Learned the plan and read articles generally to know the current progress.
Came up with the general ideas to achieve bleaching resistance.(1)
Discussed the ways to operate, such as CRISPR and iRNA. But Dr. Brewer analyzed their strength and weakness. The two ways are not suitable for this project.(1)
(1)
Set up Wechat group to ensure easy and timely communication in COVID-19 situation.(1)
Read many papers about transcriptome of Symbiodinium.
Found Gene microarray branch companies and price of transcriptome measurement.
Searched and compared the feasibility and finally planned to use microarray to test the genes’ expression between normal and high temperature situation to find the key resistant gene.(2)
Found the genome information of Symbiodium (SRR9613609) and Dunaliella from CNGBdp and NCBI.(3)(4)
Discussed methods to compare and find resistant gene
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Found and shared the most useful paper.(1)(2)(3)
Made the waiting list of resistant genes from that paper.(4)
Did a heat map to compare easily based on the data in this paper.(5)
Don’t need to do sequence!
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Came up with and analyzed some selecting ways of these genes (Pathways, Differences’ degree, Phylogenetic Trees).
Found more information, such as protein sequence of these genes. (1)
Another useful paper.(2)(3)(4)
Searched some tools to do the pathway and Phylogenetic Trees screening, such as KEGG, TBtools, MEGA and iTOL and so on.
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August
Learned and discussed the difference between Orthologous gene and Paralogous gene in phylogenetic trees.(1)(2)
Discussed the different role of phylogenetic trees in screening down and up regulation genes.
Need read more papers to decide up or down one gene to achieve the goal
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Did research on every waiting list gene’s functions from NCBI papers and GO database.(1)(2)(3)
Excluded some genes whose major functions are not relevant to heat-resistance.(4)(5)
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Did more research on “not recommended genes” and “possible genes” to exclude genes due to feasibility.(1)
Compared two important papers and found the similarity in genes.(2)
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Pathways and interaction relationships of the final genes from KEGG and String. Excluded genes that pathways are not clearly or could not be found from database.(1)(2)(3)
HSF is the upstream gene of HSP70 and HSP90 and also DnaJ, which are mentioned in the two papers. So it’s a possible gene to use.
HSF Types’ introduction, we needed to ensure if it’s A type that can regulate the expression of HSP and DnaJ independently.
Found more clear information of genome sequence.
(1)
(2)
September
Found many websites and papers about HSF types and promoter analysis (HSEAT). Prepared some A type HSF organisms to do BLAST. (1)(2)
After the discussion with Professor Zhou, we found it’s the wrong direction! We need to find HSP types.
Discuss what kinds of the symbiodium clades that we are cultured to ensure the genome database.(3)
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Introduced the IGEM calendar and divided the detailed work.
Was in HSP problems. It’s hard to find papers about it.
Found the nucleotide sequence and promoter sequence of HSP.
Solved the “type problem”!
Found the HSE sequence and the difference between the three types of HSP.(1)
After the comparison, can ensure the HSP in symbiodium is A type, which means we can regulate HSF gene to achieve the goal.(2)(3)(4)
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October
Build a phylogenetic tree about heat shock protein to see the relationships.(1)
