Melanie Blokesch

Wow - big congrats Jörg 🍾🎉🎊

Brave genomes book cover

Brave genomes is finally out!😎

shop.elsevier.com/books/brave-...

www.amazon.de/Brave-Genome...

CryoET of microbes inside an animal organ? Yes it’s possible! Check out our new preprint showing how we did it! What an amazing collaboration with amazing scientists who made this possible!

Structural mechanism of the Retron-Eco7 anti-phage defense system - Nature Communications The Retron-Eco7 is a genetic element involved in anti-phage defense that encodes two effector proteins (PtuA and PtuB) and cleaves the host tRNA. Here, the authors solved the Retron-Eco7 complex struc...

www.nature.com/articles/s41...

Structural mechanism of the Retron-Eco7 anti-phage defense system

📢 We have multiple open PhD positions to study bacterial immune systems using cutting-edge cryo-EM, microbiology, and biochemistry in our group! Join us and uncover how bacterial defenses eliminate predators and engineer next-gen biotech tools.

🔥 Apply by Jan 8, 2026

Details: phd.pages.ista.ac.at

The SMC Hinge is a Selective Gate for Obstacle Bypass - Nature Communications SMC complexes are ring-shaped motors that fold DNA by extruding loops, but how they navigate large DNA obstacles is unclear. Here, Liu et al., show that SMC complexes bypass obstacles by threading obs...

The hinge bypass gate paper is finally out! doi.org/10.1038/s414...

We show how loop-extruding SMC complexes can maintain DNA entrapment while bypassing obstacles on DNA — including transcription machinery & potentially other SMCs.

A lucky convergence of 3 projects lead to the initial discovery!

Multi-omics profiling reveals atypical sugar utilization and a key membrane composition regulator in Streptococcus pneumoniae - Nature Communications The pathogen Streptococcus pneumoniae can adapt to diverse microenvironments in the human body. Here, De Bakker et al. study these adaptation responses, showing unusual sugar utilization and identifyi...

Really cool paper from @vincentdebakker.bsky.social @jonbakerlab.bsky.social now published @natcomms.nature.com #MicroSky www.nature.com/articles/s41...

Portrait von Jörg Vogel mit Zitat: Wenn es uns gelingt, das Potenzial von Phagen nutzbar zu machen, wäre das angesichts zunehmender Antibiotikaresistenzen ein vielversprechender Therapie-Ansatz.“

Angesichts zunehmender #Antibiotikaresistenzen können #Phagen ein vielversprechender Therapieansatz sein, so @jorg-vogel-lab.bsky.social @helmholtz-hiri.bsky.social. Mehr über das Potenzial von #Bakteriophagen erfahrt ihr hier: www.helmholtz-hzi.de/media-center... #WAAW2025 #Weltantibiotikawoche

🚀New preprint from our lab!
I am very excited to finally share what has been the main focus of my PhD for the past almost 3 years! It is about viral dark matter and a powerful tool we built to shed light on it. 🧬💡
Continue reading (🧵)

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.

Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.

A thread 1/8

Bacterial networks #BacNet26 in September 2026 will be chaired by @lalouxlab.bsky.social and co-chaired by @s-lab.bsky.social with @coralietesseur.bsky.social

Sneak peak on invited speakers and preliminary program:
meetings.embo.org/event/26-bac...

Why does daptomycin resistance appear so fast in Enterococcus? We finally have a clue.

DAP resistance in enterococci pops up quickly. What’s been missing is why resistance-associated membrane changes look the way they do, and why the classic path of mutations is so predictable.

Happy to share our latest NAR paper on Rel toxins targeting M. tuberculosis anti-SD region, with Tim Blower’s team (@durham.ac.uk @nebiolabs.bsky.social) and Laurent Falquet
Thanks to FRM @frm-officiel.bsky.social and CNRS @cnrsbiologie.bsky.social
academic.oup.com/nar/article-...

A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year.

A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision.

A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year.

The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.

We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...

Thanks Jesse 🤩
It’s indeed hard & some non-native English speakers know that they can never express themselves as well / effortless in their 2nd & 3rd language as in their mother tongue.
What helps nowadays is ChatGPT and we would appreciate native speakers not bitching about us using it 🫣

Shout out to people routinely working in their 2nd or 3rd language.

Yesterday I gave a 1-hour research seminar in French. Afterwards, my brain was pretty much done for the day.

Respect to the loads of scientists who do this daily (and usually a lot more effectively than me!)

Prix scientifique Suisse Marcel Benoist 2025 - Tobias J. Kippenberg Enjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.

How can we calibrate instruments that analyse planets outside our solar system and operate the computers of the future? With chip-based optical frequency combs. 🌌 🖥️

Learn more in the profile of Tobias Kippenberg, winner of the #MarcelBenoist Swiss Science Prize 2025.

Un immense merci à nos doctorants, au comité organisateur et à nos orateurs invités @mblokesch.bsky.social, F. Mechta-Grigoriou & E. Crubezy, pour la réussite de ce superbe 10e Symposium des étudiants de l’IPBS.
Bravo à toutes et à tous !

Cap sur le 11e Symposium !

Many thanks again for the kind invitation—and for the PhD students’ excellent organization and wonderful hospitality 🤩

A huge thank you to our PhD students, the organizing committee, and our guest speakers @mblokesch.bsky.social, F. Mechta-Grigoriou & E. Crubezy for making the 10th IPBS Student Symposium such a success.
Kudos to everyone involved!

On to the 11th Symposium! 🎉

#DRC faces one of the worst cholera outbreaks in a decade. Since January, over 58,000 suspected cases and 1,700 deaths have been reported.

MSF calls for coordinated action to ensure the provision of medical care, drinking water and proper sanitation.

www.doctorswithoutborders.ca/democratic-r...

Cholera is spreading fast, yet it can be stopped. Why haven’t we consigned it to history? | Hakainde Hichilema and Tedros Adhanom Ghebreyesus Vaccine production must be expanded to combat this ancient disease, especially in Africa, but a lack of political will is holding us back

Cholera is spreading fast, yet it can be stopped. Why haven’t we consigned it to history? | Hakainde Hichilema and Tedros Adhanom Ghebreyesus

Welcome to EPFL 🤩

I’m excited to announce the launch of my lab at EPFL in Jan 2026 🎉. We’ll combine evolution & synthetic biology to study and (re)engineer bacterial communication.
I’m recruiting PhD students to start in the first semester of 2026.
Apply via EPFL PhD programs by Nov 1
drive.google.com/file/d/1cm-t...

Sign up for our annual Impromptu Symposium on Nov. 21 in the Biophore @unil.bsky.social organized by Christophe Keel and Jordan Vacheron, which will explore the fascinating world of microbe–plant interactions with an exciting speaker line up!
Registration (lunch included): forms.gle/t4fC8uQV5HQF...

Structure and activation mechanism of a Lamassu phage and plasmid defense system Nature Structural & Molecular Biology, Published online: 14 October 2025; doi:10.1038/s41594-025-01677-4Li et al. show that a Lamassu defense system protects bacteria from phage infection by activating a lethal tetrameric DNA-cutting enzyme. In the absence of phages, a protein clamp holds the enzyme as an inactive monomer, preventing self-damage.

New online: Structure and activation mechanism of a Lamassu phage and plasmid defense system

Yipeee.....finally out.
Thanks for this awesome collaboration Yan @yli18smc.bsky.social , Stephan @gruberlab.bsky.social & co.....
So much fun! 🤩

Happy that the final version of our Lamassu work @yli18smc.bsky.social is now out:

www.nature.com/articles/s41...

Thanks again to our awesome collaborators @mblokesch.bsky.social and David and co and Mark Szczelkun and @steven-shaw.bsky.social and the DCI Lausanne @fbm-unil.bsky.social

WHO warns of widespread resistance to common antibiotics worldwide One in six laboratory-confirmed bacterial infections causing common infections in people worldwide in 2023 were resistant to antibiotic treatments, according to a new World Health Organization (WHO) r...

WHO reports 1 in 6 bacterial infections worldwide are antibiotic-resistant, with resistance rising sharply since 2018. Gram-negative bacteria like E. coli and K. pneumoniae pose the biggest threat. Action on #AMR surveillance and responsible antibiotic use is needed.

www.who.int/news/item/13...

Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...

Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...