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James Lloyd 🧬

@jamespblloyd.bsky.social
2.3K followers 2.1K following 472 posts

Synthetic AstroBotanist Engineer of synthetic gene circuits in plants. 🇬🇧🇪🇺 now in 🇦🇺. He/They. Google Scholar: shorturl.at/dnHVZ Compbio blog: .com

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Reposted by James Lloyd 🧬
emmasebunyakato.bsky.social @emmasebunyakato.bsky.social · 22h
Webinar recording now available YouTube: youtu.be/xgrt8m19IjA Website: synbioforall.org How can we make whole plasmid sequencing accessible for resource limited labs? Dr. James Lloyd, University of Western Australia @synbio4allafrica.bsky.social @jamespblloyd.bsky.social
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Reposted by James Lloyd 🧬
synbio4allafrica.bsky.social @synbio4allafrica.bsky.social · 22h
Webinar recording now available YouTube: youtu.be/xgrt8m19IjA Website: synbioforall.org How can we make whole plasmid sequencing accessible for resource limited labs? Dr. James Lloyd, University of Western Australia @jamespblloyd.bsky.social
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Reposted by James Lloyd 🧬
Robert Arkowitz @robertarkowitz.bsky.social · 08/10/2026
www.nature.com/articles/s41...
nature.com
Overcoming key challenges in the evolutionary transition to multicellularity - Nature
This Review synthesizes an evolutionary framework for understanding the key stages, challenges and microevolutionary processes through which single cells evolve into functionally integrated multi...
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Reposted by James Lloyd 🧬
Matthew Cobb @matthewcobb.bsky.social · 06/10/2026
A lot of excitement on here about the article in Science summarising the discoveries of @alistairsponsel.bsky.social and Brian Sutton, just published in the Journal of the History of Biology. Some people have asked, so here is what I think they show, and what are the implications:
link.springer.com
Photograph 49 is the Key to Understanding the History of Rosalind Franklin’s DNA Photograph 51 - Journal of the History of Biology
This essay, co-authored by a historian of science and an X-ray crystallographer, sheds new light on Rosalind Franklin’s Photograph 51. We refute the infamous claim that, unlike James Watson, Franklin ...
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James Lloyd 🧬 @jamespblloyd.bsky.social · 02/10/2026
They seem to only want to experimental data and not hypothesis from what I can tell with a nice suggestion
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James Lloyd 🧬 @jamespblloyd.bsky.social · 02/10/2026
I do not think a hypothesis paper would fit into their categories, but it's a nice suggestion
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James Lloyd 🧬 @jamespblloyd.bsky.social · 02/10/2026
I have a short one figure hypothesis paper that I would like to get out rapidly. But sadly @biorxivpreprint.bsky.social do not take hypothesis papers without new results. Does anyone have a suggestion for how I can get this idea out? It relates to the origins of complex multicellular life 
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Reposted by James Lloyd 🧬
Philipp Radler @radler92.bsky.social · 01/10/2026
The first paper of my PostDoc in Christa Schlepers group (@archaea-vienna.bsky.social) on the dynamics of Asgard archaea is now out in Nature! www.nature.com/articles/s41... This was a great team effort and I am looking forward to uncover the complex behavior of these cells further!
nature.com
Dynamic protrusions mediate crawling motility in Asgard archaea - Nature
Anoxic live-cell imaging shows actin-dependent crawling motility and dynamic protrusions in Asgard archaea, providing insights into cellular innovations that may have contributed to eukaryotic evoluti...
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Reposted by James Lloyd 🧬
Andreas P.M. Weber 🌾🌱🧬 @apmweber.bsky.social · 01/10/2026
Asgard archaea can actively crawl, using protrusions that are filled with an actin-based "cytoskeleton". Speed in the range of µm / s. www.nature.com/articles/s41...
nature.com
Dynamic protrusions mediate crawling motility in Asgard archaea - Nature
Anoxic live-cell imaging shows actin-dependent crawling motility and dynamic protrusions in Asgard archaea, providing insights into cellular innovations that may have contributed to eukaryotic evoluti...
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Reposted by James Lloyd 🧬
MAdLand @watertoland.bsky.social · 01/10/2026
Now we'll hear from Norina Noor from the Frank Lab in Munich, who will present her work on the functional analysis of small RNA pathways in bryophytes. #MAdLand2026 #plantsci
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Reposted by James Lloyd 🧬
MAdLand @watertoland.bsky.social · 01/10/2026
We are very happy to welcome our next guest speaker, Liam Dolan @liamdolanlab.bsky.social from the GMI in Vienna. He is telling us more about the development of the Marchantia polymorpha sporeling #MAdLand2026 #plantsci
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Reposted by James Lloyd 🧬
MAdLand @watertoland.bsky.social · 01/10/2026
And we’ve reached the final talk of the session! Mina Kazemianrouhi from the Reumann lab in Hamburg is exploring how peroxisome functions evolved and assembled during plant terrestrialization. #MAdLand2026 #plantsci
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MAdLand @watertoland.bsky.social · 01/10/2026
Starting fresh into a new day! 🌱 We’re very happy to welcome @moodytomato.bsky.social from Oxford as our next guest speaker, who will be unravelling the origins of multidimensional growth in plants with us. #MAdLand2026 #plantsci
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Reposted by James Lloyd 🧬
MAdLand @watertoland.bsky.social · 01/10/2026
Our first short talk of the day 🌱 @dvarshney.bsky.social from @rensingstefan.bsky.social lab in Freiburg is exploring the origins of land plants through gene family evolution and a reproducible Galaxy workflow. #MAdLand2026 #plantsci
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Reposted by James Lloyd 🧬
MAdLand @watertoland.bsky.social · 01/10/2026
Next up, @clinton-sa.bsky.social from @grandpahiro.bsky.social lab is exploring the evolution of SA signalling and NPR protein function using Marchantia polymorpha and Physcomitrium patens as research models. #MAdLand2026 #plantsci
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James Lloyd 🧬 @jamespblloyd.bsky.social · 01/10/2026
I don’t think so and have thought this way for about a decade.
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Reposted by James Lloyd 🧬
MAdLand @watertoland.bsky.social · 30/09/2026
Alisha Alisha from @plantphotobiology.bsky.social lab in Freiburg is focusing on investigating the role of FHY1 in phytochrome signaling in the moss Physcomitrium patens #MAdLand2026 #plantsci
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Reposted by James Lloyd 🧬
MAdLand @watertoland.bsky.social · 30/09/2026
Starting our short talk sessions with James Walker from San Diego, telling us more about linking live-cell dynamics to single- cell molecular states across plant evolution #MAdLand2026 #plantsci
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Reposted by James Lloyd 🧬
James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
I’m delighted to share our new pre-print: Make it so: Rapid and affordable plasmid sequencing on ONT platforms with PICARD-seq www.biorxiv.org/content/10.6... I wanted to use a MinION to sequence my large repetitive plasmids in-house. Luckily @jwdebler.bsky.social was willing to help. 1/14
biorxiv.org
Make it so: Rapid and affordable plasmid sequencing on ONT platforms with PICARD-seq
Plasmid construction underpins molecular biology and synthetic biology, yet validation is often limited to the inserted fragment rather than the whole plasmid, and around a third of laboratory-made pl...
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James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
I can see many labs wanting to adopt this especially given the buying for equipment is significantly less than for other sequencing platforms like Illumina. This pipeline is fast and affordable and we hope others find this protocol and manuscript helpful. 14/14
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James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
Being able to do in-house plasmid sequencing that takes only <1 day to go from DNA to full analysis is an incredibly helpful tool - we believe could be a democratising aspect for many. Some labs have services that can deliver something similar overnight but not in remote cities like Perth. 13/14
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James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
Finally we found a highly repetitive plasmid ended up as a mixed population likely due to recombination events, suggesting difficulties in downstream cloning may occur. 12/14
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James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
We also were able to detect a mixup in assembly parts where one promoted part was exchanged for another. These can easily be missed by a restriction enzyme digest due to similar size of the expected fragments. Therefore sequencing of plasmid at every stage of cloning is very helpful. 11/14
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James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
Finally, we present a rogue's gallery of plasmid errors that can be detected through such whole plasmid sequencing approaches. We found one plasmid with concatenated backbones including antibiotic resistance for both amp & kan. 10/14
Plasmids
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James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
For example, it ruled out the spurious deletions that EPI2ME had predicted earlier. Mapping also highlighted why one plasmid could never be assembled, because it did not have reads to cover the whole region due to low impact of DNA into the starting reaction. 9/14
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James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
We finally tried mapping reads to the expected plasmid sequence as an additional verification process. Mapping stats were not a good predictor of whether the plasma was intact. However, a visual inspection of the mapped reads is a useful step in validation. 8/14
Mapped reads and a table.
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James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
autocycler did have problems assembling one plasmid successfully but this was related to a homopolymer stretch of a residues, a known problem with Nanopore sequencing. Therefore we suggest that uses use autocycler over EPI2ME, but also it is worth manually inspecting all discrepancies. 7/14
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James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
We then decided to test an alternative software called autocycler. While autocycler was slower, it led to a much higher rate of successful assemblies & a much higher percentage of those matching the expected sequence. 6/14
Bar plot and DNA sequence.
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James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
We created a simple dilution series and even 2.5 fmol you still had many full length reads of the plasmid. Our problem plasmids had few long reads suggesting a cause. Changing the software settings from a expected coverage of 60x down to 40x/20x allowed for these plasmids to be assembled. 5/14
Histograms and bar plots
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James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
We started using the official Nanopore pipeline called EPI2ME to assemble. The assemblies were sarcastic & would sometimes introduce errors into the assemblies. Therefore this approach should be used precaution. Some plasmids could never be assembled despite a reasonable number of long rates. 4/14
Bar plots and DNA alignments.
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James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
But in this preprint we outline the computational analysis options, highlighting issues with some approaches and present examples of what sequencing can capture. It has-been reported over a 3rd of plasmids contain errors, so we need to be vigilant. 3/14
Workflow diagram of your plasmid being cut and sequenced
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James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
We have dubbed our version of this Plasmid Integrity by Complete Assembly and Rapid Determination sequencing (PICARD-seq) and a full wet lab protocol is available here: dx.doi.org/10.17504/pro... 2/14
dx.doi.org
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James Lloyd 🧬 @jamespblloyd.bsky.social · 25/09/2026
I’m delighted to share our new pre-print: Make it so: Rapid and affordable plasmid sequencing on ONT platforms with PICARD-seq www.biorxiv.org/content/10.6... I wanted to use a MinION to sequence my large repetitive plasmids in-house. Luckily @jwdebler.bsky.social was willing to help. 1/14
biorxiv.org
Make it so: Rapid and affordable plasmid sequencing on ONT platforms with PICARD-seq
Plasmid construction underpins molecular biology and synthetic biology, yet validation is often limited to the inserted fragment rather than the whole plasmid, and around a third of laboratory-made pl...
13514
Reposted by James Lloyd 🧬
bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 24/09/2026
Make it so: Rapid and affordable plasmid sequencing on ONT platforms with PICARD-seq www.biorxiv.org/content/10.64898/20…
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Reposted by James Lloyd 🧬
Human Pangenome Reference Consortium @humanpangenome.bsky.social · 24/09/2026
Shredtools is making it easier to explore regions across a pangenome by quickly finding matching genomic regions across hundreds of genomes. The tool can identify a gene region across 476 human genomes in approximately half a second.  Read more: www.biorxiv.org/content/10.6...
biorxiv.org
Navigating the pangenome coordinate system with Shredtools
Existing notions of pangenome coordinates rely on hard-to-compute multiple sequence alignments. On the other hand, pangenome-wide exact unique matches (multi-MUMs) can be computed efficiently, and rep...
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Reposted by James Lloyd 🧬
bioRxivpreprint @biorxivpreprint.bsky.social · 23/09/2026
An atlas of eukaryotic centromere architecture reveals recurrent evolutionary dynamics www.biorxiv.org/content/10.64898/20…
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Reposted by James Lloyd 🧬
bioRxivpreprint @biorxivpreprint.bsky.social · 21/09/2026
Gravlax: an annotation-independent molecular evidence archive for single-cell RNA-seq www.biorxiv.org/content/10.64898/20…
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Reposted by James Lloyd 🧬
The Arabidopsis Information Resource (TAIR) @tairnews.bsky.social · 21/09/2026
What's new with TAIR12? The TAIR curatorial team is hard at work integrating the latest TAIR12 updates into the live TAIR database and toolset. 🧪 #PlantScience #PlantBiology #Arabidopsis #TAIR #TAIR12
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Reposted by James Lloyd 🧬
bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 22/09/2026
An Open-Source 3D-Printed Vacuum Manifold for Automated DNA Isolation in the Opentrons Flex and OT-2 www.biorxiv.org/content/10.64898/20…
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James Lloyd 🧬 @jamespblloyd.bsky.social · 21/09/2026
Great to see this work out in the wild - congrats @c-jake-harris.bsky.social and team!
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Reposted by James Lloyd 🧬
bioRxivpreprint @biorxivpreprint.bsky.social · 14/09/2026
Engineering chromatin to encode transcriptional immune memory in Arabidopsis www.biorxiv.org/content/10.64898/20…
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Reposted by James Lloyd 🧬
Jake Harris @c-jake-harris.bsky.social · 18/09/2026
Very excited to share the new preprint from our lab on transcriptional memory and immune priming! Herculean effort from first authors Linhao and Jenia. Epigenome-engineering experiments provide evidence that H3K4me3 plays a causal role!  doi.org/10.64898/202...
doi.org
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Reposted by James Lloyd 🧬
Tominaga K. (tomiken) @pacyc184.bsky.social · 31/07/2026
pLAST - a tool for rapid comparison and classification of bacterial plasmid sequences | Bioinformatics | Oxford Academic
dx.doi.org
pLAST - a tool for rapid comparison and classification of bacterial plasmid sequences
AbstractMotivation. The increasing number of fully sequenced bacterial plasmids being annotated and catalogued has prompted the development of computationa
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Reposted by James Lloyd 🧬
Olivier Borkowski @oborkowski.bsky.social · 21/09/2026
Characterization of recombinase-based genetic parts and circuits using nanopore sequencing doi.org/10.1038/s414...
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Reposted by James Lloyd 🧬
Olivier Borkowski @oborkowski.bsky.social · 21/09/2026
Modular synthetic cross-kingdom promoters enable coordinated expression in Escherichia coli and Saccharomyces cerevisiae doi.org/10.1093/nar/...
doi.org
Modular synthetic cross-kingdom promoters enable coordinated expression in Escherichia coli and Saccharomyces cerevisiae
Abstract. Synthetic biology and metabolic engineering increasingly demand predictable and interoperable gene expression across phylogenetically distant org
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Reposted by James Lloyd 🧬
Sophien Kamoun @kamounlab.bsky.social · 21/09/2026
Our second keynote speaker is Alain Tissier @atissier.bsky.social @ipbhalle.bsky.social on enhancing HDR and its use in engineering cis-genic disease resistance and other traits
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Reposted by James Lloyd 🧬
Molecular Plant & Plant Communications @mplantpcom.bsky.social · 20/09/2026
De novo Genes in Plants: Origins, Mechanisms, and Functional Implications #review #PlantCommunications cell.com/plant-commun...
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Reposted by James Lloyd 🧬
emmasebunyakato.bsky.social @emmasebunyakato.bsky.social · 20/09/2026
Check our website and support synthetic biology education in Africa synbioforall.org
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Reposted by James Lloyd 🧬
synbio4allafrica.bsky.social @synbio4allafrica.bsky.social · 20/09/2026
Check our website and support synthetic biology education in Africa synbioforall.org
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Reposted by James Lloyd 🧬
Plant Physiology @plantphys.bsky.social · 20/09/2026
The ZmBBM2-BBIP1-RCC1-4 module enhances callus growth and genetic transformation efficiency in maize (Qinghui Fu , Qianhan Wei , Chunlai Qi , Anqi Zhao , Xiaojie Yuan , Yuan Yuan , Yunjun Liu) doi.org/10.1093/plph... #PlantScience @aspbofficial
doi.org
The ZmBBM2-BBIP1-RCC1-4 module enhances callus growth and genetic transformation efficiency in maize
Dear Editor,
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