Tag Archives: Howard Hughes Medical Institute (HHMI)

“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?

Iridescent giant clams could point the way to safety, climatologically speaking

Giant clams in Palau (Cynthia Barnett)

These don’t look like any clams I’ve ever seen but that is the point of Cynthia Barnett’s absorbing Sept. 10, 2018 article for The Atlantic (Note: A link has been removed),

Snorkeling amid the tree-tangled rock islands of Ngermid Bay in the western Pacific nation of Palau, Alison Sweeney lingers at a plunging coral ledge, photographing every giant clam she sees along a 50-meter transect. In Palau, as in few other places in the world, this means she is going to be underwater for a skin-wrinkling long time.

At least the clams are making it easy for Sweeney, a biophysicist at the University of Pennsylvania. The animals plump from their shells like painted lips, shimmering in blues, purples, greens, golds, and even electric browns. The largest are a foot across and radiate from the sea floor, but most are the smallest of the giant clams, five-inch Tridacna crocea, living higher up on the reef. Their fleshy Technicolor smiles beam in all directions from the corals and rocks of Ngermid Bay.

… Some of the corals are bleached from the conditions in Ngermid Bay, where naturally high temperatures and acidity mirror the expected effects of climate change on the global oceans. (Ngermid Bay is more commonly known as “Nikko Bay,” but traditional leaders and government officials are working to revive the indigenous name of Ngermid.)

Even those clams living on bleached corals are pulsing color, like wildflowers in a white-hot desert. Sweeney’s ponytail flows out behind her as she nears them with her camera. They startle back into their fluted shells. Like bashful fairytale creatures cursed with irresistible beauty, they cannot help but draw attention with their sparkly glow.

Barnett makes them seem magical and perhaps they are (Note: A link has been removed),

It’s the glow that drew Sweeney’s attention to giant clams, and to Palau, a tiny republic of more than 300 islands between the Philippines and Guam. Its sun-laden waters are home to seven of the world’s dozen giant-clam species, from the storied Tridacna gigas—which can weigh an estimated 550 pounds and measure over four feet across—to the elegantly fluted Tridacna squamosa. Sweeney first came to the archipelago in 2009, while working on animal iridescence as a post-doctoral fellow at the University of California at Santa Barbara. Whether shimmering from a blue morpho butterfly’s wings or a squid’s skin, iridescence is almost always associated with a visual signal—one used to attract mates or confuse predators. Giant clams’ luminosity is not such a signal. So, what is it?

In the years since, Sweeney and her colleagues have discovered that the clams’ iridescence is essentially the outer glow of a solar transformer—optimized over millions of years to run on sunlight and algal biofuel. Giant clams reach their cartoonish proportions thanks to an exceptional ability to grow their own photosynthetic algae in vertical farms spread throughout their flesh. Sweeney and other scientists think this evolved expertise may shed light on alternative fuel technologies and other industrial solutions for a warming world.

Barnett goes on to describe Palau’s relationship to the clams and the clams’ environment,

Palau’s islands have been inhabited for at least 3,400 years, and from the start, giant clams were a staple of diet, daily life, and even deity. Many of the islands’ oldest-surviving tools are crafted of thick giant-clam shell: arched-blade adzes, fishhooks, gougers, heavy taro-root pounders. Giant-clam shell makes up more than three-fourths of some of the oldest shell middens in Palau, a percentage that decreases through the centuries. Archaeologists suggest that the earliest islanders depleted the giant clams that crowded the crystalline shallows, then may have self-corrected. Ancient Palauan conservation law, known as bul, prohibited fishing during critical spawning periods, or when a species showed signs of over-harvesting.

Before the Christianity that now dominates Palauan religion sailed in on eighteenth-century mission ships, the culture’s creation lore began with a giant clam called to life in an empty sea. The clam grew bigger and bigger until it sired Latmikaik, the mother of human children, who birthed them with the help of storms and ocean currents.

The legend evokes giant clams in their larval phase, moving with the currents for their first two weeks of life. Before they can settle, the swimming larvae must find and ingest one or two photosynthetic alga, which later multiply, becoming self-replicating fuel cells. After the larvae down the alga and develop a wee shell and a foot, they kick around like undersea farmers, looking for a sunny spot for their crop. When they’ve chosen a well-lit home in a shallow lagoon or reef, they affix to the rock, their shell gaping to the sky. After the sun hits and photosynthesis begins, the microalgae will multiply to millions, or in the case of T. gigas, billions, and clam and algae will live in symbiosis for life.

Giant clam is a beloved staple in Palau and many other Pacific islands, prepared raw with lemon, simmered into coconut soup, baked into a savory pancake, or sliced and sautéed in a dozen other ways. But luxury demand for their ivory-like shells and their adductor muscle, which is coveted as high-end sashimi and an alleged aphrodisiac, has driven T. gigas extinct in China, Taiwan, and other parts of their native habitat. Some of the toughest marine-protection laws in the world, along with giant-clam aquaculture pioneered here, have helped Palau’s wild clams survive. The Palau Mariculture Demonstration Center raises hundreds of thousands of giant clams a year, supplying local clam farmers who sell to restaurants and the aquarium trade and keeping pressure off the wild population. But as other nations have wiped out their clams, Palau’s 230,000-square-mile ocean territory is an increasing target of illegal foreign fishers.

Barnett delves into how the country of Palau is responding to the voracious appetite for the giant clams and other marine life,

Palau, drawing on its ancient conservation tradition of bul, is fighting back. In 2015, President Tommy Remengesau Jr. signed into law the Palau National Marine Sanctuary Act, which prohibits fishing in 80 percent of Palau’s Exclusive Economic Zone and creates a domestic fishing area in the remaining 20 percent, set aside for local fishers selling to local markets. In 2016, the nation received a $6.6 million grant from Japan to launch a major renovation of the Palau Mariculture Demonstration Center. Now under construction at the waterfront on the southern tip of Malakal Island, the new facility will amp up clam-aquaculture research and increase giant-clam production five-fold, to more than a million seedlings a year.

Last year, Palau amended its immigration policy to require that all visitors sign a pledge to behave in an ecologically responsible manner. The pledge, stamped into passports by an immigration officer who watches you sign, is written to the island’s children:

Children of Palau, I take this pledge, as your guest, to preserve and protect your beautiful and unique island home. I vow to tread lightly, act kindly and explore mindfully. I shall not take what is not given. I shall not harm what does not harm me. The only footprints I shall leave are those that will wash away.

The pledge is winning hearts and public-relations awards. But Palau’s existential challenge is still the collective “we,” the world’s rising carbon emissions and the resulting upturns in global temperatures, sea levels, and destructive storms.

F. Umiich Sengebau, Palau’s Minister for Natural Resources, Environment, and Tourism, grew up on Koror and is full of giant-clam proverbs, wisdom and legends from his youth. He tells me a story I also heard from an elder in the state of Airai: that in old times, giant clams were known as “stormy-weather food,” the fresh staple that was easy to collect and have on hand when it was too stormy to go out fishing.

As Palau faces the storms of climate change, Sengebau sees giant clams becoming another sort of stormy-weather food, serving as a secure source of protein; a fishing livelihood; a glowing icon for tourists; and now, an inspiration for alternative energy and other low-carbon technologies. “In the old days, clams saved us,” Sengebau tells me. “I think there’s a lot of power in that, a great power and meaning in the history of clams as food, and now clams as science.”

I highly recommend Barnett’s article, which is one article in a larger series, from a November 6, 2017 The Atlantic press release,

The Atlantic is expanding the global footprint of its science writing today with a multi-year series to investigate life in all of its multitudes. The series, “Life Up Close,” created with support from Howard Hughes Medical Institute’s Department of Science Education (HHMI), begins today at TheAtlantic.com. In the first piece for the project, “The Zombie Diseases of Climate Change,” The Atlantic’s Robinson Meyer travels to Greenland to report on the potentially dangerous microbes emerging from thawing Arctic permafrost.

The project is ambitious in both scope and geographic reach, and will explore how life is adapting to our changing planet. Journalists will travel the globe to examine these changes as they happen to microbes, plants, and animals in oceans, grasslands, forests, deserts, and the icy poles. The Atlantic will question where humans should look for life next: from the Martian subsurface, to Europa’s oceans, to the atmosphere of nearby stars and beyond. “Life Up Close” will feature at least twenty reported pieces continuing through 2018.

“The Atlantic has been around for 160 years, but that’s a mere pinpoint in history when it comes to questions of life and where it started, and where we’re going,” said Ross Andersen, The Atlantic’s senior editor who oversees science, tech, and health. “The questions that this project will set out to tackle are critical; and this support will allow us to cover new territory in new and more ambitious ways.”

About The Atlantic:
Founded in 1857 and today one of the fastest growing media platforms in the industry, The Atlantic has throughout its history championed the power of big ideas and continues to shape global debate across print, digital, events, and video platforms. With its award-winning digital presence TheAtlantic.com and CityLab.com on cities around the world, The Atlantic is a multimedia forum on the most critical issues of our times—from politics, business, urban affairs, and the economy, to technology, arts, and culture. The Atlantic is celebrating its 160th anniversary this year. Bob Cohn is president of The Atlantic and Jeffrey Goldberg is editor in chief.

About the Howard Hughes Medical Institute (HHMI) Department of Science Education:
HHMI is the leading private nonprofit supporter of scientific research and science education in the United States. The Department of Science Education’s BioInteractive division produces free, high quality educational media for science educators and millions of students around the globe, its HHMI Tangled Bank Studios unit crafts powerful stories of scientific discovery for television and big screens, and its grants program aims to transform science education in universities and colleges. For more information, visit www.hhmi.org.

Getting back to the giant clams, sometimes all you can do is marvel, eh?