The standard university response to a new challenge takes years. AI is not waiting.

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Female PhD students "disciplined" with a cane by their professor - absurd? Female professors losing their positions under dubious circums...

As a labor-augmenting technology, large language models (LLMs) have the potential to accelerate scientific activity across the research pipeline. But even if LLMs perform on par with human experts at ...

Manifeste pour l’enseignement supérieur et l’éducation nationale [Vous pouvez signer ce manifeste (version pdf ici) dans ce formulaire. Un document de mise en perspective critique des discours de défe...

Abstract. A general theory of adaptation is one that accounts for both the quantitative and functional properties of adaptive evolution. To date, the field

Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig

Advances in genomics, proteomics, and bioinformatics have uncovered the existence of thousands of translated small open reading frames less than 100–150 codons in length that encode microproteins. In ...

Dismissal of the National Science Board is widely seen as latest move to erase NSF’s independence

OR: the long overdue forest fire

YouTube video by Université de Lille

Page Unil Center for Theory in Ecology and Evolution of site Faculty of Biology and Medicine hosted by the University of Lausanne

The analysis of ribosome profiling (Ribo-Seq) data has provided evidence that many eukaryotic mRNAs contain translated upstream or downstream ORFs (uORFs/dORFs), but the biological significance of this translation activity remains, for the most part, unknown. One of the principal limitations has been the lack of Ribo-Seq data from several closely related species, precluding the identification of cases in which translation is phylogenetically conserved. Here, by combining Ribo-Seq data from 100 different experiments, we identify 2,332 translated uORFs and 1,008 translated dORFs in S. cerevisiae, which result in microproteins that tend to be highly hydrophobic or positively charged. To study their phylogenetic conservation, we have generated Nanopore direct RNA sequencing data, together with Ribo-Seq data, from six additional Saccharomyces species, spanning an evolutionary period of around 16 million years. We have identified 195 translated S. cerevisiae uORFs that are also translated in other Saccharomyces species; these uORFs are translated at levels comparable to the main coding sequence and display signatures of purifying selection at the level of the encoded microproteins. In contrast, dORFs are translated at very low levels and they are rarely conserved, suggesting much more limited microprotein functionalization. We have also discovered that uORF translation is associated with the formation of alternative transcript isoforms encompassing the region containing the uORFs but not the main protein coding sequence, implying that some microproteins can be produced independently of the main protein product. This work significantly advances our understanding of how initially pervasive uORF translation can result in new microproteins, providing many new candidates for further functional studies. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, 101052538 Ministerio de Ciencia, Innovación y Universidades, PID2021- 122726NBI00, PGC2018-094091- B-I00, PID2022-136939OBI00, CEX2024-001431-M, MICIU/AEI/10.13039/501100011033 Generalitat de Catalunya, https://ror.org/01bg62x04, 2021SGR00042, 2021SGR00176

Cells are the fundamental units of life, shaped by evolution into a remarkable diversity of forms and functions. Much is known about the roles of genes and proteins, the regulation of molecular proce…

A structural catalogue of the Asgard archaeal pangenome reveals hundreds of eukaryotic-like proteins that suggest a higher degree of cellular complexity in the archaeal ancestor of eukaryotes.

Abstract. The origin of life is one of the great mysteries of science. Of the multiple unsolved problems, the origin of the translation system (the means b

De novo gene evolution entails the birth of new genes from previously non-coding DNA. In this Review, Bornberg-Bauer and Eicholt overview how protein-coding de novo genes are identified, the mechanist...

Nature Reviews Genetics - De novo gene evolution entails the birth of new genes from previously non-coding DNA. In this Review, Bornberg-Bauer and Eicholt overview how protein-coding de novo genes...

Students use AI to write papers, professors use AI to grade them, degrees become meaningless, and tech companies make fortunes. Welcome to the death of higher education.

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

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

ALT: a woman says " would you like to join us " with her eyes closed

Open Positions – GEvol – DFG SPP 2349

Abstract. The current economics of scientific publishing reveal a profound imbalance: academia pays prices far exceeding the actual costs of publication. R

Abstract. The current economics of scientific publishing reveal a profound imbalance: academia pays prices far exceeding the actual costs of publication. R

The FlyBase team’s fundraising efforts have proven successful in the short term, but restoration of its federal grant remains uncertain.

The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...

Speciation, the process by which new reproductively isolated species emerge from ancestral populations, results from the gradual accumulation of barriers to gene flow within genomes. To date, the noti...