Next step taken to #GiveGenesAChance in the EU 🇪🇺
Today, the European Council, i.e. the memeber states of the EU, has adopted the new regulation for plants obtained by New Genomic Techniques (NGTs).
Next step will be the decision of the European Parliament on 18th May.
Ooh, someone cited my research about indoles! Looked at their review... Hmm, their Figure 1 looks AI generated. Structure of Sunitinib is terribly wrong. What's Motinib and Oximeindolol, lol? and according to AI, ferroptosis is a compound, ferroZptosis is a mechanism of action...
#chemsky
Screenshot of a Facebook report dialog asking "What's going on?" with four radio button options: "It's annoying or not interesting," "I'm in this photo and I don't like it" (selected), "I think it shouldn't be on Facebook," and "It's spam."
Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.
Postdoctoral Scholar position in the Coaker group University of California, Davis We are seeking a Postdoctoral Scholar to join our research program focused on immune receptor engineering and spatial analyses of plant pathogens interactions using computational and imaging approaches. The position will involve integration of molecular, imaging, and computational approaches. Relevant publications from the laboratory include Nature Plants (2025, PMID: 40721669), Proceedings of the National Academy of Sciences (2024, PMID: 38814867), and Cell Reports (2023, PMID: 37342910). https://www.coakerlab.org/ Qualifications: • Ph.D. in plant biology, molecular biology, genetics, computational biology, or a related field • Strong background in genomics and/or computational biology • First author publications in peer-reviewed journals • Ability to work both independently and collaboratively in a multidisciplinary environment • Experience in plant innate immunity is preferred Application Instructions: The position is initially available for two years, with the possibility of extension based on performance and funding. Salary is based on the University of California postdoctoral salary scale (https://www.ucop.edu/academic-personnel-programs/_files/2025-26/represented-oct-2025-scales/t23.pdf). The salary range for this position is $69,073-$82,836 US Dollars/year. Review of applications will begin June 1, 2026 and will continue until the position is filled. Please submit a CV, a brief statement of research interests (~1 page), and contact information for three references to glcoaker@ucdavis.edu. The research statement should describe your previous work, how your expertise aligns with ongoing research in the lab, and potential future research directions.
We are hiring! We’re excited to recruit a postdoc to our lab at UC Davis to work on plant immune engineering and single-cell analyses of plant pathogen interactions. Apply by June 1. Please repost. www.coakerlab.org/postdoctoral...
I picked up a copy of the new LightBio trial pink autoluminescent petunia to add to my collection. Looking forward to seeing how well it glows once it recovers from a rough shipment. Gotta support fellow flower designers any way I can!
Best comment:
Any postdocs in Microscopy/Microbiology/Host-Pathogen/AMR looking to set up their own labs? Look here: www.uts.edu.au/research/exp...
Life in Sydney is pretty darn good! ☀️🏄🏻♂️🦘 Reach out for more info.
A picture of the contamination club calendar showing a picture of a fungus on an agar plate
It's @gerrich.bsky.social 's month, let's goooo
Hahaha , it actually is my month. ✨🌈
The first published article of my PhD. As described by @gerrich.bsky.social, we equipped R. sphaeroides with a MoClo system, characterized genetic elements, and applied a semi-automated approach for rapid strain construction. Such a nice collaboration!
If you are curious for more, here is my original post from 2024 on the Zymo-Parts toolbox. That was when I moved to bsky.
@altmetric.com notice me, Senpai!
#openscience
10/10
Screenshot of a tweet by Howard Salis (@hsalis) from 2022. Text reads: "Great paper! Zymo-Parts: A Golden Gate Modular Cloning Toolbox for Heterologous Gene Expression in Zymomonas mobilis. It's the first time someone has used the Promoter Calculator to design synthetic promoters for another organism. P100k* is 💪💪💪". Below the tweet text, a figure from the Zymo-Parts paper shows a schematic of the Golden Gate cloning system: a library of regulatory elements (promoter, RBS, GOI, terminator) in individual entry plasmids with ColE1 ori and AmpR, assembled via Golden Gate cloning into an acceptor plasmid containing a Zymomonas mobilis replication origin and KanR, yielding a final expression plasmid depicted next to a Z. mobilis cell. A link preview to the Zymo-Parts paper on pubs.acs.org is shown at the bottom.
This project started back in the days of science twitter. @hsalis.bsky.social reposted my first first-author paper, so @matick.bsky.social noticed it and saw potential.
It is amazing how projects can start, I love the online science community and hope that it will thrive here.
9/10
This is it ... for now!
More applications of Rhodo-Box will follow.
I am more than happy, that this collaboration worked out. I visited the Netherlands three times and got to meet amazing people and an amazing community.
If you are interested in adapting our assembly framework, reach out!
8/10
Three-panel figure showing combinatorial part characterization using a semiautomated cloning workflow. Panel A: top left, network diagram showing combinatorial assembly of 5 promoters (red squares, varying shades) with 6 RBSs (green squares, varying shades) driving eGFP, connected to 4 terminators (blue squares); top right, photograph of a fluorescent colony plate showing green-yellow fluorescent colonies of varying intensity on amber-colored agar; bottom, timeline of the semiautomated workflow using an Opentrons OT2 liquid handling robot: Day 1 — Golden Gate assembly and chemical transformation; Day 2 — conjugation into R. sphaeroides; Days 3-4-5 — strain recovery. 38 strains built in 5 days. Panel B: heatmap of combinatorial promoter-RBS expression strengths; promoters (PJ23100, PJ95025, PcrtE, PrpmI, PJ95027) on y-axis, RBSs (B0034, B0030, J95018, J95016, J95019, J95015) on x-axis; color scale from 10³ (dark purple) to 10⁵ (yellow); crosses indicate failed assemblies. Panel C: bar chart comparing four terminator performances (T0, B0010, B0015, J95029) across four promoter-RBS combinations; J95029 consistently lowest.
Finally, this is where standardized parts pay off.
5 promoters × 6 RBSs × 4 terminators assembled combinatorially on an Opentrons OT2.
38 plasmids in 5 days, hands-on time cut from ~4h to ~2h.
961-fold dynamic range across the full combinatorial space.
This is were collaborations shine!
7/10
Two-panel figure characterizing ribosome binding site (RBS) strength in R. sphaeroides. Panel A: horizontal bar chart ranking 11 RBSs by biomass-normalized eGFP fluorescence (a.u./OD, log scale from 10² to 10⁵), all assessed with promoter PrpmI. Strongest RBSs (dark green): B0034, J61100, B0030. Medium strength (medium green): J95028, J95018, J95017, J95019, B0032, J95016. Weakest (light green): B0031, J95015. Overall 49-fold dynamic range. E. coli-based RBSs B0034, J61100 and B0030 outperform the strongest R. sphaeroides-native designs. Panel B: scatter plot correlating RBS strengths when coupled with promoter PrpmI (y-axis) versus promoter PcrtE (x-axis), both on log scale from 10² to 10⁶. Points colored by RBS strength group. Linear regression line shown. Pearson r = 0.97, p < 0.0001, indicating highly predictable RBS behavior across two different promoter contexts.
11 RBSs characterized, with 49-fold range.
Interestingly, again E. coli-based elements (B0034, J61100, B0030) outperform the strongest R. sphaeroides-native designs.
Source your RBSs from iGEM registry!
6/10
Three-panel figure characterizing inducible expression systems in R. sphaeroides. Panel A: schematics of three transcriptional unit constructs, each with a constitutive promoter driving a regulatory gene (NahR, LacI, or VanR) and an inducible promoter (PsalTTC, PlacT7A1_O3O4, or PvanCC) driving eGFP with RBS J61100 and T0 terminator, all in a pBBR1-based vector with kanamycin resistance. Panel B: dose-response curves for three inducible systems on log-log scale; inducer concentration (mM) on x-axis, biomass-normalized fluorescence (a.u./OD) on y-axis. NahR-PsalTTC (dark orange circles): 136-fold range. LacI-PlacT7A1 (medium orange diamonds): 27-fold range. VanR-PvanCC (light orange squares): 432-fold range with near-zero basal expression. Fitted Hill equation curves shown. Panel C: bar chart comparing maximum expression levels of the three systems relative to reference promoter PrpmI-J61100; NahR-PsalTTC highest (~7.2×), followed by LacI-PlacT7A1 (~5×) and VanR-PvanCC (~2×).
A proper selection of inducible promoters had been mostly missing for R. sphaeroides #synbio, but no longer:
NahR-PsalTTC (salicylic acid), 136-fold range
LacI-PlacT7A1 (IPTG), 27-fold range
VanR-PvanCC (vanillic acid), 432-fold range
Their characterization inspired me, more to follow soon!
5/10
Two-panel figure assessing promoter strength in R. sphaeroides. Panel A: horizontal bar chart ranking 13 promoters by biomass-normalized eGFP fluorescence (a.u./OD, log scale from 10² to 10⁶), assessed with RBS J61100. Strongest promoters (dark red): PJ23100, Pstrong100K, PJ23104, PJ95025. Medium strength (medium red): PJ23116, PJ95027, PcrtE, PJ23105, PrpmI. Weakest (light red/pink): PJ23114, Pstrong1K, Pstrong10K, PJ95023. Overall 270-fold dynamic range. Panel B: scatter plot correlating promoter strengths when combined with either RBS J61100 (y-axis) or RBS J95017 (x-axis), both on log scale from 10² to 10⁶. Points colored by promoter strength group. Linear regression line shown. Pearson r = 0.94, p < 0.0001, indicating high correlation of promoter ranking across the two RBS contexts.
13 constitutive promoters characterized, 270-fold range
Synthetic σ70-based elements designed for E. coli (Anderson) are among the strongest in R. sphaeroides, despite the different RNAP architecture of Alphaproteobacteria.
Worth trying your E. coli parts in your non-model host!
4/10
Four-panel figure characterizing origins of replication (ORIs) in R. sphaeroides. Panel A: schematic of assessed constructs showing a transcriptional unit with promoter PrpmI, RBS J95017, eGFP and T0 terminator, cloned into plasmid backbones carrying either pBBR1, RK2, or RSF1010 ORI with kanamycin resistance marker. Panel B: schematic of the extended Level 1 and 2 broad-host entry plasmid collection, showing three ORIs (pBBR1, RK2, RSF1010) combined with four antibiotic resistance markers (kanamycin, spectinomycin, chloramphenicol, gentamicin) and a dropout cassette. Panel C: bar chart of biomass-normalized eGFP fluorescence (a.u./OD) for the three ORI-containing plasmids; RSF1010 highest (~700), followed by RK2 (~575) and pBBR1 (~510). Panel D: bar chart of relative plasmid copy number determined by qPCR; RSF1010 highest (~17), followed by pBBR1 (~13) and RK2 (~10). Error bars represent standard deviation.
As they are interested in R. sphaeroides and other Proteobacteria they added new broad-host-range vectors to the framework.
pBBR1, RK2, RSF1010
Each combined with 4 antibiotic markers as lvl 1 or lvl 2 entry vectors, all conjugateable.
3/10
Diagram of the Zymo-Parts Golden Gate MoClo assembly system showing four hierarchical levels. Level −1: individual RBS-GOI operon fragments in entry plasmids, assembled using BbsI. Level 0: basic parts (Promoter, RBS, Operon, GOI, Terminator) in E. coli-based entry plasmids, assembled using BsaI. Level 1: complete transcriptional units (Promoter-RBS-Gene-Terminator) in R. sphaeroides-compatible plasmids with antibiotic resistance marker, assembled using BsaI. Level 2: multi-transcriptional unit plasmids in R. sphaeroides-compatible backbone, assembled using BbsI. Arrows indicate double-loop architecture allowing recursive reassembly between Level 1 and Level 2.
The team in Wageningen @w-u-r.bsky.social outdid me with their overview of the assembly framework.
They were interested in it for the high-fidelity overhangs, loop assembly structure, but most of all the option to assemble polycistronic expression units natively inside the system.
2/10
Publication alert 🚨
A new Golden Gate MoClo toolbox for Rhodobacter sphaeroides is out and it's built on Zymo-Parts!
@matick.bsky.social & Antoine took our framework and added many new genetic tools and a new automation angle.
This adaptation is a dream come true for me. 1/10 🧪🧵
Wait is there an option for domestication for GG MoClo for CDS where it would design primers to create an overhang at the site that needs to be domesticated to switch from one codon to the closest other based of kazusa or something??
Why to choose between ants and microbes when you can have both? @khadlily.bsky.social, @adriatica.bsky.social and co. have been diving into what's happening in the honeypot ant repletes for years, and the first papers are coming out 🎉 (photo copyright: Smithsonian Institution-NMNH-Insect Zoo)
1/25 New paper out in PNAS! We show that the fitness costs of reproductive specialization, where somatic cells give up reproduction, scale inversely with organism size. Larger organisms can afford far more soma, removing a key barrier to multicellular complexity.
A new study exploring the diversity of microbial life encapsulated in global metagenomic contigs reveals there could be at least 250,000 bacterial species and potentially up to 750,000, with only a fraction that have genomic representatives
www.nature.com/articles/s41...
Every PI
What a tour de-force! Amazing study completing our knowledge of nicotine biosynthesis.
OMG, HMM/Pfam detection sounds like a great idea!
I hope, it's good karma that I acquired by being a fair reviewer myself. 🌈
I fear, it's an immediate wish for revision upon seeing my manuscript. 🙃
Screenshot of a journal manuscript tracking timeline showing five completed steps (bottom to top): Submission checks complete (24 Mar 2026), Editor assigned (24 Mar 2026), Reviewers invited (25 Mar 2026), Reviewers agreed (1 Apr 2026), Reviews received (1 Apr 2026).
Ahhh , this can't be good! 🧪
I am not prepared for rejection. 🥲
