All posts by Alun Salt

About Alun Salt

When he's not the web developer for AoB Blog, Alun Salt researches something that could be mistaken for the archaeology of science. His current research is about whether there's such a thing as scientific heritage and if there is how would you recognise it?

Inflorescences take centre stage

Inflorescences issue cover Annals of Botany has a new special issue in Free Access: Inflorescences. It’s a useful reminder to me of another area of Botany I need to read more about.

For a start, I think I’ve said elsewhere that inflorescences are the structures where there are multiple flowers on a plant and not just a single flower. In a clumsy way this might be true but it also misses the point of an inflorescence. It’s not simply that there are multiple flowers, but also that those flowers work with each other as unit. They’re not just a collection of individuals.

If you approach inflorescences from this point of view, their structure becomes a bit of a puzzle. Why the diversity? But also, can you classify them sensibly and, if you can, what is the basis of that? Do different structures correspond with different functions?

Lawrence Harder and Przemyslaw Prusinkiewicz describe the interplay between inflorescence development and function as the crucible of architectural diversity. It highlights the importance of linking structures and function. In terms of tracing plant relationships, structure is useful but it’s also worth looking at what the structure does. A similar structure could have a very different result if the phenology, the timing of the flowering, changes.

Time is key factor that is highlighted by Harder and Prusinkiewicz. Looking at a display, it’s easy to think of it as an organisation in space, but they also make a point that inflorescences are dynamic. They change with time, and how they change with time has consequences for their function.

As far as plant reproduction goes, it’s easy to focus on the success of flowers, but Harder and Prusinkiewicz argue that what you have is part of a modular system, and that to understand it you have to look at the system as a whole, instead of modules in isolation. Most angiosperms use inflorescences so it’s clearly a powerful tool for a plant. Looking at them as a unit and not just parts can put plant reproduction into a new context.

Harder L.D. & Prusinkiewicz P. (2012). The interplay between inflorescence development and function as the crucible of architectural diversity, Annals of Botany, 112 (8) 1477-1493. DOI: http://dx.doi.org/10.1093/aob/mcs252

The Guardian tackles the ethics of rewilding

The Guardian posted an interesting article yesterday from Tori Herridge: Mammoths are a huge part of my life. But cloning them is wrong.

Mammoth

Mammoth of BC by Tyler Ingram / Flickr.

I’ll concede that a mammoth is not a plant, but part of what I found interesting is that Herridge points out that mammoths didn’t exist in isolation. She tackles the idea that mammoths could somehow be part of a plan to restore the arctic steppes, but she makes an important point:

There’s a reason the terms “de-extinction” and “rewilding” are so powerful and that’s because they imply a return to a time, a state of grace, a place that was somehow unspoiled. Cloning a mammoth offers us the hope of undoing the excesses of humanity, bringing back the creatures whose extinction we helped bring about.

I think the idea of turning back the clock, to a time when things are better, is a powerful image. However it isn’t practical. Herridge points out that the mammoth was part of a wider ecosystem of arctic steppe, and it’s not certain that the plants will naturally appear if you dump a load of mammoths in Siberia.

It’s not even purely about the plants. Looking this up I saw there was a lot about remediation in the Root Biology special issue of Annals of Botany (now free access). In particular, Interactions between exotic invasive plants and soil microbes in the rhizosphere suggest that ‘everything is not everywhere’ say Rout and Callaway. They’re talking about microbes in the context of invasive species, but I wonder what ten thousand years of change has done to the soil of the arctic.

We don’t have the plants, we may not have the right soils. We are going through a big extinction event. I’d love to see a mammoth, but sadly when you look at the social problems a mammoth would have, as well as the many conservation efforts competing for limited funding, I think Tori Herridge is right, and that she does a good job of explaining all the problems.

Microgravity and chromosome damage

The Karyological Observations of Krikorian and O’Connor look at plant material from flights STS-2 and STS-3 of the Space Shuttle.

STS-2, among other things, carried a payload of Helianthus annuus, sunflowers. STS-2 was cut short from five days to two when a fuel cell for producing electricity and processing water failed. Despite this the plants had some time to grow, in a couple of cases with roots protruding from the soil. Krikorian and O’Connor say: “The soil environment of the roots in the HEFLEX-type modules was not particularly well suited to recovery of roots tips for karyological examination.” In plain English it sounds like it was extremely difficult, and they go on in the paper to explain some of the problems they had.

The key result was that when they looked at the cells, they found only around 2% were in division. The same plant in a lab would be expected to be ten times more active. They also found some plants had aneuploidy. Usually chromosomes come in pairs, (though polyploidy is common in plants too). In this case one plant was missing a partner for chromosome 6. The same was true in another plant from the sample. Given these results, similar tests followed on the STS-3 material.

Again with the oats, it was found that only a 2% of cells were in division, again about ten times less than anticipated from the lab. There was also chromosome damage. The mung beans too were found to have low counts for division, though less obvious signs of damage to the chromosomes.

It seems something was affecting the plants, but in their conclusions Krikorian and O’Connor were wary of saying exactly what. The obvious suspect is microgravity, but they also left open the possibility that it was the effect of launch and/or re-entry that was the problem. It’s this referring back to the control that marks out the value of the research on STS-3. It wasn’t simply that material was put into orbit, it was also that the same equipment was run on the ground to act as a control. If gravity is the variable you’re changing then it’s essential to get as much of the rest of the control experiment to run as closely to the orbital experiment as possible.

Like some of the other papers in this supplement, Karyological Observations has been cited this year in a paper Seed-to-Seed-to-Seed Growth and Development of Arabidopsis in Microgravity published October 2014 in Astrobiology. Link et al. also cite Kuang et al from 1996, Musgrave et al from 1998 and Kuang et al from 2000. In some ways it might be surprising that work from thirty years ago is still getting cited, but that’s how science works.

Currently NASA does plant science in orbit on the International Space Station, but this latest platform was built with the shuttle and the aging Russian Soyuz craft. In a similar way current plant research is built on the prior work of earlier scientists. Fortunately you don’t have to wait thirty years to see most research in Annals of Botany. If your library doesn’t have access to the journal, papers become free access a year after paper publication.

Space Shuttle landing

STS-3 lands at White Sands. Photo: NASA.

You can read more posts on papers from our spaceflight supplement by clicking the STS-3 tag.

Today’s Papers

Krikorian A.D. & O’Connor S.A. Karyological Observations, Annals of Botany, 54 (supp3) 49-63. DOI:

KUANG A. (1996). Cytochemical Localization of Reserves during Seed Development inArabidopsis thalianaunder Spaceflight Conditions, Annals of Botany, 78 (3) 343-351. DOI: http://dx.doi.org/10.1006/anbo.1996.0129

Kuang A. (2000). Influence of Microgravity on Ultrastructure and Storage Reserves in Seeds of Brassica rapa L., Annals of Botany, 85 (6) 851-859. DOI: http://dx.doi.org/10.1006/anbo.2000.1153

Link B.M. & Bratislav Stankovic (2014). Seed-to-Seed-to-Seed Growth and Development of Arabidopsis in Microgravity , Astrobiology, 14 (10) 866-875. DOI: http://dx.doi.org/10.1089/ast.2014.1184

MUSGRAVE M. (1998). Changes inArabidopsisLeaf Ultrastructure, Chlorophyll and Carbohydrate Content During Spaceflight Depend on Ventilation, Annals of Botany, 81 (4) 503-512. DOI: http://dx.doi.org/10.1006/anbo.1998.0585

Use it or lose it, for a plant’s sense of gravity?

Gravitropism is the ability of a plant to turn in response to gravity. Roots have gravitropism, bending to turn down and stems negative gravitropism to turn up. But what happens if you remove a plant’s ability to sense where down is?

In roots, plants feel where down is in the root cap. If you remove the root cap carefully, and then tip the plant on its side, the root will continue to grow without changing direction until the root cap regenerates. Once the root cap can signal to the root, cells on one side of the root elongate to bend the root downwards.

The flight of STS-3 posed a challenge to the plants on board. Once in orbit they would be in perpetual freefall and there’d be no sense of ‘up’. What effect would this have on the root cap? Slocum, Gaynor and Galston compared the responses of the oat and mung bean seedlings on board in their paper Cytological and Ultrastructural Studies on Root Tissues. Seedlings for both plants germinated either a few hours before launch or in orbit.

The oats were fine. Both the flight and ground-based oat seedlings had normal root structure. The same was almost true for the mung beans too. Most of the roots were normal, except for the root-cap in the flight sample. The root cap cells on the mung beans in space had had a very bad time. Most of the cells were degenerated. If you compare the control sample below (left) with the flight root (right) you can see one of them is not well.

Two roots, the one on the right looking terrible.

Light micrographs of A, ground control and B, flight-grown mung bean roots, seen in near
median longitudinal section x 75.

It seems that the ability of plants to adapt to microgravity varies on the plant, so it’s not enough to extrapolate from one to all.

This is another paper that continues to get cited today. Most recently Simple sequence repeat markers reveal multiple loci governing grain-size variations in a japonica rice (Oryza sativa L.) mutant induced by cosmic radiation during space flight by Wang et al in Euphytica 2014. There’s also research on peas citing it like Ultrastructure and metabolic activity of pea mitochondria under clinorotation in Cytology and Genetics 2012.

If gravity is essential, then it might become something we have to fake in space. The usual idea is to gently rotate a space station to give a sense of centripetal force. Spin faster and it is possible to subject plants to hypergravity, as noted by Nigel Chaffey earlier this year. Perennial favourite Arabidopisis is the subject of a 300g (yes, three hundred times the force of gravity) in this paper from AnnBot. Subjecting humans to this level of gravity would be a Very Bad Idea.

You can read more posts on papers from our spaceflight supplement by clicking the STS-3 tag.

Today’s Papers

Slocum R.D., Gaynor J.J. & Galston A.W. (1984). Cytological and Ultrastructural Studies on Root Tissues, Annals of Botany, 54 (supp3) 65-76.

Brykov V.O. & I. P. Generozova (2012). Ultrastructure and metabolic activity of pea mitochondria under clinorotation, Cytology and Genetics, 46 (3) 144-149. DOI: http://dx.doi.org/10.3103/s0095452712030036

NAKABAYASHI I. (2006). Hypergravity Stimulus Enhances Primary Xylem Development and Decreases Mechanical Properties of Secondary Cell Walls in Inflorescence Stems of Arabidopsis thaliana, Annals of Botany, 97 (6) 1083-1090. DOI: http://dx.doi.org/10.1093/aob/mcl055

Wang J., Tianqing Zheng, Xiuqin Zhao, Jauhar Ali, Jianlong Xu & Zhikang Li (2013). Simple sequence repeat markers reveal multiple loci governing grain-size variations in a japonica rice (Oryza sativa L.) mutant induced by cosmic radiation during space flight, Euphytica, 196 (2) 225-236. DOI: http://dx.doi.org/10.1007/s10681-013-1026-8

Is there a downside for plants when they can’t sense ‘up’?

Looking at a tree, it can be hard to visualise the sheer volume of water being drawn up from the roots to the canopy. That volume of was is massive, and puts cells under a lot of pressure, so lignin, the substance plants use to strengthen cell walls, is an important product. But what happens to lignin if you take gravity away? Growth and Lignification in Seedlings Exposed to Eight Days of Microgravity by Cowles et al. is a study that aims to find out.

The experiment on STS-3 was growing pine seedlings with mung beans and oat seeds. There were a couple of targets. One was to examine how gravity affected the production of lignin. The other was to test the PGU, the plant growth unit, that would be used in following missions.

Plant Growth Unit

From Cowles et al.

To see the effect of gravity a PGU with similar plants was kept on Earth, so the development of the plants could be compared.

Germination of the orbiting plants was much like the 1g plants. However, Cowles et al. point out that the seeds have to be prepared before launch, which gave them twelve hours on Earth to germinate. They found that the flying plants grew less, and in the case of the seeds, roots were growing ‘up’ as well as ‘down’. Some of the plants that grew in orbit also contained less lignin.

There have been plenty of papers that went on to cite this research, most recently Expression of stress-related genes in zebrawood (Astronium fraxinifolium, Anacardiaceae) seedlings following germination in microgravity by Inglis et al. in Genetics and Molecular Biology from this year.

Recently in Annals of Botany there’s been Xylem Development and Cell Wall Changes of Soybean Seedlings Grown in Space and in the opposite directon Hypergravity Stimulus Enhances Primary Xylem Development and Decreases Mechanical Properties of Secondary Cell Walls in Inflorescence Stems of Arabidopsis thaliana by Nakabayashi et al.

This is interesting that it still gets cited because the results weren’t all significant. While the mung beans had less lignin, the oat and pine seedlings didn’t have significantly less and the experiment was relatively small. However, this flight wasn’t just about the results, it also worked to establish a method. By laying out the experimental technique used to analyse the plant Cowles et al laid down a baseline for other researchers to compare and improve their techniques.

The basic question they studied remains important. Understanding the processes that produce lignin could help with technology on Earth. For example, it would be helpful in producing biofuel if there were less lignin in it to start with. Launching plants and growing them in space would be a spectacularly inefficient way to do that. However for small samples, it can be a useful way to isolate one variable and help figure out the mechanics of lignin production.

You can read more posts on papers from our spaceflight supplement by clicking the STS-3 tag.

Today’s Papers

Cowles J.R., Scheld H.W., Lemay R. & Peterson C. (1984). Growth and Lignification in Seedlings Exposed to Eight Days of Microgravity , Annals of Botany, 54 (supp3) 33-48. DOI:

Chapple C. & Rick Meilan (2007). Loosening lignin’s grip on biofuel production, Nature Biotechnology, 25 (7) 746-748. DOI: http://dx.doi.org/10.1038/nbt0707-746

de Micco V., J.-P. Joseleau & K. Ruel (2008). Xylem Development and Cell Wall Changes of Soybean Seedlings Grown in Space, Annals of Botany, 101 (5) 661-669. DOI: http://dx.doi.org/10.1093/aob/mcn001

Inglis P.W., Ciampi A.Y., Salomão A.N., Costa T.D.S.A. & Azevedo V.C.R. (2013). Expression of stress-related genes in zebrawood (Astronium fraxinifolium, Anacardiaceae) seedlings following germination in microgravity., Genetics and molecular biology, PMID: http://www.ncbi.nlm.nih.gov/pubmed/24688295

NAKABAYASHI I. (2006). Hypergravity Stimulus Enhances Primary Xylem Development and Decreases Mechanical Properties of Secondary Cell Walls in Inflorescence Stems of Arabidopsis thaliana, Annals of Botany, 97 (6) 1083-1090. DOI: http://dx.doi.org/10.1093/aob/mcl055

Calibrating data in a weightless environment

A Test to Verify the Biocompatibility of a Method for Plant Culture in a Microgravity Environment by Brown and Chapman is an example of the basic science people needed to do with the shuttle.

If you’re going to run plant experiments, then the plants will need to perform basic function in order to live. One example is taking up water and this was a problem. Soviet experiments and theoretical work suggested the way plants reacted to soil moisture in orbit was very different to how they behaved on Earth. This would have a major effect on any experiment results because unusual behaviour could be due to whatever it was you were experimenting for, or it could just be the way it goes in microgravity.

STS-3 carried what NASA called ‘bio-engineering tests’ to see if botanical experiments with their systems were practical. The test has HEFLEX, the Helianthus Flight Experiment. The question HEFLEX was to look at was how sunflower nutation happened in orbit. This is the spinning effect of the stem in growing seedlings. You can see Arabidopsis doing this in the time-lapse video below.

There was a problem with STS-2 which meant that the experiments for that mission were cut short. STS-3 had the opposite problem, the mission was longer than HEFLEX would be, but it still allowed researchers to compare the effects of soil moisture.

Graph of results.

Comparison of shoot lengths of 8-9-day-old plants from STS-3 Mission (solid dot) and those from 1g control test (hollow dot). The same experiment hardware was used for both tests.

Tests showed plant responses seemed to be comparable, and additional post-landing inspection also show the effects of launch and re-entry were no big problem.

This research went on to be cited in a few papers, and you can pick up Circumnutations of Sunflower Hypocotyls in Satellite Orbit for free from Plant Physiology, which had Brown and Chapman among the authors. But the chain doesn’t stop there.

Nutation remains a puzzle in plant sciences. Circumnutation as an autonomous root movement in plants in AmJBot dates from 2012 (again free access). AoB PLANTS, the open access plant journal has a paper Petiole hyponasty: an ethylene-driven, adaptive response to changes in the environment by Polko et al. Both of these papers refer back to Brown et al’s PlanyPhys paper, despite being terrestrial papers. This first paper, specialising in how a lab on the space shuttle worked, is part of a chain of research. It shows launching seedlings away from the planet can bring us closer to understanding life upon it.

You can read more posts on papers from our spaceflight supplement by clicking the STS-3 tag.

Today’s Papers

Brown A.H. & Chapman D.K. (1984). A Test to Verify the Biocompatibility of a Method for Plant Culture in a Microgravity Environment, Annals of Botany, 54 (supp3) 19-31.

Brown A.H., Chapman D.K., Lewis R.F. & Venditti A.L. (1990). Circumnutations of Sunflower Hypocotyls in Satellite Orbit, Plant Physiology, 94 (1) 233-238. DOI: 10.​1104/​pp.​94.​1.​233

Migliaccio F. & A. Fortunati (2012). Circumnutation as an autonomous root movement in plants, American Journal of Botany, 100 (1) 4-13. DOI: 10.3732/ajb.1200314

Polko J.K., A. J. M. Peeters & R. Pierik (2011). Petiole hyponasty: an ethylene-driven, adaptive response to changes in the environment, AoB Plants, 2011 plr031-plr031. DOI: 10.1093/aobpla/plr031

30 years of Astrobotany in Annals of Botany

“In the newspapers I used to read about shuttles going up and down all the time, but it bothered me a little bit that I never saw in any scientific journal any results of anything that had ever come out of the experiments on the shuttle that were supposed to be so important.”

Richard Feynman – What Do You Care What Other People Think?

STS-3 Shuttle mission launching

STS-3 departs on its mission. Photo: NASA.

On 22 March 1982, at 11:00 local time, the STS-3 mission, manned by Lousma and Fullerton launched in the space shuttle Columbia. Over the next eight days the shuttle was a platform for a few plant science experiments. A year and a half later these experiments were the basis of most of an Annals of Botany supplement Experiments on Plants Grown in Space.

It’s not that surprising Richard Feynman hadn’t seen these results. It’s easy to forget what a difference electronic communications have made. This issue of Annals of Botany would not have been issued as a PDF. Anyone wanting to see the results would have to physically locate an issue at a local library, not just click – which made it difficult for the public to access. NASA would also be issuing paper releases, and the news was the next shuttle flight not the one several missions back. So some science of immense public interest was kept to a few specialists.

The supplement has been digitised, and with current papers Annals of Botany makes its papers free access a year after print publication. In this case the delay is around thirty years. Quite a few things have changed since then, so the first paper in the supplement is a useful primer. Status and Prospects by Halstead and Dutcher gives a sense of the state of play for botany in the early 1980s.

It’s easy to be accustomed to space flight, and most ISS launches are not inherently newsworthy. The space shuttle was the vehicle that started the West’s perception of space travel as a mundane event. Halstead and Dutcher looked forward to the prospect of regular and affordable spaceflight.

Hindsight comes from Paul et al. and their paper Fundamental Plant Biology Enabled by the Space Shuttle in AmJBot. They comment on how plant science changed on shuttle flights, eventually taking advantage of the long-term missions offered by the International Space Station. One of the features of their paper is they point out there’s more to botany in space than the effect of gravity. By eliminating gravity you can explore other tropisms. They give a couple of examples, you can test for phototropism obviously, by manipulating light. But they also point out that subtle effects like ionic gradients become visible, once you eliminate the effect of gravitropism.

Aside from plans to colonise Mars, basic science means that exploration of microgravity and extreme environments will continue to be growth areas in botany. Over this week, we’ll be looking at the papers in our Space Shuttle issue and the science that they inspired after publication. Posts will be going live daily.

Today’s Papers

Halstead T.W. & Dutcher F.R. (1984). Status and Prospects, Annals of Botany, 54 (supp3) 3-18.

Paul A.L., Wheeler R.M., Levine L.G. & Ferl R.J. (2013). Fundamental Plant Biology Enabled by The Space Shuttle, American Journal of Botany, 100 (1) 226-234. DOI: 10.3732/ajb.1200338

The Martian by Andy Weir

TheMartianA while back I asked for recommendations for science fiction reading involving botany. On our Facebook page Claire Soulsby suggested The Martian by Andy Weir. I’ve had a stroke of luck* and have been stuck in bed feeling sorry for myself. This has given me plenty of time to read it.

The story begins after a freak dust storm on Mars causes the Ares 3 team to abandon their mission, leaving behind their dead crew member, Mark Watney. Watney awakes to find himself alone with the habitat and no hope of rescue for years, and enough food for months. The challenge is to produce food, water and oxygen to keep him alive and then to establish contact with NASA to coördinate a rescue.

The key to survival is first botany. It’s Watney’s ability to grow food on Mars that keeps him alive long enough to get a fighting chance. As everybody knows Botanists are pretty much the closest thing we have to superhero geniuses, so Watney is able to engineer all the fixes he needs to make in the hab to make farming, and everything else he needs, happen.

The book reads like hard-SF for the most part. The science is plausible and by relying on near-future science it means that Weir puts his character in a believable danger. The start of the writing process was planning a hypothetical Mars mission, including contingency plans for what might go wrong. Then he realised the contingency plans would make the basis of a story.

Most of the story is told through log entries. This works to explain the problems and the solutions. It also gives a plausible reason for why the character comes across the way he does. I vaguely remember someone saying there are no characters in Shakespeare plays, just plot devices. In a similar way, I’m not sure there are many characters in this book. In a couple of other reviews, people think the characterisation is weak. Watney does things, but he’s not changed much by them. When the next problem comes along in the book, he simply settles down to solve it so while there are many problems, I don’t know if there are many setbacks or catastrophes. Watney’s job at times seems to be to set up the next problem.

Fortunately, the problems are interesting enough to pull the story along. It’s also a change to read something where not every scientific problem can be solved by basic physics.

There’s a video of a talk he gave at, including a reading of the first chapter.

*Not good luck. I tend to avoid that.

Other reviews