Out Now! Tryptophanase disruption promotes insect–bacterium mutualism #MicroSky
28.02.2026 06:41
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Out Now! Tryptophanase disruption promotes insect–bacterium mutualism #MicroSky
Out Now! Skin androgens regulate Staphylococcus aureus pathogenicity via quorum sensing #MicroSky
New paper alert: Paralog interference contributes to the preservation of genetic redundancy www.cell.com/current-biol...
Reposting this paper now with a working link! 😅 www.sciencedirect.com/science/arti...
I try reaching out and wasn’t so lucky, if you do get an answer, could you please let me know? Thanks so much!
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.
#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
A new paper from the lab on virus-like particles called eCISs www.nature.com/articles/s41...
How bacteria evolved thousands of precision nanoinjectors?
Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
50 million tons of PET are produced annually, and from this, only 10% is recycled. PETBuster opens the door for PET fermentation, helping us close the PET carbon cycle. Moreover, P. putida is “easy” to engineer, so we can further optimize PETBuster - stay tuned!
Put together, breaking the polymer, plus eating the resulting small molecules, PETBuster can degrade 90% of PET in 21 days while maintaining robust growth.
PET is broken down into ethylene glycol and terephthalic acid. Thus, we also engineered P. putida to metabolize those molecules.
To engineer PETBuster, we used Pseudomonas putida as a chassis and expressed an enzyme extracellularly, capable of breaking the plastic polyethylene terephthalate, PET, into small molecules.
Paper alert!
We have created a bacterium that eats plastic! We named it PETBuster! Great work by PhD student Dekel Freund @dekel-freund.bsky.social.
www.biorxiv.org/content/10.1...
🚨 News on bioremediation! A study published in Nature reveals how by genetically modifying the bacterium Vibrio natriegens, it simultaneously degrades five toxic contaminants in industrial wastewater and saline soils. Read the full article: www.nature.com/articles/d41...
🔊New perspective piece out @genomebiolevol.bsky.social.
"The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity" 💡🌀🌈
doi.org/10.1093/gbe/...
Co-led with @mbrasovives.bsky.social and @diegoharta.bsky.social
Check out our thread! 🧵👇 (1/n)
Design stable, folded proteins using only the 10 "ancient" amino acids.
www.biorxiv.org/content/10.1...
🫵 Our daily bread: Experimental evolution of gene essentiality in bacteria!
| mBio journals.asm.org/doi/10.1128/...
@mbio.bsky.social
A wonderful collaboration between my lab and Andy Ellington and Edward Marcotte here at UT.
We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)
Looking forward to seeing David Moi's talk about Foldtree and the upcoming Foldtree II at #APSPM2026 in sunny Brisbane.
biosig.lab.uq.edu.au/strphy26/spe...
@official-smbe.bsky.social
Beautiful work from my friend @kiranrpatil.bsky.social . Gut bacteria can accumulate Forever chemicals and help us get rid of them! Happy we could contribute! www.nature.com/articles/s41...
Molecular fossils may not always be what they seem.
“Just as archaeologists know to be careful in how they interpret physical fossils, historians of protein evolution could take similar care in their interpretation of molecular fossils.”
- @lynnkamerlin.bsky.social in this co-authored article⤵️
Great work by Nitay Ahituv, Dekel Freund, and Raul Mireles @raulmireles.bsky.social
New Paper Alert! “The diversity of PET-degrading enzymes: A review”. We present a database of PET-plastic hydrolases, including sequence, structure, and function. From this, we discuss the distribution, efficiency, stability, and potential for biodegradation of PETases.
@asaflevylab.bsky.social suffers from it often, maybe he can help. I would produce a lot of biomas and then activate the expression of the toxic gene.
The future of bioremediation? Not seeding sites with super-degrader bacteria, but super-fortifying microbiomes of target locations with catabolic genes via HGT. Nature has been doing it forever 💪🏻! Eng community-level function is the way! enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
Have fun!
Good luck!
Do people in the same household share strains when they have the same species?
How many cells transmit when a strain is shared?
Can strain composition be dynamic when species composition is stable?
We answer these and related questions for the facial skin microbiome in our latest paper.
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Bite-sized solutions
A recent study found high amounts of microplastics in the human brain. This could spur funding and technological advances for plastic degradation go.nature.com/3QL4L0b
