Feed on
Posts
Comments

Public Domain

Public Domain

Double helix in the sky tonight
Throw out the hardware
Let’s do it right
” – Steely Dan

Here A CRISPR, There A CRISPR, Everywhere A CRISPR, CRISPR….

Yikes! You can hardly go through a week these days without reading some headline with “CRISPR” in the title. (Even in Time magazine!)

Yes, “CRISPR” currently is (and has been for about the past year or so) a pretty big deal in the popular press. (In mainstream scientific journals, such as Nature and Science, it’s been a big deal since about 2013.)

Why?

Well, because CRISPR, or more precisely the CRISPR/Cas9 system, is a powerful new way to edit DNA.

If you’re unfamiliar with CRISPR, here’s a nice YouTube video (from my old home town, btw) that I think does a pretty good job explaining it.

Nota bene: This is an excellent example of how a basic research project can lead to a major technological advance and of why it’s so critically important to support basic research (a.k.a., fundamental or pure research), in addition to “applied” research.

OK, so molecular biologists now have a new “toolkit” for tinkering with the genomes of biological organisms.

But why do many plant scientists say that CRISPR may “change everything” when it comes to the realm of plant genetic engineering and, ultimately, the fundamental nature of plant “GMO’s”?

Please allow me to explain….

Using a “Scalpel” Instead of a “Shotgun”

Up until recently, most plant GMOs have pretty much been the result of a “shotgun” approach to plant genetic engineering.

That is, using Agrobacterium or a “gene gun” to deliver foreign genes into plant cells, these genes were randomly inserted into the plant genome, sometimes multiple times, in several different locations within the genome.

“In addition, and due to the random transfer process, insertion may disrupt a resident gene and, accordingly, bring on unwanted phenotypic side-effects.”

“From 2006 to 2012, a few crop plants were successfully and precisely modified using zinc-finger nucleases. A third wave of improvement in genome editing, which led to a dramatic decrease in off-target events, was achieved in 2009-2011 with the TALEN technology.”

“…zinc-finger and TALEN nucleases, were based on specific polypeptide-to-DNA binding which is tedious to optimize; CRISPR-Cas9 is based on DNA-RNA hybridization which is well mastered. CRISPR-Cas9 nowadays appears as the most efficient system to achieve site-specific genome editing–easiest, more reliable and cheapest as well.” (From: Quetier below)

With CRISPR/Cas9, plant genetic engineers now have the ability to relatively easily and precisely “edit” the plant genome, that is, with a molecular “scalpel” instead of a “shotgun”.

Are CRISPR-modified plants GMOs?

What’s especially important to the whole anti-GMO debate is that researchers have recently devised a way to use CRISPR to precisely modify a plant’s genome without introducing any foreign DNA. (See Cyranoski below)

This whole issue has been nicely summarized by Dr. Johannes Fütterer, a Senior researcher at the Institute of Agricultural Sciences, ETH Zurich, in an article entitled The future of plant breeding”:
“The special feature of CRISPR/Cas is that the modifications produced in the genome do not differ from naturally occurring mutations in plants and animals caused by environmental influences on the genome, such as natural radioactive radiation, reactive metabolites or even by defects in DNA replication and inheritance. Random mutagenesis by chemical treatment or irradiation has been used in mutation breeding for many years and contributed to major yield gains in our crops in the 20th century. Worldwide this type of mutation breeding led to currently more than 3088 varieties from 190 species.
As plants modified with CRISPR/Cas cannot be distinguished from those modified with conventional breeding techniques, the question arises: if a new breeding method triggers a targeted modification in the genome of the given species that can also be achieved through conventional breeding – admittedly with significantly greater effort – or accidental mutation, should the resulting product be regarded as a GMO (genetically modified organism) or not? The current debate focuses accordingly on whether a regulation should be process- or product-related.

And what’s amazing is that some have suggested that this new “toolkit” for precise gene editing in plants is compatible with organic farming, since it will facilitate the “rewilding” of crop plants. (See Andersen et al below)

I’m skeptical that organic farmers would accept crop plants genetically modified using these “new breeding techniques”. But these are early days for CRISPR/Cas 9, and it’s possible that this new technology may eventually overcome zealotry.

Online Resources

  • On the usefulness of CRISPR for exploring how genomes work: CRISPR: gene editing is just the beginning
  • Are CRISPR-modified plants GMOs? :

    “GREEN LIGHT IN THE TUNNEL”! SWEDISH BOARD OF AGRICULTURE: A CRISPR-CAS9-MUTANT BUT NOT A GMO (13 May 2016)

    Are plants engineered with CRISPR technology genetically modified organisms? (14 June 2016)

    Brave New Crops: Gene Editing Comes to Agriculture (17 June 2016)

    Recent CRISPR News: 9/22/2016 – Titanic Clash Over CRISPR Patents Turns Ugly

    References

    Andersen, M. M., et al. (2015) “Feasibility of new breeding techniques for organic farming.” Trends in Plant Science, Vol. 20, pp. 426–434. DOI: 10.1016/j.tplants.2015.04.011 (Abstract)

    Belhaj, K., A. Chaparro-Garcia, S. Kamoun and V. Nekrasov (2013) “Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system.” Plant Methods, 20139:39, DOI: 10.1186/1746-4811-9-39. (Full Text)

    Cyranoski, D. (2015) “CRISPR tweak may help gene-edited crops bypass biosafety regulation.” Nature, DOI:10.1038/nature.2015.18590. (Full text)

    Khatodia, S., et al. (2016) “The CRISPR/Cas Genome-Editing Tool: Application in Improvement of Crops.” Frontiers in Plant Science, Vol 7, pp. 506. DOI: 10.3389/fpls.2016.00506 (Full Text)

    Quetier, F. (2016) “The CRISPR-Cas9 technology: Closer to the ultimate toolkit for targeted genome editing.” Plant Science, Vol. 242, pp. 65–76. DOI: 10.1016/j.plantsci.2015.09.003 (Abstract)

    © 2008-2016 All Rights Reserved.

  • Firstly, What Is A Roundup Ready® Crop?

    Well, let’s start out with: What’s Roundup®?

    Briefly, Roundup® is the commercial name for the herbicide glyphosate, first made and sold by Monsanto in the 1970’s.

    You can read more about Roundup® HERE.

    “Roundup Ready®” is Monsanto’s trade name for crops (soybean, maize, cotton & alfalfa, e.g.) that have been genetically engineered to tolerate glyphosate.

    Simply put, a bacterial gene (or genes) coding for an enzyme that promotes the breakdown of glyphosate has been transferred to these plants. (You can see how HERE.)

    Thus, farmers can spray Roundup® on Roundup Ready® crops, and they don’t die, because they can detoxify the herbicide.

    Glyphosate-resistant soybean was the first crop launched and marketed under the Roundup Ready brand in the USA in 1996.” (from Ref. 1 below)

    Secondly, What Is A “Superweed”?

    To answer this question, I wanted to know what professional weed scientists thought. Here’s the official answer from the Weed Science Society of America (WSSA):

    Use of superweed has snowballed in recent years, along with considerable misinformation that isn’t supported by scientific facts.  Most online dictionaries, for example, associate superweeds with herbicide resistance caused by the suspected transfer of resistance genes from crops to weeds.  To date, there is no scientific evidence to indicate that crop to weed gene transfer is contributing to the herbicide resistance issues faced by farmers.

    And the official definition, from the WSSA:

    Superweed:  Slang used to describe a weed that has evolved characteristics that make it more difficult to manage due to repeated use of the same management tactic. Over-dependence on a single tactic as opposed to using diverse approaches can lead to such adaptations.”
    “The most common use of the slang refers to a weed that has become resistant to one or more herbicide mechanisms of action (www.weedscience.org) due to their repeated use in the absence of more diverse control measures.”

    OK, I’ll go with this definition.

    But the WSSA is careful to point out that so-called “superweeds” can arise not only from the overuse of a herbicide, but also ““Dependence on a single mechanical, biological, or cultural management tactic….

    So, if a single herbicide is used, year-after-year, to kill “weeds”, then this selection pressure promotes the proliferation of individual “weeds” that resist, even tolerate, the herbicide, eventually leading to populations of so-called “superweeds”.

    But why are Roundup Ready® crops often blamed for a rise in “superweeds” in recent years?

    Cause: Predominance of Roundup Ready® Crops

    The estimated annual agricultural use of glyphosate in the USA for 2014 equaled over 250 million pounds, over 10 times more than in 1994.

    Why this massive increase?

    I think the graph below provides pretty good clues for answering the question. (“HT” = “herbicide-tolerant” & “Bt” = Bacillus thuringiensis. By the way, the “HT” crops are mostly Roundup Ready® crops.)

    ImageGen ashx

    Effect: Relatively Rapid Appearance Glyphosate-Tolerant “Superweeds”

    It seems to me that the evidence that the excess and wide-spread use of Roundup®, due primarily to the huge increase in the adoption of Roundup Ready® crops in the past twenty years (see above graph), have led to the current problems with “superweeds”. But I’m no weed science expert.

    What do the experts say?

    “…herbicides exert a high selection pressure on weed populations, and density and diversity of weed communities change over time in response to herbicides and other control practices imposed on them. Repeated and intensive use of herbicides with the same mechanisms of action (MOA; the mechanism in the plant that the herbicide detrimentally affects so that the plant succumbs to the herbicide; e.g., inhibition of an enzyme that is vital to plant growth or the inability of a plant to metabolize the herbicide before it has done damage) can rapidly select for shifts to tolerant, difficult-to-control weeds and the evolution of herbicide-resistant weeds, especially in the absence of the concurrent use of herbicides with different mechanisms of action or the use of mechanical or cultural practices or both.” (from Ref. 2 below)

    And from the USDA plant physiologist Dr. Stephen O. Duke: “Just as with overuse of certain antibiotics in medicine, overuse of a superior technology has been a recipe for accelerated evolution of resistance. Nature abhors a vacuum, and even though evolution of resistance to glyphosate was thought to be unlikely, or at the most, to occur very slowly and only to low levels, the massive selection pressure caused by the world’s most-used herbicide, has resulted in weeds evolving often novel and unpredicted mechanisms of resistance that can impart resistance to glyphosate doses far above those that are recommended.” (from Ref. 3 below)

    OK, now what are farmers to do?

    The Road To Nowhere?

    In response to increasing number of agronomically-significant glyphosate-tolerant “superweeds”, the chemical companies have developed GMO crops with tolerance to multiple herbicides.

    Though this may be a really bad idea, these GMO crops have recently been approved (e.g., see here and here) and are currently being propagated in the fields, already with some unintended consequences.

    Will this approach be the ultimate solution to weed control?

    Likely not. (Please see here, for example.)

    Recent News: Monsanto Seeds Unleash Unintended Consequences Across U.S. Farms.

    Online Resources:

    1. What Do We Really Know About Roundup Weed Killer? by Elizabeth Grossman, National Geographic

    2. History of Roundup Ready Crops

    3. Selection Pressure, Shifting Populations, and Herbicide Resistance and Tolerance by University of California, Riverside

    4. Why Roundup Ready Crops Have Lost their Allure, by Jordon Wilkerson, Harvard University

    References

    1. Dill, G. M. (2005) “Glyphosate-resistant crops: history, status and future.” Pest Management Science, Vol. 61, pp. 219–224. (Full Text PDF)

    2. Vencill, W. K., et al. (2012) “Herbicide Resistance: Toward an Understanding of Resistance Development and the Impact of Herbicide-Resistant Crops.” Weed Science, Vol. 60, pp. 2-30. (Full Text)

    3. Duke, S. O. (2015) “Perspectives on transgenic, herbicide-resistant crops in the United States almost 20 years after introduction.” Pest Management Science, Vol. 71, pp. 652–657. Abstract

    4. Keim, B. (2015) “Monsanto’s Newest GM Crops May Create More Problems Than They Solve.” Wired, (Full Text)

    Talking Heads – “Road to Nowhere”

    © 2008-2016 All Rights Reserved.

    From Decaf Coffee Plants To Non-Browning Apples

    Have you ever had a really good cup of decaf coffee?

    Me neither.

    This is likely because most decaf coffee results from chemical processing of normal coffee beans.

    But why would anyone want coffee without caffeine? And why do plants make caffeine in the first place?

    These questions have been addressed in a previous post, but suffice it to say here that there certainly is a very large potential market for coffee beans that naturally have very low or no caffeine.

    Indeed, coffee plant breeders have been trying to develop such varieties for decades, with very little success.

    In 2003, a more efficient gene-silencing technology was used in order to shut off caffeine production in coffee plants. (See Ref. 1 below.)

    This approach is called RNA interference (RNAi).

    The Benitec Biopharma website has provided a nice summary of this biological process:
    RNA interference (RNAi) is a natural process that cells use to ‘turn off’ or silence unwanted or harmful genes. The initial discovery of this phenomenon was in 1991, by scientists trying to deepen the colour of petunias. Surprisingly, by introducing a gene for colour, they found that they had turned off the gene.
    Several years after the petunia experiments, the mechanism of RNA interference was revealed: it is triggered by double-stranded RNA (dsRNA), not usually found in healthy cells, but needed to turn genes off, if the cell is threatened or damaged by invading viruses.

    To learn more about how this technology may impact plant breeding, please see Ref. 2 below.

    Back to decaf coffee plants….Unfortunately, it’s been difficult to produce coffee plants that don’t make caffeine because its biosynthesis involves a complex metabolic pathway. Thus, to develop “decaf” coffee plants has been especially challenging for plant genetic engineers, but they’re still trying. (e.g., see Ref. 3 below.)

    There are, however, plant products produced using RNAi gene-silencing that you will likely soon encounter.

    Arctic® Apples and Innate® Potatoes

    According to the official Arctic® apples website: “Arctic® apples aren’t slow browning. They aren’t low browning. They’re nonbrowning! By silencing the enzyme that causes apples to brown when bitten, sliced or bruised popular apple varieties like Golden Delicious and Granny Smith can be enhanced with the Arctic Advantage™. Our goal? To help consumers eat more apples by making them more convenient, and reducing food waste while we’re at it!

    What is the “Arctic Advantage™”?

    Briefly, these apple plants were genetically modified using RNA interference to silence genes coding for the enzyme polyphenol oxidase, which is primarily responsible for the browning of apples and other fruits and vegetables.

    These apple trees were approved for commercial planting by the USDA in 2015.

    A year earlier, another crop plant with specific genes silenced by RNAi was USDA-approved, namely, the Innate® potato.

    According to the official Innate® potato website:
    “Innate® potatoes are less prone to bruising and black spots, which means consumers waste less and fewer potatoes end up in landfills. Innate potatoes also contain less asparagine. By producing less asparagine, Innate potatoes provide the potential for the formation of acrylamide to be reduced by 58-72% when potatoes are baked, fried or roasted at high temperatures.”

    As I understand it, in the first generation of Innate® potatoes, RNAi gene-silencing was used to block the production of two enzymes, namely, polyphenol oxidase (see Arctic® apples, above) and asparagine synthetase.

    The second generation of Innate® potatoes blocked the biosynthesis of these two enzymes, plus two more – starch-associated R1 and phosphorylase-L. These two enzymes are involved in converting starch into reducing sugars, such as glucose and fructose. By blocking the production of these two enzymes, this results in a decrease in reducing sugars in stored potatoes, which also contributes to the lowering of acrylamide in French fries, for example.

    Online Resources: More thorough considerations of Innate® potatoes can be found at:

  • A look at the Innate Potato
  • Q&A with Haven Baker on Simplot’s Innate™ Potatoes
  • Recent News: Genetic improvement of tomato by targeted control of fruit softening

    References

    1. Ogita, S., et al. (2003) “Producing decaffeinated coffee plants.” Nature, Vol. 243, p. 823. (Full Text)

    2. Younis, A., et al. (2014) “RNA Interference (RNAi) Induced Gene Silencing: A Promising Approach of Hi-Tech Plant Breeding.” International Journal of Biological Sciences, Vol. 10, pp. 1150–1158. (Full Text)

    3. Borrell, B. (2012) “Plant biotechnology: Make it a decaf.” Nature, Vol. 483, pp. 264–266. (Full Text + Extras)

    *Please Note: The subject of RNAi mediated gene-silencing has also popped up on this blog in a previous post, entitled “Spray and Pray? – Will Spraying RNA on Plants Revolutionize Agriculture?”.

    HowPlantsWork © 2008-2016 All Rights Reserved.

    Diagrammatic illustration of the process of Plant Molecular Farming (PMF). (Figure 1 from Ref. 5 below)

    Diagrammatic illustration of the process of Plant Molecular Farming (PMF). (Figure 1 from Ref. 5 below)

    Plant-Based Vaccines – A Great Idea

    It’s been over 20 years since I introduced students in my plant sciences classes to the idea of using genetically-engineered plants (GMOs) as a source of edible vaccines.

    Basically, the idea was that some crop plants could be genetically engineered to
    produce vaccines in their edible parts, which could then be eaten when inoculations were needed.

    I think it’s safe to say that one of the chief proponents of this idea, since the early 1990’s, has been Dr. Charles Arntzen.

    When Dr. Charles Arntzen of Arizona State University visited Thailand in 1992, he was not expecting a moment of scientific “eureka” that would redirect his career. However, after observing a young Thai mother soothing her fussy infant with bits of banana, this plant molecular biologist was struck with an idea that is both startling and ingenious. What if, in addition to quieting her child, the mother could also administer a life-saving vaccine – in the banana?” (from Ref. 1 below)

    (By the way, a recent review of plant-made pharmaceuticals by Dr. Arntzen – please see Ref. 2 below – is what prompted this post.)

    –> Fast-Forward to 2016 –> Despite the scientific progress (e.g., see Ref. 3) and all the interest and excitement with regard to this idea (e.g., see Ref. 4) that existed nearly 20 years ago, to date, there is no commercially-available plant-based edible vaccine.

    Why not?

    Reality Bites….The Banana

    Brilliant ideas are often tempered, even sometimes crushed, by reality. And such appears to be the case for edible vaccines.

    By 2004, the cumulative number of antigens from pathogens of humans and/or animals successfully expressed in GMO plants had reached almost 50 (from Ref. 5 below). But, by then, the limitations of edible vaccines was also becoming evident.

    These limitations included the following:

  • Effectiveness of plant-derived oral vaccines – The stability and immunogenicity of orally-delivered antigens from plants appears to be highly variable, often producing unsatisfactory results. Also, a related concern, especially from a regulatory point of view, is how to deliver a specific dose of vaccine.
  • Human risks – Oral ingestion of food containing antigens may elicit an immune tolerance. Also, there may occur adverse allergic reactions to plant-specific compounds in the edible vaccines.
  • Ecological risks – The risks from field-grown GMO plants expressing vaccine components are not fully known. For example, of serious concern is the potential contamination of non-GMO crop plants and/or wild plants by the “escape” from GMO plants of transgenes coding for antigens “into the wild” – typically via pollen.
  • Government approval – The regulatory obstacles to orally-delivered, plant-derived vaccines may, indeed, be insurmountable at the present time.
  • Social resistance to GMOs – The last, but by no means the least, concern is the anti-GMO attitude of many people, especially with regard to the ingestion of GMO crops.

    These problems have undermined interest from the vaccine industry, and unless financial incentives are found, serious work on edible vaccines will be likely be confined to research labs. But, even though much progress been made in research laboratories, the practical applications of edible vaccines in the “real world” may be up against seemingly overwhelming odds.

    In his own words, Dr. Arntzen explains why promoting the idea of edible vaccines was probably a mistake:

    As I have said in recent years that [the term “edible vaccine”] may have attracted attention in the plant biology realm, but it probably has been much more counterproductive in the traditional vaccine industry. I have come to regret coining the term. In my naiveté, I was ignoring the rigorous regulatory requirements that government agencies and the vaccine industry follow to give us today’s highly effective and wonderfully safe vaccines. I still believe that using plant tissue for low-cost delivery of unpurified (or partially purified) antigens, perhaps as a dry powder, is technically feasible for mucosal vaccination. I see progress in this direction for animal vaccines, which is needed.” (from Ref. 2 below)

    Still, There Is Hope Down On The “Pharm”

    Although it’s unlikely that plant-grown “edible vaccines” will ever be used as originally envisioned, the interest in plants as biosynthetic factories for human and livestock pharmaceuticals, including vaccines, is alive and well. (For example, please see Refs. 6 and 7.)

    The West Africa Ebola virus outbreak of 2014-15 is a good example. As described in a previous post, tobacco plants were used to make an Ebola therapeutic called ZMappTM. (See YouTube video below.)

    And, more recently, tobacco plants were again in the news as “anti-malaria drug factories”.

    With the 2012 FDA approval of plant-made pharmaceutical (PMP) Elelyso for human use, the stage is set for other forthcoming PMPs. So, the future looks bright for “pharming” after all.

    Down on the “Pharm” (Some companies producing biologics and vaccines made in GMO plants that are in clinical development.)

    1. Mapp Biopharmaceutical, Inc. – Using tobacco plants to make components of Ebola vaccine ZMappTM.

    2. Medicago – Making vaccines against viruses (e.g., influenza and HIV) using tobacco plants.

    3. Ventria Bioscience – Making human lactoferrin (VEN 100) in rice as treatment against antibiotic-associated diarrhea.

    4. Planet Biotechnology – Using plants to produce treatment of MERS coronavirus infection.

    References

    1. Mandy, R. (2005) “Banana Vaccines: A Conversation with Dr. Charles Arntzen.”, Journal of Young Investigators, published online September 2005. (Full Text)

    2. Arntzen, C. (2015) “Plant-made pharmaceuticals: from ‘Edible Vaccines’ to Ebola therapeutics.” Plant Biotechnology Journal, Vol. 13, pp. 1013-1016; DOI:10.1111/pbi.12460 (Full Text)

    3. Walmsley, A. M. and C. J. Arntzen (2000) “Plants for delivery of edible vaccines.” Current Opinion in Biotechnology, Vol. 11, pp. 126-129. (Abstract)

    4. Langridge, W. H. R. (2000) “Edible Vaccines.”, Scientific American, Vol. 283, pp. 66-71. (Full Text – PDF)

    5. Arntzen, C., S. Plotkin and B. Dodet (2005) “Plant-derived vaccines and antibodies: potential and limitations.” Vaccine, Vol. 23, pp. 1753–1756.

    6. Yao, J., et al. (2015) “Plants as Factories for Human Pharmaceuticals: Applications and Challenges.” International Journal of Molecular Sciences, Vol. 16, pp. 28549-28565; doi:10.3390/ijms161226122 (Full Text)

    7. Liew, P.S. and M. Hair-Bejo (2015) “Farming of Plant-Based Veterinary Vaccines and Their Applications for Disease Prevention in Animals.” Advances in Virology, Vol. 2015, Article ID 936940; doi.org/10.1155/2015/936940 (Full Text)

    YouTube Video – How to grow an Ebola vaccine with a tobacco plant

    HowPlantsWork © 2008-2016 All Rights Reserved.

    Tags: ,

  • A Flowering Uber?

    Batman has the Batmobile.

    Dr. Who has the Tardis.

    Is it possible that the protein that triggers flowering in plants also has its own special transport vehicle?

    A paper from Prof. Hao Yu’s lab at National University of Singapore published in the 6 June 2016 issue of Nature Plants appears to support this idea. (Please see Ref. 1 below.)

    Before I tell you about this report, let me remind you that:

  • 1 In many plants, flowering may be regulated by photoperiod, that is, the relative lengths of day and night, over a 24-hr period.
  • 2 This photoperiod is sensed in the leaves of the plant, mediated by the photoreceptor phytochrome.
  • 3 When the plant experiences a flower-inducing photoperiod, the leaves produce a substance long-known as “florigen”, whose true identity was discovered only about 10 years ago (see Ref. 2 below), namely, FT protein.
  • 4 The FT proteins are then transported via the phloem to the shoot apical meristems (SAMs).
  • 5 At the SAMs, the FT proteins interact with specific transcription factors called FD proteins to activate floral identity genes, thus inducing flowering.

    Today’s paper (Ref. 1) has to do with step 4 above, namely, how FT proteins are transported from leaves to SAMs.

    Briefly, Yang Zhu and co-investigators present several pieces of evidence that are consistent with the idea that proteins, with the unwieldy name of “SODIUM POTASSIUM ROOT DEFECTIVE 1”, abbreviated NaKR1, mediate the phloem transport of FT proteins from leaves to SAMs.

    First, let me tell you that the NaKR1 protein has previously been shown to travel in the phloem and to be involved in the long-distance phloem transport of sucrose and also, perhaps, mineral nutrients such as sodium (Na+) and potassium (K+). And, interestingly, it was also previously shown than NaKR1 affects flowering time under certain conditions.

    Knowing all this, Zhu and co-workers (Ref. 1) found that the expression of the genes coding for FT and NaKR1 were similarly affected by photoperiod and by flowering-related genetic factors, and that the relative levels and cellular locations of both FT and NaKR1 coincided with each other.

    Moreover, “We provide evidence that NaKR1 interacts in vivo with FT, and promotes flowering by regulating long-distance movement of FT from leaves to the shoot apex through the phloem stream. Our results suggest that NaKR1 is a hitherto unknown regulator specifically required for photoperiodic control of long-distance delivery of florigenic signals.” (From Ref. 1 below)

    Although the evidence supports the idea that NaKR1 is important in long-distance phloem transport of the flowering signal (at least in Arabidopsis), it’s unclear exactly how it does so.

    References

    1. Zhu, Y., L. Liu, L. Shen & H. Yu (2016) “NaKR1 regulates long-distance movement of FLOWERING LOCUS T in Arabidopsis.” Nature Plants, Vol. 2, Article number: 16075;
    doi:10.1038/nplants.2016.75. (Abstract)

    2. Corbesier, L., et al. (2007) “FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis.” Science, Vol. 316, pp. 1030-1033; DOI: 10.1126/science.1141752 (Abstract).

    HowPlantsWork © 2008-2016 All Rights Reserved.

  • Land Plants Do Affect the Climate

    About 70% of the Earth’s surface is covered by oceans, and marine phytoplankton likely play a significant role in cloud formation via ice nucleation (and, thus, affect the weather and climate). For example, please see Ref. 1 below.

    But a paper published in 2015 (see Ref. 2 below) suggested that we have underestimated the impact of pollen from land plants on cloud formation. (A nice summary of this report: Pollen and clouds: April flowers bring May showers?)

    So this led me to wondering about the question of whether “macroscopic” land plants significantly affect the weather. (Let’s leave the microscopic phytoplankton for another time….)

    Of course, it follows that if 70% of the Earth’s surface is covered by oceans, then the remaining 30% is land. About 1/3 of the land is cold or hot desert (few or no plants). So, roughly speaking, about 20% of the Earth’s surface is covered with vegetation. And about half of this is forests. Thus, it’s not unreasonable to presume that terrestrial plants may affect the Earth’s climate (time frame = decades), and perhaps even the weather (time frame = minutes to months).

    It’s generally accepted that terrestrial ecosystems (especially forests) may have significant effects on the climate. (See, for example, forests’ roles in climate.) Terrestrial ecosystems influence climate by affecting how much solar energy is absorbed by the land surface and by exchanging climatically important gases with the atmosphere.

    But Do Land Plants Also Affect the Weather?

    I’m skeptical,…

    However, it is surprising how much plants affect weather. Plants process and release water vapor (necessary for cloud formation) and absorb and emit energy used to drive weather. Plants also produce their own micro-weather by controlling the humidity and temperature immediately surrounding their leaves through transpiration. Most plants and forest soils have a very low albedo, (about .03 to .20) and absorb a large amount of energy. However, plants don’t contribute to overall warming because the excess warmth is offset by evaporative cooling from transpiration.” (From the excellent website Vegetation: Its Role in Weather and Climate provided by North Carolina State University)

    I also found a good online resource for explaining the relationships between forests and weather (see Ref. 3 below) In it, the authors state that:
    “1. The main mechanisms by which forests modify weather have been identified. They are the surface albedo, transpiration and evaporation of water vapour, aerodynamic effects, and emission of hydrocarbons whose oxidation can form aerosol particles.
    2. Different mechanisms are dominant for each class of forest. Boreal forests affect local weather and climate via their low albedos, causing a local warming. Temperate forests modify weather via the albedo and transpiration of moisture, but their exact impacts on climate are the least certain. Tropical forests cool climate via their very high transpiration rates; the moisture transferred to the atmosphere forms large clouds which reflect incoming solar energy and cause a further cooling.”
    (from Ref. 3 below)

    And, if you consider seaweeds in the intertidal zone land plants, then:

    (1) Stressed seaweed contributes to cloudy coastal skies, study suggests and

    (2) Iodide accumulation provides kelp with an inorganic antioxidant impacting atmospheric chemistry.

    …but now I think it’s safe to say that land plants do indeed affect the weather (at least under certain circumstances).

    References

    1. Amos, J. (2015) Ocean plants ‘can help freeze clouds’, BBC News Online

    2. Steiner, A. L., et al. (2015) “Pollen as atmospheric cloud condensation nuclei.” Geophysical Research Letters, Vol. 42, pp. 3596–3602. doi: 10.1002/2015GL064060 (Abstract)

    3. Sanderson, M., M. Santini, R. Valentini and E. Pope (2012) “Relationships between forests and weather.” EC Directorate General of the Environment. Full Text (PDF)

    HowPlantsWork © 2008-2016 All Rights Reserved.

    By Emily Stackhouse [Public domain], via Wikimedia Commons

    By Emily Stackhouse [Public domain], via Wikimedia Commons

    Potatoes And Tomatoes And Deadly Nightshade

    Two recent reports (1) that potato plants boost the chemical defenses in their leaves when their tubers are under attack (see Ref. 1 below) and (2) Why Tomato Leaves Smell “Grassy”? (see Ref. 2 below) reminded me of how fascinating the biochemistry is in solanaceous plants and, also, of a question I sometimes got when I was a botany professor.

    Is it safe to eat green potatoes?

    This question, I presume, was prompted by articles such as “Horrific Tales of Potatoes That Caused Mass Sickness and Even Death”.

    Potatoes and tomatoes are the most well-known members of the plant family Solanaceae, a.k.a., the nightshade family.

    Perhaps the most notorious member of this family, “deadly nightshade” (Atropa belladonna), is very toxic, even deadly.

    (By the way, a really good book about this and other poisonous plants is Wicked Plants: The Weed That Killed Lincoln’s Mother and Other Botanical Atrocities, which was featured in a previous post.)

    So, is it any wonder that people would expect the foliage of potatoes and tomatoes to also be very toxic?

    And, indeed, both tomato leaves and potato tubers that have turned green due to exposure to light contain relatively small amounts of toxic compounds called alkaloids.

    But according the “Curious Cook”, a.k.a., Harold McGee, the author of several books on the science of cooking (shown below), we may not have to worry too much about this.

    Please see the links below for why:

    Harold McGee on eating tomato leaves.

    Harold McGee on green potatoes.

    Though I wouldn’t eat a bunch of green potatoes, I may try a few tomato leaves in my next batch of pasta sauce.

    Thanks Curious Cook!

    Books by Harold McGee:

    The classic that every cook should own: On Food and Cooking and, more recently, The Curious Cook.

    References

    1. Kumar, P., E. V. Ortiz, E. Garrido, K. Poveda, and G. Jander (2016) “Potato tuber herbivory increases resistance to aboveground lepidopteran herbivores.” Oecologia, doi: http://dx.doi.org/10.1007/s00442-016-3633-2 (Abstract)

    2. Kunishima, M. et al. (2016) “Identification of (Z)-3:(E)-2-hexenal isomerases essential to the production of the leaf aldehyde in plants.” Journal of Biological Chemistry, doi: 10.1074/jbc.M116.726687 (Abstract)

    HowPlantsWork © 2008-2016 All Rights Reserved.

    Pk16 clip image004Here, There, and Everywhere?

    Recent headlines – China to acquire Syngenta and Chinese farmers are illegally growing GMO corn: Greenpeace – got me wondering about the proliferation (or lack of it) of GMO crop plants outside the USA.

    It’s seems well-known that biotech crops are not welcome in most of Europe. But what about the rest of the world?

    As mentioned in a previous post, some countries have banned GMOs, including most of the EU countries, Russia, Philippines, Saudi Arabia, Egypt, and Tasmania (see here for a list of 36 countries that have banned the cultivation of GMO crops).

    However, as shown in the table on the right (from: Ref. 1 below), a number of other countries all around the world have indeed been actively engaged in cultivating GMO crops.

    Please see the references below – with a particular emphasis on China – for current information regarding this topic.

    References

    1. James, C. (2014) “Global Status of Commercialized Biotech/GM Crops: 2014.” ISAAA Brief No. 49. ISAAA: Ithaca, NY. (Full Text – PDF)

    2. Talbot. D. “China’ GMO Stockpile“, MIT Technology Review online, October 21, 2014.

    3. Larson, C. “Can the Chinese Government Get Its People to Like G.M.O.s?“, The New Yorker online, August 31, 2015.

    4. Li, Y., Y. Peng, E. M. Hallerman, and K. Wu (2014) “Biosafety management and commercial use of genetically modified crops in China.”, Plant Cell Reports, Vol. 33, pp. 565-573. (Abstract).

    5. Li, Y., E. M. Hallerman, Q. Liu, K. Wu and Y. Peng (2015) “The development and status of Bt rice in China.” Plant Biotechnology Journal, doi: 10.1111/pbi.12464. (Full Text)

    6. Thomson, J. A. (2015) “Why genetically modified crops have been slow to take hold in Africa.” The Conversation, published online July 13, 2015. (Full Text).

    7. Kumar, S. (2015) “India eases stance on GM crop trials.” Nature, Vol. 521, pp. 138-139. (Full Text)

    HowPlantsWork © 2008-2016 All Rights Reserved.

    Tearing Down The Paywalls?

    Over the years scribbling this blog, I’ve often been frustrated when trying to provide readers with links to material I’ve referenced. This is because, in many cases, the scientific information in question has been published in a journal article that is blocked by a paywall.

    But just like with newspapers and magazines, the world of scientific journal publications has dramatically changed in the past 10 years.

    Frustration with blocked online-access to scientific papers, the majority of which were the result of publicly-funded research, led many people, including scientists, to demand that publishers provide less restrictive access.

    Bowing to this outcry (and likely fearing legislation requiring free access to publicly-funded research results), many publishers responded by providing partial open-access options to authors (for a fee, of course).

    Alternatively, some scientists (and even some publishers) established fully open-access scientific journals, where authors could publish peer-reviewed scientific research free to view on the Internet. (In most cases, authors are charged a “publication fee” that varies from several hundred dollars to several thousand dollars.)

    You may have noticed that almost everything involved with the Internet these days seems to be in a constant state of flux. And scientific publication on the Internet is no exception (see Addendum below, for example).

    But since I don’t have the time or space here to cover all the myriad of ways one can publish scientific information these days, please allow me to offer you a few tidbits.

    What is meant by: Open Access (Wikipedia)

    For your perusal: a Directory of Open Access Journals

    Some recent news: Handful of Biologists Went Rogue and Published Directly to Internet

    And, of course, we can’t forget Caveat emptorPredatory publishers are corrupting open access, and be sure to check potential open-access journals at the great website Scholarly Open Access.

    Here’s my list – in no particular order – of full open-access plant science journals*:

    *Please note, this list is biased. These journals tend to feature articles in the realms of plant physiology and/or plant molecular biology, because, after all, this blog is about how plants work.

    For each journal, I’ve included the year of first publication, relative ranking (citations), publisher information, and publication fee. (Please also see legend below for further explanation.) Also, I may have missed a journal or two (or even more than two), so please leave a comment if I’ve overlooked your favorite open-access plant science journal.

  • AoB Plants (0,624) [16] (Oxford) 2010 {$1,000}
  • International Journal of Plant Biology (0,107) [5] 2010 {$560}
  • Frontiers in Plant Science (1,552) [36] 2007 {$2,490}
  • Applications in Plant Science* [6] (Botanical Society of America) 2013 {$1,200}
  • Current Plant Biology* (Elsevier) 2014 {$2,000}
  • Plant Biotechnology Journal (2,034) [51] (Wiley) 2003 {$2,720}
  • PLOS ONE – Plant Science [161 for PLOS ONE] 2006 {$1,495}

    ( ) = SJR Journal Rankings – Plant Science – 2014 (* indicates journal likely too new for ranking)

    [ ] = Google Scholar Metrics value

    { } = publication fee (Please note: actual fee may differ depending on various factors, such as society membership, type of publication, type of open access, etc.)

    Partial Open-Access Plant Science Journals

    To be fair, I should also mention that some plant science journals now offer authors the option to publish open-access articles (typically, for a publication fee). However, journals published by scientific societies, such as the ASPB and BSA, discount (even waive) this fee if the corresponding authors are members of the society or if their institution subscribes to the journal (please see Ref. 1 below, for example).

    I’d like to highlight the journal Plant Physiology in this regard. If the corresponding author is a member of the ASPB, then there is no publication fee to make the paper fully open-access. A brief accounting of the number of fully open-access papers published in 2015 for this relatively high-impact plant science journal (please see here, for example) revealed that the majority of the published papers were fully open-access articles. Thanks Plant Physiology!

    Addendum: Different Categories of “Open-Access”

    Apparently there exists at least two levels of “open-access”, so-called “gold” and “green”.

    I’ll leave it to the Nature Publishing Group to define:

    Gold open access:

    “Article is made open access immediately on publication.
    Usually associated with an Article Processing Charge (APC).
    Article is freely available on our platform.
    Article is the version of record, i.e. publisher’s typeset PDF.
    CC BY licence allows unrestricted reuse of the article providing the author(s) and original source are properly cited. CC BY is the default license for all NPG-owned fully open access titles. Other licences are available.”

    versus, Green open access:

    “Open access after an embargo period (though an embargo will not apply in all cases).
    Article is made freely available but somewhere other than the publisher’s website, e.g. in a subject or university repository, or the author’s homepage.
    Open access article is not necessarily the version of record – it could be the typeset PDF or the author’s final version after peer review but before typesetting.
    Rights/re-use may be limited.”

    Update: E.U. urged to free all scientific papers by 2020

    In Related News:
    Springer Nature to extend content sharing to whole Springer Nature-owned journal portfolio

    Who’s downloading pirated papers?…Everyone!

    Reference

    1. Ort, D. (2006) “RT-Plant Physiology: Full Open Access Publishing at No Charge to ASPB Members” Plant Physiology, Vol. 142, p. 5. (Full Text)

    HowPlantsWork © 2008-2016 All Rights Reserved.

  • GMO? OMG!

    Back in the day, I used to be a member of the American Society of Plant Physiologists (ASPP), which morphed into the American Society of Plant Biologists (ASPB) in 2001 to better reflect the diverse fields of plant science (read “plant molecular biology”) emerging in the 21st century.

    Anyway, I noticed that the ASPB was recently in the news because of a petition it sponsored (which has been signed by well over 1,500 scientists, to date) supporting GMO technology for crop improvement.

    The petition has been generally perceived as a warning to the anti-GMO folks that they are hindering the next Green Revolution presumably needed to feed the 9.6 billion people that’ll likely be on this planet in about 35 more trips around the sun (that is, in 2050).

    Despite the preponderance of scientific evidence in favor of GMO crops (see here, here and here, for example, and also Refs. 1 & 2 below):

  • Some countries have banned GMOs, including most of the EU countries, Russia, Philippines, Saudi Arabia, Egypt, and Tasmania (see here for a list of 36 countries that have banned the cultivation of GMO crops).
  • Recent polls indicate that over 50% of Americans think that it’s unsafe to eat genetically modified foods.

  • Last year, Chipotle declared it was the first national restaurant chain to cook with only non-GMO ingredients (although this claim has been challenged).

    An Unconscious Decision?

    Despite the overwhelming scientific evidence in favor of the safety and efficacy of the use of plant genetic engineering for crop improvement, there exists strong public opposition to GMO’s. This opposition has motivated some companies to ban GMO-derived ingredients from their products and some countries to ban, or significantly limit, the cultivation of GMO crops (see above).

    The seemingly irrational, yet strong, objections to GMO crops has long frustrated many members of the plant science community, which presumably motivated the ASPB to sponsor its petition supporting GMO technology.

    This frustration has recently led some plant biotechnologists to collaborate with cognitive scientists in order to understand WHY there is such widespread opposition GMO’s despite the scientific evidence to the contrary.

    This collaboration resulted in a paper published last year (see Ref. 3 below) that concluded that human emotion, not reason, was why arguments against GMO’s had such resonance with the general public. They found that the human mind may be highly susceptible to negative, and frequently emotional, arguments by opponents of GMOs.

    According to the lead author of the paper Stefaan Blancke: “Negative representations of GMOs–for instance, like claims that GMOs cause diseases and contaminate the environment–tap into our feelings of disgust and this sticks to the mind. These emotions are very difficult to counter, in particular because the science of GMOs is complex to communicate.” (from: Psychology of the appeal of being anti-GMO).

    So I guess it’s no big surprise that in the case of public opposition to GMO crops, emotions often trump reason (like so many other things in life).

    Please Note: Don’t get me wrong. As discussed in a previous post, there are some rationale reasons to seriously question some GMO’s, including economic, political and ecological arguments.

    References

    1. Klümper, W. and M. Qaim (2014) “A Meta-Analysis of the Impacts of Genetically Modified Crops.” PLoS ONE, 9(11): e111629. doi:10.1371/journal.pone.0111629. (Full Text)

    2. Nicolia, A., A. Manzo, F. Veronesi and D. Rosellini (2013) “An overview of the last 10 years of genetically engineered crop safety research.” Critical Reviews in Biotechnology, Vol. 34, pp. 77-88. (Abstract)

    3. Blancke, S., F. Van Breusegem, G. De Jaeger, J. Braeckman, and M. Van Montagu (2015) “Fatal attraction: the intuitive appeal of GMO opposition.” Trends in Plant Science, Vol. 20, pp. 414-418. (Abstract)

    HowPlantsWork © 2008-2016 All Rights Reserved.

  • Older Posts »