Carlos Rodríguez

Postdoc of Plant Natural Product Biosynthesis or Transport | Fernando Geu-Flores 🌿 Postdoc position in Plant Natural Products 🌿 📍 Geu-Flores lab at the University of Copenhagen (DK) 🥼 Are you passionate about uncovering how plants make and transport complex bioactive alkaloids? ...

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Come work with us in beautiful Copenhagen!

This is the erfect position for you, if you like:
- natural products
- working with plants
- solving complex metabolism puzzles
- having an applied impact

shorturl.at/iIjW3

Honestly, any miniprep day; I was done by noon, had to wait for until the next day for sequencing results, so I had a whole afternoon free; usually wasted reading, but sometimes with a view or a beer

I forgot to ad hashtags!! #Biosynthesis #Olive #plantscience #NaturalProducts #SecMet
I may have to repost this later this week; anyone know hashtags on natural product biosynthesis or enzyme/gene discovery?

But anyway, feel free to ask me anything on this. I noticed several mistakes in this thread that I cannot edit (including an it's that should be an its) but any other discussion on the science is more than welcome!

The method has it's limitations; by checking with known enzymes, it might have a higher false negative rate than other methods (which is hard to determine for other methods with no clear threshold) so it's not a silver bullet. But it makes use of public data, so has very low cost to implement.

And in the first batch of enzymes we found an activity! And it wasn't a p450 at all, but an oxoglutarate-dependent dioxygenase! Never before I had an activity in the first batch of candidates.

I was starting my lab in México with no starter funds, so we couldn't brute force it. So I did the usual: throw more data at the problem. Jasmine and Ash have similar metabolites, so we analized public datasets, and got a reasonable number of candidates that were coexpressed in the 3 species.

Stubbornness wouldn't let me forget the issue, and we kept testing for the activity; synGenes from different assemblies, isoforms, alleles, ID%, etc. but no activity. Until we thought that maybe it wasn't a CYP72. We decided to have an open-minded approach, but how do you select from 100s of genes?

Two bi‐functional cytochrome P450 CYP72 enzymes from olive (Olea europaea) catalyze the oxidative C‐C bond cleavage in the biosynthesis of secoxy‐iridoids – flavor and quality determinants in olive oil Olive (Olea europaea) is an important crop in Europe, with high cultural, economic and nutritional significance. Olive oil flavor and quality depend on phenolic secoiridoids, but the biosynthetic ...

A key step of the pathway is the oxidation of 7-deoxy-loganic acid to 7-epi-loganic acid, assumed to be performed by a P450, as C. roseus 7DLH. So we BLASted Cr7DLH, and found homologues in Olive; some with interesting activities we reported in 2021 (doi.org/10.1111/nph....) but no hydroxylation.

Comparative transcriptomic and co-expression analyses enable the discovery of key enzymes responsible for oleuropein biosynthesis in olive (Olea europaea) Oleuropein, an oleoside-type secoiridoid, is the major determinant of olive oil flavor and quality. This study completes the biosynthetic pathway from 7-deoxy-loganic acid to 7-β-1-D-glucopyranosyl-ol...

We're closing in on oleuropein biosynthesis in Olive! Oleuropein is the reason we can't eat raw olives, and also the "spicy" taste of olive oil. People assumed (and some wrongly reported) that the pathway was the same as in Catharanthus, but that's not entirely true! 🧵
www.cell.com/plant-commun...

A structural formula of "Lysine". Wrong one.

You know, it would really add a bit credibility to your article if you would use correct structural formula of the (well-known) compound that you are studying.

#chemsky

www.mdpi.com/1999-4923/17...

I'm intrigued...I would look for forbidden m/z values, some masses cannot exist as combinations of atoms are limited. Or check the variation of intensities and symmetry of LC peaks? I'm tempted to volunteer my time to the effort; this is scary...

A graph showing the increase of executive and management staff salaries at McGill (260%) since 2014-15 compared to full time faculty (125%). A second graph shows that academic salaries have decreased in real dollars by 4.2% while director/manager salaries have increased by 5.2%.

I like to tape these graphs next to the asbestos monitoring air pumps that have been running in my building since 2014.

Profile image of Laila P. Partida-Martínez

In #Profile: Laila P. Partida-Martínez
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📖 nph.onlinelibrary.wiley.com/doi/10.1111/...

#LatestIssue

There's something that breaks inside me whenever I read "human - AI collaboration" in a formal, scientific article. I don't collaborate with Excel or R anymore than I collaborare with a pipette or a mass spec. It's a marketing term that overstates capacities that editors should not allow.

Lowry! Forgot the name of the assay! I do think that it's due to the misuse in food science spam articles, rather than the protein assay, as I've rarely seen anything that is not Bradford for that.

My guess would be the Folin assay, or the paper that first uses it to estimate total phenolics. Food science has a serious SPAM issue of people throwing Folin to a random extract and publishing the results, so it must be >100k citations.

I need to start making my exams less dependent on NCBI; good thing it's 10mins to the end of the test, and that I also taught them to use the EBI. But there was some panic.

That also works against my notion of potential autotoxicity; few things more reactive than an isothiocyanate...I need to sit and think this more thoroughly.

I always believed on the cost to produce, but then I can't explain some Caryophyllales substituting "inexpensive" (CO2) anthocyanins with costly (N2) betalains. I now think it's more about the liability of leaky production of reactive molecules. But that's on ecological time, not evolutionary time.

Good to know I'm not the only one! Yesterday I started the lecture one hour early because I misread the time zone. Had to tell the students that showed up to meet back in an hour.

A cell‐type‐specific regulon controlling monoterpene indole alkaloid biosynthesis with feedback and feedforward activation loops Monoterpene indole alkaloids (MIA) are a diverse class of plant natural products produced by a subset of lineages within the Asterid clade of eudicots. The diversity of MIAs provides a unique opport.....

Our latest New Phytologist paper has been assigned an issue. #PlantScience #SecMet

nph.onlinelibrary.wiley.com/doi/full/10....

Both papers advanced our understanding of how specialized metabolism are regulated in rare cell types to achieve cell type specificity. 1/n🧵

The Matthew Effect is alive and well in academia - always makes me wary of programs aimed at identifying rising stars in an already highly talented pool...

elifesciences.org/reviewed-pre...

That's why funders hold the power here. Funders can decide to pay for services or not. They can decide to support authors who publish in for-profit journals, or not. They can decide to pay APCs in for-profit journals, or not.

9/n

I think a huge part of this is due to admins being *very* JIF and brand-driven (brand aware?) I also think, and this is very anecdotal, that some uni admins tend to be anti-academic and perceive society journals as old school and Nature brand as more "disruptive" (at least buzzword/marketing-wise).

🌱plantiSMASH 2.0💥 is now live!

I’m very excited to share that the 2.0 version of plantiSMASH is now available online and as a preprint on bioRxiv 📄https://lnkd.in/dN4F56pf

🌱 What’s new in plantiSMASH 2.0? ⬇️

PSNA2026@Madison Save the date!! June 15 Monday - June 19 Friday, 2026

SAVE THE DATE! The annual meeting of the PSNA will be on June 15-19 in Wisconsin! Check the website go.wisc.edu/PSNA2026 and follow @psna-official.bsky.social for updates.
And if you do research in phytochemistry, consider joining the PSNA; I've found the community to be very welcoming.

Faculty opening in Cornell Chemistry at the Assistant Professor level in the area of chemical biology, broadly defined! academicjobsonline.org/ajo/jobs/30338 #chemjobs

Essentially, narratives about the efficiency and efficacy of AI have flooded our cultural conversation about AI thereby resulting in the uncritical uptake of anything branded as "AI" as inherently more valuable, more effective, than anything without AI, EVEN IF AI IS NOT NECESSARY.

Has anyone else seen an increase in manuscript submissions using triple quads for untargeted metabolomics? Are vendors telling people they can do untargeted with a TQD? Or did I miss something?