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Tsung-Ta Yu

@tsung-ta.bsky.social
43 followers 62 following 1 posts

PhD student in LundbergLand (@derekseveri.bsky.social) Studying the functional role of plasmids in Sphingomonas

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Reposted by Tsung-Ta Yu
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 02/10/2026
Regulatory and metabolic integration accompany plasmid domestication during adaptation to a plant-associated lifestyle www.biorxiv.org/content/10.64898/20…
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Ben Parker @ben-parker.bsky.social · 21/09/2026
Excited that our new paper with @henrylabsymbio.bsky.social and Kerry Oliver is out @pnas.org! We show that mobile genetic elements can spread adaptive host-benefiting traits across heritable insect symbionts on eco-evolutionary timescales.🧵 www.pnas.org/doi/10.1073/...
pnas.org
Phenotypic divergence is driven by mobile genetic elements in a heritable insect symbiont | PNAS
Heritable microbes profoundly influence insect biology, yet the traits they confer often evolve rapidly and differ among closely related symbiont s...
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Nature Microbiology @natmicrobiol.nature.com · 17/09/2026
Out Now! Bacterial growth rate in populations and single cells #MicroSky
go.nature.com
Bacterial growth rate in populations and single cells
Nature Microbiology, Published online: 17 September 2026; doi:10.1038/s41564-026-02449-6In this Perspective, Levin and Wang give a brief history of bacterial growth rate and discuss how it is connected to nutrient availability and macromolecule synthesis, with a focus on (p)ppGpp as a central hub regulating resource allocation and, indirectly, growth rate at the single-cell level.
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Will Matlock @wtmatlock.bsky.social · 09/09/2026
Does an AMR gene on a plasmid diversify differently to an AMR gene on a chromosome? We are looking for a PhD student to work on this question in Bath!
gw4biomed.ac.uk
Turning up the volume: plasmid copy number and gene duplications as drivers of antimicrobial resistance evolution - GW4 BioMed MRC DTP
Project Code IIAR27Ba Matlock Project Type Wet lab Research Theme Infection, Immunity, and Antimicrobial Resistance Project Summary Download Summary Plasmids are important drivers of antimicrobial res...
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 06/06/2026
Extreme envelope plasticity drives temperature-dependent morphogenesis in the LPS-free bacterium Sphingobium yanoikuyae www.biorxiv.org/content/10.64898/20…
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Reposted by Tsung-Ta Yu
EMBO @embo.org · 29/06/2026
Deadline tomorrow! Submit your abstract now for the Hybrid EMBO Workshop "Molecular mechanisms in #evolution and #ecology," 6–9 October 2026. www.embl.org/about/info/course-and-… #EMBOevents #EMBOEvoEco 🧪
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Reposted by Tsung-Ta Yu
Ching-Yi Huang @chingyi.bsky.social · 29/06/2026
Back on social media for SMBE 2026! I'll be presenting the fascinating microbe Hyaloperonospora arabidopsidis at Poster A048!
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Maliheh Mehrshad @mehrshmali.bsky.social · 04/06/2026
🔬 We have an open PhD position at SLU Uppsala! We're looking for a curious & driven PhD student to join the #ECOPHARM project funded by @kawresearch.bsky.social and investigate plasmid-dependent phages in aquatic ecosystems. Pls share with anyone who might be interested! www.slu.se/en/about-slu...
slu.se
Diversity of Plasmid-Dependent Phages in Aquatic Ecosystems | slu.se
SLU - Science and Education for Sustainable Life
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Eduardo Rocha @epcrocha.bsky.social · 23/07/2025
Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
graphical abstract of the article the extended mobility of plasmids
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Reposted by Tsung-Ta Yu
Nature Microbiology @natmicrobiol.nature.com · 01/05/2026
Out Now! Unravelling bacterial complexity at high resolution with single-cell transcriptomics #MicroSky
go.nature.com
Unravelling bacterial complexity at high resolution with single-cell transcriptomics
Nature Microbiology, Published online: 01 May 2026; doi:10.1038/s41564-026-02333-3This Review summarizes recent advances in bacterial single-cell transcriptomics approaches, while also discussing technological and computational challenges remaining to be met and the need for standardization going forwards.
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Reposted by Tsung-Ta Yu
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 09/04/2026
Single-cell genomics reveals opportunistic Enterobacterales carrying putative cationic antimicrobial peptide resistance genes in red crown rot-affected soybean rhizoplanes www.biorxiv.org/content/10.64898/20…
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Derek Severi Lundberg @derekseveri.bsky.social · 09/04/2026
the sensitivity of "tagIMseq" will be broadly useful for CRISPR-associated transposon work. Ruling out off-target insertions in resuspended colonies with minimal effort and cost investment is critical because targeting isn't always perfect.
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Reposted by Tsung-Ta Yu
Ezgi Mehmetoglu Boz @ezgiboz.bsky.social · 07/04/2026
A quick thread summarizing our new bioRxiv preprint on using CASTs for DNA barcoding to tell "look-alike" bacteria apart (Sphingomonas edition)!! Enjoy the read! ✨
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Reposted by Tsung-Ta Yu
Derek Severi Lundberg @derekseveri.bsky.social · 07/04/2026
When organisms look similar, you can use a tag to tell them apart. We wanted to tag our collection of diverse Sphingomonas bacteria with DNA barcodes to distinguish them. We planned to use Tn7, until we saw new reports about CRISPR-associated transposons (CASTs).
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Cell Reports @cp-cellreports.bsky.social · 26/02/2026
Unveiling hidden variables in stressed bacteria
dlvr.it
Unveiling hidden variables in stressed bacteria
Noise in bacterial stress responses is often dismissed as mere randomness. While true stochasticity exists, much variation reflects hidden variables—cell state, history, and microenvironment—that are only now becoming measurable. Choudhary and Vincent review emerging tools that disentangle chance from determinism, moving microbiology toward more mechanistic and predictive frameworks.
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Reposted by Tsung-Ta Yu
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 25/02/2026
Programmed strain tagging and gene disruption throughout a diverse bacterial genus www.biorxiv.org/content/10.64898/20…
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Asiya Gusa @asiya-gusa.bsky.social · 17/01/2026
Sharing our lab’s first publication! Probing clinical isolates of Cryptococcus, a disease-causing fungus of the lungs and brain, we found multiple heat-mobile elements that ‘jump’ in the genome at body temperature (!) with the ability to drive adaptive changes. journals.plos.org/plosgenetics...
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Reposted by Tsung-Ta Yu
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 13/01/2026
Integrative mobilizable elements are pervasive throughout Pseudomonadota www.biorxiv.org/content/10.64898/20…
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Tominaga K. (tomiken) @pacyc184.bsky.social · 31/12/2025
Replicon family of Vibrionaceae plasmids as a reservoir of antimicrobial and phage resistance genes in marine ecosystems | The ISME Journal | Oxford Academic academic.oup.com/ismej/article/19/1…
dx.doi.org
Replicon family of Vibrionaceae plasmids as a reservoir of antimicrobial and phage resistance genes in marine ecosystems
Abstract. Plasmids are mobile genetic elements that drive horizontal gene transfer among bacteria, influencing microbial community composition and function
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ivanraimondi.bsky.social @ivanraimondi.bsky.social · 14/10/2025
🚀 Excited to share SMART-PTA (miniaturized Primary Template Amplification) a high-throughput single-cell whole-genome amplification method that preserves clonal lineage information while enabling deep genomic and transcriptomic profiling.
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Derek Severi Lundberg @derekseveri.bsky.social · 13/08/2025
www.sciencedirect.com/science/arti... How much environmental chaos to embrace in plant-microbe research, and to what end? A commentary on setting (with all choices OK as long as all options considered) w/ bergelsonlab.org, @fabriceroux7.bsky.social, @plantevolution.bsky.social, tkarasovlab.org
authors.elsevier.com
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Wannes Nauwynck @wannesn.bsky.social · 24/07/2025
New Review Out! We explore how droplet microfluidics is opening new doors in microbial ecology - enabling single-cell functional insights into growth, metabolism & interactions. 🔗 doi.org/10.1093/fems... #MicrobialEcology #DropletMicrofluidics #Microbiology
doi.org
Droplet microfluidics for single-cell studies: a frontier in ecological understanding of microbiomes
Abstract. Recent advances in single-cell technologies have profoundly impacted our understanding of microbial communities—shedding light on cell-to-cell va
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Team Thomma @teamthomma.bsky.social · 24/07/2025
📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social rdcu.be/exBSp
rdcu.be
Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution
Nature Communications - Giant transposons, known as ‘Starships’, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions...
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Paula Ramiro-Martínez @paularamiro.bsky.social · 02/07/2025
Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨 doi.org/10.1038/s414... We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇
doi.org
Universal rules govern plasmid copy number - Nature Communications
Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...
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Tsung-Ta Yu @tsung-ta.bsky.social · 15/07/2025
Thanks to everyone who came by my poster today for discussion! #2025ISMPMI If you weren’t able to make it but still interested in the potential role native plasmids play within Sphingomonas-plant interactions. Can check it out now on Zenodo zenodo.org/records/1591...
zenodo.org
Small DNA, Big Impact? Exploring the role of plasmids in Sphingomonas – plant interactions
This poster was presented at the 2025 IS-MPMI, Cologne Submitted Abstract Plasmids provide traits that can enable bacteria to adapt to unique and changing environments. Sphingomonas, an often-benefici...
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Reposted by Tsung-Ta Yu
Derek Severi Lundberg @derekseveri.bsky.social · 15/07/2025
This work started nearly 10 years ago and was once my main postdoctoral project at @plantevolution.bsky.social before I slowed work on it to a trickle because it became confusing. But it always remained extremely interesting. journals.plos.org/plosbiology/...
journals.plos.org
A major trade-off between growth and defense in Arabidopsis thaliana can vanish in field conditions
In controlled greenhouse conditions, Arabidopsis thaliana plants with a hyperactive allele of the ACD6 gene have stronger pathogen defenses but are smaller and make fewer seeds, in a classic fitness t...
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Ezgi Mehmetoglu Boz @ezgiboz.bsky.social · 13/07/2025
Last week, I had a great time at the New Phytologist EiC Symposium: “Microbes as hidden or prominent players in plant life” in Tartu, Estonia! Honored and very happy to receive the Best Poster Award! ✨ Big thanks to the organizers and all the inspiring scientists I met! 🌱 @newphyt.bsky.social
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