David Bikard
@dbikard.bsky.social
Bacterial Immunity and Synthetic Biology enthusiast. Head of Lab at Institut Pasteur. Co-Founder of Eligo Bioscience.
Congratulations Rotem Sorek @soreklab.bsky.social on receiving the Gruber prize today in Stockholm
August 23, 2025 at 9:24 AM
Congratulations Rotem Sorek @soreklab.bsky.social on receiving the Gruber prize today in Stockholm
I will be recruiting new postdocs with start dates end 2025 - early 2026. If you'd like to work at the Pasteur Institute in the heart of Paris surrounded by amazing scientists, reach out to discuss possible projects on SynBio / Bacterial Immunity!
May 18, 2025 at 3:20 PM
I will be recruiting new postdocs with start dates end 2025 - early 2026. If you'd like to work at the Pasteur Institute in the heart of Paris surrounded by amazing scientists, reach out to discuss possible projects on SynBio / Bacterial Immunity!
Typical lab meeting in France with a few small pastries :-) Thank you Paul !
March 12, 2025 at 4:51 PM
Typical lab meeting in France with a few small pastries :-) Thank you Paul !
More importantly, in an infant rabbit disease model, EB003 mitigated clinical symptoms and accelerated epithelial repair at therapeutically relevant doses.
March 4, 2025 at 12:31 PM
More importantly, in an infant rabbit disease model, EB003 mitigated clinical symptoms and accelerated epithelial repair at therapeutically relevant doses.
We could further show that EB003 can drastically reduce bacterial burden in mouse colonization model.
March 4, 2025 at 12:31 PM
We could further show that EB003 can drastically reduce bacterial burden in mouse colonization model.
Critically, EB003 kills target bacteria with no detectable toxin release.
March 4, 2025 at 12:31 PM
Critically, EB003 kills target bacteria with no detectable toxin release.
To overcome this, we had to engineer our capsid to make it resistant to intestinal proteases.
March 4, 2025 at 12:31 PM
To overcome this, we had to engineer our capsid to make it resistant to intestinal proteases.
When checking the stability of our delivery vehicle during passage through the mouse GI tract, we however had the bad surprise that the side tail fibers were degraded.
March 4, 2025 at 12:31 PM
When checking the stability of our delivery vehicle during passage through the mouse GI tract, we however had the bad surprise that the side tail fibers were degraded.
The side tail fibers were modified to recognize the O157 antigen, ensuring efficient delivery into the vast majority of clinical isolates of O157 E. coli. High-throughput screening of tail fiber chimeras was used to identify the best candidate.
March 4, 2025 at 12:31 PM
The side tail fibers were modified to recognize the O157 antigen, ensuring efficient delivery into the vast majority of clinical isolates of O157 E. coli. High-throughput screening of tail fiber chimeras was used to identify the best candidate.
To ensure targeted delivery, we engineered a capsid derived from bacteriophage λ. The tail tip, gpJ, was modified to ensure recognition of a primary receptor, OmpC, that is consistently expressed by E. coli in the gut environment.
March 4, 2025 at 12:31 PM
To ensure targeted delivery, we engineered a capsid derived from bacteriophage λ. The tail tip, gpJ, was modified to ensure recognition of a primary receptor, OmpC, that is consistently expressed by E. coli in the gut environment.
Finally we show how AriB is a 2-metal ion ribonuclease which leaves 3'OH and 5'P extremities after cleavage.
February 5, 2025 at 2:43 PM
Finally we show how AriB is a 2-metal ion ribonuclease which leaves 3'OH and 5'P extremities after cleavage.
AF3 models with nucleic acids are not always reliable, but in our case AF3 placed the catalytic site of AriB right in front of the tRNA cleavage sites that we mapped experimentally! This gave us some confidence in the model.
February 5, 2025 at 2:43 PM
AF3 models with nucleic acids are not always reliable, but in our case AF3 placed the catalytic site of AriB right in front of the tRNA cleavage sites that we mapped experimentally! This gave us some confidence in the model.
A puzzling observation regarding AriB is that it forms a symmetric homo-dimer but recognizes an asymmetric molecule and makes a single nick. AF3 gave use great insights into this interaction.
February 5, 2025 at 2:43 PM
A puzzling observation regarding AriB is that it forms a symmetric homo-dimer but recognizes an asymmetric molecule and makes a single nick. AF3 gave use great insights into this interaction.
We found that base modifications are not required for AriB recognition. AriB will even efficiently a fully unmodified in vitro transcript. Specific base interactions in the stem of the anti-codon stem-loop are however critical.
February 5, 2025 at 2:43 PM
We found that base modifications are not required for AriB recognition. AriB will even efficiently a fully unmodified in vitro transcript. Specific base interactions in the stem of the anti-codon stem-loop are however critical.
We showed with @artemisaev.bsky.social that expressing the Lysine, Threonine and Asparagine tRNA from T5 can fully rescue E. coli growth when PARIS is triggered.
February 5, 2025 at 2:43 PM
We showed with @artemisaev.bsky.social that expressing the Lysine, Threonine and Asparagine tRNA from T5 can fully rescue E. coli growth when PARIS is triggered.
But phages are not phazed :-) Some of them encode their own tRNA variants in order to bypass this immunity mechanism. This includes T5 which carries 24 tRNAs including a Lysine and a Threonine tRNA with mutations that block AriB cleavage.
February 5, 2025 at 2:43 PM
But phages are not phazed :-) Some of them encode their own tRNA variants in order to bypass this immunity mechanism. This includes T5 which carries 24 tRNAs including a Lysine and a Threonine tRNA with mutations that block AriB cleavage.
Ma chronique pour les Echos sur la grande migration académique de X vers BlueSky
www.lesechos.fr/idees-debats...
La dernière décennie a connu une adoption massive des réseaux sociaux par le milieu académique, Twitter devenant un outil essentiel pour suivre les dernières avancées scientifiques.(1/X)
www.lesechos.fr/idees-debats...
La dernière décennie a connu une adoption massive des réseaux sociaux par le milieu académique, Twitter devenant un outil essentiel pour suivre les dernières avancées scientifiques.(1/X)
January 27, 2025 at 8:19 AM
Ma chronique pour les Echos sur la grande migration académique de X vers BlueSky
www.lesechos.fr/idees-debats...
La dernière décennie a connu une adoption massive des réseaux sociaux par le milieu académique, Twitter devenant un outil essentiel pour suivre les dernières avancées scientifiques.(1/X)
www.lesechos.fr/idees-debats...
La dernière décennie a connu une adoption massive des réseaux sociaux par le milieu académique, Twitter devenant un outil essentiel pour suivre les dernières avancées scientifiques.(1/X)
You can easily save figures for publications in svg, png or html formats.
December 13, 2024 at 4:48 PM
You can easily save figures for publications in svg, png or html formats.
You can add tracks which are fully customizable (they are basically just Bokeh figures). We provide a few handy track types to easily display data from pandas DataFrames.
December 13, 2024 at 4:48 PM
You can add tracks which are fully customizable (they are basically just Bokeh figures). We provide a few handy track types to easily display data from pandas DataFrames.
No server required, everything happens in the browser. You can provide GFF, GenBank, or GFF + FASTA. It's as easy to use as this.
December 13, 2024 at 4:48 PM
No server required, everything happens in the browser. You can provide GFF, GenBank, or GFF + FASTA. It's as easy to use as this.
Great talk by my student Paul Rochette at the BioConvS innovation day. It's great to see so much SynBio / Biotech energy in the Paris region!
November 28, 2024 at 11:46 AM
Great talk by my student Paul Rochette at the BioConvS innovation day. It's great to see so much SynBio / Biotech energy in the Paris region!