Tag Archives: plants

CRISPR patent decision: Harvard’s and MIT’s Broad Institute victorious—for now

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I have written about the CRISPR patent tussle (Harvard & MIT’s [Massachusetts Institute of Technology] Broad Institute vs the University of California at Berkeley) previously in a Jan. 6, 2015 posting and in a more detailed May 14, 2015 posting. I also mentioned (in a Jan. 17, 2017 posting) CRISPR and its patent issues in the context of a posting about a Slate.com series on Frankenstein and the novel’s applicability to our own time. This patent fight is being bitterly fought as fortunes are at stake.

It seems a decision has been made regarding the CRISPR patent claims. From a Feb. 17, 2017 article by Charmaine Distor for The Science Times,

After an intense court battle, the US Patent and Trademark Office (USPTO) released its ruling on February 15 [2017]. The rights for the CRISPR-Cas9 gene editing technology was handed over to the Broad Institute of Harvard University and the Massachusetts Institute of Technology (MIT).

According to an article in Nature, the said court battle was between the Broad Institute and the University of California. The two institutions are fighting over the intellectual property right for the CRISPR patent. The case between the two started when the patent was first awarded to the Broad Institute despite having the University of California apply first for the CRISPR patent.

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Heidi Ledford’s Feb. 17, 2017 article for Nature provides more insight into the situation (Note: Links have been removed),

It [USPTO] ruled that the Broad Institute of Harvard and MIT in Cambridge could keep its patents on using CRISPR–Cas9 in eukaryotic cells. That was a blow to the University of California in Berkeley, which had filed its own patents and had hoped to have the Broad’s thrown out.

The fight goes back to 2012, when Jennifer Doudna at Berkeley, Emmanuelle Charpentier, then at the University of Vienna, and their colleagues outlined how CRISPR–Cas9 could be used to precisely cut isolated DNA1. In 2013, Feng Zhang at the Broad and his colleagues — and other teams — showed2 how it could be adapted to edit DNA in eukaryotic cells such as plants, livestock and humans.

Berkeley filed for a patent earlier, but the USPTO granted the Broad’s patents first — and this week upheld them. There are high stakes involved in the ruling. The holder of key patents could make millions of dollars from CRISPR–Cas9’s applications in industry: already, the technique has sped up genetic research, and scientists are using it to develop disease-resistant livestock and treatments for human diseases.

But the fight for patent rights to CRISPR technology is by no means over. Here are four reasons why.

1. Berkeley can appeal the ruling

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2. European patents are still up for grabs

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3. Other parties are also claiming patent rights on CRISPR–Cas9

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4. CRISPR technology is moving beyond what the patents cover

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As for Ledford’s 3rd point, there are an estimated 763 patent families (groups of related patents) claiming CAS9 leading to the distinct possibility that the Broad Institute will be fighting many patent claims in the future.

Once you’ve read Distor’s and Ledford’s articles, you may want to check out Adam Rogers’ and Eric Niiler’s Feb. 16, 2017 CRISPR patent article for Wired,

The fight over who owns the most promising technique for editing genes—cutting and pasting the stuff of life to cure disease and advance scientific knowledge—has been a rough one. A team on the West Coast, at UC Berkeley, filed patents on the method, Crispr-Cas9; a team on the East Coast, based at MIT and the Broad Institute, filed their own patents in 2014 after Berkeley’s, but got them granted first. The Berkeley group contended that this constituted “interference,” and that Berkeley deserved the patent.

At stake: millions, maybe billions of dollars in biotech money and licensing fees, the future of medicine, the future of bioscience. Not nothing. Who will benefit depends on who owns the patents.

On Wednesday [Feb. 15, 2017], the US Patent Trial and Appeal Board kind of, sort of, almost began to answer that question. Berkeley will get the patent for using the system called Crispr-Cas9 in any living cell, from bacteria to blue whales. Broad/MIT gets the patent in eukaryotic cells, which is to say, plants and animals.

It’s … confusing. “The patent that the Broad received is for the use of Crispr gene-editing technology in eukaryotic cells. The patent for the University of California is for all cells,” says Jennifer Doudna, the UC geneticist and co-founder of Caribou Biosciences who co-invented Crispr, on a conference call. Her metaphor: “They have a patent on green tennis balls; we have a patent for all tennis balls.”

Observers didn’t quite buy that topspin. If Caribou is playing tennis, it’s looking like Broad/MIT is Serena Williams.

“UC does not necessarily lose everything, but they’re no doubt spinning the story,” says Robert Cook-Deegan, an expert in genetic policy at Arizona State University’s School for the Future of Innovation in Society. “UC’s claims to eukaryotic uses of Crispr-Cas9 will not be granted in the form they sought. That’s a big deal, and UC was the big loser.”

UC officials said Wednesday [Feb. 15, 2017] that they are studying the 51-page decision and considering whether to appeal. That leaves members of the biotechnology sector wondering who they will have to pay to use Crispr as part of a business—and scientists hoping the outcome won’t somehow keep them from continuing their research.

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Happy reading!

SWEET, sweet transporters

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A Sept. 4, 2014 news item on Azonano is all about sugar,

Sugars are an essential source of energy for microrganisms, animals and humans. They are produced by plants, which convert energy from sunlight into chemical energy in the form of sugars through photosynthesis.

These sugars are taken up into cells, no matter whether these are bacteria, yeast, human cells or plant cells, by proteins that create sugar-specific pores in the membrane that surrounds a cell. These transport proteins are thus essential in all organisms. It is not surprising that the transporters of humans and plants are very similar since they evolved from their bacterial ancestors.

Sugar transporters can also be a source of vulnerability for plants and animals alike. In plants they can be susceptible to takeover by pathogens, hijacking the source of the plant’s food and energy. In animals, mutations in sugar transporters can lead to diseases, such as diabetes.

New work from a team led by the Stanford University School of Medicine’s Liang Feng and including Carnegie’s [Carnegie Institution for Science] Wolf Frommer has for the first time elucidated the atomic structures of the prototype of the sugar transporters (termed “SWEET” transporters) in plants and humans. These are bacterial sugar transporters, called SemiSWEETs (because they are just half the size of the human and plant ones). …

A Sept. 3, 2014 Carnegie Institution for Science news release, which originated the news item, describes the importance of understanding these transporters,

Until now, there was very limited information about the unique structures of these important transport proteins, which it turns out are different from all other known sugar transporters.

Discovering the structure of these proteins is important, as it is the key to unlocking the mechanism by which they work. And understanding their mechanism is crucial for figuring out what happens when these functions fail to work properly, because that knowledge can help in addressing the resulting diseases or growth problems in both plants and animals.

The research team performed a combination of structural and functional analyses of SemiSWEETs and SWEETs and was able to crystallize two examples in different states, demonstrating not only the protein’s structure, but much about its functionality as well.

They found that the SemiSWEETs do not act as a sugar channel, or tunnel, which allow sugars to pass across the membrane. Rather they act like an airlock, moving the sugars in multiple stages, two of which can be observed in the crystal structures. The SemiSWEETs, among the smallest known transport proteins, assemble in pairs, thereby creating a structure that looks like their bigger plant and human SWEET homologs. This marks the SWEET family of proteins as drastically different from other sugar transport proteins.

“One of the most-exciting parts of this discovery is the speed with which we were able to move from discovering these novel sugar transporters, to determining their actual structure, to showing how they work,” Frommer said. “Fantastic progress made possible by a collaboration with a structural biologist from Stanford University. Our findings highlight the potential practical applications of this information in improving crop yields as well as in addressing human diseases.”

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

Structures of bacterial homologues of SWEET transporters in two distinct conformations by Yan Xu, Yuyong Tao, Lily S. Cheung, Chao Fan, Li-Qing Chen, Sophia Xu, Kay Perry, Wolf B. Frommer, & Liang Feng. Nature (2014) doi:10.1038/nature13670 Published online 03 September 2014

This paper is behind a paywall.

Using microwaves to test for carbon nanotube toxicity in soil

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It’s been a while since I’ve mentioned soil or environmental testing for this this Oct. 19, 2012 news item by Karen Slyker on physorg.com, which highlights some research on environmental testing of carbon nanotubes, lets me redress the situation,

Industrial uses are growing, as are concerns that these novel nanomaterials may have negative or unintended effects on organisms and the environment. With this in mind, environmental toxicologists at Texas Tech are exploring the fate of CNTs in biological environments and their ability to accumulate in soil, plants or other organisms.

One recurring question has slowed these studies: How can anyone be certain the tiny CNTs are present in the given sample?

“It’s like a needle in a haystack,” Green said [Micah Green, assistant professor of chemical engineering]. “How can you prove the effects of the needle, if you’re not sure that it’s really in there?”

The impetus for the work initially began with a conversation between Green and Jaclyn Cañas, associate professor of environmental toxicology at The Institute for Environmental and Human Health at Texas Tech. Cañas described the problem of detecting CNTs in crop samples. Green suggested that exposing samples to microwaves could reveal the presence of even trace quantities of nanotubes.

The Texas Technical University Oct. 19, 2012 news release (which originated the news item) provides more detail about the approach,

CNTs have the unusual property of evolving extreme amounts of heat upon exposure to microwaves, much more so than typical materials. In fact, nanotube powder will quickly and spontaneously ignite if placed in a conventional kitchen microwave. Green’s idea was to expose the sample to low-power microwaves and measure the resulting increase in temperature.

Mohammad Saed, an associate professor in electrical and computer engineering, joined the team to contribute his expertise in the area of microwave physics.

Together, the three research groups successfully built a testing apparatus and proved the concepts that microwave-based heating can quantify CNT loading inside a plant sample.

The team has refined its testing protocols and extended the scope from soil testing only to including earthworms,

Continued development of the device led to a double-blind test, where a student was given samples of a specified CNT loading but was not told what the concentration was. Graduate student Fahmida Irin was principally responsible for applying the method. The double-blind test successfully duplicated the true values, and was then applied to studying the uptake of nanotubes into alfalfa plant roots grown in soil spiked with nanotubes.

“Since we started the method, we have started collaborating with other groups as well to look at the presence of nanotubes in organisms like earthworms,” Green said.

The method was recently published in a paper entitled “Detection of carbon nanotubes in biological samples through microwave-induced heating” by Irin et al. in the journal Carbon.

I’m not quite sure how to take this research. They do mention that nanotube powder will ignite in a kitchen microwave. Here’s hoping the researchers have designed an apparatus that cannot accidentally ignite carbon nanotubes in soil, plants, or earthworms.