DNA and RNA

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Tero
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Re: DNA and RNA

Post by Tero » Thu Aug 19, 2021 11:10 am

Pfizer and BioNTech are manufacturing the vaccine in their own facilities in the United States and in Europe. The license to distribute and manufacture in China was purchased by Fosun, alongside its investment in BioNTech.[24][88]

Pfizer indicated in its 9 November press release that 50 million doses could be available by the end of 2020, with about 1.3 billion doses provided globally by 2021.[28]

Manufacturing the vaccine requires a three-stage process. The first stage involves the molecular cloning of DNA plasmids that code for the spike protein by infusing them into Escherichia coli bacteria. For all markets, this stage is conducted in the United States,[89] at a small Pfizer pilot plant in Chesterfield, Missouri[90][91] (near St. Louis). After four days of growth, the bacteria are killed and broken open, and the contents of their cells are purified over a week and a half to recover the desired DNA product. The DNA is bottled and frozen for shipment. Safely and quickly transporting the DNA at this stage is so important that Pfizer has used its company jet and helicopter to assist.[92]

The second stage is being conducted at a Pfizer plant in Andover, Massachusetts,[93] in the United States, and at BioNTech's plants in Germany.[89] The DNA is used as a template to build the desired mRNA strands,[92] which takes about four days.[89] Once the mRNA has been created and purified, it is frozen in plastic bags about the size of a large shopping bag, of which each can hold up to 10 million doses. The bags are placed on trucks which take them to the next plant.[92]

The third stage is being conducted at Pfizer plants in Portage, Michigan[94] (near Kalamazoo) in the United States, and Puurs in Belgium. This stage involves combining the mRNA with lipid nanoparticles, then filling vials, boxing vials, and freezing them.[92] Croda International subsidiary Avanti Polar Lipids is providing the requisite lipids.[95] As of November 2020, the major bottleneck in the manufacturing process is combining mRNA with lipid nanoparticles.[92] At this stage, it takes only four days to go from mRNA and lipids to finished vials, but each lot must then spend several weeks in deep-freeze storage while undergoing verification against 40 quality-control measures.[89]
https://en.wikipedia.org/wiki/Pfizer%E2 ... ufacturing

From the template link (no real detail on what the source of the polymerase is...there are plants to make these
Initiation
Transcription begins with the binding of RNA polymerase, together with one or more general transcription factors, to a specific DNA sequence referred to as a "promoter" to form an RNA polymerase-promoter "closed complex". In the "closed complex" the promoter DNA is still fully double-stranded.[7]

RNA polymerase, assisted by one or more general transcription factors, then unwinds approximately 14 base pairs of DNA to form an RNA polymerase-promoter "open complex". In the "open complex" the promoter DNA is partly unwound and single-stranded. The exposed, single-stranded DNA is referred to as the "transcription bubble."[7]

RNA polymerase, assisted by one or more general transcription factors, then selects a transcription start site in the transcription bubble, binds to an initiating NTP and an extending NTP (or a short RNA primer and an extending NTP) complementary to the transcription start site sequence, and catalyzes bond formation to yield an initial RNA product.[7]
Elongation

Simple diagram of transcription elongation
One strand of the DNA, the template strand (or noncoding strand), is used as a template for RNA synthesis. As transcription proceeds, RNA polymerase traverses the template strand and uses base pairing complementarity with the DNA template to create an RNA copy (which elongates during the traversal). Although RNA polymerase traverses the template strand from 3' → 5', the coding (non-template) strand and newly formed RNA can also be used as reference points, so transcription can be described as occurring 5' → 3'. This produces an RNA molecule from 5' → 3', an exact copy of the coding strand (except that thymines are replaced with uracils, and the nucleotides are composed of a ribose (5-carbon) sugar where DNA has deoxyribose (one fewer oxygen atom) in its sugar-phosphate backbone).[citation needed]

mRNA transcription can involve multiple RNA polymerases on a single DNA template and multiple rounds of transcription (amplification of particular mRNA), so many mRNA molecules can be rapidly produced from a single copy of a gene.[citation needed] The characteristic elongation rates in prokaryotes and eukaryotes are about 10-100 nts/sec.[42] In eukaryotes, however, nucleosomes act as major barriers to transcribing polymerases during transcription elongation.[43][44] In these organisms, the pausing induced by nucleosomes can be regulated by transcription elongation factors such as TFIIS.[44]
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Re: DNA and RNA

Post by Tero » Thu Aug 19, 2021 11:21 am

A year ago, the materials for these vaccines were being made for research purposes only, enough for maybe a few hundred doses at a time. Now Pfizer expects to pump out two billion doses by the end of this year.

It has made scaling up the manufacturing process a herculean feat, said Morin. There are 25 different suppliers involved, spanning 19 different countries. Some of them, said Morin, were making milligrams of liquid at the start. Then they were asked to make kilograms of it, and finally hundreds of kilograms.

The 475,000 doses Canada received last week began their lives before Christmas. Morin said it used to take four months to make a single dose of the vaccine, which is officially called BNT162b2. Morin said the process has recently been streamlined to half that time.
https://www.ctvnews.ca/health/coronavir ... -1.5327003
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Said Peter...what you're requesting just isn't my bag
Said Daemon, who's sorry too, but y'see we didn't have no choice
And our hands they are many and we'd be of one voice
We've come all the way from Wigan to get up and state
Our case for survival before it's too late

Turn stone to bread, said Daemon Duncetan
Turn stone to bread right away...

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Re: DNA and RNA

Post by JimC » Thu Aug 19, 2021 9:24 pm

Australia is (hopefully) going to develop its own mRNA technology (in Melbourne, apparently), and have the ability to quickly produce vaccines against new covid variants or new emerging diseases of the future.
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Re: DNA and RNA

Post by Tero » Tue Sep 14, 2021 1:54 am

paper on Australian Fairy Wrens
analyzed.
Our paternity assignments indicated a high level of extrapair
paternity in this population. Across the six years, an average of
55.3% of all broods analyzed contained offspring sired by
males other than the dominant male in the social group, and
42% of all offspring were the result of such matings (Table 3).
Reproductive promiscuity in the splendid fairy-wrenhttps://academic.oup.com › beheco › article-pdf › arh093
by MS Webster · 2004 · Cited by 100 — We employed microsatellite markers to examine patterns of parentage in the cooperatively breeding splendid fairy-wren (Malurus splendens melanotus).
9 pages
https://academic.oup.com/beheco/article ... arh093.pdf

The strings of noncoding DNA are listed in Table 1. I wish they had explained a bit more on the method, rather than just the percenatage results.
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Said Peter...what you're requesting just isn't my bag
Said Daemon, who's sorry too, but y'see we didn't have no choice
And our hands they are many and we'd be of one voice
We've come all the way from Wigan to get up and state
Our case for survival before it's too late

Turn stone to bread, said Daemon Duncetan
Turn stone to bread right away...

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Re: DNA and RNA

Post by Tero » Tue Sep 14, 2021 8:42 pm

https://esapolitics.blogspot.com
http://esabirdsne.blogspot.com/
Said Peter...what you're requesting just isn't my bag
Said Daemon, who's sorry too, but y'see we didn't have no choice
And our hands they are many and we'd be of one voice
We've come all the way from Wigan to get up and state
Our case for survival before it's too late

Turn stone to bread, said Daemon Duncetan
Turn stone to bread right away...

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Re: DNA and RNA

Post by Tero » Fri Oct 01, 2021 10:51 am

The Merck (purchased, off Emory univeristy) Covid drug is a nucleoside. Other than that I don't know its involvement in RNA.
https://en.wikipedia.org/wiki/Molnupiravir
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Said Peter...what you're requesting just isn't my bag
Said Daemon, who's sorry too, but y'see we didn't have no choice
And our hands they are many and we'd be of one voice
We've come all the way from Wigan to get up and state
Our case for survival before it's too late

Turn stone to bread, said Daemon Duncetan
Turn stone to bread right away...

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Re: DNA and RNA

Post by Tero » Fri Oct 01, 2021 11:36 am

It is involved in viral RNA replication. Just like cells need to duplicate DNA, viruses need to produce and package their RNA. The drug is involved in the viral (only) RNA production. You need your (human) RNA.
Coronaviruses use an RNA-dependent RNA polymerase (RdRp) for the replication and transcription of their RNA genome1,2,3,4,5,6. RdRp is an important target for the development of antiviral drugs against coronaviruses1,7,8,9,10. Structures of RdRp have been reported for SARS-CoV-111 and SARS-CoV-212,13,14,15,16 and provide insights into the mechanisms of RNA-dependent RNA synthesis17. The structures also enable mechanistic studies that can rationalize the molecular processes underlying the antiviral activity of compounds targeting RdRp.
https://www.nature.com/articles/s41594-021-00651-0

this might need a bit more testing to see long term effects of the drug in volunteers. That is, it is 1000% more effective than horse dewormer, but the side effeects often get logged in the first year of use. If you are already on a ventilator you don't care about that. If you are home with covid and no serious effects appear, hold off on this.
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Said Peter...what you're requesting just isn't my bag
Said Daemon, who's sorry too, but y'see we didn't have no choice
And our hands they are many and we'd be of one voice
We've come all the way from Wigan to get up and state
Our case for survival before it's too late

Turn stone to bread, said Daemon Duncetan
Turn stone to bread right away...

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Re: DNA and RNA

Post by Tero » Sat Oct 02, 2021 1:26 am

OK, I changed my mind. Those sick at home and risk factors (obesity etc) should take it. So as not to tie up so much hospital space.
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Said Peter...what you're requesting just isn't my bag
Said Daemon, who's sorry too, but y'see we didn't have no choice
And our hands they are many and we'd be of one voice
We've come all the way from Wigan to get up and state
Our case for survival before it's too late

Turn stone to bread, said Daemon Duncetan
Turn stone to bread right away...

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Re: DNA and RNA

Post by Tero » Sat Oct 09, 2021 12:08 pm

mRNA vaccine

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Said Peter...what you're requesting just isn't my bag
Said Daemon, who's sorry too, but y'see we didn't have no choice
And our hands they are many and we'd be of one voice
We've come all the way from Wigan to get up and state
Our case for survival before it's too late

Turn stone to bread, said Daemon Duncetan
Turn stone to bread right away...

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Re: DNA and RNA

Post by Tero » Thu Dec 02, 2021 7:07 pm

Fairly complete summary of manufacture steps now included
https://en.wikipedia.org/wiki/Pfizer%E2 ... ufacturing

plasmids are the key commercial thing to buy
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Said Peter...what you're requesting just isn't my bag
Said Daemon, who's sorry too, but y'see we didn't have no choice
And our hands they are many and we'd be of one voice
We've come all the way from Wigan to get up and state
Our case for survival before it's too late

Turn stone to bread, said Daemon Duncetan
Turn stone to bread right away...

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Re: DNA and RNA

Post by Tero » Fri Apr 01, 2022 2:56 pm

07224BEE-A233-41F3-BEEC-2023DA7B3E66.jpeg
Stuff they don't teach in college biology for the general science major crowd. The stem cells are the ones with all of DNA available to make protein. All the other ones have most of the DNA tagged and turned off. Thus only pancreas cells make insulin etc.
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Said Peter...what you're requesting just isn't my bag
Said Daemon, who's sorry too, but y'see we didn't have no choice
And our hands they are many and we'd be of one voice
We've come all the way from Wigan to get up and state
Our case for survival before it's too late

Turn stone to bread, said Daemon Duncetan
Turn stone to bread right away...

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Re: DNA and RNA

Post by Tero » Thu Nov 17, 2022 8:43 pm

Vaccines again. A plasmid (see wikipedia, it invades bacteria) is designed with the added DNA for, in covid, the spike protein. It is at this point DNA. It goes into the cells and they are killed and processed to trap DNA.
Manufacturing the vaccine requires a three-stage process. The first stage involves the molecular cloning of DNA plasmids that code for the spike protein by infusing them into Escherichia coli bacteria. For all markets, this stage is conducted in the United States,[132] at a small Pfizer pilot plant in Chesterfield, Missouri[133][134] (near St. Louis). After four days of growth, the bacteria are killed and broken open, and the contents of their cells are purified over a week and a half to recover the desired DNA product. The DNA is bottled and frozen for shipment. Safely and quickly transporting the DNA at this stage is so important that Pfizer has used its company jet and helicopter to assist.[135]

The second stage is being conducted at a Pfizer plant in Andover, Massachusetts,[136] in the United States, and at BioNTech's plants in Germany.[132] The DNA is used as a template to build the desired mRNA strands,[135] which takes about four days.[132] Once the mRNA has been created and purified, it is frozen in plastic bags about the size of a large shopping bag, of which each can hold up to 10 million doses. The bags are placed on trucks which take them to the next plant.
This plasmid picture is the part missing from the Wikipedia article.
plasmid dna.jpg
Wikipedia
https://en.wikipedia.org/wiki/Pfizer%E2 ... 19_vaccine
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Said Peter...what you're requesting just isn't my bag
Said Daemon, who's sorry too, but y'see we didn't have no choice
And our hands they are many and we'd be of one voice
We've come all the way from Wigan to get up and state
Our case for survival before it's too late

Turn stone to bread, said Daemon Duncetan
Turn stone to bread right away...

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Tero
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Re: DNA and RNA

Post by Tero » Thu Nov 17, 2022 10:15 pm

The plasmids are also covered under this
https://en.wikipedia.org/wiki/Recombinant_DNA
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http://esabirdsne.blogspot.com/
Said Peter...what you're requesting just isn't my bag
Said Daemon, who's sorry too, but y'see we didn't have no choice
And our hands they are many and we'd be of one voice
We've come all the way from Wigan to get up and state
Our case for survival before it's too late

Turn stone to bread, said Daemon Duncetan
Turn stone to bread right away...

User avatar
Tero
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Re: DNA and RNA

Post by Tero » Thu Dec 08, 2022 9:50 pm

Not now mitochondria in sperm!
OR
Dawkins was wrong. As were most others.

In "The Blind Watchmaker” (ref. 57, p. 176): “All the mitochondria in you are descended from the small population that traveled from your mother in her egg. Sperms are too small to contain mitochondria (our italics), so mitochondria travel exclusively down the female line, and male bodies are dead ends as far as mitochondrial reproduction is concerned. Incidentally, this means that we can use mitochondria to trace our ancestry strictly down the female line.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC19448/
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Said Peter...what you're requesting just isn't my bag
Said Daemon, who's sorry too, but y'see we didn't have no choice
And our hands they are many and we'd be of one voice
We've come all the way from Wigan to get up and state
Our case for survival before it's too late

Turn stone to bread, said Daemon Duncetan
Turn stone to bread right away...

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Re: DNA and RNA

Post by macdoc » Thu Dec 08, 2022 10:25 pm

one of those "oops" moments. aka all swans are white
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