Tag Archives: University of California at Riverside (UCR)

“transforming a plant is still an art” even with CRISPR

“Plus ça change, plus c’est la même chose (the more things change, the more things stay the same), is an old French expression that came to mind when I stumbled across two stories about genetic manipulation of food-producing plants.

The first story involves CRISPR (clustered regularly interspersed short palindromic repeats) gene editing and the second involves more ancient ways to manipulate plant genetics.

Getting ‘CRISPR’d’ plant cells to grow into plants

Plants often don’t grow from cells after researchers alter their genomes. Using a new technology, a team coaxed wheat (above) and other crops to more readily produce genome-edited healthy adult plants. Credit: Juan Debernardi

An October 13, 2020 news item on phys.org announces research about getting better results after a plant’s genome has been altered,

Researchers know how to make precise genetic changes within the genomes of crops, but the transformed cells often refuse to grow into plants. One team has devised a new solution.

Scientists who want to improve crops face a dilemma: it can be difficult to grow plants from cells after you’ve tweaked their genomes.

A new tool helps ease this process by coaxing the transformed cells, including those modified with the gene-editing system CRISPR-Cas9, to regenerate new plants. Howard Hughes Medical Institute Research Specialist Juan M. Debernardi and Investigator Jorge Dubcovsky, together with David Tricoli at the University of California, Davis [UC Davis] Plant Transformation Facility, Javier Palatnik from Argentina, and colleagues at the John Innes Center [UK], collaborated on the work. The team reports the technology, developed in wheat and tested in other crops, October 12, 2020, in the journal Nature Biotechnology.

An October 12, 2020 Howard Hughes Medical Institute (HHMI) news release, which originated the news item, provides more detail,

“The problem is that transforming a plant is still an art [emphasis mine],” Dubcovsky says. The success rate is often low – depending on the crop being modified, 100 attempts may yield only a handful of green shoots that can turn into full-grown plants. The rest fail to produce new plants and die. Now, however, “we have reduced this barrier,” says Dubcovsky, a plant geneticist at UC Davis. Using two genes that already control development in many plants, his team dramatically increased the formation of shoots in modified wheat, rice, citrus, and other crops.

Although UC Davis has a pending patent for commercial applications, Dubcovsky says the technique is available to any researcher who wants to use it for research, at no charge. A number of plant breeding companies have also expressed interested in licensing it. “Now people are trying it in multiple crops,” he says.

Humans have worked to improve plants since the dawn of agriculture, selecting wild grasses to produce cultivated maize and wheat, for example. Nowadays, though, CRISPR has given researchers the ability to make changes to the genome with surgical precision. They have used it to create wheat plants with larger grains, generate resistance to fungal infection, design novel tomato plant architectures, and engineer other traits in new plant varieties.

But the process isn’t easy. Scientists start out with plant cells or pieces of tissue, into which they introduce the CRISPR machinery and a small guide to the specific genes they’d like to edit. They must then entice the modified cells into forming a young plant. Most don’t sprout – a problem scientists are still working to understand.

They have tried to find work-arounds, including boosting the expression of certain genes that control early stages of plant development. While this approach has had some success, it can lead to twisted, stunted, sterile plants if not managed properly.Dubcovsky and his colleagues looked at two other growth-promoting genes, GRF and GIF, that work together in young tissues or organs of plants ranging from moss to fruit trees. The team put these genes side-by-side, like a couple holding hands, before adding them to plant cells. “If you go to a dance, you need to find your partner,” Dubcovsky says. “Here, you are tied with a rope to your partner.”

Dubcovsky’s team found that genetically altered wheat, rice, hybrid orange, and other crops produced many more shoots if those experiments included the linked GRF and GIF genes. In experiments with one variety of wheat, the appearance of shoots increased nearly eight-fold. The number of shoots in rice and the hybrid orange, meanwhile, more than doubled and quadrupled, respectively. What’s more, these shoots grew into healthy plants capable of reproducing on their own, with none of the defects that can result when scientists boost other development-controlling genes. That’s because one of the genes is naturally degraded in adult tissues, Dubcovsky says.

Caroline Roper, a plant pathologist at University of California, Riverside who was not involved in the work, plans to use the new technology to study citrus greening, a bacterial disease that kills trees and renders oranges hard and bitter.

To understand how citrus trees can protect themselves, she needs to see how removing certain genes alters their susceptibility to the bacterium — information that could lead to ways to fight the disease. With conventional techniques, it could take at least two years to generate the gene-edited plants she needs. She hopes Dubcovsky’s tool will shorten that timeline.  

“Time is of the essence. The growers, they wanted an answer yesterday, because they’re at the brink of having to abandon cultivating citrus,” she says.

For anyone who noticed the reference to citrus greening in the last paragraphs of this news release, I have more information aboutthe disease and efforts to it in an August 6, 2020 posting.

As for the latest in gene editing and regeneration, here’s a link to and a citation for the paper,

A GRF–GIF chimeric protein improves the regeneration efficiency of transgenic plants by Juan M. Debernardi, David M. Tricoli, Maria F. Ercoli, Sadiye Hayta, Pamela Ronald, Javier F. Palatnik & Jorge Dubcovsky. Nature Biotechnology volume 38, pages 1274–1279(2020) DOI: https://doi.org/10.1038/s41587-020-0703-0 First Published Online: 12 October 2020 Journal Issue Date: November 2020

This paper is behind a paywall.

Ancient farming techniques for engineering crops

I stumbled on this story by Gabriela Serrato Marks for Massive Science almost three years late (it’s a Dec. 5, 2017 article),

There are more than 50 strains of maize, called landraces, grown in Mexico. A landrace is similar to a dog breed: Corgis and Huskies are both dogs, but they were bred to have different traits. Maize domestication worked the same way.

Some landraces of maize can grow in really dry conditions; others grow best in wetter soils. Early maize farmers selectively bred maize landraces that were well-adapted to the conditions on their land, a practice that still continues today in rural areas of Mexico.

If you think this sounds like an early version of genetic engineering, you’d be correct. But nowadays, modern agriculture is moving away from locally adapted strains and traditional farming techniques and toward active gene manipulation. The goal of both traditional landrace development and modern genetic modification has been to create productive, valuable crops, so these two techniques are not necessarily at odds.

But as more farmers converge on similar strains of (potentially genetically modified) seeds instead of developing locally adapted landraces, there are two potential risks: one is losing the cultural legacy of traditional agricultural techniques that have been passed on in families for centuries or even millennia, and another is decreasing crop resilience even as climate variability is increasing.

Mexico is the main importer of US-grown corn, but that imported corn is primarily used to feed livestock. The corn that people eat or use to make tortillas is grown almost entirely in Mexico, which is where landraces come in.

It is a common practice to grow multiple landraces with different traits as an insurance policy against poor growth conditions. The wide range of landraces contains a huge amount of genetic diversity, making it less likely that one adverse event, such as a drought or pest infestation, will wipe out an entire crop. If farmers only grow one type of corn, the whole crop is vulnerable to the same event.

Landraces are also different from most commercially available hybrid strains of corn because they are open pollinating, which means that farmers can save seeds and replant them the next year, saving money and preserving the strain. If a landrace is not grown anymore, its contribution to maize’s genetic diversity is permanently lost.

This diversity was cultivated over generations from maize’s wild cousin, teosinte, by 60 groups of indigenous people in Mexico. Teosinte looks like a skinny, hairier version of maize. It still grows wild in some parts of Central America, but its close relatives have been found, domesticated, at archaeological sites in the region over 9,000 years old. These early maize cobs could easily fit in the palm of your hand – not big enough to be a staple crop that early farmers could depend upon for sustenance. Genetically, they were more similar to wild teosinte than to modern maize.

[] archaeologists also found that the cobs in Honduras, which is outside the natural range of teosinte, were larger than cobs of the same age from the original domestication region in southern Mexico. The scientists think that people in Honduras were able to develop more productive maize landraces because their crops were isolated from wild teosinte.

The size and shape of the ancient cobs from Honduras show that early farmers engineered the maize crop [emphasis mine] to make it more productive. They developed unique landraces that were well adapted to local conditions and successfully cultivated enough maize to support their communities. In many ways, they were early geneticists. [emphasis mine] …

We have a lot to learn from the indigenous farmers who were growing maize 4,000 years ago. Their history provides examples of both environmentally sound genetic modification and effective adaptation to climate variability. [emphases mine] …

Plus ça change …, eh?

Effective treatment for citrus-destroying disease?

Citrus greening is a worldwide problem. A particularly virulent disease that destroys citrus fruit, it’s a problem that is worsening. Before getting to the research from the University of California at Riverside (UCR), here’s more about the disease and how it’s developing from the UCR Huanglongbing, (HLB, Citrus Greening webpage,

The Situation: Citrus huanglongbing (HLB), previously called citrus greening disease, is one of the most destructive diseases of citrus worldwide.  Originally thought to be caused by a virus, it is now known to be caused by unculturable phloem-limited bacteria.  There are three forms of greening that have been described.  The African form produces symptoms only under cool conditions and is transmitted by the African citrus psyllid Trioza erytreae, while the Asian form prefers warmer conditions and is transmitted by the Asian citrus psyllid Diaphorina citri.  Recently a third American form transmitted by the Asian citrus psyllid was discovered in Brazil.  This American form of the disease apparently originated in China.  In North America, the psyllid vector, Diaphorina citri, of HLB is found in Florida, Louisiana, Georgia, South Carolina, Texas and Hawaii, and recently arrived in Southern California from Mexico. HLB is known to occur in Florida Lousiana, South Carolina, Georgia, Cuba, Belize and the Eastern Yucatan of Mexico.  A federal quarantine restricts all movement of citrus and other plants in the family Rutaceae from Asian Citrus Psyllid or HLB-infested areas into California in order to prevent introduction of the disease.

 Damage:  The HLB bacteria can infect most citrus cultivars, species and hybrids and even some citrus relatives.  Leaves of newly infected trees develop a blotchy mottle appearance.  On chronically infected trees, the leaves are small and exhibit asymmetrical blotchy mottling (in contrast to Zinc deficiency that causes symmetrical blotching).  Fruit from HLB-infected trees are small, lopsided, poorly colored, and contain aborted seeds. The juice from affected fruit is low in soluble solids, high in acids and abnormally bitter.  The fruit retains its green color at the navel end when mature, which is the reason for the common name “citrus greening disease.”  This fruit is of no value because of poor size and quality.  There is no cure for the disease and rapid tree removal is critical for prevention of spread.

Economic Impact: HLB is one of the most devastating diseases of citrus and since its discovery in Florida in 2005, citrus acreage in that state has declined significantly.  If the disease were to establish in California, the nursery industry would be required to move all of their production under screenhouses, pesticide treatments for the vector would be instituted resulting in greatly increased pesticide costs (3-6 treatments per year) and indirect costs due to pesticide-induced disruption of integrated pest management programs for other citrus pests.  A costly eradication program would need to be instituted to remove infected trees in order to protect the citrus industry.

Distribution of HLB: In April 2012, after about a week of testing, the California Department of Food and Agriculture (CDFA) removed a pumelo tree with a lemon graft from Hacienda Heights in Los Angeles County after the tree and an Asian citrus psyllid found on the tree both tested positive for Huanglongbing. In 2005, HLB was also found in Florida and it is now known to occur in Louisiana, Georgia, South Carolina, Cuba, Belze and Eastern Mexico.  Worldwide, HLB is also present in China, eastern and southern Africa, the Indian subcontinent, Mauritius, Reunion, the Saudi Arabian peninsula, and southeast Asia.

Research:  Research is focusing on characterization of the bacteria, development of detection methods, and control of the disease and the psyllid.  To date, control of the disease is based on planting HLB-free citrus germplasm, eradication of infected citrus plants, and control of the vector with systemic insecticides.  Countries with HLB learn to manage the disease so that they can still produce citrus.  In California, the best strategy is to keep this disease out. This goal is supported by both federal and state quarantine regulations and the University of California’s Citrus Clonal Protection Program, which provides a mechanism for the safe introduction of citrus germplasm into California.

A July 7, 2020 news item on phys.org announces what researchers hope can be used commercially as a new treatment for citrus greening disease from researchers University of California at Riverside (UCR), Note: Links have been removed,

UC Riverside scientists have found the first substance capable of controlling Citrus Greening Disease, which has devastated citrus farms in Florida and also threatens California.

The new treatment effectively kills the bacterium causing the disease with a naturally occurring molecule found in wild citrus relatives. This molecule, an antimicrobial peptide, offers numerous advantages over the antibiotics currently used to treat the disease.

UCR geneticist Hailing Jin, who discovered the cure after a five-year search, explained that unlike antibiotic sprays, the peptide is stable even when used outdoors in high heat, easy to manufacture, and safe for humans.

A July 7, 2020 UCR news release (also on EurekAlert) by Jules Bernstein, which originated the news item, provides technical detail and information about plans to commercialize the product,

“This peptide is found in the fruit of Australian finger limes, which can naturally tolerate Citrus Greening bacteria and has been consumed for hundreds of years,” Jin said. “It is much safer to use this natural plant product on agricultural crops than other synthetic chemicals.”

Currently, some growers in Florida are spraying antibiotics and pesticides in an attempt to save trees from the CLas bacterium that causes citrus greening, also known as Huanglongbing or HLB.

“Most antibiotics are temperature sensitive, so their effects are largely reduced when applied in the hot weather,” Jin said. “By contrast, this peptide is stable even when used in 130-degree heat.”

Jin found the peptide by examining plants such as the Australian finger lime known to possess natural tolerance for the bacteria that causes Citrus Greening Disease, and she isolated the genes that contribute to this innate immunity. One of these genes produces the peptide, which she then tested over the course of two years. Improvement was soon visible.

“You can see the bacteria drastically reduced, and the leaves appear healthy again only a few months after treatment,” Jin said.

Because the peptide only needs to be reapplied a few times per year, it is highly cost effective for growers. This peptide can also be developed into a vaccine to protect young healthy plants from infection, as it is able to induce the plant’s innate immunity to the bacteria.

Jin’s peptide can be applied by injection or foliage spray, and it moves systemically through plants and remains stable, which makes the effect of the treatment stronger.

The treatment will be further enhanced with proprietary injection technology made by Invaio Sciences. UC Riverside has entered into an exclusive, worldwide license agreement with Invaio, ensuring this new treatment goes exactly where it’s needed in plants.

“Invaio is enthusiastic to partner with UC Riverside and advance this innovative technology for combating the disease known as Citrus Greening or Huanglongbing,” said Invaio Chief Science Officer Gerardo Ramos. “The prospect of addressing this previously incurable and devastating crop disease, helping agricultural communities and improving the environmental impact of production is exciting and rewarding,” he said. “This is crop protection in harmony with nature.”

The need for an HLB cure is a global problem, but hits especially close to home as California produces 80 percent of all the fresh citrus in the United States, said Brian Suh, director of technology commercialization in UCR’s Office of Technology Partnerships, which helps bring university technology to market for the benefit of society through licenses, partnerships, and startup companies.

“This license to Invaio opens up the opportunity for a product to get to market faster,” Suh said. “Cutting edge research from UCR, like the peptide identified by Dr. Jin, has a tremendous amount of commercial potential and can transform the trajectory of real-world problems with these innovative solutions.”

You can find out more about Invaio Sciences here.

Citrus greening has been featured here before in an April 7, 2015 posting titled, Citrus canker, Florida, and Zinkicide. There doesn’t seem to have been much progress made with this Florida solution for citrus greening. This 2018 document on nano.gov was the most recent I could find, ZinkicideTM- a systemic nano-ZnO based bactericide/fungicide for crop protection by Swadeshmukul Santra.

Chameleon skin (nanomaterial made of gold nanoparticles) for robots

A June 17, 2020 news item on Nanowerk trumpets research into how robots might be able to sport chameleon-like skin one day,

A new film made of gold nanoparticles changes color in response to any type of movement. Its unprecedented qualities could allow robots to mimic chameleons and octopi — among other futuristic applications.

Unlike other materials that try to emulate nature’s color changers, this one can respond to any type of movement, like bending or twisting. Robots coated in it could enter spaces that might be dangerous or impossible for humans, and offer information just based on the way they look.

For example, a camouflaged robot could enter tough-to-access underwater crevices. If the robot changes color, biologists could learn about the pressures facing animals that live in these environments.

Although some other color-changing materials can also respond to motion, this one can be printed and programmed to display different, complex patterns that are difficult to replicate.

This video from the University of California at Riverside researchers shows the material in action (Note: It gets more interesting after the first 20 secs.),

A June 15, 2020 University of California at Riverside (UCR) news release (also on EurekAlert but published on June 17, 2020) by Jules Bernstein, which originated the news item, delves further,

Nanomaterials are simply materials that have been reduced to an extremely small scale — tens of nanometers in width and length, or, about the size of a virus. When materials like silver or gold become smaller, their colors will change depending on their size, shape, and the direction they face.

“In our case, we reduced gold to nano-sized rods. We knew that if we could make the rods point in a particular direction, we could control their color,” said chemistry professor Yadong Yin. “Facing one way, they might appear red. Move them 45 degrees, and they change to green.”

The problem facing the research team was how to take millions of gold nanorods floating in a liquid solution and get them all to point in the same direction to display a uniform color.

Their solution was to fuse smaller magnetic nanorods onto the larger gold ones. The two different-sized rods were encapsulated in a polymer shield, so that they would remain side by side. That way, the orientation of both rods could be controlled by magnets.

“Just like if you hold a magnet over a pile of needles, they all point in the same direction. That’s how we control the color,” Yin said.

Once the nanorods are dried into a thin film, their orientation is fixed in place and they no longer respond to magnets. “But, if the film is flexible, you can bend and rotate it, and will still see different colors as the orientation changes,” Yin said.

Other materials, like butterfly wings, are shiny and colorful at certain angles, and can also change color when viewed at other angles. However, those materials rely on precisely ordered microstructures, which are difficult and expensive to make for large areas. But this new film can be made to coat the surface of any sized object just as easily as applying spray paint on a house.

Though futuristic robots are an ultimate application of this film, it can be used in many other ways. UC Riverside chemist Zhiwei Li, the first author on this paper, explained that the film can be incorporated into checks or cash as an authentication feature. Under normal lighting, the film is gray, but when you put on sunglasses and look at it through polarized lenses, elaborate patterns can be seen. In addition, the color contrast of the film may change dramatically if you twist the film.

The applications, in fact, are only limited by the imagination. “Artists could use this technology to create fascinating paintings that are wildly different depending on the angle from which they are viewed,” Li said. “It would be wonderful to see how the science in our work could be combined with the beauty of art.”

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

Coupling magnetic and plasmonic anisotropy in hybrid nanorods for mechanochromic responses by Zhiwei Li, Jianbo Jin, Fan Yang, Ningning Song & Yadong Yin. Nature Communications volume 11, Article number: 2883 (2020) DOI: https://doi.org/10.1038/s41467-020-16678-8 Published: 08 June 2020

This paper is open access.

Anyone have a spare portabella (also known as, portobello) mushroom? I need for my phone

Scientists as the University of California at Riverside (UCR) have developed a type of lithium-ion battery with portabella mushrooms, from a Sept. 29, 2015 news item on ScienceDaily,

Can portabella mushrooms stop cell phone batteries from degrading over time?

Researchers at the University of California, Riverside Bourns College of Engineering think so.

They have created a new type of lithium-ion battery anode using portabella mushrooms, which are inexpensive, environmentally friendly and easy to produce. The current industry standard for rechargeable lithium-ion battery anodes is synthetic graphite, which comes with a high cost of manufacturing because it requires tedious purification and preparation processes that are also harmful to the environment.

A Sept. 29, 2015 UCR news release (also on EurekAlert) by Sean Nealon, which originated the news item, expands on the theme,

With the anticipated increase in batteries needed for electric vehicles and electronics, a cheaper and sustainable source to replace graphite is needed. Using biomass, a biological material from living or recently living organisms, as a replacement for graphite, has drawn recent attention because of its high carbon content, low cost and environmental friendliness.

UC Riverside engineers were drawn to using mushrooms as a form of biomass because past research has established they are highly porous, meaning they have a lot of small spaces for liquid or air to pass through. That porosity is important for batteries because it creates more space for the storage and transfer of energy, a critical component to improving battery performance.

In addition, the high potassium salt concentration in mushrooms allows for increased electrolyte-active material over time by activating more pores, gradually increasing its capacity.

A conventional anode allows lithium to fully access most of the material during the first few cycles and capacity fades from electrode damage occurs from that point on. The mushroom carbon anode technology could, with optimization, replace graphite anodes. It also provides a binderless and current-collector free approach to anode fabrication.

“With battery materials like this, future cell phones may see an increase in run time after many uses, rather than a decrease, due to apparent activation of blind pores within the carbon architectures as the cell charges and discharges over time,” said Brennan Campbell, a graduate student in the Materials Science and Engineering program at UC Riverside.

Nanocarbon architectures derived from biological materials such as mushrooms can be considered a green and sustainable alternative to graphite-based anodes, said Cengiz Ozkan, a professor of mechanical engineering and materials science and engineering.

The nano-ribbon-like architectures transform upon heat treatment into an interconnected porous network architecture which is important for battery electrodes because such architectures possess a very large surface area for the storage of energy, a critical component to improving battery performance.

One of the problems with conventional carbons, such as graphite, is that they are typically prepared with chemicals such as acids and activated by bases that are not environmentally friendly, said Mihri Ozkan, a professor of electrical and computer engineering. Therefore, the UC Riverside team is focused on naturally-derived carbons, such as the skin of the caps of portabella mushrooms, for making batteries.

It is expected that nearly 900,000 tons of natural raw graphite would be needed for anode fabrication for nearly six million electric vehicle forecast to be built by 2020. This requires that the graphite be treated with harsh chemicals, including hydrofluoric and sulfuric acids, a process that creates large quantities of hazardous waste. The European Union projects this process will be unsustainable in the future.

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

Hierarchically Porous Carbon Anodes for Li-ion Batteries by Brennan Campbell, Robert Ionescu, Zachary Favors, Cengiz S. Ozkan, & Mihrimah Ozkan. [Nature] Scientific Reports 5, Article number: 14575 (2015)  doi:10.1038/srep14575 Published online: 29 September 2015

This is an open access paper