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Lotus Lofgren

@lotuslofgren.bsky.social
1.4K followers 299 following 28 posts

Fungal evolutionary ecology, genomics, bioinformatics, sci-art, code, data viz. She/her. Asst. Prof. at UC Berkeley.

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Reposted by Lotus Lofgren
The Rokas Lab at Vanderbilt University @rokaslab.bsky.social · 22/03/2026
What an honor and privilege to organize #fungal26 with the one and only Meritxell Riquelme! Thank you fungal community and @genetics-gsa.bsky.social for making this such a great meeting !
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Lotus Lofgren @lotuslofgren.bsky.social · 20/03/2026
Hey #fungal26 our lab is hiring a postdoctoral researcher for an NSF funded project in ectomycorrhizal competition. Come find me for more info! www.lotuslofgren.com/pd2026
lotuslofgren.com
PD ad 2026 — The Lofgren Lab
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Lotus Lofgren @lotuslofgren.bsky.social · 12/03/2026
www.nature.com/articles/s41...
nature.com
Cross-kingdom RNA interference promotes arbuscular mycorrhiza development - Nature Plants
The authors provide evidence that symbiotic fungi forming widespread arbuscular mycorrhiza symbioses use cross-kingdom RNA interference to silence plant genes and promote their colonization of host ro...
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Reposted by Lotus Lofgren
PLOS Biology @plosbiology.org · 03/02/2026
#Antifungal resistance is a global threat, but epigenetic mechanisms drive rapid, reversible adaptation in fungi. This study shows that #RNAi or #heterochromatin driven #epimutations transiently silence the gene fkbA to confer FK506 #tacrolimus resistance in #Mucor @plosbiology.org 🧪 plos.io/4qdttWc
Top: FK506-resistant strains isolated from the Mucor circinelloides complex. Phenotypic analysis of FK506-resistant isolates in Mucor janssenii CBS185.68 (PS1), Mucor bainieri CBS293.63 (PS3), and Mucor atramentarius CBS202.28 (PS6). WT, wild-type; M, mendelian mutant; E, epimutant. Bottom: Schematic overview of epigenetic silencing contributing to antifungal resistance in Mucor species. fkbA expression enables FKBP12 production and FK506 sensitivity (yeast-like morphology). Epigenetic silencing of fkbA via RNAi and/or heterochromatin leads to FK506 resistance and hyphal growth. Generated with BioRender.com.
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Lotus Lofgren @lotuslofgren.bsky.social · 31/01/2026
SuilluCamp No. 2 is coming to Portland July 11, 2026! Join us for featured talks, networking, and community building around Suillus as a model genus for ectomycorrhizal biology, ecology, and evolution. Abstract submissions open now through June 1.
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Eva Stukenbrock @estukenbrock.bsky.social · 27/01/2026
What enables a fungus to invade a mammal host? @marco-guerreiro.bsky.social unravels signatures of translation adaptation among pathogenic and non-pathogenic species of Trichosporonales. See more: www.nature.com/articles/s41...
nature.com
Genomic and physiological signatures of adaptation in pathogenic fungi - Nature Communications
Emerging fungal pathogens have detrimental impacts on crops, animals, and humans, however little is known about their transition to a pathogenic lifestyle. This study demonstrates that the transition ...
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Sara Branco @sbranco.bsky.social · 03/12/2025
Everything you always wanted to know about mushroom-forming fungi! Great collab with amazing mycologists. Thanks Laszlo Nagy for leading this effort! www.nature.com/articles/s44...
nature.com
The biodiversity, genomics, ecology and evolution of mushroom-forming fungi - Nature Reviews Biodiversity
Mushroom-forming fungi have along evolutionary history and a suite of important ecological roles. This Review highlights advances in understanding of Agaricomycetes evolution and ecology driven by gen...
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Jean-Michel Ané @jeanmichelane.bsky.social · 05/12/2025
Terpenoids are associated with cytokinin and auxin signaling during mycorrhiza formation in the Suillus bovinus–Pinus yunnanensis symbiosis - ScienceDirect
sco.lt
Terpenoids are associated with cytokinin and auxin signaling during mycorrhiza formation in the Suillus bovinus
Suillus bovinus is an ecologically significant wild ectomycorrhizal fungus that forms symbiotic associations with pine trees. Terpenoids are known to play a key role in interactions between fungi and plants. However, the molecular mechanisms underlying the effects of terpenoids on the formation of symbiotic associations with S. bovinus remain poorly understood. Here, we investigated the effect of S. bovinus terpenoids on root development and mycorrhizal formation in Pinus yunnanensis using physiological, transcriptomic, and phytohormone assays. Our findings revealed that terpenoids from S. bovinus were associated with alterations in the synthesis and signaling of cytokinin in P. yunnanensis, evidenced by changes in the expression of specific genes in the mevalonate synthesis pathway and signaling transduction, such as CKXs, AHP, and A-ARRs. Similarly, these terpenoids correlated with changes in auxin synthesis and signaling, indicated by modulated tryptophan levels and the expression of specific enzyme genes, such as GH3, AUX1, AUX/IAA, and SAUR. This suggests that terpenoids from S. bovinus may contribute to lateral root development and mycorrhizal formation in P. yunnanensis, potentially by influencing the relative levels of cytokinin and auxin. These results shed light on the potential involvement of terpenoids produced by S. bovinus in establishing symbiotic interactions between ectomycorrhizal fungi and their host plants, warranting further direct functional validation.
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Toby Baril @tobybarilbio.bsky.social · 12/11/2025
TEs aren’t just genomic parasites, they’re also engines of genomic novelty. Our new study with ~2,000 Z. tritici genomes shows repeated TE mobilization waves during global expansion. With @danielcroll.bsky.social & @guidopuccetti.bsky.social 🧬 www.nature.com/articles/s41... #TEworldwide
nature.com
Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen - Nature Communications
In this study, the authors analysed a large genomic dataset to trace how jumping genes shaped the global spread of a major wheat pathogen and reveal bursts of activity over decades that drove adaptati...
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Jo Rhodes @drjorhodes.com · 11/11/2025
Genomic and phenotypic insights into the expanding phylogenetic landscape of the Cryptococcus genus journals.plos.org/plosgenetics...
journals.plos.org
Genomic and phenotypic insights into the expanding phylogenetic landscape of the Cryptococcus genus
Author summary Cryptococcus is a genus of fungi that includes both pathogenic species capable of causing life-threatening infections in humans and many environmental species that inhabit soil, fruit, ...
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Emily Josephs @emjo.bsky.social · 24/10/2025
Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...
ybrandvain.github.io
Applied Biostatistics
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Jason Stajich @hyphaltip.bsky.social · 16/10/2025
Registration open for #Fungal26 genetics-gsa.org/fungal-2026/ at Asilomar.
genetics-gsa.org
Homepage - 33rd Fungal Genetics Conference
Visit our website to learn more.
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Toby Kiers @tobykiers.bsky.social · 10/10/2025
This week, I was awarded a MacArthur ‘Genius’ Grant. So proud to be included among individuals recognized for “extraordinary originality & dedication in their creative pursuits”. This research has been possible because I collaborate with the most incredible teams. www.nytimes.com/2025/10/08/a...
nytimes.com
MacArthur Foundation Announces 2025 ‘Genius Grant’ Winners
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New Phytologist @newphyt.bsky.social · 04/10/2025
Invasive ectomycorrhizal fungi in South America 📖 buff.ly/ZgIX5IC #TansleyInsight by @nahpo.bsky.social and @martin-nunez.bsky.social @uh.edu @WileyPlantSci #PlantSci Image source: Colección y Archivo Visual Patagónico; Photographer: Antonio Lynch; courtesy of Federico Silin.
nph.onlinelibrary.wiley.com
Ectomycorrhizal fungi being introduced together with their plant hosts on Isla Victoria, Bariloche, Patagonia, Argentina, in 1936.
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Lotus Lofgren @lotuslofgren.bsky.social · 01/10/2025
www.nature.com/articles/s41...
nature.com
A timetree of Fungi dated with fossils and horizontal gene transfers - Nature Ecology & Evolution
Combining fossil-based and molecular calibrations with data on horizontal gene transfer events, the authors develop a time-calibrated phylogeny of Fungi. This timescale, which integrates analytic uncertainties, suggests an older age of crown Fungi (1,401–896 million years ago), as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma).
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Prof. Keiko Torii @keikoutorii.bsky.social · 01/10/2025
🌱Tenure-track Assistant Professor Position OPEN🌱 -Plant Interkingdom/Environment Interactions & Plant Immunity- at The Univ. Texas at Austin, Molecular BioSciences. Deadline Nov 1st. Please spread the words and APPLY! Contact me if you have any questions. apply.interfolio.com/175001
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Hugues Renault @huguesrenault.bsky.social · 23/09/2025
Transposable elements are vectors of recurrent transgenerational epigenetic inheritance | Science www.science.org/doi/10.1126/...
science.org
Transposable elements are vectors of recurrent transgenerational epigenetic inheritance
DNA methylation loss at transposable elements (TEs) can affect neighboring genes and be epigenetically inherited in plants, yet the determinants and significance of this additional system of inheritan...
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Lotus Lofgren @lotuslofgren.bsky.social · 23/09/2025
Excited to share our latest paper, now out in FPS: "Diverse nitrogen acquisition strategies of conifer-associated ectomycorrhizal fungi shape unique responses to changing nitrogen regimes" www.frontiersin.org/journals/pla...
frontiersin.org
Frontiers | Diverse nitrogen acquisition strategies of conifer-associated ectomycorrhizal fungi shape unique responses to changing nitrogen regimes
Ectomycorrhizal fungi are critical mediators of nitrogen acquisition in forest ecosystems, exhibiting variation in both host association and metabolic traits...
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Andres Bendesky @bendeskylab.com · 20/09/2025
Tenure-track Assistant Professor in Computational Ecology and/or Evolution @columbiauniversity.bsky.social. Deadline to apply September 30. Reach out if you have questions. apply.interfolio.com/172496
apply.interfolio.com
Apply - Interfolio {{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
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Ákos T Kovács @evolvedbiofilm.bsky.social · 09/09/2025
Comparing EcoFab 2.0 results from 5 labs on 3 continents‼️ Breaking the reproducibility barrier with standardized protocols for plant–microbiome research @plosbiology.org by Vlastimil Novak et al from Trent Northen @jgi.doe.gov journals.plos.org/plosbiology/...
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Ben Auxier @benauxier.bsky.social · 09/09/2025
Really cool new results from @fritzlaylin.bsky.social , they got actual working homology-directed transformation working in a chytrid fungus! There are so, so many interesting questions that still need explaining in this group, and molecular genetics can answer a lot! www.biorxiv.org/content/10.1...
biorxiv.org
Homology-mediated transformation of frog-killing fungus Batrachochytrium dendrobatidis illuminates chytrid development and pathogenesis
The chytrid fungus Batrachochytrium dendrobatidis ( Bd ) infects amphibians and causes chytridiomycosis, a disease linked to global amphibian decline. Despite its ecological importance, Bd has lacked ...
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Neta Shlezinger @shlezingerlab.bsky.social · 24/08/2025
Our study on a mycovirus that boosts fungal virulence is now out — and beautifully covered in this Behind the Paper piece by Amariliz Rivera Huge thanks for capturing the heart of the story so thoughtfully. @natmicrobiol.nature.com rdcu.be/eB9yg
rdcu.be
Mycoviruses steer fungal fitness
Nature Microbiology - A mycovirus drives the fitness of the lung-infecting fungus Aspergillus fumigatus under stress, helping it to survive within immune cells, and thus shaping its pathogenesis.
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Jo Rhodes @drjorhodes.com · 11/08/2025
Stellar work by graduate students to build this comprehensive dataset of antifungal resistance mechanisms. Kudos and congratulations to the Landry lab @christianlandry.bsky.social www.nature.com/articles/s41...
nature.com
FungAMR: a comprehensive database for investigating fungal mutations associated with antimicrobial resistance - Nature Microbiology
An online, manually curated and continually updating database of fungal antimicrobial resistance mutations provides a starting point for further research in fungal AMR.
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Lotus Lofgren @lotuslofgren.bsky.social · 02/09/2025
Our department (Berkeley PMB) is hiring an asst. prof. in Plant Resilience to Climate Change! aprecruit.berkeley.edu/JPF05049
aprecruit.berkeley.edu
Assistant Professor - Plant Resilience to Climate Change - Department of Plant and Microbial Biology
University of California, Berkeley is hiring. Apply now!
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Mycological Society of America @msafungi.bsky.social · 21/08/2025
📢🍄Mycology job alert🍄📢 The Department of Plant Biology at @michiganstateu.bsky.social has a job opening for a herbarium/fungarium director at the Assistant, Associate or Full professor level. Review of applications start on 3rd October 2025. careers.msu.edu/jobs/assista...
careers.msu.edu
Assistant/Associate/Full Professor Tenure System - East Lansing, Michigan, United States
Working/Functional Title Assistant/Associate/Full Professor Tenure System Position Summary The Department of Plant Biology (PLB) at Michigan State University (MSU) seeks applications for a director of...
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Jason Stajich @hyphaltip.bsky.social · 21/08/2025
Assistant/ Associate Professor of Mycology at UGA - Go be part of a Legendary Fungal Group fungi.franklinresearch.uga.edu and dept of plant pathology plantpath.caes.uga.edu www.ugajobsearch.com/postings/445...
ugajobsearch.com
Assistant or Associate Professor - Fungal Biology/Mycology
The Department of Plant Pathology in the College of Agricultural and Environmental Sciences (CAES) at the University of Georgia is recruiting for the position of Assistant or Associate Professor in Fu...
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Tadashi Fukami @fukamit.bsky.social · 06/08/2025
Assistant Professor position in Traditional Ecological Knowledge at Stanford University. Applications due Sept 30, 2025 facultypositions.stanford.edu/en-us/job/49...
facultypositions.stanford.edu
Stanford | Faculty Positions: Details - Assistant Professor in Traditional Ecological Knowledge
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Louis Mielke @myconet.bsky.social · 30/06/2025
New Article Out 📣 Open Access 📣 @newphyt.bsky.social “Fungal guild interactions slow decomposition of boreal forest pine litter and humus” nph.onlinelibrary.wiley.com/doi/10.1111/...
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Lotus Lofgren @lotuslofgren.bsky.social · 29/06/2025
Inspired and overwhelmed after SuilluCamp No.1 - amazing science, nearly 50 attendees, and an outline for a new strategic plan for the International Suillus Consortium. I *could not be* more grateful for this community, or more excited for what we’re building together. Thank you #TeamSlime!
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Sebastian Schornack @dromius.bsky.social · 24/06/2025
Plz repost. Fresh Preprint led by @alexguyon.bsky.social When a pathogen pushes into a cell already occupied by a symbiotic fungus, things change. New membrane phospholipids at pathogen haustoria! This may impact immune receptor positioning & defense secretion. - And the roots are more resistant!
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Vasilis Kokkoris @vkokkoris.bsky.social · 20/06/2025
🧪🧬Should we reignite genetic manipulation attempts on #arbuscular #mycorrhizal #fungi? Our review in @cp-trendsmicrobiol.bsky.social suggests the time is ripe. With: Midge Woodward @paszkowskilab.bsky.social @alexdallaire.bsky.social Open access🔗 doi.org/10.1016/j.ti... #scicomm
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Yan Gong @yangong.bsky.social · 19/06/2025
Happy to announce that I will be opening my lab in the PMB department at UC Berkeley this July. Our lab will study nectary development and evolution using non-conventional models. We are actively recruiting. Join us if you are also enthusiastic about development or evolution!
yangonglab.com
Gong Lab @ UC Berkeley PMB
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Francis M. Martin @fmartin54.bsky.social · 10/06/2025
Saprotrophy-to-symbiosis continuum in fungi I enjoyed writing this piece with Tan Hao for the Current Biology special issue on Fungi www.sciencedirect.com/science/arti...
sciencedirect.com
Saprotrophy-to-symbiosis continuum in fungi
Fungi are one of the most diverse and ecologically important groups of organisms on Earth. They exhibit remarkable diversity in their ecological roles…
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Burstein lab @bursteinlab.bsky.social · 07/06/2025
1/6 🧬📊 Curious about the buzz around NLP in biology? Feeling overwhelmed by the rapid developments? We've got you covered! Our review on NLP applications in genomics, by the wonderful Ella Rannon, is now out as a pre-print! #NLP #Bioinformatics arxiv.org/abs/2506.02212
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Jenn Coughlan @jenncoughlan.bsky.social · 04/06/2025
Yale School of the Environment is hiring an open-rank professor in temperate forest resilience! Come be my colleague!!!!! environment.yale.edu/jobs/faculty...
environment.yale.edu
Faculty Position in Temperate Forest Resilience
The Yale School of the Environment (YSE) invites applications for an open-rank tenured or tenuretrack faculty position with research and teaching interests in the broad area of temperate forest resili...
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LaBella Lab @lablabella.bsky.social · 04/06/2025
We are looking for a Postdoc in the LaBella Lab! Do you love fungi 🍄, genetics 🧬and bioinformatics 💻 - then this might be a good fit for you! jobs.charlotte.edu/postings/63307 Applications accepted through July 1
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Lotus Lofgren @lotuslofgren.bsky.social · 31/05/2025
Students of Slime! Reminder that today is the last day to submit an abstract for trainee lightning talks at SuilluCamp - the inaugural Suillus pre-meeting on June 28th! Submission portal here: msa.joynconference.com/v2/?c=submis...
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Lotus Lofgren @lotuslofgren.bsky.social · 28/05/2025
imafungus.pensoft.net/article/1556... Sharing this important roadmap for other scientific societies in unprecedented times. To my colleagues who contributed to this writing, and all the work it encompasses over the last decade, but remain unnamed because of concerns over retaliation- thank you.
imafungus.pensoft.net
10 years of advancing diversity within the Mycological Society of America
Like most Science, Technology, Engineering, and Mathematics (STEM) fields, mycology has been dominated by white male scientists, while representation of marginalised groups (e.g., women, persons from ...
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Wright Laboratory @labofwright.bsky.social · 28/04/2025
Proud to announce a new publication from the lab: EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals www.nature.com/articles/s41...
nature.com
EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals - Nature Communications
Despite having structures for most proteins, we still do not know their function. Here, authors introduce EvoWeaver, a de novo method to identify genes working together using evolutionary information....
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Marc Chevrette @wildtypemc.bsky.social · 27/04/2025
antiSMASH8: The Ocho Manuscript is out! doi.org/10.1093/nar/...
doi.org
antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry, enzymology, and regulation
Abstract. Microorganisms synthesize small bioactive compounds through their secondary or specialized metabolism. Those compounds play an important role in
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Ran Blekhman @blekhman.bsky.social · 18/04/2025
Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics www.nature.com/articles/s42...
nature.com
Metabolites are not genes — avoiding the misuse of pathway analysis in metabolomics - Nature Metabolism
Pathway analysis, originally developed for gene expression data, has been adapted for metabolomics. However, owing to the unique characteristics and constraints of metabolites compared with genes, pat...
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Lotus Lofgren @lotuslofgren.bsky.social · 18/04/2025
www.biorxiv.org/content/10.1...
biorxiv.org
Comparative transcriptomics uncovers plant and fungal genetic determinants of mycorrhizal compatibility
Ectomycorrhizal symbiosis supports tree growth and is crucial for nutrient cycling and temperate and boreal ecosystems functioning. The establishment of functional ECM first requires the association o...
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Ethan White @ethanwhite.weecology.org · 06/03/2025
Every US scientist needs to 100% clear that this is a fundamental attack on the process of science itself. If allowed to stand it will be the end of US science as we know it. Staying quiet because it does not (yet) target your work is not an option. www.nature.com/articles/d41...
nature.com
Exclusive: NIH to terminate hundreds of active research grants
Studies that touch on LGBT+ health, gender identity and DEI in the biomedical workforce could be terminated, according to documents obtained by Nature.
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Aaron Vogan @fungage-lab.bsky.social · 11/02/2025
Interested in #fungal accessory chromosomes or toxin/antidote genes? Check out our new preprint! We show that the Spok gene family in Fusarium include active toxin/antidote genes. We present a model for how these genes influence the evolution of fungal genomes. www.biorxiv.org/content/10.1...
Illustration of FuSpok killing a cell which has lost an accessory chromosome. Core chromosome in blue, accessory chromosome in red. Black circle: FuSpok. Green circle: antidote function. Red triangle: toxin function.
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Leslie Rissler @ljrissler.bsky.social · 03/03/2025
NSF plans to reinstate all probationary employees who were fired on 18 Feb! NSF’s decision. 👏🏻👏🏻❤️
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Jean-Michel Ané @jeanmichelane.bsky.social · 24/02/2025
A must read for AM symbiosis afficionados nph.onlinelibrary.wiley.com/doi/10.1111/...
nph.onlinelibrary.wiley.com
A fungal sRNA silences a host plant transcription factor to promote arbuscular mycorrhizal symbiosis
Cross-kingdom RNA interference (ckRNAi) is a mechanism of interspecies communication where small RNAs (sRNAs) are transported from one organism to another; these sRNAs silence target genes in trans ...
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Morgan Carter @morgancarterphd.bsky.social · 19/02/2025
Collaborators fired at USDA. Program officers fired at NSF. Study sections suspended indefinitely at NIH (also firings). It's impossible to just keep your head down and do the work, as the work and the people are vanishing in front of us. 🧪
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Laura Lautz @llautz.bsky.social · 19/02/2025
Yesterday was the darkest day of my professional life so far. Many of NSF’s best and brightest people fired indiscriminately. The terms of their firing cruel. My colleagues matter, they are valued and they make a difference. I have no words. www.npr.org/2025/02/18/n...
npr.org
National Science Foundation fires roughly 10% of its workforce
NSF fired 168 employees, leaving the agency less equipped to fund a wide range of scientific research.
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Lotus Lofgren @lotuslofgren.bsky.social · 06/02/2025
Hivemind- as we get up and running, I’m looking for formalize how we track and inventory our culture collection with a QR or barcode system. Anyone have recommendations for set up (batch QR generators, database, label printer etc.)?
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Nonia Pariente @npariente.bsky.social · 22/01/2025
To end the morning, Solene Moulin tells us about a fascinating symbiosis that allowed Episthemia spp to fix nitrogen. Can Crocosphera-based symbioses teach us how to make N-fixing plants? For more about the wonderful world of symbiosis, see this fantastic @plosbiology.org collection plos.io/3UncV1j
collections.plos.org
Symbiosis across the tree of life
The aim of this collection is to showcase symbiotic relationships across the tree of life, exploring their evolutionary basis and underlying mechanisms.
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