James Lloyd 🧬's Avatar

James Lloyd 🧬

@jamespblloyd.bsky.social

Synthetic AstroBotatnist. Engineer of synthetic gene circuits in plants. πŸ‡¬πŸ‡§πŸ‡ͺπŸ‡Ί now in πŸ‡¦πŸ‡Ί. He/They. Google Scholar: http://shorturl.at/dnHVZ Compbio blog: badgrammargoodsyntax.com

2,155 Followers  |  1,922 Following  |  338 Posts  |  Joined: 17.09.2023
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Posts by James Lloyd 🧬 (@jamespblloyd.bsky.social)

GeneWiz have worked for me in the past. Anda recently applied something very large and repetitive for us (not promoter but I am still in awe). Twist rarely bother with anything remotely tricky and then give up pretty easily other times, so I’m not surprised by this.

05.03.2026 14:11 β€” πŸ‘ 2    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
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Assembly of Arundinella anomala genome to facilitate single-cell resolved functional and developmental characterization of C4 distinctive cells - Nature Plants The genome of Arundinella anomala, a C4 grass with variant Kranz anatomy and interveinal distinctive cells, is sequenced and annotated, followed by single-cell transcriptomes for comparative analyses ...

Assembly of #Arundinella anomala #genome to facilitate #single-cell resolved functional and #developmental characterization of #C4 distinctive #cells

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

#PlantScience #StressBiology @natureportfolio.nature.com @natplants.nature.com @alliancegenome.bsky.social

05.03.2026 13:49 β€” πŸ‘ 1    πŸ” 1    πŸ’¬ 0    πŸ“Œ 0
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Systematic investigation of interindividual variation of DNA methylation in human whole blood - Genome Biology Background Interindividual genetic variability is well characterised, but we still lack a complete catalogue of loci displaying variable and stable epigenetic patterns. Results Here, we report a catal...

Excited to share our latest publication on interindividual variation of DNA methylation in human whole blood, spearheaded by the amazing Olivia Grant and co-led with @leo-schalkwyk.bsky.social and Meena Kumari.

link.springer.com/article/10.1...

05.03.2026 10:56 β€” πŸ‘ 16    πŸ” 9    πŸ’¬ 2    πŸ“Œ 0
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Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling - Nature Microbiology A structural catalogue of the Asgard archaeal pangenome reveals hundreds of eukaryotic-like proteins that suggest a higher degree of cellular complexity in the archaeal ancestor of eukaryotes.

🧡 1/10 New paper out in @natmicrobiol.nature.com from my postdoc at @mib-wur.bsky.social! πŸŽ‰

How eukaryote-like was the archaeal ancestor of eukaryotes? Sequence searches alone can't tell us β€” so we used protein structure prediction to look deeper. 🧬
www.nature.com/articles/s41...

05.03.2026 10:46 β€” πŸ‘ 54    πŸ” 28    πŸ’¬ 1    πŸ“Œ 2

Check out our new review in Nature Reviews Genetics on de novo emerged genes and proteins. How they emerge, are lost and persist - and how de novo emerged proteins relate to randomized proteins! @bornberglab.bsky.social www.nature.com/articles/s41...

28.01.2026 18:23 β€” πŸ‘ 58    πŸ” 28    πŸ’¬ 3    πŸ“Œ 2

Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now?
www.nature.com/articles/s41...

More functional data, many thousands of words removed, and a few other updates from last year's preprint.

12.02.2026 11:22 β€” πŸ‘ 134    πŸ” 57    πŸ’¬ 7    πŸ“Œ 5
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The results are finally in! πŸ†πŸ’»πŸ§¬

I'm thrilled to announce that the manuscript for the Bits to Binders protein design competition is out on bioRxiv! Here's a summary of our findings, including some simple criteria that nearly *double* success rates when applied as a filter 🧡

04.03.2026 15:01 β€” πŸ‘ 31    πŸ” 17    πŸ’¬ 1    πŸ“Œ 2

Wow I did not know that RNA-seq was being used to inform treatment. My current chemo has just been informed by genome sequencing of the biopsy but I have been given limited access to it. And certainly no mention of RNA-seq.

04.03.2026 15:02 β€” πŸ‘ 1    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0
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Assessing and mitigating batch effects in large-scale omics studies Batch effects in omics data are notoriously common technical variations unrelated to study objectives, and may result in misleading outcomes if uncorrected, or hinder biomedical discovery if over-corrected. Assessing and mitigating batch effects is ...

Paper: Yu et al. (2024) Genome Biology
pmc.ncbi.nlm.nih.gov/articles/PM...

04.03.2026 14:45 β€” πŸ‘ 4    πŸ” 2    πŸ’¬ 0    πŸ“Œ 0
Spatial distribution of isoprenoid enzymes and MpABCG1 transporter influences sesquiterpene accumulation in Marchantia polymorpha oil bodies - Communications Biology A study maps terpene biosynthesis in Marchantia polymorpha oil bodies and identifies the ABC transporter MpABCG1 as a key factor for endogenous sesquiterpene accumulation in oil bodies, informing futu...

New paper from the lab. Important insights into the compartmentalisation of terpene biosynthesis in Marchantia oil body cells. #PlantScience #SynBio www.nature.com/articles/s42...

04.03.2026 11:46 β€” πŸ‘ 18    πŸ” 13    πŸ’¬ 0    πŸ“Œ 0
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New preprint from
@novoalab.bsky.social !

Which tRNAs are used by ribosomes during translation?

We introduce tRIBO-seq, a nanopore method to sequence ribosome-associated tRNAs and track how the active tRNA pool changes across stress conditions.

www.biorxiv.org/content/10.6...

Thread πŸ‘‡

04.03.2026 09:25 β€” πŸ‘ 32    πŸ” 13    πŸ’¬ 2    πŸ“Œ 1

Please check out our latest #preprint to study #ACTIVELY TRANSLATING #tRNA populations and their dynamics upon #stress :) This was an wonderful collaborative effort between @novoalab.bsky.social @immagina.bsky.social and #Soares teams - thank you for making this possible!

04.03.2026 10:11 β€” πŸ‘ 17    πŸ” 6    πŸ’¬ 0    πŸ“Œ 0
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13/ Overall, our data suggest that GA-independent developmental phenotypes are evolutionary conserved in #MyMarchantia, while AMS-related phenotypes are not. We propose that GA-dependent DELLA functions evolved in vascular plants and were co-opted as an additional layer of control during AMS.

04.03.2026 05:41 β€” πŸ‘ 4    πŸ” 1    πŸ’¬ 1    πŸ“Œ 0

1/ ✨ New preprint alert ✨

It is my pleasure to share:
"Stepwise evolution of the developmental and symbiotic functions of DELLA in land plants"

Here we investigated the role of the single GRAS transcription factor DELLA in #MyMarchantia

doi.org/10.64898/202...

#PlantScience
A thread...

04.03.2026 05:20 β€” πŸ‘ 47    πŸ” 36    πŸ’¬ 5    πŸ“Œ 2
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As we lead up to #IWD2026, we’re celebrating Kristina Gagalova, Bioinformatics Scientist and part of AGGI, whose work bridges cutting‑edge genomics with real‑world agricultural impact.
@curtinuniversity.bsky.social, #GRDC

04.03.2026 03:00 β€” πŸ‘ 3    πŸ” 2    πŸ’¬ 0    πŸ“Œ 0

Nah eukaryotes are just ribosomes making ribosomes but with extra steps.

Meiosis seems to be the central innovation in eukaryotes that sets the stage of a lot of other things including multicellularity. I have written something on this but trying to find a good venue for it.

03.03.2026 13:37 β€” πŸ‘ 3    πŸ” 0    πŸ’¬ 0    πŸ“Œ 0

And there's also this

bsky.app/profile/mkru...

03.03.2026 13:23 β€” πŸ‘ 1    πŸ” 1    πŸ’¬ 0    πŸ“Œ 0
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A symbiotic origin of the ribosome? Abstract. The origin of life is one of the great mysteries of science. Of the multiple unsolved problems, the origin of the translation system (the means b

"we propose that the protoribosome was a parasite (...). If this view is correct, then like the spliceosome in the stem eukaryote, a repurposed host-parasite interaction led to a dramatic change in cell biology at the base of the tree of life, in this case leading to the exit from an RNA world"

02.03.2026 18:43 β€” πŸ‘ 30    πŸ” 15    πŸ’¬ 1    πŸ“Œ 0
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Very happy about this nice piece of work by @eugeniapitsili.bsky.social on developmentally controlled cell death in plants @dev-journal.bsky.social‬ !
Special thanks also to @ingridtsang.bsky.social for a terrific editorial job bringing out the best of this manuscript!!
doi.org/10.1242/dev....

03.03.2026 08:21 β€” πŸ‘ 31    πŸ” 15    πŸ’¬ 2    πŸ“Œ 0
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Morning.

23.11.2025 05:31 β€” πŸ‘ 14141    πŸ” 1377    πŸ’¬ 140    πŸ“Œ 2
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With Eugene Koonin, we propose a concept of β€œthe selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268

03.03.2026 08:58 β€” πŸ‘ 221    πŸ” 95    πŸ’¬ 5    πŸ“Œ 13
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RNA Splicing Lab - JOIN US Are you interested in investigating basic mechanisms in splicing regulation and gene expression? Our research group was launched in September 2024 and is hosted at the Institute of Molecular Infection...

We have an open position for a #PhD student (last week to apply!) & a lab technician/TA. For more information see: www.beuschlab.org/join-us
Interested in understanding post-transcriptional regulation and how #RNA #splicing decisions are made? Then take a look or share with people who might be! πŸ§ͺ🧫

02.03.2026 15:44 β€” πŸ‘ 12    πŸ” 12    πŸ’¬ 0    πŸ“Œ 0

Prepare your best art for AR(t)RBMP

Plant Molecular Biology Meeting
πŸ“ Bilbao
πŸ—“οΈ July 1-3
rbmp2026.com/RBMP/en/info

Thanks to #RBMP2026 organizing committee, @danielmarinoehu.bsky.social
@ibmcp.bsky.social support & my partner in crime for these fun initiatives @javijevi.bsky.social
#PlantScience

02.03.2026 09:39 β€” πŸ‘ 3    πŸ” 5    πŸ’¬ 1    πŸ“Œ 0

How should I keep spores of Marchantia polymorpha subsp. ruderalis? Although I have kept them at -30˚C for 1-2 months, they don't germinate so far.

02.03.2026 08:00 β€” πŸ‘ 2    πŸ” 2    πŸ’¬ 2    πŸ“Œ 0

Great to see this one out. I agree it was challenging but watching it unfold was definitely exciting. The team worked brilliantly, truly thankful!

02.03.2026 08:51 β€” πŸ‘ 4    πŸ” 3    πŸ’¬ 0    πŸ“Œ 0
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Dynamics of genetic circuits in Pseudomonas protegens Genetic circuit engineering enables new cellular functions, yet most circuits are developed in the model host Escherichia coli, limiting their availab…

Latest paper out! This piece was a challenge: logic, predictability, decidability, non-model organisms, design... Kudos to @juanricomol.bsky.social & Pablo JapΓ³n #syntheticbiology #synbio #biocomputation (I'll post more on this next week) www.sciencedirect.com/science/arti...

27.02.2026 16:38 β€” πŸ‘ 12    πŸ” 8    πŸ’¬ 1    πŸ“Œ 2

Previous studies reported a correlation between presence of gBM and gene expression noise. Here, we used a series of epigenetic mutants in plants together with epigenetic recombinant inbred lines and showed that loss of CpG methylation in gBM leads to increase in noise in gene expression. 3/3

17.02.2026 13:41 β€” πŸ‘ 3    πŸ” 1    πŸ’¬ 0    πŸ“Œ 0

gBM is present in many organisms (humans, animals and plants) and while DNA methylation is often associated with transcription silencing, gBM has been found at a subset of highly expressed genes. This raised the question of why some expressed genes have gene body methylation and others don't. 2/3

17.02.2026 13:41 β€” πŸ‘ 2    πŸ” 1    πŸ’¬ 1    πŸ“Œ 0
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Gene body methylation buffers noise in gene expression in plants Abstract. Non-genetic variability in gene expression is an inevitable consequence of the stochastic nature of processes driving transcription and translati

Hot off the press, our latest publication on the functional role of gene body methylation (gBM).

academic.oup.com/nar/article/...

Work spearheaded by Jakub Zastapilo with help from @robynemm.bsky.social and Liudmila Mikheeva and co-led by Marco Catoni and @ubechtold.bsky.social 1/3

17.02.2026 13:41 β€” πŸ‘ 16    πŸ” 11    πŸ’¬ 2    πŸ“Œ 0
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Ultra-sensitive CAR T cells eliminate hard-to-treat tumours in mice Nature - A proof-of-concept study opens up an avenue for treating solid tumours that express low levels of a target antigen.

Ultra-sensitive CAR T cells eliminate hard-to-treat tumours in mice

A proof-of-concept study opens up an avenue for treating solid tumours that express low levels of a target antigen.

www.nature.com/artic...
1/3

01.03.2026 21:39 β€” πŸ‘ 28    πŸ” 10    πŸ’¬ 1    πŸ“Œ 0