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  • NATURE PODCAST

Five years in the coldest fridge in the known Universe

Listen to the latest from the world of science, with Nick Petrić Howe and Benjamin Thompson.

In this episode:

00:46 The very cool experiment looking for a proposed particle

Physics tells us that when matter is created, antimatter should be as well. But while the Universe is full of matter, there’s surprisingly little antimatter to be found. To try and understand this imbalance, a team have built a detector kept just above absolute zero which they are using to look for a hypothesised, ultra-rare type of particle decay that could create matter without antimatter.

Research article: The CUORE Collaboration

News and Views: Cryogenic mastery aids bid to spot matter creation

09:43 Research Highlights

Subsidence of coastal cities makes them more vulnerable to sea-level rise, and tackling ‘crazy ants’ with a parasitic fungus.

Research Highlight: Global cities are sinking — and humans are partly to blame

Research Highlight: Marauding crazy ants come to grief when a fungus comes to call

12:17 Solving the puzzle of the missing plasmids

Bacteria are well known for their ability to share genes, which they often do using small circles of DNA called plasmids. But while plasmids are common in bacteria, a long-standing mystery has been why they are absent in a group of cholera-causing strains of Vibrio cholerae. Now, a team might have solved this mystery, by discovering two previously unknown DNA defence systems that eliminate plasmids, hidden in the bacteria's genomes.

Research article: Jaskólska et al.

News and Views: Bacterial defence systems degrade plasmid invaders

18:41 Briefing Chat

We discuss some highlights from the Nature Briefing. This time, what smelling jars from an Egyptian tomb has revealed about ancient burial practices, and the latest report from the IPCC.

Science: Ancient smells reveal secrets of Egyptian tomb

Nature: IPCC’s starkest message yet: extreme steps needed to avert climate disaster

Subscribe to Nature Briefing, an unmissable daily round-up of science news, opinion and analysis free in your inbox every weekday.

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doi: https://doi.org/10.1038/d41586-022-00993-9

Transcript

Listen to the latest from the world of science, with Nick Petrić Howe and Benjamin Thompson.

Host: Nick Petrić Howe

Welcome back to the Nature Podcast. This week, why physicists built the coldest cubic metre in the known Universe.

Host: Benjamin Thompson

And solving a long-standing microbial mystery. I’m Benjamin Thompson.

Host: Nick Petrić Howe

And I’m Nick Petrić Howe.

[Jingle]

Interviewer: Nick Petrić Howe

This week, physicists have a newish weapon in their arsenal to attempt to find evidence of a theoretical phenomenon that’s never been observed. Deep underground, frozen to near absolute zero and filled with tellurium dioxide crystals is The Cryogenic Underground Observatory for Rare Events (CUORE), also known as the coldest cubic metre in the known Universe. With this technological marvel, physicists hope to find evidence of a process that could explain one of the key mysteries of the Universe: why is there so much matter?

Interviewee: Carlo Bucci

So, there is no explanation for us on why the Universe is full of matter and there is a very scarce amount of antimatter.

Interviewer: Nick Petrić Howe

This is physicist Carlo Bucci, one of the team behind CUORE.

Interviewee: Carlo Bucci

Because all the physics laws that we know postulate that for every creation of a matter particle there should be a simultaneous creation of an antimatter particle.

Interviewer: Nick Petrić Howe

So then how is the Universe filled with so much stuff? Well, it could be due to a process known as neutrinoless double beta decay.

Interviewee: Carlo Bucci

It’s a peculiar decay that happens, if it happens, very, very rarely.

Interviewer: Nick Petrić Howe

Let me break down this neutrinoless double beta decay for you. Now, beta decay is where a neutron transforms into a proton, emitting an electron and an antineutrino while it’s at it. Double beta decay is where this happens twice at same time, so two electrons and two anti-neutrinos are emitted. With me so far? Both single and double beta decay happen often in nature and have been observed. But then we come to something that’s only been theorised to exist: neutrinoless double beta decay.

Interviewee: Carlo Bucci

In which the double beta decay can happen without the emission of the two antineutrinos.

Interviewer: Nick Petrić Howe

This could explain the mystery of why there’s so much matter around. Without the emission of two antineutrinos, you would end up with more matter than antimatter, which is basically the current state of the Universe. Unsurprisingly, physicists are kind of keen to see if this theoretical neutrinoless double beta decay exists. So, how would you go about finding it? Here’s Carlo to explain.

Interviewee: Carlo Bucci

What you have to do experimentally is to look for a specific energy release in your detector. What I mean is the following: you take, let’s say, a nucleus that can theoretically have this neutrinoless double beta decay and then you wait and see if these two electrons come out without neutrinos. This is, let’s say, the basic idea.

Interviewer: Nick Petrić Howe

This may sound straightforward – just observe and see if it happens – but in practice it is, to put it mildly, tricky. The first of many problems is that the process seems to happen very rarely.

Interviewee: Carlo Bucci

What we call the half-life of the process is extremely long, is the order of 1025-1027 years, means billions of billions of billions of years, and so you cannot wait so much.

Interviewer: Nick Petrić Howe

Much as physicists are keen to solve the mystery, they're not that patient. One way to potentially speed up the process is to use a whole bunch of nuclei instead of just one, as the more you have, the more likely it is one of them will decay while you’re watching them. But then you still need to actually be able to measure when this rare event occurs. The method Carlo and his team used was to make everything cold, and I mean really cold. Their experiment was kept just above absolute zero, which meant that when, and if, neutrinoless double beta decay occurred, they would be able to see a small spike in temperature due to the energy released. But then there’s another problem.

Interviewee: Carlo Bucci

Cosmic rays are something that can mimic the signal that we are looking for, so we have to reduce the number of them in order to reduce also the possibility that they can interfere with our measurement.

Interviewer: Nick Petrić Howe

Cosmic rays are protons and nuclei that rain down on us from space, and they can spoof the signature of neutrinoless double beta decay. As such, it’s best to limit the amount of them that hit the detector. So, Carlo and his team’s experiment was placed deep underground, underneath the Gran Sasso mountains in Italy, to shield it from these rays. But that isn’t the only process that can mimic neutrinoless double beta decay. Another problem is radiation from things a bit closer to home. Tiny amounts of radiation are emitted by just about everything and, with the sensitivity of CUORE, even negligible amounts can get picked up. So, the team shielded their detector with lead, but not just any lead.

Interviewee: Carlo Bucci

The most internal shield of the CUORE experiment is made of ancient Roman lead. The reason is because lead is an excellent material for making shielding against radioactivity because it’s very dense, but contains an isotope that is radioactive. And so, you are building a shielding against radioactivity with something that is a bit radioactive. But this radioactivity, if you wait enough, meaning many, many years, it disappears.

Interviewer: Nick Petrić Howe

After many, many years, a few hundred – or thousand if you want to be safe – lead loses its radioactive qualities, making Roman lead the perfect, non-radioactive shielding material. So, once you’ve got a detector, in this case a very cold detector, that can detect neutrinoless double beta decay and other processes are as blocked out as possible, then the next step is to wait. And that’s what Carlo and his colleagues have been doing. The detector has been up and running, barring a little maintenance, since around 2017, and it’ll run until 2024, overall ending up with five continuous years of data. So, the killer question is, have they found this elusive process?

Interviewee: Carlo Bucci

Not yet.

Interviewer: Nick Petrić Howe

They're in good company. Many other experiments of this ilk are running around the world, and so far none of them have happened upon this potentially matter-forming process of neutrinoless double beta decay. The key result of this experiment is the technical achievement. Running such an experiment so close to absolute zero for so long is extraordinarily difficult. But Carlo and the team have proved it possible, which could potentially have other applications, such as in quantum computing. But Carlo and the team aren’t done yet. They’re using the advances made in this experiment to inspire the next. The search will certainly continue, as many physicists, including Carlo, are optimistic that they will find this neutrinoless double beta decay.

Interviewee: Carlo Bucci

Yeah, we strongly believe that we can see it. I mean, it’s clear that no one really knows when we can say, ‘Okay, it does not exist,’ but there are many, many physicists that believe that neutrinoless double beta decay exists. And so, at the moment, the effort of all the experimentalists is to improve the sensitivities of the experiments because we strongly believe that we will see it. What we don’t know is when we will see it, and it’s a bit frustrating because it can be a very, very long search.

Interviewer: Nick Petrić Howe

That was Carlo Bucci from Laboratori Nazionali del Gran Sasso and the Istituto Nazionale di Fisica Nucleare, both in Italy. To find out more about CUORE, check out the paper and an associated News and Views article in the show notes.

Host: Benjamin Thompson

Coming up, we’ll be hearing how researchers have answered a question that’s had microbiologists scratching their heads for years. Right now, though, it’s time for the Research Highlights with Dan Fox.

[Jingle]

Dan Fox

As sea levels rise around the globe, coastal cities are faced with a second problem: many are also sinking. Researchers analysed satellite data gathered between 2015 and 2020 for 99 coastal cities. By comparing measurements of the ground surface taken every two months, the researchers could watch as the land subsided in various parts of a city. Most of the cities had at least some neighbourhoods where land was sinking faster than the rate of sea-level rise. In Karachi, Pakistan, the land dropped by as much as 10 millimetres per year – 5 times the mean sea-level rise. While Tianjin in China and Jakarta in Indonesia subsided by more than 30 millimetres a year. In most cases, the cause was thought to be pumping groundwater from beneath cities. The improved global view could help officials to develop better policies to track groundwater extraction and reduce the risks of flooding. Read that research in full in Geophysical Research Letters.

[Jingle]

Dan Fox

Swarms of tawny crazy ants are known to invade houses, cause electrical short circuits and overrun birds’ nests, but they have met their match in a naturally occurring single-celled parasite. Originally native to South America, crazy ants are now established in countries such as Cuba and the US, and not only damage human infrastructure but also harm reptiles and birds. However, in 2015, researchers observed that a single-celled fungal parasite was infecting some crazy-ant populations in the United States. To understand the parasite’s effects, researchers analysed 15 populations of ants, finding that the infected crazy-ant populations dwindled and disappeared over 4-7 years. When the researchers exposed two previously uninfected ant populations, both disappeared within three years. Laboratory experiments suggest that the parasite can rapidly kill worker ants in winter, leaving queens with too few workers to rear the next generation of brood in spring. The authors suggest that such pathogens could be used to control invasive insect species. Find that paper in the Proceedings of the National Academy of Sciences of the United States of America.

[Jingle]

Interviewer: Benjamin Thompson

This week in Nature, a paper has been published that appears to have solved a microbial mystery that centres on the bacterial species Vibrio cholerae. Now, while most strains of Vibrio cholerae are natural inhabitants of marine environments, some can cause a serious disease in humans: cholera. In fact, the world is currently in the midst of what’s known as the seventh cholera pandemic, but the strains responsible for it have puzzled researchers because they've got something missing, as paper author and microbiologist Melanie Blokesch explains.

Interviewee: Melanie Blokesch

Why do the pandemic strains specifically not keep plasmids, because plasmids are very common in environmental strains of the same species of Vibrio cholerae. So, the question is, where are the plasmids? Why are they not there?

Interviewer: Benjamin Thompson

Plasmid are circles of DNA found in bacteria that are separate from their own genomes. They can be small, carrying only a couple of genes, or much bigger. And the thing is, they’re found all over the bacterial tree of life, where they’re shared all the time. Sharing plasmids is one way that bacteria can acquire new genes and potentially new abilities, so it’s unusual, to say the least, that they’re rare in strains of the seventh cholera pandemic. Researchers can introduce them into these bacteria in the lab, but they don’t stick around. This was a bit of a head-scratcher, but no one had really taken the time to find out why.

Interviewee: Melanie Blokesch

I guess everyone has asked themselves the question but nobody followed up on it. People just accept that these strains don’t have plasmids, and then people have looked at many, many isolates from patients, and they’ve found that some few strains in the past had large plasmids, but these seem to have also disappeared in the last 10-15 years. So, I think people have observed it, they’ve thought about it, but nobody looked at what the mechanism behind it is.

Interviewer: Benjamin Thompson

That is until now. And not only did these strains seem unhappy to keep the plasmids, in some cases they also actively destroyed them. In their new paper, Melanie and her team did some genomic digging and found out how this happened. They identified two areas containing clusters of genes that were important.

Interviewee: Melanie Blokesch

And so these gene clusters encode two DNA defence systems that can then do the job in the cell.

Interviewer: Benjamin Thompson

And in this case ‘do the job’ means ‘get rid of the plasmids’. But there’s an important question here: why? After all, sharing plasmids gives bacteria a way of acquiring new genes, so the fact that these cholera strains don’t have them is a bit weird. It’s a tough one to answer, but Melanie’s got an idea.

Interviewee: Melanie Blokesch

So, I think this really depends on where the bacterium usually lives. If it’s in an environment where you have constant changes, it’s probably good for the whole population if they can acquire new genetic information and share a lot, and so some part of the population that might have an advantage when there’s an extreme conditional change. But of course, there might also be a cost to have a new plasmid because it’s costly to keep it, to replicate it, to make new copies of the plasmid, so that is energy that the cell will invest for this plasmid. Now, the pandemic strains of Vibrio cholerae are very much adapted to human infection. So, in a way, they might have less changing conditions so they might not need more plasmids because they have already evolved to really do this cycle of infection well. So, in a way, by not keeping plasmids, they don’t have this extra burden that a plasmid might have, at the cost that they might not get new plasmids with new superpowers and new genes, but they might not need that.

Interviewer: Benjamin Thompson

Now, defence systems that target plasmids have been seen before in other bacteria, but the two that Melanie has identified appear to be new, and they work in a different way. These two systems can cooperate to quickly degrade small plasmids, but the second also appears to work in quite a particular way to get rid of large plasmids – by making bacteria containing them grow more slowly. This negative selection pressure means that, in time, bacteria containing these large plasmids are outgrown by those without them. Didier Mazel from the Pasteur Institute in France also works on cholera, and has written a News and Views article about the new work. He says he found it fascinating because it offers an answer to a long-standing question, but he says it asks a lot of new ones as well.

Interviewee: Didier Mazel

One of the fascinating questions is how these systems are able to recognise the difference between a chromosome and a plasmid, which is fascinating because they are both made of DNA, I mean essentially the same molecule, they encode different things, but they are basically made of the same four bases, so it is very intriguing and exciting to find how they recognise the difference.

Interviewer: Benjamin Thompson

While there’s a long way to go before these new systems and the roles they play are fully understood, Melanie’s work does shed light on the long-standing curiosity among microbiologists as to why plasmids are so rare in seventh cholera pandemic strains. But could this curiosity be used in other settings? After all, the discovery of CRISPR – another system that bacteria use to defend themselves from external DNA – has opened up a lot of research potential. For Didier, there’s one avenue of particular interest, tackling something problematic that bacteria often share via plasmid – namely, antibiotic resistance.

Interviewee: Didier Mazel

One of the things is that in many cases, the antibiotic-resistant gene clusters are carried on plasmids. So, you can imagine that you are potentially able to develop something that will get rid of these plasmids. And so, you can think that domesticating such systems may allow to re-sensitise resistant bacteria by destroying the plasmid that carried the antibiotic-resistant gene. So, that’s an obvious application of this kind of thing.

Interviewer: Benjamin Thompson

That was Didier Mazel. You also heard from Melanie Blokesch from Ecole Polytechnique Fédérale de Lausanne in Switzerland. Look out for a link to Melanie’s paper, and Didier’s News and Views article, in the show notes.

Host: Nick Petrić Howe

Finally on the show, it’s time for the Briefing chat, where we discuss a couple of articles that have been featured in the Nature Briefing. Ben, what have you bought for us to discuss this time?

Host: Benjamin Thompson

Well, Nick, we’re going to go back to ancient Egypt, in fact more than 3,400 years ago, and this is a story that I read about in Nature, and it’s looking at how researchers are analysing smells to get a little window into the past.

Host: Nick Petrić Howe

Wow, this sounds very intriguing. I mean, my first thought is this is a long time ago. Are there any smells left?

Host: Benjamin Thompson

Well, Nick, that is actually central to this, right, because smells do tend to linger, it turns out, and this story kind of centres on a discovery in 1906 of the tombs of a husband and wife, and their remains apparently remain the most complete non-royal ancient burial ever found in Egypt, and it gave lots of info about high-ranking individuals and how they were treated after death.

Host: Nick Petrić Howe

Right, and, well, I’m assuming researchers haven’t just been giving this couple a sniff. What exactly are they doing to analyse the smells here?

Host: Benjamin Thompson

Well, I mean, weirdly, you’re kind of not far off, but the story continues then. So, these tombs were discovered and, unusually, the people who discovered them didn’t start opening stuff up and having a look. They just kind of left it. And so, a bunch of urns and jars and what have you were taken to a museum in Italy where they remained, and apparently the curators there noticed that, in some of the display cases, they could sometimes get a bit of a fruity aroma, and so researchers have actually said, okay, well, let’s try and work out what was going on then. And what they’ve done is, they’ve taken some of these vessels, put them in kind of plastic bags for a few days, and then used mass spectrometry to analyse these volatile compounds, these smell compounds, that kind of wafted off them as they were sitting there.

Host: Nick Petrić Howe

So, you mentioned there a fruity sort of smell. What other sorts of smells did they find when they were analysing this?

Host: Benjamin Thompson

Well, there were some smells associated with dried fish and fruits, and there were also things called aldehydes and these long-chain hydrocarbons associated with beeswax, and the researchers said that, actually, two thirds of the things that they tested gave up a result as to what was causing the smell, which is kind of neat. And this is all part of a project to reanalyse the tomb’s contents and maybe give an insight into what burial customs were like for non-royals back in ancient Egypt.

Host: Nick Petrić Howe

That’s really interesting. I had no idea they would be able to find smells after so long. But what can it tell us about the distant past?

Host: Benjamin Thompson

Well, I get the sense, Nick, that some researchers are saying that smells is really kind of an underexplored area of archaeology. Obviously, I think people just assume they would have dissipated over these thousands of years, but it turns out that this isn’t the case, as this work has shown. But it’s not the first time then that the kind of sniffing stuff has given a sense about what’s going on in ancient Egypt. Back in 2014, researchers extracted some of these volatile molecules from linen bandages that were used to wrap bodies that were over 5,000 years old, so even older, from some of the earliest known Egyptian cemeteries. And what they’ve found is that antibacterial embalming agents were used, by sniffing these bandages, showing that Egyptians were experimenting with mummification much, much earlier than was previously thought, so it really is giving a more accurate window into what society was like back in antiquity.

Host: Nick Petrić Howe

Well, that sounds absolutely fascinating, Ben. Thanks for telling me about that. For my story this week, I’ve been looking at the latest findings from the IPCC, and I’ve been reading about them in Nature.

Host: Benjamin Thompson

Yeah, and we’ve covered the IPCC’s work before on the podcast, right? What’s going on at the moment?

Host: Nick Petrić Howe

So, what I’m referring to is actually the third part of the sixth assessment, and so this report is all about mitigation. So, it’s all about the things that we can do to actually tackle climate change. And the findings of this one are maybe not too surprising, but it’s quite stark. Essentially, what they’ve found is we’re probably not going to be able to stop warming above 1.5 °C, and the window to try and do so is closing quickly.

Host: Benjamin Thompson

I mean, if you say there are reports about mitigation then, is it saying, well, if we’re going to miss this target, we need to work out ways to try and avoid the worst-case scenarios happening? Is that right?

Host: Nick Petrić Howe

So, yeah, really this report is about this closing window and the fact that we don’t have a lot of time to actually make the aggressive changes required to attempt to get to 1.5 °C, or if we get to 1.5 °C, how we can bring the temperatures back down afterwards. So, the key findings are essentially that we need to do things more quickly and we need to implement clean energy and new technologies far more quickly and take very aggressive action.

Host: Benjamin Thompson

And what does that aggressive action look like then, Nick?

Host: Nick Petrić Howe

Well, one thing that they’ve found is that emissions need to peak by 2025 and, yes, you heard that right, that’s in three years’ time. And after 2025, they need to rapidly decline. So, to achieve the net zero by 2050 goals, we need to halve emissions by 2030. There is some good news, though, in the report. The prices of renewables has been plummeting. Battery technologies, wind power, solar power – this is all getting far cheaper. And the energy intensity that runs the global economy is declining, so that means that we need less energy to keep the economy going. So, there is a bit of good news in there as well. But of course, there are other aspects as well, like we need to keep some fossil fuels in the ground, and we need to start pulling some carbon dioxide from the air.

Host: Benjamin Thompson

Well, obviously a lot to get done then, Nick, in a very, very short space of time. Obviously these reports put forward evidence. What are climate scientists saying about what this report is saying and the chances of these things happening?

Host: Nick Petrić Howe

So, as I said, it seems unlikely that we’re going to hit the 1.5 °C target. We’ll probably go over, and so what some scientists are now saying is we need to have a plan of how to deal with the overshoot because once we get over 1.5 °C, that’s when you start to get more serious consequences of climate change. So, we need to start thinking about what we’re going to do there, and really we just need to speed up the transition because we not only need to be reducing emissions, we need to be pulling them out of the air. And that could be carbon capture and things like that that you may have heard of, but it could also be more low-tech things like changes in agricultural practices or planting more forests. But really, I think scientists are like, okay, we need to actually make these changes now. Pledges are fine but we need to actually see action, and this is the starkest warning from the IPCC yet.

Host: Benjamin Thompson

Well, Nick, let’s leave it there then for this week’s Briefing chat. Listeners, if you’d like to know more about these stories, we’ll put links to them in the show notes as always, and we’ll also put a link on where you can sign up for the Nature Briefing to have more stories like these delivered directly to your inbox.

Host: Nick Petrić Howe

That’s all for this week. As always, you can reach out to us on Twitter – we’re @NaturePodcast. Or you can send us an email to podcast@nature.com. I’m Nick Petrić Howe.

Host: Benjamin Thompson

And I’m Benjamin Thompson. See you next time.

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