Head Shepherd

Exploring Genetics in Agriculture: From Beef Breeding to Medical Cannabis with Dr Gemma Jenkins

January 15, 2024 Dr Gemma Jenkins Season 2024
Head Shepherd
Exploring Genetics in Agriculture: From Beef Breeding to Medical Cannabis with Dr Gemma Jenkins
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With extensive experience working with AgResearch, Abacus Bio, the Irish Cattle Breeding Federation, the New Zealand Medical Cannabis Council and (in her current role) as Genetics Programme Manager at Beef + Lamb New Zealand (B+LNZ), our guest this week, Dr Gemma Jenkins, has a passion for genetics.

Gemma's primary focus at B+LNZ is genetic improvement in the beef industry via the Informing New Zealand Beef Programme (INZB).

“Our main objectives are to drive genetic gain in the beef industry; enhancing it through superior genetics, AI use and promoting genomic selection by stud breeders," she explains. "The goal is to generate an additional $460 million in income for the beef industry by 2045. We aim to create genetic evaluations tailored for New Zealand, focusing on traits important to local farmers, and develop easy-to-use genetic tools like n-Prove, but for beef. These tools will assist farmers in making informed breeding decisions.”

Listen in for Gemma's excellent explanation of industry indexes and how the weightings of individual traits work to drive overall industry improvement.

We also dive into the world of medicinal cannabis. Gemma shares her experience as a science and technical advisor for the New Zealand Medical Cannabis Council. The complexity of the cannabis plant and its chemical components presents unique challenges for the pharmaceutical industry, particularly when it comes to replicating its components.

“There's lots of different parts of the plant and so it’s very hard for pharmaceutical companies to replicate because it wasn't just looking at a single product like THC or CBD. There's what they call the “entourage effect”. So it's more than just the sum of the parts, it's not just the THC and CBD together but it's all of them combined.”

Gemma explains the parallels between cannabis breeding and animal breeding, emphasising the importance of considering genetic background and interactions.

“I guess that's the same as animal breeding, at the end of the day. Some genes have a major effect, but then you know there's a different genetic landscape for each individual and ultimately, the way the genes express each other can be different based on what the genetic background is for the animal too.”

Whatever we're breeding, genetics plays a pivotal role in shaping the future of agriculture.


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Mark:

Welcome to Ed Sheppard, Gemma Jenkins.

Gemma:

I'll think through much for having me.

Mark:

Excellent, great to have you along. I should have said Dr Gemma Jenkins. We do these PhDs, so we should probably should claim them every now and again to justify them. These days, you're a genetics program manager at Beef and Lamb New Zealand, but we might start prior to that and go back to how you got interested in genetics way back when, and then that's making you sound ancient, sorry. How you got interested in genetics originally and then we'll go forward.

Gemma:

Yeah. So yeah, I did genetics at Otago University. It was quite a while ago now and actually I was sort of just interested in science in general in my first year and then genetics was reasonably new back then actually, and there was a lot of human genetic stuff within that, just a little bit of agricultural genetics. Like it was still very early in the piece and there wasn't actually that much on that at the university at the time. And so I did my undergrad and then I actually went to Brisbane and I did a masters in genetic counselling over there.

Gemma:

My intention was basically that I didn't want to work in a lab. I wanted to do something to do with genetics, but I didn't actually want to be stuck in a lab. So that was why I did that. And then I came back and I got offered a summer student ship at Ag Research with John McEwen. So that was my first sort of foray into the agricultural genetic side of things and I think I looked at identifying simple sequence repeats in the cattle genome and we actually ended up being, you know, co-authors and I mean very, very nestled down in the author list of the cattle genome science paper that came out. So that was my first foray into it.

Gemma:

And then I ended up working at Ag Research for about three years after that in the Animal Genomics Research Unit and also in the Genomes Lab as well, and that was, you know, obviously commercially genotyping with micro satellites back in the day. And then after that I actually had a three-month stint over at the Irish Cattlebreeding Federation. So I lived in court for a few months and I was working alongside Epicus Bio there to set up the sheep genetic evaluation system in Ireland, which was a pretty cool thing to be part of. And then I came back and did my PhD. So I was based at Ag Research with John McEwen as one of my supervisors. I also had McBlack from the University of Otago and my main supervisor was Mike Goddard so I did it at the University of Melbourne.

Gemma:

So yeah, so after that I that was in. I should actually mention what my PhD was about. It's funny, it's a thesis that sits on my desk at home, but it doesn't. It really just collects dust these days. But it was in sheep genetic. So I was identifying copy number variants in the sheep genome and also developing genetic evaluations as well, and I was looking to see if any of the copy number variations were associated with any of the variations that we could see in some sheep traits. So that was my PhD.

Gemma:

And then I went on to work for Epicus Bio for eight years and that was primarily in the dairy, for the dairy industry. So a lot of work with dairy and Z, some work around developing genetic evaluations for fertility traits. We also did some work for the Irish Kettle Breeding Federation as well and just everything related to breeding indexes and breeding objectives and stuff like that. So the last thing I sort of did at Epicus was I was involved in the national review of the breeding objectives and indexes for dairy and Z and that was actually really awesome to be part of. So it's quite similar to some of the stuff that we're doing now as part of the Informa New Zealand Beef Program. So that's how I got to where I am now.

Mark:

Awesome, that was a quick tour through life. We'll drill into the dairy cow bit for a minute. So the fertility is obviously for the last I don't know 20, 30 years. We started to understand that single trait selection for milk production wasn't ideal for other parts of dairy cow. So what was the, I guess, through that work, what was the strategy to improve fertility?

Gemma:

Yeah, so one of the things that can happen when you apply a lot of selection pressure on one particular trait is that it can obviously have unintended consequences on other traits. So what you were talking about is that you know, by selecting heavily for milk production, we ultimately then got a reduction in fertility in the national herd. So there was a shift in focus that was a little bit before my time, but around increasing the amount of selection pressure that was put on fertility. So that's all done through breeding worth for dairy cows, well, for bull selection in the dairy industry. So breeding worth is basically a combination of traits.

Gemma:

So the way I always describe it as a breeding objective is effectively, we want to go as an industry and a selection index is the tool that you use to get there. So the selection index contains, you know, the different traits that have economic ramifications, basically to get to your goal, where you're heading. So obviously, if we want to increase well you know, get more favourable fertility in the national herd, then what you need to do is increase the amount of weighting that's put on that trait within the selection index. So that's ultimately what happened, so that we could increase the genetic gains that we were seeing you know, at an industry level in fertility.

Gemma:

Hopefully that makes sense.

Mark:

Yeah, that makes sense and I guess it's similar to other industries where the obviously fertility is not the main game in dairy production. But if you have a decline, then you have issues with replacement cows and the zollip of unintended consequences or will flow on costs of that dropping fertility. So while obviously milk production was the primary aim and that's the classic case of you have your breeding objective, of your sort of wish list almost, and then you have to be careful as careful about what you put on there as what you don't put on there, because if you leave something off and it doesn't get any selection pressure, then it can wander off in a direction you weren't hoping for, either through correlation or just through drift. So if we get back into the main game, so genetics program manager at Beef and Lamb New Zealand, tell me what that means and the kind of work you're up to there.

Gemma:

Yeah, cool. So primarily I'm involved with the Informa New Zealand Beef Programme so INZB is what we call that and it's a $16.7 million seven-year project that's funded by Beef and Lamb and the New Zealand Meat Board as well, and MPI through their Sustainable Food and Fibre Futures Fund. So I'm in the program manager for that particular program and we are just entering our fourth year of the program and really the main objectives of the program are to drive genetic gain in the beef industry. So we've already got an awesome beef industry in New Zealand, but the idea is to supercharge it and that's all true, you know using superior genetics, use of AI and also promoting genomic selection by stud brewers as well, all which obviously can increase the selection pressure in a population. So the ultimate goal is that we'd like to achieve $460 million extra income in the beef industry by 2045.

Gemma:

So that's sort of over the next 40 odd years, and the key outcome is really that we want from the program to create genetic evaluations that are really fit for New Zealand's purposes, so traits that are important to New Zealand farmers, and to do that we're going to produce, you know, sort of easy to use genetic tools for farmers.

Gemma:

You might have heard of M-Proof for sheep, so we'll be doing the same for beef and that will really allow them to look at, you know, the bulls that are available to them, what their estimated breeding values are, what their selection index values are, and it will allow them to make the right selection decisions for their farming operations. So obviously, a really key part of that is we can produce all the tools we want, but we actually need it to get into the hands of farmers. So a large part of the program as well is around using a different extension sorry, a different approach to extension and looking at how we can really drive adoption and provide extension services around the tools that we're producing as part of the program. So, yeah, really, you know, we're looking for commercial farmers to have an easy to use tool to help with their selection decisions, which will ultimately increase the genetic gain within the industry.

Mark:

Yeah, it's interesting work. There's obviously a lot of, I guess, us in the know or that get close to us. We see the power of breeding bays on a daily basis. We're very lucky to work across hundreds or over 100 businesses and see the power of genetics. But others often farm with their same genetics in their same system. So don't, unless you run a progeny test or do something, genetics can be a little bit kind of hidden in the background. Yet we know how powerful they can be to change the things you can see and change lots of things you can't see as well.

Mark:

Yeah, so I guess important work there to try and to get the beef industry moving forward. I see a fair bit of use of data in the beef industry, but I guess there is still a lot of confusion around, like some people will just have a focus on a single trade or a couple of trades, and fair enough to a lot of these people are buying two or three bulls, one or two, three bulls a year and it's it is 12 months between jobs and so it's hard to remember exactly which trades you're focusing on. So it's good to hear there's going to be a lot of work in different extension approaches. Is that being underway now, or is it?

Gemma:

later in the project.

Gemma:

Yep, no, so we've already started the extension stuff. We we actually started it sort of during COVID times, but obviously that had to be online workshops and stuff like that. But just over the last year we have actually started holding workshops and they're called like Imperson workshops. They're called Beta Beef Breeding workshops, so they're run by we've got facilitators, but also our extension managers throughout the country. So I think we had about eight or nine of those this year and that really focuses on you know, choosing what your breeding objective is for your it's relevant for your operation and aligning your breeding objective with your breeder as well, to make sure you know you're selecting a breeder that has a similar objective to you and then really looking at how you use the EBVs to you know select based on what your overall breeding objective is. So so we've we've actually got just over 20 of those workshops planned for next year, so I think April, may and potentially a little bit later on as well in the year.

Gemma:

So yeah, 20 odd workshops throughout the country that will be focused specifically on that, and we also will hold an online workshop as well for people who can't actually get there in person.

Gemma:

But yeah, so that work has already started and we're also using an extension design approach as well. So we're sort of in the process of doing that at the moment and and McVetridge, who leads the extension design project, has gone out with her team and talked to a number of different farmers across the country and different stakeholders in the industry to really look at what influences decision making when it comes to using genetics and the genetic tools that we're going to provide. So the insights from that she's really working through the insights from there at the moment and looking at how we can actually, you know, adjust what we're doing in the extension space to ensure that farmers can use the tools that we're producing and that we give it through them in the way that they they want it, so that you know they can use it and it's insured of. So, yeah, the extension work is well underway already.

Mark:

Yeah, excellent. I've stated several times that I'm not going to live long enough to understand Ram buying and bull buying behaviour, but hopefully Ange can beat me to that.

Gemma:

I think there's a number of. You know like it's really complex and it doesn't just that you know, it's just not someone sitting in a room and making a decision purely based on that. Like you know, there's a number of different things that play into it as well, especially for farmers at the moment. You know there's economic pressures, social pressures, different policies and regulations that you know they're all having to work within the nexus of all of that stuff when they're making these decisions, so they're not decisions that happen in isolation. And so that's the extension. Design works really around understanding what that is and what that landscape looks like.

Mark:

Cool. So I'm not 100% understand, but so there'll be. So the Informing New Zealand Beef project will develop independent breeding bays of breed plan, or are they just helping get data into breed plan?

Gemma:

No. So at the moment we're looking at different options for producing those EBVs. We are developing prototype genetic evaluations for a number of different modules at the moment and we'll be developing genetic evaluations for new traits as well. So last year, I think it was, we went out and asked farmers what traits were important to them and to rank them. You know which ones are a priority for them and the traits that came through with things like fertility and structural traits and stuff like that obviously production too. So we are actually developing those traits as part of the program too. So we, by the end of the program we should have EBVs for the likes of body condition scoring and other scoring and fertility as well.

Gemma:

So we just started on a couple of pilot farms doing some fertility related data recording and we're doing that using cow manager tags. So they're basically wearables for cows and they go in their ears and it detects heat activity and what we're looking at doing is breaking because obviously fertility is lowly heritable. But there's also questions around. You know the accuracy of the fertility trait and so at the moment it kind of captures time to conception as well as gestation length. So what we're doing with these wearable devices is looking to see if we can break the fertility trait up into gestation length and time to conception as well, to ultimately create more accurate fertility breeding values. And then the other piece of work that we're doing, which we won't actually be developing genetic evaluations for in this program, but we have actually done this year a proof of concept trial with Ag research on putting cows from our beef progeny test herd, our Kepla site, through the portable accumulation chambers that they've had made up for cattle. So they were the first beef animals to actually be put through those chambers and it was really awesome to see actually. So they're doing that down at the bottom of the chamber.

Gemma:

And for me here in Taneven, where I'm based, and effectively they had six of these chambers, big steel boxes lined up beside each other, and they run the cattle up the race and take methane measures from them.

Gemma:

They stand there for 45 minutes and they take methane measures from them and they do that again. So they run the cows through once each and then they do that again in another few weeks and in between those times as well, they also take Rumen samples and then they do sequence analysis on the microbes that are present in those samples. And what we're looking for is whether there's any correlation with the methane outputs in the beef cattle. So obviously the power won't be big enough because we did 120 cattle. We probably need a lot more than that to identify any correlations. Maybe getting a bit technical here for you, but the moral of the story is we're looking at proxy type traits, so that would be the likes of the Rumen or Chexel samples. You know that could be. If we find, once we've done more animals, that they are correlated with methane output, then ultimately we could test a whole lot more animals, many more animals than we could put through the packed chambers and then ultimately develop a breeding value for greenhouse gas emissions.

Mark:

Yeah, for sure. I mean I can have shoved sheep into chambers before, but the concept of shoving a cow into a steel box doesn't sound like a whole heap of fun.

Gemma:

Yeah, well, it was really interesting. They had put some dairy cows through there previously, earlier on in the year, but obviously dairy cows are different to beef cows and yeah, so it was actually just really interesting to see them go through. They just walked in and stood there nicely. It was quite amazing actually.

Mark:

It is amazing.

Gemma:

So they're sort of yearling cattle or yeah, so they were our 20, what year are we now 23? They were our 2022 born heifers from our Kepler beef progeny test site. Yeah so they obviously have to be assured and they can't be too big to go through there, so they're at the right sort of weight to be going through.

Mark:

Yeah, we've talked on the show before with a couple of the AgriSearch team around the, around the yeah, the greenhouse gas stuff and obviously it's pretty cool that the sort of biology of the ruminant can control the ruminant bugs and therefore control how much methane is produced.

Gemma:

Yeah, it's really interesting it is an interesting space.

Mark:

So at the workshops you'd be covering sort of the combination of like, because a farmer out there are we going to end up with a ball catalogue with breeding vows from different evaluations in the same catalogue. How's that? What's your vision?

Gemma:

So all the brief societies will probably still do their own catalogs, but so I'm not sure if you've seen the improved tool for sheep.

Mark:

Yeah, yeah.

Gemma:

That's available online now if people wanted to go and check it out. But effectively, we'll be doing the same thing for beef. So what that is is you can log on on your computer and you can look at all the different balls that are available and there's little sliders and things like that where you can actually say fertility is very important to me, like that's part of my breeding objective. That's where I really want to be putting my focus. Obviously, I still want to put some focus on production as well, or it might be that, like parasite resistance or something, is really that's another trait that we're actually investigating to is really important, and so you can move your sliders around, effectively filter the balls that are available to you based on what the EBVs are, and that will help with making selection decisions.

Mark:

Yeah, and so that'll be an across breed analysis, or?

Gemma:

correct. Yes, so I haven't even talked about that. So so part of the one of the projects within the program is our beef progeny test site. So we've got Kepler and also Lockenberg Station as well. So Kepler I think we're three cohorts deep now at Kepler and we run Angus balls over Angus and Hereford cows and Hereford balls over here for Angus cows at Kepler and we run the same balls over cementiles at Lockenberg. So effectively, what that allows us to do is, you know, estimate heterosis and the basically breed effects, and that means that you're comparing apples with apples when you're looking at balls from different breeds when the EBVs come out of the genetic evaluation.

Mark:

Yeah, which has been. We've been lucky in shape for a long time, but obviously in cattle, as always, that's been the highly grail to this. Lots of reasons why that becomes quite difficult to do. So it's going to be good to well, not difficult scientifically, but fairly difficult politically generally. So I guess, amanda's. Obviously IGS are running the world's biggest across breed evaluation and we're going to see more of that as the industry advances forward.

Gemma:

Yeah.

Mark:

In your mind what is it that stops genetics? I mean, obviously, production. Other production factors are important that farmers need to manage, but why does genetics sort of sit down the list in terms of things that people might focus on in their beef herds or in their sheep flocks?

Gemma:

I think that's really dependent on the operation, isn't it? And you know, I guess, like how people are used to operating as well, but just like, as I mentioned earlier, just all the other factors that come into play, you know, like at the moment, with the economic pressures and stuff that are on farmers, then you know how much money have I got to play around with here. When it comes to selecting a ball, like you know, it's obviously got to be within your price range and stuff like that as well. So I think that's probably the million dollar question.

Mark:

And if we get that?

Gemma:

then that will. Yeah, if we get the answer to that, then that will obviously help drive the adoption of the tools that we produce as part of the program and, yeah, that's what we really need to get those, you know, the four hundred and sixty million over the next 20 odd years. So, yeah.

Mark:

So if we drill into body condition school because that's one of my favourite traits, obviously beef breeders have tried or some beef breeders have tried to have used positive fats to try and achieve that outcome.

Mark:

But obviously what we're really trying to achieve in doing that is is cow condition school, because we know that. I think the way that was put to me once is really relevant If you've got fat cows, you've got options, if they're skinny, you haven't kind of thing, and I think if they're, as in cows, in good condition scores. What I mean by fat cows, yeah, yeah, and I think that's true in particularly in New Zealand, which is I haven't travelled other than or done lots of travel around Australia, but the Southern beef herd in Australia runs on pretty good country generally, whereas in New Zealand they really are. Their job mainly is to keep pastures nice and tidy for sheep and get up and push into areas that the sheep are eating tag with the sheep's not going to eat. So it's, yeah, the job of a beef cow on a high country or a heel in a high country farm in New Zealand is actually, as most of the year, is, not eating, not sitting around eating nice ryegrass pastures on the flat, that's for sure.

Gemma:

Yeah, yeah. So we so as far as body condition scoring goes, and what?

Gemma:

we're doing around that is, we are looking to work with breeders to get them to record body condition score for us so that we've got some data to develop a chair evaluation for that trait. So we're actually running four workshops in February next year for breeders. There'll be till in the North Island and till in the South Island and that will be around body condition scoring and then really it will be up to the breeders to go out and record that trait and give us information on it so we can develop those evaluations. The body condition score is an interesting one and it's probably the same for a number of different traits. But it's sort of a non-linear trait in that you don't want them to be obese, but obviously you don't want them to be too skinny either. So again I come back to the indexes, as you can sort of put non-linear weightings, which is getting quite technical, but it just basically means that you're selecting for an intermediate optimum for that particular trait.

Mark:

Most people listen to us the keen on genetics, so they'll be happy to chat oh great. Yeah, yeah, yeah. The ad is definitely an optimum trait in something that we're always and differs a lot between farming or farms and farming methods, I think, in terms of its value, which makes it difficult to put a value on.

Gemma:

Yeah, so the other thing about body condition scoring is just ensuring that nationally we do actually have standardized traits so that we're all scoring on the same wing system as well. So that's obviously something that we'll cover within those workshops that we hold to.

Mark:

Yeah, great and that actually was my next question is the we do a lot of work in machine learning and cameras. Obviously the beauty of cows is they don't grow wool. Is there any movement to sort of automate that condition? Scoring of cattle because it should be pretty, should be pretty possible.

Gemma:

Not at this stage, but I mean, I think all of that AI type stuff is really awesome and you know, I'm sure there'll be entrepreneurial farmers out there that will start looking at that kind of thing. It'll be really interesting to see, sort of over the next probably 10 years, where things go and what things get automated, because obviously there is like facial recognition sort of technology and stuff like that out there. Now, I mean, we're quite excited about using just the activity monitors, basically like putting a garment on your cow, but in this case the tags in the air for the fertility work that we're doing. So yeah, it's going to be really interesting to see where technology goes over the next five to 10 years.

Mark:

Yeah, definitely I think it'll be. So we're working lots that area, which is really interesting, and I think something like a water conditions score and cattle would be fairly well. Apart from the boring bit of training, this training the machine should be quite possible. So it'd be interesting where that goes.

Gemma:

Yeah.

Mark:

Before we pull up on your LinkedIn page, it says you used to have a job as a science and technical advisor in medical cannabis. I thought that'd be a lot of cannabis and cows would be a nice title for a podcast, so I thought we should touch on the cannabis side of things.

Gemma:

Yeah, what was that?

Mark:

Was that genetics or was that just management?

Gemma:

Yeah, so it's actually a really interesting job. So obviously when I worked at EBCAS I was a consultant. I primarily worked in the dairy industry, but one of the things I also did was the science and technical advisor for the Medical Cannabis Council, and that was really interesting actually, just because it was a new industry that was just getting set up and there were a bunch of different companies looking at growing medical cannabis and obviously we had quite a close relationship with the Ministry of Health as well, because they were developing their regulations and guidelines and everything like that as to how the industry was going to play out and what regulations there'd be and who could actually have a license to grow for research purposes or production purposes. I mean, obviously I haven't really kept up to date with what's happening in the industry, but it does seem like there are a couple of companies that are going quite well in that space.

Gemma:

But I probably didn't have to do too much. You know I wasn't actually too much science at the time. It was more advising them on you know what breeding programs looks like and you know different traits that might be important and things like that, which obviously they had great knowledge of already anyway, and there were lots of international experts coming in as well. So, yeah, it was a really interesting time to be part of that industry, but yeah, Definitely, I guess yeah, you'd be adaptive traits for farming as well as THC.

Mark:

They're active.

Gemma:

Yeah, yeah, so THC and CBD as well. So cannabidiol, but you know it was really interesting because cannabis obviously has a number of different chemicals I'm not sure if that's what you'd call it molecules within the plant. So CBD is one of them, thc is one of them, but there's, you know, there's heaps of those cannabinoids and there's also terpenes, profiles and stuff like that as well. So a number of different terpenes within the different plants that are grown, the different strains, and it all sort of contributes to the overall effect of the plant. And there was, you know, in the Cochrane Reviews.

Gemma:

So Cochrane Reviews, aware, there's a whole lot of data analysed from a whole lot of different studies. It wasn't really that clear what health impacts the plant had, but I think that was primarily due to the heterogeneous nature of the plant itself and its chemical composition. So, you know, some studies would find that it really helped with sleep, others would find that it didn't. You know, there was obviously treatment for like nausea and stuff around those who were receiving chemotherapy treatment. So it was really interesting. There's lots of different parts of the plant and also very hard for pharmaceutical companies to replicate because it wasn't just looking at you know a single product like THC or CBD, and you know, for the producers in New Zealand, obviously you need to create standardized products.

Gemma:

So you know there's all the they call it the entourage effect. So it's, you know, the sum of more than just the sum of the parts, and you know it's not just the THC and CBD together but it's all of the. You know the background and you know, like I guess that's the same as animal breeding, really, at the end of the day, like you know, there are some genes that have a major effect, but then you know there's a different genetic landscape for each individual and you know, ultimately, the way the genes express each other can, you know, be different based on what the genetic background is for the animal too.

Mark:

Yeah, exactly, there's lots of small things interacting that we only really scratch the surface of, but we try and. I guess the power of breeding ways is we and the prow of combining those breeding ways in a sensible way through a carefully constructed index. You can kind of put all that together in a sensible way. Yeah, all right, that's awesome, gemma. Thanks very much for your time. I think we can. We can wrap it up there anything that we've missed in informing New Zealand beef or anything else.

Gemma:

Oh, I think we've probably covered. I really appreciate your time today, so thanks for having me.

Mark:

Excellent, great to have you on and we look forward to seeing those cows chucked in steel tanks all over the all over the country.

Gemma:

Thank you.

Mark:

Cheers Gemma.

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