Tag Archives: DuPont

The CRISPR yogurt story and a hornless cattle update

Leave a reply

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.

“Breaking Me Softly” at the nanoscale

Leave a reply

“Breaking Me Softly” sounds like a song title but in this case the phrase as been coined to describe a new technique for controlling materials at the nanoscale according to a June 6, 2016 news item on ScienceDaily,

A finding by a University of Central Florida researcher that unlocks a means of controlling materials at the nanoscale and opens the door to a new generation of manufacturing is featured online in the journal Nature.

Using a pair of pliers in each hand and gradually pulling taut a piece of glass fiber coated in plastic, associate professor Ayman Abouraddy found that something unexpected and never before documented occurred — the inner fiber fragmented in an orderly fashion.

“What we expected to see happen is NOT what happened,” he said. “While we thought the core material would snap into two large pieces, instead it broke into many equal-sized pieces.”

He referred to the technique in the Nature article title as “Breaking Me Softly.”

A June 6, 2016 University of Central Florida (UCF) news release (also on EurekAlert) by Barbara Abney, which originated the news item, expands on the theme,

The process of pulling fibers to force the realignment of the molecules that hold them together, known as cold drawing, has been the standard for mass production of flexible fibers like plastic and nylon for most of the last century.

Abouraddy and his team have shown that the process may also be applicable to multi-layered materials, a finding that could lead to the manufacturing of a new generation of materials with futuristic attributes.

“Advanced fibers are going to be pursuing the limits of anything a single material can endure today,” Abouraddy said.

For example, packaging together materials with optical and mechanical properties along with sensors that could monitor such vital sign as blood pressure and heart rate would make it possible to make clothing capable of transmitting vital data to a doctor’s office via the Internet.

The ability to control breakage in a material is critical to developing computerized processes for potential manufacturing, said Yuanli Bai, a fracture mechanics specialist in UCF’s College of Engineering and Computer Science.

Abouraddy contacted Bai, who is a co-author on the paper, about three years ago and asked him to analyze the test results on a wide variety of materials, including silicon, silk, gold and even ice.

He also contacted Robert S. Hoy, a University of South Florida physicist who specializes in the properties of materials like glass and plastic, for a better understanding of what he found.

Hoy said he had never seen the phenomena Abouraddy was describing, but that it made great sense in retrospect.

The research takes what has traditionally been a problem in materials manufacturing and turned it into an asset, Hoy said.

“Dr. Abouraddy has found a new application of necking” –  a process that occurs when cold drawing causes non-uniform strain in a material, Hoy said.  “Usually you try to prevent necking, but he exploited it to do something potentially groundbreaking.”

The necking phenomenon was discovered decades ago at DuPont and ushered in the age of textiles and garments made of synthetic fibers.

Abouraddy said that cold-drawing is what makes synthetic fibers like nylon and polyester useful. While those fibers are initially brittle, once cold-drawn, the fibers toughen up and become useful in everyday commodities. This discovery at DuPont at the end of the 1920s ushered in the age of textiles and garments made of synthetic fibers.

Only recently have fibers made of multiple materials become possible, he said.  That research will be the centerpiece of a $317 Million U.S. Department of Defense program focused on smart fibers that Abouraddy and UCF will assist with.   The Revolutionary Fibers and Textiles Manufacturing Innovation Institute (RFT-MII), led by the Massachusetts Institute of Technology, will incorporate research findings published in the Nature paper, Abouraddy said.

The implications for manufacturing of the smart materials of the future are vast.

By controlling the mechanical force used to pull the fiber and therefore controlling the breakage patterns, materials can be developed with customized properties allowing them to interact with each other and eternal forces such as the sun (for harvesting energy) and the internet in customizable ways.

A co-author on the paper, Ali P. Gordon, an associate professor in the Department of Mechanical & Aerospace Engineering and director of UCF’s Mechanics of Materials Research Group said that the finding is significant because it shows that by carefully controlling the loading condition imparted to the fiber, materials can be developed with tailored performance attributes.

“Processing-structure-property relationships need to be strategically characterized for complex material systems. By combining experiments, microscopy, and computational mechanics, the physical mechanisms of the fragmentation process were more deeply understood,” Gordon said.

Abouraddy teamed up with seven UCF scientists from the College of Optics & Photonics and the College of Engineering & Computer Science (CECS) to write the paper.   Additional authors include one researcher each from the Massachusetts Institute of Technology, Nanyang Technological University in Singapore and the University of South Florida.

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

Controlled fragmentation of multimaterial fibres and films via polymer cold-drawing by Soroush Shabahang, Guangming Tao, Joshua J. Kaufman, Yangyang Qiao, Lei Wei, Thomas Bouchenot, Ali P. Gordon, Yoel Fink, Yuanli Bai, Robert S. Hoy & Ayman F. Abouraddy. Nature (2016) doi:10.1038/nature17980 Published online  06 June 2016

This paper is behind a paywall.

Corporate influence, nanotechnology regulation, and Friends of the Earth (FoE) Australia

Leave a reply

The latest issue of the newsletter, Chain Reaction # 121, July 2014, published by Friends of the Earth (FoE) Australia features an article by Louise Sales ‘Corporate influence over nanotechnology regulation‘ that has given me pause. From the Sales article,

I recently attended an Organisation for Economic Co-operation and Development (OECD) seminar on the risk assessment and risk management of nanomaterials. This was an eye-opening experience that graphically illustrated the extent of corporate influence over nanotechnology regulation globally. Representatives of the chemical companies DuPont and Evonik; the Nanotechnology Industries Association; and the Business and Industry Advisory Committee to the OECD (BIAC) sat alongside representatives of countries such as Australia, the US and Canada and were given equal speaking time.

BIAC gave a presentation on their work with the Canadian and United States Governments to harmonise nanotechnology regulation between the two countries. [US-Canada Regulatory Cooperative Council] [emphasis mine] Repeated reference to the involvement of ‘stakeholders’ prompted me to ask if any NGOs [nongovernmental organizations] were involved in the process. Only in the earlier stages apparently − ‘stakeholders’ basically meant industry.

A representative of the Nanotechnology Industries Association told us about the European NANoREG project they are leading in collaboration with regulators, industry and scientists. This is intended to ‘develop … new testing strategies adapted to innovation requirements’ and to ‘establish a close collaboration among authorities, industry and science leading to efficient and practically applicable risk management approaches’. In other words industry will be helping write the rules.

Interestingly, when I raised concerns about this profound intertwining of government and industry with one of the other NGO representatives they seemed almost dismissive of my concerns. I got the impression that most of the parties concerned thought that this was just the ‘way things were’. As under-resourced regulators struggle with the regulatory challenges posed by nanotechnology − the offer of industry assistance is probably very appealing. And from the rhetoric at the meeting one could be forgiven for thinking that their objectives are very similar − to ensure that their products are safe. Right? Wrong.

I just published an update about the US-Canada Regulatory Cooperation Council (RCC; in  my July 14, 2014 posting) where I noted the RCC has completed its work and final reports are due later this summer. Nowhere in any of the notices is there mention of BIAC’s contribution (whatever it might have been) to this endeavour.

Interestingly. BIAC is not an OECD committee but a separate organization as per its About us page,

BIAC is an independent international business association devoted to advising government policymakers at OECD and related fora on the many diversified issues of globalisation and the world economy.

Officially recognised since its founding in 1962 as being representative of the OECD business community, BIAC promotes the interests of business by engaging, understanding and advising policy makers on a broad range of issues with the overarching objectives of:

  • Positively influencing the direction of OECD policy initiatives;

  • Ensuring business and industry needs are adequately addressed in OECD policy decision instruments (policy advocacy), which influence national legislation;

  • Providing members with timely information on OECD policies and their implications for business and industry.

Through its 38 policy groups, which cover the major aspects of OECD work most relevant to business, BIAC members participate in meetings, global forums and consultations with OECD leadership, government delegates, committees and working groups.

I don’t see any mention of safety either in the excerpt or elsewhere on their About us page.

As Sales notes in her article,

Ultimately corporations have one primary driver and that’s increasing their bottom line.

I do wonder why there doesn’t seem to have been any transparency regarding BIAC’s involvement with the RCC and why no NGOs (according to Sales) were included as stakeholders.

While I sometimes find FoE and its fellow civil society groups a bit shrill and over-vehement at times, It never does to get too complacent. For example, who would have thought that General Motors would ignore safety issues (there were car crashes and fatalities as a consequence) over the apparently miniscule cost of changing an ignition switch. From What is the timeline of the GM recall scandal? on Vox.com,

…

March 2005: A GM project engineering manager closed the investigation into the faulty switches, noting that they were too costly to fix. In his words: “lead time for all solutions is too long” and “the tooling cost and piece price are too high.” Later emails unearthed by Reuters suggested that the fix would have cost GM 90 cents per car. [emphasis mine]

…

March 2007: Safety regulators inform GM of the death of Amber Rose, who crashed her Chevrolet Cobalt in 2005 after the ignition switch shut down the car’s electrical system and air bags failed to deploy. Neither the company nor regulators open an investigation.

…

End of 2013: GM determines that the faulty ignition switch is to blame for at least 31 crashes and 13 deaths.

…

According to a July 17, 2014 news item on CBC (Canadian Broadcasting Corporation) news online, Mary Barra, CEO of General Motors, has testified on the mater before the US Senate for a 2nd time, this year,

A U.S. Senate panel posed questions to a new set of key players Thursday [July 17, 2014] as it delves deeper into General Motors’ delayed recall of millions of small cars.

…

An internal report found GM attorneys signed settlements with the families of crash victims but didn’t tell engineers or top executives about mounting problems with ignition switches. It also found that GM’s legal staff acted without urgency.

GM says faulty ignition switches were responsible for at least 13 deaths. It took the company 11 years to recall the cars.

…

Barra will certainly be asked about how she’s changing a corporate culture that allowed a defect with ignition switches to remain hidden from the car-buying public for 11 years. It will be Barra’s second time testifying before the panel.

H/T ICON (International Council on Nanotechnology) July 16, 2014 news item. Following on the topic of transparency, ICON based at Rice University in Texas (US) has a Sponsors webpage.

US Dept. of Agriculture wants to commercialize cellulose nanomaterials

Leave a reply

Lynn Bergeson in an April 7, 2014 posting on the Nanotechnology Now website announced an upcoming ‘nano commercialization’ workshop (Note: A link has been removed),

The U.S. Department of Agriculture (USDA) and National Nanotechnology Initiative (NNI) will hold a May 20-21, 2014, workshop entitled “Cellulose Nanomaterial — A Path Towards Commercialization.” See http://www.nano.gov/ncworkshop The workshop is intended to bring together high level executives from government and multiple industrial sectors to identify pathways for the commercialization of cellulose nanomaterials and facilitate communication across industry sectors to determine common challenges.

You can find out more about the Cellulose Nanomaterial — A Path Towards Commercialization workshop here where you can also register and find an agenda, (Note: Links have been removed),

The primary goal of the workshop is to identify the critical information gaps and technical barriers in the commercialization of cellulose nanomaterials with expert input from user communities. The workshop also supports the announcement last December by USDA Secretary Thomas Vilsack regarding the formation of a public-private partnership between the USDA Forest Service and the U.S. Endowment for Forestry and Communities to rapidly advance the commercialization of cellulose nanomaterials. In addition, the workshop supports the goals of the NNI Sustainable Nanomanufacturing Signature Initiative/

The workshop is open to the public, after registration, on a first-come, first-served basis.

There is an invitation letter dated Feb. 7, 2014, which provides some additional detail,

The primary goals of the workshop are to identify critical information gaps and technical barriers in the commercialization of cellulose nanomaterials with expert input from user communities. We plan to use the outcome of the workshop to guide research planning in P3Nano and in the Federal Government.

The Cellulose Nanomaterial — A Path Towards Commercialization workshop agenda lists some interesting names. The names I’ve chosen from the list are the speakers from the corporate sectors, all eight of them with two being tentatively scheduled; there are 22 speakers listed in total at this time,

Tom Connelly – DuPont (Tentative)
Travis Earles, Technology Manager, Lockheed Martin
Beth Cormier, Vice President for R&D and Technology, SAPPI Paper
Ed Socci, Director of Beverage Packaging, PepsiCo Advanced Research
Mark Harmon, DuPont (tentative)
Kim Nelson, Vice President for Government Affairs, API
Jean Moreau, CEO, CelluForce
Yoram Shkedi, Melodea

For the most part the speakers will be academics or government bureaucrats and while the title is ‘cellulose nanomaterials’ the speaker list suggests the topic will be heavily weighted to CNC/NCC (cellulose nanocrystals, aka, nanocrystalline cellulose). Of course, I recognize the Canadian, Jean Moreau of CelluForce, a Canadian CNC production facility. I wonder if he will be discussing the stockpile, which was first mentioned here in my Oct. 3, 2013 posting,

I stumbled across an interesting little article on the Celluforce website about the current state of NCC (nanocrystalline cellulose aka CNC [cellulose nanocrystals]) production, Canada’s claim to fame in the nanocellulose world. From an August 2013 Natural Resources Canada, Canadian Forest Service, Spotlight series article,

The pilot plant, located at the Domtar pulp and paper mill in Windsor, Quebec, is a joint venture between Domtar and FPInnnovations called CelluForce. The plant, which began operations in January 2012, has since successfully demonstrated its capacity to produce NCC on a continuous basis, thus enabling a sufficient inventory of NCC to be collected for product development and testing. Operations at the pilot plant are temporarily on hold while CelluForce evaluates the potential markets for various NCC applications with its stockpiled material. [emphasis mine]

I also recognized Melodea which I mentioned here in an Oct. 31, 2013 posting titled: Israeli start-up Melodea and its nanocrystalline cellulose (NCC) projects.

A couple of final notes here, NCC (nanocrystalline cellulose) is also known as cellulose nanocrystals (CNC) and I believe the second term is becoming the more popular one to use. As for the final of these two notes, I had an illuminating conversation earlier this year (2014) about CNC and its accessibility. According to my source, there’s been a decision that only large industry players will get access to CNC for commercialization purposes. I can’t verify the veracity of the statement but over the last few years I’ve had a few individual entrepreneurs contact me with hopes that i could help them access the materials. All of them of them had tried the sources I was to suggest and not one had been successful. As well, I note the speaker list includes someone from PepsiCo, someone from Dupont, and someone from Lockheed Martin, all of which could be described as large industry players. (I’m not familiar with either API or SAPPI Paper so cannot offer any opinions as to their size or importance.) Melodea’s access is government-mandated due to research grants from the European Union’s Seventh Framework Program (FP7).

I’m not sure one can encourage innovation by restricting access to raw materials to large industry players or government-funded projects as one might be suspected from my back channel experience, the conversation as reported to me, and the speaker list for this workshop.