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Daniel Zhen Ye Sin

@danielsin909.bsky.social
126 followers 287 following 9 posts

Phages! Microbiota! MGEs! All about the little critters living around and in us :) PhD Student at the Penadés lab, Imperial College London

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Reposted by Daniel Zhen Ye Sin
Clément Canonne @ccanonne.github.io · 17h
This point regarding AI-produced proofs is of course not new, but is beautifully put here. www.quantamagazine.org/is-ai-the-en... @quantamagazine.org
It’s as if you were teleported to the peak of a tall mountain. Surrounded by fog, you have no idea where you are, or what’s around you. You do not know how your mountain connects to others, and you have no equipment to help you explore, no way to help someone else join you. If you had climbed the mountain yourself, you would have experienced how the human body adapts to altitude and changes in oxygen levels. You might have had to invent tools to navigate, to climb steep cliffs, or to make a shelter. You might have encountered a fellow explorer, gotten lost together in a hidden valley, and found a plant that could be turned into a life-saving medicine.

Instead you’re perched on the peak but in the dark, while the maker of the teleportation machine tells you that it can explore the wilderness better than any human.
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Jorge Moura de Sousa @jmouradesousa.bsky.social · 20/09/2026
Happy to see our work on the evolution of antiviral repertoires in P4-like satellites and their P2-like helper phages (check out the 🧵 👇) out in @narjournal.bsky.social 🔗 doi.org/10.1093/nar/... #phagesky #MicroSky #evosky
doi.org
Shuttling, swapping, and mixing: the rapid modular evolution of antiviral repertoires in temperate phages and their satellites
Abstract. Interactions between bacteria, bacteriophages, and their satellites are shaped by a myriad of defence and counter-defence mechanisms. Here, we id
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Daniel Zhen Ye Sin @danielsin909.bsky.social · 16/09/2026
Super happy to see this story out!! Congrats Thomas!!
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Reposted by Daniel Zhen Ye Sin
Jakob T Rostøl @jakob-tr.bsky.social · 12/08/2026
Congratulations to @antiphagexu.bsky.social for passing his viva and being a newly minted doctor 🍾🧬🥼And big thanks to Franklin Nobrega and Nick Croucher for their (allegedly) thorough examination 🤝 @jrpenades.bsky.social
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Jakob T Rostøl @jakob-tr.bsky.social · 17/06/2026
Came across phage Sushi supporting Norway at the pub yesterday. Likely place for her to be
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Tiago Costa @tcostalab.bsky.social · 28/05/2026
Our new study reveals how bacterial toxins are physically captured through a sequential, concentration-dependent assembly mechanism before secretion via the T6SS. Fantastic collaboration with @fillouxlab.bsky.social. Congrats Patricia & Ambre for leading this work. Paper here: shorturl.at/O31Vn
shorturl.at
Molecular basis of type VI secretion system effector loading - Nature Microbiology
Structural analysis reveals that the type VI secretion system effector cargo is enclosed within hexameric Hcp3 rings that form sequentially to enable effector loading and delivery by the Pseudomonas aeruginosa H3-type VI secretion system.
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Jakob T Rostøl @jakob-tr.bsky.social · 20/05/2026
Like a prophage being awakened from its slumber, the phage field has seen a lot of renewed activity during the last decade. Check out our new @natrevmicro.nature.com review on the temperate phage life cycle here to stay up-to-date 🧫🦠 www.nature.com/articles/s41...
nature.com
Revisiting the life cycle of temperate phages - Nature Reviews Microbiology
The life cycle of temperate bacteriophages involves lytic or lysogenic cycles and has historically served as a model for studying genetic regulation. This Review provides an updated overview of these ...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 20/05/2026
Phages communicate across species to shape microbial ecosystems -in @cellcellpress.bsky.social by Francisca Gallego-del-Sol, @danielsin909.bsky.social, and Cora Chmielowska et al from @albertomarina.bsky.social, José Penadés www.cell.com/cell/fulltex... #PhageSky #Bacillus #AimP
cell.com
Phages communicate across species to shape microbial ecosystems
Gallego-del-Sol et al. show that arbitrium-coding phages can sense non-cognate peptide signals from other phages to regulate lysis-lysogeny decisions. This crosstalk affects lysis-lysogeny outcomes of...
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Daniel Cazares @danielcazares.bsky.social · 11/05/2026
Happy to share that our latest research on the eco-evolutionary dynamics of MDR plasmids and PDPs is now out (open access vAuthor) in The ISME Journal doi.org/10.1093/isme... Here, we explored how plasmid-dependent phages (PDPs) act as a selective pressure against the spread of multidrug resistance
doi.org
Eco-evolutionary responses to plasmid-dependent phage constrain the spread of multidrug resistance plasmids
Abstract. Phage therapy offers a promising alternative to antibiotics for treating multidrug-resistant infections. Plasmid-dependent phages (PDPs) are part
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Rafal Mostowy @rafalmostowy.bsky.social · 29/04/2026
🎉 New in @plosbiology.org: Temperate phages of Klebsiella pneumoniae show capsule-driven host tropism — but how? The working assumption was depolymerases: enzymes that chew through the bacterial sugar capsule. Turns out that's not the whole story. 🧵 journals.plos.org/plosbiology/...
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Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
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Simon Hammann @simonhammann.bsky.social · 20/04/2026
Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.
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Kotaro Chihara @kochihara.bsky.social · 20/04/2026
Happy to share our new work on how phages escape bacterial immunity. We show that a phage homing endonuclease drives segmental amplification of anti-defense genes, pointing to a versatile and rapid mode of adaptation. www.nature.com/articles/s41... #PhageSky #MicroSky
nature.com
Phage homing endonuclease amplifies anti-defense genes to evade bacterial immunity - Nature Communications
Phages employ diverse counter-defense strategies to overcome bacterial immune systems. Here, the authors reveal that the phage homing nuclease SegB facilitates immune evasion by promoting the segmenta...
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Wendy Figueroa @wfigueroac3.bsky.social · 06/04/2026
Out in @natcomms.nature.com! We show that while most MGEs are blocked by RM systems🛡️, the chromosome is still mobile! 🧬And that cells with defective systems act as "gateways" for HGT. Can you find the hidden Easter egg🐇🥚? Hint: There's a nod to my 🇲🇽 heritage in one of the figures! rdcu.be/fbUC8
rdcu.be
Immune-deficient bacteria serve as gateways to genetic exchange and microbial evolution
Nature Communications - The efficiency of horizontal gene transfer between different bacterial lineages is often unclear. Here, Figueroa et al. show that lateral transduction is the primary driver...
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José R Penadés @jrpenades.bsky.social · 05/04/2026
Latest from the lab! Between clinical S. aureus, most gene transfer mechanisms are blocked, yet lateral transduction remains highly efficient. Restriction modification-defective strains act as gateways for horizontal gene transfer, enabling DNA flow across populations. rdcu.be/fbNQK
rdcu.be
Immune-deficient bacteria serve as gateways to genetic exchange and microbial evolution
Nature Communications - The efficiency of horizontal gene transfer between different bacterial lineages is often unclear. Here, Figueroa et al. show that lateral transduction is the primary driver...
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Aude Bernheim @audeber.bsky.social · 02/04/2026
How diverse is bacterial immunity ? We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems. 👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie... Explore them here defensefinder.mdmlab.fr/wiki/refseq_...
science.org
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José R Penadés @jrpenades.bsky.social · 31/03/2026
This paper started as an idea @albertomarina.bsky.social had many years ago… which of course means he was right all along 😄. Some of us just needed a few years (and a lot of experiments) to catch up. Grateful (and slightly humbled) to be part of this. Thanks Alberto! www.cell.com/cell/fulltex...
cell.com
Phages communicate across species to shape microbial ecosystems
Gallego-del-Sol et al. show that arbitrium-coding phages can sense non-cognate peptide signals from other phages to regulate lysis-lysogeny decisions. This crosstalk affects lysis-lysogeny outcomes of...
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Daniel Zhen Ye Sin @danielsin909.bsky.social · 01/04/2026
Hey #Phagesky [Ph]ans! My first work with the Penadés lab is out! Come read how arbitrium-coding phages sense non-cognate Arbitrium signals from other phages to influence their lysis-lysogeny decisions. www.cell.com/cell/fulltex...
cell.com
Phages communicate across species to shape microbial ecosystems
Gallego-del-Sol et al. show that arbitrium-coding phages can sense non-cognate peptide signals from other phages to regulate lysis-lysogeny decisions. This crosstalk affects lysis-lysogeny outcomes of...
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Reposted by Daniel Zhen Ye Sin
Franklin Nobrega @fnobrega.bsky.social · 03/03/2026
In our latest work, we characterise the Tmn defence system. We reveal plasmolysis as a new way to block phage infection, dramatically reducing secondary infections.
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Jorge Moura de Sousa @jmouradesousa.bsky.social · 02/03/2026
➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔 🧵👇
biorxiv.org
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Paula Ramiro-Martínez @paularamiro.bsky.social · 27/01/2026
New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...
pnas.org
Plasmid mutation rates scale with copy number | PNAS
Plasmids are extrachromosomal DNA molecules that spread by horizontal transfer and shape bacterial evolution. Plasmids are typically present at mul...
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Daniel Zhen Ye Sin @danielsin909.bsky.social · 05/02/2026
MGE fans! Come check out this amazing story from my great friend (and passable labmate) @tomipou.bsky.social!
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Alvaro San Millan @sanmillan.bsky.social · 22/10/2025
New paper with my (amazing) friend and mentor @jrpenades.bsky.social Really looking forward to see what plasmid aficionados think of this one!! With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others www.cell.com/cell-reports...
cell.com
Non-conjugative plasmids limit their mobility to persist in nature
Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...
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José R Penadés @jrpenades.bsky.social · 14/10/2025
Our latest work reveals that arbitrium phages cross-communicate across species! These tiny viruses “listen” to signals from others, coordinating lysis-lysogeny decisions across species. Original idea from @albertomarina.bsky.social and, as usual, he was right. www.biorxiv.org/content/10.1...
biorxiv.org
Phages communicate across species to shape microbial ecosystems
Arbitrium is a communication system that helps bacteriophages decide between lysis and lysogeny via secreted peptides. In arbitrium, the AimP peptide binds its cognate AimR receptor to repress aimX ex...
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Daniel Zhen Ye Sin @danielsin909.bsky.social · 14/10/2025
Good morning Phage [Ph]ans! I'm so stoked to share my first preprint with the @jrpenades.bsky.social lab! We show that phages can use the arbitrium system to crosstalk and regulate lysis-lysogeny, which has huge implications in how phages shape microbial communities! www.biorxiv.org/content/10.1...
biorxiv.org
Phages communicate across species to shape microbial ecosystems
Arbitrium is a communication system that helps bacteriophages decide between lysis and lysogeny via secreted peptides. In arbitrium, the AimP peptide binds its cognate AimR receptor to repress aimX ex...
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Reposted by Daniel Zhen Ye Sin
Zamin Iqbal @zaminiqbal.bsky.social · 25/09/2025
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n
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Daniel Zhen Ye Sin @danielsin909.bsky.social · 10/09/2025
Incredible work!! Go check it out!
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RM @rsbmilne.bsky.social · 08/05/2025
Virtual Virology is back - our first ever phage session. Do join us...
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Fernando Rossine @fernpizza.bsky.social · 21/02/2025
I'm so happy that I can finally share the results of my first postdoc paper with @baym.lol!!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics! (1/n) www.biorxiv.org/content/earl...
biorxiv.org
Intracellular competition shapes plasmid population dynamics
Conflicts between levels of biological organization are central to evolution, from populations of multicellular organisms to selfish genetic elements in microbes. Plasmids are extrachromosomal, self-r...
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Xu Kuang @antiphagexu.bsky.social · 26/02/2025
It’s a rare day these days when me and my boss are both at work! But it’s always wonderful when he’s here - he buy me clothes from NYC and he help me with preparing todays lab meeting on the weekend! Really grateful to have such an amazing D2D supervisor!
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 12/02/2025
Chimeric infective particles expand species boundaries in phage inducible chromosomal island mobilization www.biorxiv.org/content/10.1101/202…
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