PomBase: The S. pombe knowledgebase
@pombase.bsky.social
https://www.pombase.org/ Knowledgebase for Schizosaccharomyces pombe (a fission yeast). Supporting scientific discovery for cell-level processes; #OpenScience, #FAIR data #CommunityCuration; Monitoring #UnknownProteins; Elixir and GBC Core Data Resource.
Our scientific program ranged from chalk talks and "odds & ends" to brainstorming future research and improving lab onboarding & mentoring. A real highlight: the hands-on workshop on curating papers for @pombase.bsky.social , led by the one & only Valerie Wood. Huge thank you for joining us, Val!
Thank you, @Pombase.bsky.social, for your kind words about our work! This study would not have been possible without the incredible support and resources provided by PomBase. We truly appreciate everything you do for the S. pombe community!
There are often legitimate complaints about the fun photos illustrating news articles on climate change and heat waves, so here's @TheGuardian doing it well.
Another game changer from @grewalsh.bsky.social lab. We look forward to integrating this data and pathways @pombase.bsky.social
Shiv Grewal@grewalsh.bsky.social · 4w agoIntrons have a hidden regulatory role! 🧬🎉 Delighted to share our latest paper showing that inefficiently spliced introns and spliceosomal proteins direct RNA methylation, engaging RNAi to silence retrotransposons and regulate gene expression nature.com/articles/s41...
Congratulations Pascal. Really well deserved.
International Society for Biocuration@biocurator.bsky.social · 2mo agoPascal has been a PomBase (@pombase.bsky.social) curator for just over 2 years where he has taken on community curation review, developed a series of outreach seminars, “Just One Thing”, and was lead author of the recent PomBase resource update.
Is it time to blacklist authors identified as papermill users? They clearly have integrity problems which raise concerns about the rest of their work.
michael veale@michae.lv · 3mo agoAcademics amass large database of paper mill services, depicting a global academic fraud network. www.nature.com/articles/d41.... In some jurisdictions , you may be able to get takedown for these ads under contract cheating laws (Aus, E&W), based on PhD students submitting them as work.
@Pombase links to SOGs from every gene page. See the ortholog section.
Yeast Journal@yeast-journal.bsky.social · 4mo agoThe latest #Yeast research article features a tool developed by Guo-Song Jia, @lilindu.bsky.social & team: www.sogweb.org. Based on genome assemblies and annotations of Schizosaccharomyces species, users can explore gene alignments and phylogenetic trees. 👇 onlinelibrary.wiley.com/doi/10.1002/...
Updates from: Caenorhabditis Genetics Center CartograPlant, @treegenes.bsky.social CottonGen Genome Database for Vaccinium GrainGenes Legume Information System @maizegdb.bsky.social Mondo PeanutBase @pombase.bsky.social @sorghumbase.bsky.social SoyBase @tairnews.bsky.social @xenbase.bsky.social 2/2🧵
2 more Proteins from the PomBase Exploration of the proxiOME of large subunit ribosomal proteins reveals Acl1 and Bcl1 as cooperating dedicated chaperones of Rpl1 url: academic.oup.com/nar/article/...
Exploration of the proxiOME of large subunit ribosomal proteins reveals Acl1 and Bcl1 as cooperating dedicated chaperones of Rpl1
Abstract. In eukaryotes, most newly synthesized ribosomal proteins (r-proteins) need to rapidly and safely get into the nucleus to reach their assembly sit
academic.oup.com
#UnknownProtein #NewGeneCharacterization 2 more proteins from the @pombase #Unknome Exploration of the proxiOME of large subunit ribosomal proteins reveals Acl1 and Bcl1 as cooperating dedicated chaperones of Rpl1 url: academic.oup.com/nar/article/...
Exploration of the proxiOME of large subunit ribosomal proteins reveals Acl1 and Bcl1 as cooperating dedicated chaperones of Rpl1
Abstract. In eukaryotes, most newly synthesized ribosomal proteins (r-proteins) need to rapidly and safely get into the nucleus to reach their assembly sit
academic.oup.com
Proud to share the yeast telomerase structure, led by the talented @hongmiaohu.bsky.social in collaboration with the Wellinger and Chartrand labs. Discovered 37 years ago and took us nearly 7 years but totally worth the wait 😍. www.science.org/doi/10.1126/... www.youtube.com/watch?v=gFE4...
Cryo-EM structure of yeast telomerase
YouTube video by MRC Laboratory of Molecular Biology
youtube.com
MRC Laboratory of Molecular Biology@mrclmb.ac.uk · 4mo agoLed by Investigator Scientist @hongmiaohu.bsky.social, @kellythd-nguyen.bsky.social’s group in the LMB’s Structural Studies Division have produced the first ever structure of telomerase from yeast. Read more here: mrclmb.ac.uk/news-events/... #LMBResearch #cryoEM 🧪
🧬 Phage recombinases just landed in hashtag#OpenCloning Simulate site-specific recombination defining your own recognition sites. 🎥 See it in action below 👇 Links in the comments 🔗
Corrections: Note that we have detailed gene function annotations for over 80% of proteins (not 20%). The 20% (should be 25%) is the number now linked into the GO-CAM pathway models! The community makes a HUGE amount to our curation, but these models were made by PomBase curators.
I can only recommend...
Sophie G Martin@sophiemartinlab.bsky.social · 5mo agoYou are finishing your PhD and looking to continue in science? The Martin lab @biology-unige.bsky.social has an open postdoctoral position in cell biology to study cell-cell fusion. For more information, please consult mocel.unige.ch/research-gro.... Thanks for reposting!
These scientists and medical experts are taking to social media to counter climate denialism, vaccine scepticism and wellness pseudoscience go.nature.com/4tFXSjb
The science influencers going viral on TikTok to fight misinformation
Nature - Scientists and medical experts are countering climate denialism, vaccine scepticism and wellness pseudoscience on social media.
go.nature.com
Empowering biological knowledgebases: advances in human-in-the-loop AI-driven literature curation url: academic.oup.com/bioinformati... @elixiruknode.org @biocurator.bsky.social
Empowering biological knowledgebases: advances in human-in-the-loop AI-driven literature curation
Abstract. Biological knowledgebases facilitate discovery across the life sciences by structuring experimental findings into human-readable and computable f
academic.oup.com
This week I participated in the excellent @biocurator.bsky.social virtual AI workshop. I presented some general tips for learning about agents. zenodo.org/records/1861... A lot of the advice comes down to: find time to learn+don't wait for the perfect curation tool, start using existing agent tools!
Staying in the Loop: A Biocurator's Guide to Agentic AI Developments
Staying in the Loop: A Biocurator’s Guide to Agentic AI Developments Large language models have rapidly become part of everyday scientific workflows, yet most biocurators still interact with AI primar...
zenodo.org
🚀 Update from @pombase.bsky.social! Gene pages now link to OpenCloning. Load the gene region instantly and design primers + cloning strategies in one click 🧬🧪✨ To get started with OpenCloning, check the docs: docs.opencloning.org
Over the last few months I've been helping organize various tutorials and workshops on agentic AI, aimed mostly at biocurators, ontology developers, and PIs of knowledge bases / data resources. Some of this might be generally useful to folks who don't identify as a 'technical' or an 'AI' person.🧵
Very excited about this new preprint, in which @juliacoronasserna.bsky.social shows how cells ensure that fusion with another cell is irreversible! www.biorxiv.org/content/10.6... @biology-unige.bsky.social 👇
PAK-family kinases promote cell fusion irreversibility by preventing cell wall repair
Cell-cell fusion is critical for the sexual life cycle, as it drives the unidirectional transition between haploid and diploid phases. In eukaryotes where fusion occurs between partners with cell wall, fusion requires not only plasma membrane merging but also local removal of the intervening cell wall. However, the integrity of the cell wall, which resists the strong internal turgor pressure and is essential for survival, is normally monitored by signaling pathways that promote repair upon damage. How cell wall integrity pathways allow localized cell wall degradation is not known. In the fission yeast Schizosaccharomyces pombe, we previously identified pak2 deletion mutants that exhibit transient fusion: cells briefly fuse and exchange cytoplasmic contents that signal meiosis but then reseal their fusion pore. This reversal of fusion directionality induces meiosis in haploid cells, with catastrophic consequences. Here, we show that PAK activity is essential for cell-cell fusion, with major contribution for Pak2 and a more minor role for the essential Pak1. Pak2 accumulates at the fusion site, where its kinase activity is controlled to promote both fusion pore opening and expansion, thereby preventing post-fusion pore closure. Strikingly, osmotic stabilization largely suppresses all PAK-associated fusion defects, pointing to a role in cell-wall remodeling rather than plasma-membrane merging. Indeed, correlative light and cryo-soft-X-ray tomography reveals that resealed pores in PAK mutants rebuilt an intact cell wall. Thus, PAKs enforce fusion directionality by antagonizing cell-wall repair mechanisms that otherwise restore separation between mating partners. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, https://ror.org/00yjd3n13, 310030_207909 European Research Council, https://ror.org/0472cxd90, SexYeast; 101019630 European Molecular Biology Organization, ALTF 351-2021
biorxiv.org
Julia Coronas-Serna@juliacoronasserna.bsky.social · 6mo ago📢 Happy to share our new preprint from @sophiemartinlab.bsky.social ! Check our latest work on cell–cell fusion, uncovering how PAK kinases promote cell-cell fusion irreversibility by preventing cell wall repair.
The first release of 2026 of the Rhea database is out! Release 140 (2026-01-28) contains 18,343 unique reactions and 15,125 unique reaction participants, with 25M protein sequence entries annotated with Rhea reactions in UniProtKB.
📣 NuQuest consortium update: Our first joint publication is out! Review on quiescence—A milestone for our initiative laying out the scientific groundwork & collaborative vision for our MSCA-DN application coordinated by @jlugiessen.bsky.social 1/n www.mdpi.com/3700996 #NuQuest #MSCA #DoctoralNetwork
mdpi.com
Another removal from the #UnknownProteins inventory! This is pombe SPAC630.06c and human 'Custos' ortholog -There are still plenty of broadly conserved eukaryotic proteins to study: www.pombase.org/status/prote... 144 in our high priority list (well 143 tomorrow)
PomBase, the S. pombe genome database
PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets
pombase.org
Saccharomyces Genome Database@yeastgenome.bsky.social · 6mo ago🧬 Meet Sni445, a newly discovered #Yeast ribosome assembly factor! Ynl050c/Sni445 recruits specialized snoRNPs (snR4 & snR45) that guide precise rRNA acetylation during ribosome synthesis. Another piece of the puzzle solved! 🧪 #YeastResearch #SGD www.yeastgenome.org/reference/S1...
🧬 Meet Sni445, a newly discovered #Yeast ribosome assembly factor! Ynl050c/Sni445 recruits specialized snoRNPs (snR4 & snR45) that guide precise rRNA acetylation during ribosome synthesis. Another piece of the puzzle solved! 🧪 #YeastResearch #SGD www.yeastgenome.org/reference/S1...
Structure of the adaptor protein 4 (AP-4) complex revealed! AP-4 exists in a dynamic equilibrium between closed and open conformations in solution. ARF1 does not shift this equilibrium but is required—together with cargo—for membrane recruitment. rdcu.be/e1ozM
🚀 InterPro 108.0 is live! ✨ Updated to Pfam 38.1 and NCBIFam 18.0 ✨ 1,911 InterPro entries Explore the latest annotations and discover new protein insights. Explore it now: www.ebi.ac.uk/interpro/
Micropublication @micropub7n.bsky.social is peer reviewed and PubMed indexed. A great way to get the data out in uncertain times 👇🏼
Needhi Bhalla 💅🏽@needhibhalla.bsky.social · 9mo ago"Due to a variety of circumstances...many science projects will never be finished, despite years of invested resources and effort. By carefully and strategically documenting scientific work achieved, components of unfinished projects can be salvaged and preserved to benefit future researchers." 🧪
As a final nod to 2025, #GeneOntology announces our latest paper in @narjournal.bsky.social! Updates include expanded #Ontology & annotations in #Metabolism, multi-org interactions, #chromatin remodeling, & more. Also ft. #Functionome v2 and 1500+ GO-CAM pathway models! 🧬🧪 doi.org/10.1093/nar/...
The Gene Ontology knowledgebase in 2026
Abstract. The Gene Ontology (GO) knowledgebase (https://geneontology.org) is a comprehensive resource describing the functions of genes. The GO knowledgeba
doi.org
This week, Professor James Hansen and colleagues published projections that the global temperature record could reach +1.7°C by 2027. And if that number lands in your gut the way it landed in mine, good. It should. #climatecrisis #auspol www.lyrebirddreaming.com/post/two-yea...
Two Years to 1.7°C: the “Prediction Game” We Can’t Afford to Lose
Australia’s sweltering through another early-summer heatwave, and I’m trying to decide whether to write about the weather outside my window - or the bigger climate system we’re reengineering on this p...
lyrebirddreaming.com