Notebook
Establishing the subject—multi-site editing—after taking other projects and skills of our members into consideration.
Interviewed Prof. Yi Wu.
April 29
Chinese characters stored in the computer was outputted in binary, then converted into ternary, and we coded the character/base conversion program based on ternary system.
Around May 12
TPrevious plan of ternary system went through a few difficulties and had problems with realization. Inspired by opinions from other universities, especially some art schools, we decided to modify songs via base editing technique.
May 29
We realized that music has become universal as a form of digital information. Therefore, the coding system focused on already digitalized music, and designed music tracks based on MIDI.
End of May
Questionnaire 1.
June 8
We designed the first generational coding rules focusing on music editing, with hopes of combining Chinese characters coding in gRNA design to increase density of the characters.
June 9
Previous code's lack of density led to further thinking, we were inspired after communicating with members from other crews and went through other projects, began to plan for the second generational code.
June 11
The base sequences we acquired cannot satisfy our requirements for gRNA design, so we turned to another coding system: we generated pseudo-random numbers, converted them into ternary, each group of numbers were transformed into six bases. Next step, estimated whether the base sequence is suitable for gRNA design and, if the answer is yes, define it as the base expression of one character.
We basically shaped the second generation, largely increased degrees of freedom. Concepts such as events, branches and switches were brought in with our combination of tip tree. Code density went up but needed further improvement.
June 20
The second generational code was used to design the information plasmid DNA sequence.
June 30
Repeat the transfer of the carotene plasmid into SY14 cells.
June 24
Dry lab made first attempt to construct gRNA sequences, the original plan was to combine gRNA sequences with both textual information and musical information. However, due to the long period of designing gRNA, the textual part was postponed.We used constructed gRNA arrays to design DNA.
Coded for viewing image size; acquired microvenus.png; coded for image cropping.
June 25
Coded Chinese character search and replace program.
June 26
Coded to generate the empty pixels and created the black and white pixel units; Coded program for pixel segmentation and converting them into 0s and 1s.
June 27
Interviewed Dr. Mingzhe Han.
July 1
First and second generational decoding took off. Information plasmid design completed.
July 3
Coded the first generational encoding program and decoding program of images.
July 8
Decoding part is completed, and we started to code the music module (.MID) which can be played by the system according to the decoding rules. We used winhex software to decipher and reverse the low-level code, iterating the file to obtain the corresponding track (inputted as DNA fragments).
Coded the second generational encoding program of images.
July 9
Coded the second generational decoding program of images.
July 10
Coded the GIF generating program.
July 13
Coded the program to generate original image; coded generating program for modifying target points.
July 14
Coded the program for decoding second type of sequence.
July 15
Design of information plasmid storing Ode to Joy accomplished and sent to a biotech company for synthesis.
Coding and music track are basically completed, also generally connected with wet lab experiment.
Starting to optimize the code itself, aiming to increase coding efficiency and information density.
Due to the time cycle length and shortage of time, third generational code did not go through wet experiment verification, but it is theoretically achievable.
July 16-July 17
Participated in the meetup.
Communicated with TJU_SLS offline.
July 18
Coded the program to generate images from 0s and 1s.
Acquired the GIF generated in second type of sequence; generated informative sequences 1 and 2.
July 20
Accomplished combination of informative sequences 1 and 2, DNA sequence synthesis was outsourced to a company.
Coding the GUI.
July 21
Information plasmid storing GIF was successfully designed and sent to a biotech company for synthesis.
July 22
Formation of third generational code was completed, we started to use software such as C, Python, eclipse (JAVA) and winhex to code the third generation. (Modifying input and output according to the underlying code, iterating file format and fine-tuning internal parameters).
July 25
We began to practice yeast galactose-induction, modified the metabolic pathways of violacein in yHX0378 to check the modification efficiency of gRNA array.
Inoculated X-16-2, X-16-4, X-22-4 to SC-L-H-U liquid medium for cell expansion.
Designed premiers for metabolic pathways of violacein to check the effect of our modification.
July 26
Transferred X-16-2, X-16-4, X-22-4 to SG-L-H-U+1/3ade liquid medium for inducing.
July 27
We coated Induced X-16-2, X-16-4, X-22-4 on SC-L-H-U+1/3ade medium.
July 29
Obtained premiers for metabolic pathways of violacein.
July 30
We performed PCR to verify the modification of metabolic pathways of violacein.
July 31-September 7
Coded the first edition of GUI for GIF generating program.
End of July
Interviewed Prof. Yingxiu Cao
August 1- August 2
First time to have acquired results of modifying metabolic pathways of violacein.
August 4
First time to have selected successfully grown red colonies of yNuwa002 to streak plate culture on SC-L-U+1/3ade medium.
Secondary inoculated X-16-2, X-16-4, X-22-4 to SC-L-H-U liquid medium for cell expansion.
Third generational coding basically finished, we were able to code simple music tracks, as for more complex tracks, coding is still in progress due to technical problems and lack of time.
August 5
Secondary transferred X-16-2, X-16-4, X-22-4 to SG-L-H-U+1/3ade liquid medium for inducing.
August 6
The red colonies streak plate cultured once were streak plate cultured again.
Second time to have coated Induced X-16-2, X-16-4, X-22-4 on SC-L-H-U+1/3ade medium.
August 11
Lectured about DNA storage on Bilibili.com.
August 13
Second time to have selected successfully grown red colonies of X-16-2 on SC-L-U+1/3ade medium to first time streak plate culture.
August 17
Red colonies successfully grown were streak plate cultured again.
August 19
We obtained Escherichia coli with integrated GIF plasmid from GENERAL BIOL.
August 20
Used streak plate technique to culture GIF plasmid integrated Escherichia coli.
August 21
Lectured for international students.
August 26
Designed premiers for GIF plasmid for synthesis.
August 27
We inoculated eight tubes of Escherichia coli with GIF plasmid integrated to LB+AMP liquid medium.
Inoculated one tube of yHX0362 primary yeast to SC-U liquid medium.
August 28
We inoculated one tube of yHX0362 secondary yeast to SC-U liquid medium.
Extracted 50μL×8 GIF plasmids.
Performed transformation of constitutive and inducible yeast.
August 29
Constitutive yeast coated on SC-L-U-H+1/3ade+hyg medium.
Inducible yeast coated on SC-L-U+1/3ade+hyg medium.
August 30
We obtained premiers for GIF plasmid.
August 31
We obtained successfully synthesized Ode to Joy plasmid from GENERAL BIOL.
End of August
Questionnaire 2
Interviewed Prof. Yunzi Luo
September 1
We acquired successfully transformed inducible GIF strain: yNuwa002.
Inoculated yNuwa002 to SC-L-U+hyg liquid medium for cell expansion.
We gathered our current possessed software and programs to form a keyboard game.
September 2
Transferred yNuwa003 to SG-L-U+1/3ade+hyg liquid medium for inducing.
September 3
Induced yNuwa003 were coated on SC-L-U+1/3ade+hyg medium.
We designed premiers for Ode to Joy plasmid and sent them for synthesis.
Basically accomplished modifying the metabolic pathways of violacein.
Communications with freshmen.
September 5
We obtained successfully synthesized premiers for Ode to Joy plasmid.
September 6
We selected successfully grown red colonies of yNuwa002 to streak plate culture on SC-L-U+1/3ade medium.
September 8-September 25
Coded the second edition of GUI for GIF generating program.
Decoding of Sequencing results.
September 11
Construction of Ode to Joy plasmid accomplished.
September 14
Extracted Ode to Joy plasmid.
September 16
We inoculated one tube of yHX0362 primary yeast to SC-U liquid medium.
September 17
We inoculated one tube of yHX0362 secondary yeast to SC-U liquid medium.
Performed transformation of constitutive and inducible yeast.
September 18
Constitutive yeast coated on SC-L-U-H+1/3ade+hyg medium.
Inducible yeast coated on SC-L-U+1/3ade+hyg medium.
September 21
We acquired successfully transformed inducible Ode to Joy strain: yNuwa003.
First batch of GIF red colonies were performed PCR and sent for sequencing.
September 22
Inoculated yNuwa003 to SC-L-U+hyg liquid medium for cell expansion.
Obtained first batch of GIF plasmid modification results.
September 22-September 27
Improved the decoding program, successfully acquired the decoding results for single-cell sequencing.
September 23
Transferred yNuwa003 to SG-L-U+1/3ade+hyg liquid medium for inducing.
September 24
Induced yNuwa003 were coated on SC-L-U+1/3ade+hyg medium.
September 27
Second batch of GIF red colonies were performed PCR and sent for sequencing.
September 28
Obtained second batch of GIF plasmid modification results.
October 5
Red colonies of yNuwa003 were picked out for PCR and sent to GENEWIZ for sequencing.
October 6
Obtained modification results of Ode to Joy plasmid.
October 8
Summarizing information plasmid modification results accomplished.