Tag Archives: cheese

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.

Fantastic Fungi Futures: a multi-night ArtSci Salon event in late November/early December 2019 in Toronto

In fact, I have two items about fungi and I’m starting with the essay first.

Giving thanks for fungi

These foods are all dependent on microorganisms for their distinctive flavor. Credit: margouillat photo/Shutterstock.com

Antonis Rokas, professor at Venderbilt University (Nashville, Tennessee, US), has written a November 25, 2019 essay for The Conversation (h/t phys.org Nov.26.19) featuring fungi and food, Note: Links have been removed),

I am an evolutionary biologist studying fungi, a group of microbes whose domestication has given us many tasty products. I’ve long been fascinated by two questions: What are the genetic changes that led to their domestication? And how on Earth did our ancestors figure out how to domesticate them?

The hybrids in your lager

As far as domestication is concerned, it is hard to top the honing of brewer’s yeast. The cornerstone of the baking, brewing and wine-making industries, brewer’s yeast has the remarkable ability to turn the sugars of plant fruits and grains into alcohol. How did brewer’s yeast evolve this flexibility?

By discovering new yeast species and sequencing their genomes, scientists know that some yeasts used in brewing are hybrids; that is, they’re descendants of ancient mating unions of individuals from two different yeast species. Hybrids tend to resemble both parental species – think of wholpins (whale-dolphin) or ligers (lion-tiger).

… What is still unknown is whether hybridization is the norm or the exception in the yeasts that humans have used for making fermented beverages for millennia.

To address this question, a team led by graduate student Quinn Langdon at the University of Wisconsin and another team led by postdoctoral fellow Brigida Gallone at the Universities of Ghent and Leuven in Belgium examined the genomes of hundreds of yeasts involved in brewing and wine making. Their bottom line? Hybrids rule.

For example, a quarter of yeasts collected from industrial environments, including beer and wine manufacturers, are hybrids.

The mutants in your cheese

Comparing the genomes of domesticated fungi to their wild relatives helps scientists understand the genetic changes that gave rise to some favorite foods and drinks. But how did our ancestors actually domesticate these wild fungi? None of us was there to witness how it all started. To solve this mystery, scientists are experimenting with wild fungi to see if they can evolve into organisms resembling those that we use to make our food today.

Benjamin Wolfe, a microbiologist at Tufts University, and his team addressed this question by taking wild Penicillium mold and growing the samples for one month in his lab on a substance that included cheese. That may sound like a short period for people, but it is one that spans many generations for fungi.

The wild fungi are very closely related to fungal strains used by the cheese industry in the making of Camembert cheese, but look very different from them. For example, wild strains are green and smell, well, moldy compared to the white and odorless industrial strains.

For Wolfe, the big question was whether he could experimentally recreate, and to what degree, the process of domestication. What did the wild strains look and smell like after a month of growth on cheese? Remarkably, what he and his team found was that, at the end of the experiment, the wild strains looked much more similar to known industrial strains than to their wild ancestor. For example, they were white in color and smelled much less moldy.

… how did the wild strain turn into a domesticated version? Did it mutate? By sequencing the genomes of both the wild ancestors and the domesticated descendants, and measuring the activity of the genes while growing on cheese, Wolfe’s team figured out that these changes did not happen through mutations in the organisms’ genomes. Rather, they most likely occurred through chemical alterations that modify the activity of specific genes but don’t actually change the genetic code. Such so-called epigenetic modifications can occur much faster than mutations.

Fantastic Fungi Futures (FFF) Nov. 29, Dec. 1, and Dec. 4, 2019 events in Toronto, Canada

The ArtSci Salon emailed me a November 23, 2019 announcement about a special series being presented in partnership with the Mycological Society of Toronto (MST) on the topic of fungi,

Fantastic Fungi Futures a discussion, a mini exhibition, a special screening, and a workshop revolving around Fungi and their versatile nature.

NOV 29 [2019], 6:00-8:00 PM Fantastic Fungi Futures (FFF): a roundtable discussion and popup exhibition.

Join us for a roundtable discussion. what are the potentials of fungi? Our guests will share their research, as well as professional and artistic practice dealing with the taxonomy and the toxicology, the health benefits and the potentials for sustainability, as well as the artistic and architectural virtues of fungi and mushrooms. The Exhibition will feature photos and objects created by local and Canadian artists who have been working with mushrooms and fungi.

This discussion is in anticipation of the special screening of Fantastic Fungi at the HotDocs Cinema on Dec 1 [2019] our guests:James Scott,Occupational & Environmental Health, Dalla Lana School of Public Health, UofT; Marshall Tyler, Director of Research, Field Trip, Toronto; Rotem Petranker, PhD student, Social Psychology, York University; Nourin Aman, PhD student, fungal biology and Systematics lab, Punjab University; Sydney Gram, PhD student, Ecology & Evolutionary Biology student researcher (UofT/ROM); [and] Tosca Teran, Interdisciplinary artist.

DEC. 1 [2019], 6:15 pm join us to the screening of Fantastic Fungi, at the HotDocs Cinemaget your tickets herehttps://boxoffice.hotdocs.ca/websales/pages/info.aspx?evtinfo=104145~fff311b7-cdad-4e14-9ae4-a9905e1b9cb0 afterward, some of us will be heading to the Pauper’s Pub, just across from the HotDocs Cinema

DEC. 4 [2019], 7:00-10:00PM Multi-species entanglements:Sculpting with Mycelium, @InterAccess, 950 Dupont St., Unit 1 

This workshop is a continuation of ArtSci Salon’s Fantastic Fungi Futures event and the HotDocs screening of Fantastic Fungi.this workshop is open to public to attend, however, pre-registration is required. $5.00 to form a mycelium bowl to take home.

During this workshop Tosca Teran introduces the amazing potential of Mycelium for collaboration at the intersection of art and science. Participants learn how to transform their kitchens and closets in to safe, mini-Mycelium biolabs and have the option to leave the workshop with a live Mycelium planter/bowl form, as well as a wide array of possibilities of how they might work with this sustainable bio-material. 

Bios

Nourin Aman is a PhD student at fungal biology and Systematics lab at Punjab University, Lahore, Pakistan. She is currently a visiting PhD student at the Mycology lab, Royal Ontario Museum. Her research revolves around comparison between macrofungal biodiversity of some reserve forests of Punjab, Pakistan.Her interest is basically to enlist all possible macrofungi of reserve forests under study and describe new species as well from area as our part of world still has many species to be discovered and named. She will be discussing factors which are affecting the fungal biodiversity in these reserve forests.

Sydney Gram is an Ecology & Evolutionary Biology student researcher (UofT/ROM)

Rotem Petranker- Bsc in psychology from the University of Toronto and a MA in social psychology from York University. Rotem is currently a PhD student in York’s clinical psychology program. His main research interest is affect regulation, and the way it interacts with sustained attention, mind wandering, and creativity. Rotem is a founding member oft the Psychedelic Studies Research Program at the University of Toronto, has published work on microdosing, and presented original research findings on psychedelic research in several conferences. He feels strongly that the principles of Open Science are necessary in order to do good research, and is currently in the process of starting the first lab study of microdosing in Canada.

James Scott– PhD, is a ARMCCM Professor and Head Division of Occupational & Environmental Health, Dalla Lana School of Public Health, University of TorontoUAMH Fungal Biobank: http://www.uamh.caUniversity Profile: http://www.dlsph.utoronto.ca/faculty-profile/scott-james-a/Research Laboratory: http://individual.utoronto.ca/jscottCommercial Laboratory: http://www.sporometrics.com

Marshall Tyler– Director of Research, Field Trip. Marshall is a scientist with a deep interest in psychoactive molecules. His passion lies in guiding research to arrive at a deeper understanding of consciousness with the ultimate goal of enhancing wellbeing. At Field Trip, he is helping to develop a lab in Jamaica to explore the chemical and biological complexities of psychoactive fungi.

Tosca Teran, aka Nanotopia, is an Multi-disciplinary artist. Her work has been featured at SOFA New York, Culture Canada, and The Toronto Design Exchange. Tosca has been awarded artist residencies with The Ayatana Research Program in Ottawa and The Icelandic Visual Artists Association through Sím, Reykjavik Iceland and Nes artist residency in Skagaströnd, Iceland. In 2019 she was one of the first Bio-Artists in residence at the Museum of Contemporary Art Toronto in partnership with the Ontario Science Centre as part of the Alien Agencies Collective. A recipient of the 2019 BigCi Environmental Award at Wollemi National Park within the UNESCO World Heritage site in the Greater Blue Mountains. Tosca started collaborating artistically with Algae, Physarum polycephalum, and Mycelium in 2016, translating biodata from non-human organisms into music.@MothAntler @nanopodstudio www.toscateran.com www.nanotopia.net8 

A trailer has been provided for the movie mentioned in the announcement (from the Fantastic Fungi screening webpage on the Mycological Society of Toronto website),

You can find the ArtSci Salon here and the Mycological Society of Toronto (MST) here.