Tag Archives: plants

Are plants and brains alike?

The answer to the question about whether brains and plants are alike is the standard ‘yes and no’. That said, there are some startling similarities from a statistical perspective (from a July 6, 2017 Salk Institute news release (also received via email; Note: Links have been removed),

Plants and brains are more alike than you might think: Salk scientists discovered that the mathematical rules governing how plants grow are similar to how brain cells sprout connections. The new work, published in Current Biology on July 6, 2017, and based on data from 3D laser scanning of plants, suggests there may be universal rules of logic governing branching growth across many biological systems.

“Our project was motivated by the question of whether, despite all the diversity we see in plant forms, there is some form or structure they all share,” says Saket Navlakha, assistant professor in Salk’s Center for Integrative Biology and senior author of the paper. “We discovered that there is—and, surprisingly, the variation in how branches are distributed in space can be described mathematically by something called a Gaussian function, which is also known as a bell curve.”

Being immobile, plants have to find creative strategies for adjusting their architecture to address environmental challenges, like being shaded by a neighbor. The diversity in plant forms, from towering redwoods to creeping thyme, is a visible sign of these strategies, but Navlakha wondered if there was some unseen organizing principle at work. To find out, his team used high-precision 3D scanning technology to measure the architecture of young plants over time and quantify their growth in ways that could be analyzed mathematically.

“This collaboration arose from a conversation that Saket and I had shortly after his arrival at Salk,” says Professor and Director of the Plant Molecular and Cellular Biology Laboratory Joanne Chory, who, along with being the Howard H. and Maryam R. Newman Chair in Plant Biology, is also a Howard Hughes Medical Investigator and one of the paper’s coauthors. “We were able to fund our studies thanks to Salk’s innovation grant program and the Howard Hughes Medical Institute.”

The team began with three agriculturally valuable crops: sorghum, tomato and tobacco. The researchers grew the plants from seeds under conditions the plants might experience naturally (shade, ambient light, high light, high heat and drought). Every few days for a month, first author Adam Conn scanned each plant to digitally capture its growth. In all, Conn scanned almost 600 plants.

“We basically scanned the plants like you would scan a piece of paper,” says Conn, a Salk research assistant. “But in this case the technology is 3D and allows us to capture a complete form—the full architecture of how the plant grows and distributes branches in space.”

From left: Adam Conn and Saket Navlakha
From left: Adam Conn and Saket Navlakha Credit: Salk Institute

Each plant’s digital representation is called a point cloud, a set of 3D coordinates in space that can be analyzed computationally. With the new data, the team built a statistical description of theoretically possible plant shapes by studying the plant’s branch density function. The branch density function depicts the likelihood of finding a branch at any point in the space surrounding a plant.

This model revealed three properties of growth: separability, self-similarity and a Gaussian branch density function. Separability means that growth in one spatial direction is independent of growth in other directions. According to Navlakha, this property means that growth is very simple and modular, which may let plants be more resilient to changes in their environment. Self-similarity means that all the plants have the same underlying shape, even though some plants may be stretched a little more in one direction, or squeezed in another direction. In other words, plants don’t use different statistical rules to grow in shade than they do to grow in bright light. Lastly, the team found that, regardless of plant species or growth conditions, branch density data followed a Gaussian distribution that is truncated at the boundary of the plant. Basically, this says that branch growth is densest near the plant’s center and gets less dense farther out following a bell curve.

The high level of evolutionary efficiency suggested by these properties is surprising. Even though it would be inefficient for plants to evolve different growth rules for every type of environmental condition, the researchers did not expect to find that plants would be so efficient as to develop only a single functional form. The properties they identified in this work may help researchers evaluate new strategies for genetically engineering crops.

Previous work by one of the paper’s authors, Charles Stevens, a professor in Salk’s Molecular Neurobiology Laboratory, found the same three mathematical properties at work in brain neurons. “The similarity between neuronal arbors and plant shoots is quite striking, and it seems like there must be an underlying reason,” says Stevens. “Probably, they both need to cover a territory as completely as possible but in a very sparse way so they don’t interfere with each other.”

The next challenge for the team is to identify what might be some of the mechanisms at the molecular level driving these changes. Navlakha adds, “We could see whether these principles deviate in other agricultural species and maybe use that knowledge in selecting plants to improve crop yields.”

Should you not be able to access the news release, you can find the information in a July 6, 2017 news item on ScienceDaily.

For the paper, here’s a link and a citation,

A Statistical Description of Plant Shoot Architecture by Adam Conn, Ullas V. Pedmale4, Joanne Chory, Charles F. Stevens, Saket Navlakha. Current Biology DOI: http://dx.doi.org/10.1016/j.cub.2017.06.009 Publication stage: In Press Corrected Proof July 2017

This paper is behind a paywall.

Here’s an image that illustrates the principles the researchers are attempting to establish,

This illustration represents how plants use the same rules to grow under widely different conditions (for example, cloudy versus sunny), and that the density of branches in space follows a Gaussian (“bell curve”) distribution, which is also true of neuronal branches in the brain. Credit: Salk Institute

Tree-on-a-chip

It’s usually organ-on-a-chip or lab-on-a-chip or human-on-a-chip; this is my first tree-on-a-chip.

Engineers have designed a microfluidic device they call a “tree-on-a-chip,” which mimics the pumping mechanism of trees and other plants. Courtesy: MIT

From a March 20, 2017 news item on phys.org,

Trees and other plants, from towering redwoods to diminutive daisies, are nature’s hydraulic pumps. They are constantly pulling water up from their roots to the topmost leaves, and pumping sugars produced by their leaves back down to the roots. This constant stream of nutrients is shuttled through a system of tissues called xylem and phloem, which are packed together in woody, parallel conduits.

Now engineers at MIT [Massachusetts Institute of Technology] and their collaborators have designed a microfluidic device they call a “tree-on-a-chip,” which mimics the pumping mechanism of trees and plants. Like its natural counterparts, the chip operates passively, requiring no moving parts or external pumps. It is able to pump water and sugars through the chip at a steady flow rate for several days. The results are published this week in Nature Plants.

A March 20, 2017 MIT news release by Jennifer Chu, which originated the news item, describes the work in more detail,

Anette “Peko” Hosoi, professor and associate department head for operations in MIT’s Department of Mechanical Engineering, says the chip’s passive pumping may be leveraged as a simple hydraulic actuator for small robots. Engineers have found it difficult and expensive to make tiny, movable parts and pumps to power complex movements in small robots. The team’s new pumping mechanism may enable robots whose motions are propelled by inexpensive, sugar-powered pumps.

“The goal of this work is cheap complexity, like one sees in nature,” Hosoi says. “It’s easy to add another leaf or xylem channel in a tree. In small robotics, everything is hard, from manufacturing, to integration, to actuation. If we could make the building blocks that enable cheap complexity, that would be super exciting. I think these [microfluidic pumps] are a step in that direction.”

Hosoi’s co-authors on the paper are lead author Jean Comtet, a former graduate student in MIT’s Department of Mechanical Engineering; Kaare Jensen of the Technical University of Denmark; and Robert Turgeon and Abraham Stroock, both of Cornell University.

A hydraulic lift

The group’s tree-inspired work grew out of a project on hydraulic robots powered by pumping fluids. Hosoi was interested in designing hydraulic robots at the small scale, that could perform actions similar to much bigger robots like Boston Dynamic’s Big Dog, a four-legged, Saint Bernard-sized robot that runs and jumps over rough terrain, powered by hydraulic actuators.

“For small systems, it’s often expensive to manufacture tiny moving pieces,” Hosoi says. “So we thought, ‘What if we could make a small-scale hydraulic system that could generate large pressures, with no moving parts?’ And then we asked, ‘Does anything do this in nature?’ It turns out that trees do.”

The general understanding among biologists has been that water, propelled by surface tension, travels up a tree’s channels of xylem, then diffuses through a semipermeable membrane and down into channels of phloem that contain sugar and other nutrients.

The more sugar there is in the phloem, the more water flows from xylem to phloem to balance out the sugar-to-water gradient, in a passive process known as osmosis. The resulting water flow flushes nutrients down to the roots. Trees and plants are thought to maintain this pumping process as more water is drawn up from their roots.

“This simple model of xylem and phloem has been well-known for decades,” Hosoi says. “From a qualitative point of view, this makes sense. But when you actually run the numbers, you realize this simple model does not allow for steady flow.”

In fact, engineers have previously attempted to design tree-inspired microfluidic pumps, fabricating parts that mimic xylem and phloem. But they found that these designs quickly stopped pumping within minutes.

It was Hosoi’s student Comtet who identified a third essential part to a tree’s pumping system: its leaves, which produce sugars through photosynthesis. Comtet’s model includes this additional source of sugars that diffuse from the leaves into a plant’s phloem, increasing the sugar-to-water gradient, which in turn maintains a constant osmotic pressure, circulating water and nutrients continuously throughout a tree.

Running on sugar

With Comtet’s hypothesis in mind, Hosoi and her team designed their tree-on-a-chip, a microfluidic pump that mimics a tree’s xylem, phloem, and most importantly, its sugar-producing leaves.

To make the chip, the researchers sandwiched together two plastic slides, through which they drilled small channels to represent xylem and phloem. They filled the xylem channel with water, and the phloem channel with water and sugar, then separated the two slides with a semipermeable material to mimic the membrane between xylem and phloem. They placed another membrane over the slide containing the phloem channel, and set a sugar cube on top to represent the additional source of sugar diffusing from a tree’s leaves into the phloem. They hooked the chip up to a tube, which fed water from a tank into the chip.

With this simple setup, the chip was able to passively pump water from the tank through the chip and out into a beaker, at a constant flow rate for several days, as opposed to previous designs that only pumped for several minutes.

“As soon as we put this sugar source in, we had it running for days at a steady state,” Hosoi says. “That’s exactly what we need. We want a device we can actually put in a robot.”

Hosoi envisions that the tree-on-a-chip pump may be built into a small robot to produce hydraulically powered motions, without requiring active pumps or parts.

“If you design your robot in a smart way, you could absolutely stick a sugar cube on it and let it go,” Hosoi says.

This research was supported, in part, by the Defense Advance Research Projects Agency [DARPA].

This research’s funding connection to DARPA reminded me that MIT has an Institute of Soldier Nanotechnologies.

Getting back to the tree-on-a-chip, here’s a link to and a citation for the paper,

Passive phloem loading and long-distance transport in a synthetic tree-on-a-chip by Jean Comtet, Kaare H. Jensen, Robert Turgeon, Abraham D. Stroock & A. E. Hosoi. Nature Plants 3, Article number: 17032 (2017)  doi:10.1038/nplants.2017.32 Published online: 20 March 2017

This paper is behind a paywall.

Harvesting plants for electricity

A Feb. 27, 2017 article on Nanowerk describes research which could turn living plants into solar cells and panels (Note: Links have been removed),

Plants power life on Earth. They are the original food source supplying energy to almost all living organisms and the basis of the fossil fuels that feed the power demands of the modern world. But burning the remnants of long-dead forests is changing the world in dangerous ways. Can we better harness the power of living plants today?

One way might be to turn plants into natural solar power stations that could convert sunlight into energy far more efficiently. To do this, we’d need a way of getting the energy out in the form of electricity. One company has found a way to harvest electrons deposited by plants into the soil beneath them. But new research (PNAS, “In vivo polymerization and manufacturing of wires and supercapacitors in plants”) from Finland looks at tapping plants’ energy directly by turning their internal structures into electric circuits.

A Feb. 27, 2017 essay by Stuart Thompson for The Conversation (which originated the article) explains the principles underlying the research (Note: A link has been removed),

Plants contain water-filled tubes called “xylem elements” that carry water from their roots to their leaves. The water flow also carries and distributes dissolved nutrients and other things such as chemical signals. The Finnish researchers, whose work is published in PNAS, developed a chemical that was fed into a rose cutting to form a solid material that could carry and store electricity.

Previous experiments have used a chemical called PEDOT to form conducting wires in the xylem, but it didn’t penetrate further into the plant. For the new research, they designed a molecule called ETE-S that forms similar electrical conductors but can also be carried wherever the stream of water travelling though the xylem goes.

This flow is driven by the attraction between water molecules. When water in a leaf evaporates, it pulls on the chain of molecules left behind, dragging water up through the plant all the way from the roots. You can see this for yourself by placing a plant cutting in food colouring and watching the colour move up through the xylem. The researchers’ method was so similar to the food colouring experiment that they could see where in the plant their electrical conductor had travelled to from its colour.

The result was a complex electronic network permeating the leaves and petals, surrounding their cells and replicating their pattern. The wires that formed conducted electricity up to a hundred times better than those made from PEDOT and could also store electrical energy in the same way as an electronic component called a capacitor.

I recommend reading Thompson’s piece in its entirety.

CRISPR patent decision: Harvard’s and MIT’s Broad Institute victorious—for now

I have written about the CRISPR patent tussle (Harvard & MIT’s [Massachusetts Institute of Technology] Broad Institute vs the University of California at Berkeley) previously in a Jan. 6, 2015 posting and in a more detailed May 14, 2015 posting. I also mentioned (in a Jan. 17, 2017 posting) CRISPR and its patent issues in the context of a posting about a Slate.com series on Frankenstein and the novel’s applicability to our own time. This patent fight is being bitterly fought as fortunes are at stake.

It seems a decision has been made regarding the CRISPR patent claims. From a Feb. 17, 2017 article by Charmaine Distor for The Science Times,

After an intense court battle, the US Patent and Trademark Office (USPTO) released its ruling on February 15 [2017]. The rights for the CRISPR-Cas9 gene editing technology was handed over to the Broad Institute of Harvard University and the Massachusetts Institute of Technology (MIT).

According to an article in Nature, the said court battle was between the Broad Institute and the University of California. The two institutions are fighting over the intellectual property right for the CRISPR patent. The case between the two started when the patent was first awarded to the Broad Institute despite having the University of California apply first for the CRISPR patent.

Heidi Ledford’s Feb. 17, 2017 article for Nature provides more insight into the situation (Note: Links have been removed),

It [USPTO] ruled that the Broad Institute of Harvard and MIT in Cambridge could keep its patents on using CRISPR–Cas9 in eukaryotic cells. That was a blow to the University of California in Berkeley, which had filed its own patents and had hoped to have the Broad’s thrown out.

The fight goes back to 2012, when Jennifer Doudna at Berkeley, Emmanuelle Charpentier, then at the University of Vienna, and their colleagues outlined how CRISPR–Cas9 could be used to precisely cut isolated DNA1. In 2013, Feng Zhang at the Broad and his colleagues — and other teams — showed2 how it could be adapted to edit DNA in eukaryotic cells such as plants, livestock and humans.

Berkeley filed for a patent earlier, but the USPTO granted the Broad’s patents first — and this week upheld them. There are high stakes involved in the ruling. The holder of key patents could make millions of dollars from CRISPR–Cas9’s applications in industry: already, the technique has sped up genetic research, and scientists are using it to develop disease-resistant livestock and treatments for human diseases.

But the fight for patent rights to CRISPR technology is by no means over. Here are four reasons why.

1. Berkeley can appeal the ruling

2. European patents are still up for grabs

3. Other parties are also claiming patent rights on CRISPR–Cas9

4. CRISPR technology is moving beyond what the patents cover

As for Ledford’s 3rd point, there are an estimated 763 patent families (groups of related patents) claiming CAS9 leading to the distinct possibility that the Broad Institute will be fighting many patent claims in the future.

Once you’ve read Distor’s and Ledford’s articles, you may want to check out Adam Rogers’ and Eric Niiler’s Feb. 16, 2017 CRISPR patent article for Wired,

The fight over who owns the most promising technique for editing genes—cutting and pasting the stuff of life to cure disease and advance scientific knowledge—has been a rough one. A team on the West Coast, at UC Berkeley, filed patents on the method, Crispr-Cas9; a team on the East Coast, based at MIT and the Broad Institute, filed their own patents in 2014 after Berkeley’s, but got them granted first. The Berkeley group contended that this constituted “interference,” and that Berkeley deserved the patent.

At stake: millions, maybe billions of dollars in biotech money and licensing fees, the future of medicine, the future of bioscience. Not nothing. Who will benefit depends on who owns the patents.

On Wednesday [Feb. 15, 2017], the US Patent Trial and Appeal Board kind of, sort of, almost began to answer that question. Berkeley will get the patent for using the system called Crispr-Cas9 in any living cell, from bacteria to blue whales. Broad/MIT gets the patent in eukaryotic cells, which is to say, plants and animals.

It’s … confusing. “The patent that the Broad received is for the use of Crispr gene-editing technology in eukaryotic cells. The patent for the University of California is for all cells,” says Jennifer Doudna, the UC geneticist and co-founder of Caribou Biosciences who co-invented Crispr, on a conference call. Her metaphor: “They have a patent on green tennis balls; we have a patent for all tennis balls.”

Observers didn’t quite buy that topspin. If Caribou is playing tennis, it’s looking like Broad/MIT is Serena Williams.

“UC does not necessarily lose everything, but they’re no doubt spinning the story,” says Robert Cook-Deegan, an expert in genetic policy at Arizona State University’s School for the Future of Innovation in Society. “UC’s claims to eukaryotic uses of Crispr-Cas9 will not be granted in the form they sought. That’s a big deal, and UC was the big loser.”

UC officials said Wednesday [Feb. 15, 2017] that they are studying the 51-page decision and considering whether to appeal. That leaves members of the biotechnology sector wondering who they will have to pay to use Crispr as part of a business—and scientists hoping the outcome won’t somehow keep them from continuing their research.

….

Happy reading!

SWEET, sweet transporters

A Sept. 4, 2014 news item on Azonano is all about sugar,

Sugars are an essential source of energy for microrganisms, animals and humans. They are produced by plants, which convert energy from sunlight into chemical energy in the form of sugars through photosynthesis.

These sugars are taken up into cells, no matter whether these are bacteria, yeast, human cells or plant cells, by proteins that create sugar-specific pores in the membrane that surrounds a cell. These transport proteins are thus essential in all organisms. It is not surprising that the transporters of humans and plants are very similar since they evolved from their bacterial ancestors.

Sugar transporters can also be a source of vulnerability for plants and animals alike. In plants they can be susceptible to takeover by pathogens, hijacking the source of the plant’s food and energy. In animals, mutations in sugar transporters can lead to diseases, such as diabetes.

New work from a team led by the Stanford University School of Medicine’s Liang Feng and including Carnegie’s [Carnegie Institution for Science] Wolf Frommer has for the first time elucidated the atomic structures of the prototype of the sugar transporters (termed “SWEET” transporters) in plants and humans. These are bacterial sugar transporters, called SemiSWEETs (because they are just half the size of the human and plant ones). …

A Sept. 3, 2014 Carnegie Institution for Science news release, which originated the news item, describes the importance of understanding these transporters,

Until now, there was very limited information about the unique structures of these important transport proteins, which it turns out are different from all other known sugar transporters.

Discovering the structure of these proteins is important, as it is the key to unlocking the mechanism by which they work. And understanding their mechanism is crucial for figuring out what happens when these functions fail to work properly, because that knowledge can help in addressing the resulting diseases or growth problems in both plants and animals.

The research team performed a combination of structural and functional analyses of SemiSWEETs and SWEETs and was able to crystallize two examples in different states, demonstrating not only the protein’s structure, but much about its functionality as well.

They found that the SemiSWEETs do not act as a sugar channel, or tunnel, which allow sugars to pass across the membrane. Rather they act like an airlock, moving the sugars in multiple stages, two of which can be observed in the crystal structures. The SemiSWEETs, among the smallest known transport proteins, assemble in pairs, thereby creating a structure that looks like their bigger plant and human SWEET homologs. This marks the SWEET family of proteins as drastically different from other sugar transport proteins.

“One of the most-exciting parts of this discovery is the speed with which we were able to move from discovering these novel sugar transporters, to determining their actual structure, to showing how they work,” Frommer said. “Fantastic progress made possible by a collaboration with a structural biologist from Stanford University. Our findings highlight the potential practical applications of this information in improving crop yields as well as in addressing human diseases.”

Here’s a link to and a citation for the paper,

Structures of bacterial homologues of SWEET transporters in two distinct conformations by Yan Xu, Yuyong Tao, Lily S. Cheung, Chao Fan, Li-Qing Chen, Sophia Xu, Kay Perry, Wolf B. Frommer, & Liang Feng. Nature (2014) doi:10.1038/nature13670 Published online 03 September 2014

This paper is behind a paywall.

Using microwaves to test for carbon nanotube toxicity in soil

It’s been a while since I’ve mentioned soil or environmental testing for this this Oct. 19, 2012 news item by Karen Slyker on physorg.com, which highlights some research on environmental testing of carbon nanotubes, lets me redress the situation,

Industrial uses are growing, as are concerns that these novel nanomaterials may have negative or unintended effects on organisms and the environment. With this in mind, environmental toxicologists at Texas Tech are exploring the fate of CNTs in biological environments and their ability to accumulate in soil, plants or other organisms.

One recurring question has slowed these studies: How can anyone be certain the tiny CNTs are present in the given sample?

“It’s like a needle in a haystack,” Green said [Micah Green, assistant professor of chemical engineering]. “How can you prove the effects of the needle, if you’re not sure that it’s really in there?”

The impetus for the work initially began with a conversation between Green and Jaclyn Cañas, associate professor of environmental toxicology at The Institute for Environmental and Human Health at Texas Tech. Cañas described the problem of detecting CNTs in crop samples. Green suggested that exposing samples to microwaves could reveal the presence of even trace quantities of nanotubes.

The Texas Technical University Oct. 19, 2012 news release (which originated the news item) provides more detail about the approach,

CNTs have the unusual property of evolving extreme amounts of heat upon exposure to microwaves, much more so than typical materials. In fact, nanotube powder will quickly and spontaneously ignite if placed in a conventional kitchen microwave. Green’s idea was to expose the sample to low-power microwaves and measure the resulting increase in temperature.

Mohammad Saed, an associate professor in electrical and computer engineering, joined the team to contribute his expertise in the area of microwave physics.

Together, the three research groups successfully built a testing apparatus and proved the concepts that microwave-based heating can quantify CNT loading inside a plant sample.

The team has refined its testing protocols and extended the scope from soil testing only to including earthworms,

Continued development of the device led to a double-blind test, where a student was given samples of a specified CNT loading but was not told what the concentration was. Graduate student Fahmida Irin was principally responsible for applying the method. The double-blind test successfully duplicated the true values, and was then applied to studying the uptake of nanotubes into alfalfa plant roots grown in soil spiked with nanotubes.

“Since we started the method, we have started collaborating with other groups as well to look at the presence of nanotubes in organisms like earthworms,” Green said.

The method was recently published in a paper entitled “Detection of carbon nanotubes in biological samples through microwave-induced heating” by Irin et al. in the journal Carbon.

I’m not quite sure how to take this research. They do mention that nanotube powder will ignite in a kitchen microwave. Here’s hoping the researchers have designed an apparatus that cannot accidentally ignite carbon nanotubes in soil, plants, or earthworms.