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Bert Hubert 🇪🇺 Profile picture
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31 Dec 20, 6 tweets, 4 min read
New leader in the BioNTech vaccine RNA optimization challenge: @pkuhar! With some pretty Python code that can server as a great starting point for other entries: github.com/unrelatedlabs/…. Context: berthub.eu/articles/posts…
New leader @naomicodes, 76% , using DNA Chisel from edinburgh-genome-foundry.github.io/DnaChisel/ - well done!
New leader @sanxiyn! 78.3% using codon frequency optimization.
New leader @pvieito! His modified dnschisel setup is now at 90.9%, even further than the tweet below:
A very interesting new entry from Harry Harpel. He found a static codon mapping that achieved a 79.4% match. Several people meanwhile are tweaking DNA Chisel parameters to improve the match. It may be that there is a random arbitrary factor to the mapping though!
Two new entries, one from @hyc_symas (author of the famous LMDB!), who has found an even better codon mapping table, plus the new leader Erik Brauer who squeezed 91.08% out of DNA Chisel!

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More from @PowerDNS_Bert

Bert Hubert 🇪🇺 Profile picture
31 Dec 20
Reverse engineers! Cryptographers! I have a fun challenge & contest for you. The BioNTech SARS-CoV-2 vaccine contains copy-pasted RNA from the actual virus. The vaccine RNA encodes for (almost) the unmodified virus S protein. But, the RNA has been optimized somehow. But how? 1/
You can change RNA quite a lot without changing the protein that comes out. It is known that replacing RNA letters to G and C to the RNA enhances vaccine efficiency. And lo, the designers of the vaccine have done just that - GC content went from ~36% to ~57%: 2/
In the graph above, the red dots are vaccine changes that _lower_ the number of G and C though. And we don't know why they did that. In other places, it appears simpler rules have been used to optimize the RNA. The goal is now: can we reverse engineer the algorithm they used? 3/
Read 6 tweets
Bert Hubert 🇪🇺 Profile picture
24 Dec 20
Preparing a blog post on the BioNTech/Pfizer vaccine & compared the live SARS-CoV-2 spike protein to the one in the mRNA vaccine. And indeed as described, it only differs by two amino-acids. The two Proline substitutions that make the vaccine work (KV -> PP, with the !!): 1/3
If the vaccine would have contained the unmodified Spike protein, this would have "looked" different from the real one. The real one is mounted in the virus body, which gives it a certain shape. With these two changes, the vaccine protein "looks normal" to our immune system. 2/3
This proline substitution trick was discovered in *2017* based on studies on SARS-CoV-1 and MERS, two related viruses. These studies noted that this tiny change made the protein *50 times* more recognizable. Iow we'd be toast without this invention ncbi.nlm.nih.gov/pmc/articles/P… 3/3
Read 4 tweets
Bert Hubert 🇪🇺 Profile picture
24 Dec 20
"S glycoprotein signal peptide (extended leader sequence), which guides translocation of the nascent polypeptide chain into the endoplasmic reticulum" - part of the BioNTech/Pfizer vaccine. I don't ever want to hear anyone question fundamental science again. 1/2
The level of control and understanding we now have over our biology came from literally millions of person-years spent working on things that at the time were obscure and "useless". And now? We can leverage all this into a 95% efficient vaccine _at the first try_. 2/2
Coda:
Read 4 tweets
Bert Hubert 🇪🇺 Profile picture
23 Dec 20
Shout out to @BioNTech_Group who found time to answer this small time blogger's question! @hildabast I have it in writing now, a 30 microgram dose of BNR162b2 actually contains 30 micrograms of mRNA. And in addition, there are the lipids, salts, sucrose and water.
This means that by my calculations, every shot of this vaccine contains around 2000 billion mRNA strands that encode the stabilised spike protein. At 0,53*10^-21 grams per RNA nucleotide, this represents ~25 petabyte of mRNA per injection. #cantwait
If this doesn't give you the shivers I don't know what will:
Read 7 tweets
Bert Hubert 🇪🇺 Profile picture
15 Jul 20
So the fine writeup of SIGRed (CVE-2020-1350) includes a brief discussion of a neat technique to make a Microsoft browser perform DNS lookups to arbitrary nameservers, which can then also be infected. /cc @EyalItkin & @omriher 1/9 research.checkpoint.com/2020/resolving…
Normally, you can't really do DNS lookups using the DNS protocol from browsers. Sure, the browser will resolve names for you, but it chooses how to do that. You can't direct the query anywhere, or do non-standard lookups. This is pretty good. 2/9
But what if you really really want to talk to a nameserver, for example to attack it? Browsers do speak HTTP, and do so very well. Some browsers, notably from Microsoft, are even prepared to send HTTP queries to the DNS port (53). 3/9
Read 11 tweets
Bert Hubert 🇪🇺 Profile picture
7 Apr 20
Governments are pondering if apps can help them perform contact tracing for COVID-19 infected people. The "why" of this is explained very well here: 1/16
Some countries just track the location of everyone all the time and perform matching on a government server. This is a privacy nightmare. 2/16
www1.cbn.com/cbnnews/israel…
Can we do better? An international team has designed a protocol that allows tracing, while preserving privacy: DP-3T
/cc @marcelsalathe @mikarv 3/16
Read 16 tweets

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