Plants in the City: Plants respond to vibrators

Recently there's been a lot of noise in the popular press about plants responding to the sounds of leaf-chewing insects.

Even the New York Times published an article entitled "Noisy Predators Put Plants on Alert, Study Finds".

Such a headline calls into the question the validity of a previous blog here, What a Plant Hears and Chapter 4 of WHAT A PLANT KNOWS where I concluded "in lieu of any hard data to the contrary, we must conclude for now that plants are deaf".

So what's going on here? Is there finally hard data indicating that plants hear?

To really answer this question, one has to read the primary literature, and that is the research paper, "Plants respond to leaf vibrations caused by insect herbivore chewing, that was published recently in Oecologia.

Let's briefly read how the experiment was carried out: 

The green vibrator attached under the leaf

Chewing vibrations were recorded with laser Doppler vibrometry. To experimentally reproduce the caterpillar feeding vibrations, we used piezoelectric actuators supported under a leaf and attached to the leaf using accelerometer mounting wax." (see picture on right)

In other words, the scientists recorded the vibrations caused by chewing, and then reproduced these vibration with a vibrator attached to the leaf. These physical vibration elicited a chemical response in the plant similar to the chemical response to insect chewing.  This is a very interesting finding. But what it shows is the plants respond to physical vibrations induced by being attached to a microvibrator.

So if the popular press insists on bombastic news items, perhaps it would be better to say: "Scientists Find That Plants are Similar to Samantha - They Respond to Vibrators"

No sibling rivalry for Petunias

NOTE: THIS WAS ORIGINALLY PUBLISHED ON APRIL 1, 2013!

Petunias grown in a nursery together with their sibling petunias thrived much better post-separation than did a single petunia grown on its own. This conclusion jives with numerous studies which show that puppies kept with their litter-mates for at least 8 weeks develop better than puppies separated from their siblings soon after birth, and also fits with accumulating evidence showing the importance to human development of keeping a baby in physical contact with people, rather than isolating a baby in a crib.

Seeds of Petunia hybrida were germinated in two different environments. In the green house termed “Petunia Patch”, the seeds were sown 5 cm from each other.

Petunias in the "Petunia Patch"

In the second green house termed “Onion Patch”, individual petunias were planted at least 50 m from each other. 5, 10, 20 and 45 days post-germination, individual plants from the Petunia Patch were transplanted to the Onion Patch. Control plants remained in each plot from germination until the end of the experiment. Each plot received the same watering and fertilizer regimen. Growth parameters (germination rate, height, leaf number, flowering time, flower diameter, seed set) were gathered daily over a two-month period.

The results were astounding. The longer the petunia stayed in the Petunia Patch, the more the individual plants thrived (see graph on left). The effect was especially significant for the first 10 days. Most of the petunias germinated in the Onion Patch, or transplanted early in life, failed to thrive. When asked to comment on the flowers that didn’t bloom, Drs. John N.Kamano, William E. Faber and Maurice Merl  said, “They were just lonely little petunias in an onion patch”.

These results have implications for home gardeners who are asked to purchase neighboring petunias in their local nursery so as to lessen the separation stress of plants upon leaving the nursery.

Guest blog: Jonathan Gressel - Exposing anti-GMO propaganda veiled as science

Danny: The following is a public letter written by my colleague Prof. Jonathan Gressel at the Weizmann Institute, in response to talk from an ecologist decrying the use of transgenics in agriculture. I edited the letter, shortening it for use here. I should point out that Dr. X. is a zoologist at a well known university. As the gossip is less important than the content, I decided to leave her anonymous as "X" here.   I should also point out that no response was received from "X" to this letter.

Dear Dr X,

I was rather disturbed by some of the disinformatory remarks that you made yesterday at the symposium [Genetic Engineering in Agriculture - Dream or Necessity?], especially in relationship to transgene flow. You categorically stated that there have been no studies on this (or any) area of ecology/population genetics of transgenics in Israel. My students, colleagues, and I have published over 40 papers on the subject since 1999 demonstrating that you have hardly done your homework  - or in the parlance of journal editors - this is an ethical defect known as "citation amnesia".

You also made dire warnings about gene flow (via pollen or seed) to the wild, and claimed in a slide that there was evidence for this. A careful reading of the data behind the slide would have led you to a different conclusion. Competent ecologists distinguish between agro-ecosystems, ruderal (human-disturbed) ecosystems, and wild ecosystems. There is no published evidence that there has been gene flow to any wild ecosystem, and as you should know, there are exceedingly few instances of crops growing anywhere near wild interbreeding relatives. The real issue is gene flow to weeds in agroecosystems, which is controllable, and regulators should assure that there are transgenic failsafe mechanisms installed to prevent such problems.

You implied that organic agriculture is incompatible with transgenics - I strongly suggest that you read the book co-authored by a professor of organic agriculture, and head of the program at UC-Davis, who rather considers otherwise [Tomorrow’s Table: organic Farming, Genetics and the Future of Food. Pamela C. Ronald and Raoul W. Adamchak].

You also implied that there was a consensus among ecologists that transgenics were highly dangerous (I believe you put it as "all the ecologists I talked with"). There are highly competent ecologists (including the only ecologist among the founders of Greenpeace) who argue strongly for transgenics as being an exceedingly invaluable tool for protecting the environment [Confessions of a Greenpeace Dropout: The Making of a Sensible Environmentalist].

Indeed many meta-analyses performed by ecologists have shown the distinct environmental benefits of transgenics over current conventional agricultural practices (and even moreso over organic agriculture).

Thus, it is hard to conclude that you presented an impartial review of the ecological implications of transgenics that would have been expected of an academic ecologist at an important university.

This is very unfortunate.

Sincerely,

Prof. Jonathan Gressel
Plant Sciences
Weizmann Institute of Science
Rehovot, Israel 76100

The Harbinger of Summer's End

Sea squill (Drimia maritima)

My favorite plant is easily the sea squill, which in Hebrew is called hatzav (with a hard "h" like your clearing your throat). The sea squill is wondrous because it grows and flowers like a Swiss clock in August in Israel, heralding the end of the summer and the approaching fall. Out of nowhere, the hatzav sprouts and rapidly grows a two-to-three-foot stalk with hundreds of little white flowers. The flowers open over several weeks progressively from the base to the tip, resulting in a very impressive floral display.

How does the hatsav know when August has arrived? It knows this because of the lengthening nights. The sea squill is what's known in scientific terms as a "short day" plant, which is a misnomer, as they are actually "long night" plants. "Short day" plants like sea squill and tobacco flower when the length of the night surpasses a threshold specific for that plant. This is as opposed to "long day" plants like carnations and oats, which flower when the night gets shorter than a set threshold.

Plants "know how long the night is thanks to a group of photoreceptors called phytochromes. In a simple model, phytochromes are activated by red light, and are turned on in the morning; they are deactivated by far-red light, the long waves at the end of sunset, so are turned off as night begins. Plants measure the time the phytochromes are turned off, and use this information to determine season.

Sea squill leaves in winter

Getting back to the seq squill, its floral stalk has no leaves, so where does this plant get energy from photosynthesis? The sea squill has two different life cycles. In the summer and fall, it flowers, but in the winter, when there's pleanty of water for to support photosynthesis and growth it produces large green leaves. Theses leaves produce the sugars that are stored underground in a large bulb. As the dry season starts these leaves wilt and dry up. But the bulb uses these stored sugars as energy to produce the flowering stalk in August.

What's an individual?

We expect then that within our bodies, each cell has the same genetic code, the same sequence of DNA, since all of our cells originated from the same fertilized egg. We understand that children are novel genetic combination of their parents, that twins share the same genetic code, and that individuals differ genetically one from the other. Overtime, these genetic differences provide the basis for evolution.

How strange then is the recent report that different parts of the same tree have different DNA sequences!

Ed Yong, reporting from the Ecological Society of America Annual Meeting , tells of the results from the laboratory of Brett Olds, where they determined the DNA sequence from different parts of the same black cottonwood. They found differences in thousands of genes between the topmost bud, the lowermost branch, and the roots.

As Olds told Yong, “This could change the classic paradigm that evolution only happens in a population rather than at an individual level.” 

The differences in the DNA sequences between the branches could conceivably lead to advantageous characteristics. Perhaps different branches of the same tree compete with one another for light, nutrients and pollinators, and this competition leads to Darwinian selection, whereby the most fit branches out-compete their neighboring branches.  The differences in DNA sequence would then be more likely carried on in the next generation by the branches that produced  more or heartier seeds.

Of course the caveat is that this is a blog reporting on a report of a report. i can't wait to see the research article, and for this paradigm to be tested by additional labs using other tree species. If it holds up, we'll have to rewrite some of our textbooks!

Reblog: Why a Tomato Has Stronger Survival Instincts Than a Human

The chemistry of pot

We all know that THC (Δ⁹-Tetrahydrocannabinol) is the main active ingredient of marijuana. However, you may not be aware of the high-tech research going into figuring out how pot plants make THC.

A recent paper published in the Proceedings of the National Academy of Sciences of the United States of America (affectionately known as PNAS) illustrates how some of this research is carried out.

To produce THC, cannabis employs a number of differenet enymes which work in a linear series simplified below:

hexanoyl-CoA + malonylCoA --> OA --> CBGA --> THCA --> THC

Each of the arrows is a different enzyme. A big challenge in understanding how cannabis makes THC (and maybe to be able to make it artificially) is identifying each of the enzymes. As the biochemistry behind this pathway is very complex, this has not been a simple matter.

trichomes on a Cannabis sativa leaf

The lab of Jonathan Page in Saskatchewan figures that the genes encoding these enzymes should be specifically enriched in the THC-rich trichomes, the sticky, furry things on cannabis leaves. They first identified all the genes that are expressed in these trichomes, and then, using their knowledge of enzymology, sought out particular genes that looked like a particular class of enzymes that could potentially take part in the chemistry of the first arrow. They found three candidate genes, and then put each into E.coli to make the proteins. When they added these proteins to hexanoyl-CoA and malonylCoA, the precuursors of OA, they found OA is the mixture. In other words, they identified gene encoding the enzyme for the first arrow. 


When they put this gene in yeast, the yeast started making OA. Just think of the possibilities for beer if they wold add the genes for the arrows...

An enigmatic petunia

I love when performance art and hardcore science meet.

Enigma is a petunia that was genetically engineered by the artist Eduardo Kac. Enigma is a normal petunia except its genome contains one of Kac's genes, specifically the gene called IGK. This gene encodes for part of the imunoglobulin protein which functions in our immune system. Kac engineered engima so that it expresses his IGK gene, but only in the flower's veins. He did this by first cloning the IGK gene behind a promoter from a plant virus which is usually only turned on in plant veins. This is a rather simple but cool project that can be carried out in most plant molecular biology labs.

Eduardo Kac, Natural History of the Enigma, transgenic flower with artist's own DNA expressed in the red veins, 2003/2008. Collection Weisman Art Museum. Photo: Rik Sferra.

In the picture or enigma  the red color signifies where his IGK gene is being expressed. While this is visually pleasing, its also a bit misleading, leading the unwary reader to think this "red" is due to blood. While Kac isolated his IGK gene from his own blood, imunoglobulins are colorless. The reason enigma's veins is not due to Kac's gene, but rather due to a plant gene which controls the expression of genes necessary for making anthocyanins, the plant's red pigments.


Kac calls enigma a "plantimal, a new life form [he] created that ... is a hybrid of myself and Petunia".


This is also could be misleading. Enigma is not a "hybrid", which implies a true mixing of parts [see comments below]. Enigma is at best 0.003% Kac, 99.997% petunia. Considering that plants contain many genes normally thought of as human, such as BrcA and Cftr (encoding the genes for breast cancer and cystic fibrosis), perhaps all plants are actually "plantimals". Or maybe considering that humans normally contain many genes originally thought of as plant, such as Det1 and Cop9 (genes necessary for photomorphogenesis, plant development in the light), maybe we ought to be considered "aniplants"?

In any event, I think Kac is to be applauded for pushing the boundaries of art and science, and for carrying out research project which well exemplifies how genetic engineering works! If you're interested, you can by your own enigma seeds on Kac's website.

Who's afraid of "superweeds"?

A recent post in The Atlantic decries that appearance of RoundUp-resistant weeds popping up in fields of GM crops, and uses this a call for the abandonment of GM technology.

Amaranthus hybridus

The only problem in his thinking is that "superweeds" started popping up way before the advent of GM technology and the deployment of RoundUp-resistant crops. For example, atrazine was one of the most widely used herbicides in eradicating plant growth on road shoulders, and is still widely used in agriculture. Weeds resistant to atrazine started to be noticed in the 1970s. My Ph.D. adviser Joseph Hirschberg isolated the first gene for herbicide resistance in 1983 from an atrazine-resistant Amarnthus hybridus that had been isolated from the side of a highway. This was way before any GM crops had been developed.

So as long as herbicides will be used in modern agriculture, there will always be the problem of spontaneous resistance, just as as long as we use antibiotics, antibiotic-resistant bacteria will also crop up.  GM technology is not the cause of the resistance. The challenge is in designing the best use of herbicides to ensure the best agricultural yields for the farmers, while protecting our environment as best as possible.But that's the subject of another blog.

The genes of Arabidopsis

Arabidopsis thaliana plants being grown in the Manna
Center for Plant Biosciences at Tel Aviv University

Arabidopsis isn't the most impressive plant in the world to look at. Chances are that you may even have walked on this little mustard plant and not given it a second thought. But arabidopsis has a few qualities that have made it the most influential plant in the world.

Arabidopsis has a very short life cycle, less than two months, is small, and each plant yields hundreds of not thousands of seeds. These three characteristics, coupled with the evolutionary quirk that arabidopsis has relatively a small amount of DNA, has made it the most studied plant in the world.

While Arabidopsis has almost the same number of genes (~25,000, but this is open to debate) as found in most plants and animals, it contains very little of a type of DNA that’s called "non-coding DNA" which made determining its sequence relatively easy to do. To put things in perspective, while Arabidopsis contains about 25,000 genes in 120 million nucleotides (the building blocks of DNA), wheat has the same number of genes in 16 billion nucleotides, and human beings have about 22,000 genes, less than the petite Arabidopsis, and in 2.9 billion nucleotides.  These numbers should be taken with a grain of salt as the precise definition of “gene” is evolving and with it the numbers. But the general trends and scales are correct.  Almost all of the genes found in Arabidopsis are also present in plants that are important agriculturally and economically, such as cotton and potato and poplar trees.