Tag Archives: Yi Li

The CRISPR yogurt story and a hornless cattle update

Clustered regularly interspaced short palindromic repeats (CRISPR) does not and never has made much sense to me. I understand each word individually it’s just that I’ve never thought they made much sense strung together that way. It’s taken years but I’ve finally found out what the words (when strung together that way) mean and the origins for the phrase. Hint: it’s all about the phages.

Apparently, it all started with yogurt as Cynthia Graber and Nicola Twilley of Gastropod discuss on their podcast, “4 CRISPR experts on how gene editing is changing the future of food.” During the course of the podcast they explain the ‘phraseology’ issue, mention hornless cattle (I have an update to the information in the podcast later in this posting), and so much more.

CRISPR started with yogurt

You’ll find the podcast (almost 50 minutes long) here on an Oct. 11, 2019 posting on the Genetic Literacy Project. If you need a little more encouragement, here’s how the podcast is described,

To understand how CRISPR will transform our food, we begin our episode at Dupont’s yoghurt culture facility in Madison, Wisconsin. Senior scientist Dennis Romero tells us the story of CRISPR’s accidental discovery—and its undercover but ubiquitous presence in the dairy aisles today.

Jennifer Kuzma and Yiping Qi help us understand the technology’s potential, both good and bad, as well as how it might be regulated and labeled. And Joyce Van Eck, a plant geneticist at the Boyce Thompson Institute in Ithaca, New York, tells us the story of how she is using CRISPR, combined with her understanding of tomato genetics, to fast-track the domestication of one of the Americas’ most delicious orphan crops [groundcherries].

I featured Van Eck’s work with groundcherries last year in a November 28, 2018 posting and I don’t think she’s published any new work about the fruit since. As for Kuzma’s point that there should be more transparency where genetically modified food is concerned, Canadian consumers were surprised (shocked) in 2017 to find out that genetically modified Atlantic salmon had been introduced into the food market without any notification (my September 13, 2017 posting; scroll down to the Fish subheading; Note: The WordPress ‘updated version from Hell’ has affected some of the formatting on the page).

The earliest article on CRISPR and yogurt that I’ve found is a January 1, 2015 article by Kerry Grens for The Scientist,

Two years ago, a genome-editing tool referred to as CRISPR (clustered regularly interspaced short palindromic repeats) burst onto the scene and swept through laboratories faster than you can say “adaptive immunity.” Bacteria and archaea evolved CRISPR eons before clever researchers harnessed the system to make very precise changes to pretty much any sequence in just about any genome.

But life scientists weren’t the first to get hip to CRISPR’s potential. For nearly a decade, cheese and yogurt makers have been relying on CRISPR to produce starter cultures that are better able to fend off bacteriophage attacks. “It’s a very efficient way to get rid of viruses for bacteria,” says Martin Kullen, the global R&D technology leader of Health and Protection at DuPont Nutrition & Health. “CRISPR’s been an important part of our solution to avoid food waste.”

Phage infection of starter cultures is a widespread and significant problem in the dairy-product business, one that’s been around as long as people have been making cheese. Patrick Derkx, senior director of innovation at Denmark-based Chr. Hansen, one of the world’s largest culture suppliers, estimates that the quality of about two percent of cheese production worldwide suffers from phage attacks. Infection can also slow the acidification of milk starter cultures, thereby reducing creameries’ capacity by up to about 10 percent, Derkx estimates.
In the early 2000s, Philippe Horvath and Rodolphe Barrangou of Danisco (later acquired by DuPont) and their colleagues were first introduced to CRISPR while sequencing Streptococcus thermophilus, a workhorse of yogurt and cheese production. Initially, says Barrangou, they had no idea of the purpose of the CRISPR sequences. But as his group sequenced different strains of the bacteria, they began to realize that CRISPR might be related to phage infection and subsequent immune defense. “That was an eye-opening moment when we first thought of the link between CRISPR sequencing content and phage resistance,” says Barrangou, who joined the faculty of North Carolina State University in 2013.

One last bit before getting to the hornless cattle, scientist Yi Li has a November 15, 2018 posting on the GLP website about his work with gene editing and food crops,

I’m a plant geneticist and one of my top priorities is developing tools to engineer woody plants such as citrus trees that can resist the greening disease, Huanglongbing (HLB), which has devastated these trees around the world. First detected in Florida in 2005, the disease has decimated the state’s US$9 billion citrus crop, leading to a 75 percent decline in its orange production in 2017. Because citrus trees take five to 10 years before they produce fruits, our new technique – which has been nominated by many editors-in-chief as one of the groundbreaking approaches of 2017 that has the potential to change the world – may accelerate the development of non-GMO citrus trees that are HLB-resistant.

Genetically modified vs. gene edited

You may wonder why the plants we create with our new DNA editing technique are not considered GMO? It’s a good question.

Genetically modified refers to plants and animals that have been altered in a way that wouldn’t have arisen naturally through evolution. A very obvious example of this involves transferring a gene from one species to another to endow the organism with a new trait – like pest resistance or drought tolerance.

But in our work, we are not cutting and pasting genes from animals or bacteria into plants. We are using genome editing technologies to introduce new plant traits by directly rewriting the plants’ genetic code.

This is faster and more precise than conventional breeding, is less controversial than GMO techniques, and can shave years or even decades off the time it takes to develop new crop varieties for farmers.

There is also another incentive to opt for using gene editing to create designer crops. On March 28, 2018, U.S. Secretary of Agriculture Sonny Perdue announced that the USDA wouldn’t regulate new plant varieties developed with new technologies like genome editing that would yield plants indistinguishable from those developed through traditional breeding methods. By contrast, a plant that includes a gene or genes from another organism, such as bacteria, is considered a GMO. This is another reason why many researchers and companies prefer using CRISPR in agriculture whenever it is possible.

As the Gatropod’casters note, there’s more than one side to the gene editing story and not everyone is comfortable with the notion of cavalierly changing genetic codes when so much is still unknown.

Hornless cattle update

First mentioned here in a November 28, 2018 posting, hornless cattle have been in the news again. From an October 7, 2019 news item on ScienceDaily,

For the past two years, researchers at the University of California, Davis, have been studying six offspring of a dairy bull, genome-edited to prevent it from growing horns. This technology has been proposed as an alternative to dehorning, a common management practice performed to protect other cattle and human handlers from injuries.

UC Davis scientists have just published their findings in the journal Nature Biotechnology. They report that none of the bull’s offspring developed horns, as expected, and blood work and physical exams of the calves found they were all healthy. The researchers also sequenced the genomes of the calves and their parents and analyzed these genomic sequences, looking for any unexpected changes.

An October 7, 2019 UC Davis news release (also on EurekAlert), which originated the news item, provides more detail about the research (I have checked the UC Davis website here and the October 2019 update appears to be the latest available publicly as of February 5, 2020),

All data were shared with the U.S. Food and Drug Administration. Analysis by FDA scientists revealed a fragment of bacterial DNA, used to deliver the hornless trait to the bull, had integrated alongside one of the two hornless genetic variants, or alleles, that were generated by genome-editing in the bull. UC Davis researchers further validated this finding.

“Our study found that two calves inherited the naturally-occurring hornless allele and four calves additionally inherited a fragment of bacterial DNA, known as a plasmid,” said corresponding author Alison Van Eenennaam, with the UC Davis Department of Animal Science.

Plasmid integration can be addressed by screening and selection, in this case, selecting the two offspring of the genome-edited hornless bull that inherited only the naturally occurring allele.

“This type of screening is routinely done in plant breeding where genome editing frequently involves a step that includes a plasmid integration,” said Van Eenennaam.

Van Eenennaam said the plasmid does not harm the animals, but the integration technically made the genome-edited bull a GMO, because it contained foreign DNA from another species, in this case a bacterial plasmid.

“We’ve demonstrated that healthy hornless calves with only the intended edit can be produced, and we provided data to help inform the process for evaluating genome-edited animals,” said Van Eenennaam. “Our data indicates the need to screen for plasmid integration when they’re used in the editing process.”

Since the original work in 2013, initiated by the Minnesota-based company Recombinetics, new methods have been developed that no longer use donor template plasmid or other extraneous DNA sequence to bring about introgression of the hornless allele.

Scientists did not observe any other unintended genomic alterations in the calves, and all animals remained healthy during the study period. Neither the bull, nor the calves, entered the food supply as per FDA guidance for genome-edited livestock.

WHY THE NEED FOR HORNLESS COWS?

Many dairy breeds naturally grow horns. But on dairy farms, the horns are typically removed, or the calves “disbudded” at a young age. Animals that don’t have horns are less likely to harm animals or dairy workers and have fewer aggressive behaviors. The dehorning process is unpleasant and has implications for animal welfare. Van Eenennaam said genome-editing offers a pain-free genetic alternative to removing horns by introducing a naturally occurring genetic variant, or allele, that is present in some breeds of beef cattle such as Angus.

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

Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull by Amy E. Young, Tamer A. Mansour, Bret R. McNabb, Joseph R. Owen, Josephine F. Trott, C. Titus Brown & Alison L. Van Eenennaam. Nature Biotechnology (2019) DOI: https://doi.org/10.1038/s41587-019-0266-0 Published 07 October 2019

This paper is open access.

Red wine for making wearable electronics?

Courtesy: University of Manchester [1920_stock-photo-red-wine-pouring-58843885-927462.jpg]

A July 12, 2019 news item on Nanowerk may change how you view that glass of red wine,

A team of scientists are seeking to kick-start a wearable technology revolution by creating flexible fibres and adding acids from red wine.

Extracting tannic acid from red wine, coffee or black tea, led a team of scientists from The University of Manchester to develop much more durable and flexible wearable devices. The addition of tannins improved mechanical properties of materials such as cotton to develop wearable sensors for rehabilitation monitoring, drastically increasing the devices lifespan.

A July 11, 2019 University of Manchester press release, which originated the news item, describes how this new approach could affect the scientists’ previous work,

The team have developed wearable devices such as capacitive breath sensors and artificial hands for extreme conditions by improving the durability of flexible sensors. Previously, wearable technology has been subject to fail after repeated bending and folding which can interrupt the conductivity of such devices due to tiny micro cracks. Improving this could open the door to more long-lasting integrated technology.

Dr Xuqing Liu who led the research team said: “We are using this method to develop new flexible, breathable, wearable devices. The main research objective of our group is to develop comfortable wearable devices for flexible human-machine interface.

“Traditional conductive material suffers from weak bonding to the fibers which can result in low conductivity. When red wine, or coffee, or black tea, is spilled on a dress, it’s difficult to get rid of these stains. The main reason is that they all contain tannic acid, which can firmly adsorb the material on the surface of the fiber. This good adhesion is exactly what we need for durable wearable, conductive devices.”

The new research published in the journal Small demonstrated that without this layer of tannic acid, the conductivity is several hundred times, or even thousands of times, less than traditional conductive material samples as the conductive coating becomes easily detached from the textile surface through repeated bending and flexing.

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

A Nature‐Inspired, Flexible Substrate Strategy for Future Wearable Electronics by Chuang Zhu, Evelyn Chalmers, Liming Chen, Yuqi Wang, Ben Bin Xu, Yi Li, Xuqing Liu. Small Online Version of Record before inclusion in an issue 1902440 DOI: https://doi.org/10.1002/smll.201902440 First published: 19 June 2019

This paper is behind a paywall.

Robotics where and how you don’t expect them: a wearable robot and a robot implant for regeneration

Generally I  expect robots to be machines that are external to my body but recently there were two news bits about some different approaches. First, the wearable robot.

A robot that supports your hip

A January 10, 2018 news item on ScienceDaily describes research into muscles that can be worn,

Scientists are one step closer to artificial muscles. Orthotics have come a long way since their initial wood and strap designs, yet innovation lapsed when it came to compensating for muscle power — until now.

A collaborative research team has designed a wearable robot to support a person’s hip joint while walking. The team, led by Minoru Hashimoto, a professor of textile science and technology at Shinshu University in Japan, published the details of their prototype in Smart Materials and Structures, a journal published by the Institute of Physics.

A January 9, 2018 Shinshu University press release on EurekAlert, which originated the news item, provides more detail,

“With a rapidly aging society, an increasing number of elderly people require care after suffering from stroke, and other-age related disabilities. Various technologies, devices, and robots are emerging to aid caretakers,” wrote Hashimoto, noting that several technologies meant to assist a person with walking are often cumbersome to the user. “[In our] current study, [we] sought to develop a lightweight, soft, wearable assist wear for supporting activities of daily life for older people with weakened muscles and those with mobility issues.”

The wearable system consists of plasticized polyvinyl chloride (PVC) gel, mesh electrodes, and applied voltage. The mesh electrodes sandwich the gel, and when voltage is applied, the gel flexes and contracts, like a muscle. It’s a wearable actuator, the mechanism that causes movement.

“We thought that the electrical mechanical properties of the PVC gel could be used for robotic artificial muscles, so we started researching the PVC gel,” said Hashimoto. “The ability to add voltage to PVC gel is especially attractive for high speed movement, and the gel moves with high speed with just a few hundred volts.”

In a preliminary evaluation, a stroke patient with some paralysis on one side of his body walked with and without the wearable system.

“We found that the assist wear enabled natural movement, increasing step length and decreasing muscular activity during straight line walking,” wrote Hashimoto. The researchers also found that adjusting the charge could change the level of assistance the actuator provides.

The robotic system earned first place in demonstrations with their multilayer PVC gel artificial muscle at the, “24th International Symposium on Smart Structures and Materials & Nondestructive Evaluation and Health Monitoring” for SPIE the international society for optics and photonics.

Next, the researchers plan to create a string actuator using the PVC gel, which could potentially lead to the development of fabric capable of providing more manageable external muscular support with ease.

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

PVC gel soft actuator-based wearable assist wear for hip joint support during walking by Yi Li and Minoru Hashimoto. Smart Materials and Structures, Volume 26, Number 12 DOI: 10.1088/1361-665X/aa9315 Published 30 October 2017

© 2017 IOP Publishing Ltd

This paper is behind a paywall and I see it was published in the Fall of 2017. Either they postponed the publicity or this is the second wave. In any event, it was timely as it allowed me to post this along with the robotic research on regeneration.

Robotic implants and tissue regeneration

Boston Children’s Hospital in a January 10, 2018 news release on EurekAlert describes a new (to me) method for tissue regeneration,

An implanted, programmable medical robot can gradually lengthen tubular organs by applying traction forces — stimulating tissue growth in stunted organs without interfering with organ function or causing apparent discomfort, report researchers at Boston Children’s Hospital.

The robotic system, described today in Science Robotics, induced cell proliferation and lengthened part of the esophagus in a large animal by about 75 percent, while the animal remained awake and mobile. The researchers say the system could treat long-gap esophageal atresia, a rare birth defect in which part of the esophagus is missing, and could also be used to lengthen the small intestine in short bowel syndrome.

The most effective current operation for long-gap esophageal atresia, called the Foker process, uses sutures anchored on the patient’s back to gradually pull on the esophagus. To prevent the esophagus from tearing, patients must be paralyzed in a medically induced coma and placed on mechanical ventilation in the intensive care unit for one to four weeks. The long period of immobilization can also cause medical complications such as bone fractures and blood clots.

“This project demonstrates proof-of-concept that miniature robots can induce organ growth inside a living being for repair or replacement, while avoiding the sedation and paralysis currently required for the most difficult cases of esophageal atresia,” says Russell Jennings, MD, surgical director of the Esophageal and Airway Treatment Center at Boston Children’s Hospital, and a co-investigator on the study. “The potential uses of such robots are yet to be fully explored, but they will certainly be applied to many organs in the near future.”

The motorized robotic device is attached only to the esophagus, so would allow a patient to move freely. Covered by a smooth, biocompatible, waterproof “skin,” it includes two attachment rings, placed around the esophagus and sewn into place with sutures. A programmable control unit outside the body applies adjustable traction forces to the rings, slowly and steadily pulling the tissue in the desired direction.

The device was tested in the esophagi of pigs (five received the implant and three served as controls). The distance between the two rings (pulling the esophagus in opposite directions) was increased by small, 2.5-millimeter increments each day for 8 to 9 days. The animals were able to eat normally even with the device applying traction to its esophagus, and showed no sign of discomfort.

On day 10, the segment of esophagus had increased in length by 77 percent on average. Examination of the tissue showed a proliferation of the cells that make up the esophagus. The organ also maintained its normal diameter.

“This shows we didn’t simply stretch the esophagus — it lengthened through cell growth,” says Pierre Dupont, PhD, the study’s senior investigator and Chief of Pediatric Cardiac Bioengineering at Boston Children’s.

The research team is now starting to test the robotic system in a large animal model of short bowel syndrome. While long-gap esophageal atresia is quite rare, the prevalence of short bowel syndrome is much higher. Short bowel can be caused by necrotizing enterocolitis in the newborn, Crohn’s disease in adults, or a serious infection or cancer requiring a large segment of intestine to be removed.

“Short bowel syndrome is a devastating illness requiring patients to be fed intravenously,” says gastroenterologist Peter Ngo, MD, a coauthor on the study. “This, in turn, can lead to liver failure, sometimes requiring a liver or multivisceral (liver-intestine) transplant, outcomes that are both devastating and costly.”

The team hopes to get support to continue its tests of the device in large animal models, and eventually conduct clinical trials. They will also test other features.

“No one knows the best amount of force to apply to an organ to induce growth,” explains Dupont. “Today, in fact, we don’t even know what forces we are applying clinically. It’s all based on surgeon experience. A robotic device can figure out the best forces to apply and then apply those forces precisely.”

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

In vivo tissue regeneration with robotic implants by Dana D. Damian, Karl Price, Slava Arabagi, Ignacio Berra, Zurab Machaidze, Sunil Manjila, Shogo Shimada, Assunta Fabozzo, Gustavo Arnal, David Van Story, Jeffrey D. Goldsmith, Agoston T. Agoston, Chunwoo Kim, Russell W. Jennings, Peter D. Ngo, Michael Manfredi, and Pierre E. Dupont. Science Robotics 10 Jan 2018: Vol. 3, Issue 14, eaaq0018 DOI: 10.1126/scirobotics.aaq0018

This paper is behind a paywall.