A Russian jet-powered drone hit Ukraine’s National Academy of Sciences, the source of almost all of the country’s major scientific discoveries.

Breathless claims about AGI and new capabilities fall apart pretty quickly under scrutiny.

Abstract. Orphan genes (OGs)—genes lacking detectable homologs outside a species—are widespread in microbial genomes and are thought to contribute to their

Recent AI developments and what they mean for us Quick primer on general AI models* State-of-the-art in AI agent capabilities AI agents in biology (examples) Discussion - what does this mean for our r...

The Department of Biochemistry and Biophysics   SciLifeLab ( SciLifeLab ) is a national center for molecular biosciences with a focus on health and environmental research. The center combines frontl

Understanding the history and diversity of life inspires awe and wonder.

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Determining whether sponges or ctenophores root the animal tree has important implications for understanding early animal evolution. Here, we examined support for these competing hypotheses by constru...

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

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

An Owner's Guide to the Human Genome

Seamus O'Reilly warns of AI maximum bubbledrive this year.

Abstract. The recent Society for Molecular Biology and Evolution Satellite Meeting on De Novo Gene Birth, hosted at Texas A&M University on November 6

Meta's metaverse division posts massive Q3 loss despite beating expectations

Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...

Genomes contain orders of magnitude more open reading frames (ORFs) than known protein coding genes, and recent work suggests there may be unannotated proteins present in even the best studied organisms. To address this gap, we used a high throughput reverse genetic toolkit to construct precise C-terminal fusions of a reporter (and control) to >120,000 ORFs in model E. coli . We found hundreds of unannotated significant hits, and individually detected >50 novel polypeptides by western blot, including ORFs within tRNA loci. Many ORFs overlap annotated genes in the sense orientation, and we found these are likely chimeric polypeptides produced by ribosomal frameshifting. Using degron based knockdowns, we identified unannotated proteins that have putative fitness effects, and we found a novel small protein that displays phenotypes consistent with a role in the mRNA degradosome. The observation of a range of unannotated translation products should lead to better annotation and understanding of the bacterial domain of life and motivates the continued exploration of genomes broadly. ### Competing Interest Statement The authors have declared no competing interest.

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...

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Structurally complex regions of the genome are increasingly recognized as engines of evolutionary convergence due to their propensity to generate recurrent gene duplications that give rise to similar ...