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Ebola Virus (CC BY 2.0) by NIAID

Ebola Virus (CC BY 2.0) by NIAID
Scanning electron micrograph of Ebola virus budding from the surface of a Vero cell (African green monkey kidney epithelial cell line).

“On Thursday, Dr. Kent Brantly thought he was going to die.
It was the ninth day since the American missionary worker came down sick with Ebola in Liberia.
His condition worsening by the minute, Brantly called his wife to say goodbye.
Thankfully, the call was premature.
Brantly is back on his feet — literally — after receiving a last-ditch, highly experimental drug.”
(from Ref. 1 below)

This drug is called ZMappTM.

…having received one dose of ZMapp out of the required three doses, and a blood transfusion from a fourteen-year-old boy who had recovered from Ebola, Kent Brantly walked onto the evacuation plane. At Emory University Hospital, in Atlanta, he received two more doses of ZMapp, which had been sent from the tobacco facility in Kentucky, and was discharged from the hospital after two weeks, free of the virus.” (from Ref. 2 below)

Yes, the ZMappTM that likely saved Kent Brantly’s life was produced in tobacco plants. (see Ref. 3 below)

In the many stories about ZMappTM and the Ebola virus I’ve read in the past few weeks, I’ve never seen a good explanation about how ZMappTM is made in tobacco, and why.

So, what follows, dear reader, is MY take on HOW this drug is manufactured in plants, and WHY.

But first, I think it’s important to find out a bit more about ZMappTM.

What The Heck Is ZMappTM ?

According to the manufacturer of this drug:
ZMappTM is not a serum or serum derived product. It is composed of three monoclonal antibodies directed against the Ebola Zaire virus strain. The component monoclonal antibodies were licensed from Defyrus (Toronto) and USAMRIID, humanized and recombinantly manufactured in a variety of tobacco (Nicotiana benthamiana).” (from: ZMappTM FAQ (PDF) from Mapp Biopharmaceutical)

My interpretation of the above:

  • ZMappTM is not derived from animal or human blood. Simply put, it is produced not by animals, but by plants.
  • ZMappTM = 3 antibody proteins that very specifically bind to the surface of a particular strain of the Ebola virus.
  • These antibodies were first produced (and licensed) by Defyrus and USAMRIID (see “Cast of Characters” below)
  • The monoclonal antibodies were “humanized”. Briefly, this means that the antibody genes (typically developed using animals such as mice) are modified to produce proteins that resemble human antibodies so that they won’t induce a severe allergic reaction when administered to patients.
  • Once so modified, these humanized monoclonal antibody genes are inserted – via recombinant DNA techniques – into a genetic vector. Millions of copies of this vector are then introduced into living tobacco plants.
  • In theory, how does injecting these monoclonal antibodies to Ebola virus into people sick with Ebola work? Briefly, giving a person antibodies against a particular pathogen is an example of passive immunization. This is in contrast to “active immunity”, which is when people produce their own antibodies when exposed to a pathogen or are vaccinated against a pathogen.

    Does ZMappTM work?
    We don’t know. The ZMappTM combination of antibodies was identified in January 2014. As an experimental product only limited supplies were manufactured for testing in animals. ZMappTM has shown efficacy in a monkey model of Ebola in studies conducted by the Public Health Agency of Canada (submitted for publication). Available data in humans are extremely limited. Larger trials are necessary to determine whether ZMappTM is safe and effective.
    ” (from: ZMappTM FAQ (PDF) from Mapp Biopharmaceutical)

    (By the way, you can also read about ZMappTM at Wikipedia.)

    How Is ZMappTM Made In Tobacco Plants?

    First, a bit of background on plant genetic engineering:

    Back in the day, when I was boring undergraduates, I’d tell students that, because plant and animal cells are likely derived from common eukaryotic ancestors, they have many cellular and metabolic processes in common.

    The molecular machinery of plant cells is closely related to that of animal cells. Thus, plant cells are able to synthesize and process relatively complex biologics. Indeed, GE [Genetically Engineered] plants have been shown to be able to produce human antibodies (immunoglobulins). Such so-called “plantibodies” appear to have the same biochemical properties as antibodies produced in animal cell cultures.” (from “Plant Trek”)

    The first proof of concept for functional antibody production in plants was provided in 1989, when two transgenic tobacco plants, each expressing light or heavy chains, were produced by Agrobacterium-mediated transformation of tobacco leaf discs. Crossing these two transgenic tobacco lines led to the expression of assembled functional IgG antibodies, accumulating up to 1.3% of total soluble protein. From then on, numerous antibodies and other proteins have been expressed in plants, demonstrating that plants can express and assemble components into functional, complex multimeric proteins.” (from Ref. 4 below)

    According to ZMappTM FAQ (PDF) from Mapp Biopharmaceutical: “Nicotiana [tobacco] seeds are planted in flats carried on mechanized roller trays similar to those used in large warehouses. The plants are grown for several weeks with careful control of light, temperature, and humidity. The plants are treated with the antibody vector system and grown for an additional week allowing the plants to manufacture humanized antibody proteins. The plants are harvested and homogenized in a large vat followed by separation of the antibody proteins using a series of specialized purification techniques. The resultant antibody is tested for purity and potency before being formulated into the drug.

    By the way, a series of photos of the process at Icon Genetics (see “Cast of Characters” below) can be viewed at at Zimbio.

    Why Is ZMappTM Made In Tobacco Plants?

    Why plants?

    1. “Plant expression systems are an attractive platform for the production of antibodies, for several reasons. Predominantly due to the possibility of production scale-up at a fraction of the costs compared to conventional systems.
    2. “Another advantage is that many plant species have a ‘generally regarded as safe’ status, since they do not contain mammalian viruses or pathogens, or produce endotoxins.
    3. “The ease of purification and downstream processing of plant-made antibodies is often postulated to result in a low cost of the final product, which can be applied parenterally, topically or orally.
    4. “Moreover, the developments in glyco-engineering of plants has made it possible to produce antibodies with desired glycoforms. Modification of glycans has also been perfected in comparative expression systems like mammalian cell cultures, but it has been seen that glyco-engineered plants have a much higher degree of glycan homogeneity.” (all of the above from Ref. 4 below)

    Why tobacco plants?

    Then there is the merit of speed: using the established state of the art tobacco leaf-based transient expression system [see Ref. 5 below, for example], bulk quantities of antibodies can be manufactured in a record time as compared to any other established expression system.” (from Ref. 4 below)

    In summary, the time it takes to grow and to genetically modify tobacco plants is much faster, and way less expensive, than to genetically engineer mice, for example. And plant cells also seem to produce higher quality antibodies, with less complicating factors, than animal cells.

    Cast of Characters:

    Mapp Biopharmaceutical (San Diego, CA, USA) “…was founded in 2003 to develop novel pharmaceuticals for the prevention and treatment of infectious diseases, focusing on unmet needs in global health and biodefense.”

    LeafBio, Inc. (San Diego, CA, USA) is the commercialization arm of Mapp Biopharmaceutical.

    Defyrus Inc. (Toronto, Canada) is “…a private life sciences biodefence company that collaborates with public health agencies and military R&D partners in the United States, United Kingdom and Canada to develop and sell broad spectrum anti-viral drugs and vaccine system as medical countermeasures to bioterrorist threats and emerging infectious diseases.”

    Icon Genetics (Halle, Germany) – pioneered genetic vectors for engineering tobacco (genus Nicotiana) plants to produce biopharmaceuticals.

    Kentucky Bioprocessing (Owensboro, KY, USA) – specializes in the good manufacturing practices (GMP) production of therapeutic proteins in Nicotiana.

    U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) (Frederick, MD, USA) is the “...the Department of Defense’s (DoD) lead laboratory for medical biological defense research. While our core mission is to protect the warfighter from biological threats, we also investigate disease outbreaks and threats to public health.”

    For Further Reading:
    A Possible Ebola Vaccine
    WHO plans for millions of doses of Ebola vaccine by 2015

    References

    1. Gupta, S. and D. Dellorto (2014) “Experimental drug likely saved Ebola patients.” CNN, August 5, 2014, online. (Full Text)

    2. Preston, R. (2014) “The Ebola Wars: How genomics research can help contain the outbreak.” The New Yorker, October 27, 2014 issue, online.
    (Full Text)

    3. Qui, X., et al. (2014) “Reversion of advanced Ebola virus disease in nonhuman primates with ZMapp.” Nature, doi:10.1038/nature13777. (Full Text)

    4. Virdi, V. and A. Depicker (2013) “Role of plant expression systems in antibody production for passive immunization.” The International Journal of Developmental Biology, Vol. 57, pp.587-593. (Full Text PDF)

    5. Sainsbury Laboratory (2012) “High Efficiency Transient Expression System for Plants- Methods to highly express proteins in plants in days not months.” www.pbltechnology.com (Full Text PDF).

    HowPlantsWork © 2008-2014 All Rights Reserved.

    The disclaimer: This is not meant to be an exhaustive review of the recent literature regarding abscission in plants. Instead, think of this as a selection of “recent highlights” (my opinion) in the study of abscission.

    Let’s focus on three steps of abscission: (1) the development of the abscission zone (AZ), (2) the signals that activate the abscission process, and (3) some key abscission-related genes and what proteins they code for.

  • 1. Setting The Stage - It’s clear that the abscission zone is formed long before abscission actually takes place, often when the organ in question (leaf, flower petal, seed, etc.) is being formed. Unraveling the precise sequence of events that takes place in forming the abscission zone has been very difficult. The approach has generally been to identify developmental mutants showing abnormal organ shedding in Arabidopsis and tomato, for example, and to isolate the genes responsible. To date, around dozen genes have been shown to be involved abscission zone development, many of them coding for transcriptional factors. (Please see Ref. 2 below for a thorough list.) Although these mutants have revealed several aspects of abscission zone formation, the “…expected set of factors necessary for AZ differentiation have proved surprisingly elusive.” (from Ref. 4 below)

  • 2. Signaling to Go (or Stop) - Another confounding aspect of abscission in plants is what triggers it, specifically which plant hormones are involved, and how. Both auxin (IAA) and ethylene have been shown to be involved in the regulation of the timing of abscission. It’s generally accepted (at least in the textbooks I’ve read) that ethylene acts as a natural accelerator of abscission and that auxin usually functions as a brake. Other plant hormones have also been implicated, including the one called “abscisic acid” (a.k.a., ABA), which unfortunately turns out NOT to have a very important direct role in triggering abscission in most plants. (But that’s a story for another day.) The general consensus seems to be that factors such as stress, senescence, and ABA may actually stimulate abscission through increasing the production of ethylene. Ethylene, in turn, then stimulates the expression of key abscission-related genes in the cells of the AZ.

    But recent results (e.g., see Ref. 1 below) have somewhat complicated the story. The prevailing theory is “…that the auxin/ethylene balance ultimately dictates the triggering of abscission and the rate at which it proceeds. However, much of the evidence of an involvement of auxin in the regulation of abscission is correlative and is based on manipulating hormone concentrations by tissue excision and auxin application. In this study [Ref. 1 below], endogenous IAA activity and signaling, to our knowledge for the first time, have been specifically manipulated within the cells that constitute the AZ. The data reveal that auxin not only regulates the timing of organ shedding in planta but that there is also an absolute requirement for IAA signaling to be maintained for abscission to take place.” (from Ref. 1 below)

  • 3. Breaking Up is Hard To Do - To shed part of itself, a plant must selectively self-digest a small portion of its most fundamental structure, the plant cell wall. During abscission, the walls of the cells in the AZ are digested by enzymes such as cellulase and polygalacturonase, which are synthesized by the AZ cells and then secreted into the cell wall space. This causes the cell walls to become soft and weak, leading to the eventual breakage and separation from the main plant body. But this is sort of the end of the story.

    What happens between the triggering of the process of abscission in the AZ by ethylene (let’s say this is the beginning of the story, for now) and the end of the story (namely, cell wall digestion)? In other words, what’s happening in the AZ cell in between these two events?

    Well, much of what’s happening in this middle section of the story is signal transduction. That is, how does the initial signal – ethylene – cause the biochemical chain of events inside the AZ cells leading to abscission? This is also called the “abscission signaling cascade”, which has been the focus of much research in the past decade or so.

    Briefly, both protein kinases located on the plasma membrane of AZ cells and membrane vesicle trafficking appear to play key roles in disseminating and amplifying the initial signals involved in activating abscission and production and secretion of enzymes involved in cell wall degradation. (For detailed information about this, please see Ref. 3 below.)

    Despite the fact that dozens of genes have been identified, there are still many questions regarding their precise role in abscission.

    “Abscission signaling cascades…have been extensively elucidated, although our understanding of the many identified genes remains fragmentary and incomplete. Moreover, it remains to be determined whether a general regulatory mechanism for abscission may exist among different organs and whether the mechanism may be conserved in different plant species.” (from Ref. 5 below).

    Cellular signaling cascades are somewhat analogous to a cellular Rube Goldberg machine – for instance:

    In conclusion: “If letting go is never easy, neither is it easy to understand the reasons why. Moving forward, there are large gaps in our knowledge of abscission that remain to be filled.” (from Ref. 3 below)

    References

    1. Basu, M. M., Z. H. González-Carranza, S. Azam-Ali, S. Tang, A. A. Shahid and J. A. Roberts (2013) “The manipulation of auxin in the abscission zone cells of Arabidopsis flowers reveals that indoleacetic acid signaling is a prerequisite for organ shedding.” Plant Physiology, Vol. 162, pp. 96-106. (Full Text)

    2. Estornell, L. H., J. Agustí, P. Merelo, M. Talón, and F. R. Tadeo (2013) “Elucidating mechanisms underlying organ abscission.”, Plant Science, Vols. 199–200, pp. 48–60. (Full Text)

    3. Chad E. Niederhuth, Sung Ki Cho, Kati Seitz, and John C. Walker (2013) “Letting go is never easy: Abscission and receptor-like protein kinases.” Journal of Integrative Plant Biology, Vol. 55, pp. 1251–1263. (Full Text)

    4. Liljegren, S. J. (2012) “Organ abscission: exit strategies require signals and moving traffic.”, Current Opinion in Plant Biology, Vol. 15, pp. 670–676. (Abstract)

    5. Nakano, T. and Y. Ito (2013) “Molecular mechanisms controlling plant organ abscission.”, Plant Biotechnology, Vol. 30, pp. 209–216. (PDF)

    HowPlantsWork © 2008-2014 All Rights Reserved.

  • “..And all the leaves on the trees are falling
    To the sound of the breezes that blow…”

    - Van Morrison

    How Can I Miss You, If You Won’t Go Away?

    Ah, November in the Pacific Northwest, when the autumn leaves are being scoured from the trees by blustery winds and driving rain,… and a plant physiologist’s thoughts turn to….abscission. Yes, abscission.

    You probably already knew that abscission refers to the process by which a plant sheds one or more of its parts, such as a leaf, fruit, flower, or seed. (“Abscission”, from the Latin “ab“, meaning “away“, and “scindere“, meaning “to cut“.)

    The shedding of autumn leaves, the dropping of petals from an old rose flower, and the dispersal of dandelion seeds in the wind are all the result of abscission in plants.

    Why do plants do this?

    It’s because abscission “…can limit the spread of systemic invasion by pathogens, provide a mechanism to remove damaged or inefficiently functioning tissues, remove competition for pollinators from fertilized flowers, and contribute to seed dispersal in dry and fleshy fruits.” (from Ref. 1 below)

    And why should anybody care about this?

    The timing of flower and fruit abscission is a process of substantial interest to the horticultural and agricultural industries, as it can affect both the quantity and quality of yield.” (from Ref. 1 below)

    Some basic information about abscission was explored in a previous post.

    Basically, the story goes like this: During plant development, the plant will form a so-called abscission zone (AZ) typically in a region at the base of a leaf, flower, fruit, or other plant part. Later on (often months later), the activation of the plant cells in the AZ by certain signals (primarily the plant hormone ethylene) ultimately results in the separation of that part from the plant body.

    There are many questions about the cellular mechanisms of abscission that remain unanswered. Such as: How does the plant “pre-determine” which of its parts to shed? (Why shed leaves, for example?); What triggers abscission?; What genes are directly involved the separation process?

    Even from the simplification of abscission depicted in the illustration below, it appears likely that multiple pathways and processes must somehow be integrated to bring about abscission in plants.

    The basic story of abscission (by the way, the little green circles are plant cells) – a simplified version of Fig. 2 from Ref. 2 below.

    1 s2 0 S0168945212002191 gr2

    Plant scientists have used different approaches – physiological and genetic – to discover various parts of the story. The challenge, of course, is fitting all the pieces together in order to reveal the “big-picture” of abscission’s “clockwork”. When I last investigated this a few years ago, many parts of the story were missing, and, also, it was unclear how some of the parts actually fit into the story.

    Several reviews have been published in the past couple of years regarding recent (past decade or so) research into the mechanisms of abscission in plants. Two that are openly accessible online are Refs. 2 and 3 below. (Many thanks to the publishers of these journals, by the way, for allowing such open access.)

    I read these and a couple of other such reviews (so that you don’t have to). What I found out was a bit encouraging, but also a bit disappointing.

    Next Time: What’s new about abscission. (The good, the bad , and the ugly.)

    References

    1. Basu, M. M., Z. H. González-Carranza, S. Azam-Ali, S. Tang, A. A. Shahid and J. A. Roberts (2013) “The manipulation of auxin in the abscission zone cells of Arabidopsis flowers reveals that indoleacetic acid signaling is a prerequisite for organ shedding.” Plant Physiology, Vol. 162, pp. 96-106. (Full Text)

    2. Estornell, L. H., J. Agustí, P. Merelo, M. Talón, and F. R. Tadeo (2013) “Elucidating mechanisms underlying organ abscission.”, Plant Science, Vols. 199–200, pp. 48–60. (Full Text)

    3. Chad E. Niederhuth, Sung Ki Cho, Kati Seitz, and John C. Walker (2013) “Letting go is never easy: Abscission and receptor-like protein kinases.” Journal of Integrative Plant Biology, Vol. 55, pp. 1251–1263. (Full Text)

    HowPlantsWork © 2008-2014 All Rights Reserved.

    m4s0n501

    We’re In A Jam

    Let’s face it, humanity is NOT going to back off anytime soon on it’s production of greenhouse gases, especially carbon dioxide from the combustion of fossil fuels.

    Just last year, for example, atmospheric CO2 emissions increased at their fastest rate for 30 years.

    So, how are we to respond to the agricultural challenges posed by the forthcoming high-CO2 (and probably much warmer) world?

    Devoting a lot of research time and effort to developing biofuels is probably NOT the answer (see here, for example).

    Perhaps a better approach would be to learn as much as we can about how plants respond to high CO2 (and to high temperatures) and to use this basic knowledge in developing the crops of the future.

    A paper published in the journal Nature last July (see Ref. 1 below) is a good example of what I’m talking about.

    In a previous post I said that elevated levels of CO2 may decrease the ability of many plants to cope with heat stress. But not for the reason that you might think. Here’s a good explanation:

    “For each carbon dioxide molecule that is incorporated into plants through photosynthesis, plants lose about 200 hundred molecules of water through their stomata,” explains Julian Schroeder, a professor of biology who headed the research effort. “Because elevated CO2 reduces the density of stomatal pores in leaves, this is, at first sight beneficial for plants as they would lose less water. However, the reduction in the numbers of stomatal pores decreases the ability of plants to cool their leaves during a heat wave via water evaporation. Less evaporation adds to heat stress in plants, which ultimately affects crop yield.” (From: Ref. 2 below)

    Scanning electron micrograph of leaf surface featuring stomata.

    Scanning electron micrograph of leaf surface featuring stomata.

    Simply put, because of this research, we now have a much better understanding of the genes involved in controlling the development of stomata in plants.

    What are some of the implications to future crop development of this research?

    “The discoveries of these proteins and genes have the potential to address a wide range of critical agricultural problems in the future, including the limited availability of water for crops, the need to increase water use efficiency in lawns as well as crops and concerns among farmers about the impact heat stress will have in their crops as global temperatures and CO2 levels continue to rise.
    “At a time where the pressing issues of climate change and inherent agronomic consequences which are mediated by the continuing atmospheric CO2 rise are palpable, these advances could become of interest to crop biologists and climate change modelers,” says Engineer.
    (From: Ref. 2 below)

    So, can we bioengineer plants for a high-CO2 world?

    I think the answer is: YES!

    But to do so effectively, we will need lots more basic knowledge about plants, such as that recently provided by the Schroeder research lab at UCSD (Ref. 1 below).

    Bottom Line: We are currently spending hundreds of millions of dollars on plant biofuels research. Perhaps this money would be better spent on basic research aimed at understanding (and at preparing for) the effects of high CO2 on plants. (Or better yet, increase funding for basic plant research to levels equivalent to the amount we spend on biofuels research.)

    References

    1. Engineer, C. B., M. Ghassemian, J. C. Anderson, S. C. Pack, H. Hu, and J. I. Schroeder (2014) “Carbonic anhydrases, EPF2 and a novel protease mediate CO2 control of stomatal development.” Nature, Vol. 513, pp. 246-250. (Abstract)

    2. Kim McDonald (2014) “Discovery provides insights on how plants respond to elevated CO2 levels.” Press Release (July 6, 2014), UC San Diego News Center. Full Text

    HowPlantsWork © 2008-2014 All Rights Reserved.

    Back To The Eocene?

    eocene_rainforest2

    From Anthropocene To Eocene II?

    A mountainside near where I live gave way in January 2009 (as a result of torrential rains) resulting in Racehorse Creek rock slide.

    This landslide revealed a treasure-trove of fossils, mainly 55-million-year old fossils of plants that were alive during the Eocene. Most interestingly, perhaps, this time corresponds to to a period called the Paleocene–Eocene Thermal Maximum (PETM), which is characterized by a rapid (about 20,000 years) increase in atmospheric CO2 (primarily of volcanic origin) and global warming.

    On a recent trip to the Racehorse fossil field, I couldn’t help thinking that not only was I revisiting the Eocene but also maybe getting a glimpse of what the predominant plant life may look like here in the Pacific northwest in a few thousands of years.

    Do these Eocene plant fossils provide clues to the ultimate botanical outcomes of the Anthropocene?

    Related Links:

  • The BBC view of the Eocene
  • Could human CO2 emissions cause another PETM?
  • The Emerald Planet
  • HowPlantsWork © 2008-2014 All Rights Reserved.

    By 2050, What Will Be The Greatest Human Impact on Plants?

    I first encountered the term “anthropocene” back in 2007 when I was writing a manuscript regarding some of our research in Yellowstone National Park (see Ref. 1 below).

    A more detailed view regarding the nature and implications of the anthropocene is presented on YouTube here. Yet another YouTube video that’s a bit more technical can be viewed here. (And if you’re really pressed for time, then check out this 2-min YouTube video.)

    If you’ve watched any of these videos, then you probably have a pretty good basic understanding of the anthropocene. If you didn’t, then the anthropocene can be briefly defined as the current geologic age in which “…human impacts such as land use and industrial pollution have grown to become significant geological forces, frequently overwhelming natural processes.” (from Ref. 1 below)

    There are several major impacts on plants as result of the anthropocene.

  • Increase in Atmospheric Carbon Dioxide (CO2) Some of the impacts on plants are a direct result of the burning of fossil fuels. One major impact is the increase in atmospheric CO2 (please see previous post). Other effects include elevated ground-level ozone and “acid” rain, both of which can negatively impact plants.
  • “Global Weirding” The increased greenhouse gases carbon dioxide and methane resulting from the combustion of fossil fuels have significant indirect effects on plants primarily by causing significant global climate changes (e.g., drought, heat), otherwise known as “global weirding”.
  • Loss/Degradation of Native Plant Habitats Agriculture, logging and land “development” also contribute to the anthropocene not only because of increasing atmospheric CO2 but also because of causing loss of natural habitats, thus decreasing plant biodiversity, including plant extinctions. (Agriculture is also the main contributor to nitrate pollution, another attribute of the anthropocene that can decrease biodiversity.)
  • Genome Engineering Technologies And, finally, let’s not forget plant genetic engineering, which already has major impacts on agriculture and will likely have ever-increasing impacts on plants, not only within the realm of agriculture but also, perhaps, even in natural ecosystem management.

    OK, but let’s get back to the question I’m posing here: Which of the above will probably have the greatest overall impact on plants within the next 35 years?

    I’m Placing My Bet On CO2

    First off, let’s acknowledge that atmospheric CO2 levels will likely continue to increase within the next 35 years, and probably well beyond that, primarily from human activities (please see here, for example). At the current rate of increase (please see here for the data), atmospheric CO2 will likely reach 500 to 600 ppmv by 2050. (It was about 310 ppmv in 1950 and is currently at about 400 ppmv.)

    Although this may not seem like a big increase, it will likely have profound effects on plants, for several reasons.

    As mentioned in the previous post, most green plants will likely benefit photosynthetically from this increase in CO2.

    Why?

    Mainly because the enzyme in plants that captures CO2 from the atmosphere for photosynthesis is currently working at a sub-optimal rate. This is because the current level of atmospheric CO2 is so low (relative to when green plants colonized the land, for example) that it may actually limit the activity of this key enzyme, known as RuBisCo.

    Tumblr lr3navql0Q1qh1rkuLet me put it this way: Imagine that RuBisCo is like a high-performance car that can go 100 mph when you give it high-octane gasoline (petrol). But now, only low-octane gas is available, so the car can only go 50 mph max.

    By steadily increasing the CO2 available to green plants, we are enabling RuBisCo to “fix” CO2 into sugars at a faster and faster rate, resulting in improved photosynthetic productivity of the plants.

    This is great, right? More productive plants means higher crop yields, bigger vegetables, more fruit….without having to add any more fertilizer or water.

    WOOHOO!

    But wait. This isn’t the whole story…

    Other Effects of Elevated CO2 on Plants

    Increasing the rate of photosynthesis by accelerating RuBisCo is not the only effect that elevated levels of CO2 have on most green plants.

    And some of these other effects may actually negatively impact crop plants.

    Homer simpson doh

  • Decrease in Heat Resistance?
  • Elevated CO2 levels have at least two effects on leaf stomata:
    1. High CO2 tends to close stomata.
    2. High CO2 may lead to fewer stomata per leaf during plant development.

    Perhaps above all else, land plants try to minimize water loss via transpiration, which occurs mainly through the stomata. Thus, it makes sense that, if there is a relative abundance of CO2 for doing photosynthesis, plants would tend to close stomata, make fewer of them, or both.

    But isn’t this another good thing? On the one hand, yes. But on the other hand, keep in mind that leaves cool themselves via leaf transpiration through stomata. So less transpiration may mean that the plants become more susceptible to heat stress, which many believe is on the increase do to global warming. And plant heat stress typically inhibits photosynthesis. (For example, please see Ref. 4 below.)

  • Less Nutritious Crop Plants?
  • A recently published report (see Ref. 5 below) provides evidence that high-CO2 crop plants may have less protein, zinc and iron (see news report about this paper here).

    Scientists are uncertain why elevated levels of CO2 cause a decrease in zinc and iron in plants, though variation among different species indicates that it’s likely a complex mechanism. “Of all the elements, changes in nitrogen content at elevated [CO2] have been the most studied, and inhibition of photorespiration and malate production, carbohydrate dilution, slower uptake of nitrogen in roots and decreased transpiration-driven mass flow of nitrogen may all be significant.” (from Ref. 5 below)

  • Loss of Plant Biodiversity?
  • In a previous post we explored the origin of C4 plants in a past, relatively low-CO2 world and their fate in a future high-CO2 world. Though C4 plants likely arose as a result of decreased levels of atmospheric CO2, their fate is very uncertain in the face of the increasing levels of CO2 that will likely occur in the centuries to come. (If some C4 plant species are displaced by C3 species, primarily as a result of elevated levels of atmospheric CO2, then this may contribute to a loss in plant biodiversity.)

    Though it seems reasonable that many C4 plant species might lose their CO2-concentrating edge over C3 plants in relatively higher CO2 environments and be displaced, there is little evidence for this to date. Admittedly, this hypothesis is very difficult test, and, indeed, there is evidence to the contrary (e.g., see Ref. 6 below).

    Bottom Line: In 2011, I posted on how increased CO2 will affect plants. It was clear then that, because plants’ responses to elevated levels of CO2 were so significant and complex, it was difficult to make reliable predictions. Three years later, though we know more about how some crop plants will likely respond to a high-CO2 world, it’s still hard to make general predictions with high confidence. What I think is clear, however, is that, considering all the major impacts of the anthropocene, increased atmospheric CO2 will probably have the greatest overall effect on plants.

    “Prediction is very difficult, especially if it’s about the future.” – Nils Bohr, Nobel laureate in Physics

    “I never think of the future, it comes soon enough.” – Albert Einstein

    References

    1. Tercek, M. T., T. S. Al-Niemi and R. G. Stout (2008) “Plants exposed to high levels of carbon dioxide in Yellowstone National Park: A glimpse into the future?” Yellowstone Science, Vol. 16, pp. 12-19. (PDF)

    2. Terashima,I., S. Yanagisawa and H. Sakakibara (2014) “Plant responses to CO2: Background and Perspectives.” Plant & Cell Physiology, Vol. 55, pp. 237-240. (Full Text)

    3. Leakey, A. D. B., et al. (2009) “Elevated CO2 effects on plant carbon, nitrogen, and water relations: six important lessons from FACE.” Journal of Experimental Botany, Vol. 60, pp. 2859-2876. (Full Text)

    4. Ruiz-Vera, U. M., et al. (2013) “Global warming can negate the expected CO2 stimulation in photosynthesis and productivity for soybean grown in the midwestern United States.” Plant Physiology, Vol. 162, pp. 410-423 (Full Text)

    5. Myers, S. S., et al. (2014) “Increasing CO2 threatens human nutrition.” Nature, Vol. 510, pp. 139-142. (Abstract)

    6. Morgan, J. A., et al. (2011) “C4 grasses prosper as carbon dioxide eliminates desiccation in warmed semi-arid grassland.” Nature, Vol. 476, pp. 202–205. (Abstract)

    Acknowledgment

    Thanks to Prof. Lisa Ainsworth (USDA/ARS & University of Illinois) for generous input regarding the potential displacement of C4 plants by C3 plants in a high-CO2 world.

    HowPlantsWork © 2008-2014 All Rights Reserved.

    It’s All About The CO2

    Sell all your bicycles. Forget about buying a Prius®. Drive the biggest gas-guzzler you can find. Crank up that home and work air conditioning, especially if you get your electricity from coal-fired power plants.

    Yes, your houseplants – all green (photosynthetic) plants, for that matter (with, perhaps, a few exceptions) – want you to increase your carbon footprint. That is, burn as much fossil fuel as humanly possible, so that you maximize your CO2 output. This is because most green plants currently need and want more CO2.

    Why?

    Well, at the present time, most plants are “gasping” for CO2, somewhat like you would probably be “gasping” for O2 if you were hiking around Machu Picchu, at nearly 8,000 feet (2,430 meters) in elevation.

    Allow me to explain.

    When plants were colonizing the land – roughly, 400 to 500 million years ago (MYA) – Earth’s atmosphere may have had over 20 times the current level of CO2. (Please see here for atmospheric carbon dioxide through geologic time.)

    By the way, do you know what the amount of CO2 is in our atmosphere?

    In general, Earth’s atmosphere currently contains about 0.04% CO2 by volume (often expressed at 400 parts per million or ppm). Sometimes people have a hard time getting their heads around proportions expressed in this way. Most, however, can understand relative amounts of money. So let’s say that all the gases in the Earth’s atmosphere add up to $100 (analogous to 100%). If so, then carbon dioxide’s share would only amount to about four pennies. In contrast, oxygen’s share would be about $21 (or 21%).

    The early photosynthetic land plants (400 to 500 MYA) were probably luxuriating in nearly 1% atmospheric CO2, compared to today’s paltry 0.04% CO2. It’s no wonder that plants are “cheering us on” as we continue to burn fossil fuels, releasing more and more CO2 into the air.

    So, can we expect ever-increasing plant growth leading to improved crop yields as we continue to pump more CO2 into the atmosphere?

    Unfortunately, probably not.

    Why?

    Well, partly because of CO2‘s “greenhouse effect” on climate (which, I presume, you’re already familiar with) that is causing “global weirding”.

    But also, it turns out that increased atmospheric CO2 has profound short-term (minutes) and long-term (days to years) effects on plant physiology and plant development, such as a decrease in leaf stomata.

    More on this to come…

    HowPlantsWork © 2008-2014 All Rights Reserved.

    FCWhat’s That Plant? What’s That Mushroom? And More…

    On this brief tour of botanical apps, we previously had a look at Garden Compass. This plant identification app is for IOS devices, such as iPhones and iPads.

    But what about all those millions of people who use Android-based smartphones and tablets? Is there something equivalent to Garden Compass for them?

    I’m pleased to say that the answer is yes. And, somewhat surprisingly, this Android app may actually be better than Garden Compass, which I think is quite an impressive app.

    So, why may this Android app be better than Garden Compass?

    Well, for one thing, this Android app maybe useful for identifying not only garden plants, but also wild plants, and even mushrooms, mosses, and lichens.

    And, also, I prefer the way they have “monetized” this app compared to the Garden Compass model. To wit:

    Bucks For Botanists

    With Garden Compass, plant identifications are “free” (limited to 20 per month, however), but you must provide them your location and device identification information (so that they can attempt to sell you other stuff).

    Wouldn’t it be better to simply pay (say, for example, a dollar) for each plant ID?

    This is the primary monetization model used by the Android app I’ve been talking about, which is:

  • FlowerChecker

    FlowerChecker is a free (to install) plant identification app for Android devices (not yet available for iPhones and iPads, but they are working on it – from an email I received from a member of the FlowerChecker development team on 6/20/2014: “The development of iOS app starts next week so that the betaversion is expected to be released in August or September. We have a waiting list for those who want to try a betaversion — http://www.flowerchecker.com/waiting-ios (we’ll send them e-mail when it is finished)“.

  • According to the FlowerChecker website:
    This app provides plant identification service. You simply take a picture of an unknown plant (or moss, lichen and even fungi) and get it identified by international team of experts.
    The identification process is not computer-based, it requires human involvement. Therefore each identification is paid using Google’s in-app purchase. One plant identification costs 1 USD / 0.7 EUR. If we can’t identify your plant, you don’t pay anything.
    Everybody gets one identification for free as a trial.
    Our team will respond as soon as possible, but the identification usually takes minutes or hours. So far, we have been able to identify 90% plants in average.

    Please Note: Before installing the FlowerChecker app on your Android device, you should be aware that, like Garden Compass, this app can access personal information on your device, including location. (Of course, you should always carefully read the capabilities of any app before you install it on your device.)

    Anyway, I was OK with all this, and I installed the free FlowerChecker app on a Nexus 7 (2013 version), got my free identification, and prepaid for five more (prepaid, it’s $1 for one, $4.50 for five, and $15 for twenty identifications). By the way, according to an email I received from FlowerChecker, “the income is half-half divided between botanists and developers“.

    Thus, I sent FlowerChecker six different photos to test their identification skills – 3 garden plants, 2 wild plants & 1 mushroom.

    Untitled How did they do? All of the identifications were spot on.

    Briefly, here’s how FlowerChecker works:

    1. After installing and launching the app for the first time, you have one free identification credit to use.
    2. Select “New Request” and you’re then presented with a fresh screen allowing you (a) to ask a question, most commonly, “What is this plant?”, (b) to select a category, such as “garden plant”, “wild plant”, “mushroom”, etc., and (c) finally, to take a photo or to select one or more photos from your “Gallery”. (Please see here for a series of screen shots.)
    3. After you submit your request, the FlowerChecker team will process it within 24 hours.
    4. Nice Feature: Unlike Garden Compass, all of this occurs within the FlowerChecker app rather than via email.
    5. After a few hours, check back with your FlowerChecker app, and the team most likely will have processed your request and identified your plant. You don’t pay unless you accept, and, if so, then your request is marked “Resolved”.

    Two Thumbs Up (Way Up!) For FlowerChecker

    If you are looking for a plant identification app for your Android device, I highly recommend
    FlowerChecker.

    I found that their identifications were both accurate and delivered within the time they promised.

    However, as I didn’t have them try to identify any lichens or mosses, and only one mushroom, I can’t vouch for their competence in identifying these categories of “plants”.

    But, based on the positive feedback for this app posted on the Google Play store, I’m confident that the FlowerChecker team can do about as well as one could expect.

    Please keep in mind that even the best botanists can only go so far in identifying plants from merely pictures. Frankly, I’m amazed how well the FlowerChecker team did in my cases, considering that all they had to go on were my crappy photos.

    It’s said that “actions speak louder than words”. So, perhaps my most sincere endorsement is that, after using the FlowerChecker app for this blog post, I purchased 20 more identifications for $15.

    Personally, I prefer paying developers and botanists directly for their services, rather than indirectly, via advertising.

    Finally, as previously mentioned, can providing employment for botanists (and developers) be a bad thing? I think not!

    Disclaimer: I receive no financial remuneration or any other support (that I know of) from the makers of these apps.

    HowPlantsWork © 2008-2014 All Rights Reserved.

    IMG 0097What’s That Plant?

    Though I’m very interested in plants, I’m terrible at identifying plant species and remembering plant names. (That’s probably why I’m a plant physiologist.) I’m pretty sure there are other folks reading this blog that also have this “problem”.

    For people like us, wouldn’t it be great if we could take photos of plants with our smartphones or tablets and have an online botanist or horticulturist identify the plant for us? (Dream on, right?)

    But it’s not a just a dream, it’s now a reality. There are at least a couple of remarkable apps available that may help you to determine a plant from your photos.

    First up:

  • Garden Compass

    One app that I’ve recently used is Garden Compass (Compatible with iPhone, iPad, and iPod touch and requires iOS 6.0 or later. This app is optimized for iPhone 5.)

    To visit the Garden Compass website, click here, and to watch a 90-second video about this app, please click here.

  • Here’s the way it works:
    (1) After installing the app, you can take a photo inside the app or select a photo from your camera role. (Note: The first time you use the plant identification function, the app asks your permission to access your camera role. The app may also ask you to turn on location services under the “Privacy” settings on your device – this turns on the GPS.)
    (2) Once you snap a photo or select a picture from your camera roll, a text box appears below the photo to allow you to add comments about the plant.
    (3) When you touch the “send e-mail” button, the app will likely ask you for permission to use your location. (This, I presume, is mainly to help them ID the plant. But I notice that after you send e-mail, the app asks you if you want to see closest garden retailers in your area. So this is likely part of how they make money. More about this below.)
    (4) If you are okay with the app using your location, then you are redirected to your e-mail app where you can see/edit your draft e-mail message before you send it to Garden Compass. (I noticed that not only is your geolocation included in the e-mail but also your device ID.) If you’re cool with this (I didn’t mind), then touch “Send” and your e-mail message blasts off into the “cloud”.
    (5) If Garden Compass has received your e-mail message, you will receive e-mail confirmation within a few minutes. They also tell you what position you are in their queue. (The times I used Garden Compass, I ended up with 500 to 600 people ahead of me.)
    (6) Despite the long line ahead of me, I received e-mail messages from Garden Compass with my plant identifications in under 5 hours. Each was spot on.

    Two thumbs up for Garden Compass

    I must say I was pretty impressed with the Garden Compass app, and I didn’t even use all of its features. In addition to garden plant ID, they also provide a “Problem ID” service. This is to help you identify plant diseases or plant insect pests. Since I didn’t use this feature I can’t comment on its accuracy.

    I also can’t comment on how well this app works on the identification of wild plants. I presume their aim is mostly restricted to domesticated plants.

    Since this app is free, you may be wondering how they monetize it. Well, along with providing you plant information, they also facilitate you buying stuff, mainly from them. This app is part of a larger venture called Garden Compass that you can read about here.

    Perhaps the Garden Compass app is a marketing strategy for the Garden Compass online store. If so, it may be a brilliant one. My hat’s off to them, because, in my experience, this app delivers accurate garden plant IDs within several hours…for “free”. (Yes, you do provide them your information, however, and photo submissions are limited to 20 per month.)

    But can providing employment for botanists and horticulturists be bad? I think not.

    Next Time: Another plant identification app…for Android devices.

    Disclaimer: I receive no financial remuneration or any other support (that I know of) from the makers of these apps.

    HowPlantsWork © 2008-2014 All Rights Reserved.

    There’s An App For That?

    I can’t believe it’s only been seven years since the iPhone was first introduced by Steve Jobs in 2007 and only four years since Jobs introduced the iPad.

    Since then, hundreds of millions of iPhones and iPads have been sold, and dozens of other types mobile-computing devices with cameras have been developed and sold in the millions.

    And as you can see if you cruise through the iTunes App store or through Google Play app store, software developers have been busy filling virtually every imaginable niche with computer applications for your smartphone or tablet.

    Among these hundreds of thousands of different apps are some that are botany related. What I’d like to do is offer you a sampling of some of my favorite plant-related apps.

    (Please Note: This is NOT a comprehensive list of plant-related apps. And most of such apps I’ve used are for North America (particularly the U.S.) because that’s where I live. There are lots of other botany-related apps out there, which you can find by searching online, including the various app stores.)

    OK. Here we go……

  • leafsnap
  • Way back in 2011, I scribbled a post about one of the earliest botany-related iPhone apps leafsnap.

    Well, leafsnap is still available (requires iOS 4.2 or later. Compatible with iPhone, iPad, and iPod touch), and it’s only gotten better.

    (And now there’s even a version for our friends in the UK, named, appropriately, leafsnap UK.)

    Simply put, leafsnap helps you identify trees from snaps (photos) of leaves that you take with your smartphone or tablet.

    Leafsnap works by using technology similar to facial-recognition software, by matching a simple photograph of a leaf against a database of tree species.

    Perhaps the best place to go in order to understand and to use leafsnap is Leafsnap: An Electronic Field Guide.

    According to the leafsnap website and iTunes app store: “Leafsnap currently includes the trees of the Northeast and will soon grow to include the trees of the entire continental United States.

    Did I mention that leafsnap is a FREE app?

  • HighCountry Apps

    Slide 1If you live in the Western United States or plan to visit there this summer, and you’re interested in electronic field guides of the wildflower kind for your smartphone or tablet, you should probably check out HighCountry Apps.

    These folks provide wildflower field guide apps not only for the major national parks such as Yellowstone, Glacier and Yosemite, but also for the states of Idaho, Colorado and Washington.

    Newly added for 2014 are apps for the wildflowers of Oregon state and also for the grasses of Montana. (I suspect my former colleague Prof. Matt Lavin may have had something to do with the Montana grass guide.)

    I’ve used their Washington state wildflower guide app, and I think it’s great. (But don’t take my word for it. Check out the many positive reviews on their website and the various app stores.)

    Most of the Highcountry apps cost $7.99. All of them work on iPhone, iPad, and Android devices, and many of them also work on the Kindle Fire.

    Quoting from their website: “High Country Apps is dedicated to developing applications that deliver high quality natural history information with an intuitive, easy-to-use interface. Our goal is to enable discovery! We present information in simple, non-technical language that will delight and empower the rank amateur who loves the outdoors and wants to learn more. Yet we are also meticulous about creating scientifically accurate apps, thus making them excellent tools for serious biologists.”

    Disclaimer: I receive no financial remuneration nor any other support (that I know of) from the makers of these apps.

    HowPlantsWork © 2008-2014 All Rights Reserved.

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