www.newyorker.com/magazine/2022/03/07/a-journey-to-the-center-of-our-cells A Journey to the Center of Our Cells (2022) by James Somers comments on M. genitalium in general, and in particular on the JCVI strains.
www.biorxiv.org/content/10.1101/2022.09.19.508583v1.fullIt is also interesting to see how they are interested in co-culture with HeLa cells, presumably to enable infectious bacterial disease studies.
CVI-syn3B strains differ from JCVI-syn3.0 by the presence of 19 additional non-essential genes that result in a more easily manipulated cell. JCVI-syn3B additionally includes a dual loxP landing pad that enables easy Cre recombinase mediated insertion of genes
At biology.indiana.edu/news-events/news/2023/lennon-minimal-cells.html (2023) they let it re-evove to it it would regain some fitness, and it did.
Name of the clade of archaea plus eukarya proposed at: www.frontiersin.org/articles/10.3389/fmicb.2015.00717/full. Much better term than prokaryote as that is not a clade. Let's hope it catches on!
But one thing you should really know, as often mentioned in Power, Sex, Suicide by Nick Lane (2006): they are all eukaryotes.
Because prokaryotes are fundamentally unable to do phagocytosis, because they have a rigid cell wall. Changing cell shape at will requires a cytoskeleton.
You read the name and think: hmm, neural cords!
But then you see that his is one of its members:
Yup. That's your cousin. And it's a much closer cousin than something like arthropods, which at least have heads eyes and legs like you.
Convergent evolution is crazy!
The hard part then is how to make any predictions from it:
- 2024 www.nature.com/articles/d41586-024-02935-z Fly-brain connectome helps to make predictions about neural activity. Summary of "Connectome-constrained networks predict neural activity across the fly visual system" by J. K. Lappalainen et. al.
2024: www.nature.com/articles/d41586-024-03190-y Largest brain map ever reveals fruit fly's neurons in exquisite detail
As of 2022, it had been almost fully decoded by post mortem connectome extraction with microtome!!! 135k neurons.
- 2021 www.nytimes.com/2021/10/26/science/drosophila-fly-brain-connectome.html Why Scientists Have Spent Years Mapping This Creature’s Brain by New York Times
That article mentions the humongous paper elifesciences.org/articles/66039 elifesciences.org/articles/66039 "A connectome of the Drosophila central complex reveals network motifs suitable for flexible navigation and context-dependent action selection" by a group from Janelia Research Campus. THe paper is so large that it makes eLife hang.
Includes:
- amphibians
- amniotes, which includes:
- sauropsida: reptiles and birds, which really are reptiles
- mammals
The exact relationships between those clades is not very clear as there's a bunch of extinct species in the middle we are not sure exactly where they go exactly, some hypothesis are listed at: en.wikipedia.org/w/index.php?title=Tetrapod&oldid=1053601110#Temnospondyl_hypothesis_(TH)
Pinned article: Introduction to the OurBigBook Project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
Intro to OurBigBook
. Source. We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivativeVideo 2. OurBigBook Web topics demo. Source. - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 3. Visual Studio Code extension installation.
Figure 4. Visual Studio Code extension tree navigation.
Figure 5. Web editor. You can also edit articles on the Web editor without installing anything locally.Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension.Video 4. OurBigBook Visual Studio Code extension editing and navigation demo. Source. 
- Infinitely deep tables of contents:
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact