iGEM 2020 — Team GA_State_SW_Jiaotong

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# Team:GA State SW Jiaotong/Notebook

GSU & SWJT iGEM

[![](https://static.igem.org/mediawiki/2019/2/23/T--Georgia_State--logo.png)](../Team%3AGeorgia_State)

* [Home](../Team%3AGA_State_SW_Jiaotong)
* [Team](../Team%3AGA_State_SW_Jiaotong/Team)
  + [- Team Members](../Team%3AGA_State_SW_Jiaotong/Team)
  + [- Collaborations](../Team%3AGA_State_SW_Jiaotong/Collaborations)
  + [- Attributions](../Team%3AGA_State_SW_Jiaotong/Attributions)
* [Project](../Team%3AGA_State_SW_Jiaotong/Description)
  + [- Description](../Team%3AGA_State_SW_Jiaotong/Description)
  + [- Design](../Team%3AGA_State_SW_Jiaotong/Design)
  + [- Engineering Success](../Team%3AGA_State_SW_Jiaotong/Engineering)
  + [- Culturing](../Team%3AGA_State_SW_Jiaotong/Culturing)
  + [- Model](../Team%3AGA_State_SW_Jiaotong/Model)
  + [- Notebook](../Team%3AGA_State_SW_Jiaotong/Notebook)
  + [- Protocols](../Team%3AGA_State_SW_Jiaotong/Protocols)
  + [- Results](../Team%3AGA_State_SW_Jiaotong/Results)
  + [- Hardware](../Team%3AGA_State_SW_Jiaotong/Hardware)
  + [- Proposed Implementation](../Team%3AGA_State_SW_Jiaotong/Implementation)
* [Parts](../Team%3AGA_State_SW_Jiaotong/Parts)
  + [- Contribution](../Team%3AGA_State_SW_Jiaotong/Contribution)
  + [- Basic Parts](../Team%3AGA_State_SW_Jiaotong/Basic_Part)
  + [- Composite Parts](../Team%3AGA_State_SW_Jiaotong/Composite_Part)
* [Human Practices](../Team%3AGA_State_SW_Jiaotong/Human_Practices)
  + [- Human Practices](../Team%3AGA_State_SW_Jiaotong/Human_Practices)
  + [- Public Engagement](../Team%3AGA_State_SW_Jiaotong/Public_Engagement)
* [Safety](../Team%3AGA_State_SW_Jiaotong/Safety)
* [Judging Form](https://igem.org/2020_Judging_Form?team=GA_State_SW_Jiaotong)

## Notebook

1. [Home](../Team%3AGA_State_SW_Jiaotong)
2. Notebook

![](https://static.igem.org/mediawiki/2020/b/bf/T--GA_State_SW_Jiaotong--cartoon3.png)

[##### Fall: Post Quarantine](https://static.igem.org/mediawiki/2020/4/41/T--GA_State_SW_Jiaotong--post_quarantine_notebook.pdf)

[##### Corals](https://static.igem.org/mediawiki/2020/3/37/T--GA_State_SW_Jiaotong--corals_notebook.pdf)

[##### Algae](https://static.igem.org/mediawiki/2020/a/a0/T--GA_State_SW_Jiaotong--algae_notebook.pdf)

![](/wiki/images/2/23/T--Georgia_State--logo.png)

Copyright © All rights reserved | This template is made with  by [Colorlib](https://colorlib.com) | Modified by GSU iGEM

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#### Contact Us

Tel: (+1) 404 413 5344

E-mail: igemgsu@gmail.com

Address: iGEM 50 Decatur St SE, Atlanta GA 30303

[![](https://static.igem.org/mediawiki/2020/8/8b/HQ_page_logo.jpg)](https://2020.igem.org)

# Team:GA State SW Jiaotong/Engineering

GSU & SWJT iGEM

[![](https://static.igem.org/mediawiki/2019/2/23/T--Georgia_State--logo.png)](../Team%3AGeorgia_State)

* [Home](../Team%3AGA_State_SW_Jiaotong)
* [Team](../Team%3AGA_State_SW_Jiaotong/Team)
  + [- Team Members](../Team%3AGA_State_SW_Jiaotong/Team)
  + [- Collaborations](../Team%3AGA_State_SW_Jiaotong/Collaborations)
  + [- Attributions](../Team%3AGA_State_SW_Jiaotong/Attributions)
* [Project](../Team%3AGA_State_SW_Jiaotong/Description)
  + [- Description](../Team%3AGA_State_SW_Jiaotong/Description)
  + [- Design](../Team%3AGA_State_SW_Jiaotong/Design)
  + [- Engineering Success](../Team%3AGA_State_SW_Jiaotong/Engineering)
  + [- Culturing](../Team%3AGA_State_SW_Jiaotong/Culturing)
  + [- Model](../Team%3AGA_State_SW_Jiaotong/Model)
  + [- Notebook](../Team%3AGA_State_SW_Jiaotong/Notebook)
  + [- Protocols](../Team%3AGA_State_SW_Jiaotong/Protocols)
  + [- Results](../Team%3AGA_State_SW_Jiaotong/Results)
  + [- Hardware](../Team%3AGA_State_SW_Jiaotong/Hardware)
  + [- Proposed Implementation](../Team%3AGA_State_SW_Jiaotong/Implementation)
* [Parts](../Team%3AGA_State_SW_Jiaotong/Parts)
  + [- Contribution](../Team%3AGA_State_SW_Jiaotong/Contribution)
  + [- Basic Parts](../Team%3AGA_State_SW_Jiaotong/Basic_Part)
  + [- Composite Parts](../Team%3AGA_State_SW_Jiaotong/Composite_Part)
* [Human Practices](../Team%3AGA_State_SW_Jiaotong/Human_Practices)
  + [- Human Practices](../Team%3AGA_State_SW_Jiaotong/Human_Practices)
  + [- Public Engagement](../Team%3AGA_State_SW_Jiaotong/Public_Engagement)
* [Safety](../Team%3AGA_State_SW_Jiaotong/Safety)
* [Judging Form](https://igem.org/2020_Judging_Form?team=GA_State_SW_Jiaotong)

## Engineering Success

1. [Home](../Team%3AGA_State_SW_Jiaotong)
2. Engineering Success

Although this year we were unable to get into the lab as often as we would have liked, we
focused on the research phase of our project. One aspect of modifying the symbiotic algae is
performing a genomic analysis on different Symbiodinium clades in order to identify bleaching
resistant genes that we can insert or regulate into the algal genome. During our research, we
learned about the transcriptome of Symbiodinium, discovered drafts of its genome, and performed
a phylogenetic analysis of stress and metabolic genes in Symbiodinium. This led us to
hypothesize that the regulation of heat shock proteins and heat shock factors play a role in
thermal stress of the algae.

![](https://static.igem.org/mediawiki/2020/d/d7/T--GA_State_SW_Jiaotong--logo2.jpg)

In addition to identifying bleaching resistant genes in the algal genome, we designed experiments to successfully transform Symbiodinium. We engineered a codon optimized RFP reporter gene and inserted it into a dinoflagellate-optimized expression plasmid called DinoIII in order to confirm if our transformation was successful using flow cytometry. With this plasmid, we have attempted to transform the algae by electroporation via Lonza-4D Nucleofector, agrobacterium mediation, glass beads mediation, silica carbide whiskers, and yeast electroporation via Bio-Rad.

![](https://static.igem.org/mediawiki/2020/7/7c/T--GA_State_SW_Jiaotong--cartoon5.png)

From these transformations, we learned the plasmid we designed, DinoIII RFP cannot be used to yield accurate flow cytometry results because Symbiodinium naturally expresses red autofluorescence. Subsequently, we improved our plasmid by engineering a GUS reporter gene into DinoIII, which will produce a distinguishable blue pigment when measured via GUS assay. Also, we have learned that the transformation methods performed on Symbiodinium may not be feasible for delivering genes to its nucleus. Additional research revealed that Symbiodium has permanently condensed nuclear chromosomes, so there is limited access to relevant gene sites for the transient genes to be integrated into the genome. Instead, we want to target the DNA containing chloroplasts of Symbiodinium using a biolistics gene gun particle delivery system. Using this method, we will be able to insert our plasmid without integrating it into the nuclear genome.

[Read More About Our Design](./Design)

![](/wiki/images/2/23/T--Georgia_State--logo.png)

Copyright © All rights reserved | This template is made with  by [Colorlib](https://colorlib.com) | Modified by GSU iGEM

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#### Contact Us

Tel: (+1) 404 413 5344

E-mail: igemgsu@gmail.com

Address: iGEM 50 Decatur St SE, Atlanta GA 30303

[![](https://static.igem.org/mediawiki/2020/8/8b/HQ_page_logo.jpg)](https://2020.igem.org)

# Team:GA State SW Jiaotong/Experiments

# Experiments

Describe the research, experiments, and protocols you used in your iGEM project. These should be detailed enough for another team to repeat your experiments.

If you made Parts this year, please remember to put all information, characterization, and measurement data on the Part's Main Page on the [Registry](http://parts.igem.org/Main_Page).

### What should this page contain?

* Protocols
* Experiments

### Inspiration

* [2014 Colombia](https://2014.igem.org/Team%3AColombia/Protocols)
* [2014 Imperial](https://2014.igem.org/Team%3AImperial/Protocols)
* [2014 Caltech](https://2014.igem.org/Team%3ACaltech/Project/Experiments)

[![](https://static.igem.org/mediawiki/2020/8/8b/HQ_page_logo.jpg)](https://2020.igem.org)

# Team:GA State SW Jiaotong/Results

GSU & SWJT iGEM

[![](https://static.igem.org/mediawiki/2019/2/23/T--Georgia_State--logo.png)](../Team%3AGeorgia_State)

* [Home](../Team%3AGA_State_SW_Jiaotong)
* [Team](../Team%3AGA_State_SW_Jiaotong/Team)
  + [- Team Members](../Team%3AGA_State_SW_Jiaotong/Team)
  + [- Collaborations](../Team%3AGA_State_SW_Jiaotong/Collaborations)
  + [- Attributions](../Team%3AGA_State_SW_Jiaotong/Attributions)
* [Project](../Team%3AGA_State_SW_Jiaotong/Description)
  + [- Description](../Team%3AGA_State_SW_Jiaotong/Description)
  + [- Design](../Team%3AGA_State_SW_Jiaotong/Design)
  + [- Engineering Success](../Team%3AGA_State_SW_Jiaotong/Engineering)
  + [- Culturing](../Team%3AGA_State_SW_Jiaotong/Culturing)
  + [- Model](../Team%3AGA_State_SW_Jiaotong/Model)
  + [- Notebook](../Team%3AGA_State_SW_Jiaotong/Notebook)
  + [- Protocols](../Team%3AGA_State_SW_Jiaotong/Protocols)
  + [- Results](../Team%3AGA_State_SW_Jiaotong/Results)
  + [- Hardware](../Team%3AGA_State_SW_Jiaotong/Hardware)
  + [- Proposed Implementation](../Team%3AGA_State_SW_Jiaotong/Implementation)
* [Parts](../Team%3AGA_State_SW_Jiaotong/Parts)
  + [- Contribution](../Team%3AGA_State_SW_Jiaotong/Contribution)
  + [- Basic Parts](../Team%3AGA_State_SW_Jiaotong/Basic_Part)
  + [- Composite Parts](../Team%3AGA_State_SW_Jiaotong/Composite_Part)
* [Human Practices](../Team%3AGA_State_SW_Jiaotong/Human_Practices)
  + [- Human Practices](../Team%3AGA_State_SW_Jiaotong/Human_Practices)
  + [- Public Engagement](../Team%3AGA_State_SW_Jiaotong/Public_Engagement)
* [Safety](../Team%3AGA_State_SW_Jiaotong/Safety)
* [Judging Form](https://igem.org/2020_Judging_Form?team=GA_State_SW_Jiaotong)

## Results

1. [Home](../Team%3AGA_State_SW_Jiaotong)
2. Results

July

5
July

- Everyone decided their groups.
- 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)

![](https://static.igem.org/mediawiki/2020/e/e1/T--GA_State_SW_Jiaotong--ppt5.png)

(1)

12
July

- 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

![](https://static.igem.org/mediawiki/2020/9/96/T--GA_State_SW_Jiaotong--wechat.png)

(1)

![](https://static.igem.org/mediawiki/2020/5/56/T--GA_State_SW_Jiaotong--ppt6.png)

(2)

![](https://static.igem.org/mediawiki/2020/8/84/T--GA_State_SW_Jiaotong--ppt7.png)

(3)

![](https://static.igem.org/mediawiki/2020/c/c6/T--GA_State_SW_Jiaotong--ppt8.png)

(4)

20
July

- 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!**

![](https://static.igem.org/mediawiki/2020/d/df/T--GA_State_SW_Jiaotong--ppt9.png)

(1)

![](https://static.igem.org/mediawiki/2020/4/49/T--GA_State_SW_Jiaotong--ppt10.png)

(2)

![](https://static.igem.org/mediawiki/2020/8/81/T--GA_State_SW_Jiaotong--ppt11.png)

(3)

![](https://static.igem.org/mediawiki/2020/c/ca/T--GA_State_SW_Jiaotong--ppt12.png)

(4)

![](https://static.igem.org/mediawiki/2020/2/20/T--GA_State_SW_Jiaotong--ppt13.png)

(5)

27
July

- **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.

![](https://static.igem.org/mediawiki/2020/9/9f/T--GA_State_SW_Jiaotong--ppt14.png)

(1)

![](https://static.igem.org/mediawiki/2020/f/f2/T--GA_State_SW_Jiaotong--ppt15.png)

(2)

![](https://static.igem.org/mediawiki/2020/b/b5/T--GA_State_SW_Jiaotong--ppt16.png)

(3)

![](https://static.igem.org/mediawiki/2020/9/95/T--GA_State_SW_Jiaotong--ppt17.png)

(4)

August

2
Aug

- 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

![](https://static.igem.org/mediawiki/2020/b/bd/T--GA_State_SW_Jiaotong--ppt18.png)

(1)

![](https://static.igem.org/mediawiki/2020/0/09/T--GA_State_SW_Jiaotong--ppt19.png)

(2)

10
Aug

- 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)

![](https://static.igem.org/mediawiki/2020/4/4e/T--GA_State_SW_Jiaotong--ppt20.png)

(1)

![](https://static.igem.org/mediawiki/2020/0/06/T--GA_State_SW_Jiaotong--ppt21.png)

(2)

![](https://static.igem.org/mediawiki/2020/f/ff/T--GA_State_SW_Jiaotong--ppt22.png)

(3)

![](https://static.igem.org/mediawiki/2020/c/cb/T--GA_State_SW_Jiaotong--ppt23.png)

(4)

![](https://static.igem.org/mediawiki/2020/e/e6/T--GA_State_SW_Jiaotong--ppt24.png)

(5)

17
Aug

- 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)

![](https://static.igem.org/mediawiki/2020/7/74/T--GA_State_SW_Jiaotong--ppt25.png)

(1)

![](https://static.igem.org/mediawiki/2020/a/a0/T--GA_State_SW_Jiaotong--ppt26.png)

(2)

31
Aug

- **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.

![](https://static.igem.org/mediawiki/2020/f/ff/T--GA_State_SW_Jiaotong--ppt27.png)

(1)

![](https://static.igem.org/mediawiki/2020/3/31/T--GA_State_SW_Jiaotong--ppt28.png)

(2)

September

14
Sept

- 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)

![](https://static.igem.org/mediawiki/2020/c/cc/T--GA_State_SW_Jiaotong--ppt30.png)

(1)

![](https://static.igem.org/mediawiki/2020/3/3e/T--GA_State_SW_Jiaotong--ppt31.png)

(2)

![](https://static.igem.org/mediawiki/2020/f/f5/T--GA_State_SW_Jiaotong--ppt32.png)

(3)

23
Sept

- Introduced the IGEM calendar and divided the detailed work.
- Was in HSP problems. It’s hard to find papers about it.

29
Sept

- 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)

![](https://static.igem.org/mediawiki/2020/a/a2/T--GA_State_SW_Jiaotong--ppt33.png)

(1)

![](https://static.igem.org/mediawiki/2020/2/2c/T--GA_State_SW_Jiaotong--ppt34.png)

(2)

![](https://static.igem.org/mediawiki/2020/e/ef/T--GA_State_SW_Jiaotong--ppt35.png)

(3)

![](https://static.igem.org/mediawiki/2020/d/dd/T--GA_State_SW_Jiaotong--ppt36.png)

(4)

October

7
Oct

- **Build a phylogenetic tree about heat shock protein to see the relationships.(1)**
- Prepared human practice.

![](https://static.igem.org/mediawiki/2020/2/25/T--GA_State_SW_Jiaotong--ppt37.png)

(1)

![](/wiki/images/2/23/T--Georgia_State--logo.png)

Copyright © All rights reserved | This template is made with  by [Colorlib](https://colorlib.com) | Modified by GSU iGEM

![](/wiki/images/2/2a/T--Georgia_State--13.png)

#### Contact Us

Tel: (+1) 404 413 5344

E-mail: igemgsu@gmail.com

Address: iGEM 50 Decatur St SE, Atlanta GA 30303