Patrick Barendse

55 posts

Patrick Barendse

Patrick Barendse

@BarendsePatrick

#PhD candidate Biochemistry @DCSwarts @WUR @patrickbarendse.bsky.social

Wageningen, Netherlands Katılım Ağustos 2013
185 Takip Edilen129 Takipçiler
Patrick Barendse retweetledi
Daan C. Swarts
Daan C. Swarts@DCSwarts·
Out now in @MolecularCell: Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA cell.com/molecular-cell… Most long-A pAgos interfere with invading DNA solo. Why then are cyanobacterial pAgos co-encoded with a Cas4-like protein? A 🧵
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Patrick Barendse
Patrick Barendse@BarendsePatrick·
Check this out if you work on prokaryotic immunity! Amazing how a 'simple' question to @SumanthMutte 4 years ago turned into this. Did not expect the first co-first author story of my PhD on prokaryotic Argonautes to be a bioinformatic study into DNA repair proteins
Daan C. Swarts@DCSwarts

🔥New paper! 🔥 Distribution of bacterial DNA repair proteins and their co-occurrence with immune systems (cell.com/cell-reports/f…) It started with a simple question: Are certain prokaryotic immune systems always (or never) encoded with specific DNA repair proteins?...

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Patrick Barendse retweetledi
Daan C. Swarts
Daan C. Swarts@DCSwarts·
This is 🔥🔥🔥! @MartinPacesa, Lennart Nickel, @befcorreia @sokrypton, et al. developed BindCraft - an open-source pipeline to design de novo binders for basically any protein of interest. We asked if we could design binders for CbAgo - a DNA-guided DNA interfering Argonaute..
Martin Pacesa@MartinPacesa

We updated our BindCraft preprint with lots of new exciting results! We release all our binder sequences and models, include more in silico analysis, novel design targets, and present AAV retargeting to specific cell types using de novo binders! biorxiv.org/content/10.110…

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Patrick Barendse
Patrick Barendse@BarendsePatrick·
Did you know that no natural inhibitors of prokaryotic Argonautes have been described (yet)? Together with @MartinPacesa and Lennart Nickel, we designed our own de novo pAgo inhibitors! Check out these and other de novo protein designs in the updated Bindcraft preprint!
Martin Pacesa@MartinPacesa

Additionally, we designed binders against another large nuclease – the prokaryotic Argonaute protein. Together with @BarendsePatrick and @DCSwarts we show that are our binders can inhibit Argonaute cleavage activity!

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Patrick Barendse
Patrick Barendse@BarendsePatrick·
Such a powerful protein binder design pipeline, and now with even more useful applications! Like guiding AAVs to specific cell surface receptors, neutralizing allergens, and inhibiting nucleases like Cas9 and pAgo!
Martin Pacesa@MartinPacesa

We updated our BindCraft preprint with lots of new exciting results! We release all our binder sequences and models, include more in silico analysis, novel design targets, and present AAV retargeting to specific cell types using de novo binders! biorxiv.org/content/10.110…

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Patrick Barendse retweetledi
Martin Pacesa
Martin Pacesa@MartinPacesa·
v1.2.0 of BindCraft released on github. Includes improvements to the Colab notebook, new design protocol options, several critical bug fixes in the run script, QoL improvements, and streamlining of the installation script.
Martin Pacesa@MartinPacesa

Have you ever wanted to design protein binders with ease? Today we present 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕, a user-friendly and open-source pipeline that allows to anyone to create protein binders de novo with high experimental success rates. @befcorreia @sokrypton biorxiv.org/content/10.110…

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Patrick Barendse retweetledi
The Nobel Prize
The Nobel Prize@NobelPrize·
BREAKING NEWS The 2024 #NobelPrize in Physiology or Medicine has been awarded to Victor Ambros and Gary Ruvkun for the discovery of microRNA and its role in post-transcriptional gene regulation.
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Patrick Barendse retweetledi
Martin Pacesa
Martin Pacesa@MartinPacesa·
Have you ever wanted to design protein binders with ease? Today we present 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕, a user-friendly and open-source pipeline that allows to anyone to create protein binders de novo with high experimental success rates. @befcorreia @sokrypton biorxiv.org/content/10.110…
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Patrick Barendse retweetledi
green mechanobiology
green mechanobiology@GreenMechanobio·
Cell walls are crucial in all aspects of plant life, yet challenging to study. PhD Maarten Besten, our chemistry superman, likes a challenge and designed a modular probe toolbox for live 5D plant cell wall imaging. We present: CarboTag. A 🧵 biorxiv.org/content/10.110…
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Patrick Barendse retweetledi
Daan C. Swarts
Daan C. Swarts@DCSwarts·
Super proud on @BalwinaK , who successfully defended her PhD thesis "short and sweet, on short pAgos", and was awarded with a cum laude PhD degree! Excellent thesis, defense, and defense party ;) Bel is the first PhD graduating from my group. Thanks for the adventure Bel!
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Patrick Barendse retweetledi
Daan C. Swarts
Daan C. Swarts@DCSwarts·
The long-expected manuscript on the characterization of catalytically inactive long-b pAgos. Like short pAgos, they act together with (variable) associated effector proteins. Great work! nature.com/articles/s4146…
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Patrick Barendse retweetledi
Daan C. Swarts
Daan C. Swarts@DCSwarts·
❗️preprint alert!❗️ Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA biorxiv.org/content/10.110… We are excited to share our newest study where we uncover how the SPARTA immune system is activated! 🧵(1/14)
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Patrick Barendse retweetledi
Daan C. Swarts
Daan C. Swarts@DCSwarts·
I am very excited and grateful to be awarded a Vidi grant to further consolidate the Argonaute research in my group! Many thanks to everyone who made this possible. Vacancies for PhD and PD positions will be posted soon :)
NWO Funding@NWOFunding

Researchers from the NWO domains, as well as from @ZonMw will receive Vidi grants of up to 800,000 euro. This will enable the laureates to develop an innovative line of research over the next five years and further expand their own research group. nwo.nl/en/news/97-lea…

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Patrick Barendse retweetledi
Daan C. Swarts
Daan C. Swarts@DCSwarts·
We are looking for a new colleague! The Laboratory of Biochemistry has a vacancy for a staff scientist proteomics expert. Come join us :D wur.nl/nl/vacature/se…
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Keşfet

@MolecularCell @SumanthMutte @pilar_bobadilla @DCSwarts @MartinPacesa @befcorreia @sokrypton @LOlijslager