Monday, July 30, 2012

Berry-Go-Round, July 2012

This month's Berry Go Round features an eclectic collection of 11 posts from 10 contributors. 

1. Kathryn Turner at Alien Plantation gives a great overview of the recently published banana genome. I agree with her that the Venn diagram in this article is one of the best, or at least most original, ever.

2. Hollis from In the Company of Plants and Rocks has two interesting posts this past month. What's an old oak for? discusses the variation in oak morphology, and wistfully remembers swings hung from old oaks.

3. Hollis's second post describes her recent jaunt to the Black Hills of South Dakota, in an attempt to make a comprehensive inventory of the mountain meadows originally described by none other than that known humanitarian, Lt. Col. George A. Custer back in 1874. Sadly only about 10% of the meadows surveyed appeared to be undisturbed by invasive species.

4. The Berry-Go-Round has a new contributor this month, Kathryn Kostka de Tanzi.  Kathryn was born in Memphis, and has lived in Costa Rica for over 35 years. She contributes this striking photograph:
It was a rainy day in the mountains near the Turrialba Volcano in Costa Rica.  I was up early to observe the foraging birds, to watch tip-toeing clouds passing through, and to savor the crisp fresh air.  Along my walk I came across a beautiful Callistemon laden with bushy crimson  flowers and heavy with raindrops.  A variety of Hummingbirds, Blue-Gray Tanagers, and and migratory Orioles decorated its branches and it was a splendid sight.

5. Molly Day from All the Dirt on Gardening teaches us a thing or two about using plants to attract butterflies.

6. Yuval Sapir this month explains how plants move. No, plants haven't learned to pull up their roots and migrate. But their seeds are very mobile when they hitch onto Yuval's sock!

7. Phil Gates from Beyond the Human Eye uses a microscope to show the rough world of aphids navigating trichomes, in his post Aphids in a Savage Landscape.

8. Mary Williams suggests we all read the paper "Interspecific RNA Interference of SHOOT MERISTEMLESS-Like Disrupts Cuscuta pentagona Plant Parasitism" which was just published in The Plant Cell. in Mary's words: "This gets my vote for 'best paper to give undergraduates'."

9. Richard Stout, a.k.a plantguy, writes in How Plants Work about plant "social networks" and companion planting.

10. The Phytoreactor examines the transparent windows in the leaves of the seaside ox-eye (Borrichia frutescens).

11. And lastly, I wrote this month about the marriage of art and GMO technology in An enigmatic petunia.

Laurent from Seeds Aside will host next month's carnival!

Wednesday, July 25, 2012

The war in Syria and Global Food Security

Wild barley cultivars grown in ICARDA
Of all the implications of the civil war in Syria, probably very few of us have thought about the effect of the uprising on world agriculture and food security.

While this may strike you as strange, Syria houses one of the world's foremost research institutes - ICARDA, International Center for Agriculture in Dry Areas. Among other activities, ICARDA holds seeds from over 100,000 accessions of wild and cultivated crops in its gene bank, including 55,000 cereals. As part of Fertile Crescent, Syria contains  As reported in The Independent :

"As the birthplace of agriculture – the Euphrates is only 70 miles to the east – Aleppo is also the headquarters of the International Centre for Agricultural Research in Dry Areas (Icarda), one of the finest institutions of its kind in the world. It increases food production in Asia and Africa in an area containing a billion people, 50 per cent of whom earn their living from agriculture. Donors include Britain, Canada, the US, Germany, Holland, the World Bank – you name it. And its 500 employees are still operating in Aleppo.

Alas, its principal research station at Tel Hadya, 20 miles from Aleppo, was raided by gunmen who stole vehicles – to use them as "technicals" mounted with machine guns – along with farm machinery and computers. Mercifully, Icarda's gene bank is safe and has been duplicated outside Syria. The Syrian government moved a military checkpoint closer to Icarda's property at Tel Hadya – the Syrian ministry of agriculture was always one of the more progressive offices in Damascus – but what use this will be in the coming days, we shall see."

The uprising in Syria also reflects on a similar research center in Israel - The Institute for Cereal Crop Improvement (ICCI) at Tel Aviv University. The ICCI holds seeds from about 20,000 accessions fo barley, wild wheat and wild wheat relatives. Both Syria and Israel are located within the Fertile Crescent, the center
Resistant and susceptible wheat cultivars
infected with yellow rust
 of origin of a number of wild ancestors of major crops such as wheat, barley, oats, legumes, olive, almond and more. These wild species, still growing in this region, serve as a rich gene pool for crop improvement with tolerance to drought and salinity and with resistance to different diseases. While direct contacts between ICARDA and the ICCI are for political reasons impossible, both institutes are part of the global effort to fight wheat rust disease funded by the Gates Foundation. All efforts must be made to ensure that the collections in both institutes are immune to toe regional conflicts that plague the Middle East.

(Thanks to Agricultural Biodiversity Weblog for leading me to The Independent article)

Sunday, July 22, 2012

Fun with Gat

Catha edulis (gat)
Catha edulis, better known as gat or khat, is native to Yemen and the Horn of Africa.  Locals chew on the leaves, which releases small concentrations of a neuroactive alkaloid called cathinone.  This stimulates the cental nervous system, and according to gat chewers, increase endurance, gives a feeling of strength and health, suppresses hunger (which is an advantage in areas known for chronic famine) and tiredness (which is an adavantage during hard labor and long walks). Because the leaves contain so little cathinone, large qauntitites of leaves have to be cchewed to get any effect. Consequently, gat-chewing is a social experience with groups of men or women sitting around and chewing and conversing together. In Yemen gat is so popular that 40% of the county's water supply is dedicated to gat agriculture!

Hagigat in Tel Aviv
Of course western culture doesn't have time for hours of leaf chewing (or the stomachs to see people spitting out the leaves and juice, though this to me seems no different than chewing tobacco). An Israeli biochemistry student working for some shady characters isolated cathinone from gat, who then marketed it in a concentrated pill called hagigat, which loosely translates to "party gat". While initially legal, hagigat soon became abused in the local party scene, was connected to several hospitalizations due to damage to the cardiac and central nervous systems, and was added to the list of illegal drugs. 

Gat itself though is still legal in Israel and many other countries. Apparently, its difficult to abuse something that you have to chew for hours. 

Wednesday, July 18, 2012

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...

Sunday, July 15, 2012

ReBlog - The Legumes of War: How Peanuts Fed the Confederacy

I found this on  Rather than summarize, I'm just showing the entire blog post. the original link is Good thing for the confederacy that peanut allergies are a modern epidemic!

April 19, 2012

The Legumes of War: How Peanuts Fed the Confederacy

Peanuts. Image Courtesy of Flickr user La.blasco.
When it came to fighting the Civil War, the South may have been rich in military leadership, but the North had superior resources, especially when it came to industrial strength. Still a largely agrarian society, the Southern states had to import most of their manufactured products, and with a poor railway system, keeping troops well-stocked was a battle in and of itself, especially when enemy blockades interrupted supply lines. Combined with inflation and scorched-earth military campaigns—such as General Sherman’s march through South Carolina—food shortages were a problem for both military and civilians. But even in those hard times, people could find relief in peanuts.
Before the Civil War, peanuts were not a widely cultivated crop in the United States—Virginia and North Carolina were the principal producers—and were generally viewed as a foodstuff fit for the lowest social classes and for livestock. When they were consumed, they were usually eaten raw, boiled or roasted, although a few cookbooks suggested ways to make dessert items with them. The goober pea’s status in the Southern diet changed during the war as other foods became scarce. An excellent source of protein, peanuts were seen as a means of fighting malnutrition. (And they still are, with products such as Plumpy’nut being used in famine-plagued parts of the world.) In addition to their prewar modes of consumption, people used peanuts as a substitute for items that were no longer readily available, such as grinding them to a paste and blending them with milk and sugar when coffee was scarce. “This appreciation [for peanuts] was real,” Andrew F. Smith wrote inPeanuts: The Illustrious History of the Goober Pea. “Southerners continued to drink peanut beverages decades after the war ended.” Peanut oil was used to lubricate locomotives when whale oil could not be obtained—and had the advantage of not gumming up the machinery—while housewives saw it as a sound stand-in for lard and shortening as well as lamp fuel.
Peanuts became ingrained in the culture, going so far as to crop up in music. For Virginian soldiers wanting to take a dig at North Carolina’s peanut crop, there was:
The goobers they are small
Over thar!
The goobers they are small
Over thar!
The goobers they are small,
And they digs them in the fall,
And they eats them, shells and all,
Over thar!
The humorous song “Eatin’ Goober Peas” also surfaced during the war wears. (You can hear the song in full as performed by Burl Ives and Johnny Cash.)
Just before the battle the General hears a row,
He says, “The Yanks are coming, I hear the rifles now,”
He turns around in wonder, and what do you think he sees?
The Georgia militia eating goober peas!
There is also an account of a July 1863 episode where the Confederate Army’s Fifth Company of the Washington Artillery of New Orleans was entrenched in Jackson, Mississippi, and burned down a mansion in order to clear their view of the battlefield—although not before saving a piano. As the Union Army drew nearer, one soldier took to the ivories, encouraging his compatriots to join in song, including a round of “You Shan’t Have Any of My Peanuts”:
The man who has plenty of good peanuts,
And giveth his neighbor none,
He shan’t have any of my peanuts when his peanuts are gone.
While the Fifth Company succeeded in keeping the enemy at bay that day, peanuts just weren’t enough to save the Confederacy in the long haul.

Thursday, July 12, 2012

Calling all blogs botanical

Since starting this blog, I've become slowly aware of a small community of bloggers committed to plants in all and any aspect. This communtiy publishes a compendium of the latest plant-replated blogs in its monthly "Berry Go Round".

What's a Berry Go Round? According to its website:

Berry Go Round Badge by Mary at
Berry Go Round covers all thing botanical. That is, featured articles should just be about plants, from cells & chemistry to plant ecology and communities. Pictures can also be submitted whenever a minimum amount of information is given (such as scientific name, family and the like), and recipes may also be featured if the main ingredient is a plant and provided a decent botanical account follows.

I have the honor of hosting next month's Berry Go Round. If  you've recently come across any cool plant-related blogs, or written one yourself, submit it to this months Berry Go Round by clicking here.  The The Berry Go Round will be up an published on August 1. And of course, feel free to pass on this information to further publicize the Berry Go Round!  

I'm looking forward to hearing from you!

Monday, July 9, 2012

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.

Wednesday, July 4, 2012

Carrots weren't always orange!

The orange-colored carrots so ubiquitous today weren't around forever. Actually orange carrots were only first documented in the 17th century by Flemish painters. Before that, European carrots were commonly white, purple, yellow and even red. But by the 18th century, orange carrots had not only taken over culinarily, but have also influenced language. For example, carrots were an incentive for donkeys to move forward, which led to the "carrot or stick" approach to motivation.

Evelyne Bloch-Dano tells the story of the carrot and other under-appreciated vegetables in her new book, aptly named Vegetables, a Biography.

Sunday, July 1, 2012

Yuval Sapir: When plants move - seeds on my sock

Dr. Yuval Sapir is Director of the Tel Aviv University Botanical Gardens 

As taught in basic biology classes, plants differ from animals in several substantial ways, including mobility. While animals are mobile and can choose their environment, plants are stationary, rooted in one place.

However, while this might be true for an individual plant, on a different level, plant do indeed move, just at a different speed and with unexpected parts.  

While animals move their entire body, including all related organs, plants move only their embyos. Plants pack their embryos in a bag that is on the one hand resistant to environmental harshness, and on the other hand "opens" immediately to the right set of cues, which are a complex mixture of light, temperature and moisture. This package is of course the seed. This is the real moving part of the plant, moving sometime as far and as rapid as animals do, and even more.

Seed movement requires agents of transportation, and different types of seeds are adapted to different agents of transportation. These could be physical, such as wind, carrying light-weight seeds (sometimes equipped with wing-like appendices) to circle the globe like dust. Such are, for example, seeds of orchids. Animals, just to close the circle, are good transportation agents because they... well, move. Fury animals, like dogs and cats, are especially adept at transporting seeds, as so also are, surprisingly, (relatively) hairless humans.  In place of fur, our clothes become the furry vehicle that seeds hitch a ride on. See the picture of my leg, my sock covered with seeds of Daucus carota (the wild carrot) and other seeds. All are spiny and adapted to catch the fur on my (or on other mammal's) leg.