Tag Archives: explainer

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.

Probing the physical limits of plasmons in organic molecules with fewer than 50 atoms

A Sept. 5, 2018  news item on ScienceDaily introduces the work,

Rice University [Texas, US] researchers are probing the physical limits of excited electronic states called plasmons by studying them in organic molecules with fewer than 50 atoms.

A Sept. 4, 2018 Rice University news release (also on EurekAlert published on Sept. 5, 2018), which originated the news item, explains what plasmons are and why this research is being undertaken,

Plasmons are oscillations in the plasma of free electrons that constantly swirl across the surface of conductive materials like metals. In some nanomaterials, a specific color of light can resonate with the plasma and cause the electrons inside it to lose their individual identities and move as one, in rhythmic waves. Rice’s Laboratory for Nanophotonics (LANP) has pioneered a growing list of plasmonic technologies for applications as diverse as color-changing glass, molecular sensing, cancer diagnosis and treatment, optoelectronics, solar energy collection and photocatalysis.

Reporting online in the Proceedings of the National Academy of Sciences, LANP scientists detailed the results of a two-year experimental and theoretical study of plasmons in three different polycyclic aromatic hydrocarbons (PAHs). Unlike the plasmons in relatively large metal nanoparticles, which can typically be described with classical electromagnetic theory like Maxwell’s [James Clerk Maxwell] equations, the paucity of atoms in the PAHs produces plasmons that can only be understood in terms of quantum mechanics, said study co-author and co-designer Naomi Halas, the director of LANP and the lead researcher on the project.

“These PAHs are essentially scraps of graphene that contain five or six fused benzene rings surrounded by a perimeter of hydrogen atoms,” Halas said. “There are so few atoms in each that adding or removing even a single electron dramatically changes their electronic behavior.”

Halas’ team had experimentally verified the existence of molecular plasmons in several previous studies. But an investigation that combined side by side theoretical and experimental perspectives was needed, said study co-author Luca Bursi, a postdoctoral research associate and theoretical physicist in the research group of study co-designer and co-author Peter Nordlander.

“Molecular excitations are a ubiquity in nature and very well studied, especially for neutral PAHs, which have been considered as the standard of non-plasmonic excitations in the past,” Bursi said. “Given how much is already known about PAHs, they were an ideal choice for further investigation of the properties of plasmonic excitations in systems as small as actual molecules, which represent a frontier of plasmonics.”

Lead co-author Kyle Chapkin, a Ph.D. student in applied physics in the Halas research group, said, “Molecular plasmonics is a new area at the interface between plasmonics and molecular chemistry, which is rapidly evolving. When plasmonics reach the molecular scale, we lose any sharp distinction of what constitutes a plasmon and what doesn’t. We need to find a new rationale to explain this regime, which was one of the main motivations for this study.”

In their native state, the PAHs that were studied — anthanthrene, benzo[ghi]perylene and perylene — are charge-neutral and cannot be excited into a plasmonic state by the visible wavelengths of light used in Chapkin’s experiments. In their anionic form, the molecules contain an additional electron, which alters their “ground state” and makes them plasmonically active in the visible spectrum. By exciting both the native and anionic forms of the molecules and comparing precisely how they behaved as they relaxed back to their ground states, Chapkin and Bursi built a solid case that the anionic forms do support molecular plasmons in the visible spectrum.

The key, Chapkin said, was identifying a number of similarities between the behavior of known plasmonic particles and the anionic PAHs. By matching both the timescales and modes for relaxation behaviors, the LANP team built up a picture of a characteristic dynamics of low-energy plasmonic excitations in the anionic PAHs.

“In molecules, all excitations are molecular excitations, but select excited states show some characteristics that allow us to draw a parallel with the well-established plasmonic excitations in metal nanostructures,” Bursi said.

“This study offers a window on the sometimes surprising behavior of collective excitations in few-atom quantum systems,” Halas said. “What we’ve learned here will aid our lab and others in developing quantum-plasmonic approaches for ultrafast color-changing glass, molecular-scale optoelectronics and nonlinear plasmon-mediated optics.”

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

Lifetime dynamics of plasmons in the few-atom limit by Kyle D. Chapkin, Luca Bursi, Grant J. Stec, Adam Lauchner, Nathaniel J. Hogan, Yao Cui, Peter Nordlander, and Naomi J. Halas. PNAS September 11, 2018 115 (37) 9134-9139; published ahead of print August 27, 2018 DOI: https://doi.org/10.1073/pnas.1805357115

This paper is behind a paywall.

Nanoparticles and strange forces

An April 10, 2017 news item on Nanowerk announces work from the University of New Mexico (UNM), Note: A link has been removed,

A new scientific paper published, in part, by a University of New Mexico physicist is shedding light on a strange force impacting particles at the smallest level of the material world.

The discovery, published in Physical Review Letters (“Lateral Casimir Force on a Rotating Particle near a Planar Surface”), was made by an international team of researchers lead by UNM Assistant Professor Alejandro Manjavacas in the Department of Physics & Astronomy. Collaborators on the project include Francisco Rodríguez-Fortuño (King’s College London, U.K.), F. Javier García de Abajo (The Institute of Photonic Sciences, Spain) and Anatoly Zayats (King’s College London, U.K.).

An April 7,2017 UNM news release by Aaron Hill, which originated the news item, expands on the theme,

The findings relate to an area of theoretical nanophotonics and quantum theory known as the Casimir Effect, a measurable force that exists between objects inside a vacuum caused by the fluctuations of electromagnetic waves. When studied using classical physics, the vacuum would not produce any force on the objects. However, when looked at using quantum field theory, the vacuum is filled with photons, creating a small but potentially significant force on the objects.

“These studies are important because we are developing nanotechnologies where we’re getting into distances and sizes that are so small that these types of forces can dominate everything else,” said Manjavacas. “We know these Casimir forces exist, so, what we’re trying to do is figure out the overall impact they have very small particles.”

Manjavacas’ research expands on the Casimir effect by developing an analytical expression for the lateral Casimir force experienced by nanoparticles rotating near a flat surface.

Imagine a tiny sphere (nanoparticle) rotating over a surface. While the sphere slows down due to photons colliding with it, that rotation also causes the sphere to move in a lateral direction. In our physical world, friction between the sphere and the surface would be needed to achieve lateral movement. However, the nano-world does not follow the same set of rules, eliminating the need for contact between the sphere and the surface for movement to occur.

“The nanoparticle experiences a lateral force as if it were in contact with the surface, even though is actually separated from it,” said Manjavacas. “It’s a strange reaction but one that may prove to have significant impact for engineers.”

While the discovery may seem somewhat obscure, it is also extremely useful for researchers working in the always evolving nanotechnology industry. As part of their work, Manjavacas says they’ve also learned the direction of the force can be controlled by changing the distance between the particle and surface, an understanding that may help nanotech engineers develop better nanoscale objects for healthcare, computing or a variety of other areas.

For Manjavacas, the project and this latest publication are just another step forward in his research into these Casimir forces, which he has been studying throughout his scientific career. After receiving his Ph.D. from Complutense University of Madrid (UCM) in 2013, Manjavacas worked as a postdoctoral research fellow at Rice University before coming to UNM in 2015.

Currently, Manjavacas heads UNM’s Theoretical Nanophotonics research group, collaborating with scientists around the world and locally in New Mexico. In fact, Manjavacas credits Los Alamos National Laboratory Researcher Diego Dalvit, a leading expert on Casimir forces, for helping much of his work progress.

“If I had to name the person who knows the most about Casimir forces, I’d say it was him,” said Manjavacas. “He published a book that’s considered one of the big references on the topic. So, having him nearby and being able to collaborate with other UNM faculty is a big advantage for our research.”

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

Lateral Casimir Force on a Rotating Particle near a Planar Surface by Alejandro Manjavacas, Francisco J. Rodríguez-Fortuño, F. Javier García de Abajo, and Anatoly V. Zayats. Phys. Rev. Lett. (Vol. 118, Iss. 13 — 31 March 2017) 118, 133605 DOI:https://doi.org/10.1103/PhysRevLett.118.133605 Published 31 March 2017

This paper is behind a paywall.

3D bioprinting: a conference about the latest trends (May 3 – 5, 2017 at the University of British Columbia, Vancouver)

The University of British Columbia’s (UBC) Peter Wall Institute for Advanced Studies (PWIAS) is hosting along with local biotech firm, Aspect Biosystems, a May 3 -5, 2017 international research roundtable known as ‘Printing the Future of Therapeutics in 3D‘.

A May 1, 2017 UBC news release (received via email) offers some insight into the field of bioprinting from one of the roundtable organizers,

This week, global experts will gather [4] at the University of British
Columbia to discuss the latest trends in 3D bioprinting—a technology
used to create living tissues and organs.

In this Q&A, UBC chemical and biological engineering professor
Vikramaditya Yadav [5], who is also with the Regenerative Medicine
Cluster Initiative in B.C., explains how bioprinting could potentially
transform healthcare and drug development, and highlights Canadian
innovations in this field.

WHY IS 3D BIOPRINTING SIGNIFICANT?

Bioprinted tissues or organs could allow scientists to predict
beforehand how a drug will interact within the body. For every
life-saving therapeutic drug that makes its way into our medicine
cabinets, Health Canada blocks the entry of nine drugs because they are
proven unsafe or ineffective. Eliminating poor-quality drug candidates
to reduce development costs—and therefore the cost to consumers—has
never been more urgent.

In Canada alone, nearly 4,500 individuals are waiting to be matched with
organ donors. If and when bioprinters evolve to the point where they can
manufacture implantable organs, the concept of an organ transplant
waiting list would cease to exist. And bioprinted tissues and organs
from a patient’s own healthy cells could potentially reduce the risk
of transplant rejection and related challenges.

HOW IS THIS TECHNOLOGY CURRENTLY BEING USED?

Skin, cartilage and bone, and blood vessels are some of the tissue types
that have been successfully constructed using bioprinting. Two of the
most active players are the Wake Forest Institute for Regenerative
Medicine in North Carolina, which reports that its bioprinters can make
enough replacement skin to cover a burn with 10 times less healthy
tissue than is usually needed, and California-based Organovo, which
makes its kidney and liver tissue commercially available to
pharmaceutical companies for drug testing.

Beyond medicine, bioprinting has already been commercialized to print
meat and artificial leather. It’s been estimated that the global
bioprinting market will hit $2 billion by 2021.

HOW IS CANADA INVOLVED IN THIS FIELD?

Canada is home to some of the most innovative research clusters and
start-up companies in the field. The UBC spin-off Aspect Biosystems [6]
has pioneered a bioprinting paradigm that rapidly prints on-demand
tissues. It has successfully generated tissues found in human lungs.

Many initiatives at Canadian universities are laying strong foundations
for the translation of bioprinting and tissue engineering into
mainstream medical technologies. These include the Regenerative Medicine
Cluster Initiative in B.C., which is headed by UBC, and the University
of Toronto’s Institute of Biomaterials and Biomedical Engineering.

WHAT ETHICAL ISSUES DOES BIOPRINTING CREATE?

There are concerns about the quality of the printed tissues. It’s
important to note that the U.S. Food and Drug Administration and Health
Canada are dedicating entire divisions to regulation of biomanufactured
products and biomedical devices, and the FDA also has a special division
that focuses on regulation of additive manufacturing – another name
for 3D printing.

These regulatory bodies have an impressive track record that should
assuage concerns about the marketing of substandard tissue. But cost and
pricing are arguably much more complex issues.

Some ethicists have also raised questions about whether society is not
too far away from creating Replicants, à la _Blade Runner_. The idea is
fascinating, scary and ethically grey. In theory, if one could replace
the extracellular matrix of bones and muscles with a stronger substitute
and use cells that are viable for longer, it is not too far-fetched to
create bones or muscles that are stronger and more durable than their
natural counterparts.

WILL DOCTORS BE PRINTING REPLACEMENT BODY PARTS IN 20 YEARS’ TIME?

This is still some way off. Optimistically, patients could see the
technology in certain clinical environments within the next decade.
However, some technical challenges must be addressed in order for this
to occur, beginning with faithful replication of the correct 3D
architecture and vascularity of tissues and organs. The bioprinters
themselves need to be improved in order to increase cell viability after
printing.

These developments are happening as we speak. Regulation, though, will
be the biggest challenge for the field in the coming years.

There are some events open to the public (from the international research roundtable homepage),

OPEN EVENTS

You’re invited to attend the open events associated with Printing the Future of Therapeutics in 3D.

Café Scientifique

Thursday, May 4, 2017
Telus World of Science
5:30 – 8:00pm [all tickets have been claimed as of May 2, 2017 at 3:15 pm PT]

3D Bioprinting: Shaping the Future of Health

Imagine a world where drugs are developed without the use of animals, where doctors know how a patient will react to a drug before prescribing it and where patients can have a replacement organ 3D-printed using their own cells, without dealing with long donor waiting lists or organ rejection. 3D bioprinting could enable this world. Join us for lively discussion and dessert as experts in the field discuss the exciting potential of 3D bioprinting and the ethical issues raised when you can print human tissues on demand. This is also a rare opportunity to see a bioprinter live in action!

Open Session

Friday, May 5, 2017
Peter Wall Institute for Advanced Studies
2:00 – 7:00pm

A Scientific Discussion on the Promise of 3D Bioprinting

The medical industry is struggling to keep our ageing population healthy. Developing effective and safe drugs is too expensive and time-consuming to continue unchanged. We cannot meet the current demand for transplant organs, and people are dying on the donor waiting list every day.  We invite you to join an open session where four of the most influential academic and industry professionals in the field discuss how 3D bioprinting is being used to shape the future of health and what ethical challenges may be involved if you are able to print your own organs.

ROUNDTABLE INFORMATION

The University of British Columbia and the award-winning bioprinting company Aspect Biosystems, are proud to be co-organizing the first “Printing the Future of Therapeutics in 3D” International Research Roundtable. This event will congregate global leaders in tissue engineering research and pharmaceutical industry experts to discuss the rapidly emerging and potentially game-changing technology of 3D-printing living human tissues (bioprinting). The goals are to:

Highlight the state-of-the-art in 3D bioprinting research
Ideate on disruptive innovations that will transform bioprinting from a novel research tool to a broadly adopted systematic practice
Formulate an actionable strategy for industry engagement, clinical translation and societal impact
Present in a public forum, key messages to educate and stimulate discussion on the promises of bioprinting technology

The Roundtable will bring together a unique collection of industry experts and academic leaders to define a guiding vision to efficiently deploy bioprinting technology for the discovery and development of new therapeutics. As the novel technology of 3D bioprinting is more broadly adopted, we envision this Roundtable will become a key annual meeting to help guide the development of the technology both in Canada and globally.

We thank you for your involvement in this ground-breaking event and look forward to you all joining us in Vancouver for this unique research roundtable.

Kind Regards,
The Organizing Committee
Christian Naus, Professor, Cellular & Physiological Sciences, UBC
Vikram Yadav, Assistant Professor, Chemical & Biological Engineering, UBC
Tamer Mohamed, CEO, Aspect Biosystems
Sam Wadsworth, CSO, Aspect Biosystems
Natalie Korenic, Business Coordinator, Aspect Biosystems

I’m glad to see this event is taking place—and with public events too! (Wish I’d seen the Café Scientifique announcement earlier when I first checked for tickets  yesterday. I was hoping there’d been some cancellations today.) Finally, for the interested, you can find Aspect Biosystems here.