© 2016 by Allan Dyen-Shapiro

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February 8, 2016

I've reached the point that I now need a website for my fiction career. Welcome. Here you'll find a list of all the short stories I've sold with links...

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Either a Solution to a Major Cause of Famine or Shoddy Science—I Don’t Know

October 13, 2019

By 2050, half of the world’s arable land will be salt-stressed due to rising sea levels. Although transgenic tomatoes that are more salt-tolerant have been around since the 1990s, even ignoring the political issues, the challenges surrounding making every variety of plant out there transgenic are daunting to the point of unfeasible in developing countries. This is a big deal—a major cause of famine currently has lacked a viable solution.

 

Until now. Maybe. In a paper coming out this week, scientists from research institutions in Egypt and Saudi Arabia have characterized the infection of tomato plant roots with a fungus (Piriformospora indica) that can be added to soil. The fungus is endophytic—it isn’t inside the plant cells, but close apposition of fungal cell membrane to highly invaginated plant root cell membrane with very thin cell walls allows transfer of material and information between fungus and plant.

 

The fungal infection doesn't do much in non-salty soil. However, in salty soil, it leads to lower sodium levels and higher potassium levels in plant roots. It also activates defenses against reactive oxygen and improves plant growth and fruit yield.

 

Salt toxicity to roots is mediated by loss of potassium in the cytoplasm, reactive oxygen accumulation, and direct toxicity of sodium ions. It is prevented under low-salt conditions because of the vacuoles, an organelle that takes up 90% of the space in mature plant cells and acts as a storage depot for ions. Sodium ions are pumped into the vacuole, away from where they can cause damage, powered by a gradient in hydrogen ions. (The vacuoles are acidic.)

 

Excess sodium causes potassium loss. In plants, this loss has two causes: (1) A depolarization-activated potassium channel—cells normally have a voltage across the membrane with the outside positive and the inside negative. Positively charged sodium ions moving inside the cell means a decreased voltage because the difference in voltage across the membrane is reduced. This change in electronic environment alters the shape of the channel so that more potassium ions leak out of the cells; (2) There is also a channel in the membrane that allows all types of positive ions, including potassium, to leak out. This one is activated by reactive oxygen. Fungal infection seems to prevent all of this.

 

The flaw in this paper is the explanation for how the fungus does it. The authors show a two-fold increase in expression (RNA synthesis from) the gene that codes for the transporter in the vacuole. If that were to translate into more of the exchange of hydrogen for sodium, it would explain everything else. However, the simple experiment that should have been done—seeing if the increase in RNA levels for this gene correlated with an increase in protein levels—was not reported. The harder, but still very feasible experiment—looking for an increase in this transport activity in isolated vacuoles—wasn’t reported either.

 

Two possible explanations: either there’s something wrong with the work, or these scientists did the experiments and will publish them in a separate paper. These experiments are important because they would prove that the RNA increases aren’t just a red herring and would suggest comparatively quick, cheap, and simple experiments to do on all the other crops that seem to be infected by this fungus. We can eliminate lack of funding as an explanation because the Saudi institution is rather flush with cash.

 

The principal investigator, who also has an affiliation with an Austrian university, published a similar paper recently using the model plant Arabidopsis, and the corresponding genes were not upregulated. Tellingly, the experiments I am proposing were not performed for this paper either.

 

More problematically, if you look at the reported data for the gene expression, it’s just too pretty. The error bars are tiny. I’ve done RNA analysis from plants grown in growth chambers with exquisite control over physiologically relevant conditions (and I was good at it—a team from Harvard sent representatives to Berkeley when I was a post-doc to figure out how I was getting such good results), and my data was never this pretty. Moreover, this group is growing the plants in greenhouses, not in growth chambers, and they are averaging the data from two different growing seasons, three samples from each season.

 

I’d like to believe these results. So would others—I was alerted to this paper by a science news article in Science Magazine, and generally that journalism is quite good. Aside from the New York Times science section, this venue may be the most prominent in the world for this type of journalism. The approach is quite promising, as this fungus can be grown axenically (in pure culture, so it can be mass-produced, rather than growing only on the roots of growing plants). If this pans out, it is the cheap solution to salt stress-caused famine in Africa and elsewhere.

 

But I have a hard time trusting the data. Did they snooker the journalist into believing their hype? Does the principal investigator not understand the details of what his people are doing (a very possible scenario)? If not, why aren’t they doing the necessary control experiments? Experiments on microbial influence on plant growth are notoriously messy and misleading because the experiments are hard to do well and influenced by a huge number of variables. Could they just be selecting whatever data looks pretty and ignoring everything else? And the journal in which they chose to publish—Scientia Horticulturae—is not one of the top journals in the field, so the quality of peer review is suspect.

 

I’m skeptical. Those with a science background can read the original paper for themselves. The lower left panel of Figure 5 shows the data I singled out for criticism. Here’s the link.

 

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