James Lloyd 🧬

**GROUP LEADER VACANCY**

Discovery Plant Sciences

Got burning questions about how plants grow and respond to their environment? So do we. Come join us!

#johninnescentre
#plantscijobs

Snappy: de novo identification of DNA methylation sites based on Oxford Nanopore reads https://www.biorxiv.org/content/10.1101/2025.08.03.668330v1

I feel that one should be comfortable enough with R to use it when it is the only or clearly right tool. At the same time, I'm highly in favor of recreating as much of the useful R ecosystem in Python as we can. I don't love Python, but as a computer scientist, I find it more palatable than R. 9/9

I often use Python as my comfort language in simple scripts or Jupyter notebooks to do straightforward parsing of data to count, reformat or combine. Should I bother to use Rust instead?

What about Julia?

What about R, as most RNA-seq packages are written in it? (DESeq2, tximport, edgeR, RATS)

I talk a lot about Rust for building high-perf (& even non-perf critical) software, & scientific software in particular. I often discuss what's interesting to me, but wanted to offer the chance to those interested for me to answer their questions about Rust in science. Fire away with questions!🧬🖥️

My first first author manuscript has posted! I’m very excited to share SWIF-TE with yall. It is a fast, memory efficient tool to identify novel TE insertions from short-read data. 🧬 #TEworldwide #transposons

One thing we never talk about when we talk about NIH funded jobs is how underpaid most people are. My work has been a labor of love. I’m getting a significant pay bump as my research career ends. The world gets great research at bargain rates and we never talk about that.

Better access of synthetic biology knowledge and tools will help democracies the technology and help people who need it the most. Please support financially or just by spreading the word!!!

Please, if you can, financially support them so that they can take part in iGEM (international synthetic biology competition) and further grow Africa's locally grown synthetic biology industry. We should not see synthetic biology gate kept from those it could most improve the lives for!!!

Donate to Synthetic Biology Initiative Africa Limited Help support Synthetic Biology Initiative Africa Limited by donating or sharing with your friends.

This team based in Uganda, Africa is a community led effort of people eager to learn synthetic biology and make an important impact on the world! I have had the pleasure of interacting with this passionate team.

Their paypal donation page: www.paypal.com/donate/?host...

New method drop:
HCR-Proxy, a modular proximity labelling approach to profile local proteome composition around RNA at nanoscale, subcompartmental resolution. Thereby we resolved nested nucleolar layers and uncovered the grammar of spatial protein partitioning.
www.biorxiv.org/content/10.1...

How I Would Learn Bioinformatics From Scratch 12 Years Later: A Roadmap. If I were starting over, these FREE resources would be my go-to. 🧵👇
divingintogeneticsandgenomics.com/post/bioinf...

Graphic with seedlings undergoing a heat stress and illustrating how plants with thermotolerence have a higher survival rate. Gene circuits will be tested for their ability to enhance traits like thermotolerance and drought resistance in Arabidopsis thaliana plants. Graphic by Chris Micklem.

🌱 Flipping the script on plant engineering!
New ‪‪@aria-research.bsky.social‬ grant for James Locke & Chris Micklem to pioneer stochastic synthetic biology using gene expression noise as a tool to design more resilient, climate-adaptive plants.
🔗 www.slcu.cam.ac.uk/news/aria-gr...
#synbio #plantsci

After 10 years of work, a complete telomere-to-telomere gap-free genome for C. elegans finally exists: it has 106 Mb rather than the textbook 100.3 Mb, and up to 366 additional genes.
genome.cshlp.org/content/35/8...

Glyphosate: 10 Lessons from 10 Years After IARC - Dr. David Zaruk In this episode of the Talking Biotech podcast, Kevin Folta and Dr....

🎙️ Just published a new episode of Talking Biotech with Dr. Kevin Folta: Glyphosate: 10 Lessons from 10 Years After IARC - Dr. David Zaruk. Have a listen:

Asymmetry in the bryophyte, Physcomitrium patens Cell polarity and asymmetric division are fundamental to plant development, governing growth, differentiation, and stress responses. The filamentous t…

Asymmetry in the bryophyte, Physcomitrium patens | Review article

www.sciencedirect.com/science/arti...

Engineered lignin composition in Brachypodium distachyon modulates the root-associated microbiome https://www.biorxiv.org/content/10.1101/2025.07.30.667798v1

Dynamics and distribution of eccDNA in Arabidopsis. Left: Schematic representation of eccDNA amplification and sequencing via CIDER-Seq pipeline. Top right: EccDNA size distribution in Arabidopsis Col-0 leaf tissues (n = 4,158). The x-axis shows eccDNA size in kb and the y-axis shows the percentage of eccDNAs belonging to each window. Middle right: Size ranges of eccDNAs with marked median and quantiles (n = 4,190). Bottom right: Percentages of eccDNA reads mapping to TAIR CDS, TE, or intergenic databases (values represent the average of three replicates).

Previous studies of extrachromosomal circular DNA #eccDNA in #plants are based on short-read seq. @vanderschuren-lab.bsky.social uses long-read seq to obtain a map of full-length eccDNAs from #Arabidopsis, identifying their genomic origins & epigenetic regulation @plosbiology.org 🧪 plos.io/44Mq3RI

(But my memory might be especially bad as I just had some minor surgery and I am on some potent painkillers, so take what I say with a pinch of all. But I wanted to get back to you while I saw the message instead of hoping to remember later)

I have used “Slido” as a moderator for this in the past. And as a panel member. I didn’t choose it and don’t have a lot of experience with setting it up, as colleague did that. But seemed to work very well

(From memory, scan QR code as audience member on slide and write question on phone to ask)

Any suggestions/recommendations for a tool that would allow the audience at a conference to ask questions, but...

a. Those could only be seen by a moderator, with the relevant app and permissions (so that the moderator would ask the question on the person's behalf)
b. can be asked anonymously

Thx!

InSillyClo, a user-friendly web application to assist large-scale Golden Gate Cloning and MoClo workflows https://www.biorxiv.org/content/10.1101/2025.07.31.667881v1

Ancient hybridization underlies tuberization and radiation of the potato lineage Genomic and functional analyses reveal that the potato lineage originated from a homoploid interspecific hybridization event between the Tomato and Etuberosum lineages 8–9 million years ago. The alter...

The hybrid origin of potato tuberization.

From: www.cell.com/cell/fulltex...

Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals - Genome Biology Background Because transposable elements (TEs) can cause heritable genetic changes, past work on TE mobility in Arabidopsis thaliana has mostly focused on new TE insertions in the germline of hypometh...

Paper led by @movillome.bsky.social on unbiased detection of (somatic) #TE insertions in #Arabidopsis with @pacbio.bsky.social long reads out after peer review. Thanks to academic editor Leandro Quadrana for shepherding it through the review process.
#plantscience
link.springer.com/article/10.1...?

We are pleased to share that P4S Research Fellow @jamespblloyd.bsky.social from the University of Western Australia was recently awarded a Grains Research and Development Corporation Mid-Career Research Fellowship 🌟

Read more 👉 www.linkedin.com/feed/update/...

Repressive cytosine methylation is a marker of viral gene transfer across divergent eukaryotes Abstract. Cytosine DNA methylation patterns vary widely across eukaryotes, with its ancestral roles being understood to have included both transposable ele

Happy to see our latest work out in @molbioevol.bsky.social. We revisit the evolution of 5-methylcytosine across neglected eukaryotic supergroups, establishing an ancestral repressive role silencing genome invaders, both transposons and viral elements👾: academic.oup.com/mbe/advance-... 🧵 1/7

Maize and wild relatives show distinct patterns of genome downsizing following polyploidy Plant genomes are smaller than expected despite the ubiquity of polyploidy due to the process of genome downsizing called fractionation. This process causes loss of DNA sequences, including genes, unt...

Excellent talk and question answers by Samantha Snodgrass. #PlantBio2025 www.biorxiv.org/content/10.1...

Here I am at #PlantBio2025 in Milwaukee
Curious about plants under space stressors? 🚀👽🛸Come and visit poster number 200-21
@aspbofficial.bsky.social

Multimodal Learning Reveals Plants' Hidden Sensory Integration Logic https://www.biorxiv.org/content/10.1101/2025.07.25.666865v1

Correct.

I see a lot of people saying that if an N95 is not fit tested, it's worthless.

The science says no, an N95 that is not fit tested is basically just as good as a fit tested N95.

The more you know. 🌈

journals.plos.org/plosone/arti...