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CSI: Botany – Using Plants And Forensic Science To Solve Crimes

Dec 19th, 2011 by

51qxFlFAUaLForensic Botany?

In the last few decades, forensic science has seen a large growth in research and application. This site that profiles forensic science college programs does a decent job of explaining how the forensic science profession operates. While there may be fewer car explosions and shoot-outs than on television, it’s still a very cool field of science. Forensics has worked its way into other disciplines of study, including nursing, accounting and psychology.

What do the Lindbergh baby kidnapping in 1935, a murder in the Arizona desert in 1992, the assault of a young woman in New Zealand in 1997, and the infamous Soham murders in 2002 all have in common?

They were all solved, at least in part, by forensic evidence from plants. (To find out how, please see below.)

Recent musings by Dr. Nigel Chaffey (see Ref. 1 below) regarding the apparent paucity of plant-based evidence in most episodes of the ever-popular CSI (Crime Scene Investigation) TV programs prompted me to investigate the subject, namely, Forensic Botany.

I must say that I was a bit surprised by what I found out.

First off, yes, indeed, there is a literature devoted to the subject (see Ref. 2 below) – even entire books (see right, e.g.), with more on the way.

So, apparently, there is a burgeoning interest in forensic botany.

Some creative teachers have even incorporated forensic botany as an alternative to the traditional lab practical used to assess students’ skills and knowledge in plant cell biology and anatomy. (see Ref 3 below, e.g.)

However, it seems that efforts to solve crimes by employing such botanical evidence is under-utilized. One reason I found often-cited for this is that there are insufficient numbers of people with a knowledge of plant taxonomy, plant anatomy, palynology, etc., qualified to expertly assist in such investigations. Also, “In great part, the failure to incorporate botanical evidence in investigations is due to lack of knowledge about plants by personnel who study crime scenes and so fail to collect it.” (from: Crime Scene Botanicals)

Briefly, What Is Forensic Botany?

From Wikipedia: “Forensic botanists look to plant life in order to gain information regarding possible crimes. Leaves, seeds and pollen found either on a body or at the scene of a crime can offer valuable information regarding the timescales of a crime and also if the body has been moved between two or more different locations. The forensic study of pollen is known as forensic palynology and can often produce specific findings of location of death, decomposition and time of year.“

While the field of forensic botany encompasses a variety of sub-disciplines ranging from plant taxonomy to palynology, applications involving DNA profiling of plant material have been relatively limited.

Palo Verde A somewhat well-known case involved seed pods of the Palo Verde tree (Cercidium sp.) recovered from the pick-up truck of a suspect.

Randomly Amplified Polymorphic DNA (RAPD) genetic profiling was used to link the seed pods to an individual tree found at the murder site (Please see Ref 4 below).

Recent advances in DNA fingerprinting technology (see Refs 5 & 6, e.g.) have shown that this technique may be a valuable resource for forensic applications, primarily to provide physical evidence that links plant materials to live plants at or near crime scenes.

Perhaps a more common use of this technology will be to identify individual plants, plant species, and plant populations and provide this as legal evidence for court proceedings against illegal loggers, drug dealers, and plant patent infringers.

Botanical Witnesses For The Prosecution

How was plant-based evidence used to help solve the cases mentioned at the beginning of this post?

In the Lindbergh kidnapping case, Dr. Arthur Koehler, an expert on wood anatomy and identification, provided dendrological evidence that a ladder found at the scene of the crime belonged to the chief suspect, Bruno Richard Hauptmann. The wood anatomical evidence ultimately was one of the most incriminating and unshakable pieces of evidence that led to Hauptmann’s conviction and his eventual electrocution for the kidnapping.

In the murder case of Denise Johnson in 1992, whose body was found in the desert near Phoenix, Arizona, forensic botanical evidence linked the murderer’s pickup truck to the crime scene. As previously mentioned, this was the first case in which DNA analysis was used to match the “tree fingerprints” of an individual tree at the murder site with seed pods from the tree in the bed of the suspect’s truck. (Please see Ref 4 below for more about this story.)

In the New Zealand case, unusual fungal spores and pollen from soil at the scene of the assault was shown to match those found in dirt-stains on the suspect’s clothes. This pollen and spore evidence was presented at the trial, the suspect was convicted, and he was given an 8-year prison sentence.

PollenAnd, finally, it was Patricia Wiltshire, “the queen of forensic science” (see Selected Links below), who established that pollen from the murderer’s shoes and his car exactly matched the type found in the ditch near where the victims’ bodies had been discovered.

Selected Links:

If one “Googles” the phrase “forensic botany”, quite a few links pop up. After exploring many of these links, I found the following especially interesting and informative (to me, at least):

Crime Scene Botanicals An excerpt from Plant Science Bulletin, Vol. 52, #3, Fall 2006 (PDF) – This is a very informative and comprehensive resource. (My hat’s off to the Botanical Society of America for making this publication freely available online.)

Forensic botany (This Forensic Botany site was created in 2002 by Jennifer Van Dommelen as a project in the Web Literacy For the Natural Sciences class at Dalhousie University, Halifax, Canada.)

Forensic Botany and Ecology by L. Labate, J. Lee & S. Kim – A PowerPoint slideshow nicely introducing the subjects, with references. PowerPoint (PPT) File (Please Note: Clicking on link may trigger download of a 7MB PPT file.)

Another PowerPoint slideshow introducing Forensic Botany (looks like a class project): PPT Quick View – This link will take you to the PowerPoint slideshow at Google docs.

Famous Forensic Botanist: Here’s a profile of Britain’s foremost forensic botanist Patricia Wiltshire.

Want to take a college course in Forensic Botany? Here you go: Forensic Botany offered by The University of Oklahoma Biological Station, taught by Dr. Adam Ryburn.

…or a career in forensic botany?

References

1. Chaffey, N. (2011) “Plant Cuttings: Forensic botany collections.” Annals of Botany, Vol. 109, pp. v-vii. (Full Text)

2. Coyle, H. M., C. Ladd, T. Palmbach, and H. C. Lee (2001) “The Green Revolution: Botanical contributions to forensics and drug enforcement.” Croatian Medical Journal, Vol. 42, pp. 340-345. (PDF)

3. Barratt, N.M (2011) “The case for forensic botany.” The American Biology Teacher, Vol. 73, pp. 414-417. (Abstract & References) (Full Online Text)

4. Yoon, C. K. (1993) “Botanical witness for the prosecution.” Science, Vol. 260, pp. 894-895. (PDF)

5. Craft, K. J., J. D. Owens, and M. V. Ashley (2007) “Application of plant DNA markers in forensic botany: Genetic comparison of Quercus evidence leaves to crime scene trees using microsatellites.” Forensic Science International, Vol. 165, pp. 64–70. (PDF)

6. Tnah, L. H. , et al. (2010) “Forensic DNA profiling of tropical timber species in Peninsular Malaysia.” Forest Ecology and Management, Vol. 259, pp. 1436-1446. (Abstract)

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Do Plants Have an Immune System?

Dec 10th, 2011 by

Rice diseaseIt Depends on How You Define “Immune System”

Plants get sick. That is, they can be infected by pathogens.

But after hundreds of millions of years of pathogen attacks, plants are still here. So, they must have ways to get well after being sick.

Plants can defend themselves against disease-causing organisms (pathogens) such as viruses, bacteria, and fungi.

They do so by producing physical barriers (e.g., plant cells walls), some antibiotic compounds (e.g., phytoalexins), and even enzymes that perturb pathogens.

In a broad sense, these are all part of a plant’s immune response, that is, biological processes that an organism uses to defend itself against disease.

But do plants have an immune system similar to that in animals? One that can “remember” exposure to specific pathogens?

Recognizing (and Remembering) Self from Non-Self

Humans, along with most other vertebrates, have a multifaceted immune system called an adaptive immune system, which is the culmination of complex interactions at the biochemical, genetic and cellular levels.

Restricted Key parts of this adaptive system are the organism’s ability to (1) biochemically distinguish between it’s own cells (self) and foreign (non-self) entities AND (2) remember specific features of the foreigner.

All pathogens – from viruses to fungi – have so-called macromolecules on their surfaces that distinguish them.

Adaptive immune systems (AIS) use these macromolecules as antigens. That is, the immune system uses these characteristic surface features as a way to specifically identify foreign (non-self) entities.

The AIS uses the antigens to generate specific antibodies, which are used to tag the “foreigner” for destruction by specialized blood cells called lymphocytes. These specific antibodies then allow for the rapid detection of subsequent infections with a particular pathogen, which allows for relatively quick defensive responses.

Although plants don’t possess such a sophisticated AIS, there are instances of self/non-self recognition in plants, mainly having to do with issues of self-pollination. (A topic for another time.)

JasminePlants Have an Innate (Passive) Immune System

A more generic, non-specific response to infection characterizes a plant’s immune system.

This type of response is called an innate immune system, in contrast to AIS.

Plants don’t have antibodies or special cells that search for and destroy pathogens.

Plants do, however, have cell-surface receptors to identify certain patterns characteristic of pathogens.

Such receptors, when activated, trigger the production of chemical signals, such as methyl jasmonate (think jasmine perfume or jasmine tea) that may elicit both local and systemic defense responses.

Local defensive responses included the so-called “hypersensitive response” characterized by the self-destruction of the plant cells in a localized area around the site of infection. (See Refs. 2 & 3 below for recent news regarding this.)

Plants also possess inducible systemic defense responses when locally infected by pathogens (e.g., see Ref. 4 below). That is, a single, localized infection may elicit defensive responses throughout the plant.

Bottom Line: Although plants do have the ability to defend themselves against disease-causing organisms (sort of a rudimentary immune system), plants don’t have an immune system as complex as humans.

References

1. Jones, J. D. G and J. L. Dangl (2006) “The plant immune system.”, Nature, Vol. 444, pp. 323-329. (Full Text)

2. Bhattacharjee, S., M. K. Halane, S. H. Kim and W. Gassmann (2011) “Pathogen effectors target Arabidopsis EDS1 and alter its interactions with immune regulators.” Science, Vol. 334, pp. 1405-1408. (Full Text)

3. Heidrich, K., L. Wirthmueller, C. Tasset, C. Pouzet, L. Deslandes and J. E. Parker (2011) “Arabidopsis EDS1 connects pathogen effector recognition to cell compartment–specific immune responses.” Science, Vol. 334, pp. 1401-1404. (Full Text)

4. Jung, H. W., et al. (2009) “Priming in systemic plant immunity.” Science, Vol. 324, p. 89-91. (Abstract)

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A New Master Plant Hormone?

Nov 30th, 2011 by

BranchesWhat if the roots of flowering plants produced chemical signals that regulated the branching and thickening of their shoots, i.e., secondary growth?

Chemical signals used by plants to regulate their development and physiology are called plant hormones.

Very small amounts of these compounds, acting alone or in tandem, often elicit dramatic effects on plant development.

For many years there were only five plant hormones known, but advances in plant sciences have recently revealed others.

Evidence in support of the discovery of another new class of plant hormones called strigolactones was reported in the September 11 2008 issue of Nature magazine (summarized here).

Cover natureBriefly, an international team of scientists used several complementary experimental approaches to show that strigolactones produced in the roots travel up the plant in the xylem to the aerial parts of the plant and somehow suppress developmental pathways resulting in stem branching. (more info here)

(Strigolactones are likely chemically derived from carotenes, the orange-colored pigments in plants that give carrots their color, for example.)

Strigolactones are also suspected of being involved in mediating the formation of fungal symbioses in plants as well as promoting the germination of seeds of some plants (such as Striga ) that parasitize the roots of host plants and can cause significant crop damage.

Could there be any practical uses for strigolactones?

Conceivably, they may be agriculturally useful to induce premature germination of parasitic plants. By affecting shoot branching in flowering plants, and thus plant achitecture, strigolactones also may be useful to horticulturalists. (In a previous post, I discussed strigolactones as they may relate to apical dominance.)

Recent News

In a recent report, summarized here, a new, more extensive role for strigolactones in mediating auxin signaling is proposed.

According to the authors of this paper: “Our results provide a model of how auxin-based long-distance signaling is translated into cambium activity and suggest that SLs [strigolactones] act as general modulators of plant growth forms linking the control of shoot branching with the thickening of stems and roots.” (from Ref 1 below)

Bottom line: Plants may use strigolactones as hormones produced in the roots to regulate not only the branching of shoots, but also secondary growth in general. (Moreover, some soil fungi and some parasitic plants use this chemical as a proximity signal in order for them to better colonize the roots of their plant hosts.)

Reference

1. Agusti, J., et al. (2011) “Strigolactone signaling is required for auxin-dependent stimulation of secondary growth in plants.” Proceedings of the National Academy of Sciences (USA), published online before print November 28, 2011, doi: 10.1073/pnas.1111902108.
(Abstract)

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A New Twist On “You Are What You Eat”

Nov 3rd, 2011 by

FaceDoes Ingested Plant Material Regulate Your Gene Expression?

Research results published in the journal Cell Research provide evidence that small bits of genetic material from ingested plants may regulate gene expression in animals. (for the original paper, see Ref 1 below; and summaries of these findings can be found in refs. 2 & 3 below)

These small bits of plant genetic material are called micro RNAs (miRNA).

Briefly, these very small pieces of RNA are found in both animals and plants. They “…were recently revealed as master chief regulators of gene expression in all organisms.” (from ref 2 below)

These micro RNAs regulate gene expression by interfering with translation. They do so by binding to complementary regions of specific message RNAs (mRNAs) to prevent translation of these mRNAs into proteins.

In other words, miRNAs may inhibit or prevent the final outcome of gene expression by interfering with the final step, that is, protein biosynthesis.

Because of this, small RNAs have been recognized as significant factors in the regulation of gene expression in both animals and plants.

But is it possible that the small RNAs present in the plant material you eat may actually affect the regulation of your own genes?

This is the question was investigated by researchers at the Nanjing University of Life Sciences, and their answer appears to be: YES!

MouseWhat’s the evidence?

These investigators were studying specific miRNA in plants. They found that such plant derived small RNAs were present in human serum, presumably from ingested plant material.

They also investigated the presence of these plant-derived miRNAs in mice fed with either rice or mouse chow. The rice-fed mice had a higher levels of plant-derived miRNAs compared to the mice fed with chow. And when the researchers added plant miRNAs to the chow, this resulted in higher plant miRNAs in the mouse serum.

Cooking the rice had no effect. That is, the plant-derived miRNAs apparently survived not only the digestive process, but also cooking temperatures.

Apparently what happens is that the plant-derived miRNAs are absorbed by the cells in the intestines. These intestinal cells then package the miRNAs and secrete them into the bloodstream.

What are the implications?

Well, of course, the main implication is that the cooked or uncooked plant material you eat may actually affect the regulation of some of your genes through the effects of plant-derived miRNAs.

Does meat also contain miRNAs? You bet! Indeed, meat miRNA content may be at much higher levels compared to plant material.

All of this adds a whole new twist to the phrase “You are what you eat”.

New implications to eating genetically-modified organisms (GMOs).Corn seed

If natural miRNAs that you ingest can be absorbed by your body and have effects on your gene regulation, what about artificial genes present in GMOs?

Indeed, one of the new strategies that genetic engineers have been using in pest control is through the use of small RNAs in genetically-modified crop plants to interfere with the production of specific proteins in insects and nematodes. (see ref 2)

Now that there is evidence that such small RNAs may actually be absorbed from ingested cooked or uncooked plant material and may be active in humans could have major implications on the use transgenic plants for food.

Caveat Emptor

Though the implications of this report are far-reaching, it’s important to keep in mind that it’s a single study.

I’m sure other labs are actively engaged in attempting to confirm and to expand on these results.

Stay tuned.

Nevertheless, the more things we learn about the nature of plants, the more things get interestinger and interestinger.

References:

1. Zhang, L., et al. (2011) “Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA.” Cell Research, advance online publication 20 September 2011; doi: 10.1038/cr.2011.158.
(Full Text)

2. Vaucheret, H. and Y. Chupeau (2011) “Ingested plant miRNAs regulate gene expression in animals.” Cell Research, advance online publication 25 October 2011; doi: 10.1038/cr.2011.164. (Full Text)

3. Science Daily, (Sept. 19, 2011) “Plant miRNAs Could Enter Host Blood and Tissues Via Food Intake, Study Suggests.” (Full Text)

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Self-Digesting Plants = The Ultimate Solution to Biofuel Production from Plant Biomass?

Oct 15th, 2011 by

I’m Melting!!

Remember the melting witch in The Wizard of Oz?

What if corn stalks, for instance, could be induced to “melt” – that is, to go from tough biomass into a sugary puddle?

In biochemical terms, it would be the equivalent to the conversion of cellulosic biomass into a solution of its components, that is, glucose and other sugars.

If this could be easily accomplished, then would be much more cost-effective to use corn biomass as a source of raw material to make biofuels than is currently the case.

This is because lignocellulosic biomass is very difficult to enzymatically digest in the laboratory, or ethanol production plant, as a preliminary step to the production of cellulosic ethanol.

Typically, such plant material is cooked in sulfuric acid to render it suitable for commercial conversion to ethanol.

Thus, despite the fact that cellulosic biomass is by far the most abundant source of material for biofuel production, it is currently not cost effective because of the extensive pretreatment required to make it useful.

But what if digestive enzymes were embedded within the plant biomass itself, to be activated only by special conditions?

“Plant biomass” consists mainly of plant cell wall material, chiefly cellulose (see pie chart right). As cellulose and the other plant cell wall structural components are the plant’s chief line of defense against herbivorous insects and microbes, this is tough stuff.

Some bacteria and fungi, however, have evolved to produce enzymes such as cellulases that can digest plant cell walls. (Even plants have genes that code for cellulase – used in fruit softening and leaf abscission, for example.)

Some especially effective plant biomass-digesting microbes live in the guts of some insects (termites) and animals (cows and even Pandas!). Indeed, cell wall-digesting enzymes obtained from such animals and microbes can be used in the laboratory to breakdown – albeit slowly – plant biomass in vitro.

One of the reasons this process is slow is that the enzymes must digest the material from the outside in. But what if these enzymes could digest plant cell walls from the inside out?

Some recent research (see also ref. 1 below) is aimed at doing just that. This idea has also attracted interest from the private sector (see PDF file describing such a project here).

Basically, the idea works like this. Microbial genes coding for potent cell wall-digesting enzymes are incorporated into transgenic corn, for example. These enzymes are designed to be deposited in the plant cell walls. But the key to this plan is to make sure these enzymes remain inactive until “turned-on” by conditions that typically are not experienced naturally, such as temperatures above 140o F.

After corn stalks, for example, are harvested, they then are heated to such temperatures, which activates the digestive enzymes embedded in the biomass itself.

Using cellulosic biomass for biofuel production instead of corn kernels, for example, would help to ease pressure on food prices.

But am I the only one that thinks it’s a bit scary to release transgenes into the wild that code for enzymes designed specifically for the super-efficient self-digestion of plants?

Bottom line: Until lignocellulosic material can be cheaply rendered appropriate for fermentation to ethanol, biofuels will likely remain an impractical solution to America’s current and future energy needs.

Links:

Could “putting the cow inside the plant” make a new biofuel?

Potential key found for unlocking biomass energy.

The ethanol scam.

References

1. Jiang, X-r., X-y. Zhou, W-y. Jiang, X-r. Gao, and W-l. Li (2011) “Expressions of thermostable bacterial cellulases in tobacco plant.” Biotechnology Letters, Vol. 33, pp. 1797-1803. (Abstract)

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Flowering Hormone Florigen Also Triggers Tuber Formation in Potatoes

Sep 28th, 2011 by

Grumpy potatoFlorigen = Tuberigen

In an online report (ref 1 below) published this week in Nature, researchers in Spain and Japan have provided evidence that a protein similar to FT, currently regarded as the flowering signal florigen in plants, not only initiates flowering in potatoes, but also triggers tuber formation.

“Seasonal fluctuations in day length regulate important aspects of plant development such as the flowering transition or, in potato (Solanum tuberosum), the formation of tubers. Day length is sensed by the leaves, which produce a mobile signal transported to the shoot apex or underground stems to induce a flowering transition or, respectively, a tuberization transition.” (from ref. 1 below)

As previously discussed here and here, much has been learned about the flowering signal in plants over the past few years.

Briefly, plants that form flowers in response to a particular photoperiod sensed by the leaves produce a flower-initiation signal in the leaves.

This signal, named florigen nearly 100 years ago, travels from the leaves to the shoot apical meristem where it triggers genes that initiates flower formation. (For lots more about this story, please see here.)

Until recently, the identity of florigen was unknown.

Most plant scientists now agree that florigen is a protein named FT (coded for by gene named “Flowering Locus T”). Its analog in rice is called Hd3a.

Interestingly, the onset of tuber formation in potatoes is also sensitive to the photoperiod. (Most potato varieties are “long-night plants”, that is, tuber formation is induced by relatively long nights, uninterrupted by light.)

It’s long been suspected by scientists that study potatoes that florigen and “tuberigen” were likely one in the same signal (see, for example, ref. 2 below).

Indeed, interspecific grafting experiments demonstrated that the flower-inducing (florigen) and tuber- inducing (tuberigen) signals were functionally exchangeable.

So, perhaps it not so surprising that an analog to FT in potato may induce tuber formation as well as flowering.

References

1. Navarro, C., J. A. Abelenda, E. Cruz-Oro, C. A. Cuellar, S. Tamaki, J. Silva, K. Shimamoto, and S. Prat (2011) “Control of flowering and storage organ formation in potato by FLOWERING LOCUS T.” Nature, Vol. 478, pp. 119-122. (Abstract)

2. Jackson, S. D. (1999) “Multiple signalling pathways control tuber induction in potato.” Plant Physiology, Vol. 119, pp. 1–8. (Full Text)

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Falling of Autumn Leaves – A Biological Separation Process Triggered by a Gaseous Plant Hormone

Sep 22nd, 2011 by

Much can be found online about why leaves change colors in the fall…

…but relatively little about the final part of the story, namely leaf drop.

Components of this terminal process, called leaf abscission, are actually put into place at the beginning of the leaf’s life. At the end, a chemical signal from the leaf itself triggers this “end game”, a sequence of events involving the self-digestion of plant cells.

Abscission is not restricted to autumn leaves, however. It is a process plants use to discard spent flowers (see below), ripening fruits, and other dead or diseased parts.

Relevance anyone?: Some of the enzymes involved in this process may have relevance to commercial biofuel production from plant biomass. (Much more about this later on.)

The Pre-Fab Structure:

The Abscission Zone (AZ) consists of several layers of cells typically located at the base of the leaf petiole. The first step in abscission, then, is the formation of the AZ during leaf development. The second step occurs when the AZ gains the ability to respond to the gaseous plant hormone that triggers abscission.

The Plant Hormone:

The third step in this process involves ethylene, a plant hormone long implicated in plant aging (senescence). The generally accepted story is that ethylene is produced in aging leaves, which, in turn, acts as a chemical signal to cells in the AZ to begin the process of leaf abscission.

Ironically, there is another plant hormone called Abscisic Acid (ABA) that originally was thought to trigger abscission in plants. This turned out NOT to be the case, but, alas, the name stuck.

The Enzymes:

The final stage in the process of leaf abscission is the digestion of the plant cell walls in the AZ. This weakens the petiole in the region of the AZ, thus producing a separation point. Enzymes that digest the cellulose, hemicelluloses, and pectins in the plant cell walls are produced and then secreted by the cells in the AZ.

It’s interesting to realize that plants apparently have genes that code for enzymes that can literally be used to digest themselves.

The Genetics:

Published research (see ref. 1 below) regarding floral abscission in Arabidopsis has revealed a key network of genes involved in this process.

These genes apparently code for proteins that act in a sequential manner, culminating in abscission.

Bottom line: Abscission is used by plants as a way to jettison aging or diseased parts. Understanding the cellular and genetic mechanisms involved in abscission may have significant economic implications in horticulture (e.g., longer flower life) and agriculture (e.g., simultaneous fruit drop.)

Reference

1. Cho, S. K., et al. (2008) “Regulation of floral organ abscission in Arabidopsis thaliana.” Proceedings of the National Academy of Sciences (USA), vol. 105, pp. 15629-15634. (Full Text)

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Why Are Plants Important?

Sep 13th, 2011 by


No Respect?

A recent online news item entitled Why We Need Plant Scientists attracted my attention a few days ago.

It’s mostly about a paper published in the scientific journal New Phytologist (see ref. 1 below) that prioritizes research questions currently facing “the few, the proud and the chronically underfunded” (my quote) scientists that work primarily on plants.

Included in this paper is a succinct explanation of why plants are important:

“Plants are fundamental to all life on Earth. They provide us with food, fuel, fibre, industrial feedstocks, and medicines. They render our atmosphere breathable. They buffer us against extremes of weather and provide food and shelter for much of the life on our planet. However, we take plants and the benefits they confer for granted. Given their importance, we should pay plants greater attention and give higher priority to improving our understanding of them.”
 (from ref. 1 below)

Respect

In addition to this is a call for more respect for plant scientists:
“Everyone knows that we need doctors, and the idea that our best and brightest should go into medicine is embedded in our culture. However, even more important than medical care is the ability to survive from day to day; this requires food, shelter, clothes, and energy, all of which depend on plants.

“Plant scientists are tackling many of the most important challenges facing humanity in the twenty-first century, including climate change, food security, and fossil fuel replacement. Making the best possible progress will require exceptional people. We need to radically change our culture so that ‘plant scientist’ (or, if we can rehabilitate the term, ‘botanist’) can join ‘doctor’, ‘vet’ and ‘lawyer’ in the list of top professions to which our most capable young people aspire.” (from ref. 1 below)

It would be nice if this turned out to happen, but, sadly, I sincerely doubt that it will, especially in the USA.

For decades plant research in this country has not been very well funded. Relatively little money has been available to plant scientists from the NSF and the NIH.

Unfortunately, the main funding source for plant research in the USA is the USDA, which has received criticism from the scientific community over the years for not supporting much innovative research.

But I’ll save my diatribe regarding this subject for another day. Instead, I’ll refer you to ref. 2 below.

References

1. Grierson, C. S., et al. (2011) “One hundred important questions facing plant science research.” New Phytologist, Vol. 192, pp.6-12. (Full Text)

2. Law, M. T., G. J. Miller and J. M. Tonon (2005) Earmarked: The Political Economy of Agricultural Research Appropriations. (PDF)

3. Wood, C. and N. Habgood (2010) Why People Need Plants

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Plants That “Remember” (Part 2) – “Secret Life of Plants” Redux

Sep 5th, 2011 by

ForgetmenotsA Brief Stroll Down Memory Lane

Previously, we delved into the subject of “long-term” (weeks to months) plant “memory” by exploring what’s new on the subject of vernalization, that is, how some plants “remember” that they have experienced winter.

In this case, a “cold” treatment of some plant species over the course of weeks leads to the suppression of the expression of a gene that codes for a protein that inhibits flowering. Because this gene suppression is due to an actual physical, but epigenetic, modification of the plant cells’ DNA, it remains in place even after multiple cell divisions, though not after meiosis.

I’ve also recently posted about how plants may erase their “memories”.

But in my wanderings through the recent plant scientific literature on the subject, I bumped into a old, but familiar, title: Secret Life of Plants. (Please see ref. 1 below)

If you were a college student in the 1970′s, then you probably are familiar with the book and the documentary film (if not, please see here and here, respectively).

Probably the most notable thing about the movie is that the soundtrack is by Stevie Wonder.

If you’d like to watch the whole movie on YouTube, please go ahead. We’ll still be here after you finish…..

….welcome back!

Short-Term Memory

The latest incarnation of the “secret life of plants” is courtesy of Prof. Stanisław Karpiński and colleagues at the Warsaw University of Life Sciences, Warsaw, Poland. They published a paper in 2010 (ref. 2 below) providing experimental evidence that Arabidopsis plants are able to “remember” and “react” to information contained in light, at least over the short-term (hours).

Well, these experiments got noticed by the BBC, which published an online article entitled Plants “can think and remember”. And, of course, this story went sort of viral on the internet.

Fortunately, the whole topic was more intelligently discussed a few days later on the Scientific American blog network by Ferris Jabr entitled “Plants cannot “think and remember,” but there’s nothing stupid about them: They’re shockingly sophisticated”, which I highly recommend. It’s an excellent post.

Anyway, Prof. Karpiński and colleague Dr. Magdalena Szechynska-Hebda followed up this paper a few months later with a review entitled “Secret life of plants” (please see ref. 1 below). There’s even a YouTube video of Prof. Karpiński presenting a talk called “Do Plants Think” at the 2011 TED conference in Warsaw. (But all of us who can not understand Polish are out of luck.)

ThinkerBriefly, the gist of the new “Secret life of plants” (ref. 1 below) is summarized by the authors in their Discussion section: “Our results suggest that plants are intelligent organisms capable of performing a sort of thinking process (understood as at the same time and non-stress conditions capable of performing several different scenarios of possible future definitive responses), and capable of memorizing this training. Indeed leaves in the dark are able to not only “see” the light, but also are able to differently remember its spectral composition and use this memorized information to increase their Darwinian fitness.”

Like many plant scientists, I get a bit uncomfortable with the terms “plant intelligence” and “plant thinking” because it sort of confers a level of sentience to plants, analogous to animals, which plants certainly don’t possess. (And, let’s face it, an iPhone may be more “intelligent” than most plants.)

Perhaps the most thoughtful discussion of “plant intelligence” has been provided by Prof. Tony Trewavas from the University of Edinburgh (please see ref. 3 below).

But a more concise take on the subject is from Jabr’s Scientific Ameican blog post mentioned above: “A big mistake people make is speaking as if plants ‘know’ what they’re doing,” says Elizabeth Van Volkenburgh, a botanist at the University of Washington. “Biology teachers, researchers, students and lay people all make the same mistake. I’d much rather say a plant senses and responds, rather than the plant ‘knows.’ Using words like ‘intelligence’ or ‘think’ for plants is just wrong. Sometimes it’s fun to do, it’s a little provocative. But it’s just wrong. It’s easy to make the mistake of taking a word from another field and applying it to a plant.”

See also: The Roots of Plant Intelligence. (Video of TED talk by Stefano Mancuso.)

References

1. Karpiński S. and M. Szechyńska-Hebda (2010) “Secret life of plants: from memory to intelligence.” Plant Signaling & Behavior, Vol. 5, pp. 1391-1394. (Full Text)

2. Szechyńska-Hebdaa, M., J. Krukc, M. Góreckaa, B. Karpińskaa and S. Karpińskia (2010) “Evidence for light wavelength-specific photoelectrophysiological signaling and memory of excess light episodes in Arabidopsis.” The Plant Cell, Vol. 22, pp. 2201-2218. (Full Text)

3. Trewavas, A. (2003) “Aspects of plant intelligence.” Annals of Botany, Vol. 92, pp. 1-20. (Full Text)

HowPlantsWork © 2008-2011 All Rights Reserved.

Posted in Plant Cells, Plant Science, Plant Signaling | No Comments »

Plants That “Remember” – Some Plants Can Record Environmental Experiences For Future Reference By Altering Their DNA

Aug 30th, 2011 by

Plant memory?

Can some plants access past experiences so that this information can be incorporated into new responses, such as flowering?

The answer is: Yes! (as illustrated in the photo on the the left).

This picture shows a cabbage plant that was grown for five years in the laboratory of Dr. Rick Amasino. (For size comparison the little girl – who was the same age as the cabbage – is shown.)

Cabbage is a biennial plant and requires exposure to the environmental cue of prolonged winter cold in order to flower the second spring after planting. This promotion of flowering by cold is called vernalization.

The large cabbage shown in this picture has never been vernalized and cannot flower. The little girl is holding a cabbage plant (presumably between 1 to 2 years old) that has been vernalized.

In biennial plants, such as cabbage, competence to flower in the spring requires a previous “cold” treatment, sometimes months earlier.

A requirement for vernalization permits biennials to become established during the fall without the risk of flowering as winter begins. During the winter, these plants experience and “remember” a cold treatment, which enables them to flower during the favorable conditions of spring.

But how do such plants retain a “memory” of winter?

Much of what we currently know about how this works comes from the work of Dr. Amasino and his colleagues at the University of Wisconsin using the experimental plant Arabidopsis thaliana (see figure below right).

Briefly, the cold treatment elicits epigenetic changes in the cells of the shoot apical meristem (SAM) of the plant. (The SAM will ultimately give rise to the flower.)

Simply put, cold somehow causes parts of the SAM cells’ DNA to be physically blocked so that no gene transcription can take place in selected regions of the DNA. (Histones likely serve as the “padlocks” on the DNA.)

Remarkably, these blocks remain on the DNA even through the process of cell division (mitosis). Thus, even though vernalized cells divide, they retain this “memory” of a cold treatment.

These blocks do NOT persist through meiosis, however, so that the next generation of plants can use this vernalization strategy.

How do these epigenetic changes promote spring flowering?

The key appears to be the removal of a factor that actually blocks flowering. This factor, a transcription factor called FLC, blocks flowering by inhibiting genes required to switch the SAM from vegetative to floral development in Arabidopsis. (To learn much more about how this works, please see here.)

The epigenetic changes in response to the cold treatment result in the blockage of the gene coding for FLC. Thus, by the time warm spring temperatures role around, the absence of FLC renders the plant competent to flower.

If, however, vernalization does not occur, then the presence of FLC either delays or completely blocks flowering (e.g., see the 5-year old cabbage above).

A similar story appears to take place in winter wheat and winter barley.

Recent findings re. vernalization:

Research reported from the lab of Dr. Caroline Dean indicates that vernalization involves polycomb proteins, which suggests that gene silencing in plants – at least in connection with vernalization – may resemble that in insects and mammals.

Briefly, polycomb proteins actually alter the structure of small parts of the chromatin itself, thus, effectively silencing the genes in this section of the DNA by adding a “bend” or “kink” in the chromatin.

This would be analogous to having a bend or kink in a zipper, so that when the slider hits the kink, it can’t unzip the chain. It’s physically blocked.

From results published in January of 2011 by Jae Bok Heo and Sibum Sung (University of Texas, Austin), it looks like RNA also plays a role in this story.

Simply put, these investigators showed that a small strand of RNA that they named “COLDAIR” (ha ha) actually serves to help direct the polycomb proteins to the gene coding for the FLC, thus helping to shut it off. And what’s even more remarkable is that COLDAIR is a transcript of a non-coding region (intron) of the FLC gene itself. (Pretty cool, huh?)

Bottom line: Biennial plants have evolved a cellular mechanism that allows them to “remember” that they have experienced winter, so that they don’t flower prematurely.

Reference

Müller, R. and J. Goodrich (2011) “The Footprints of Winter: Epigenetic marks laid down during the cold months of the year allow flowering in spring and summer.” The Scientist, Vol. 25, p.57. (Full Text)

HowPlantsWork © 2008-2011 All Rights Reserved.

Posted in Flowering, Plant Development | No Comments »

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