chalamydomonas.jpg
File:Chlamydomonas-reinhardtii-Agrisera-antibodies.png
File:Grunalge-chlamydomonas.jpg
</gallery>

===VIDEO ESSAY===

[[File:Video essay still1.png|frameless|center|600x600px]]

Link :<nowiki> https://youtu.be/pK4iSMGivBQ?si=6y7W-pbcQaKUgvQc </nowiki>

===Still cut===
<gallery mode="nolines">
File:Video essay still1.png
File:Video essay still2.png
File:Video essay still3.png
File:Video essay still4.png
File:Video essay still7.png
File:Video essay still8.png
File:Video essay still9.png
File:Video essay still10.png
File:Video essay still11.png
File:Video essay still12.png
File:Video essay still13.png
File:Video essay still14.png
File:Video essay still15.png
</gallery>

GMU:Life in an aquatic ecosystem/Ecosystem of our pond

2025-01-26T17:33:04Z

Dahyeseo:

==Ecosystem of our pond==

=== '''Observation of the our pond's Ecology on January 22, 2025''' ===
It was a cold day, and the water and soil of the pond were completely frozen. Using a stone, I broke through approximately 5 cm of ice to collect a water sample from the pond. Under the microscope, the movement of a single species was particularly active. According to Alessandro Vopato, it is identified as ''Chlamydomonas''.

====== '''Chlamydomonas''' ======
Chlamydomonas is a genus of unicellular green algae comprising approximately 150 species. These microscopic organisms are predominantly found in freshwater environments, such as ponds and lakes, but can also inhabit damp soils and even snow. They are characterized by their spherical or oval shape and possess two anterior flagella, which facilitate movement. A notable feature is their cup-shaped chloroplast, essential for photosynthesis.

In scientific research, Chlamydomonas, particularly the species ''Chlamydomonas reinhardtii'', serves as a valuable model organism. It is extensively utilized to study various cellular processes, including photosynthesis, flagellar motility, and light perception. Research on this alga has significantly advanced our understanding of plant biology and cellular functions.

Under the microscope, Chlamydomonas exhibits active movement due to its flagella. Its adaptability allows it to thrive in diverse environments, making it a common subject of study in ecological and biological research.
<gallery mode="nolines">
File:Chalamydomonas.jpg
File:Chlamydomonas-reinhardtii-Agrisera-antibodies.png
File:Grunalge-chlamydomonas.jpg
</gallery>

===VIDEO ESSAY===

[[File:Video essay still1.png|frameless|center|600x600px]]

Link :<nowiki> https://youtu.be/gMjgVnIXREU?si=jZQQuwfXvkn0ITV7 </nowiki>

===Still cut===
<gallery mode="nolines">
File:Video essay still1.png
File:Video essay still2.png
File:Video essay still3.png
File:Video essay still4.png
File:Video essay still7.png
File:Video essay still8.png
File:Video essay still9.png
File:Video essay still10.png
File:Video essay still11.png
File:Video essay still12.png
File:Video essay still13.png
File:Video essay still14.png
File:Video essay still15.png
</gallery>

File:Grunalge-chlamydomonas.jpg

2025-01-26T17:31:38Z

Dahyeseo:

Grunalge-chlamydomonas

File:Chlamydomonas-reinhardtii-Agrisera-antibodies.png

2025-01-26T17:31:12Z

Dahyeseo:

Chlamydomonas-reinhardtii-Agrisera-antibodies

GMU:Life in an aquatic ecosystem/Ecosystem of our pond

2025-01-26T17:27:34Z

Dahyeseo:

==Ecosystem of our pond==

=== '''Observation of the our pond's Ecology on January 22, 2025''' ===
It was a cold day, and the water and soil of the pond were completely frozen. Using a stone, I broke through approximately 5 cm of ice to collect a water sample from the pond. Under the microscope, the movement of a single species was particularly active. According to Alessandro Vopato, it is identified as ''Chlamydomonas''.

====== '''Chlamydomonas''' ======
Chlamydomonas is a genus of unicellular green algae comprising approximately 150 species. These microscopic organisms are predominantly found in freshwater environments, such as ponds and lakes, but can also inhabit damp soils and even snow. They are characterized by their spherical or oval shape and possess two anterior flagella, which facilitate movement. A notable feature is their cup-shaped chloroplast, essential for photosynthesis.

In scientific research, Chlamydomonas, particularly the species ''Chlamydomonas reinhardtii'', serves as a valuable model organism. It is extensively utilized to study various cellular processes, including photosynthesis, flagellar motility, and light perception. Research on this alga has significantly advanced our understanding of plant biology and cellular functions.

Under the microscope, Chlamydomonas exhibits active movement due to its flagella. Its adaptability allows it to thrive in diverse environments, making it a common subject of study in ecological and biological research.
[[File:Chalamydomonas.jpg|left|thumb|197x197px]]

===VIDEO ESSAY===

[[File:Video essay still1.png|frameless|center|600x600px]]

Link :<nowiki> https://youtu.be/gMjgVnIXREU?si=jZQQuwfXvkn0ITV7 </nowiki>

===Still cut===
<gallery mode="nolines">
File:Video essay still1.png
File:Video essay still2.png
File:Video essay still3.png
File:Video essay still4.png
File:Video essay still7.png
File:Video essay still8.png
File:Video essay still9.png
File:Video essay still10.png
File:Video essay still11.png
File:Video essay still12.png
File:Video essay still13.png
File:Video essay still14.png
File:Video essay still15.png
</gallery>

GMU:Life in an aquatic ecosystem/Ecosystem of our pond

2025-01-26T17:26:08Z

Dahyeseo:

==Ecosystem of our pond==
'''Observation of the our pond's Ecology on January 22, 2025'''

It was a cold day, and the water and soil of the pond were completely frozen. Using a stone, I broke through approximately 5 cm of ice to collect a water sample from the pond. Under the microscope, the movement of a single species was particularly active. According to Alessandro Vopato, it is identified as ''Chlamydomonas''.

'''Chlamydomonas'''

Chlamydomonas is a genus of unicellular green algae comprising approximately 150 species. These microscopic organisms are predominantly found in freshwater environments, such as ponds and lakes, but can also inhabit damp soils and even snow. They are characterized by their spherical or oval shape and possess two anterior flagella, which facilitate movement. A notable feature is their cup-shaped chloroplast, essential for photosynthesis.

In scientific research, Chlamydomonas, particularly the species ''Chlamydomonas reinhardtii'', serves as a valuable model organism. It is extensively utilized to study various cellular processes, including photosynthesis, flagellar motility, and light perception. Research on this alga has significantly advanced our understanding of plant biology and cellular functions.

Under the microscope, Chlamydomonas exhibits active movement due to its flagella. Its adaptability allows it to thrive in diverse environments, making it a common subject of study in ecological and biological research.
[[File:Chalamydomonas.jpg|left|thumb|197x197px]]

===VIDEO ESSAY===

[[File:Video essay still1.png|frameless|center|600x600px]]

Link :<nowiki> https://youtu.be/gMjgVnIXREU?si=jZQQuwfXvkn0ITV7 </nowiki>

===Still cut===
<gallery mode="nolines">
File:Video essay still1.png
File:Video essay still2.png
File:Video essay still3.png
File:Video essay still4.png
File:Video essay still7.png
File:Video essay still8.png
File:Video essay still9.png
File:Video essay still10.png
File:Video essay still11.png
File:Video essay still12.png
File:Video essay still13.png
File:Video essay still14.png
File:Video essay still15.png
</gallery>

GMU:Life in an aquatic ecosystem/Ecosystem of our pond

2025-01-26T17:25:41Z

Dahyeseo: Created page with "==Ecosystem of our pond== '''Observation of the our pond's Ecology on January 22, 2025''' It was a cold day, and the water and soil of the pond were completely frozen. Using a stone, I broke through approximately 5 cm of ice to collect a water sample from the pond. Under the microscope, the movement of a single species was particularly active. According to Alessandro Vopato, it is identified as ''Chlamydomonas''. '''Chlamydomonas''' Chlamydomonas is a genus of unicel..."

File:Chalamydomonas.jpg

2025-01-26T17:14:00Z

Dahyeseo:

Chalamydomonas

File:Video essay still15.png

2025-01-26T16:54:19Z

Dahyeseo:

video essay_still15

File:Video essay still14.png

2025-01-26T16:53:46Z

Dahyeseo:

video essay_still14

File:Video essay still13.png

2025-01-26T16:53:17Z

Dahyeseo:

video essay_still13

File:Video essay still12.png

2025-01-26T16:52:50Z

Dahyeseo:

video essay_still12

File:Video essay still11.png

2025-01-26T16:52:25Z

Dahyeseo:

video essay_still11

File:Video essay still10.png

2025-01-26T16:51:56Z

Dahyeseo:

video essay_still10

File:Video essay still9.png

2025-01-26T16:51:30Z

Dahyeseo:

video essay_still9

File:Video essay still8.png

2025-01-26T16:51:00Z

Dahyeseo:

video essay_still8

File:Video essay still7.png

2025-01-26T16:50:32Z

Dahyeseo:

video essay_still7

File:Video essay still6.png

2025-01-26T16:50:09Z

Dahyeseo:

video essay_still6

File:Video essay still4.png

2025-01-26T16:49:45Z

Dahyeseo:

video essay_still4

File:Video essay still3.png

2025-01-26T16:49:19Z

Dahyeseo:

video essay_still3

File:Video essay still2.png

2025-01-26T16:48:49Z

Dahyeseo:

video essay_still2

File:Video essay still1.png

2025-01-26T16:48:00Z

Dahyeseo:

video essay_still1

GMU:Life in an aquatic ecosystem/Dahye Seo

2025-01-06T16:53:05Z

Dahyeseo:

GMU:Cybernetic Subjects - Ursula Damm (Georg Trogemann)/Dahye Seo

2025-01-06T13:02:35Z

Dahyeseo:

{{#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 2..jpg|center|frameless|800x800px]]

====Technical solution====

=====1. Biological part=====
Instruction of DNA analysis<gallery>
File:Instruction1 DNAworkshop.jpg
File:Instruction2 DNAworkshop.jpg
</gallery>1) DNA Extraction of Persimmons <gallery>
File:Kaki gelElectrophoresis 2.jpeg
File:Kaki gelElectrophoresis 3.jpeg
File:Kaki gelElectrophoresis 4.jpeg
File:Kaki gelElectrophoresis 5.jpeg
File:Kaki gelElectrophoresis 6.jpeg
File:Kaki gelElectrophoresis 7.jpeg
File:Kaki gelElectrophoresis 8.jpeg
</gallery>

2) PCR Experiment (DNA amplification) / Gel electrophoresis (DNA movement & visualization) . <gallery>
File:Kaki gelElectrophoresis 10.jpeg
File:Kaki gelElectrophoresis 9.jpeg
File:Kaki gelElectrophoresis 11.jpeg
File:Kaki gelElectrophoresis 12.jpeg
File:Kaki gelElectrophoresis 13.jpeg
File:Gelelectrophoresis workshop 20230428 Large.jpeg
</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

=====2. Sound part=====
1) Sonification of DNA movementMax/Msp patch

Convert continuously changing number of RGB data (could be change to other data) of DNA movement animation to midi or frequency.{{#ev:youtube|bGzmhJ9kQi4}}

2) Sound Design

====Work in Biolab====

====='''2024.11.16. Sat'''=====
Introduction

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.

Procedure

''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.

<gallery>
File:DNA ladder1.jpg
File:DNA Ladder2.jpg
File:Prepare GelElectrophoresis.jpg
File:Gel electrophoresis1.jpg
File:GelElectrophoresis.jpg
File:Note.jpg
</gallery>

Result

First Column: 1 kb DNA ladder

Last to first and second Columns: 100 bp DNA ladder <gallery>
File:First round 5V-40min.jpg
File:2round 5v-40min.jpg
File:3round 6v-60min.jpg
</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?

ps. after around 50 hours. Still there remains the trace of the DNA movement.
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>

=====''' 2024.11.18. Mon'''=====
Introduction

The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.

Procedure

A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.

* Note

1. Reused the gel from 2 days ago.

2. Did not put stain green in the TBE buffer covering the gel.

Result

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'''=====
Introduction

DNA Extraction Exercise_ Kaki,Blueberry

Procedure

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>
Result

Blueberries were successful in extracting DNA, but kaki failed again.
<gallery>
File:Dna Ex5.jpg
File:Dna Ex6.jpg
</gallery>

====='''2024.11.20. Wed'''=====
Introduction

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.

Procedure

-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.

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:

### Materials Needed:

- 3-4 kaki fruits

- 5g washing up liquid or hand soap

- 2g salt

- 100ml tap water

- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)

- Knife and fork for cutting and mashing

- Beaker or large bowl

- Coffee filter or fine sieve

- Saucepan for hot water bath

- Ice water bath

### Procedure:

1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.

2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.

3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.

4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.

5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.

6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.

7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.

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.

9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.
<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>

Result

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'''=====
Introduction

Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry.

Procedure

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>Result

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'''=====
Introduction

Exercise for DNA centrifugation and PCR Experiment

Procedure

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)

*sample B11, B12 are dirtier than B2

*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. 
<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'''=====
Introduction

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.

Procedure

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>

Result

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.

GMU:Life in an aquatic ecosystem/Dahye Seo

2025-01-06T13:01:45Z

Dahyeseo:

{{#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 2..jpg|center|frameless|800x800px]]

====Technical solution====

=====1. Biological part=====
Instruction of DNA analysis<gallery>
File:Instruction1 DNAworkshop.jpg
File:Instruction2 DNAworkshop.jpg
</gallery>1) DNA Extraction of Persimmons <gallery>
File:Kaki gelElectrophoresis 2.jpeg
File:Kaki gelElectrophoresis 3.jpeg
File:Kaki gelElectrophoresis 4.jpeg
File:Kaki gelElectrophoresis 5.jpeg
File:Kaki gelElectrophoresis 6.jpeg
File:Kaki gelElectrophoresis 7.jpeg
File:Kaki gelElectrophoresis 8.jpeg
</gallery>

2) PCR Experiment (DNA amplification) / Gel electrophoresis (DNA movement & visualization) . <gallery>
File:Kaki gelElectrophoresis 10.jpeg
File:Kaki gelElectrophoresis 9.jpeg
File:Kaki gelElectrophoresis 11.jpeg
File:Kaki gelElectrophoresis 12.jpeg
File:Kaki gelElectrophoresis 13.jpeg
File:Gelelectrophoresis workshop 20230428 Large.jpeg
</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

=====2. Sound part=====
1) Sonification of DNA movementMax/Msp patch

Convert continuously changing number of RGB data (could be change to other data) of DNA movement animation to midi or frequency.{{#ev:youtube|bGzmhJ9kQi4}}

2) Sound Design

====Work in Biolab====

====='''2024.11.16. Sat'''=====
Introduction

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.

Procedure

''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.

<gallery>
File:DNA ladder1.jpg
File:DNA Ladder2.jpg
File:Prepare GelElectrophoresis.jpg
File:Gel electrophoresis1.jpg
File:GelElectrophoresis.jpg
File:Note.jpg
</gallery>

Result

First Column: 1 kb DNA ladder

Last to first and second Columns: 100 bp DNA ladder <gallery>
File:First round 5V-40min.jpg
File:2round 5v-40min.jpg
File:3round 6v-60min.jpg
</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?

ps. after around 50 hours. Still there remains the trace of the DNA movement.
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>

=====''' 2024.11.18. Mon'''=====
Introduction

The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.

Procedure

A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.

* Note

1. Reused the gel from 2 days ago.

2. Did not put stain green in the TBE buffer covering the gel.

Result

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'''=====
Introduction

DNA Extraction Exercise_ Kaki,Blueberry

Procedure

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>
Result

Blueberries were successful in extracting DNA, but kaki failed again.
<gallery>
File:Dna Ex5.jpg
File:Dna Ex6.jpg
</gallery>

====='''2024.11.20. Wed'''=====
Introduction

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.

Procedure

-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.

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:

### Materials Needed:

- 3-4 kaki fruits

- 5g washing up liquid or hand soap

- 2g salt

- 100ml tap water

- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)

- Knife and fork for cutting and mashing

- Beaker or large bowl

- Coffee filter or fine sieve

- Saucepan for hot water bath

- Ice water bath

### Procedure:

1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.

2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.

3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.

4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.

5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.

6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.

7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.

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.

9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.
<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>

Result

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'''=====
Introduction

Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry.

Procedure

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>Result

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'''=====
Introduction

Exercise for DNA centrifugation and PCR Experiment

Procedure

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)

*sample B11, B12 are dirtier than B2

*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. 
<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'''=====
Introduction

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.

Procedure

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>

Result

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]]
Introduction

PCR / Gel electrophoresis

I did PCR 3 samples which are DNA of leaves extracted by DNA EXTRACT KIT, Banana, Blueberry.

Result

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''' =====
Introduction

Electrophoresis was performed under constant UV light and the movement of the dna was filmed live. Experiments with DNA Ladder.

Result

<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.

GMU:Cybernetic Subjects - Ursula Damm (Georg Trogemann)/Dahye Seo

2025-01-05T11:48:37Z

Dahyeseo:

{{#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 sound and movement of DNA. This work 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 2..jpg|center|frameless|800x800px]]

====Technical solution====

=====1. Biological part=====
Instruction of DNA analysis<gallery>
File:Instruction1 DNAworkshop.jpg
File:Instruction2 DNAworkshop.jpg
</gallery>1) DNA Extraction of Persimmons <gallery>
File:Kaki gelElectrophoresis 2.jpeg
File:Kaki gelElectrophoresis 3.jpeg
File:Kaki gelElectrophoresis 4.jpeg
File:Kaki gelElectrophoresis 5.jpeg
File:Kaki gelElectrophoresis 6.jpeg
File:Kaki gelElectrophoresis 7.jpeg
File:Kaki gelElectrophoresis 8.jpeg
</gallery>

2) PCR Experiment (DNA amplification) / Gel electrophoresis (DNA movement & visualization) . <gallery>
File:Kaki gelElectrophoresis 10.jpeg
File:Kaki gelElectrophoresis 9.jpeg
File:Kaki gelElectrophoresis 11.jpeg
File:Kaki gelElectrophoresis 12.jpeg
File:Kaki gelElectrophoresis 13.jpeg
File:Gelelectrophoresis workshop 20230428 Large.jpeg
</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

=====2. Sound part=====
1) Sonification of DNA movementMax/Msp patch

Convert continuously changing number of RGB data (could be change to other data) of DNA movement animation to midi or frequency.{{#ev:youtube|bGzmhJ9kQi4}}

2) Sound Design

====Work in Biolab====

====='''2024.11.16. Sat'''=====
Introduction

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.

Procedure

''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.

<gallery>
File:DNA ladder1.jpg
File:DNA Ladder2.jpg
File:Prepare GelElectrophoresis.jpg
File:Gel electrophoresis1.jpg
File:GelElectrophoresis.jpg
File:Note.jpg
</gallery>

Result

First Column: 1 kb DNA ladder

Last to first and second Columns: 100 bp DNA ladder <gallery>
File:First round 5V-40min.jpg
File:2round 5v-40min.jpg
File:3round 6v-60min.jpg
</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?

ps. after around 50 hours. Still there remains the trace of the DNA movement.
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>

=====''' 2024.11.18. Mon'''=====
Introduction

The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.

Procedure

A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.

* Note

1. Reused the gel from 2 days ago.

2. Did not put stain green in the TBE buffer covering the gel.

Result

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'''=====
Introduction

DNA Extraction Exercise_ Kaki,Blueberry

Procedure

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>
Result

Blueberries were successful in extracting DNA, but kaki failed again.
<gallery>
File:Dna Ex5.jpg
File:Dna Ex6.jpg
</gallery>

====='''2024.11.20. Wed'''=====
Introduction

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.

Procedure

-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.

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:

### Materials Needed:

- 3-4 kaki fruits

- 5g washing up liquid or hand soap

- 2g salt

- 100ml tap water

- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)

- Knife and fork for cutting and mashing

- Beaker or large bowl

- Coffee filter or fine sieve

- Saucepan for hot water bath

- Ice water bath

### Procedure:

1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.

2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.

3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.

4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.

5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.

6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.

7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.

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.

9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.
<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>

Result

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'''=====
Introduction

Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry.

Procedure

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>Result

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'''=====
Introduction

Exercise for DNA centrifugation and PCR Experiment

Procedure

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)

*sample B11, B12 are dirtier than B2

*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. 
<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'''=====
Introduction

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.

Procedure

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>

Result

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.

GMU:Life in an aquatic ecosystem/Dahye Seo

2025-01-05T11:47:55Z

Dahyeseo:

{{#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 sound and movement of DNA. This work 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 2..jpg|center|frameless|800x800px]]

====Technical solution====

=====1. Biological part=====
Instruction of DNA analysis<gallery>
File:Instruction1 DNAworkshop.jpg
File:Instruction2 DNAworkshop.jpg
</gallery>1) DNA Extraction of Persimmons <gallery>
File:Kaki gelElectrophoresis 2.jpeg
File:Kaki gelElectrophoresis 3.jpeg
File:Kaki gelElectrophoresis 4.jpeg
File:Kaki gelElectrophoresis 5.jpeg
File:Kaki gelElectrophoresis 6.jpeg
File:Kaki gelElectrophoresis 7.jpeg
File:Kaki gelElectrophoresis 8.jpeg
</gallery>

2) PCR Experiment (DNA amplification) / Gel electrophoresis (DNA movement & visualization) . <gallery>
File:Kaki gelElectrophoresis 10.jpeg
File:Kaki gelElectrophoresis 9.jpeg
File:Kaki gelElectrophoresis 11.jpeg
File:Kaki gelElectrophoresis 12.jpeg
File:Kaki gelElectrophoresis 13.jpeg
File:Gelelectrophoresis workshop 20230428 Large.jpeg
</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

=====2. Sound part=====
1) Sonification of DNA movementMax/Msp patch

Convert continuously changing number of RGB data (could be change to other data) of DNA movement animation to midi or frequency.{{#ev:youtube|bGzmhJ9kQi4}}

2) Sound Design

====Work in Biolab====

====='''2024.11.16. Sat'''=====
Introduction

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.

Procedure

''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.

<gallery>
File:DNA ladder1.jpg
File:DNA Ladder2.jpg
File:Prepare GelElectrophoresis.jpg
File:Gel electrophoresis1.jpg
File:GelElectrophoresis.jpg
File:Note.jpg
</gallery>

Result

First Column: 1 kb DNA ladder

Last to first and second Columns: 100 bp DNA ladder <gallery>
File:First round 5V-40min.jpg
File:2round 5v-40min.jpg
File:3round 6v-60min.jpg
</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?

ps. after around 50 hours. Still there remains the trace of the DNA movement.
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>

=====''' 2024.11.18. Mon'''=====
Introduction

The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.

Procedure

A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.

* Note

1. Reused the gel from 2 days ago.

2. Did not put stain green in the TBE buffer covering the gel.

Result

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'''=====
Introduction

DNA Extraction Exercise_ Kaki,Blueberry

Procedure

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>
Result

Blueberries were successful in extracting DNA, but kaki failed again.
<gallery>
File:Dna Ex5.jpg
File:Dna Ex6.jpg
</gallery>

====='''2024.11.20. Wed'''=====
Introduction

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.

Procedure

-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.

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:

### Materials Needed:

- 3-4 kaki fruits

- 5g washing up liquid or hand soap

- 2g salt

- 100ml tap water

- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)

- Knife and fork for cutting and mashing

- Beaker or large bowl

- Coffee filter or fine sieve

- Saucepan for hot water bath

- Ice water bath

### Procedure:

1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.

2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.

3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.

4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.

5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.

6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.

7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.

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.

9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.
<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>

Result

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'''=====
Introduction

Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry.

Procedure

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>Result

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'''=====
Introduction

Exercise for DNA centrifugation and PCR Experiment

Procedure

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)

*sample B11, B12 are dirtier than B2

*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. 
<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'''=====
Introduction

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.

Procedure

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>

Result

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]]
Introduction

PCR / Gel electrophoresis

I did PCR 3 samples which are DNA of leaves extracted by DNA EXTRACT KIT, Banana, Blueberry.

Result

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''' =====
Introduction

Electrophoresis was performed under constant UV light and the movement of the dna was filmed live. Experiments with DNA Ladder.

Result

<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.

GMU:Life in an aquatic ecosystem/Dahye Seo

2024-12-18T15:55:48Z

Dahyeseo:

{{#ev:youtube|bGzmhJ9kQi4}}

=== '''Dead Life Live Life (working title)''' ===

''Dead Life Live Life'' is a sound installation work that sonifies the movement of DNA. This work was inspired by the poetic movement of DNA in electrophoresis experiments. ''Dead Life Live Life'' explores the materiality of DNA itself rather than genetic analysis, which is the general purpose of DNA. “Dead life got the same material as live life”, biologist Lynn Margulis said in an interview. This could be paraphrased as “Dead life got the same DNA as live life”. ''Dead Life Live Life'' poetically represents the connection between life and death by sonifying the DNA movement of an old persimmon tree planted in my grandmother's house.

[[File:Diagram Dead LifeLiveLife.jpg|center|thumb|800x800px]]

[[File:Dlll 1.001.jpg|center|frameless|800x800px]]
[[File:Dlll 2..jpg|center|frameless|800x800px]]

====Technical solution====

=====1. Biological part=====
Instruction of DNA analysis<gallery>
File:Instruction1 DNAworkshop.jpg
File:Instruction2 DNAworkshop.jpg
</gallery>1) DNA Extraction of Persimmons <gallery>
File:Kaki gelElectrophoresis 2.jpeg
File:Kaki gelElectrophoresis 3.jpeg
File:Kaki gelElectrophoresis 4.jpeg
File:Kaki gelElectrophoresis 5.jpeg
File:Kaki gelElectrophoresis 6.jpeg
File:Kaki gelElectrophoresis 7.jpeg
File:Kaki gelElectrophoresis 8.jpeg
</gallery>

2) PCR Experiment (DNA amplification) / Gel electrophoresis (DNA movement & visualization) . <gallery>
File:Kaki gelElectrophoresis 10.jpeg
File:Kaki gelElectrophoresis 9.jpeg
File:Kaki gelElectrophoresis 11.jpeg
File:Kaki gelElectrophoresis 12.jpeg
File:Kaki gelElectrophoresis 13.jpeg
File:Gelelectrophoresis workshop 20230428 Large.jpeg
</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

=====2. Sound part=====
1) Sonification of DNA movementMax/Msp patch

Convert continuously changing number of RGB data (could be change to other data) of DNA movement animation to midi or frequency.{{#ev:youtube|bGzmhJ9kQi4}}

2) Sound Design

====Work in Biolab====

====='''2024.11.16. Sat'''=====
Introduction

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.

Procedure

''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.

<gallery>
File:DNA ladder1.jpg
File:DNA Ladder2.jpg
File:Prepare GelElectrophoresis.jpg
File:Gel electrophoresis1.jpg
File:GelElectrophoresis.jpg
File:Note.jpg
</gallery>

Result

First Column: 1 kb DNA ladder

Last to first and second Columns: 100 bp DNA ladder <gallery>
File:First round 5V-40min.jpg
File:2round 5v-40min.jpg
File:3round 6v-60min.jpg
</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?

ps. after around 50 hours. Still there remains the trace of the DNA movement.
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>

=====''' 2024.11.18. Mon'''=====
Introduction

The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.

Procedure

A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.

* Note

1. Reused the gel from 2 days ago.

2. Did not put stain green in the TBE buffer covering the gel.

Result

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'''=====
Introduction

DNA Extraction Exercise_ Kaki,Blueberry

Procedure

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>
Result

Blueberries were successful in extracting DNA, but kaki failed again.
<gallery>
File:Dna Ex5.jpg
File:Dna Ex6.jpg
</gallery>

====='''2024.11.20. Wed'''=====
Introduction

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.

Procedure

-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.

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:

### Materials Needed:

- 3-4 kaki fruits

- 5g washing up liquid or hand soap

- 2g salt

- 100ml tap water

- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)

- Knife and fork for cutting and mashing

- Beaker or large bowl

- Coffee filter or fine sieve

- Saucepan for hot water bath

- Ice water bath

### Procedure:

1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.

2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.

3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.

4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.

5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.

6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.

7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.

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.

9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.
<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>

Result

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'''=====
Introduction

Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry.

Procedure

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>Result

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'''=====
Introduction

Exercise for DNA centrifugation and PCR Experiment

Procedure

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)

*sample B11, B12 are dirtier than B2

*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. 
<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'''=====
Introduction

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.

Procedure

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>

Result

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]]
Introduction

PCR / Gel electrophoresis

I did PCR 3 samples which are DNA of leaves extracted by DNA EXTRACT KIT, Banana, Blueberry.

Result

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''' =====
Introduction

Electrophoresis was performed under constant UV light and the movement of the dna was filmed live. Experiments with DNA Ladder.

Result

<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.

GMU:Life in an aquatic ecosystem/Dahye Seo

2024-12-16T10:17:58Z

Dahyeseo:

GMU:Life in an aquatic ecosystem/Dahye Seo

2024-12-11T11:26:08Z

Dahyeseo:

{{#ev:youtube|bGzmhJ9kQi4}}

=== '''Dead Life Live Life (working title)''' ===

''Dead Life Live Life'' is a sound installation work that sonifies the movement of DNA. This work was inspired by the poetic movement of DNA in electrophoresis experiments. ''Dead Life Live Life'' explores the materiality of DNA itself rather than genetic analysis, which is the general purpose of DNA. “Dead life got the same material as live life”, biologist Lynn Margulis said in an interview. This could be paraphrased as “Dead life got the same DNA as live life”. ''Dead Life Live Life'' poetically represents the connection between life and death by sonifying the DNA movement of an old persimmon tree planted in my grandmother's house.

[[File:Diagram Dead LifeLiveLife.jpg|center|thumb|800x800px]]

[[File:Dlll 1.001.jpg|center|frameless|800x800px]]
[[File:Dlll 2..jpg|center|frameless|800x800px]]

====Technical solution====

=====1. Biological part=====
Instruction of DNA analysis<gallery>
File:Instruction1 DNAworkshop.jpg
File:Instruction2 DNAworkshop.jpg
</gallery>1) DNA Extraction of Persimmons <gallery>
File:Kaki gelElectrophoresis 2.jpeg
File:Kaki gelElectrophoresis 3.jpeg
File:Kaki gelElectrophoresis 4.jpeg
File:Kaki gelElectrophoresis 5.jpeg
File:Kaki gelElectrophoresis 6.jpeg
File:Kaki gelElectrophoresis 7.jpeg
File:Kaki gelElectrophoresis 8.jpeg
</gallery>

2) PCR Experiment (DNA amplification) / Gel electrophoresis (DNA movement & visualization) . <gallery>
File:Kaki gelElectrophoresis 10.jpeg
File:Kaki gelElectrophoresis 9.jpeg
File:Kaki gelElectrophoresis 11.jpeg
File:Kaki gelElectrophoresis 12.jpeg
File:Kaki gelElectrophoresis 13.jpeg
File:Gelelectrophoresis workshop 20230428 Large.jpeg
</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

=====2. Sound part=====
1) Sonification of DNA movementMax/Msp patch

Convert continuously changing number of RGB data (could be change to other data) of DNA movement animation to midi or frequency.{{#ev:youtube|bGzmhJ9kQi4}}

2) Sound Design

====Work in Biolab====

====='''2024.11.16. Sat'''=====
Introduction

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.

Procedure

''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.

<gallery>
File:DNA ladder1.jpg
File:DNA Ladder2.jpg
File:Prepare GelElectrophoresis.jpg
File:Gel electrophoresis1.jpg
File:GelElectrophoresis.jpg
File:Note.jpg
</gallery>

Result

First Column: 1 kb DNA ladder

Last to first and second Columns: 100 bp DNA ladder <gallery>
File:First round 5V-40min.jpg
File:2round 5v-40min.jpg
File:3round 6v-60min.jpg
</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?

ps. after around 50 hours. Still there remains the trace of the DNA movement.
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>

=====''' 2024.11.18. Mon'''=====
Introduction

The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.

Procedure

A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.

* Note

1. Reused the gel from 2 days ago.

2. Did not put stain green in the TBE buffer covering the gel.

Result

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'''=====
Introduction

DNA Extraction Exercise_ Kaki,Blueberry

Procedure

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>
Result

Blueberries were successful in extracting DNA, but kaki failed again.
<gallery>
File:Dna Ex5.jpg
File:Dna Ex6.jpg
</gallery>

====='''2024.11.20. Wed'''=====
Introduction

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.

Procedure

-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.

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:

### Materials Needed:

- 3-4 kaki fruits

- 5g washing up liquid or hand soap

- 2g salt

- 100ml tap water

- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)

- Knife and fork for cutting and mashing

- Beaker or large bowl

- Coffee filter or fine sieve

- Saucepan for hot water bath

- Ice water bath

### Procedure:

1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.

2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.

3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.

4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.

5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.

6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.

7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.

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.

9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.
<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>

Result

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'''=====
Introduction

Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry.

Procedure

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>Result

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'''=====
Introduction

Exercise for DNA centrifugation and PCR Experiment

Procedure

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)

*sample B11, B12 are dirtier than B2

*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. 
<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'''=====
Introduction

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.

Procedure

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>

Result

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]]
Introduction

PCR / Gel electrophoresis

I did PCR 3 samples which are DNA of leaves extracted by DNA EXTRACT KIT, Banana, Blueberry.

File:Pcr 29241211.jpg

2024-12-11T11:25:48Z

Dahyeseo:

pcr_29241211

GMU:Cybernetic Subjects - Ursula Damm (Georg Trogemann)/Dahye Seo

2024-12-09T21:53:17Z

Dahyeseo:

GMU:Life in an aquatic ecosystem/Dahye Seo

2024-12-09T21:51:59Z

Dahyeseo: /* 2024.11.20. Wed */

GMU:Life in an aquatic ecosystem/Dahye Seo

2024-12-09T16:56:25Z

Dahyeseo:

{{#ev:youtube|bGzmhJ9kQi4}}

=== '''Dead Life Live Life (working title)''' ===

''Dead Life Live Life'' is a sound installation work that sonifies the movement of DNA. This work was inspired by the poetic movement of DNA in electrophoresis experiments. ''Dead Life Live Life'' explores the materiality of DNA itself rather than genetic analysis, which is the general purpose of DNA. “Dead life got the same material as live life”, biologist Lynn Margulis said in an interview. This could be paraphrased as “Dead life got the same DNA as live life”. ''Dead Life Live Life'' poetically represents the connection between life and death by sonifying the DNA movement of an old persimmon tree planted in my grandmother's house.

[[File:Diagram Dead LifeLiveLife.jpg|center|thumb|800x800px]]

[[File:Dlll 1.001.jpg|center|frameless|800x800px]]
[[File:Dlll 2..jpg|center|frameless|800x800px]]

====Technical solution====

=====1. Biological part=====
Instruction of DNA analysis<gallery>
File:Instruction1 DNAworkshop.jpg
File:Instruction2 DNAworkshop.jpg
</gallery>1) DNA Extraction of Persimmons <gallery>
File:Kaki gelElectrophoresis 2.jpeg
File:Kaki gelElectrophoresis 3.jpeg
File:Kaki gelElectrophoresis 4.jpeg
File:Kaki gelElectrophoresis 5.jpeg
File:Kaki gelElectrophoresis 6.jpeg
File:Kaki gelElectrophoresis 7.jpeg
File:Kaki gelElectrophoresis 8.jpeg
</gallery>

2) PCR Experiment (DNA amplification) / Gel electrophoresis (DNA movement & visualization) . <gallery>
File:Kaki gelElectrophoresis 10.jpeg
File:Kaki gelElectrophoresis 9.jpeg
File:Kaki gelElectrophoresis 11.jpeg
File:Kaki gelElectrophoresis 12.jpeg
File:Kaki gelElectrophoresis 13.jpeg
File:Gelelectrophoresis workshop 20230428 Large.jpeg
</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

=====2. Sound part=====
1) Sonification of DNA movementMax/Msp patch

Convert continuously changing number of RGB data (could be change to other data) of DNA movement animation to midi or frequency.{{#ev:youtube|bGzmhJ9kQi4}}

2) Sound Design

====Work in Biolab====

====='''2024.11.16. Sat'''=====
Introduction

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.

Procedure

''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.

<gallery>
File:DNA ladder1.jpg
File:DNA Ladder2.jpg
File:Prepare GelElectrophoresis.jpg
File:Gel electrophoresis1.jpg
File:GelElectrophoresis.jpg
File:Note.jpg
</gallery>

Result

First Column: 1 kb DNA ladder

Last to first and second Columns: 100 bp DNA ladder <gallery>
File:First round 5V-40min.jpg
File:2round 5v-40min.jpg
File:3round 6v-60min.jpg
</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?

ps. after around 50 hours. Still there remains the trace of the DNA movement.
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>

=====''' 2024.11.18. Mon'''=====
Introduction

The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.

Procedure

A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.

* Note

1. Reused the gel from 2 days ago.

2. Did not put stain green in the TBE buffer covering the gel.

Result

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'''=====
Introduction

DNA Extraction Exercise_ Kaki,Blueberry

Procedure

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>
Result

Blueberries were successful in extracting DNA, but kaki failed again.
<gallery>
File:Dna Ex5.jpg
File:Dna Ex6.jpg
</gallery>

====='''2024.11.20. Wed'''=====
Introduction

DNA Extraction Exercise_ Kaki (ChatGPT), Leaf

- I failed to extract Kaki's DNA in my experiment yesterday. This time i followed Chat GPT's guide 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.

Procedure

-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.

<nowiki>*</nowiki>Chat GPT's guide

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:

### Materials Needed:

- 3-4 kaki fruits

- 5g washing up liquid or hand soap

- 2g salt

- 100ml tap water

- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)

- Knife and fork for cutting and mashing

- Beaker or large bowl

- Coffee filter or fine sieve

- Saucepan for hot water bath

- Ice water bath

### Procedure:

1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.

2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.

3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.

4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.

5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.

6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.

7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.

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.

9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.
<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>

Result

Both the leaves and the persimmon failed to extract DNA. I was a little frustrated.

The guide for chat GPT seems unreliable. 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'''=====
Introduction

Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry.

Procedure

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>Result

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'''=====
Introduction

Exercise for DNA centrifugation and PCR Experiment

Procedure

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)

*sample B11, B12 are dirtier than B2

*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. 
<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'''=====
Introduction

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.

Procedure

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>

Result

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.

GMU:Life in an aquatic ecosystem/Dahye Seo

2024-12-09T16:56:05Z

Dahyeseo:

{{#ev:youtube|bGzmhJ9kQi4}}

=== '''Dead Life Live Life''' ===

''Dead Life Live Life'' is a sound installation work that sonifies the movement of DNA. This work was inspired by the poetic movement of DNA in electrophoresis experiments. ''Dead Life Live Life'' explores the materiality of DNA itself rather than genetic analysis, which is the general purpose of DNA. “Dead life got the same material as live life”, biologist Lynn Margulis said in an interview. This could be paraphrased as “Dead life got the same DNA as live life”. ''Dead Life Live Life'' poetically represents the connection between life and death by sonifying the DNA movement of an old persimmon tree planted in my grandmother's house.

[[File:Diagram Dead LifeLiveLife.jpg|center|thumb|800x800px]]

[[File:Dlll 1.001.jpg|center|frameless|800x800px]]
[[File:Dlll 2..jpg|center|frameless|800x800px]]

====Technical solution====

=====1. Biological part=====
Instruction of DNA analysis<gallery>
File:Instruction1 DNAworkshop.jpg
File:Instruction2 DNAworkshop.jpg
</gallery>1) DNA Extraction of Persimmons <gallery>
File:Kaki gelElectrophoresis 2.jpeg
File:Kaki gelElectrophoresis 3.jpeg
File:Kaki gelElectrophoresis 4.jpeg
File:Kaki gelElectrophoresis 5.jpeg
File:Kaki gelElectrophoresis 6.jpeg
File:Kaki gelElectrophoresis 7.jpeg
File:Kaki gelElectrophoresis 8.jpeg
</gallery>

2) PCR Experiment (DNA amplification) / Gel electrophoresis (DNA movement & visualization) . <gallery>
File:Kaki gelElectrophoresis 10.jpeg
File:Kaki gelElectrophoresis 9.jpeg
File:Kaki gelElectrophoresis 11.jpeg
File:Kaki gelElectrophoresis 12.jpeg
File:Kaki gelElectrophoresis 13.jpeg
File:Gelelectrophoresis workshop 20230428 Large.jpeg
</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

=====2. Sound part=====
1) Sonification of DNA movementMax/Msp patch

Convert continuously changing number of RGB data (could be change to other data) of DNA movement animation to midi or frequency.{{#ev:youtube|bGzmhJ9kQi4}}

2) Sound Design

====Work in Biolab====

====='''2024.11.16. Sat'''=====
Introduction

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.

Procedure

''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.

<gallery>
File:DNA ladder1.jpg
File:DNA Ladder2.jpg
File:Prepare GelElectrophoresis.jpg
File:Gel electrophoresis1.jpg
File:GelElectrophoresis.jpg
File:Note.jpg
</gallery>

Result

First Column: 1 kb DNA ladder

Last to first and second Columns: 100 bp DNA ladder <gallery>
File:First round 5V-40min.jpg
File:2round 5v-40min.jpg
File:3round 6v-60min.jpg
</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?

ps. after around 50 hours. Still there remains the trace of the DNA movement.
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>

=====''' 2024.11.18. Mon'''=====
Introduction

The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.

Procedure

A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.

* Note

1. Reused the gel from 2 days ago.

2. Did not put stain green in the TBE buffer covering the gel.

Result

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'''=====
Introduction

DNA Extraction Exercise_ Kaki,Blueberry

Procedure

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>
Result

Blueberries were successful in extracting DNA, but kaki failed again.
<gallery>
File:Dna Ex5.jpg
File:Dna Ex6.jpg
</gallery>

====='''2024.11.20. Wed'''=====
Introduction

DNA Extraction Exercise_ Kaki (ChatGPT), Leaf

- I failed to extract Kaki's DNA in my experiment yesterday. This time i followed Chat GPT's guide 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.

Procedure

-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.

<nowiki>*</nowiki>Chat GPT's guide

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:

### Materials Needed:

- 3-4 kaki fruits

- 5g washing up liquid or hand soap

- 2g salt

- 100ml tap water

- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)

- Knife and fork for cutting and mashing

- Beaker or large bowl

- Coffee filter or fine sieve

- Saucepan for hot water bath

- Ice water bath

### Procedure:

1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.

2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.

3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.

4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.

5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.

6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.

7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.

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.

9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.
<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>

Result

Both the leaves and the persimmon failed to extract DNA. I was a little frustrated.

The guide for chat GPT seems unreliable. 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'''=====
Introduction

Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry.

Procedure

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>Result

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'''=====
Introduction

Exercise for DNA centrifugation and PCR Experiment

Procedure

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)

*sample B11, B12 are dirtier than B2

*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. 
<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'''=====
Introduction

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.

Procedure

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>

Result

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.

GMU:Life in an aquatic ecosystem/Dahye Seo

2024-12-09T16:54:53Z

Dahyeseo:

{{#ev:youtube|bGzmhJ9kQi4}}

=== '''Dead Life Live Life''' ===

''Dead Life Live Life'' is a sound installation work that sonifies the movement of DNA. This work was inspired by the poetic movement of DNA in electrophoresis experiments. ''Dead Life Live Life'' explores the materiality of DNA itself rather than genetic analysis, which is the general purpose of DNA. “Dead life got the same material as live life”, biologist Lynn Margulis said in an interview. This could be paraphrased as “Dead life got the same DNA as live life”. ''Dead Life Live Life'' poetically represents the connection between life and death by sonifying the DNA movement of an old persimmon tree planted in my grandmother's house.
[[File:Dlll 1.001.jpg|center|frameless|800x800px]]
[[File:Dlll 2..jpg|center|frameless|800x800px]]

[[File:Diagram Dead LifeLiveLife.jpg|center|thumb|800x800px]]

==== Technical solution ====

===== 1. Biological part =====
Instruction of DNA analysis<gallery>
File:Instruction1 DNAworkshop.jpg
File:Instruction2 DNAworkshop.jpg
</gallery>1) DNA Extraction of Persimmons <gallery>
File:Kaki gelElectrophoresis 2.jpeg
File:Kaki gelElectrophoresis 3.jpeg
File:Kaki gelElectrophoresis 4.jpeg
File:Kaki gelElectrophoresis 5.jpeg
File:Kaki gelElectrophoresis 6.jpeg
File:Kaki gelElectrophoresis 7.jpeg
File:Kaki gelElectrophoresis 8.jpeg
</gallery>

2) PCR Experiment (DNA amplification) / Gel electrophoresis (DNA movement & visualization) . <gallery>
File:Kaki gelElectrophoresis 10.jpeg
File:Kaki gelElectrophoresis 9.jpeg
File:Kaki gelElectrophoresis 11.jpeg
File:Kaki gelElectrophoresis 12.jpeg
File:Kaki gelElectrophoresis 13.jpeg
File:Gelelectrophoresis workshop 20230428 Large.jpeg
</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

===== 2. Sound part =====
1) Sonification of DNA movementMax/Msp patch

Convert continuously changing number of RGB data (could be change to other data) of DNA movement animation to midi or frequency.{{#ev:youtube|bGzmhJ9kQi4}}

2) Sound Design

==== Work in Biolab ====

===== '''2024.11.16. Sat''' =====
Introduction

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.

Procedure

''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.

<gallery>
File:DNA ladder1.jpg
File:DNA Ladder2.jpg
File:Prepare GelElectrophoresis.jpg
File:Gel electrophoresis1.jpg
File:GelElectrophoresis.jpg
File:Note.jpg
</gallery>

Result

First Column: 1 kb DNA ladder

Last to first and second Columns: 100 bp DNA ladder <gallery>
File:First round 5V-40min.jpg
File:2round 5v-40min.jpg
File:3round 6v-60min.jpg
</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?

ps. after around 50 hours. Still there remains the trace of the DNA movement.
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>

===== ''' 2024.11.18. Mon''' =====
Introduction

The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.

Procedure

A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.

* Note

1. Reused the gel from 2 days ago.

2. Did not put stain green in the TBE buffer covering the gel.

Result

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''' =====
Introduction

DNA Extraction Exercise_ Kaki,Blueberry

Procedure

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>
Result

Blueberries were successful in extracting DNA, but kaki failed again.
<gallery>
File:Dna Ex5.jpg
File:Dna Ex6.jpg
</gallery>

===== '''2024.11.20. Wed''' =====
Introduction

DNA Extraction Exercise_ Kaki (ChatGPT), Leaf

- I failed to extract Kaki's DNA in my experiment yesterday. This time i followed Chat GPT's guide 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.

Procedure

-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.

<nowiki>*</nowiki>Chat GPT's guide

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:

### Materials Needed:

- 3-4 kaki fruits

- 5g washing up liquid or hand soap

- 2g salt

- 100ml tap water

- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)

- Knife and fork for cutting and mashing

- Beaker or large bowl

- Coffee filter or fine sieve

- Saucepan for hot water bath

- Ice water bath

### Procedure:

1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.

2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.

3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.

4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.

5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.

6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.

7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.

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.

9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.
<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>

Result

Both the leaves and the persimmon failed to extract DNA. I was a little frustrated.

The guide for chat GPT seems unreliable. 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''' =====
Introduction

Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry.

Procedure

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>Result

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'''=====
Introduction

Exercise for DNA centrifugation and PCR Experiment

Procedure

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)

*sample B11, B12 are dirtier than B2

*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. 
<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''' =====
Introduction

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.

Procedure

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>

Result

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.

GMU:Life in an aquatic ecosystem/Dahye Seo

2024-12-09T16:54:15Z

Dahyeseo:

=== '''Dead Life Live Life''' ===

{{#ev:youtube|bGzmhJ9kQi4}}

''Dead Life Live Life'' is a sound installation work that sonifies the movement of DNA. This work was inspired by the poetic movement of DNA in electrophoresis experiments. ''Dead Life Live Life'' explores the materiality of DNA itself rather than genetic analysis, which is the general purpose of DNA. “Dead life got the same material as live life”, biologist Lynn Margulis said in an interview. This could be paraphrased as “Dead life got the same DNA as live life”. ''Dead Life Live Life'' poetically represents the connection between life and death by sonifying the DNA movement of an old persimmon tree planted in my grandmother's house.
[[File:Dlll 1.001.jpg|center|frameless|800x800px]]
[[File:Dlll 2..jpg|center|frameless|800x800px]]

[[File:Diagram Dead LifeLiveLife.jpg|center|thumb|800x800px]]

==== Technical solution ====

===== 1. Biological part =====
Instruction of DNA analysis<gallery>
File:Instruction1 DNAworkshop.jpg
File:Instruction2 DNAworkshop.jpg
</gallery>1) DNA Extraction of Persimmons <gallery>
File:Kaki gelElectrophoresis 2.jpeg
File:Kaki gelElectrophoresis 3.jpeg
File:Kaki gelElectrophoresis 4.jpeg
File:Kaki gelElectrophoresis 5.jpeg
File:Kaki gelElectrophoresis 6.jpeg
File:Kaki gelElectrophoresis 7.jpeg
File:Kaki gelElectrophoresis 8.jpeg
</gallery>

2) PCR Experiment (DNA amplification) / Gel electrophoresis (DNA movement & visualization) . <gallery>
File:Kaki gelElectrophoresis 10.jpeg
File:Kaki gelElectrophoresis 9.jpeg
File:Kaki gelElectrophoresis 11.jpeg
File:Kaki gelElectrophoresis 12.jpeg
File:Kaki gelElectrophoresis 13.jpeg
File:Gelelectrophoresis workshop 20230428 Large.jpeg
</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

===== 2. Sound part =====
1) Sonification of DNA movementMax/Msp patch

Convert continuously changing number of RGB data (could be change to other data) of DNA movement animation to midi or frequency.{{#ev:youtube|bGzmhJ9kQi4}}

2) Sound Design

==== Work in Biolab ====

===== '''2024.11.16. Sat''' =====
Introduction

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.

Procedure

''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.

<gallery>
File:DNA ladder1.jpg
File:DNA Ladder2.jpg
File:Prepare GelElectrophoresis.jpg
File:Gel electrophoresis1.jpg
File:GelElectrophoresis.jpg
File:Note.jpg
</gallery>

Result

First Column: 1 kb DNA ladder

Last to first and second Columns: 100 bp DNA ladder <gallery>
File:First round 5V-40min.jpg
File:2round 5v-40min.jpg
File:3round 6v-60min.jpg
</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?

ps. after around 50 hours. Still there remains the trace of the DNA movement.
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>

===== ''' 2024.11.18. Mon''' =====
Introduction

The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.

Procedure

A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.

* Note

1. Reused the gel from 2 days ago.

2. Did not put stain green in the TBE buffer covering the gel.

Result

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''' =====
Introduction

DNA Extraction Exercise_ Kaki,Blueberry

Procedure

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>
Result

Blueberries were successful in extracting DNA, but kaki failed again.
<gallery>
File:Dna Ex5.jpg
File:Dna Ex6.jpg
</gallery>

===== '''2024.11.20. Wed''' =====
Introduction

DNA Extraction Exercise_ Kaki (ChatGPT), Leaf

- I failed to extract Kaki's DNA in my experiment yesterday. This time i followed Chat GPT's guide 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.

Procedure

-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.

<nowiki>*</nowiki>Chat GPT's guide

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:

### Materials Needed:

- 3-4 kaki fruits

- 5g washing up liquid or hand soap

- 2g salt

- 100ml tap water

- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)

- Knife and fork for cutting and mashing

- Beaker or large bowl

- Coffee filter or fine sieve

- Saucepan for hot water bath

- Ice water bath

### Procedure:

1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.

2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.

3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.

4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.

5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.

6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.

7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.

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.

9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.
<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>

Result

Both the leaves and the persimmon failed to extract DNA. I was a little frustrated.

The guide for chat GPT seems unreliable. 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''' =====
Introduction

Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry.

Procedure

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>Result

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'''=====
Introduction

Exercise for DNA centrifugation and PCR Experiment

Procedure

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)

*sample B11, B12 are dirtier than B2

*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. 
<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''' =====
Introduction

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.

Procedure

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>

Result

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.

GMU:Life in an aquatic ecosystem/Dahye Seo

2024-12-09T16:54:02Z

Dahyeseo:

GMU:Cybernetic Subjects - Ursula Damm (Georg Trogemann)/Dahye Seo

2024-11-29T22:37:00Z

Dahyeseo:

=== '''Dead Life Live Life''' ===

==== Description ====
<nowiki>*</nowiki> This project was started but not completed in SS 2023 and will be continued this semester.

''Dead Life Live Life'' is a sound installation work that sonifies the movement of DNA. This work was inspired by the poetic movement of DNA in electrophoresis experiments. ''Dead Life Live Life'' explores the materiality of DNA itself rather than genetic analysis, which is the general purpose of DNA. “Dead life got the same material as live life”, biologist Lynn Margulis said in an interview. This could be paraphrased as “Dead life got the same DNA as live life”. ''Dead Life Live Life'' poetically represents the connection between life and death by sonifying the DNA movement of an old persimmon tree planted in my grandmother's house.
[[File:Dlll 1.001.jpg|center|frameless|800x800px]]
[[File:Dlll 2..jpg|center|frameless|800x800px]]

[[File:Diagram Dead LifeLiveLife.jpg|center|thumb|800x800px]]

==== Technical solution ====

===== 1. Biological part =====
Instruction of DNA analysis<gallery>
File:Instruction1 DNAworkshop.jpg
File:Instruction2 DNAworkshop.jpg
</gallery>1) DNA Extraction of Persimmons <gallery>
File:Kaki gelElectrophoresis 2.jpeg
File:Kaki gelElectrophoresis 3.jpeg
File:Kaki gelElectrophoresis 4.jpeg
File:Kaki gelElectrophoresis 5.jpeg
File:Kaki gelElectrophoresis 6.jpeg
File:Kaki gelElectrophoresis 7.jpeg
File:Kaki gelElectrophoresis 8.jpeg
</gallery>

2) PCR Experiment (DNA amplification) / Gel electrophoresis (DNA movement & visualization) . <gallery>
File:Kaki gelElectrophoresis 10.jpeg
File:Kaki gelElectrophoresis 9.jpeg
File:Kaki gelElectrophoresis 11.jpeg
File:Kaki gelElectrophoresis 12.jpeg
File:Kaki gelElectrophoresis 13.jpeg
File:Gelelectrophoresis workshop 20230428 Large.jpeg
</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

===== 2. Sound part =====
1) Sonification of DNA movementMax/Msp patch

Convert continuously changing number of RGB data (could be change to other data) of DNA movement animation to midi or frequency.{{#ev:youtube|bGzmhJ9kQi4}}

2) Sound Design

==== Work in Biolab ====

===== '''2024.11.16. Sat''' =====
Introduction

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.

Procedure

''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.

<gallery>
File:DNA ladder1.jpg
File:DNA Ladder2.jpg
File:Prepare GelElectrophoresis.jpg
File:Gel electrophoresis1.jpg
File:GelElectrophoresis.jpg
File:Note.jpg
</gallery>

Result

First Column: 1 kb DNA ladder

Last to first and second Columns: 100 bp DNA ladder <gallery>
File:First round 5V-40min.jpg
File:2round 5v-40min.jpg
File:3round 6v-60min.jpg
</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?

ps. after around 50 hours. Still there remains the trace of the DNA movement.
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>

===== ''' 2024.11.18. Mon''' =====
Introduction

The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.

Procedure

A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.

* Note

1. Reused the gel from 2 days ago.

2. Did not put stain green in the TBE buffer covering the gel.

Result

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''' =====
Introduction

DNA Extraction Exercise_ Kaki,Blueberry

Procedure

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>
Result

Blueberries were successful in extracting DNA, but kaki failed again.
<gallery>
File:Dna Ex5.jpg
File:Dna Ex6.jpg
</gallery>

===== '''2024.11.20. Wed''' =====
Introduction

DNA Extraction Exercise_ Kaki (ChatGPT), Leaf

- I failed to extract Kaki's DNA in my experiment yesterday. This time i followed Chat GPT's guide 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.

Procedure

-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.

<nowiki>*</nowiki>Chat GPT's guide

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:

### Materials Needed:

- 3-4 kaki fruits

- 5g washing up liquid or hand soap

- 2g salt

- 100ml tap water

- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)

- Knife and fork for cutting and mashing

- Beaker or large bowl

- Coffee filter or fine sieve

- Saucepan for hot water bath

- Ice water bath

### Procedure:

1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.

2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.

3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.

4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.

5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.

6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.

7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.

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.

9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.
<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>

Result

Both the leaves and the persimmon failed to extract DNA. I was a little frustrated.

The guide for chat GPT seems unreliable. 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''' =====
Introduction

Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry.

Procedure

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>Result

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'''=====
Introduction

Exercise for DNA centrifugation and PCR Experiment

Procedure

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)

*sample B11, B12 are dirtier than B2

*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. 
<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''' =====
Introduction

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.

Procedure

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>

Result

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.

GMU:Life in an aquatic ecosystem/Dahye Seo

2024-11-27T23:39:51Z

Dahyeseo: /* 2024.11.26. Tue */

GMU:Life in an aquatic ecosystem/Dahye Seo

2024-11-27T23:39:30Z

Dahyeseo: /* 2024.11.26. Tue */

=== '''Dead Life Live Life''' ===

==== Description ====
<nowiki>*</nowiki> This project was started but not completed in SS 2023 and will be continued this semester.

''Dead Life Live Life'' is a sound installation work that sonifies the movement of DNA. This work was inspired by the poetic movement of DNA in electrophoresis experiments. ''Dead Life Live Life'' explores the materiality of DNA itself rather than genetic analysis, which is the general purpose of DNA. “Dead life got the same material as live life”, biologist Lynn Margulis said in an interview. This could be paraphrased as “Dead life got the same DNA as live life”. ''Dead Life Live Life'' poetically represents the connection between life and death by sonifying the DNA movement of an old persimmon tree planted in my grandmother's house.
[[File:Dlll 1.001.jpg|center|frameless|800x800px]]
[[File:Dlll 2..jpg|center|frameless|800x800px]]

[[File:Diagram Dead LifeLiveLife.jpg|center|thumb|800x800px]]

==== Technical solution ====

===== 1. Biological part =====
Instruction of DNA analysis<gallery>
File:Instruction1 DNAworkshop.jpg
File:Instruction2 DNAworkshop.jpg
</gallery>1) DNA Extraction of Persimmons <gallery>
File:Kaki gelElectrophoresis 2.jpeg
File:Kaki gelElectrophoresis 3.jpeg
File:Kaki gelElectrophoresis 4.jpeg
File:Kaki gelElectrophoresis 5.jpeg
File:Kaki gelElectrophoresis 6.jpeg
File:Kaki gelElectrophoresis 7.jpeg
File:Kaki gelElectrophoresis 8.jpeg
</gallery>

2) PCR Experiment (DNA amplification) / Gel electrophoresis (DNA movement & visualization) . <gallery>
File:Kaki gelElectrophoresis 10.jpeg
File:Kaki gelElectrophoresis 9.jpeg
File:Kaki gelElectrophoresis 11.jpeg
File:Kaki gelElectrophoresis 12.jpeg
File:Kaki gelElectrophoresis 13.jpeg
File:Gelelectrophoresis workshop 20230428 Large.jpeg
</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

===== 2. Sound part =====
1) Sonification of DNA movementMax/Msp patch

Convert continuously changing number of RGB data (could be change to other data) of DNA movement animation to midi or frequency.{{#ev:youtube|bGzmhJ9kQi4}}

2) Sound Design

==== Work in Biolab ====

===== '''2024.11.16. Sat''' =====
Introduction

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.

Procedure

''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.

<gallery>
File:DNA ladder1.jpg
File:DNA Ladder2.jpg
File:Prepare GelElectrophoresis.jpg
File:Gel electrophoresis1.jpg
File:GelElectrophoresis.jpg
File:Note.jpg
</gallery>

Result

First Column: 1 kb DNA ladder

Last to first and second Columns: 100 bp DNA ladder <gallery>
File:First round 5V-40min.jpg
File:2round 5v-40min.jpg
File:3round 6v-60min.jpg
</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?

ps. after around 50 hours. Still there remains the trace of the DNA movement.
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>

===== ''' 2024.11.18. Mon''' =====
Introduction

The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.

Procedure

A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.

* Note

1. Reused the gel from 2 days ago.

2. Did not put stain green in the TBE buffer covering the gel.

Result

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''' =====
Introduction

DNA Extraction Exercise_ Kaki,Blueberry

Procedure

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>
Result

Blueberries were successful in extracting DNA, but kaki failed again.
<gallery>
File:Dna Ex5.jpg
File:Dna Ex6.jpg
</gallery>

===== '''2024.11.20. Wed''' =====
Introduction

DNA Extraction Exercise_ Kaki (ChatGPT), Leaf

- I failed to extract Kaki's DNA in my experiment yesterday. This time i followed Chat GPT's guide 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.

Procedure

-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.

<nowiki>*</nowiki>Chat GPT's guide

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:

### Materials Needed:

- 3-4 kaki fruits

- 5g washing up liquid or hand soap

- 2g salt

- 100ml tap water

- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)

- Knife and fork for cutting and mashing

- Beaker or large bowl

- Coffee filter or fine sieve

- Saucepan for hot water bath

- Ice water bath

### Procedure:

1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.

2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.

3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.

4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.

5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.

6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.

7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.

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.

9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.
<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>

Result

Both the leaves and the persimmon failed to extract DNA. I was a little frustrated.

The guide for chat GPT seems unreliable. 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''' =====
Introduction

Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry.

Procedure

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>Result

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'''=====
Introduction

Exercise for DNA centrifugation and PCR Experiment

Procedure

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)

*sample B11, B12 are dirtier than B2

*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. 
<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''' =====
Introduction

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.

Procedure

The protocol below was followed.

[[File:DNeasy protocol.pdf|left|thumb]]
<nowiki>https://youtu.be/c1WOBy5vSg8?si=ksFltpYkG1ytvugT</nowiki>

<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>

Result

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.

GMU:Life in an aquatic ecosystem/Dahye Seo

2024-11-27T23:38:56Z

Dahyeseo:

=== '''Dead Life Live Life''' ===

==== Description ====
<nowiki>*</nowiki> This project was started but not completed in SS 2023 and will be continued this semester.

''Dead Life Live Life'' is a sound installation work that sonifies the movement of DNA. This work was inspired by the poetic movement of DNA in electrophoresis experiments. ''Dead Life Live Life'' explores the materiality of DNA itself rather than genetic analysis, which is the general purpose of DNA. “Dead life got the same material as live life”, biologist Lynn Margulis said in an interview. This could be paraphrased as “Dead life got the same DNA as live life”. ''Dead Life Live Life'' poetically represents the connection between life and death by sonifying the DNA movement of an old persimmon tree planted in my grandmother's house.
[[File:Dlll 1.001.jpg|center|frameless|800x800px]]
[[File:Dlll 2..jpg|center|frameless|800x800px]]

[[File:Diagram Dead LifeLiveLife.jpg|center|thumb|800x800px]]

==== Technical solution ====

===== 1. Biological part =====
Instruction of DNA analysis<gallery>
File:Instruction1 DNAworkshop.jpg
File:Instruction2 DNAworkshop.jpg
</gallery>1) DNA Extraction of Persimmons <gallery>
File:Kaki gelElectrophoresis 2.jpeg
File:Kaki gelElectrophoresis 3.jpeg
File:Kaki gelElectrophoresis 4.jpeg
File:Kaki gelElectrophoresis 5.jpeg
File:Kaki gelElectrophoresis 6.jpeg
File:Kaki gelElectrophoresis 7.jpeg
File:Kaki gelElectrophoresis 8.jpeg
</gallery>

2) PCR Experiment (DNA amplification) / Gel electrophoresis (DNA movement & visualization) . <gallery>
File:Kaki gelElectrophoresis 10.jpeg
File:Kaki gelElectrophoresis 9.jpeg
File:Kaki gelElectrophoresis 11.jpeg
File:Kaki gelElectrophoresis 12.jpeg
File:Kaki gelElectrophoresis 13.jpeg
File:Gelelectrophoresis workshop 20230428 Large.jpeg
</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

===== 2. Sound part =====
1) Sonification of DNA movementMax/Msp patch

Convert continuously changing number of RGB data (could be change to other data) of DNA movement animation to midi or frequency.{{#ev:youtube|bGzmhJ9kQi4}}

2) Sound Design

==== Work in Biolab ====

===== '''2024.11.16. Sat''' =====
Introduction

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.

Procedure

''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.

<gallery>
File:DNA ladder1.jpg
File:DNA Ladder2.jpg
File:Prepare GelElectrophoresis.jpg
File:Gel electrophoresis1.jpg
File:GelElectrophoresis.jpg
File:Note.jpg
</gallery>

Result

First Column: 1 kb DNA ladder

Last to first and second Columns: 100 bp DNA ladder <gallery>
File:First round 5V-40min.jpg
File:2round 5v-40min.jpg
File:3round 6v-60min.jpg
</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?

ps. after around 50 hours. Still there remains the trace of the DNA movement.
<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>

===== ''' 2024.11.18. Mon''' =====
Introduction

The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.

Procedure

A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.

* Note

1. Reused the gel from 2 days ago.

2. Did not put stain green in the TBE buffer covering the gel.

Result

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''' =====
Introduction

DNA Extraction Exercise_ Kaki,Blueberry

Procedure

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>
Result

Blueberries were successful in extracting DNA, but kaki failed again.
<gallery>
File:Dna Ex5.jpg
File:Dna Ex6.jpg
</gallery>

===== '''2024.11.20. Wed''' =====
Introduction

DNA Extraction Exercise_ Kaki (ChatGPT), Leaf

- I failed to extract Kaki's DNA in my experiment yesterday. This time i followed Chat GPT's guide 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.

Procedure

-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.

<nowiki>*</nowiki>Chat GPT's guide

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:

### Materials Needed:

- 3-4 kaki fruits

- 5g washing up liquid or hand soap

- 2g salt

- 100ml tap water

- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)

- Knife and fork for cutting and mashing

- Beaker or large bowl

- Coffee filter or fine sieve

- Saucepan for hot water bath

- Ice water bath

### Procedure:

1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.

2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.

3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.

4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.

5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.

6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.

7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.

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.

9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.
<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>

Result

Both the leaves and the persimmon failed to extract DNA. I was a little frustrated.

The guide for chat GPT seems unreliable. 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''' =====
Introduction

Various sample preparations for pcr and gel electrophoresis : DNA extraction of banana and blueberry.

Procedure

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>Result

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'''=====
Introduction

Exercise for DNA centrifugation and PCR Experiment

Procedure

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)

*sample B11, B12 are dirtier than B2

*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. 
<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''' =====
Introduction

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.

Procedure

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>

Result

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.