Gene-Editing: Food of the Future?

It’s 10 years since the recently restarted particle accelerator in CERN, the Large Hadron Collider, discovered the elusive Higgs Boson or “God Particle” as some also refer to it. So let’s talk particle physics now! Most of the time in science, researchers tell us about what they have found. But occasionally important papers are presented that tell us what hasn't been found; and this can help to rule out how something doesn’t work or what something doesn't look like and points us more in the right direction for where we should look. This week Ben McAllister, from the University of Western Australia and Swinburne University of Technology, has done just this in grappling with what is literally a massive problem in physics, as he explained to Chris Smith...

本,我们一直试图弄清真相one of the biggest mysteries in the universe, as I like to call it. For about a hundred years, we have known that all of the stuff we can see in the universe, that's the kind of matter that makes up you and me and the planet and the sun, is not even close to all the stuff that there is. We can't explain the way things move around. If we only consider the stuff we can see, particularly, it seems like the gravity that's provided by the stuff that we see, wouldn't be strong enough to pull stuff in space around as strongly as we see it pulled, if you like. So we infer that there must be a lot of invisible stuff out there about five times as much as there is of all the stuff we can see providing additional gravity. So it's this huge cosmic mystery. And we've known it's for a long time. And we just don't know exactly what it is.

克里斯-如果我们只是推断它的存在,我们can't see it. And we don't actually know how to detect it. How can we therefore work out what it is?

本——是的,这是一个很好的问题。所以有很多of different ways that people try and get to the bottom of dark matter. The most popular theories rely on introducing new particles. So new kinds of matter that are different to the kinds of things we already know about that can account for the dark matter. But generally speaking, the lines of attack for detecting dark matter are you can do something like what they do at the large Hadron Collider at CERN. Take particles we already know about and smash them together and hope that some interactions occur that cause them to generate dark matter. Or you can look in space with telescopes and hope that maybe some dark matter particles out there are interacting in such a way that they generate particles we can see like photons, particles of light, or other things like that, and we can catch them with telescopes. Or you can do what we are doing here in the study that we're talking about today, which is called direct detection, where you build a detector on earth and you try and catch an interaction of one of the dark matter particles that's passing through the earth with something in your detector.

Chris - You've therefore, presumably got in mind some kind of model for what shape or structure that dark matter entity might take. So you are saying, if it looks like this, it should do the following things in our detector, can we detect it?

Ben - Yeah, that's exactly right. So again, you need a hypothesis to start with of what the dark matter is. There are a few of them. In particular, the work we're talking about here is trying to detect, a very popular dark matter candidate, a thing called an axion, which is a new particle that was proposed in the seventies. Funny story it's actually named after a brand of dish soap, for the way it cleans up problems. And the nice thing about the axion is that it is supposed to have an interaction with photons, which are particles of light, which is great because it means we can take dark matter, this invisible thing that we can't see at all and convert it into a little flash of light, a thing that we're great at trying to detect. So that's what we do with the organ experiment, which is the work that is being published this week.

Chris - And what have you seen so far?

本,这是有趣的。当you do these kinds of experiments, you obviously hope to see something you hope to see that little flash of light in excess of the background that says, oh great, we found this dark matter signal, but more often than not, you don't. What you can then do as we've done here, and as other experiments have done in the past is you can place stringent limits on the existence of the dark matter. You can say, okay, our experiment is this sensitive in this region of parameter space of dark matter? And we didn't see anything, which means we can put a big block through it and say, okay, the dark matter is not here. So what you can do is you set it to be sensitive to a certain axion mass. You wait some amount of time to see if you get a signal and then you move to another axion mass and you do that for some range of masses. And if you don't see the axons, you say, okay, we can rule them out to this level of sensitivity within this mass range. And that's what we've done here. We've ruled out some new parameter space, the most sensitive search for axions to date in the mass ranging question.

Chris - How do you know your machine's just not broken?

Ben - Yeah. Right. Well, you can do all kinds of different calibrations and tests where you inject signals. That would mimic what you'd expect to see from an axion converting into photons and see if you pick those up. But the fundamental answer is really that it does depend on your model. You're saying, we're assuming for this thing, where the axion is the dark matter and it's interacting in this way inside the detector. And then we can generate simulated versions of that signal and see that we would see them and, say with some confidence, some degree of confidence that we have ruled out the axions in that range.

Chris - If they don't exist in that range and your experiments are correct. What effect does that have in terms of constraining what axion are?

Ben - Yeah, it's quite funny to be reporting a negative result, but it is really the way science works isn't it? I mean, we're doing a big search here. It's sort of like the wild west. There's all this territory that we have to go out and search. And what we're doing is essentially saying in concordance with the international community, well, we've looked here and it's not here, so we don't need to spend any more time looking here and we can start moving our detectors into other ranges and work with international collaborators in the field to gradually sweep through this huge range and hopefully eventually detect the dark matter.

Chris - And if it turns out your right and you find the elusive axion, what does that do to physics?

本——好吧,我的意思是,这就像一个巨大的对位digm shift because we would have answered one of the biggest mysteries in the universe, what the nature of the dark matter is. And at the same time detected this new particle, and it would be the start of a sort of new era of axion physics. You could imagine doing all kinds of interesting things. You can do astronomy using these axons. People have various proposals for different kinds of seemingly futuristic technologies that they might be able to be used for. But it is one of those questions where we almost don't wanna get too far ahead of ourselves in terms of possible applications of these things at the moment. I think it's more like we know there's this huge unexplored realm out there. There's all this dark matter and we just don't know what it is. And we will never learn anything new if we only ask questions we already know the answer to, like we never would've discovered radio waves, we never would've discovered modern electricity, if we'd only set out to do experiments where we said, okay, we know exactly what's gonna come out of this by the time we're finished doing it. We just need to start probing away at these mysterious things that seem at the time, like just unexplained physical phenomena. And that's exactly what we have here. And we know throughout history, when we probe these big unexplained physical phenomena, we make big discoveries and we change the way the world works.

F1 fans were treated to a thrilling race last weekend with the British Grand Prix. But, for all the dramatic overtakes and frantic final laps, many will reflect gratefully on what, fortunately, didn’t happen. The race was delayed for an hour after a spectacular crash at the first corner when Alfa Romeo’s Zhou Guanyu (JO GWAN-YOO) was flipped upside down onto the tarmac and span into - and over - the barriers at nearly 200mph. James Tytko spoke with science journalist Kit Chapman to find out how Guanyu came out of the incident unscathed…

Kit - When you go round a track at 195 miles per hour, there is of course an element of risk. There has been since the early days of formula one. But since the 1990s, in particular the death of Ayrton Senna, safety has become a major priority. There have been countless accidents where people have learnt, they've improved the cars and they've made them safer.

James - It's quite unfathomable for someone like me, who doesn't watch that much F1, to get my head around how someone comes out of a crash like that. And I think the term that was officially used to pronounce his state was 'uninjured.'

Kit - Absolutely. So Zhou was completely uninjured in the crash and that's for several different reasons. When you look at the design of a formula one car, what you've got is the monocoque, which is where the cockpit, where the driver is sitting, and that is designed around a crush zone. So that crush zone will dissipate energy when there's an impact. That's why the tyres end up twisted and bent around. Behind them, in the fuel tank, that's protected by kevlar and so it's very unlikely you're going to get a sort of spectacular fireball. Then, if you look at the actual design around the cockpit, you've got this roll bar, which basically is designed to protect the driver if the car does flip around. But of course the most important part is the halo, and this is a titanium beam that is just above the cockpit, and that is able to withstand the impact of 15 cars on top of it. And that is really what saved Zhou's life. Even if you have a perfect situation with your car and all the crumpling happens exactly where you need it to be, your halo works, your roll bars work, you're still suffering a huge amount of G force. Now 1 G is normal for us, six G is what you get on a roller coaster - this could be an impact of 60 to 80 G, which is huge. And that normally would be fatal for humans. They'll suffer what's called a basilar skull fracture, which is basically the bottom of your neck, your skull, fracturing and snapping. And so drivers also use something called the Hans device. It's basically a yoke that goes over your shoulder, and then there's a tether that attaches to your helmet and that prevents your neck from snapping forward. It keeps everything in line and it protects the head and neck and makes sure that you don't get that injury.

James - And if we can go back to talking about the halo, because there was some controversy wasn't there when it was initially introduced?

Kit - Yeah. The halo was one of the most unpopular ideas. People thought, "why do we need this extra layer of safety?" It was influenced by the death of a driver called Jules Bianchi, who was killed from complications during a race and drivers weren't particularly happy with it. Roman Grosjean was actually a huge critic of it when it was introduced. After the 2020 crash in Bahrain, the halo unquestionably saved his life. It actually bent over a barrier that would otherwise have decapitated him. He has become a complete convert. And now when we look at the halos, multiple drivers, including Lewis Hamilton, who had Max Verstappen's car land on him last season, have been saved because of this halo device.

James - And what have the F1 organization and community learnt from this, other than the effectiveness of the halo? Is this time for a pat on the back for everyone involved, or is this more of a reason to re-energise, to redouble the efforts on making sure the sport is as safe as possible?

Kit - It's always something that you have to improve. Formula one operates on a Swiss cheese model. Famously, Mark Gallagher of Red Bull has talked about this. And the whole idea is that you don't want a hole going all the way through the cheese, you want to make sure that there are barriers in place. And so those barriers are human; training, making sure that the medical staff are there. They're technological, making sure that there's safety features. They're just things like track layouts and making sure that the right type of barriers are used. But this crash will be analysed and poured over by F1's teams. Already, there's a load of dissection going on about the roll bar, on whether or not it crumpled effectively, or whether or not that's something that needs to be improved. And so they're going to look at this from every single angle, from angles we are never going to see. They've got black boxes on the cars and they're going to figure out exactly how they can prevent it ever happening again.

目标基因的改变游戏规则的编辑是侦探hnique called CRISPR-Cas9. This won a Nobel Prize in 2020, and allows researchers to target and alter precise parts of the DNA genetic code. Using CRISPR-cas9 to edit crops could lead to a revolution in food production. One of those foods is tomatoes augmented to make Vitamin D. Vitamin D is essential to human health, but we do not make it naturally. During the COVID19 pandemic, the UK government permitted the prescription of vitamin D tablets as its levels were correlated with reduced severity of illness. Having a food product packed with this vitamin may have huge knock-on implications for the health of the population. And Cathie Martin, a plant scientist at the John Innes Centre in Norwich, decided to use CRISPR-cas9 in attempts to generate such a product using the world's most popular fruit. Julia Ravey popped to the John Innes Centre to speak to Cathie and see these tomatoes for myself. Firstly, Jie Lie, a researcher in Cathie’s lab, explained why tomatoes were prime candidates for making a vitamin-D enriched food…

Jie - Because tomatoes naturally accumulate provitamin D3 in leaves, but at very low levels - in ripe fruit it is not detectable at all. We targeted a specific enzyme, which converts this provitamin D3 to other molecules. If we block the function of this enzyme, it should accumulate the substrate, which is provitamin D3.

Julia - So it's almost like if you think of the tomato as a factory, and you've got this enzyme, it's like a worker and they're doing a specific job to move this one thing on the line, along to the next. You've taken that worker out of the chain. And what you'll get is the provitamin D that would have been moved along the line to become the next substrate that it's going to be. That's just building up and building up because the worker isn't there to move it along.

Jie - Yeah, exactly. And the good thing is, this pathway is a partially duplicated pathway from brassinosteroid. Brassinosteroid is really important for plant growth. If you block or touch this pathway, you may get dwarfism.

Julia - And with the tomatoes, we're getting a buildup of provitamin D which is great for us, but what does it mean for the tomato? What does the tomato normally use that provitamin D for down the line that we are now taking for ourselves?

Jie - Oh yes. Vitamin D is a converted to cholesterol, and then to these anti-pathogen compounds. The good thing is we've reduced, but not eliminated this process. So we can still maintain the pathogen resistance of the plant.

Julia - After learning about the method behind how gene editing can be used to generate provitamin D3-enriched tomatoes, Cathie Martin, the plant scientist behind this project, took me to their greenhouse to see the resulting fruit with my own eyes. And they look like, well, tomatoes.

Cathie - I don't think you can tell the ones that are enriched in provitamin D compared to the wild type. So that one's a wild type and that one's a provitamin D enriched one as are these. That's a good thing in terms of getting something that people will grow and use, because we don't want to have a big yield impact or anything like that.

Julia - Are the conditions exactly the same? So you've just grown these in the exact same way as the regular wild type tomatoes?

Cathie - Yes. We had to make sure that following the edit that we made, that the machinery that we use to make the mutation has all segregated away. So these are the progeny of the initial transformation event. So we've lost all the machinery that we use to make the edit and just has the edit left in the lines. And that's very important that we can classify them as qualifying higher plants that don't contain any foreign DNA.

Julia - A big player in this process was the leaves and the plant itself. Also containing these enriched levels of provitamin D.

Cathie - I think that it's really important for any consumer trait that you have something that makes farmers, producers, growers want to grow it because otherwise it tends to be a boutique variety that disappears off the shelves. But if you have a producer trait, whether it's disease resistance or improved nitrogen use efficiency or improved water use efficiency, then you've got something that will make people grow it because you get lower inputs. And for these provitamin D enriched rich tomatoes, there's massive levels of provitamin D in the leaves. And although these plants don't look fantastic at the moment, that can be taken and you can make extracts of provitamin D or vitamin D from the leaves, and those can go to feed supplements. And so you can get value from the waste.

Julia - And side by side. I couldn't tell the difference.

Cathie - No, I can't either.

Julia - I have to look at the labels, because they're all mixed in with the wild type plants next to each other. But in terms of, they may look the same, but are these plants exactly the same, except for that one change? Can we see if there's any other knock-on impacts within the tomato itself?

Cathie - We've done quite a bit of metabolite characterisation to check that. I mean, that's part of the process of engineering a new step, you want to know whether there are any knockout effects and we have done a lot of analysis to show that there was no effect. For example, there was a risk that we might affect brassinosteroid production, which is a hormone that affects the height of the plants. But as you can see, they're normal height -these ones are a bit bigger than the wild type over there. As far as we can tell so far, we can say that that's the only change in the genome.

Julia - Have you tasted them? Are they allowed to be tasted yet?

Cathie - Yes. I think the one I tasted was a bit over ripe. But they taste like a tomato.

Julia - That's brilliant. So you couldn't tell the difference?

Cathie - I'd say squishy, but that was what was available.

Julia - And these tomatoes are enriched with provitamin D but what if we want vitamin D from them? What has to happen next?

凯蒂,在人类中,前维生素D3是欺诈verted to vitamin D3 and you need exposure to UV light to do that. So we've done it experimentally in the lab, we've taken leaves or fruit and exposed them to UV light. And you can get the conversion at about 30% efficiency to vitamin D3. In humans you're recommended to go out for half an hour, a day in sunlight to be able to convert your provitamin D3 to vitamin D3. So we're quite interested to test whether that works in tomatoes as well. Simple kind of idea but maybe we can get away from having to treat with UV by growing the plant outside. So that's why we have applied for a field trial to expose them to the sunlight. And we've been very lucky the last few weeks that there's been plenty of sunlight. So they're just growing down the corridor.

Julia - Cathie took me along the corridor to see the vitamin D three field trial.

Cathie - You Ready?

Julia - Ready for this. The field trial field trial! It's less of a field and more of a stoney patch in between greenhouses.

Cathie - That's right. And I don't know which ones which, again, you have to look at the label on the plants to know whether they're edited or not. So we've got wild type in here as well as provitamin D enriched ones, but we're waiting to see what the effect of sunlight, which is really quite strong.

Julia - Yeah. I'm glad I've got factor 50 on!

Cathie - They're doing quite well I think. And we just have to harvest all the leaves and fruit and see how much vitamin D we get.

Julia - And obviously here, it's out with the sun from the sky coming in and there isn't a control over that. So is there a way you're going to say, okay, well, this plant we know has had this much sunlight based on the weather forecast. So you can do a correlation of sun to vitamin D?

Cathie - Of course in the UK, we do not grow tomatoes commercially outside because they don't do very well. So we were hoping to do these experiments in Italy. But because the Italians are under EU regulations, it's going to take them about two years. So we've just actually got really lucky - as is everyone else - it's been sunny for the last few weeks. And so, we're dependent on what we can get, but I think that this would give us a minimum value of whether it works outside. Of course it may not work. I don't know the answer, but that's the most exciting thing about outside doing sciences when you don't know the answer.

Julia - It's really exciting! Well, I'm definitely getting my vitamin D out here today. Move the ginger inside! Fingers crossed the tomatoes are getting it as well.

一个huge issue on the sustainability front is overfishing. Fish oils are an important part of our diets, with molecules such as EPA and DHA being beneficial for brain health. But excessive harvesting of ocean stocks is damaging marine ecosystems. Johnathan Napier, research leader at Rothamsted research, has potentially found a solution to this problem using genetic modification. This differs from gene editing, but he hopes that the precision breeding bill marks an important first step to gateway other GM produce down the line. He explained to Chris Smith what his lab has been working on…

Johnathan - What we've done after decades of effort is we can make fish oils in plants.

Chris - Isn't that what eating fish is for though? I mean, I could go out and buy some salmon and eat that, couldn't I. Why do I need plants for that?

Johnathan——实际上,很多人不吃enough fish. And contrary to popular belief, There aren't plenty more fish in the sea. There's not enough fish oils to go around to ensure that everybody on the planet gets correct nutrition.

Chris - I thought one way of combating this was we were just farming fish and growing enormous amounts of fish to make sure we don't deplete ocean stocks?

Johnathan - We do farm lots of fish. Now most of the fish that people would consume has been farmed. All the fish you buy in the supermarket, almost all of that's probably been farmed. But the Achilles heel, if you like, of fish farming, is that actually - this is the really bizarre thing - fish don't make fish oils, but they need them as part of their diet. So we have to feed the farmed fish fish oils that have been extracted out of the oceans. So you have this unsustainable cycle of extracting fish oils out of the ocean to feed to farmed fish.

Chris - Hang on a minute. So you are saying, I need to eat lots of oily fish to get fish oils, but fish need to eat oily fish to get fish oils. So where do the fish get it from then?

Johnathan - So the fish get it from their diet. You can think of our oceans as a soup of omega3 fish oils - but we've already decided that's not really a good name because fish don't make omega3 fish oils. It's actually the marine microbes; the little plankton and the microalgae that are in the base of the food web in the ocean. They're the things that are making the omega3 oils. And just in every layer in the food web in the oceans, those fatty acids are accumulating.

Chris - How did you (a) find out what the algae were doing to make these essential fatty acids in the first place? So how did you know what to take from them? And how did you get that to work in plants and indeed what sort of plants?

Johnathan - We started our project to try and make these particular omega3 fatty acids. And it was well known that algae were making them, but nobody knew what the genes were. And so we really had to embark on a project to find the genes in the algae that make the omega3 polyunsaturated fatty acids, and identify those genes and introduce them one by one into plants to effectively rebuild the algal pathway in a higher plant so that the plant was now making these long chain omega3 fatty acids.

Chris - And what plant have you put them in?

Johnathan - The one that works really well for us is a plant called camelina, which is like a cousin of oil seed rape canola.

Chris - What's the concentration that you achieve? How many cod liver oil capsules do I have to pop to be equivalent to a handful of the seeds of one of these plants?

Johnathan - In terms of the amount of EPA and DHA that we make in our oil, the levels that we make are actually a little bit higher than you would find in cod liver oil. You should be taking probably a couple of teaspoons of cod liver oil a week. Well, probably you could only take one teaspoon of our GM camelina oil. We've done human studies with these oils, and we now know that our plant fish oil replacement is exactly the same in terms of how it's taken up by the human body as a regular fish oil.

Chris - Have you actually gone through chemical by chemical what your plants make in order to prove that in stitching in these additional genes the biochemistry of the plant hasn't changed in some other unpredictable way?

Johnathan - There's always variation between one plant and another. We've done a great deal of analysis of our transgenic plants, and we've not seen any difference we think is significant or cause for concern.

Chris - At the moment, the legislation forbids you from doing what you are doing in terms of using it for direct access into the human marketplace. People are lobbying to try to change that. You've been one of those people who've been advocating for that. How's it gone down? How are your arguments being received?

Johnathan - The government, in general, knows that the legislation that was developed within the EU for covering GM and gene editing is too restrictive and impedes innovation. We've got something useful and we know that it's safe and we know that it works well. The mechanisms to bring this to market are too complicated, too burdensome, too expensive, that doesn't really help anybody, but I think we're still somewhere away from the government moving towards changing how GM foods are regulated. But I think their direction of travel is clear, which I think is really exciting and really promising.