Naked Man orchid (Orchis Italica)

My first break after the morning chores was spent lucratively on social media. I say lucratively because I found this gem in my Twitter feed:

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Who says social media is bad for you? Besides me and many other professionals, that is.

Naturally, as any 6 year old would, I felt intrigued by the orchid’s appearance and wanted to know more about it because pareidolia is strong with this one. To my surprise, a quick PubMed search revealed 15 serious publications about the genes of this plant (oh, silly me, I shouldn’t be surprised). Most of these papers are authored by Italian researchers, obviously. Not because of what you think, dirty mind, but (probably) because the orchid is widespread in Italy, as the species name indicates. All of these papers dealt with the genetics and the transcriptome of the plant. Since I have already covered the transcriptome of tomato in the previous post I thought to let these papers be and give you, my reader, a breather from the world of heavy trascriptomics.

Instead, the self-evident name of the plant and its visually striking flower got me wondering if it was used as a cure for impotence or some other ailments of the male reproductive organs as part of the doctrine of signatures wave. Let me explain. Back in the 1500s, a guy called Theophrastus von Hohenheim, a.k.a. Paracelsus posited that plants that look like an organ are good for treating diseases of that organ. This led to the practice called doctrine of signatures, meaning the healers went gallivanting in the fields in search of various plants that resemble or ‘have a signature of’ some part of human anatomy, pluck it, ground it, and give it to the suffering patients. Needless to say – or perhaps not needless, given the increase in pseudoscience bull lately – this assumption is not only false, but also dangerous. Sure, eating walnuts to help your brain manage stress because walnuts look like brains may not make you less stressed but will not harm you either. Giving birthwort to expectant mothers on the other hand may very well end up with orphaned kids.

Sure enough, it looks like even before Paracelsus the Naked Man orchid’s root was ground up and eaten as aphrodisiac or as erectile dysfunction cure in the entire Mediterranean basin, from Spain to Turkey, from Sicily to North Africa, which is the habitat of this plant. Luckily for the gentlemen in the Middle Ages, Orchis italica’s roots appear to be edible, or at least not toxic in the amounts ingested. I wish I could give you some original source for this information but I couldn’t find any that I could trust or in a language I could read.

For what is worth, it appears that although the species has been described by everybody with an intact fusiform gyrus (part of the brain responsible with, among other things, seeing faces where there aren’t), it was drawn formally by the famous botanist Heinrich Gustav Reichenbach in 1851. Alas, the internet is devoid of the exact volume where this momentous depiction took place, so I – and presumably you – were robbed of the pleasure of seeing how the plant was painted by someone with the most keen observational botanical eye. Reichenbach has drawn thousands upon thousands of plants in minute detail. So, even if I couldn’t find his plate for Orchis italica, I’ll leave you with some of his other works (excepts from Vols 3, 21, 23 of Icon. Fl. Germ. Helv., see REFERENCE).

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REFERENCE: Reichenbach, H. G. Ludwig (Heinrich Gottlieb Ludwig) & Reichenbach, H. G. (Heinrich Gustav) (1834-1912. [v. 1, 1850]). Icones florae Germanicae et Helveticae, simul Pedemontanae, Tirolensis, Istriacae, Dalmaticae, Austriacae, Hungaricae, Transylvanicae, Moravicae, Borussicae, Holsaticae, Belgicae, Hollandicae, ergo Mediae Europae. Iconographia et supplementum ad opera Willdenowii [et al.] .. 25 Volumes, Published by Leipzig and Gera: Friedrich Hofmeister, Ambrose Abel and Friedrich de Zezschwitz. Most of the 24 volumes scanned courtesy of  The New York Botanical Garden, LuEsther T. Mertz Library

By Neuronicus, 12 March 2018

Tomato transcriptome

As most children, growing up I showed little appreciation for what I had, coveting instead what I did not. Now I realize how fortunate I have been to have grown up half the time in a metropolis and the other half at the countryside. At the farm. A subsistence farm, although I truly loathe the term because we were not subsisting but thriving off the land, as we planted and harvested a bit of everything and we had a specimen or four of almost all the farm animals, from bipeds to quadrupeds.

I got on this memory lane after reading the paper of Shinozaki et al. (2018) on tomatoes. It was a difficult read for me as it was punctured by many term definition lookups since botany evolved quite steeply since the last time I checked, about 25 years or so.

Briefly, the scientists grew tomato plants in a greenhouse at Cornell, NY. They harvested the fruit from 60 plants about 5 to 50 days after the flower was at its peak (DPA, days post anthesis) following this chart:

  • Expanding [fruit] stage (harvested at 5, 10, 20, or 30 DPA)
  • Mature Green stage (full-size green fruit, ≈ 39 DPA),
  • Breaker stage (definite break in color from green to tannish-yellow with less than 10% of the surface, ≈ 42 DPA),
  • Pink stage (50% pink or red color, ≈ 44 DPA),
  • Light red stage (100% light red, ≈ 46 DPA),
  • Red ripe stage (full red for 8 days, ≈ 50 DPA).

(simplified from the Methods section, p. 10, see pic)

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Fig. 1 (partial from Shinozaki et al., 2018). A tissue/cell-based transcript profiling of developing tomato fruit. a Traced image of six targeted fruit tissues. Shaded areas of the total pericarp and the placenta were not harvested. b Traced image of five pericarp cells. c Representative pictures of harvested fruit spanning ten developmental stages. d Representative pictures of the stylar end of MG and Br stage fruit. DPA, days post anthesis; MG, mature green; Br, breaker; Pk, pink; LR, light red; RR, red ripe. Credit: DOI: 10.1038/s41467-017-02782-9. License: CC BY 4.0 IL.

Immediately after harvesting, the tomato was scanned with a micro-computed tomograph (micro-CT) to generate a 3D image of the fruit, including its internal structures. Then, the fruit was dissected by hand or laser, depending of its size, divided into various tissue types and then preserved either via snap-freezing in liquid nitrogen or standard tissue fixation for light or transmission electron microscopy. Finally, the researchers used kits to extract and analyze the RNA from their samples. And, last but not least, a lot of math & stats.

This is what I got out of it:

  1. A total of 24,660 genes were uniquely expressed in various tomato cell types and at various stages of development.
  2. The tomato ripens from within, meaning from the interior to the exterior and not the other way around.
  3. The ripening seems to be a continuous process, starting before the ‘Breaker’ stage.
  4. The ripening signals originate in the locular tissues (the goo around the seeds; it’s possible that the seeds themselves send the signals to the locular tissue to start the ripening process).
  5. The flesh of the fruit is only one part of the tomato and the most investigated, but the other types of tissue are also important. For example, some genes responsible for aroma and flavor (CTOMT1, TOMLOXC) are predominantly or even exclusively expressed in the flesh, but some genes that improve the nutritional value (SlGAD3) are expressed mostly in the placenta.
  6. The fruit can do photosynthesis, probably for the benefit of its seeds.
  7. Each developmental stage is characterized by a distinct transcriptome profile (by inference, also a distinct proteomic profile, although not necessarily in exact correspondence)
  8. Botany, like any serious science, is complicated.

Ah, I have been vindicated. By science, nonetheless! You see, in my pursuit to recapture the tomato taste of my childhood I sample various homegrown exemplars of Solanum lycopersicum derived both from more or less failed personal attempts with pots on the balcony and from various farmer’s market vendors. While I can understand – though not approve of – the industrial scale agro-growers’ practice to pick the tomatoes green, unripe and then artificially injecting them with ethylene to prolong shelf life, I completely fail to understand the picking them up when green by the sellers in the farmer’s markets. I had many surreal conversations with such vendors (I cannot call them farmers for the life of me) who more than once attempted to reassure me that 1) Everybody’s picking tomatoes green off the vine because that’s how it’s done and 2) Ripening happens on the window sill. In vain have I tried to explain the difference between ripen and rotten; in vain have I pointed out that color is only one indicator of ripening; in vain did I explain that during ripening on the vine the plant delivers certain substances to the fruit that lead to changes in the flesh composition to make it more nutritious for the future seedling, process that the aforesaid widow sill does nor partake in. Alas, ultimately, my arguments (and my family’s last 400 years of experience) hit the wall of “I am growing tomatoes for three years now and I know what I’m doing. Are you buying or not?” As you might imagine, I end up going home frustrated and yet staring at some exorbitantly expensive and looking as sad as I feel greenish tomatoes.

For me, this is what Shinozaki et al. (2018) validated: Ripening is a complex process that involves a lot of physiological changes in the fruit, not merely some extra production of ethylene that can be conveniently supplied externally by a syringe or rotting on the window sill. Of course, there is nowhere in the paper that Shinozaki et al. (2018) say that. What they do say is this: “The ripening program is revealed as comprising gradients of gene expression, initiating in internal tissues then radiating outward, and basipetally along a latitudinal axis. We also identify spatial variations in the patterns of epigenetic control superimposed on ripening gradients” (Abstract). Tomayto, tomahto…

Now we know that… simply put, I’m right. Sometimes is good to be right. I am old enough to prefer happiness and tranquility over rightness & righteousness, but still young enough that sometimes, just sometimes, it feels good to be right. Yes, the Shinozaki et al. (2018) paper exists only for my vindication in my farmer’s market squabbles and not for providing a huge comprehensive atlas on the tomato transcriptome, along with an awesome spatiotemporal map showing the place and time of the expression of genes responsible for fruit ripening, quality traits and so on.

Good job, Shinozaki et al. (2018)!

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REFERENCE: Shinozaki Y, Nicolas P, Fernandez-Pozo N, Ma Q, Evanich DJ, Shi Y, Xu Y, Zheng Y, Snyder SI, Martin LBB, Ruiz-May E, Thannhauser TW, Chen K, Domozych DS, Catalá C, Fei Z, Mueller LA, Giovannoni JJ, & Rose JKC (25 Jan 2018). High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening. Nature Communications, 9(1):364. PMID: 29371663, PMCID: PMC5785480, DOI: 10.1038/s41467-017-02782-9. ARTICLE | FREE FULLTEXT PDF | The Tomato Expression Atlas database

By Neuronicus, 7 February 2018

The FIRSTS: Magnolia (1703)

It is April and the Northern Hemisphere is enjoying the sight and smell of blooming magnolias. Fittingly, today is the birthday of the man who described and named the genus. Charles Plumier (20 April 1646 – 20 November 1704) was a French botanist known for describing many plant genera and for preceding Linnaeus in botanical taxonomy. His (Plumier’s) taxonomy was later incorporated by Linnaeus and is still in use today.

Plumier traveled a lot as part of his job as Royal Botanist at the court of Louis XIV. Don’t envy him too much though because the monk order to which he belonged, the Minims, forced him to be a vegan, living mostly on lentil.

Among thousands of other plants described was the magnolia, a genus of gorgeous ornamental flowering trees that put out spectacularly big flowers in the Spring, usually before the leaves come out. Plumier found it on the island of Martinique and named it after Pierre Magnol, a contemporary botanist who invented the concept of family as a distinct taxonomical category.

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Excerpts from the pages 38, 39 and plate 7 from Nova Plantarum Americanum Genera by Charles Plumier (Paris, 1703) describing the genus Magnolia.

Interestingly enough, Plumier named other plants either after famous botanists like fuchsia (Leonhard Fuchs) and lobelia (Mathias Obel) or people who helped his career as in begonia (Michel Begon) and suriana (Josephe Donat Surian), but never after himself. I guess he took seriously the humility tenet of his order. Never fear, the botanists Joseph Pitton de Tournefort and the much more renown Carl Linnaeus named an entire genus after him: Plumeria.

Of interest to me, as a neuroscientist, is that the bark of the magnolia tree contains magnolol which is a natural ligand for the GABAA receptor.

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REFERENCE: Plumier, C. (1703). Nova Plantarum Americanum Genera, Paris. FULLTEXT courtesy of the Biodiversity Heritage Library

By Neuronicus, 20 April 2017