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
James Lloyd 🧬
@jamespblloyd.bsky.social
· Oct 31
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 🧬
This one goes to 12
February 19, 2026 at 9:51 PM
This one goes to 12
Reposted by James Lloyd 🧬
🎉📣 #TAIR12, the latest reannotation of the Arabidopsis thaliana genome, is now available under accession number PRJEB100887 on ENA and NCBI!
Thank you all the volunteer researchers whose hard work has made this possible!
#plantscience #plantbiology 🧪
bit.ly/3ZHtneT
Thank you all the volunteer researchers whose hard work has made this possible!
#plantscience #plantbiology 🧪
bit.ly/3ZHtneT
Announcing the publication of TAIR12: Consult the fully reannotated genome on the European Nucleotide Archive - Phoenix Bioinformatics
TAIR (The Arabidopsis Information Resource), together with our nonprofit host Phoenix Bioinformatics, is pleased to announce the public release of TAIR12
bit.ly
February 19, 2026 at 6:40 PM
🎉📣 #TAIR12, the latest reannotation of the Arabidopsis thaliana genome, is now available under accession number PRJEB100887 on ENA and NCBI!
Thank you all the volunteer researchers whose hard work has made this possible!
#plantscience #plantbiology 🧪
bit.ly/3ZHtneT
Thank you all the volunteer researchers whose hard work has made this possible!
#plantscience #plantbiology 🧪
bit.ly/3ZHtneT
Reposted by James Lloyd 🧬
New paper from my team detailing a greatly expanded genomic database of Asgard archaea revealing of high energy metabolism those related to eukaryotes! Led by @katyappler.bsky.social lots of help from @jameslingford.bsky.social @valdeanda.bsky.social @kassipan.bsky.social doi.org/10.1038/s415...
February 18, 2026 at 4:00 PM
New paper from my team detailing a greatly expanded genomic database of Asgard archaea revealing of high energy metabolism those related to eukaryotes! Led by @katyappler.bsky.social lots of help from @jameslingford.bsky.social @valdeanda.bsky.social @kassipan.bsky.social doi.org/10.1038/s415...
Reposted by James Lloyd 🧬
Our editors write:
- Plant–microbe interaction: Root engineering blocks methanogens rdcu.be/e4yJc
- Marchantia immunity: Fungi genes to fight fungi rdcu.be/e4yJl
- Plant–microbe interaction: Root engineering blocks methanogens rdcu.be/e4yJc
- Marchantia immunity: Fungi genes to fight fungi rdcu.be/e4yJl
February 18, 2026 at 12:58 PM
Our editors write:
- Plant–microbe interaction: Root engineering blocks methanogens rdcu.be/e4yJc
- Marchantia immunity: Fungi genes to fight fungi rdcu.be/e4yJl
- Plant–microbe interaction: Root engineering blocks methanogens rdcu.be/e4yJc
- Marchantia immunity: Fungi genes to fight fungi rdcu.be/e4yJl
Reposted by James Lloyd 🧬
I’ve officially started my lab at Monash University! 🎉
We’re diving into #cellgrowth and #lysosome biology, through the lens of molecular #structure and mechanism.
I’m thrilled to say that PhD student scholarships are available—so please share widely and get in touch if you’re interested. 🤩
We’re diving into #cellgrowth and #lysosome biology, through the lens of molecular #structure and mechanism.
I’m thrilled to say that PhD student scholarships are available—so please share widely and get in touch if you’re interested. 🤩
February 18, 2026 at 8:35 AM
I’ve officially started my lab at Monash University! 🎉
We’re diving into #cellgrowth and #lysosome biology, through the lens of molecular #structure and mechanism.
I’m thrilled to say that PhD student scholarships are available—so please share widely and get in touch if you’re interested. 🤩
We’re diving into #cellgrowth and #lysosome biology, through the lens of molecular #structure and mechanism.
I’m thrilled to say that PhD student scholarships are available—so please share widely and get in touch if you’re interested. 🤩
Reposted by James Lloyd 🧬
🚨📢📄 Article in press in Genome Biology doi.org/10.1186/s130...
We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics #TEsky 🧵👇
We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics #TEsky 🧵👇
A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species - Genome Biology
Background The role of transposable elements (TEs) in host adaptation has gained interest in recent years. Individuals of the same species undergo independent TE insertions, providing genetic variabil...
doi.org
February 16, 2026 at 8:38 AM
🚨📢📄 Article in press in Genome Biology doi.org/10.1186/s130...
We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics #TEsky 🧵👇
We introduce panREPET, a reference-free pipeline to detect shared transposable element (TE) insertions across pangenomes and retrace their evolutionary dynamics #TEsky 🧵👇
Reposted by James Lloyd 🧬
Ever notice that when one gene is disrupted, its orthologs get upregulated? This phenomenon, known as transcriptional adaptation, has been controversial and mysterious - glad to see that we are starting to learn how it works.
Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation
Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...
www.science.org
February 13, 2026 at 9:42 PM
Ever notice that when one gene is disrupted, its orthologs get upregulated? This phenomenon, known as transcriptional adaptation, has been controversial and mysterious - glad to see that we are starting to learn how it works.
Reposted by James Lloyd 🧬
And save >80% on the cost by pooling 6 or more plasmids into a single sample using our free SAVEMONEY algorithm!
elifesciences.org/articles/88794
colab.research.google.com/github/Masaa...
elifesciences.org/articles/88794
colab.research.google.com/github/Masaa...
February 15, 2026 at 3:03 AM
And save >80% on the cost by pooling 6 or more plasmids into a single sample using our free SAVEMONEY algorithm!
elifesciences.org/articles/88794
colab.research.google.com/github/Masaa...
elifesciences.org/articles/88794
colab.research.google.com/github/Masaa...
Reposted by James Lloyd 🧬
Reading this for my ecological genomics class. Pretty mind-blowing stuff, even identifying insect-bacterial symbionts from high covariance in airborne eDNA!
Airborne eDNA captures three decades of ecosystem biodiversity - Nature Communications
Quantifying ecosystem dynamics is critical in the face of rapid environmental change. This study uses airborne eDNA to quantify changes in organism abundances across the tree of life and reveal a regi...
doi.org
February 12, 2026 at 4:48 PM
Reading this for my ecological genomics class. Pretty mind-blowing stuff, even identifying insect-bacterial symbionts from high covariance in airborne eDNA!
Reposted by James Lloyd 🧬
But why? How does a simple U-code target transposons? It’s a brilliant exploit of retrotransposon evolution: their genomes are intrinsically A-rich. When transcribed in antisense (as in clusters), they become exceptionally U-rich, placing them squarely in Yb’s crosshairs. 🎯 (11/19)
February 13, 2026 at 3:11 PM
But why? How does a simple U-code target transposons? It’s a brilliant exploit of retrotransposon evolution: their genomes are intrinsically A-rich. When transcribed in antisense (as in clusters), they become exceptionally U-rich, placing them squarely in Yb’s crosshairs. 🎯 (11/19)
Reposted by James Lloyd 🧬
Check this out: we designed "U-ramp" reporters with entirely synthetic 3’ UTRs by varying in their uridine content (20% to 45%). The result was striking: U-density behaves like a threshold—below ~30% U, barely any piRNAs; above it, output shoots up in a Yb-dependent manner. (7/19)
February 13, 2026 at 3:11 PM
Check this out: we designed "U-ramp" reporters with entirely synthetic 3’ UTRs by varying in their uridine content (20% to 45%). The result was striking: U-density behaves like a threshold—below ~30% U, barely any piRNAs; above it, output shoots up in a Yb-dependent manner. (7/19)
Reposted by James Lloyd 🧬
Evolution of oncogene amplification across 86,000 cancer cell genomes https://www.biorxiv.org/content/10.64898/2026.02.12.705658v1
February 14, 2026 at 10:34 AM
Evolution of oncogene amplification across 86,000 cancer cell genomes https://www.biorxiv.org/content/10.64898/2026.02.12.705658v1
Reposted by James Lloyd 🧬
How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller?
Excited to share our latest work in @science.org on a new small polymerase.
1/n
Excited to share our latest work in @science.org on a new small polymerase.
1/n
A small polymerase ribozyme that can synthesize itself and its complementary strand
The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...
www.science.org
February 13, 2026 at 11:42 AM
How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller?
Excited to share our latest work in @science.org on a new small polymerase.
1/n
Excited to share our latest work in @science.org on a new small polymerase.
1/n
Reposted by James Lloyd 🧬
In @science.org this week, thermospermine affects ribosome methylation, which in turn regulates translation of xylem development proteins www.science.org/doi/10.1126/...
#plantscience
#plantscience
Recruitment of bifunctional regulator thermospermine to methylated ribosomes directs xylem fate
Polyamines are often associated with ribosomes and are thought to stabilize their integrity. In Arabidopsis, the polyamine thermospermine (tSpm) affects xylem cell fate. tSpm induces translation of SU...
www.science.org
February 13, 2026 at 9:43 AM
In @science.org this week, thermospermine affects ribosome methylation, which in turn regulates translation of xylem development proteins www.science.org/doi/10.1126/...
#plantscience
#plantscience
Reposted by James Lloyd 🧬
A toolkit for programmable transcriptional engineering across eukaryotic kingdoms https://www.biorxiv.org/content/10.64898/2026.02.10.705154v1
February 12, 2026 at 5:02 AM
A toolkit for programmable transcriptional engineering across eukaryotic kingdoms https://www.biorxiv.org/content/10.64898/2026.02.10.705154v1
Reposted by James Lloyd 🧬
Great to see CCDM’s sclerotinia stem rot team preparing resistant material for this year’s experiments 🌱🧪
@curtinuniversity.bsky.social, #GRDC
@curtinuniversity.bsky.social, #GRDC
February 12, 2026 at 4:18 AM
Great to see CCDM’s sclerotinia stem rot team preparing resistant material for this year’s experiments 🌱🧪
@curtinuniversity.bsky.social, #GRDC
@curtinuniversity.bsky.social, #GRDC
Reposted by James Lloyd 🧬
Nature has a trick to evolve multimeric proteins via gene duplication.
🧬One copy compensates, the other explores.🧬
Although this has only been a theory so far.
Until now: Directed evolution of multimeric proteins by dual-compensatory gene duplication.
www.biorxiv.org/content/10.6...
🧬One copy compensates, the other explores.🧬
Although this has only been a theory so far.
Until now: Directed evolution of multimeric proteins by dual-compensatory gene duplication.
www.biorxiv.org/content/10.6...
January 14, 2026 at 6:30 PM
Nature has a trick to evolve multimeric proteins via gene duplication.
🧬One copy compensates, the other explores.🧬
Although this has only been a theory so far.
Until now: Directed evolution of multimeric proteins by dual-compensatory gene duplication.
www.biorxiv.org/content/10.6...
🧬One copy compensates, the other explores.🧬
Although this has only been a theory so far.
Until now: Directed evolution of multimeric proteins by dual-compensatory gene duplication.
www.biorxiv.org/content/10.6...
Reposted by James Lloyd 🧬
Out in @science.org this week: A decline in epigenetic silencing of TEs in older plant organs but not in the shoot meristem. TCX5 and TCX6 help regulate DNA methylation in this context.
www.science.org/doi/10.1126/...
#plantscience
www.science.org/doi/10.1126/...
#plantscience
Aging drives a program of DNA methylation decay in plant organs
Plants display a wide range of life spans and aging rates. Although dynamic changes to DNA methylation are a hallmark of aging in mammals, it is unclear whether similar molecular signatures reflect ra...
www.science.org
February 2, 2026 at 1:48 PM
Out in @science.org this week: A decline in epigenetic silencing of TEs in older plant organs but not in the shoot meristem. TCX5 and TCX6 help regulate DNA methylation in this context.
www.science.org/doi/10.1126/...
#plantscience
www.science.org/doi/10.1126/...
#plantscience
Reposted by James Lloyd 🧬
We genetically disconnected starch from the matrix in the algal pyrenoid!
A saga1;saga2 double mutant lacks a starch sheath!
Our model: SAGA1 & SAGA2 locally initiate starch on the pyrenoid surface by enriching starch precursors.
🌞🦠🔬🔌👀
www.biorxiv.org/content/10.6...
A saga1;saga2 double mutant lacks a starch sheath!
Our model: SAGA1 & SAGA2 locally initiate starch on the pyrenoid surface by enriching starch precursors.
🌞🦠🔬🔌👀
www.biorxiv.org/content/10.6...
February 1, 2026 at 6:17 PM
We genetically disconnected starch from the matrix in the algal pyrenoid!
A saga1;saga2 double mutant lacks a starch sheath!
Our model: SAGA1 & SAGA2 locally initiate starch on the pyrenoid surface by enriching starch precursors.
🌞🦠🔬🔌👀
www.biorxiv.org/content/10.6...
A saga1;saga2 double mutant lacks a starch sheath!
Our model: SAGA1 & SAGA2 locally initiate starch on the pyrenoid surface by enriching starch precursors.
🌞🦠🔬🔌👀
www.biorxiv.org/content/10.6...
Reposted by James Lloyd 🧬
Cool work, but comments like "protein centric view of the central dogma" have to stop. 1) That's not what the central dogma was about & 2) Jacob/Monod/Lwoff were awarded the Nobel in 1965 for demonstrating that genes are regulated by non-coding regions.
The protein centric view of the central dogma, ie genetic information flows from DNA to RNA to protein, completely ignores info in noncoding seqs. But > 70% conserved seqs are noncoding. We need unbiased experimental evidence, including functional annotation of noncoding seqs.
January 31, 2026 at 1:55 PM
Cool work, but comments like "protein centric view of the central dogma" have to stop. 1) That's not what the central dogma was about & 2) Jacob/Monod/Lwoff were awarded the Nobel in 1965 for demonstrating that genes are regulated by non-coding regions.
Reposted by James Lloyd 🧬
Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...
www.biorxiv.org
January 31, 2026 at 1:13 AM
Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...
Reposted by James Lloyd 🧬
🦠
Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli
Abstract. Cas9-based genome editing technologies can rapidly generate mutations to probe a diverse array of mutant genotypes. However, aberrant Cas9 nuclea
academic.oup.com
January 30, 2026 at 4:36 PM
🦠
Reposted by James Lloyd 🧬
Calling all OrthoFinder users!
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
www.biorxiv.org
January 29, 2026 at 12:07 PM
Calling all OrthoFinder users!
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
Reposted by James Lloyd 🧬
If you are looking for a distraction, this seems cool. Sticky ends++. If it works as advertised, seems like it could be a game-changer.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Construction of complex and diverse DNA sequences using DNA three-way junctions - Nature
Sidewinder enables high-fidelity DNA assembly by separating the information that guides assembly from the final assembled sequence.
www.nature.com
January 26, 2026 at 9:20 PM
If you are looking for a distraction, this seems cool. Sticky ends++. If it works as advertised, seems like it could be a game-changer.
www.nature.com/articles/s41...
www.nature.com/articles/s41...