[TOC]

# Petalsmiths Reading Group

## Logistics

No real logistics yet. Currently:

1. We're tentatively planning to meet every other Tuesday night.
1. Readings are suggested in [this Petalsmiths thread][1].
1. Group notes are written in [this HackMD note][2].
1. The group meets, as always, at [this Jitsi Meet link][3].

## Themes

:::warning
Here is where overarching themes we define as reading topics will live.
:::

## Sessions

### Assembly Standards for Plant Biotechnology

- Date
- 2021-12-07
- Primary Reading
- [GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology][4]
- Other Reading
- gbcloning.org
- FungalBraid

#### Chores for first meet

- [x] Should reading group meets be at a different time?
- Seb is making a whentomeet
- [x] What sorts of themes/topics do you want to cover?
- [x] Should we have a zotero group?
- Once we have more readings Jeremy can do it

#### Notes

- GoldenBraid versions
- GB is currently on version 4.0
- (Our reading is on version 2.0)
- Restriction enzymes
- BsaI and BsmBI are both from Bacillus stearothermophilus spp.
- [List of restriction enzyme cutting sites: Bsa - Bso][7]
- GoldenBraid Figures
- :::spoiler
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- yeah notes didn't really happen this time. more diligent next time
- Linkdump
- :::spoiler
- [Help:Standards/Assembly/Type IIS - parts.igem.org](http://parts.igem.org/Help:Standards/Assembly/Type_IIS)
- [CyanoGate: A Modular Cloning Suite for Engineering Cyanobacteria Based on the Plant MoClo Syntax | Plant Physiology | Oxford Academic](https://academic.oup.com/plphys/article/180/1/39/6117710)
- [Type IIS Assembly (Golden Gate) · Benchling](https://benchling.com/protocols/0IQQu6dn/type-iis-assembly-golden-gate)
- [Plasmids 101: Golden Gate Cloning](https://blog.addgene.org/plasmids-101-golden-gate-cloning)
- [1512×1134 | vibrio-cladistics-cake-or-death.png (58%)](https://cdn.discordapp.com/attachments/772088713164750858/918002267397955595/vibrio-cladistics-cake-or-death.png)
- [BioBrick - Wikipedia](https://en.wikipedia.org/wiki/BioBrick)
- [Golden Gate Cloning - Wikipedia](https://en.wikipedia.org/wiki/Golden_Gate_Cloning)
- [Idempotence - Wikipedia](https://en.wikipedia.org/wiki/Idempotence)
- [Solanum quitoense - Wikipedia](https://en.wikipedia.org/wiki/Solanum_quitoense)
- [GB2.0_Users_manual.pdf](https://gbcloning.upv.es/files/documents/GB2.0_Users_manual.pdf)
- [General FungalBraid page](https://gbcloning.upv.es/fungal/)
- [friendzymes/codon-optimize: A Github action to codon optimize sequences.](https://github.com/friendzymes/codon-optimize)
- [AllClo discussion · Issue #15 · friendzymes/community](https://github.com/friendzymes/community/issues/15)
- [667×603 | golden-braid-v2-kit.jpg__667x603_q85_subsampling-2_upscale.png (162%)](https://media.addgene.org/data/easy-thumbnails/filer_public/cms/filer_public/73/ec/73ec443f-c23b-4e40-bdba-54d22fd9a04a/golden-braid-v2-kit.jpg__667x603_q85_subsampling-2_upscale.png)
- [Concepts — moclo 0.4.6 documentation](https://moclo.readthedocs.io/en/latest/concepts/index.html#the-moclo-system)
- [Blazes of light reveal how plants signal danger long distances](https://news.wisc.edu/blazes-of-light-reveal-how-plants-signal-danger-long-distances/)
- [Repositorio Digital USFQ: Transformación genética de la naranjilla, Solanum quitoense, mediante Agrobacterium tumefaciens](https://repositorio.usfq.edu.ec/handle/23000/930)
- [Frontiers | MoCloFlex: A Modular Yet Flexible Cloning System | Bioengineering and Biotechnology](https://www.frontiersin.org/articles/10.3389/fbioe.2019.00271/full)
- [Golden Gate Cloning Tutorial | Geneious Prime](https://www.geneious.com/tutorials/golden-gate-cloning/)
- ['Starlight Avatar,' The World's First Light-Producing Plant, To Be Auctioned By Bioglow - Greenhouse Grower](https://www.greenhousegrower.com/crops/starlight-avatar-the-worlds-first-light-producing-plant-to-be-auctioned-by-bioglow/#:~:text='Starlight%20Avatar'%20is%20a%20nicotiana,%2D%20to%20three%2Dmonth%20lifespan.&text=Bioglow%20claims%20its%20plants%20are,for%20chemicals%20or%20UV%20light.)
- [Localization and Characterization of Photosystem II in Grana and Stroma Lamellae - PMC](https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC542412/)
- [BsmBI-v2 | NEB](https://www.neb.com/products/r0739-bsmbi-v2#Product%20Information)
- [Expanded “assembly standards” for MoClo | NEB](https://www.neb.com/tools-and-resources/usage-guidelines/expanded-assembly-standards-for-moclo-goldenbraid2-and-other-modular-golden-gate-assembly-methods)
- [RNAi – From Discovery to Nobel Prize in Record Time? - Nordic Biosite](https://www.nordicbiosite.com/blog/rnai-from-discovery-to-nobel-prize-in-record-time)
- [Strongly enhanced bacterial bioluminescence with the ilux operon for single-cell imaging | PNAS](https://www.pnas.org/content/115/5/962)
- [837×592 | The-complete-GB20-grammar-and-its-most-frequently-used-structures-A-Schematic-overview.png (94%)](https://www.researchgate.net/profile/Jose-Blanca/publication/236739651/figure/fig2/AS:299555733164034@1448431060831/The-complete-GB20-grammar-and-its-most-frequently-used-structures-A-Schematic-overview.png)
- [PCR-Based Random Mutagenesis - ScienceDirect](https://www.sciencedirect.com/science/article/abs/pii/B9780124186873000203)
- [Esp3I (BsmBI) (10 U/µL)](https://www.thermofisher.com/order/catalog/product/ER0451)
- [Type IIS Restriction Enzymes | Thermo Fisher Scientific - US](https://www.thermofisher.com/us/en/home/brands/thermo-scientific/molecular-biology/thermo-scientific-restriction-modifying-enzymes/restriction-enzymes-thermo-scientific/fastdigest-thermo-scientific/type-iis-restriction-enzymes.html)
:::

### Genome Editors

- Date
- 2021-12-21
- Primary Reading
- [Search-and-replace genome editing without double-strand breaks or donor DNA][5]

#### Notes

### Knocking Up Plants with CRISPR/CAS

- Date
- 2022-01-04
- Primary Reading
- [Towards mastering CRISPR-induced gene knock-in in plants: Survey of key features and focus on the model Physcomitrella patens][6]

#### Notes

---
## Scratchpad

:::info
Dump various clutter here.
:::

Sucrose based system instead of antibiotics:
-the idea is to have one carbon source sucrose in the medium, and the ecoli has no way to import or metabolise sucrose, unless it has the plasmid with ara genes to import and metabolise sucrose.

---
## Links

[1]: https://facebook.com/groups/390697141974598/posts/650432339334409
[2]: https://hackmd.io/@jcahill/petalsmiths-reading
[3]: https://meet.jit.si/Petalsmiths
[4]: https://doi.org/10.1104/pp.113.217661
[5]: https://doi.org/10.1038/s41586-019-1711-4
[6]: https://doi.org/10.1016/j.ymeth.2017.04.024
[7]: https://enwp.org/List_of_restriction_enzyme_cutting_sites

Golden braid diagram
https://media.addgene.org/data/easy-thumbnails/filer_public/cms/filer_public/73/ec/73ec443f-c23b-4e40-bdba-54d22fd9a04a/golden-braid-v2-kit.jpg__667x603_q85_subsampling-2_upscale.png

GB grammar graphic
https://www.researchgate.net/profile/Jose-Blanca/publication/236739651/figure/fig2/AS:299555733164034@1448431060831/The-complete-GB20-grammar-and-its-most-frequently-used-structures-A-Schematic-overview.png

Tomatoe with thorns. may culture in just ms
https://en.wikipedia.org/wiki/Solanum_quitoense

Erick Moreta says:
https://www.google.com/search?q=iridescent+begonia&sxsrf=AOaemvJT_noG4IvphYr9xGYWd_5nTOmy_g:1638937844918&tbm=isch&source=iu&ictx=1&fir=zbZS-NWO9s69DM%252CiV9hU1VlQIv84M%252C_%253BPXHFkQtj-EkKyM%252Cq3QqpGPNLZrOhM%252C_%253BurFoQ5q_oh7rUM%252CCxsercsw4Wc-4M%252C_%253B6xXPcFfejcX_fM%252CCxsercsw4Wc-4M%252C_%253BoaCL-EqxdOIVCM%252C9Rg0JIISTeQPyM%252C_%253BE0JpB7LUY46qHM%252CsbDyVFEvSCJb6M%252C_%253BqOTIiDsXgBzaZM%252CkjfJ6nCOOfEToM%252C_%253BKAL0EPTBWshzGM%252CcsVn7-4x89kJwM%252C_%253BknGbM_dhuhZFNM%252CZbiNfGbKgBkPFM%252C_%253BfXDKwto-Ul4-0M%252CkjfJ6nCOOfEToM%252C_&vet=1&usg=AI4_-kTqTfSkddFZ3tlJhJgGlFKe_akGEQ&sa=X&ved=2ahUKEwiNkbigr9P0AhX8TjABHS0gCbcQ9QF6BAgDEAE#imgrc=zbZS-NWO9s69DM