Resolution of Plants over time.

This is a follow on to last week’s post, here.

Last week I wrote about two papers from The Plant Cell about how plant cells figure out their identity.

Root meristem resolution in the 19th century (see this post for more about this image & where it’s led. Image from page 478 of “Arbeiten des Botanischen instituts in Würzburg” (1888). Author: Julius Sachs.

As part of that, I looked back in the archives of Plant Physiology (first issue 90 years ago– 1926) and The Plant Cell (first issue 1989) and scrolled through their table of contents until I found the first papers ever about root meristems (or root apices). There was one in the first issue of The Plant Cell. In Plant Physiology, that started publishing quarterly, I had to go through several issues. There were a few papers about root architecture as a whole, including one about sugar cane grown in various places in Hawaii. Then I found a paper from University of Minnesota scientists about how plants need Boron to properly develop with images of root apexes/meristems from peas (Pisum sativum)1.

Even in 1928, scientists were seeking ever finer insight into how plants work and building upon previous work:

“The great bulk of the research on the influence of the different essential elements on the development of the plant has employed, as a sole criterion, the mass of tissue produced by plants grown in solutions of varying composition and concentration. This represents only a limited front of attack on the general problem. An ultimate goal should be the determination of the actual rOle of each of the elements in the metabolism of the plant, and the consequent influence of these elements on the morphology of the cell and of the tissues.”

Root meristem resolution in the 19th century (see this post for more about this image & where it’s led. Image from page 478 of “Arbeiten des Botanischen instituts in Würzburg” (1888). Author: Julius Sachs.
From figure 3 of Dietrich et al. 1989 Plant Cell showing in-situ hybridization in root meristems of Brassica napus (darker areas mark where this gene is expressed)


In 1928, scientists knew what DNA and proteins existed,  and that genes- discrete factors on chromosomes- were units of inheritance but had no idea how they worked or stored information.

By 1989, we knew something of how genes worked and recombinant DNA technology existed, but was still only a little over a decade old. Dietrich et al. at UC Davis had sequences of 3 genes and explored their expression patterns in young Brassica napus (Canola/oilseed) seedlings2. They found some tissue specificity for some of the genes (see figure at right). What is amazing is that for one of the genes they had a sequence, they did not have any idea what kind of protein that gene coded for. They could predict a protein sequence, but didn’t have anything in databases in 1989 to compare it to.

The technique of in-situ hybridization is still around, as Molly Edwards of Science IRL demonstrates in her recent video. You may note in the video that the resolution of Molly’s in-situ hybridization is also much better than the ones at left.

It was also fun reading Plant Physiology’s first editor-in-chief’s 1926 opening letter about how articles in Plant Physiology should be structured. It has this passage3:


If C.A. Shull thought it was hard keeping up with the literature and technology in 1926, he might well have had an instant panic attack if placed in today’s academia (this is no disrespect to CA Shull as a scientist…but I imagine he’d get overwhelmed by today’s amount of knowledge).

The two papers from last week’s post and these early Plant Physiology and Plant Cell papers tell a story about the level of resolution we have into plant cells now compared to 90 and 27 years ago. The Plant Cell papers from 2016 are good science, but they are also routine molecular biology papers these days complete with confocal microscope images, proteins with fluorescent tags, and an integration of physiology and localized gene expression analyses.

WTmeristemDMSO copy
A propidum iodide stained root meristem imaged under a confocal microscope. Photo credit: Ian Street

These papers also track another arc in 20th-21st century plant science, the hour-glass like shape of using many plants for studies that led to a huge dominance of Arabidopsis as a model organism in the late 80’s/early 90’s to today where technology has opened up the number of plants scientists can ask questions about. A lot of the new work is built on Arabidopsis, which remains a popular reference organism, however, it is no longer surprising to read scientific papers about a lot more different plants serving as better models for some plant behaviors/lifestyles than Arabidopsis. Technologies like high-throughput (as in whole genome level) sequencing have enabled doing experiments on many more plant species (as well as gene prospecting).

The cover of Science a few weeks ago announced the discovery of just how sunflowers track the sun as they grow and then stop once fully mature and remain in a specific orientation, towards the rising sun4. The Berkeley scientists show that the circadian clock controls the distribution of auxin across the growing stem causing the solar tracking.

Science Cover5Aug
Cover of August 5 issue of Science featuring sunflower heliotropism.

Genome sequences of over 100 plants now exist, with over 100,000 having at least one sequence in Genbank. These are critical reference maps for designing experiments where specific gene expression will be tracked. It is also now possible to track global gene expression of a plant under various conditions.

Scientists have also figured out how to stably transform– make transgenic– more and more plant species. Making a plant transgenic with, for instance, fluorescent protein tagged genes of interest is one thing that made Arabidopsis such a dominant organism in plant science. Arabidopsis, eventually, was found to be readily transformed by the floral dip method, literally dipping flower buds of Arabidopsis plants in a solution of Agrobacterium tumifaciens containing the segment of DNA a scientist wants in the plant. After a few generations of selection, several lines containing and stably expressing the transgene can be used in experiments5.

Transgenesis and other technologies that make manipulating and moving DNA easier opens up all sorts of possibilities for research. The DNA encoding Fluorescent genes from jellyfish like Green Fluorescent Protein (GFP) can be fused to the DNA encoding a plant gene of interest, making it fluoresce where its expressed in the plant, as seen under a properly equipped microscope.

There are still frontiers and new technology that will become standard scientific tools (RNAseq and whole genome sequencing are rapidly becoming those). The curiosity of scientists leads to new tools (sometimes high tech, sometimes simple ‘MacGyvered’ solutions). CRISPR and other new DNA modifying technologies are the more precise future of not only plant modification, but opens the door to all sorts of living things as this In a Nutshell video talks about. There are of course social and ethical issues that have to be considered and these are what On Being host Krista Tippett calls ‘spiritual technologies’.

Humans are in the privileged position to build, design, and think about our environment. We can ask questions and have generated a massive amount of knowledge that we’ve applied, re-mixed, and iterated. Agriculture was a key milestone in freeing some humans to specialize. It’s become too much for any one person to keep up with, or even be aware of. The explosion of knowledge over the past 100 years and the technological innovation is truly stunning and calls for even better communication between scientists and the rest of the world.

Bit by bit, these advances in knowledge and technology have built today’s world and are building the one we’ll exist in tomorrow. Plant sciences are no exception to that. Scientists right now are pushing frontiers and it is not easy– technologically or creatively. Even if it is hard, scientists press on mapping the unknowns of the complex world, applying what is hopefully a responsible curiosity.


  2.  R A Dietrich, D J Maslyar, R C Heupel, and J J Harada. 1989. Spatial patterns of gene expression in Brassica napus seedlings: identification of a cortex-specific gene and localization of mRNAs encoding isocitrate lyase and a polypeptide homologous to proteinases. Plant Cell 1: 73-80. doi:10.1105/tpc.1.1.73
  3. C. A. Shull. Scientific Publication. 1926. Plant Physiol. January 1: 9091. doi:10.1104/pp.1.1.90
  4. Atamian H.S., Creux N.M., Brown E.A., Garner A.G., Blackman B.K., Harmer S.L. Circadian regulation of sunflower heliotropism, floral orientation, and pollinator visits. 2016. Science 353:587-590. doi: 10.1126/science.aaf9793
  5. Clough S.J. and Bent A.F. 1998. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16:735-743. doi: 10.1046/j.1365-313x.1998.00343.x

This post has been updated 2016/08/17: the title was changed to better reflect the topic of the post and some text added.

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