The Fromm Lab

Hey blueskiers! We are looking for examples of "microRNAs" that you came across in your studies that seemed weird or behaving unexpectedly.

What an amazing asset and friend to have had in the lab. Thank you Pedro for the last half year!!!

I am starting a computational lab at LIOS, Riga, Latvia, and going to recruit a few people. Please DM if you are interested in a postdoc or PhD position in my Metabolic Research Group within the TARGETWISE project. I can highly recommend Riga, it is a beautiful city with very good living conditions.

What a beautiful trip!! Thank you @enricodanielloszn.bsky.social

A genome resource for the marine annelid Platynereis spp - BMC Genomics The marine annelid Platynereis dumerilii is a model organism used in many research areas including evolution and development, neurobiology, ecology and regeneration. Here we present the genomes of P. ...

happy to have contributed to this nice paper on the Platynereis genome:
link.springer.com/article/10.1...

BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference - Nature Methods BEAST X advances Bayesian phylogenetic, phylogeographic and phylodynamic analysis by incorporating a broad range of complex models and leveraging advanced algorithms and techniques to boost statistica...

BEAST X for Bayesian phylogenetic, phylogeographic and phylodynamic inference

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

An ancient influenza genome from Switzerland allows deeper insights into host adaptation during the 1918 flu pandemic in Europe - BMC Biology Background From 1918 to 1920, the largest influenza A virus (IAV) pandemic known to date spread globally causing between 20 to 100 million deaths. Historical records have captured critical aspects of ...

Very cool work using RNA feom historic specimen to trace vieaö RNA mutations!! bmcbiol.biomedcentral.com/articles/10.... An ancient influenza genome from Switzerland allows deeper insights into host adaptation during the 1918 flu pandemic in Europe | BMC Biology

Sea Spiders Lack a Key Body Part and a Missing Gene Could Explain Why

Nice covarge of the paper we have been involved with on the genome of the sea spider! (microRNA complement is virtually complete!)
www.nytimes.com/2025/07/01/s...

Happy to have contributed to this paper!!! Convergent placental phenotypes are mechanistically shaped by the same regulators

Mammal placental phenotypes are predictable from microRNA repertoires. Despite >100 million years of mammal diversification, similar placental morphologies have independently evolved multiple times, presenting a long-standing evolutionary puzzle: what genetic mechanisms ...

When you see convergent phenotypes do u wonder about their genetic basis? Did they re-invent some genetic element to construct the phenotype? The mammal placenta-a pretty important organ-has a lot of convergent phenotypes & this paper helps explain how they come about www.biorxiv.org/content/10.1...

This is wild!
Engineering E. coli bacteria to turn plastic waste into paracetamol (Tylenol)
www.nature.com/articles/s41...
www.nature.com/articles/s41...

SedaDNA2025 is Go!
@arcecogen.bsky.social

@jptosar.bsky.social !

Substantial hierarchical reductions of genetic and morphological traits in the evolution of rotiferan parasites Abstract. Within the last 800 million years animals evolved a vast range of diversity of species exhibiting an enormous disparity of forms and lifestyles.

9/9 🧵In sum:
Parasitic rotifers have shed:
🔹85% of miRNA families
🔹50% core protein-coding genes
🔹Key morphological structures

But they gain new traits for parasitism.
This is degressive evolution—consistent with Dollo’s Law.

📖 Read the full paper:
academic.oup.com/gbe/advance-...

8/9 🔁 These results echo my 2013 study in MBE @official-smbe.bsky.social
Parasitic flatworms also show massive microRNA losses (up to ~50%)
→ Suggesting a general principle in lophotrochozoan parasite evolution:
💥 Regulatory gene loss accompanies simplification.

pubmed.ncbi.nlm.nih.gov/24025793/

7/9🧪 Curiously piRNAs are retained - unlike to flatworms that have lost them altogether!

✅ piRNAs detected in all syndermatan lineages
✅ Ping-pong signature mostly intact
❌ DNA methylation machinery lost
❓Rdrp and Zuc patterns vary

piRNAs persist where miRNAs collapse. Why?

6/9 Regression in proteins and microRNAs is mirrored by morphology!

Losses:
▪️Digestive tract
▪️Ciliated head structures
▪️Protonephridia

And just like gene losses, morphological losses track with microRNA and BUSCO reductions.

Parasitism = evolutionary pruning. 🪓

However, new features evolve, too!

5/9 🔍 The 280 lost core genes in parasitic lineages are not random.

They're enriched for regulatory functions:
⚙️ Transcription factors
⚙️ RNA Pol II complex components
⚙️ Translation regulators

→ Suggests regulatory collapse as parasitism advances.

4/9
📉 Curiously we find that microRNA loss correlates with other forms of genome simplification.

🔸 Each lost microRNA family ≈ 400 protein-coding genes lost
🔸 Strong correlation with metazoan core gene loss (BUSCO)
🔸 Not explained by genome assembly quality or size

Simplification at every level.

3/9
🧬 Figure 1: microRNA losses across Syndermata

🔹Free-living rotifers (Monogononta, Bdelloidea): mild miRNA loss
🔹Seisonidea: ~67% loss
🔹Acanthocephala: a shocking 85% microRNA family loss

This is the most extreme microRNA reduction ever reported in bilaterians.
📉🧫

Substantial loss of conserved and gain of novel MicroRNA families in flatworms - PubMed Recent studies on microRNA (miRNA) evolution focused mainly on the comparison of miRNA complements between animal clades. However, evolution of miRNAs within such groups is poorly explored despite the...

2/9 🚨 Just published in GBE!
We uncover extreme microRNA loss in parasitic rotifers—mirroring what we reported in parasitic flatworms back in 2013 (!!!) (pubmed.ncbi.nlm.nih.gov/24025793/).

🧵 Let’s walk through the findings and figures:
academic.oup.com/gbe/advance-...

#EvoDevo #Parasitology

Substantial hierarchical reductions of genetic and morphological traits in the evolution of rotiferan parasites Abstract. Within the last 800 million years animals evolved a vast range of diversity of species exhibiting an enormous disparity of forms and lifestyles.

🔥🔥🔥NEW PAPER OUT in @genomebiolevol.bsky.social
with @psarkies.bsky.social and many others who are not here, yet!🔥🔥🔥
academic.oup.com/gbe/advance-...

They tend to hang out where sea anemones are. Did you note the nemertean?

Beautiful discovery right at the beach.

#SaveNSF (Episode 134) Big Biology · Episode

Important episode of Big Biology on the proposed cuts to NSF. ( free access)
open.spotify.com/episode/7lLw...

ONE WEEK LEFT TO APPLY
Join us to discover the fascinating world of microRNAs

Visit our group webpage to meet the team members and read about the projects in the lab carrellalab.wordpress.com
Contact us: sabrina.carrella@szn.it
Apply: www.szn.it/index.php/it...

@frommlab.bsky.social

Trump’s new ‘gold standard’ rule will destroy American science as we know it | Colette Delawalla The new executive order allows political appointees to undermine research they oppose, paving the way for state-controlled science

Trump’s new ‘gold standard’ rule will destroy American science as we know it
Colette Delawalla, Victor Ambros, Carl Bergstrom, Carol Greider, Michael Mann and Brian Nosek in The Guardian.
www.theguardian.com/commentisfre...

#RNAsky #ncRNA #microRNA

Ambitious project to develop low-cost genome sequencing for pathogens known and unknown - University of Birmingham Project will build on research that helped diagnostic labs to adopt sequencing capacity for COVID-19 and permit characterisation of future infectious threats

Absolutely thrilled to announce the launch of ARTIC2 - a £5.5M 5 year project funded by @wellcometrust.bsky.social to build on the ARTIC approach of low-cost, globally accessible genome sequencing for surveillance of outbreaks, epidemics and endemic diseases: www.birmingham.ac.uk/news/2025/am...

Interested in a PhD position on microRNAs and oxidative stress with the fantastic @sabcarrella.bsky.social and co-supervised by me in beautiful Naples at the marvelous Stazione Zoologica Anton Dohrn?

Check this opportunity!!