James Lloyd 🧬
@jamespblloyd.bsky.social
Synthetic AstroBotatnist. Engineer of synthetic gene circuits in plants. 🇬🇧🇪🇺 now in 🇦🇺. He/They.
Google Scholar: http://shorturl.at/dnHVZ
Compbio blog: badgrammargoodsyntax.com
Google Scholar: http://shorturl.at/dnHVZ
Compbio blog: badgrammargoodsyntax.com
Pinned
CREation of an expanded plant memory gene circuit toolkit
Genetic circuits rely on modular, well-characterized genetic parts to achieve predictable cellular behaviour. Despite their widespread adoption, biological parts are complex and when used in a new mol...
www.biorxiv.org
I am delighted to share our latest work on memory gene circuits for plants. This work was led by the phenomenal PhD student @patrickgong.bsky.social
A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.
www.biorxiv.org/content/10.1...
A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.
www.biorxiv.org/content/10.1...
Reposted by James Lloyd 🧬
ARC are considering a restructure in which jobs there will be lost, a source tells me.
This seems ridiculous when they're about to completely overhaul the entire grants system – they've never undertaken anything so large before!
I've long said ARC needs MANY MORE staff, & should do more, not less.
This seems ridiculous when they're about to completely overhaul the entire grants system – they've never undertaken anything so large before!
I've long said ARC needs MANY MORE staff, & should do more, not less.
November 25, 2025 at 10:26 PM
ARC are considering a restructure in which jobs there will be lost, a source tells me.
This seems ridiculous when they're about to completely overhaul the entire grants system – they've never undertaken anything so large before!
I've long said ARC needs MANY MORE staff, & should do more, not less.
This seems ridiculous when they're about to completely overhaul the entire grants system – they've never undertaken anything so large before!
I've long said ARC needs MANY MORE staff, & should do more, not less.
Reposted by James Lloyd 🧬
Photosynthetic sea slugs can decapitate themselves & regenerate whole body from the detached head (without the heart or guts), while the shed body do not regenerate. The process takes ~2-3 weeks. A new model for regeneration?
From: www.cell.com/current-biol...
From: www.cell.com/current-biol...
Extreme autotomy and whole-body regeneration in photosynthetic sea slugs
Autotomy, the voluntary shedding of a body part, is common among animals. Mitoh and
Yusa report an extreme case of autotomy with the shedding of the main body, including
the whole heart, and subsequen...
www.cell.com
November 22, 2025 at 4:00 PM
Photosynthetic sea slugs can decapitate themselves & regenerate whole body from the detached head (without the heart or guts), while the shed body do not regenerate. The process takes ~2-3 weeks. A new model for regeneration?
From: www.cell.com/current-biol...
From: www.cell.com/current-biol...
Reposted by James Lloyd 🧬
Delighted to report that our group's passion project over the last 6+ years to make DNA cloning more accessible, efficient, and scalable using a software-assisted workflow called CloneCoordinate is now out in ACS Synbio!
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
CloneCoordinate: Open-Source Software for Collaborative DNA Construction
Custom DNA constructs have never been more common or important in the life sciences. Many researchers therefore devote substantial time and effort to molecular cloning, aided by abundant computer-aide...
pubs.acs.org
November 21, 2025 at 7:40 PM
Delighted to report that our group's passion project over the last 6+ years to make DNA cloning more accessible, efficient, and scalable using a software-assisted workflow called CloneCoordinate is now out in ACS Synbio!
pubs.acs.org/doi/10.1021/...
pubs.acs.org/doi/10.1021/...
Reposted by James Lloyd 🧬
And now we have Arabidopsis plants with 8 chromosomes instead of 10 and no obvious phenotypic differences, this week in @science.org
#PlantScience
Paper here: www.science.org/doi/10.1126/...
Perspective here:
www.science.org/doi/10.1126/...
#PlantScience
Paper here: www.science.org/doi/10.1126/...
Perspective here:
www.science.org/doi/10.1126/...
CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis
The genome of Arabidopsis thaliana consists of 10 chromosomes. By inducing CRISPR-Cas–mediated breaks at subcentromeric and subtelomeric sequences, we fused entire chromosome arms, obtaining two eight...
www.science.org
November 21, 2025 at 10:20 AM
And now we have Arabidopsis plants with 8 chromosomes instead of 10 and no obvious phenotypic differences, this week in @science.org
#PlantScience
Paper here: www.science.org/doi/10.1126/...
Perspective here:
www.science.org/doi/10.1126/...
#PlantScience
Paper here: www.science.org/doi/10.1126/...
Perspective here:
www.science.org/doi/10.1126/...
Reposted by James Lloyd 🧬
Therefore, the Last Eukaryotic Common Ancestor had a dual methylation system: 6mA for transcriptionally permissive chromatin and 5mC for silencing. This dual pattern is maintained in some extant eukaryotes but has diverged in many others, including ALL multicellular groups that lost AMT1. 8/9
November 18, 2025 at 12:00 PM
Therefore, the Last Eukaryotic Common Ancestor had a dual methylation system: 6mA for transcriptionally permissive chromatin and 5mC for silencing. This dual pattern is maintained in some extant eukaryotes but has diverged in many others, including ALL multicellular groups that lost AMT1. 8/9
Reposted by James Lloyd 🧬
But is 6mA directing transcription? We checked in 5 different species across stages and conditions, and we could detect plenty of transcriptional changes not followed by 6mA reprogramming. So correlation does not mean causation (as most times with chromatin features). 5/9
November 18, 2025 at 12:00 PM
But is 6mA directing transcription? We checked in 5 different species across stages and conditions, and we could detect plenty of transcriptional changes not followed by 6mA reprogramming. So correlation does not mean causation (as most times with chromatin features). 5/9
Reposted by James Lloyd 🧬
However there's been rampant simplifications across the tree of life. We then took advantage of 6mA basecalling with @nanoporetech.com to profile several eukaryotes branching in very distant groups, some encoding AMT1 or not. AMT1 encoding eukaryotes presented symmetric ApT methylation. 3/9
November 18, 2025 at 12:00 PM
However there's been rampant simplifications across the tree of life. We then took advantage of 6mA basecalling with @nanoporetech.com to profile several eukaryotes branching in very distant groups, some encoding AMT1 or not. AMT1 encoding eukaryotes presented symmetric ApT methylation. 3/9
Reposted by James Lloyd 🧬
First we traced the evolutionary history of AMT1 (aka MTA1), the main 6mA enzyme in eukaryotes. We find that a complex repertoire including AMT1 and its heterodimeric partner AMT6/7 can be traced back to the Last Eukaryotic Common Ancestor. Same goes for the RNA methyltransferases METTL3/14. 2/9
November 18, 2025 at 12:00 PM
First we traced the evolutionary history of AMT1 (aka MTA1), the main 6mA enzyme in eukaryotes. We find that a complex repertoire including AMT1 and its heterodimeric partner AMT6/7 can be traced back to the Last Eukaryotic Common Ancestor. Same goes for the RNA methyltransferases METTL3/14. 2/9
Reposted by James Lloyd 🧬
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes - Nature Genetics
Long-read sequencing in 18 unicellular eukaryotes reveals that 6mA is widespread across eukaryotes and is enriched at transcriptionally permissive regions, which are also marked by H3K4me3.
www.nature.com
November 18, 2025 at 12:00 PM
Out today, our take on 6-methyladenine #6mA evolution in Eukaryotes @natgenet.nature.com. We asked a simple question, is really DNA 6mA common across the eukaryotes? The answer is "yes" if you're a unicellular eukaryote 🦠, not so if you're multicellular 🐝🌱🍄. www.nature.com/articles/s41... 1/9
Reposted by James Lloyd 🧬
Two alternative isoforms of PRC2 accessory subunit AEBP2 modulate developmental Polycomb functions in opposite ways - with broadly-expressed AEBP2L acting as an intrinsic inhibitor in somatic cells
@adrianbracken.bsky.social @davidovichlab.bsky.social and colleagues
www.embopress.org/doi/full/10....
@adrianbracken.bsky.social @davidovichlab.bsky.social and colleagues
www.embopress.org/doi/full/10....
November 4, 2025 at 12:51 PM
Two alternative isoforms of PRC2 accessory subunit AEBP2 modulate developmental Polycomb functions in opposite ways - with broadly-expressed AEBP2L acting as an intrinsic inhibitor in somatic cells
@adrianbracken.bsky.social @davidovichlab.bsky.social and colleagues
www.embopress.org/doi/full/10....
@adrianbracken.bsky.social @davidovichlab.bsky.social and colleagues
www.embopress.org/doi/full/10....
Reposted by James Lloyd 🧬
I am looking to hire a postdoc interested in combining genetics and evolution to understand why telomeres vary so much in plants. My group has been developing Mimulus a genetic model for studying plant telomeres and we have really cool research brewing. Please check ad for detail. Deadline is 12/31.
November 16, 2025 at 8:29 PM
I am looking to hire a postdoc interested in combining genetics and evolution to understand why telomeres vary so much in plants. My group has been developing Mimulus a genetic model for studying plant telomeres and we have really cool research brewing. Please check ad for detail. Deadline is 12/31.
Reposted by James Lloyd 🧬
Latest research from the Bäurle lab on the function of our favourite memory TF - HSFA2!
Promoter and domain swap analysis delineates heat stress memory-specific determinants of heat shock factor HSFA2
The function of the transcription factor HSFA2 in heat-stress induced transcriptional memory maps to functional domains within the protein.
academic.oup.com
November 16, 2025 at 8:57 AM
Latest research from the Bäurle lab on the function of our favourite memory TF - HSFA2!
Reposted by James Lloyd 🧬
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
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
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...
www.nature.com
November 12, 2025 at 1:17 PM
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
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
Reposted by James Lloyd 🧬
Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes (Fabricio Almeida-Silva, Yves Van de Peer) doi.org/10.1093/plce... #PlantScience @aspbofficial
Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes
After gene and genome duplications, expression divergence across cell types is not random, and it can be explained by a combination of gene age, gene funct
doi.org
November 12, 2025 at 1:27 PM
Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes (Fabricio Almeida-Silva, Yves Van de Peer) doi.org/10.1093/plce... #PlantScience @aspbofficial
Reposted by James Lloyd 🧬
I am delighted to share our latest work on memory gene circuits for plants. This work was led by the phenomenal PhD student @patrickgong.bsky.social
A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.
www.biorxiv.org/content/10.1...
A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.
www.biorxiv.org/content/10.1...
CREation of an expanded plant memory gene circuit toolkit
Genetic circuits rely on modular, well-characterized genetic parts to achieve predictable cellular behaviour. Despite their widespread adoption, biological parts are complex and when used in a new mol...
www.biorxiv.org
October 31, 2025 at 9:24 AM
I am delighted to share our latest work on memory gene circuits for plants. This work was led by the phenomenal PhD student @patrickgong.bsky.social
A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.
www.biorxiv.org/content/10.1...
A lot of debugging & highlights how even simple components in synthetic biology can have unexpected properties.
www.biorxiv.org/content/10.1...
Such a cool pre-print on making sentinel plants - so much potential!
Bioluminescent sentinel plants enable autonomous diagnostics of viral infections
www.biorxiv.org/content/10.1...
Bioluminescent sentinel plants enable autonomous diagnostics of viral infections
www.biorxiv.org/content/10.1...
Bioluminescent sentinel plants enable autonomous diagnostics of viral infections
Plants engineered with synthetic genetic programs can transform how we monitor and manage the extension of crop pests and diseases. Here, we establish a bioluminescent platform in Nicotiana benthamian...
www.biorxiv.org
November 12, 2025 at 3:55 AM
Such a cool pre-print on making sentinel plants - so much potential!
Bioluminescent sentinel plants enable autonomous diagnostics of viral infections
www.biorxiv.org/content/10.1...
Bioluminescent sentinel plants enable autonomous diagnostics of viral infections
www.biorxiv.org/content/10.1...
Reposted by James Lloyd 🧬
Powerful read processing with matchbox https://www.biorxiv.org/content/10.1101/2025.11.09.685711v1
November 11, 2025 at 9:47 PM
Powerful read processing with matchbox https://www.biorxiv.org/content/10.1101/2025.11.09.685711v1
Reposted by James Lloyd 🧬
Strigolactone perception and nutrient responses
#TansleyInsight by Hu et al.
nph.onlinelibrary.wiley.com/doi/10.1111/...
#plantscience
#TansleyInsight by Hu et al.
nph.onlinelibrary.wiley.com/doi/10.1111/...
#plantscience
November 11, 2025 at 12:11 AM
Strigolactone perception and nutrient responses
#TansleyInsight by Hu et al.
nph.onlinelibrary.wiley.com/doi/10.1111/...
#plantscience
#TansleyInsight by Hu et al.
nph.onlinelibrary.wiley.com/doi/10.1111/...
#plantscience
The podcast version of my Raising the Bar talk is now online. If you are interested in "Cosmic Crops" or my work on genetic engineering of plants, please give it a listen (I have not listened to it, I hate listening to myself, so hopefully it is good, but no promises).
soundcloud.com/raising-the-...
soundcloud.com/raising-the-...
November 10, 2025 at 5:31 AM
The podcast version of my Raising the Bar talk is now online. If you are interested in "Cosmic Crops" or my work on genetic engineering of plants, please give it a listen (I have not listened to it, I hate listening to myself, so hopefully it is good, but no promises).
soundcloud.com/raising-the-...
soundcloud.com/raising-the-...
Reposted by James Lloyd 🧬
🌿🍄🟫🌱🍄We’re recruiting!!🌿🍄🟫🌱🍄
I’m looking for two postdocs and a technician to join my group @sheffielduni.bsky.social @sheffieldpps.bsky.social to work with me on my exciting @royalsociety.org Faraday Discovery Fellowship project, details for each post as follows:
I’m looking for two postdocs and a technician to join my group @sheffielduni.bsky.social @sheffieldpps.bsky.social to work with me on my exciting @royalsociety.org Faraday Discovery Fellowship project, details for each post as follows:
November 8, 2025 at 1:00 PM
🌿🍄🟫🌱🍄We’re recruiting!!🌿🍄🟫🌱🍄
I’m looking for two postdocs and a technician to join my group @sheffielduni.bsky.social @sheffieldpps.bsky.social to work with me on my exciting @royalsociety.org Faraday Discovery Fellowship project, details for each post as follows:
I’m looking for two postdocs and a technician to join my group @sheffielduni.bsky.social @sheffieldpps.bsky.social to work with me on my exciting @royalsociety.org Faraday Discovery Fellowship project, details for each post as follows:
Reposted by James Lloyd 🧬
A new method for the precise insertion of large DNA sequences into the genome using engineered recombinases that don’t require DNA cutting or rely on the cell’s repair machinery.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Site-specific DNA insertion into the human genome with engineered recombinases - Nature Biotechnology
Engineered DNA recombinases efficiently and specifically insert genetic cargos without the use of landing pads.
www.nature.com
November 6, 2025 at 9:30 PM
A new method for the precise insertion of large DNA sequences into the genome using engineered recombinases that don’t require DNA cutting or rely on the cell’s repair machinery.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by James Lloyd 🧬
Fusing transcription factors (TFs) to intrinsically disordered regions (IDRs), to drive the formation of transcriptional condensates that concentrate TFs at their target promoters.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Phase separation to buffer growth-mediated dilution in synthetic circuits
Fluctuations in host cell growth pose a critical challenge for maintaining reliable function in synthetic gene circuits. Growth-mediated dilution caus…
www.sciencedirect.com
November 8, 2025 at 11:55 AM
Fusing transcription factors (TFs) to intrinsically disordered regions (IDRs), to drive the formation of transcriptional condensates that concentrate TFs at their target promoters.
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by James Lloyd 🧬
PhD opportunity in plant developmental biology for UK based students of Black heritage!
How do they know when to grow up? Join us at the University of Bristol to find out.
Application deadline Jan 6th
www.findaphd.com/phds/project...
#PlantSciencePhDs @blackinplantsci.bsky.social
How do they know when to grow up? Join us at the University of Bristol to find out.
Application deadline Jan 6th
www.findaphd.com/phds/project...
#PlantSciencePhDs @blackinplantsci.bsky.social
November 7, 2025 at 10:37 AM
PhD opportunity in plant developmental biology for UK based students of Black heritage!
How do they know when to grow up? Join us at the University of Bristol to find out.
Application deadline Jan 6th
www.findaphd.com/phds/project...
#PlantSciencePhDs @blackinplantsci.bsky.social
How do they know when to grow up? Join us at the University of Bristol to find out.
Application deadline Jan 6th
www.findaphd.com/phds/project...
#PlantSciencePhDs @blackinplantsci.bsky.social
Reposted by James Lloyd 🧬
Rewiring protein function through genetically encoded oxidative chemistry https://www.biorxiv.org/content/10.1101/2025.11.06.686050v1
November 7, 2025 at 4:12 AM
Rewiring protein function through genetically encoded oxidative chemistry https://www.biorxiv.org/content/10.1101/2025.11.06.686050v1
Big update: My the first Lloyd Lab conceived and conducted study has been accepted and published:
Start Right to End Right: Authentic Open Reading Frame Selection Matters for Nonsense-Mediated Decay Target Identification
www.mdpi.com/2073-4425/16...
Now larger and better than the pre-print
Start Right to End Right: Authentic Open Reading Frame Selection Matters for Nonsense-Mediated Decay Target Identification
www.mdpi.com/2073-4425/16...
Now larger and better than the pre-print
www.mdpi.com
November 6, 2025 at 2:14 PM
Big update: My the first Lloyd Lab conceived and conducted study has been accepted and published:
Start Right to End Right: Authentic Open Reading Frame Selection Matters for Nonsense-Mediated Decay Target Identification
www.mdpi.com/2073-4425/16...
Now larger and better than the pre-print
Start Right to End Right: Authentic Open Reading Frame Selection Matters for Nonsense-Mediated Decay Target Identification
www.mdpi.com/2073-4425/16...
Now larger and better than the pre-print