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
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-...
Because automated protein structure prediction is becoming more common, I wondered what impact this would have on protein structure predictions. Taking the "wrong" ORF indicated a longer predicted protein, missing a small part of the C-terminal. But the reality is just a small protein would be made!
November 6, 2025 at 2:14 PM
Because automated protein structure prediction is becoming more common, I wondered what impact this would have on protein structure predictions. Taking the "wrong" ORF indicated a longer predicted protein, missing a small part of the C-terminal. But the reality is just a small protein would be made!
To show that this improvement extended beyond just two example genes I noticed manually, we re-examined some old RNA-seq from an NMD mutant in Arabidopsis. Sure enough, known NMD features were higher in the revised start/stop (open reading frame; ORF) annotations.
November 6, 2025 at 2:14 PM
To show that this improvement extended beyond just two example genes I noticed manually, we re-examined some old RNA-seq from an NMD mutant in Arabidopsis. Sure enough, known NMD features were higher in the revised start/stop (open reading frame; ORF) annotations.
So it started when I was showing a visiting High School student the Arabidopsis genome and noticed an error. The wrong start and stop codon was labelled for some NMD targets (PTB1 & RS2Z33).
Using TranSuite (modified & updated) we showed that the biologically correct start/stop were now annotated!
Using TranSuite (modified & updated) we showed that the biologically correct start/stop were now annotated!
November 6, 2025 at 2:14 PM
So it started when I was showing a visiting High School student the Arabidopsis genome and noticed an error. The wrong start and stop codon was labelled for some NMD targets (PTB1 & RS2Z33).
Using TranSuite (modified & updated) we showed that the biologically correct start/stop were now annotated!
Using TranSuite (modified & updated) we showed that the biologically correct start/stop were now annotated!
Patrick, not satisfied with the 2-input AND gate we had published in 2022, designed & built a 3-input AND gate with the new recombinases he had de-bugged, seeing a >300 activation in the 3-input on-state and negligible noise in all other conditions. Fantastic.
October 31, 2025 at 9:24 AM
Patrick, not satisfied with the 2-input AND gate we had published in 2022, designed & built a 3-input AND gate with the new recombinases he had de-bugged, seeing a >300 activation in the 3-input on-state and negligible noise in all other conditions. Fantastic.
And with all we had learned, Patrick expanded our toolkit of recombinases, bringing VCre & SCre back into the roster, after I had rejected them in the 2022 study. This builds a strong foundation to allow us to build new, more complex circuits.
October 31, 2025 at 9:24 AM
And with all we had learned, Patrick expanded our toolkit of recombinases, bringing VCre & SCre back into the roster, after I had rejected them in the 2022 study. This builds a strong foundation to allow us to build new, more complex circuits.
This goes to show that few pairs of Recombinase-Target sites behave the same. FLP site enhances, but the B3 protein enhances. The Cre family all interfere, but only the lox site has an inhibitory effect - I guess we just got epically unlucky with pairing that recombinase with that promoter!
October 31, 2025 at 9:24 AM
This goes to show that few pairs of Recombinase-Target sites behave the same. FLP site enhances, but the B3 protein enhances. The Cre family all interfere, but only the lox site has an inhibitory effect - I guess we just got epically unlucky with pairing that recombinase with that promoter!
Patrick then tested lox negation w/ a range of promoters. Act2 was repressed, but so too was TCTP & Ubi10. Only 35S & NOS did not experience negation from a lox site. Indicating interesting PRO+lox site interactions…is this common in non-plants? I think people better start checking ASAP.
October 31, 2025 at 9:24 AM
Patrick then tested lox negation w/ a range of promoters. Act2 was repressed, but so too was TCTP & Ubi10. Only 35S & NOS did not experience negation from a lox site. Indicating interesting PRO+lox site interactions…is this common in non-plants? I think people better start checking ASAP.
We ruled out Cre toxicity as a cause of the problem and confirmed Cre-interference was occurring. But to our surprise, the lox site was negating expression from the Act2 promoter we were using to drive the circuit output! But knowing this, we tried a different promoter: 35S.
October 31, 2025 at 9:24 AM
We ruled out Cre toxicity as a cause of the problem and confirmed Cre-interference was occurring. But to our surprise, the lox site was negating expression from the Act2 promoter we were using to drive the circuit output! But knowing this, we tried a different promoter: 35S.
This all started by de-bugging an OR gate from our 2022 study: Flp recombinase input worked, but Cre did not. In fact, Cre failed so badly, it stopped Flp from activating the circuit. This mystery stumped us, but through continued hard work, Patrick Gong Figured out the source of the problem:
October 31, 2025 at 9:24 AM
This all started by de-bugging an OR gate from our 2022 study: Flp recombinase input worked, but Cre did not. In fact, Cre failed so badly, it stopped Flp from activating the circuit. This mystery stumped us, but through continued hard work, Patrick Gong Figured out the source of the problem:
At the @cbsmwa.bsky.social conferences The University of Western Australia today to see the fantastic research being done across the state of WA, such a good place to be. #CBSMWA
September 19, 2025 at 1:12 AM
At the @cbsmwa.bsky.social conferences The University of Western Australia today to see the fantastic research being done across the state of WA, such a good place to be. #CBSMWA
An update to my recent pre-print:
Start right to end right: authentic open reading frame selection matters
has just gone online. In it, we look at the effect of mis-annotating an ORF on a spliced gene's predicted protein structure.
www.biorxiv.org/content/10.1...
Start right to end right: authentic open reading frame selection matters
has just gone online. In it, we look at the effect of mis-annotating an ORF on a spliced gene's predicted protein structure.
www.biorxiv.org/content/10.1...
July 13, 2025 at 11:30 AM
An update to my recent pre-print:
Start right to end right: authentic open reading frame selection matters
has just gone online. In it, we look at the effect of mis-annotating an ORF on a spliced gene's predicted protein structure.
www.biorxiv.org/content/10.1...
Start right to end right: authentic open reading frame selection matters
has just gone online. In it, we look at the effect of mis-annotating an ORF on a spliced gene's predicted protein structure.
www.biorxiv.org/content/10.1...
Great to present my synthetic biology work & considering the effects of variable gravity on root structure at the Society of Experimental Biology in Belgium. I was sad that I could not attend in person, but thank you @suruchiroy.bsky.social for getting a photo of my online talk at the meeting!
July 12, 2025 at 4:25 AM
Great to present my synthetic biology work & considering the effects of variable gravity on root structure at the Society of Experimental Biology in Belgium. I was sad that I could not attend in person, but thank you @suruchiroy.bsky.social for getting a photo of my online talk at the meeting!
Quote this with a great TV father.
June 15, 2025 at 7:30 PM
Quote this with a great TV father.
We then tested if the new ORFs led to a change in interpretation of NMD target identification from public NMD-mutant data from Arabidopsis. Short answer: Yes. Long answer YEESSSSSS!!!
Up transcripts have a longer average 3' UTR in the revised ORFs, consistent with NMD targets.
Up transcripts have a longer average 3' UTR in the revised ORFs, consistent with NMD targets.
June 11, 2025 at 10:40 PM
We then tested if the new ORFs led to a change in interpretation of NMD target identification from public NMD-mutant data from Arabidopsis. Short answer: Yes. Long answer YEESSSSSS!!!
Up transcripts have a longer average 3' UTR in the revised ORFs, consistent with NMD targets.
Up transcripts have a longer average 3' UTR in the revised ORFs, consistent with NMD targets.
We start by demonstrating that the commonly used Araport11 transcriptome for model plant Arabidopsis annotates the longest ORF of known NMD targets (internal M codon used as start after AS-NMD event). Their 3' UTRs look normal, so would be missed when looking for typical signs of an NMD target!
June 11, 2025 at 10:40 PM
We start by demonstrating that the commonly used Araport11 transcriptome for model plant Arabidopsis annotates the longest ORF of known NMD targets (internal M codon used as start after AS-NMD event). Their 3' UTRs look normal, so would be missed when looking for typical signs of an NMD target!
I am super excited to announce the first (brief) pre-print purely from my group:
Start right to end right: authentic open reading frame selection matters
www.biorxiv.org/content/10.1...
This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!
Start right to end right: authentic open reading frame selection matters
www.biorxiv.org/content/10.1...
This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!
June 11, 2025 at 10:40 PM
I am super excited to announce the first (brief) pre-print purely from my group:
Start right to end right: authentic open reading frame selection matters
www.biorxiv.org/content/10.1...
This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!
Start right to end right: authentic open reading frame selection matters
www.biorxiv.org/content/10.1...
This marks a return to NMD research for me. NMD detects early stop codons but we need to find the true stop!
Another great @xkcd.com comic. But I really hope the archaea don’t take it personally!
xkcd.com/3095/
xkcd.com/3095/
May 30, 2025 at 8:03 PM
Another great @xkcd.com comic. But I really hope the archaea don’t take it personally!
xkcd.com/3095/
xkcd.com/3095/
I went for a lovely walk now I am back in Perth and I listened to this fantastic episode of the Talking Biotech podcast with @kevinfolta.bsky.social all about the genetically modified Purple Tomatoes that are now on sale in the USA (but developed in the UK).
share.transistor.fm/s/7a058ab6
share.transistor.fm/s/7a058ab6
May 28, 2025 at 1:11 PM
I went for a lovely walk now I am back in Perth and I listened to this fantastic episode of the Talking Biotech podcast with @kevinfolta.bsky.social all about the genetically modified Purple Tomatoes that are now on sale in the USA (but developed in the UK).
share.transistor.fm/s/7a058ab6
share.transistor.fm/s/7a058ab6
Excited to be at the first @aria-research.bsky.social (Advanced Research + Invention Agency (ARIA)) in London. Learning about all sorts of great innovative science.
May 13, 2025 at 8:42 AM
Excited to be at the first @aria-research.bsky.social (Advanced Research + Invention Agency (ARIA)) in London. Learning about all sorts of great innovative science.
Great work from Jen Nemhauser and others using a gene circuit to study an essential gene!
A Hot-Swappable Genetic Switch: Building an Inducible and Trackable Functional Assay for the Essential Gene MEDIATOR
pubs.acs.org/doi/10.1021/...
A Hot-Swappable Genetic Switch: Building an Inducible and Trackable Functional Assay for the Essential Gene MEDIATOR
pubs.acs.org/doi/10.1021/...
May 10, 2025 at 5:34 PM
Great work from Jen Nemhauser and others using a gene circuit to study an essential gene!
A Hot-Swappable Genetic Switch: Building an Inducible and Trackable Functional Assay for the Essential Gene MEDIATOR
pubs.acs.org/doi/10.1021/...
A Hot-Swappable Genetic Switch: Building an Inducible and Trackable Functional Assay for the Essential Gene MEDIATOR
pubs.acs.org/doi/10.1021/...
I had a wonderful time speaking to many prospective students at The University of Western Australia Open Day on Sunday!
March 31, 2025 at 2:46 AM
I had a wonderful time speaking to many prospective students at The University of Western Australia Open Day on Sunday!
I love it! I printed a lot of the Bulbasaur (as my fav pokemon) for the lab and my student is using them to store duckweed in
March 26, 2025 at 10:29 AM
I love it! I printed a lot of the Bulbasaur (as my fav pokemon) for the lab and my student is using them to store duckweed in
Confused by your language, or how to run things for your science? Come along to UWA Hacky Hour to speak to other researchers eager to solve problems at Catalyst Cafe at 2pm today!
March 11, 2025 at 12:51 AM
Confused by your language, or how to run things for your science? Come along to UWA Hacky Hour to speak to other researchers eager to solve problems at Catalyst Cafe at 2pm today!