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Alliance of Genome Resources @alliancegenome.bsky.social · 5d

Nature has published an article on the crisis facing MODs
Model organism databases face budget cuts and closures www.nature.com/articles/d41...
@zfinmod.bsky.social @xenbase.bsky.social @yeastgenome.bsky.social @mousegenome.bsky.social @ratgenome.bsky.social @geneontology.bsky.social @nature.com

Model organism databases face budget cuts and closures

Beyond the crucial data they contain, these digital archives have provided an important space for academic communities to exchange ideas and resources.

www.nature.com

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PomBase: The S. pombe knowledgebase @pombase.bsky.social · 5d

Their potential loss would be a profound setback for the global scientific community. The staff who maintain them bring decades of expertise that cannot simply be replaced. These databases are not just helpful—they are the very foundation on which most basic biological research depends.

PomBase: The S. pombe knowledgebase @pombase.bsky.social · 5d

An important new item on the status of model organism databases: these resources, built and refined over decades, are at risk. www.nature.com/articles/d41...

Model organism databases face budget cuts and closures

Beyond the crucial data they contain, these digital archives have provided an important space for academic communities to exchange ideas and resources.

www.nature.com

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Sophie G Martin @sophiemartinlab.bsky.social · 13d

Super excited that this story by @borissieber.bsky.social is now on BioRxiv!

For decades, we thought there was no MAPK scaffold for the ERK-like cascade that promotes sexual reproduction in fission yeast ... until Boris found it !

See the thread 👇 and enjoy the paper!

doi.org/10.1101/2025...

Boris Sieber @borissieber.bsky.social · 13d

Mammalian cells have KSR, budding yeast has Ste5… and fission yeast has Sms1 as the MAPK scaffold for sexual reproduction!

Very excited to share my postdoc work where we discover that the hemi-arrestin Sms1 binds all components of the MAPK cascade, including ERK-like Spk1

doi.org/10.1101/2025...

Schematic of MAPK signalling in fission yeast, budding yeast and Metazoa. No MAPK scaffold was known for ERK-like MAPK in fission yeast, as opposed to budding yeast Ste5 and metazoan KSR1/2.

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The Braun Lab @thebraunlab.bsky.social · 11d

This one feels special: our latest work on subtelomeric heterochromatin is now on www.biorxiv.org/content/10.1....
This story was driven by the virtuoso PhD work of Agnisrota Mazumder @agnisrota.bsky.social, co-mentored with @al-sadylab.bsky.social, and grew out of our #MSCA Cell2Cell network.

Discrete Subdomains Establish Epigenetic Diversity in Subtelomeric Heterochromatin

Subtelomeres are imperfect repeats adjacent to telomeres that are repressed by heterochromatin. Although essential for genome integrity, their repetitive nature has thwarted dissection of local hetero...

www.biorxiv.org

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Omaya Dudin 𓂆 ¦🍉¦🦠¦🔬¦ @dudinlab.bsky.social · 11d

So for >30y, it was thought that #MAPK cascade in #fission #yeast lacked a scaffold ! Like in #animals, or #budding yeast.

Well this changes today !

All hail #Sms1

Congrats @borissieber.bsky.social @sophiemartinlab.bsky.social and Team !!

Boris Sieber @borissieber.bsky.social · 13d

Mammalian cells have KSR, budding yeast has Ste5… and fission yeast has Sms1 as the MAPK scaffold for sexual reproduction!

Very excited to share my postdoc work where we discover that the hemi-arrestin Sms1 binds all components of the MAPK cascade, including ERK-like Spk1

doi.org/10.1101/2025...

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Lori Passmore @lapassmore.bsky.social · 11d

We have an open post-doc position in my group to study mRNA cleavage and polyadenylation using biochemical reconstitution and cryoEM.

Please get in touch if you are interested in joining this amazing team! 🔬🧬🤩
#RNA #cryoEM

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Yale Cell Biology @yalecellbiology.bsky.social · 19d

Did you know that all nuclear pore complexes (NPCs) are not the same? @luskinglab.bsky.social propose a new hypothesis for how nuclear mechanics may impact the compositional plasticity of NPCs with implications for tissue-specific diseases caused by NPC dysfunction.

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

Nuclear mechanics as a determinant of nuclear pore complex plasticity - Nature Cell Biology

In this Review, Lusk et al. discuss emerging insights into nuclear pore complex variability with regard to composition and dilation state, and propose nuclear mechanics as a key determinant of driving...

www.nature.com

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PomBase: The S. pombe knowledgebase @pombase.bsky.social · Jul 31

PomBase introduces two new interactive views for GO-CAM pathway models: Summary Maps (high-level, visual overview) and Mega-Models (connected models). Check them out here: lnkd.in/gfxNRdua

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Henar Valdivieso @mhenarvm.bsky.social · Jul 22

@pombase.bsky.social Dear all, Kaz and I submitted this manuscript to make it accessible. We don't have active labs now, so we will not submit it to any journals. We hope that some of you will find these data interesting and can complete the work, or use them as a starting point for future projects.

Exomer cooperates with Ryh1RAB6 in regulating TORC2 activity

Exomer is a trans-Golgi protein complex involved in multiple biological processes, including lipid homeostasis and stress response. We have found that in fission yeast, the absence of exomer leads to ...

doi.org

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Colbie Reed, PhD, MS @mindandmatter.bsky.social · Jun 17

Latest paper from the de Crecy lab is out!
A finding that answers a ~40 year old question: a eukaryotic high-specificity transporter for Q/q

The oncogene SLC35F2 is a high-specificity transporter for the micronutrients queuine and queuosine | PNAS

The nucleobase queuine (q) and its nucleoside queuosine (Q) are micronutrients derived from bacteria that are acquired from the gut microbiome and/...

doi.org

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Steven Marygold @steven-flybase.bsky.social · Jun 11

European-based researchers can help support future #flybase curation by donating at this site: www.philanthropy.cam.ac.uk/give-to-camb...

Drosophila Genetic Database

The Drosophila Genetic Database, FlyBase, is on the brink of collapse due to the sudden termination of the FlyBase NIH grant, which includes salaries for 5 literature curators based at the University ...

www.philanthropy.cam.ac.uk

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FlyBase @flybase.bsky.social · Jun 3

We currently have a call for support that has gone out to European labs, to support FlyBase-UK. We are asking our colleagues from labs in the US and other countries to wait for a similar call to them that will go out in the near future, to support the US sites. We thank you for your patience.

Mark A. Hanson @hansonmark.bsky.social · Jun 3

URGENT: FlyBase has lost practically all its funding overnight; even user fees are tied up in denied grant funding. 🤬🤯

Any lab using @flybase.bsky.social please donate using the link in post below.

This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.

Marc Dionne @marcsdionne.bsky.social · Jun 3

My lab studies bacterial infections. We spend a lot of time looking at (or for) species-specific genetic and genomic databases for hosts and microbes. FlyBase is the best of all—there is literally no comparison. Its existence is under threat. Please donate.
www.philanthropy.cam.ac.uk/give-to-camb...

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PomBase: The S. pombe knowledgebase @pombase.bsky.social · Jun 4

The existence of FlyBase, the first model organism database, is under serious threat of extinction. Under the current funding, there will be no future updates after July 2025 and its curators are currently working flatout on the final release! PLEASE SUPPORT!

Marc Dionne @marcsdionne.bsky.social · Jun 3

My lab studies bacterial infections. We spend a lot of time looking at (or for) species-specific genetic and genomic databases for hosts and microbes. FlyBase is the best of all—there is literally no comparison. Its existence is under threat. Please donate.
www.philanthropy.cam.ac.uk/give-to-camb...

Drosophila Genetic Database

The Drosophila Genetic Database, FlyBase, is on the brink of collapse due to the sudden termination of the FlyBase NIH grant, which includes salaries for 5 literature curators based at the University ...

www.philanthropy.cam.ac.uk

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Tomáš Pluskal @pluskal-lab.org · May 30

Today is the registration deadline for our bioML symposium on Aug 21-22. Last chance to secure your spot! More info at tinyurl.com/bioMLPrague25

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Paul Gardner @ppgardne.bsky.social · May 29

This is terrible news, HMMER & Infernal are at the heart of DBs like Pfam, Rfam & Dfam. And vital pipelines such as AlphaFold.

Sean Eddy @cryptogenomicon.bsky.social · May 22

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

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PomBase: The S. pombe knowledgebase @pombase.bsky.social · Apr 25

Congrats Gautam, so well deserved!

Gautam Dey @gautamdey.bsky.social · Apr 24

An honour to be on this list! I’m just one of many, many early career life scientists across the globe who have benefited from the support of the Company through its storied 100 year history ❤️

The Company of Biologists @biologists.bsky.social · Apr 24

Our next extraordinary biologist for this week is Gautam Dey, who co-organised the 2023 @dev-journal.bsky.social and 2024 @jcellsci.bsky.social Journal Meetings. Gautam’s research group at @embl.org, Germany, frequently contributes to @prelights.bsky.social. #100biologists @gautamdey.bsky.social

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Manuel Lera-Ramirez @manu-lera.bsky.social · Apr 22

🧬 If you are in London and you want to learn about a free & Open Source SnapGene/Benchling alternative that also supports automation 🤖, come to our next London Synbio Network meeting this Thursday 24th in Imperial!🎓

🎤 I’ll be giving a talk about #OpenCloning!

events.humanitix.com/copy-of-lond...

London SynBio Network 8

London SynBio afterwork talks and networking event on Thursday 24th of April

events.humanitix.com

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PomBase: The S. pombe knowledgebase @pombase.bsky.social · Apr 9

Twitter is dead...

Richard Sever @richardsever.bsky.social · Mar 28

“Bluesky has won”.

Please retweet… 😉

Altmetric @altmetric.com · Mar 27

THREAD

The numbers are in. @bsky.app research sharing volumes vs X Formerly Twitter

In March 2024, on most days, Bluesky hosts more posts linked to research published in 2025 than X.

By quite a lot.

Release the Kraken...

#AcademicSky #HigherEd #Altmetrics
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PomBase: The S. pombe knowledgebase @pombase.bsky.social · Apr 9

Melania D'Angiolo @melaniadangiolo.bsky.social · Apr 9

I spent a very nice couple of days at the "Hidden Cell, Dark Genome" conference in Edinburgh last week ... and even got to win a supercute eukaryotic cell 🙂 Thanks to the organisers for arranging the meeting!

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PomBase: The S. pombe knowledgebase @pombase.bsky.social · Apr 9

A periodic reminder to cite your resources. Although no @pombase.bsky.social update in this issue, we did sneak onto the cover illustration.

Genetics Society of America @genetics-gsa.bsky.social · Mar 26

This issue of #GENETICS offers updates on 6 model organism databases & knowledgebases: buff.ly/Mn0hIzl
🔎 AgBioData Consortium
🔎 Candida Genome Database
🔎 Saccharomyces Genome Database
🔎 SpudDB
🔎 Unified Phenotype Ontology
🔎 Zebrafish Information Network

Remember to cite your community resources!

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PomBase: The S. pombe knowledgebase @pombase.bsky.social · Apr 9

Nice work @leeba.bsky.social and congrats on your thesis submission.

Vaishnavi Ananthanarayanan (She/Her) @vaishananth.bsky.social · Apr 9

How is mitochondrial volume maintained across successive generations of dividing cells? In our new preprint, we show how fission yeast cells use mitochondrial activity to control division timing and maintain mitochondrial homeostasis! (1/n)

📖 www.biorxiv.org/content/10.1...

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PomBase: The S. pombe knowledgebase @pombase.bsky.social · Apr 8

CONGRATS!!!!!!

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Snezhka Oliferenko @alebenoit.bsky.social · Apr 7

OMG IT IS OUT EUKARYOTIC HOPANOIDS DESERVE ALL CAPS

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

Horizontal acquisition of prokaryotic hopanoid biosynthesis reorganizes membrane physiology driving lifestyle innovation in a eukaryote - Nature Communications

Horizontally transferred genes must be integrated into host biology. Here, the authors show that the domestication of bacterial hopanoid synthesis has rewired lipid metabolism of a eukaryote leading t...

www.nature.com

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drpombe.bsky.social @drpombe.bsky.social · Apr 7

Pombe2025 registration will go live this week. We hope you can join us August 3-8 in Boston. We will provide computers to allow international attendees to leave their phones and laptops at home.

You can find the program here:

www.bc.edu/bc-web/sites...

Program - pombe2025

www.bc.edu

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