Molecular biology

Ciro Santilli believes that molecular biology technologies will be a large part of the next big things as shown at: Section "Molecular biology technologies".

Bibliography:

Study of the metabolome.

Some notable examples:

For a commented initial example, see: e. Coli K-12 MG1655 gene thrA.

KEGG does the visual maps well.

But BioCyc is generally better otherwise.

TODO vs KEGG.

Present at: www.roche.com/about/philanthropy/science-education/biochemical-pathways/

TODO human presumably?

I don't think it has any advantage over KEGG however, besides historical interest? Maybe slightly more manual layout and so more beautiful?

James Somers (rightly) likes to point to it as a "biology is awesome" thing.

An artificial metabolic pathway using synthetic biology technology.

Design software for synthetic biological circuit.

The input is in Verilog! Overkill?

Then it essentially maps to a standard cell library of biological primitives!

You label cells with isotopes rather than fluorescent substances. Vendors claim that this allows much wider N-way sorts, e.g. 2022 Fluidigm claims around 40/50, because the fluorecent spectrum is too wide to do much more than 7/8 way splits.

You modify the DNA of a cell and stick a fluorescent protein right before or after another protein. Then when it gets translated, the GFP is stuck to the protein of interest, which hopefully hasn't lost its function as a result, then you can just see the protein of interest.

Using green fluorescent protein as a protein tag.

The 3D structure of GFP is so cool. It is so clearly a bottle with a fluorescent bit well isolated right in the middle. Like a little lamp.

Technique widely used to measure the size of DNA strands, most often PCR output of a region of interest.

A simple sample application is gel electrophoresis alelle determination.

In the case of indel mutations (see limits of gel electrophoresis for minimal size difference issues), it is possible to determine the allele with gel electrophoresis. You can just read out the alleles right in the gel. It is a thing of beauty.

As of 2020, this method appears to be much cheaper than DNA sequencing approaches.

Biologists are obsessed with these!

These can be used to break cells apart from tissue, and also break up larger DNA or RNA molecules into smallers ones, suitable for sequencing.