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plosbiology.org
#DeepMutationalScanning (DMS) experiments are limited by gene size due to library complexity & costs. @christianlandry.bsky.social &co develop an efficient & cost-effective barcoded cloning strategy for plasmid-based DMS libraries that enables study of large genes @plosbiology.org 🧪 plos.io/4abhyUf
Strategy to generate a DMS plasmid library for Your Favorite Gene (YFG) using short, degenerate libraries. 1. Segmentation of YFG into sub-fragments, each fragment corresponding to a DNA region to be synthesized. The same approach can be applied to promoter and terminator regions, if desired. 2. Example of a pool of degenerate oligonucleotides (oPool) derived from one YFG fragment associated with DNA barcodes. Each oPool contains: (i) ~40 bp of homology upstream of the YFG fragment of interest, (ii) the YFG fragment sequence with a single NNK codon, (iii) BsaI cloning sites, (iv) a DNA barcode composed of codon-position specific regions and six degenerate nucleotides (N), and (v) a conserved i7 primer binding site (PBS_i7) present in all oPools and used for rapid and efficient sequencing library preparation. Current oligonucleotide synthesis technologies allow for a total of nine degenerate positions per fragment: three are used for the degenerate codon (NNK), and six for the barcode. A complete list of all oPool sequences and their detailed composition is provided in S1 Table. 3. Protocol for constructing YFG DMS plasmid library from oPools using two cloning steps that maintain the physical barcode-mutation association. The libraries of oPools are cloned into the plasmid template by Gibson cloning. Following this step, for each fragment, a necessary short-read sequencing using PBS_i5 (included in the 5′ sequencing primer) and PBS_i7 is performed to associate each barcode with its corresponding mutation and to assess both barcode diversity per mutation and mutation coverage for the whole fragment. The ultimate step consists in Golden Gate cloning of the missing 3′ gene fragment between the degenerate fragment and the barcode. An additional short-read sequencing step of the barcodes can be performed to make sure that coverage and diversity have been maintained. Figure created in BioRender.
February 11, 2026 at 7:19 PM
atanas-g-atanasov.bsky.social
🧵 [4/6]
Codon optimization, chaperone tuning, protease knockouts—boost expression yields with precision!

🌐 #Bioengineering #ExplorDHT #DHPSP
@castltrastondrs.bsky.social @michaeldonoian.bsky.social @mikaiaalto.bsky.social @dereksylvester.bsky.social @nicksevillaz.bsky.social
February 6, 2026 at 2:10 PM
thaisdalsasso.bsky.social
Congrats @marco-guerreiro.bsky.social. @estukenbrock.bsky.social and colleagues on this exciting study linking codon optimization and adaptive translation to lifestyle transitions in a group of fungi.
January 26, 2026 at 9:34 AM
biorxivpreprint.bsky.social
mRNAfold: Co-optimization of Global Stability, Local Structure, and Codon Choice via Suboptimal Folding https://www.biorxiv.org/content/10.64898/2026.01.23.701221v1
January 24, 2026 at 1:47 AM
avianbiology.bsky.social
NEW PAPER: vitellogenin expression and DNA methylation in the VTG2 promoter changed between pre- and early breeding in dark-eyed juncos, indicating that liver epigenetic regulation may contribute to seasonal timing of reproduction.

➡️ vist.ly/4nzre

#ornithology #birds #epigenetics 🪶
Dark-eyed junco. Photo: Wikimedia commons, Cephas. Fig. 1 from the article: Liver expression of the vitellogenin gene (VTG2) was greater in birds sampled during the early-breeding period compared with the pre-breeding period. Fig. 3 from the article: Percent DNA methylation in liver tissue of each of three CpG sites located 900–990 bp upstream from the start codon of VTG2 from individuals sampled during the pre-breeding or during the early-breeding period.
January 24, 2026 at 12:27 PM
ryanhisner.bsky.social
ORF6 is only 61 AA long, but its primary known function (shutting down nucleus-cytoplasm trafficking) is mediated by its C-terminal domain (i.e. the last few AA). This stop codon slices off those AA. This is the last variant I ever expected to see an ORF6 loss-of-function mutant in. Weird. 3/3
January 15, 2026 at 11:36 PM
labwaggoner.bsky.social
Sequences of 5′ untranslated regions in viral RNAs drive codon-usage-independent translation by blocking mRNA circularization, enabling viruses to evade the host’s codon-usage control of translation @nature.com
www.nature.com/articles/d41... on
www.nature.com/articles/s41...
January 9, 2026 at 2:33 AM
biorxiv-bioeng.bsky.social
Codon Deoptimization of Multispecific Biologics Reduces Mispairing During Transient Mammalian Protein Expression https://www.biorxiv.org/content/10.64898/2026.01.05.694717v1
January 6, 2026 at 5:46 PM
rubenlgonzalez.bsky.social
A (belated!) highlight from an excellent collaboration with
@dunhamlab.bsky.social and #HouLabTJU.

In this Nat Commun paper, we combine smFRET and cryo-EM to show how the tRNA modification m¹G37 stabilizes the reading frame—and what happens when it’s missing.
Mechanistic model for +1 frameshifting suppression. The m¹G37 tRNA modification blocks expanded codon–anticodon interactions, preserving translational fidelity.
January 4, 2026 at 6:34 PM
rubenlgonzalez.bsky.social
In the absence of m¹G37, we directly visualize the formation of four, and even five, codon-anticodon base pairs on the ribosome, thereby capturing a long-standing hypothesis for +1 frameshifting.

I’ve been behind on highlighting a few recent papers—more posts coming soon.
January 4, 2026 at 6:34 PM
zeynepbaharoglu.bsky.social
🧬❄️ RNA Modifications Newsletter - Jan 2026 is out!
RNA mods, ribosome remodeling, codon effects, nanopore detection, translation under stress - winter edition

❄️🧫From hypoxia-driven rRNA methylation to tRNA-linked virulence and ribosome structure.
#RNAsky #RNAbiology #Ribosome #microsky
RNA Modifications Newsletter - January 1st, 2026 - Winter Edition ❄️
Issue #7 - Happy new year!
rnamodifupdates.substack.com
January 2, 2026 at 10:43 AM
jnsq.org
Here you go. There's a premature stop codon in what would be their ADH7 gene, so they don't produce alcohol dehydrogenase. Same with a lot of other mammals. royalsocietypublishing.org/rsbl/article...
Genetic evidence of widespread variation in ethanol metabolism among mammals: revisiting the ‘myth' of natural intoxication
Abstract. Humans have a long evolutionary relationship with ethanol, pre-dating anthropogenic sources, and possess unusually efficient ethanol metabolism,
royalsocietypublishing.org
December 31, 2025 at 1:19 AM
narjournal.bsky.social
⭐NAR Breakthrough! ⭐

🔬 #tRNA modifications fine-tune #translation; in yeast, their loss slows #ribosomes at hard-to-read codon pairs, causing collisions ⚠️, and cells deploy quality control pathways to prevent #proteotoxicstress and ensure survival.
🧬Read more: doi.org/10.1093/nar/...
December 23, 2025 at 4:03 PM
plosbiology.org
A reduced rate of synonymous site evolution is often presented as key evidence for #selection on #SynonymousMutations. However, this study shows that paradigmatic low rate in the first 10 codons of bacterial genes is well explained by mutation, NOT selection @plosbiology.org 🧪 plos.io/4s4tIoY
Top row: Substitution rates by 5′ codon position comparing the Escherichia coli– Escherichia fergusonii ancestor to E. coli. Bottom row: Substitution rates by 5′ codon position comparing the Bacillus toyonensis–Bacillus anthracis ancestor to B. toyonensis. In each row, from left, the panels show: 1. Synonymous substitution rates (Ks); 2. non-synonymous substitution rates (Ka), and 3. the ratio between the two (Ka/Ks).
December 17, 2025 at 8:55 AM
plosbiology.org
A reduced rate of synonymous site evolution is often presented as key evidence for #selection on #SynonymousMutations. However, this study shows that paradigmatic low rate in the first 10 codons of bacterial genes is well explained by mutation, NOT selection @plosbiology.org 🧪 plos.io/4s4tIoY
Top row: Substitution rates by 5′ codon position comparing the Escherichia coli– Escherichia fergusonii ancestor to E. coli. Bottom row: Substitution rates by 5′ codon position comparing the Bacillus toyonensis–Bacillus anthracis ancestor to B. toyonensis. In each row, from left, the panels show: 1. Synonymous substitution rates (Ks); 2. non-synonymous substitution rates (Ka), and 3. the ratio between the two (Ka/Ks).
December 16, 2025 at 1:55 PM
kevinkaichuang.bsky.social
Finetune a codon-level language model with 30k tryptophan synthases, then generate diverse, functional, enzymes with broad substrate scopes.

Théophile Lambert @jsunn-y.bsky.social @francesarnold.bsky.social

www.biorxiv.org/content/10.1...
December 16, 2025 at 12:25 AM
biorxivpreprint.bsky.social
Widespread synchronization of codon usage in functionally related genes https://www.biorxiv.org/content/10.64898/2025.12.10.693408v1
December 13, 2025 at 3:32 AM
beth.lgbt
the three “stop” codons signal the halting of protein synthesis in a cell, but different organisms have different levels of tRNA that match those codons, so you can literally run out if you don’t use the right codon (while doing genetic engineering)
DNA codon table showing all combinations of 3 letter codons for the letters T C A and G and what amino acid they encode
July 11, 2023 at 4:20 PM
chasewnelson.bsky.social
So, we may be 100% certain that dN/dS=1.5 for a codon/branch is what did happen. But it might have just been chance that this is what happened, and the real expected ratio given all mutational and selective pressures (if we were omniscient) was dN/dS=1.0? 2/
November 19, 2024 at 10:23 AM
chasewnelson.bsky.social
Totally with you there. One reason I like to play devil’s advocate with dN/dS is simply that, if a “positively selected” codon is identified it’s often concluded it’s especially important. But if it’s a false-positive due to relaxation of purifying selection, the opposite is true. Such a fun topic!
November 19, 2024 at 1:10 PM
biorxivpreprint.bsky.social
A conserved opal termination codon optimizes a temperature-dependent tradeoff between protein production and processing in alphaviruses https://www.biorxiv.org/content/10.1101/2024.08.21.609082v1
A conserved opal termination codon optimizes a temperature-dependent tradeoff between protein production and processing in alphaviruses https://www.biorxiv.org/content/10.1101/2024.08.21.609082v1
Alphaviruses are enveloped, single-stranded, positive-sense RNA viruses that often require transmiss
www.biorxiv.org
August 22, 2024 at 9:17 PM
eorsi.bsky.social
This is just because ! worked with R. sphaeroides during my PhD and I was quite familiar with the system. The cas9 sequence we used is codon harmonized to the GC content of R. sphaeroides (69%) which is quite similar to the one of C. necator (66%). So, we thought to give it a try!
November 25, 2024 at 4:42 PM
cedric-gobet.bsky.social
🧬 Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation
www.biorxiv.org/content/10.1...
April 10, 2025 at 6:40 AM
atinygreencell.bsky.social
It highlights the dominant codon in each and u can flip back and forth, at least
February 13, 2025 at 8:17 PM
asimovbio.bsky.social
We built a codon optimizer that boosts expression of clinically-relevant transgenes up to 7x. We’ve compared our algorithm to five other codon optimizers available on the market, and results suggest that our algorithm is consistently superior across genes of interest.

So why does this matter?
November 22, 2024 at 8:50 PM