GMU:Life in an aquatic ecosystem/Dahye Seo: Difference between revisions

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Dahyeseo

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 ) Sound Design
-===== Work in Biolab =====
+==== Work in Biolab ====
-.11.16. Sat, 9:30 am
+===== '''2024.11.16. Sat''' =====
 <u>Introduction</u>
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 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
+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.
@@ Line 79: / Line 79: @@
-Result
+<u>Result</u>
 First Column: 1 kb DNA ladder
@@ Line 90: / Line 90: @@
 <nowiki>*</nowiki>DNA moves slow. Next time, reduce the percentage of agarose gel ?
+How to set up the current for the gel electrophoresis? Does it impact the value of current for the movement of DNA?
+<small>ps. after around 50 hours. Still there remains the trace of the DNA movement.</small>
+<gallery>File:After 50hours gelElectrophoresis.jpg</gallery>
+===== ''' 2024.11.18. Mon''' =====
+<u>Introduction</u>
+The purpose of this experiment is to find out how DNA migrates when exposed to UV light throughout the whole gel electrophoresis process.
+<u>Procedure</u>
+A 100 bp DNA ladder was electrophoresed at 50 volts, 40 minutes.
+<small>* Note</small>
+<small>1. Reused the gel from 2 days ago.</small>
+<small>2. Did not put stain green in the TBE buffer covering the gel.</small>
+<u>Result</u>
+When the UV was shined throughout the experiment, the DNA movement is very blurry compared to when it was not.
+However, I am not sure if this is due to the UV light or the reuse of the gel or the lack of stain green.
+<gallery> File:DNALadder UV lighting.jpg </gallery>
+===== '''2024.11.19. Tue''' =====
+<u>Introduction</u>
+DNA Extraction Exercise_ Kaki,Blueberry
+<u>Procedure</u>
+I followed the guide from Julian's workshop (see photo above)
+<gallery>
+File:Kaki ex.jpg
+File:Kaki ex1.jpg
+File:Blueberry dna.jpg
+File:Dna Ex.jpg
+File:Dna Ex1.jpg
+File:Dna Ex2.jpg
+File:Dna Ex3.jpg
+</gallery>
+<u>Result</u>
+Blueberries were successful in extracting DNA, but kaki failed again.
+<gallery>
+File:Dna Ex5.jpg
+File:Dna Ex6.jpg
+</gallery>
+===== '''2024.11.20. Wed''' =====
+<u>Introduction</u>
+DNA Extraction Exercise_ Kaki (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.
+<u>Procedure</u>
+-The DNA extraction experiment was performed following the guide of chat gpt for the persimmon and the existing instructions for the leaf.
+<nowiki>*</nowiki>Chat GPT's guide
+<small>To extract DNA from kaki (persimmon) fruit, you'll need about '''3-4 fruits''' to get a sufficient amount of DNA for analysis. Here's a step-by-step procedure:</small>
+<small>### Materials Needed:</small>
+<small>- 3-4 kaki fruits</small>
+<small>- 5g washing up liquid or hand soap</small>
+<small>- 2g salt</small>
+<small>- 100ml tap water</small>
+<small>- 100ml ice-cold alcohol (isopropyl alcohol or ethanol)</small>
+<small>- Knife and fork for cutting and mashing</small>
+<small>- Beaker or large bowl</small>
+<small>- Coffee filter or fine sieve</small>
+<small>- Saucepan for hot water bath</small>
+<small>- Ice water bath</small>
+<small>### Procedure:</small>
+<small>1. '''Preparation''': Peel the kaki fruits and cut them into small chunks. Remove any seeds.</small>
+<small>2. '''Mashing''': Mash the fruit chunks thoroughly in a beaker or large bowl to break down the cells.</small>
+<small>3. '''Extraction Buffer''': Mix the washing up liquid, salt, and tap water in a separate container. Stir gently to avoid creating bubbles.</small>
+<small>4. '''Mixing''': Add the extraction buffer to the mashed fruit and mix well.</small>
+<small>5. '''Incubation''': Place the mixture in a hot water bath at '''60°C''' for '''15 minutes'''. Stir occasionally to ensure even heating.</small>
+<small>6. '''Cooling''': Transfer the mixture to an ice water bath and let it cool for '''5 minutes'''.</small>
+<small>7. '''Filtration''': Filter the mixture through a coffee filter or fine sieve into a clean container. This will remove solid debris.</small>
+<small>8. '''DNA Precipitation''': Slowly pour ice-cold alcohol down the side of the container to form a layer on top of the filtered mixture. DNA will precipitate out as a white, jelly-like substance at the interface.</small>
+<small>9. '''Collection''': Use a medicine dropper or a hook made from thin wire to collect the DNA precipitate.</small>
+<gallery>
+File:Leaaaaf.jpg
+File:Leaaaaf1.jpg
+File:Dh1.jpg
+File:Dh2.jpg
+File:Dh3.jpg
+File:Dh4.jpg
+File:Dh5.jpg
+File:Dh6.jpg
+File:Dh7.jpg
+File:Dh8.jpg
+</gallery>
+<u>Result</u>
+Both the leaves and the persimmon failed to extract DNA. I was a little frustrated.
+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>