AJB Special Issue on Tropisms

I am honored to have a paper in this month’s American Journal of Botany, a special issue focused on plant tropisms. Below is a collection of links highlighting some of the work:

Scientists join forces to bring plant movement to light:

Elementary school students often learn that plants grow toward the light. This seems straightforward, but in reality, the genes and pathways that allow plants to grow and move in response to their environment are not fully understood. Leading plant scientists explore one of the most fundamental processes in plant biology—plant movement in response to light, water, and gravity—in a January Special Issue of the American Journal of Botany.

Low Phosphate Alters Lateral Root Setpoint Angle and Gravitropism (our paper):

Lateral root orientation and gravitropism are affected by Pi status and may provide an important additional parameter for describing root responses to low Pi. The data also support the conclusion that gravitropic setpoint angle reacts to nutrient status and is under dynamic regulation.

I’ll post again on the work that went into our paper, including a breakdown of the inputs of time and talent that made this work possible. In short though, three awesome students worked many hours in the lab over the course of four years to produce these insights.

All crops are genetically modified

A few days ago Kevin Folta, a colleague whose main research focuses on strawberry genetics and crop improvement, tweeted a link to an interview he did with HuffPost Science. The video sums up a lot of the same ideas I try to communicate in my classes about genetically-modified foods, both their risks and their benefits. The post on HuffPo Science has received almost 2000 comments as of this writing, so it clearly struck a nerve.

One of the points he makes is that humans have been doing genetic modification for tens of thousands of years. All of our crop plants are the result of mutation, selection, natural hybridization, and in some cases, deliberate hybridization. There is no such thing as ‘natural corn’ — it is the product of human civilization and could not survive without us. And when genetic modification happens naturally or through traditional plant breeding, whole genomes are scrambled. Modern genetic engineering allows targeted access to a single gene at a time, either by inserting a new, well-studied gene into a plant, or regulating the expression of an existing gene. But for some reason, the backlash against the modern, targeted approach is far beyond that of other techniques.

Sometimes the backlash is motivated by a disdain for the large companies that control so much of our food supply (and our politicians). But there is also a genuine fear that scientists are messing around with things they don’t understand and it will kill us all, or at least seriously mess up our lives and environments. I am all in favor of testing new crops for human and environmental safety. I believe crop biotechnology deserves neither a free pass nor impossible regulations. To hold transgenic crops to a standard that they be proven to do no harm to an ecosystem (an effectively impossible claim to uphold) when no other crop has ever been held to such a standard is hypocritical.

Journal impact factor losing impact

George Lozano, blogging about a recent study he published on journal impact facors:

Furthermore, we found that until 1990, of all papers, the proportion of top (i.e., most cited) papers published in the top (i.e., highest IF) journals had been increasing. So, the top journals were becoming the exclusive depositories of the most cited research. However, since 1991 the pattern has been the exact opposite. Among top papers, the proportion NOT published in top journals was decreasing, but now it is increasing. Hence, the best (i.e., most cited) work now comes from increasingly diverse sources, irrespective of the journals’ IFs.

To me, this is an indicator of the power of, first scholarly databases, then the internet, to make important work more discoverable. When I began graduate school, I remember doing literature work in the library and watching all the faculty come for their weekly journal check-in to “stay current” (or name-check themselves and their pals). How much more efficient and effective it is now to rely on things like saved database searches to keep us informed of important advances in our field. And database searches democratize by returning all related citations, not just those from so-called top-tier journals. This is a great step forward, I think.

Coverage of tomato discovery also tastes like cardboard

Yesterday saw a flurry of reports about a new article in Science on tomato flavor, or the lack thereof. Here are a few:

While it’s great to see such widespread coverage of a plant science discovery, as I read through each report I couldn’t help but notice the disconnect between the bold titles and the substance of each article.

Here is the science: the researchers found the molecular identity of a historical mutation in fruit development that plant breeders have selected for that makes the fruits more uniform in color and lighter green. The gene encodes a transcription factor that controls chloroplast development. When mutated, as in almost all cultivated tomatoes, it leads to fruits with fewer chloroplasts, which explains the lighter, more uniform coloration. It also leads to lower carbohydrate and pigment concentrations, which the researchers suggest could impact flavor.

The problem with the bold article titles is, the flavor of a tomato is much, much more complex than its sugar content. Tomatoes contain over 400 volatile compounds, each of which interacts with the others and nonvolatile compounds to produce the overall flavor profile. Understanding how each of those hundreds of molecules is formed and processed in the fruit throughout ripening is likely to yield better tasting tomatoes, and maybe having more total carbohydrates will be a part of that process. But the original article didn’t even begin to explore flavor, so why is that the take-home message of all the news pieces?

To me, the Science paper is extremely interesting, but not for the reasons highlighted in these articles. This is a case of classical breeding carrying out selection on a trait that seemed to improve the crop, at least from the standpoint of the grower, making it more consistent and easier to market. But now that we know what (in the molecular sense) they were selecting, we can see it was probably a poor tradeoff. This is yet another in a long line of links between classical breeding choices and molecular genetics, and this represents an excellent way to educate the public that all of our food is genetically modified! It all has DNA! Genes, even! I continue to be fascinated as we uncover the ancient — and recent — mutations that produced the foods we know, and I think it provides a great chance to inform and begin a dialog over the nature of farming, breeding, and genetics.

Gravitropism goes mainstream

How Do Plants Know Which Way Is Up And Which Way Is Down?:

Think of a seed buried in a pot (…) It’s dark down there in the potting soil. There’s no light, no sunshine. So how does it know which way is up and which way is down? It does know. Seeds routinely send shoots up toward the sky, and roots the other way. Darkness doesn’t confuse them. Somehow, they get it right…

As the resident expert on gravitropism, I had several friends send me this link, excited that they “knew all about this”. Krulwich takes this example from David Chamovitz’s new book, What a Plant Knows. He goes on to explain in words and drawings the concept of the starch-statolith theory of gravity sensing in plants. It’s an old concept that continues bearing fruitful research, as demonstrated by our recent work studying gravitropism in a starchless mutant.

The links between food, water, and climate change

By 2030, the gap between global water supply and demand is projected to be 40%, with much of the excess need due to agriculture. World population is projected to reach 10 billion by 2050, demanding greater yields in crop productivity than the current trends project. The water problem and the food problem are both occurring against the backdrop of global climate change, which exacerbates both problems and demands radical new approaches to solve these problems because of the need to cut greenhouse gas emissions.

This unholy trio of factors was highlighted in a talk by Sir John Beddington, UK Chief Scientific Adviser, at the UK Plant Sciences 2012 meeting, which he used as a point of departure for discussing the vital need for plant science research. If I had to boil down his talk into a concise summary, it would be that we need to produce more food with less greenhouse gas emission and less water on the same acreage within the next two decades. Of course none of this is news, but this talk brings all the pieces together in a single place nicely. In addition to pointing out the dangerous position humanity is in, Beddington suggests a few areas of plant science research that could address some of these issues. The rest of the conference was presumably concerned with a more detailed look at solutions, from what I can glean from the list of titles available. I’m embedding the video below and plan to write more about the areas of plant science involved in the future.

Flowering out of sync

image of pear flowers
All dressed up, but nobody's coming over. This pear's pollinators are not showing up.
As you may have noticed if you live around here, spring came really early this year. In fact, winter barely came at all, so spring has kind of been brewing since late February. But temps were in the 80’s several days this week, so spring seemed to arrive for real this week. Our silver maple began flowering a couple weeks ago, and this week our two Cleveland Select pears burst into flower. As I was walking past/under the trees, holding my breath to avoid the rank odor they emit, I noticed something unexpected. Actually, what I noticed was nothing: there was not the usual cloud of tiny flying things around the flower clusters. I’ve now spent ten or so minutes each day over the last three days observing the flowers, and I’ve counted a grand total of 3 insects.

Let me acknowledge that I am not an expert in pollinator interactions, not by a long shot. [Note: for a real treat on these kinds of natural history and phenology topics, you should read Rebecca in the Woods.] It could well be that I’m just there watching at the wrong time of day, or mis-remembering past years’ pollinators, but I don’t think so. I think what I’m observing is a plant flowering far earlier than usual due to above-average temperatures. Meanwhile, its usual pollinators aren’t yet active. I think we can probably add this to the list of unexpected results of global climate change. In our case, I’m excited at the prospect of this tree not producing fruits — they’re messy and kind of a pain. But imagine if this were a fruit tree, or a whole orchard of fruit trees with no pollinators. Yikes.

Finally some patent sanity

I’ve been casually following the litigation related to the patent mess surrounding BRCA1 and BRCA2 (see here and here for my previous comments). In short, those are two human genes linked to an increased likelihood of developing breast cancer. Their sequences were patented some years ago by the University of Utah, where they were identified, and exclusively licensed to a private company called Myriad Genetics.

Today, the US Supreme Court ruled on a separate but related case covering a patent for a medical diagnostic test. The Court found the patent invalid because it was not far removed from natural processes, which are not patentable. Experts in biotech patent law suspect that this ruling may set precedent that extends to the BRCA1 case. This would be a welcome development, and a sign of sanity in the fairly insane world that is the US patent system.

Memory of past insults

Memory of past insults:

In this sea of unknowns, there is at least one take-home message: epigenetic factors appear to be the vehicle by which plants transfer defense memories to offspring. Further evidence for this comes from the finding that the “grandchildren” of exposed plants inherit the defense memory, but the fourth generation does not. “The observation that inherited resistance reverts after three generations suggests the underlying mechanism is not a mutation or another stable genetic change,” says Georg Jander, a biologist at the Boyce Thompson Institute in Ithaca, NY who partnered with Rasmann.