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Lars Eicholt

@lacholt.bsky.social

molecular evolution.

19 Posts587 Follower1589 Folgt
Arnau Sebé-Pedrós@arnausebe.bsky.social · 2d ago

Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below

Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics

This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...

nature.com

Stanisław Dunin-Horkawicz@staszekdh.bsky.social · 6d ago

If you are into plasmid research, try pLAST. By representing plasmids as ORF chains, it enables fast searches of 700k PlasmidScope sequences in global (find similar plasmids) or local (find recurring gene modules) mode. Available as server or local package. Feedback welcome! Links below ⬇️

Similarity map of hits for a single query plasmid, with the query and selected hit highlighted.Global alignment of a single query-target plasmid pair, showing corresponding ORFs and conserved gene blocks.
Tobias Warnecke@tobiaswarnecke.bsky.social · last wk.

Bacteriocins in archaea and archaeocins in bacteria. @romainstrock.bsky.social surveys the the exchange of molecular weaponry between archaea and bacteria. www.biorxiv.org/content/10.6...

Bacteriocins in archaea and archaeocins in bacteria

Archaea and bacteria routinely live side by side in microbial communities and must interact at least on occasion. Whether such cross-Domain interactions are dominated by mutual disregard, co-operation...

biorxiv.org

Molecular Biology and Evolution@molbioevol.bsky.social · 2mo ago

Patel, @lacholt.bsky.social et al. perform cross-species gene swap assays in D. melanogaster testes, showing that several orthologs of orphan gene Gdrd have undergone lineage-specific evolutionary changes. 🔗 doi.org/10.1093/molbev/msag119 #evobio #molbio #drosophila

Orthologs of an essential orphan gene vary in their capacities for function and subcellular localization in Drosophila melanogaster

Abstract. Orphan genes evolve rapidly, raising questions about whether their functions remain conserved or diverge across species. To address this, we inve

doi.org

Mohammed AlQuraishi@moalquraishi.bsky.social · 3mo ago

Equivariance is dead! 😢 Or is it? 😈 Genie 3 is out! Our latest protein design model achieves SoTA results for binder design and motif scaffolding, greatly improving on BindCraft and Proteina-Complexa. It does so using all-atom SE(3)-equivariance based on a branched polymer representation👇

Yeqing Lin@yeqinglin.bsky.social · 3mo ago

Introducing Genie 3, a generative protein model that substantially advances the state-of-the-art for binder design, increasing in silico success rates by up to 20x on hard multimeric targets. It also debuts a form of inference-time scaling unobserved in other design models. 🧵1/8

Hassan uz Zaman@hassanzaman.bsky.social · 5mo ago

Happy to announce that our paper on orphan gene evolution in bacteria dropped in PNAS yesterday! This is a problem I've been thinking about since the start of my PhD. Very grateful for this journey, as well as All The Friends I Made Along the Way. Also, Eid Mubarak to those who celebrate!

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Genome Biology and Evolution@genomebiolevol.bsky.social · 5mo ago

Jones et al. analyzed two high-quality genomes of the cockroach genus Cryptocercus, the sister group to all termites, revealing relaxed selection in both Cryptocercus and termites. 🔗 doi.org/10.1093/gbe/evag028 #genome #evolution #sociality

Cryptocercus Genomes Expand Knowledge of Adaptations to Xylophagy and Termite Sociality

Abstract. Subsociality and wood-eating or xylophagy are understood as key drivers in the evolution of eusociality in Blattodea (cockroaches and termites),

doi.org

Bornberglab@bornberglab.bsky.social · 6mo ago

🚨 New paper in GBE! 🚨 This study analyzes two high-quality Cryptocercus genomes, the sister group to all termites, to investigate the transition to subsociality and wood-feeding (xylophagy) in Blattodea. 🪳 Check it out here: doi.org/10.1093/gbe/...

Cryptocercus genomes expand knowledge of adaptations to xylophagy and termite sociality

Abstract. Subsociality and wood-eating or xylophagy are understood as key drivers in the evolution of eusociality in Blattodea (cockroaches and termites),

doi.org

Professor Mary J O'Connell@evol-molly.bsky.social · 6mo ago

Congratulations to Eilidh Ward (first author and PhD student co-supervised by co-authors Julie Aspden, David Westhead and yours truly) on this lovely contribution - a method to visually inspect reads from novel open reading frames: doi.org/10.1093/bioa...

InspectorORF: a tool for visualising Ribo-Seq and additional genomic or transcriptomic data

AbstractMotivation. The advent of ribosome profiling (an adaptation of RNA sequencing) to determine the translatome, has led to a huge improvement in our u

doi.org

Liz Neeley@lizneeley.bsky.social · 6mo ago

Reposting w/alt text. Iranians are experiencing collective trauma. Thousands have been killed/injured, the economy is crippled & the threat of a wider conflict is real. It’s especially difficult for those living in Iran, as many have lost (or fear losing) loved ones. www.nature.com/articles/d41...

Correspondence in NATURE - 03 February 2026 Calling all scientists: Support your Iranian colleagues By Mohammad Hosseini Iranian researchers are in a difficult situation. Those in Iran face low wages, high inflation, sociopolitical instability, resource mismanagement, oppression by the authorities and longstanding international sanctions. High prices hinder conference attendance, as do difficulties obtaining visas. Unstable Internet connections, frequent power outages and lack of access to scholarly sources jeopardize collaborations. Scholars also have to contend with isolation, and sometimes biases, from the international community. And for those who work abroad, travelling to and from Iran is risky, even with visas and double citizenship. Recent tensions have further exacerbated the situation. Scientists, in shock and distress, have condemned violence against civilians. Research requires focus, concentration and a calm state of mind - rare commodities in these times. The international research community can support Iranian colleagues: send a message, show them that they are not forgotten. If your institutional policies allow it, try to work with researchers in Iran. International collaborations will help to build capacity there, strengthening civil society and enabling it to tackle systemic challenges. There is no need to be a politician to engage in science diplomacy. Do not wait for big initiatives to build bridges. At this moment, Iranian researchers can benefit from kind gestures. Show solidarity.
Mohammad Hosseini@mhmdhsini.bsky.social · 6mo ago

Iranians are experiencing a collective trauma. Thousands have been killed/injured in recent events, the economy is crippled & the threat of a wider conflict is real. This is especially difficult for those living in Iran, as many have lost (or fear losing) loved ones. www.nature.com/articles/d41...

Genome Biology and Evolution@genomebiolevol.bsky.social · 6mo ago

@ccasola.bsky.social, A. Owoyemi and @vakirlis.bsky.social test the hypothesis that many noncanonical proteins possess low stability in the cellular environment, finding that noncanonical proteins were enriched for degradation-related features. 🔗 doi.org/10.1093/gbe/evag009 #genome #evolution

Degradation Determinants Are Abundant in Human Noncanonical Proteins and Minor Annotated Isoforms

Abstract. The comprehensive characterization of human proteins, a key objective in contemporary biology, has been revolutionized by the identification of t

doi.org

Klara Hlouchova lab@hlouchova-lab.bsky.social · 9mo ago

Can proteins fold and function with half of the amino acid alphabet? Using only 10 residues, we designed stable, mutation-resilient structures—no aromatics or basics involved. A minimalist foundation for ancient biology and synthetic design. tinyurl.com/37t8br4v #ProteinDesign #OriginsOfLife

Ancient amino acid sets enable stable protein folds

Early proteins likely arose from a chemically limited set of amino acids available through prebiotic chemistry, raising a central question in molecular evolution: could such primitive compositions yie...

tinyurl.com

Claire Patiou, PhD.@cpatiou.bsky.social · 7mo ago

🧬 What does the starting material from which genes could emerge #denovo look like? 🌱 We used #RiboSeq to investigate the landscape of translated de novo ORFs in 3 #Arabidopsis species, and how they might be linked to gene birth! 📝 Check out our preprint here: doi.org/10.1101/2025...

Pervasive translation of short open reading frames and de novo gene emergence in Arabidopsis

Ancestrally non-genic sequences are now widely recognized as potential reservoirs for the de novo emergence of new genes. Across clades, some de novo genes were proven to have substantial phenotypic effects, and to contribute to the emergence of novel biological functions. Yet, still very little is known about the starting material from which de novo genes emerge, especially in plants. To fill this gap, we generated Ribosome Profiling data from the closely related species Arabidopsis halleri, A. lyrata and A. thaliana and characterized genome-wide patterns of translation across them. Synteny analysis revealed 211 Open Reading Frames (ORFs) that have emerged de novo within the Arabidopsis genus and already exhibit signs of active translation. Most of these de novo translated ORFs were species- and even accession-specific, indicating their transient nature, with patterns of polymorphism consistent with neutral evolution in natural populations. They were also significantly shorter and less expressed than conserved Coding DNA Sequences (CDS), and their GC content increased with phylogenetic conservation. While most of them were located in intergenic regions and are thus newly discovered, 34 were previously annotated as CDS in at least one genome, and are promising putative genes. Our results demonstrate the abundance of translation events outside of conserved CDS, and their role as starting material for the emergence of novel genes in plants. ### Competing Interest Statement The authors have declared no competing interest. Université de Lille, https://ror.org/0546v5182

doi.org