Ciro Santilli
OurBigBook.commolecular-biology.bigb
= Molecular biology
{tag=The next big thing}
{wiki}
<Ciro Santilli> believes that <molecular biology technologies> will be a large part of <the next big things> as shown at: <molecular biology technologies>{full}.
Bibliography:
* https://www.youtube.com/watch?v=mS563_Teges&list=PLQbPquAyEw4dQ3zOLrdS1eF_KJJbUUyBx Biophysical Techniques Course 2022 by the <MRC Laboratory of Molecular Biology>. Holy crap that playlist is a tour de force of molecular biology techniques in 2022!
= Aging
{parent=Molecular biology}
{wiki}
= Free radical theory of aging
{parent=Aging}
{wiki}
= Free radical
{parent=Free radical theory of aging}
= Central dogma of molecular biology
{parent=Molecular biology}
{wiki}
\Include[dna]{parent=molecular-biology}
\Include[protein]{parent=molecular-biology}
= Metabolism
{parent=Molecular biology}
{wiki}
= Excretion
{parent=Metabolism}
{wiki}
= Excreting
{synonym}
= Excrete
{synonym}
= Feces
{parent=Excretion}
{wiki}
= Shit
{synonym}
= Shat
{synonym}
= Shitting
{synonym}
= Shitty
{synonym}
= Poo
{synonym}
= Flatulence
{parent=Feces}
{wiki}
= Fart
{synonym}
= Bullshit
{parent=Feces}
= Urine
{parent=Excretion}
{wiki}
= Pee
{synonym}
= Peeing
{synonym}
= Flux balance analysis
{parent=Metabolism}
{wiki}
= Metabolite
{parent=Metabolism}
{wiki}
= Metabolome
{parent=Metabolism}
{wiki}
\Image[https://upload.wikimedia.org/wikipedia/en/thumb/9/98/Metabolomics_schema.png/800px-Metabolomics_schema.png]
= Metabolomics
{parent=Metabolome}
{tag=Omics}
Study of the <metabolome>.
= Metabolic pathway
{parent=Metabolism}
{wiki}
Some notable examples:
* <citric acid cycle>
= Metabolic pathway database
{c}
{parent=Metabolic pathway}
{tag=Molecular biology database}
= KEGG
{c}
{parent=Metabolic pathway database}
{title2=Kyoto Encyclopedia of Genes and Genomes}
{wiki}
https://www.genome.jp/kegg/pathway.html
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.
= WikiPathways
{c}
{parent=Metabolic pathway database}
{wiki}
TODO vs <KEGG>.
= Roche Biochemical Pathways
{parent=Metabolic pathway}
{wiki}
Present at: https://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.
= Synthetic biological circuit
{parent=Metabolic pathway}
{tag=Metabolic pathway}
{wiki}
An artificial <metabolic pathway> using <synthetic biology> technology.
= CIDARLAB/cello
{c}
{parent=Metabolic pathway}
{tag=Synthetic biological circuit}
https://github.com/CIDARLAB/cello
Design software for <synthetic biological circuit>.
The input is in <Verilog>! Overkill?
Then it essentially maps to a <standard cell library> of biological primitives!
= Molecular biology technique
{parent=Molecular biology}
= Flow cytometry
{parent=Molecular biology technique}
{wiki}
\Video[https://www.youtube.com/watch?v=EQXPJ7eeesQ]
{title=Flow Cytometry Animation by StarCellBio (2015)}
= Mass cytometry
{parent=Flow cytometry}
{wiki}
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.
= Cell sorting
{parent=Flow cytometry}
= Fluorescent protein
{parent=Molecular biology technique}
= Fluorescent tag
{parent=Fluorescent protein}
{wiki}
= Protein tag
{parent=Fluorescent tag}
{wiki}
You modify the <DNA> of a cell and stick a <fluorescent protein> right before or after another protein. Then when it gets <translated (biology)>, 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.
= GFP tagging
{c}
{parent=Protein tag}
Using <green fluorescent protein> as a <protein tag>.
= List of fluorescent proteins
{parent=Fluorescent protein}
= Green fluorescent protein
{parent=List of fluorescent proteins}
{tag=Fluorescence}
{tag=2008 Nobel Prize in Chemistry}
{title2=GFP}
{wiki}
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.
= Staining
{c}
{parent=Molecular biology technique}
{wiki}
= Molecular biology laboratory equipment
{parent=Molecular biology technique}
= Gel electrophoresis
{parent=Molecular biology laboratory equipment}
{wiki}
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>.
= Gel electrophoresis alelle determination
{parent=Gel electrophoresis}
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.
\Video[https://www.youtube.com/watch?v=dXYGYCPYKEo]
{title=Gel Electrophoresis to Determine Genotype}
= Limits of gel electrophoresis
{parent=Gel electrophoresis}
= Gel electrophoresis separation of SNPs
{parent=Limits of gel electrophoresis}
* 1982 https://www.pnas.org/doi/pdf/10.1073/pnas.80.6.1579 DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels by Fischer and Lerman (1982). It is possible then.
= Agarose gel electrophoresis
{parent=Molecular biology laboratory equipment}
{wiki}
= Microtome
{c}
{parent=Molecular biology laboratory equipment}
{wiki}
= Petri dish
{c}
{parent=Molecular biology laboratory equipment}
{wiki}
= Laboratory centrifuge
{parent=Molecular biology laboratory equipment}
{wiki}
= Eppendorf tube
{c}
{parent=Laboratory centrifuge}
= Eppendorf
{c}
{synonym}
= Centrifuge tube
{c}
{synonym}
{title2}
= Microplate
{parent=Molecular biology laboratory equipment}
{wiki}
= 96 well microplate
{parent=Microplate}
Biologists are obsessed with these!
= Pipette
{parent=Molecular biology laboratory equipment}
{wiki}
= Sonicator
{parent=Molecular biology laboratory equipment}
{wiki}
These can be used to break <cells> apart from tissue, and also break up larger <DNA> or <RNA> molecules into smaller ones, suitable for <DNA sequencing>[sequencing].
= History of molecular biology
{parent=Molecular biology}
= History of molecular biology bibliography
{parent=History of molecular biology}
= The Eighth Day of Creation
{parent=History of molecular biology bibliography}
{title2=1979}
The author <#Horace Freeland Judson> was a <MacArthur fellow>, no wonder he found the time to write this bible!
On the <Internet Archive Open Library>:
* https://archive.org/details/eighthdayofcreat0000hora
* https://archive.org/details/eighthdayofcreat0000juds
<#Max Delbrück> is quoted as saying:
> So in retrospect what the denouement was, was that both the principle of replication and the principle of readout are DNA very simple, and the actual machinery for doing it is immensely complex. That's the way it has turned out."
Nice way to put it.
When <#Thomas F. Anderson> had started taking and publishing the first <#phage> <electron microscope> images:
> Now, Anderson later wrote, "We could really see the phage as tadpole shaped particles, whose heads ranged from 600 to 800 A \[...\] Anderson wrote. "I remember particularly the reaction of Alfred Hershey's teacher, kindly old Professor J. J. Bronfenbrenner, who had worked on <bacteriophages> for many years at Washington University in St. Louis. ... When he first saw our pictures ... he clapped the palm of his hand to his forehead and exclaimed, 'Mein Gott! They've got tails!'"
Nice quote from <Pauling>'s Nobel Prize speech highlighting the power and required accuracy of chemical ball and stick models:
> The requirements are stringent ones. \[...\]. In order that the principles of modem structural chemistry may be applied with the power that their reliability justifies, molecular models must be constructed with great accuracy. For example, molecular models on the scale of 2.5 cm 1 angstrom unit, have to be made with a precision better than 0.01 cm.
The book has a few reprints:
* 1996 https://www.amazon.co.uk/Eight-Day-Creation-Revolution-Biology/dp/0879694785
= Molecular biology bibliography
{parent=Molecular biology}
= Molecular biology documentary
{parent=Molecular biology bibliography}
* https://www.reddit.com/r/labrats/comments/5kccqp/recommendations_for_molecular_biologyrelated/