Ciro Santilli @cirosantilli 37

Not done yet as of 2020! Will be done one day for sure.

The main FeathersJS hello world demo. Notable missing things...

Good list: en.wikipedia.org/wiki/Geologic_time_scale#Terminology

UniProt entry: www.uniprot.org/uniprot/P00561.

NCBI entry: www.ncbi.nlm.nih.gov/gene/945803.

The second gene in the E. Coli K-12 MG1655 genome. Part of the E. Coli K-12 MG1655 operon thrLABC.

Part of a reaction that produces threonine.

This protein is an enzyme. The UniProt entry clearly shows the chemical reactions that it catalyses. In this case, there are actually two! It can either transforming the metabolite:Also interestingly, we see that both of those reaction require some extra energy to catalyse, one needing adenosine triphosphate and the other nADP+.

TODO: any mention of how much faster it makes the reaction, numerically?

Since this is an enzyme, it would also be interesting to have a quick search for it in the KEGG entry starting from the organism: www.genome.jp/pathway/eco01100+M00022 We type in the search bar "thrA", it gives a long list, but the last entry is our "thrA". Selecting it highlights two pathways in the large graph, so we understand that it catalyzes two different reactions, as suggested by the protein name itself (fused blah blah). We can now hover over:Note that common cofactor are omitted, since we've learnt from the UniProt entry that this reaction uses ATP.

If we can now click on the L-Homoserine edge, it takes us to: www.genome.jp/entry/eco:b0002+eco:b3940. Under "Pathway" we see an interesting looking pathway "Glycine, serine and threonine metabolism": www.genome.jp/pathway/eco00260+b0002 which contains a small manually selected and extremely clearly named subset of the larger graph!

But looking at the bottom of this subgraph (the UI is not great, can't Ctrl+F and enzyme names not shown, but the selected enzyme is slightly highlighted in red because it is in the URL www.genome.jp/pathway/eco00260+b0002 vs www.genome.jp/pathway/eco00260) we clearly see that thrA, thrB and thrC for a sequence that directly transforms "L-aspartate 4-semialdehyde" into "Homoserine" to "O-Phospho-L-homoserine" and finally tothreonine. This makes it crystal clear that they are not just located adjacently in the genome by chance: they are actually functionally related, and likely controlled by the same transcription factor: when you want one of them, you basically always want the three, because you must be are lacking threonine. TODO find transcription factor!

The UniProt entry also shows an interactive browser of the tertiary structure of the protein. We note that there are currently two sources available: X-ray crystallography and AlphaFold. To be honest, the AlphaFold one looks quite off!!!

By inspecting the FASTA for the entire genome, or by using the NCBI open reading frame tool, we see that this gene lies entirely in its own open reading frame, so it is quite boring

From the FASTA we see that the very first three Codons at position 337 arewhere ATG is the start codon, and CGA GTG should be the first two that actually go into the protein:

ecocyc.org/gene?orgid=ECOLI&id=ASPKINIHOMOSERDEHYDROGI-MONOMER mentions that the enzime is most active as protein complex with four copies of the same protein:TODO image?

Published on Physical Review by Polykarp Kusch and Foley.

journals.aps.org/pr/abstract/10.1103/PhysRev.74.250, paywall as of 2021.

Dumping examples under nodejs/sequelize/raw/many_to_many.js.

Not possible without subqueries in the standard syntax, a huge shame: stackoverflow.com/questions/1293330/how-can-i-do-an-update-statement-with-join-in-sql-server

The UPDATE + FROM extension exists in a few DBMSs:

ORM:

GDM crashes sometimes when switching windows right after opening a new window: bugs.launchpad.net/ubuntu/+source/gdm/+bug/1956299

Presented e.g. at youtu.be/t0yj4hBDUsc?t=456 from Video "Silicon Photonics: The Next Silicon Revolution? by Asianometry (2022)".

Bibliography:

Spike.

Nucleocapsid phosphoprotein, sticks to the RNA inside.

www.nature.com/articles/s41467-020-20768-y mentions functions:

Dude took down a bank.

Good documentary about it: Nick Leeson and the Fall of the House of Barings by Adam Curtis (1996).

One is reminded of Annie Dookhan.

Bibliography review:

Course outline given:

Non-relativistic QFT is a limit of relativistic QFT, and can be used to describe for example condensed matter physics systems at very low temperature. But it is still very hard to make accurate measurements even in those experiments.

Defines "relativistic" as: "the Lagrangian is symmetric under the Poincaré group".

Mentions that "QFT is hard" because (a finite list follows???):But I guess that if you fully understand what that means precisely, QTF won't be too hard for you!

Notably, this is stark contrast with rotation symmetry groups (SO(3)) which appears in space rotations present in non-relativistic quantum mechanics.

www.youtube.com/watch?v=T58H6ofIOpE&t=5097 describes the relativistic particle in a box thought experiment with shrinking walls