Category Archives: Plants

Berry Go Round #31

Welcome to the September edition of Berry Go Round, the blog carnival of all things botanical!

We’ll start with the The Roaming Naturalist who went out into the desert somewhere out in the Western United States and took pictures of Bitterroot, Desert Beauty.

Ted C. MacRae of Beetles In The Bush took a trip to the Sam Baker State Park and saw a Cleft Phlox, which is found in just a handful of Missouri counties.

Christina Agapakis of Oscillator is fascinated with figs and their symbiosis with pollinating wasps so she wrote not one but two posts about them: Edible Symbiosis and Seedlessness.

Sarcozona of Gravity’s Rainbow saw a wild Impatiens with an unusually looking flower – Orange Jewelweed.

Joan Knapp from Anybody Seen My Focus? took a lot of excellent pictures of the Green Comet Milkweed (Asclepias viridiflora) in Wilkes County, Georgia.

Matt DiLeo is The Scientist Gardener. The Orange Mystery Dust that painted everyone’s shoes orange during a ballgame turned out to be from the lawn rust fungi. Matt tells us what that is all about.

Mr. Strawberry of Strawberry introduces us to a strange-looking but mouth-watering new cultivar – the Pineberry: Pineapple Strawberry.

Dave Ingram of the Dave Ingram’s Natural History Blog explains how identification of native vs. introduced grasses requires some Learning about Ligules.

Emilie Wolf of Purple Carrots & Fairy Smoke tells you more than you ever knew about apples in Don’t You Just Love Apples?

Jessica M. Budke from Moss Plants and More takes a look at the new attempt to classify 350 species of peat moss in A Tale of the Sphagnums that Weren’t.

“Where should breeders look for traits like drought resistance among the landraces and wild relatives of crops?” asked Luigi of the Agricultural Biodiversity Weblog and took a look at a new paper about tomatoes: Getting the most out of wild tomatoes.

The Phytophactor gets help from some strange flowers, like a star flower, to get students excited about Pollination biology in the greenhouse (and then you take a fruit, spice and veggie quiz).

Janet Creamer from the Midwest Native Plants, Gardens, and Wildlife took a series of pictures of a bumblebee, the only pollinator strong enough to force open the always closed flower of the Bottle Gentian.

Greg Laden of Greg Laden’s Blog gave his readers a photo quiz – Name that organism and his readers guessed them all.

Everything you ever wanted to know about Sugar beet biology you can learn from Anastasia Bodnar at Biofortified.

And that’s it for this month. Thank you all for your submissions. Next edition of Berry Go Round will be hosted by Mike Bergin at 10000 birds – make sure you send in your entries in time.

Botanicalls – plants use Twitter to tell you when they need watering!

This is awesome – Botanicalls. See one of the developer’s amazing Ignite talk:

Linnaeus’ floral clock on the island of Mainau

As you may have noticed, I am quite fascinated with the earliest beginnings of my scientific discipline, which was almost entirely involving research on plants. The most famous story from that early period is the construction of a Flower Clock by Karl Linne, the father of taxonomy.
So, of course I got really exited when I saw, on the Mainau island last Friday, a reconstructed Linnaeus’ floral clock.

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Then I looked carefully – and noticed it was not telling the correct time. This was taken at 3pm.

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So I thought about it for a second….and, well, this is what I think is going on here.

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First, Linnaeus’ clock is a 12-hour clock, not a 24-hour one. It does not include plants that flower at night. The division of the daytime into 12 hours makes sense only during the equinox. As daylength changes during the year, each hour will become gradually longer than 60 minutes for six months, then shorter then 60 minutes for six months. Thus, such a clock will not be precise on any day except the (spring) equinox.

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Second, the latitude of Mainau in Germany is different from that in Upsalla in Sweden. And yet, the same species of flowers were used in both places. Thus, the photoperiod will be different and plants will flower at different times of day at these two places (again, except on the day of spring equinox).

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Very pretty – but not a precise time-piece….

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Meetings I’d like to go to….Part V

Genetic Manipulation of Pest Species: Ecological and Social Challenges:

In the past 10 years major advances have been made in our ability to build transgenic pest strains that are conditionally sterile, harbor selfish genetic elements, and express anti-pathogen genes. Strategies are being developed that involve release into the environment of transgenic pest strains with such characteristics. These releases could provide more environmentally benign pest management and save endangered species, but steps must be taken to insure that this is the case and that there are no significant health or environmental risks associated with releases. Our conference will foster discussion of risks and benefits of these technologies among scientists, policy makers, and citizens.

March 4-6, 2009
North Carolina State University, Raleigh, NC
This is very soon – I’ll try to go to some of it if I can….

iNaturalist rocks!

Thanks Bill for drawing my attention to iNaturalist which has the makings of an awesome site!
What is it?
It is essentially a Google Map where people can add pins every time they see an interesting critter: a plant, fungus, animal, etc. What is recorded is geographical coordinates and time when it was posted.
Moreover, people can link from the pins to pictures of the sighted critters if they upload them on Flickr (nice way to interlink existing social networking sites instead of reinventing the wheel). And they can put additional information, e.g., description of the habitat where they saw the creature. They can try to identify it and others can chime in agreeing or disagreeing on the ID. One can also view maps in various ways – by time, by broader groups (e.g., insects, birds…), or by the degree of agreement people have about the ID.
The site has, apparently, just started, thus the number of people and the number of sightings is still relatively small and limited to mainly a couple of geographic locations (mostly California and Washington state).
But, imagine a couple of years from now, with millions of people pinning millions of sightings, providing additional information and then having the community agree on the ID? How about ecologists putting in all their field survey data (at least after publication if not before)? How about everyone who participates in the Christmas bird hunt? What an incredible database that will be! Something that one can search with machines, build and test models, and use the results to test ideas about, for instance, effects of weather events (hurricanes, fires, floods, El Nino, etc.) or broader weather changes (e.g., Global Warming).
In order for this database to become useful, I hope that the developers, as soon as possible, make sure it is possible for all the info to be machine searchable. And also to provide, perhaps, various fields that will lure people to put in more information. Right now, there is a date when the pin is posted, but the date of actual sighting is much more important. Exact latitude and longitude. Perhaps altitude. Perhaps depth for aquatic organisms. Exact time of day of the sighting. Description of the habitat. Number of individuals. Measurements of different kinds (one often cannot infer from pictures if the critter is 3cm or 30cm long, for instance). Behavioral observations. And of course the ID.
Such a database would be biased of course. People will tend to record when they see something unusual, or cool, or charismatic megafauna, rather than grass or field of corn or a bunch of squirrels in a tree. Also, more critters will be found in urban areas, on farms, in parks and by the roadsides than in places where one needs climbing (or diving) gear, or an hour of work with a machete in order to get to the habitat. But ecological models using the database could be made to account for these biases anyway.
In any case, I urge you to bookmark this site, and to use it. And let’s see how it shapes up over time.

Light-Responsive genes in rice

Friendly blogger Pamela Roland, the author of Tomorrow’s Table: Organic Farming, Genetics, and the Future of Food which I am reading right now (and which was recently reviewed in PLoS Biology), has just had a paper published in PLoS Genetics:
Identification and Functional Analysis of Light-Responsive Unique Genes and Gene Family Members in Rice

Rice, a model monocot, is the first crop plant to have its entire genome sequenced. Although genome-wide transcriptome analysis tools and genome-wide, gene-indexed mutant collections have been generated for rice, the functions of only a handful of rice genes have been revealed thus far. Functional genomics approaches to studying crop plants like rice are much more labor-intensive and difficult in terms of maintaining the plants than when studying Arabidopsis, a model dicot. Here, we describe an efficient method for dissecting gene function in rice and other crop plants. We identified light response-related phenotypes for ten genes, the functions for which were previously unknown in rice. We also carried out co-expression analysis of 72 genes involved in specific biochemical pathways connected in lines carrying mutations in these ten genes. This analysis led to the identification of a novel set of genes likely involved in these pathways. The rapid progress of functional genomics in crops will significantly contribute to overcoming a food crisis in the near future.

Berry Go Round #7

Welcome to the seventh edition of Berry Go Round, the carnival about all things botanical.
The previous edition was last month at Seeds Aside and the 8th issue will be at the end of August on Not Exactly Rocket Science.
The tradition for this carnival is to make it colorful (well, the plants are pretty), so I did what several other hosts of various carnivals did recently and used the LOLCat Builder to make it pretty and fun.
Since this makes the post very image-heavy and may slow down loading of the page for people with slower connections, I have placed them all under the fold.
To see from which blog the post comes from, hover your mouse/cursor over the image.
To go and read the entry, click on the image.
Also, I know, I know, there is no mycological carnival yet, so Berry Go Round has a subsection for that other sub-Domain of fungi, the Hyphae Go Round carnival, added on the bottom (last three entries). Enjoy:

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Botanical posts – you have 8 hours left!

Next edition of Berry Go Round, the carnival about all things related to plants, will alight here at A Blog Around The Clock tomorrow (probably late afternoon), so please send your submissions tonight by midnight EDT to: Coturnix AT gmail DOT com


Five species of ferns, happily cohabitating in a single large flowerpot on my porch – I have four other species, but those appear to be happier when kept seperately, one in each pot:

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Clock Classics: It all started with the plants

I was wondering what to do about the Classic Papers Chellenge. The deadline is May 31st, and I am so busy (not to mention visiting my dentist twice week which incapacitates me for the day, pretty much), so I decided to go back to the very beginning because I already wrote about it before and could just cannibalize my old posts: this one about the history of chronobiology with an emphasis on Darwin’s work, and this one about Linnaeus’ floral clock and the science that came before and immediately after it.
In the old days, when people communed with nature more closely, the fact that plants and animals did different things at different times of day or year did not raise any eyebrows. That’s just how the world works – you sleep at night and work during the day, and so do (or in reverse) many other organisms. Nothing exciting there, is it? Nobody that we know of ever wondered how and why this happens – it just does. Thus, for many centuries, all we got are short snippets of observations without any thoughts about causes:

“Aristotle [noted] that the ovaries of sea-urchins acquire greater size than usual at the time of the full moon.”(Cloudsley-Thompson 1980,p.5.)
“Androsthenes reported that the tamarind tree…, opened its leaves during the day and closed them at night.”(Moore-Ede et al. 1982,p.5.)
“Cicero mentioned that the flesh of oysters waxed and waned with the Moon, an observation confirmed later by Pliny.”(Campbell 1988, Coveney and Highfield 1990)
“…Hippocrates had advised his associates that regularity was a sign of health, and that irregular body functions or habits promoted an unsalutory condition. He counseled them to pay close attention to fluctuations in their symptoms, to look at both good and bad days in their patients and healthy people.”(Luce 1971,p.8.)
“Herophilus of Alexandria is said to have measured biological periodicity by timing the human pulse with the aid of a water clock.”(Cloudsley-Thompson 1980, p.5.)
“Early Greek therapies involved cycles of treatment, known as metasyncrasis….Caelius Aurelianus on Chronic and Acute Diseases…describes these treatments.. .”(Luce 1971, p.8.)
“Nobody seems to have noticed any biological rhythmicities throughout the Middle Ages. The lone exception was Albertus Magnus who wrote about the sleep movements of plants in the thirteenth century” (Bennet 1974).

de%20Mairan%20face.jpgThe first person to ask the question – and perform the very first experiment in the field of Chronobiology – was Jean-Jacques d’Ortous de Mairan, a French astronomer. What did he do?
In 1729, intrigued by the daily opening and closing of the leaves of a heliotrope plant (the phenomenon of ‘sleep in plants’ was well known due to Linneaus), de Mairan decided to test whether this biological “behavior” was simply a response to the sun. He took a plant (most likely Mimosa pudica but we do not know for sure as Linnean taxonomy came about a decade later) and placed it in a dark closet. He then observed it and noted that, without having access to the information about sunlight, the plant still raised its leaves during the day and let them droop down during the night.
However, De Mairan was an astronomer busy with other questions:

“….about the aurora borealis, and the relation of a prism’s rainbow colors to the musical scale, and the diurnal rotation of the earth, and the satellites of Venus, and the total eclipse of the sun that had occurred in 1706. He would waste no time writing to the Academy about the sleep of a plant!”(Ward 1971,p.43.)

de%20Mairan%20paper.jpgHe did not wanted to waste his time writing and publishing a paper on a mere plant. So his experiment was reported by his friend Marchant. It was not unusual at that time for one person to report someone else’s findings. Marchand published it in the Proceedings of the Royal Academy of Paris as he was a member, and the official citation is: De Mairan, J.J.O. 1729. Observation Botanique, Histoire de l’Academie Royale des Sciences, Paris, p.35.
In the paper Marchant wrote:

“It is well known that the most sensitive of the heliotropes turns its leaves and branches in the direction of the greatest light intensity. This property is common to many other plants, but the heliothrope is peculiar in that it is sensitive to the sun (or time of day) in another way: the leaves and stems fold up when the sun goes down, in just the same way as when touches or agutates the plant.
But M. de Mairan observed that this phenomenon was not restricted to the sunset or to the open air; it is only a little less marked when one maintains the plant continually enclosed in a dark place – it opens very appreciably during the day, and at evening folds up again for the night. This experiment was carried out towards the end of one summer, and well duplicated. The sensitive plant sense the sun without being exposed to it in any way, and is reminiscent of that delicate perception by which invalids in their beds can tell the difference between day and night. (Ward 1971)”

Marchant and de Mairan were quite careful about not automatically assuming that the capacity for time measurement resides within the plant. They could not exclude other potential factors: temperature cycles, or light leaks, or changes in other meteorological parameters. Also, the paper, being just a page long (a “short communication”), does not provide detailed “materials and methods” so we do not know if “well repeated” experiments meant that this was done a few times for a day or two, or if the same plants were monitored over many days. We also do not know how, as well as how often and when, did de Mairan check on the plants. He certainly missed that the plants opened up their leaves a little earlier each day – a freerunning rhythm with a period slightly shorter than 24 hours – a dead giveaway that the rhythm is endogenous.
The idea that clocks are endogenous, residing inside organisms, was controversial for a very long time – top botanists of Europe were debating this throughout the 19th century, and the debate lasted well into the 1970s with Frank Brown and a few others desparately inventing more and more complicated mathematical models that could potentially explain how each individual, with its own period, could actually be responding to a celestial cue (blame Skinner and behaviorism for treating all behaviors as reactive, i.e., automatic responses to the cues from the environment).
The early 18th century science did not progress at a speed we are used to today. But the paper was not obscure and forgotten either – it just took some time for others to revisit it. And revisit it they did. In 1758 and 1759 two botanists repeated the experiment: both Zinn and Duhamel de Monceau (Duhamel de Monceau 1758) controlled for both light and temperature and the plants still exhibited the rhythms. They used Mimosa pudica, which suggests to us today that this was the plant originally tested by de Mairan.
Suspecting light-leaks in de Mairan’s experiment, Henri-Louis Duhamel du Monceau repeated the same experiment several times (Duhamel du Monceau 1758). At first, he placed the plants inside an old wine cave. It had no air vent through which the light could leak in, and it had a front vault which could serve as a light lock. He observed the regular opening and closing of the leaves for many days (using a candle for observation). He once took a plant out in the late afternoon – which phase-shifted the clock with a light pulse. The plant remained open all night (i.e.., not directly responding to darkness), but then re-entrained to the normal cycle the next day. Still not happy, he placed a plant in a leather trunk, wrapped it in a blanket and placed it in a closet inside the cave – with the same result: the plant leaves opened and closed every day.
So, he was convinced that no light leaks were responsible for the plant behavior. Yet he was still not sure if the temperature in the cave was absolutely constant, so he repeated the experiment in a hothouse where the temperature was constant and quite high, suspecting that perhaps a night chill prompted the leaves to close. He had to conclude: “I have seen this plant close up every evening in the hothouse even though the heat of the stoves had been much increased. One can conclude from these experiments that the movements of the sensitive plant are dependent neither on the light nor on the heat” (Duhamel de Monceau 1758). He did not know it at the time, of course, but he was the first to demonstrate that circadian rhythms are temperature compesated – the period is the same at a broad range of constant temperatures.
The research picked up speed in the 19th century. Augustus Pyramus de Candolle repeated the experiments while making sure not just that the darkness was absolute and the temperature constant, but also that the humidity was constant, thus eliminating another potential cue. He then showed that the period of diurnal movements of Mimosa is very close to 24 hours in constant darkness, but around 22 hours in constant light (using a bank of six lamps). He also managed to reverse day and night by using artificial light to which the plants responded by reversing their rhythms (De Candolle 1832) after the initial few days of “confusion”.
Another astronomer, Svante Arrhenius argued that a mysterious cosmic Factor X triggered the movements (Arrhenius 1898). He attributed the rhythms to the “physiological influence of atmospheric electricity”. Charles Darwin published an entire book on the Movement of Plants in 1880, arguing that the plant itself generates the daily rhythms (Darwin 1880).
The most famous botanist of the 19th century, Wilhelm Pfeffer, started out favouring the “external hypothesis”, arguing that light leaks were the source of external information for de Mairan’s and Duhamel’s plants (Pfeffer 1880, 1897, 1899). But his own well-designed experiments (as well as those of Darwin) forced him to change his mind later in his career and accept the “internal” source of such rhythmic movements. Unfortunately, Pfeffer published his latter views in an obscure (surprisingly, considering the short and catchy title) German journal Abhandlungen der Mathematisch-Physischen Klasse der K√∂niglich S√§chsischen Gesellschaft der Wissenschaften, so most people were (and still are) not aware that he changed his mind on this matter.
In the early 20th century, Erwin Bunning was the first to really thoroughly study circadian rhythms in plants and to link the daily rhythms to seasonality. He and many others at the time mostly studied photoperiodism and vernalization in plants, two phenomena then thought to be closely related (we know better today). For the rest of the century, animal research took over and only recently, with the advent of molecular techniques in Arabidopsis, has the plant chronobiology rejoined the rest of the field.

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Hot Peppers – Why Are They Hot?

TITLE(First posted on July 21, 2006) Some plants do not want to get eaten. They may grow in places difficult to approach, they may look unappetizing, or they may evolve vile smells. Some have a fuzzy, hairy or sticky surface, others evolve thorns. Animals need to eat those plants to survive and plants need not be eaten by animals to survive, so a co-evolutionary arms-race leads to ever more bizzare adaptations by plants to deter the animals and ever more ingenious adaptations by animals to get around the deterrents.
One of the most efficient ways for a plant to deter a herbivore is to divert one of its existing biochemical pathways to synthetise a novel chemical – something that will give the plant bad taste, induce vomiting or even pain or may be toxic enough to kill the animal.

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Excited by milky substances?

There are many organisms that one can extract milky substances from, but cactus is NOT one of those. Which is a simple and useful way to figure out if the needly thing in front of you is a cactus or something else….

Congratulations to Karen James!

Excitement on science blogs! Karen James of the Beagle Project Blog has just today published a paper in PLoS ONE:
Diversity Arrays Technology (DArT) for Pan-Genomic Evolutionary Studies of Non-Model Organisms:

High-throughput tools for pan-genomic study, especially the DNA microarray platform, have sparked a remarkable increase in data production and enabled a shift in the scale at which biological investigation is possible. The use of microarrays to examine evolutionary relationships and processes, however, is predominantly restricted to model or near-model organisms.
Methodology/Principal Findings
This study explores the utility of Diversity Arrays Technology (DArT) in evolutionary studies of non-model organisms. DArT is a hybridization-based genotyping method that uses microarray technology to identify and type DNA polymorphism. Theoretically applicable to any organism (even one for which no prior genetic data are available), DArT has not yet been explored in exclusively wild sample sets, nor extensively examined in a phylogenetic framework. DArT recovered 1349 markers of largely low copy-number loci in two lineages of seed-free land plants: the diploid fern Asplenium viride and the haploid moss Garovaglia elegans. Direct sequencing of 148 of these DArT markers identified 30 putative loci including four routinely sequenced for evolutionary studies in plants. Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride, a lack of phylogeographic pattern in Australian G. elegans, and additive variation in hybrid or mixed samples.
These results enable methodological recommendations including procedures for detecting and analysing DArT markers tailored specifically to evolutionary investigations and practical factors informing the decision to use DArT, and raise evolutionary hypotheses concerning substrate specificity and biogeographic patterns. Thus DArT is a demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena such as adaptive radiations, population dynamics, hybridization, introgression, ecological differentiation and phylogeography.

Have no idea what it all means? Be patient. Karen will explain it all on the Beagle Project Blog in a day or two….

Fiona turns green and ogre-ish at night

‘Fiona’ Gene Controls Flower’s Physiologic Clock:

Scientists have found a new gene that regulates the daily and yearly physiological cycles of flowering and seeding.
POSTECH researchers, led by Nam Hong-gil and Kim Jeong-sik, said that they named the gene FIONA1 after the heroine in the popular animation “Shrek.” In the animation, princess Fiona is human by day but becomes an ogress at sunset. Fiona also sounds similar to the term “flowering” in Korean.
The research is a foundation for further discoveries of the plants’ clock systems, the team said. To study the gene, the POSTECH team used mutated cress, a species of weed widely used in such experiments because of its short seeding cycle and small genome size.
“We have identified the novel clock component, FIONA1 (FIO1), which is closely associated with the central oscillator and is critical to maintaining the correct period length, but it is not necessary for maintaining the amplitude of circadian rhythm,” the researchers said in the paper published on Plant Cell magazine last week.

I am assuming that, when they find the next gene whose protein interacts closely with the Fiona protein, they will name it Shrek. Who said that scientists have no sense of humor?

Olduvai George on NPR

I was lucky to be in the car at the right time this morning to catch a story about Mastodons in Manhattan: A Botanical Puzzle, i.e., why honey locust trees in NYCity have long thorns – an interesting story (click on the link and click on “Listen Now”) which, among others, features our blog-friend Carl Buell.

Darwin the Botanist – not just the orchids!

As a part of the Darwin Day celebration the North Carolina Botanical Garden has organized a series of events for today, culminating in the lecture “Darwin the Botanist” by Dr.William Kimler, a Darwinian scholar and the professor of History (of Science) at NCSU:

Most people do not think of Charles Darwin as a botanist. He is famously connected to the animals of the Galapagos Islands, and to the subjects of animal and human evolution and behavior. But Darwin’s famous curiosity did extend to plants. In fact, among his numerous publications are a book on carnivorous plants and one on orchid pollination titled, “On the Various Contrivances by which British and Foreign Orchids are Fertilised by Insects.” Dr. Kimler will discuss the influence of botany and some famous botanists on Darwin’s training and on his work as a naturalist. A look at Darwin’s lifelong interest in the biology of plants reveals some surprising insights into his scientific work on evolution.

The entrance fee of $10 rasies funds for the Botanical Garden, which is a Good Thing To Do. I’ll be there, too, so come along and bring your friends…

Gambling away the Farm

A good WaPo article: Pelosi takes heat for OK of farm bill
Ken Cook explains it very clearly: The Pelosi Farm Bill: A Corn Subsidy Windfall

Old, Hot and Pretty!

New Habanero Blasts Taste Buds — And Pepper Pests:

The super-hot, bright orange TigerPaw-NR habanero pepper offers extreme pungency for pepper aficionados, plus nematode resistance that will make it a hit with growers and home gardeners. Plant geneticist Richard L. Fery and plant pathologist Judy A. Thies at the Agricultural Research Service (ARS) U.S. Vegetable Laboratory, Charleston, S.C., put the pepper through three years of greenhouse and field tests before determining, in 2006, that it was ready for commercial fields and backyard gardens.

Exhibiting A Pepper For Every Pot:

Peppers don’t have to be just green and bell shaped and relegated to the supermarket shelf or home garden plot. This genus of plants has the genetic potential to provide a wide array of possibilities for the kitchen and the ornamental garden and sometimes both at once. Research on peppers from the Agricultural Research Service (ARS) is being featured from June to November in an exhibit called “A Pepper for Every Pot” at the U.S. Botanic Gardens in Washington, D.C. This exhibit explores the diversity of peppers, including recently introduced varieties, and celebrates peppers’ beauty, flavors and nutritional benefits.

Ancient Americans Liked It Hot: Mexican Cuisine Traced To 1,500 Years Ago:

One of the world’s tastiest and most popular cuisines, Mexican food also may be one of the oldest. Plant remains from two caves in southern Mexico analyzed by a Smithsonian ethnobotanist/archaeologist and a colleague indicate that as early as 1,500 years ago, Pre-Columbian inhabitants of the region enjoyed a spicy fare similar to Mexican cuisine today. The two caves yielded 10 different cultivars (cultivated varieties) of chili peppers.

Related: Hot Peppers – Why Are They Hot?

TreeBlogging of the Month

Festival of the Trees #7 is up on The Voltage Gate

TreeBlogging of the Month

Festival of the Trees 6 – Taking Root and Bearing Fruit – is up on Arboreality.

Another Clock Gene

Considering that circadian clocks were first discovered in plants, and studied almost exclusively in plants for almost a century before people started looking at animals in the early 20th century, it is somewhat surprising that the molecular aspects of the circadian rhythm generation mechanisms have lagged behind those in insects, vertebrates, fungi and bacteria. It is always nice to see a paper reporting a discovery of a new plant clock gene:
New function for protein links plant s circadian rhythm to its light-detection mechanism:

Plants set their clocks by detecting the light cycle, and Chua’s lab found that an accessory protein, called SPA1, is important for keeping the internal clock set. When they bred Arabidopsis plants with a mutated SPA1 protein, the plants flowered early, producing shoots and flowers weeks ahead of wild-type plants.
“The regulation of flowering initiation in response to the length of the day is mediated by the interaction of light with the plant s circadian clock system,” says Chua. Plants detect light with proteins called phytochromes and cryptochromes. SPA1 regulates one of these phytochromes, called PhyA.
The PhyA protein links light detection with the circadian clock system and directly influences when a plant flowers. But Chua’s finding suggests that SPA1 normally represses PhyA function, holding the plant back from flowering until the right time. “We knew that SPA1 negatively regulated PhyA immediately after germination, but didn t know if it played a role in the adult,” says Chua. “Our results show that SPA1 is important in the adult for regulating PhyA and the circadian period. When SPA1 is mutated, the plants precociously flower, affecting their entire reproductive cycle.”

Drinking the Clouds

Team Describes Unique Desert Cloud Forest:

Trees that live in an odd desert forest in Oman have found an unusual way to water themselves by extracting moisture from low-lying clouds, MIT scientists report.
In an area that is characterized mostly by desert, the trees have preserved an ecological niche because they exploit a wispy-thin source of water that only occurs seasonally, said Elfatih A.B. Eltahir, professor of civil and environmental engineering, and former MIT graduate student Anke Hildebrandt.
After studying the Oman site, they also expressed concern that the unusual forest could be driven into extinction if hungry camels continue eating too much of the foliage. As the greenery disappears it’s possible the trees will lose the ability to pull water from the mist and recharge underground reservoirs.

Do you write about trees? Have you ever tried? Should you?

You have until August 29th to write a post about trees, or a particular tree, or a picture of a really cool tree, or a poem about a tree…and send it to Burning Silo for the next edition of the Festival of the Trees

Friday Weird Sex Blogging – The Giant Stinkin’ Phallus!

Well, this Friday Weird Sex Blogging is not going to be so unique. After all, Janet and Zuzu have already blogged about it, but who can resist a phallic-looking, rotten-meat smelling, fly-attracting flower! And it is not a B-grade movie on the sci-fi channel. This is real! The Titan Arum (Amorphophallus titanum), in all its 3m tall glory is about to start stinking up the greenhouse at the Brooklyn Botanical Garden (follow the flowering on the blog or watch the flowering web-cam here) :

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The Quotable Tree

The second Festival of the Trees is up on Roundrock Journal. It’s big and beautiful!

Hot Peppers – Why Are They Hot?

Blogging on Peer-Reviewed Research

Some plants do not want to get eaten. They may grow in places difficult to approach, they may look unappetizing, or they may evolve vile smells. Some have a fuzzy, hairy or sticky surface, others evolve thorns. Animals need to eat those plants to survive and plants need not be eaten by animals to survive, so a co-evolutionary arms-race leads to ever more bizzare adaptations by plants to deter the animals and ever more ingenious adaptations by animals to get around the deterrents.
One of the most efficient ways for a plant to deter a herbivore is to divert one of its existing biochemical pathways to synthetise a novel chemical – something that will give the plant bad taste, induce vomiting or even pain or may be toxic enough to kill the animal.
But there are other kinds of co-evolution between plants and herbivores. Some plants need to have a part eaten – usually the seed – so they can propagate themselves. So, they evolved fruits. The seeds are enveloped in meaty, juicy, tasty packages of pure energy. Those fruits often evolve a sweet smell that can be detected from a distance. And the fruits are often advertised with bright colors – red, orange, yellow, green or purple: “Here I am! Here I am! Please eat me!”
So, the hot peppers are a real evolutionary conundrum. On one hand, they are boldly colored and sweet-smelling fruits – obvious sign of advertising to herbivores. On the other hand, once bitten into, they are far too hot and spicy to be a pleasant experience to the animal. So, what gives?
Back in 1960s, Dan Johnson had an interesting proposal he dubbed “directed deterrence” which suggested that some plants may make choices as to exactly which herbivores to attract and which to deter. Hot peppers are prime candidates for such a phenomenon. What is hot in peppers is capsaicin, a chemical that elicits a sensation of pain when it bind the vanilloid receptors in the nerve endings (usually inside the mouth) of the trigeminal nerve. As it happens, all mammals have capsaicin receptors, but it was found, relatively recently, that birds do not.
To test that hypothesis, Josh Tewksbury used two variants of hot peppers – one very hot (Capsicum annuum) and the other with a mutation that made it not hot at all (Capsicum chacoense) – and offered both as meals to rodents (packrats and cactus mice) and to birds (curve-billed thrashers).
All species ate the sweet kind about equally. When Josh offered them identically prepared meals made out of the hot stuff, the two rodents refused to eat it while the birds happily munched on it.
The study appeared in 2001 in Nature (pdf) and I saw Josh give a talk about it at that time as he was joining our department to postdoc with Dr.Nick Haddad. While my lab-buddy Chris and I gave him a lot of grief in the Q&A session on his lenient criteria of what constitutes a “hungry animal” (he needed them to be hungry for the feeding tests), still the main conclusions of the study are OK.
More importantly, it really happens in nature. Mammals avoid hot peppers out in Arizona where Josh studied them (and made videos of their behavior), but the birds gorged on peppers. When he analyzed the droppings of rodents and birds fed peppers, he saw that seeds that passed through avian intestinal tracts were fully fertile, while seeds eaten by mammals were chewed, crushed, broken or semi-digested and not fertile at all.
Additionally, the thrashers tend to spend a lot of time on fruiting shrubs of different kinds. While there, they poop. The hot pepper seeds in the droppings germinate right there and this is an ideal shady spot for them to grow.
What a great example of (co)evolutionary adaptations. Next time on this blog, the second Big Question: Why do we like to eat hot peppers?
Related: Hot Peppers

The trees, the trees, I speak for the trees!

The first edition of the Festival of the Trees, the blog carnival of tree lovers, is up on Via Negativa. It is huge and beautiful!

Chestnut Tree Circadian Clock Stops In Winter

Blogging on Peer-Reviewed Research

chestnuttree.jpgThe persistence of circadian rhythmicity during long bouts of hibernation in mammals has been a somewhat controversial topic in the literature. While some studies suggest that circadian clock is active during hibernation, other studies dispute this. Apparently, the truth is somewhere in-between – it differs between species:

Not all hibernating animals retain apparent circadian rhythmicity during the hibernation season. Whereas some species, such as bats and golden-mantled ground squirrels, maintain circadian rhythmicity in Tb throughout the hibernation season when held in constant conditions, other species, such as European hamsters, Syrian hamsters, and hedgehogs, lose circadian rhythmicity in Tb.

The outputs of the clock measured in these studies range from body temperature abd brain temperature, to timing of waking, to metabolic and behavioral parameters. But, to my knowledge, nobody has yet looked if the circadian pattern of expression of “core clock gene” persists during hibernation.
Thus, it was really interesting to see a study on the state of hibernation in a completely different kind of organism – a tree. About a year ago, a group from Spain, did exactly what was needed – they measured the levels of expression of circadian clock genes in the chestnut tree.
They measured the expression of clock genes both during naturally occuring winter dormancy and in the laboratory experiments involving chilling of seedlings combining with exposure to different photoperiods. In both cases, the core molecular mechanism of the circadian clock stopped entirely if the temperature and photoperiod both indicated ‘winter’, and was revived by warming-up the seedlings or the onset of spring.
Circadian clocks exhibit temperature independence, i.e., the period of the rhythm is not affected by temperature, within relatively broad limits. Apparently, the winter temperatures are outside the lower limit in the chestnut tree. Furthermore, it appears that the chestnut actively stops the clock with the onset of winter.
How can we interpret these data?
Overwintering is the stage in which all energetically expensive processes are minimized or shut down. However, workings of the clock itself are not very energetically expensive, so this is an unlikely reason for the elimination of rhythmicity during winter.
Second interpretation would be that, as the tree shuts down all its processes, there is nothing for the clock to regulate any more. There is also no feedback from the rest of metabolism into the clock. Thus, circadian rhythmicity fades as a by-product of overall dormancy of the plant.
Third, the clock itself may be a part of the mechanism that keeps everything else down. In other words, a clock stopped at (for instance – this is a random choice of phase) midnight will keep giving the midnight signal to the rest of the plant for months on end, keeping all the other processes at their normal midnight level (which may be very low). Thus, the clock may be central to the overal mechanism of hibernation in trees – i.e., the autumnal stopping of the clock is an evolved adaptation.