Podcast: Making plane fuel greener, synthesised yeast chromosomes, and seeking ourt hidden HIV

This week, making plane fuel greener, yeast chromosomes synthesised from scratch, and seeking out hidden HIV.Your browser does not support the audio element.Download MP3See transcript

Biofuels could cut the carbon footprint of flying, but how do they affect other pollutants. Research paper: Moore et al.

What can scientists learn by rebuilding yeast from the ground up? Research papers: Science; News: Synthetic yeast chromosomes help probe mysteries of evolution

Arctic rain; and beetle ant-ics. Research Highlight: Arctic set for rainy future; Research Highlight: Beetles repeatedly involved mimicry

Finding the infected cells that lie dormant in patients treated for HIV. Research paper: Descours et al.; News and Views: Finding latent needles in a haystack

Trump targets the Environmental Protection Agency; and scientists shed light on a fluorescent frog. News: Trump and Republicans take aim at environmental agency; News: First fluorescent frog

found

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This week: scientists synthesize a chunk of the yeast genome

I wasn’t sure whether it would be feasible but sometimes a project is just so exciting that you say, yeah, I want to be part of this.

And researchers flying behind planes to measure emissions report a turbulent ride.

The most dominant indicator that we were in the plume was you could feel it in the seat of your pants.

Plus, tracking down HIV hidden in cells. This is the Nature Podcastfor March the 16th2017. I’m Kerri Smith.

Over the past century, aviation has changed the way people travel around the world. Unfortunately, it’s also changing the world itself. Flying is currently responsible for about 2% of all

carbon dioxide emissions and it’s only expected to increase over the coming few decades. But carbon dioxide emissions only tell part of the story. David Lee runs the Centre for Aviation,

Transport and the Environment at Manchester Metropolitan University. He explains that the particles planes emit can also have big effects.

First of all, at ground level, particles are obviously a big issue to do with local air quality and human health. But at altitude, particles are involved in the formation of contrails.

Contrails are the white stripes of ice crystal clouds that you can sometimes see behind aircraft. Sometimes they remain, and they spread out and they form an ice crystal cloud formation

called contrail cirrus, and we know that that formation of contrail cirrus has a warming effect. Putting that in context with the other effects of aviation, it’s about the same order of

magnitude of effect, the contrail cirrus effect, as the cumulative CO2 effect from the global fleet.

Of course, many industries are looking for ways to lower carbon dioxide emissions and aviation is no exception but while cars can be made electric and coal power plants can be replaced with

solar and wind, things aren’t so straight forward for planes.

The possibilities are far more constrained for the aviation sector. In terms of the mitigation possibilities, they’re very efficient engines as they stand; they’re one of the finest

technological beasts on the planet already. So it’s actually difficult to squeeze more effectiveness out of them. They’re highly dependent upon liquid fuel, so we’re pretty well reliant, at

the moment, on burning a kerosene-like fuel.

But where this fuel comes from isn’t necessarily set in stone. At the moment it’s sourced from oil dug up from the ground but it could instead be made either from plant or waste materials.

Growing the materials to make these biofuels would effectively suck carbon out of the atmosphere, lowering the net carbon dioxide emissions once they’re burnt. But what about the particles

that David mentioned? A study out this week takes a look at what happens to these particles when biofuels are used in flight. Here’s Rich Moore, who led the study.

The goal here was to understand what happens when we blend half of the fuel that the jet engine is burning with biofuel. Past studies on the ground have looked at the air quality impacts of

what happens to the air around an airport or what are the emissions when a plane is on the ground when burning one of these biofuel planes. But no-one has really looked at what the engine

emissions look like in flight, at real atmospheric conditions. Those conditions are very different from what we see on the ground and it’s much colder, it’s much drier, and the pressure is a

lot lower.

But measuring the emissions under these conditions requires some pretty specialized kit. NASA has a four engine DC-8 aircraft and what we did was – the advantage of using that aircraft is

that it has different fuel tanks so we could feed different fuels to different engines. And so what we did was we had the NASA DC-8 take off from one of our centres out in California and we

chased it with three different aircrafts and we would draw air in from the outside when we were in the plume and pass it to these instruments that measured the concentrations of particles

and gases in the exhaust stream.

Taking measurements while flying is quite unlike research in the comfort of the lab. Rich was in one of the planes that was taking chase in the exhaust stream.

I would describe it like driving a car with worn shock absorbers down a rutted dirt road. The most dominant indicator that we were in the plume was that you could feel it in the seat of your

pants because you could feel that vibration.

Fortunately, this bumpy ride produced results. Rich and his team were able to measure whether burning biofuels had any effect on the particles that the plane was emitting.

We looked at the engine emissions under a variety of different conditions, at a variety of different altitudes, and what we found was that as we blend biofuel – the petroleum fuel – with a

50/50 blend of biofuel, we reduce the particle emissions, the sub-particle emissions, by about 50%. And so what these results show is that if we reduce the CO2, as a co-benefit to that, you

also reduce particle emissions and the associated warming, associated with contrails and cirrus clouds.

David Lee, who we heard from earlier, was impressed with this study. But he’s wary of assuming that reducing the particles necessarily means reducing warming.

If the reduced particles resulted in lower contrail formation then that’s a bit of a big if because that experiment didn’t actually address that. That’s certainly good for ground-level and

human health effects and it’s potentially good for lesser contrail cirrus formation.

Even so, a reduction in these particles as well as the reduction in CO2 emissions is good news. So then what’s stopping the world’s planes from switching over to biofuels tomorrow?

Technically, it’s feasible. Economically, it’s not at the moment. Even to actually undertake these experiments there is not enough biofuel around so that gives you an idea of how little is

produced at the moment. It has to be produced on commercially feasible scales. That’s likely to take a little while but the fuel producers want to do it and the aviation industry wants this.

That was David Lee. You also heard from Rich Moore who’s at NASA’s Langley Research Center in Virginia, US. Find the paper in the usual place.

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weekly, in depth reports on everything from the reality of Donald Trump’s promised border-wall to the water crisis in California.

Thanks to Stephanie Priscilla and Chiquita Brooks for recommending us to their Twitter followers.

Sometimes the best way to understand something is to take it apart and put it back together again. Any engineer will tell you that, but biologists are onto it too. This week, the journal

Science publishes seven papers which detail how scientists made chunks of the yeast genome from scratch. Here’s Kerri with more.

What I cannot create I do not understand. This phrase was on Richard Feynman’s blackboard when he died. Synthetic biologists have really taken this to heart.

There are some really interesting questions that you can only really answer by synthesizing a chromosome and seeing how it works.

This is biologist Joel Bader at Johns Hopkins University in Baltimore. He’s one of several hundred scientists who are working to synthesise the entire genome of baker’s yeast: Saccharomyces

cerevisiae. Yeast is an important biological model: a test bed. But it also has a ton of useful applications. It’s used to bake bread, brew beer, and in biotechnology to make drugs and

biofuels. Fashioning its genome from scratch is a huge undertaking: twelve million base pairs on sixteen different chromosomes.

I wasn’t sure whether it would be feasible but sometimes a project is just so exciting that you say yeah, I want to be part of this, and I’m going to do what I can to make it succeed.

The team announced they’d made the first of the sixteen chromosomes in 2014. The way it works is that they write the sequence in a computer, build it in the lab, and then insert it into a

cell to replace the natural version and then check that the cell still works normally. Now another five chromosomes are joining the list and the design for the rest is also complete. But the

team aren’t content to just reproduce the chromosomes as they are in nature, like a Xerox copy…

…Because that would only answer part of the question. That would answer: do we have the synthesis and assembly methods to replace a chromosome in a cell? But it wouldn’t answer the

additional basic science questions and applied research questions that we had for this project.

Instead, they’re tweaking the design as they go along and watching for changes that could teach them about how genetics works.

Each of these chromosomal syntheses is a major effort that involves a design stage and then synthesis assembly and then finally debugging and often during debugging we learn about functions

that we didn’t know about before because one of the changes that we’ve made in the design leads to a chromosome that doesn’t function well in the cell and then we have to track down the

reason and tracking down the reason for not functioning well shows us something that we didn’t understand before.

It might be easiest to imagine taking a book of fairytales and instead of photocopying each page as it currently is, you edit each story to see if you can make the plot more compelling or

the characters more colourful, or fit more words on a page.

Whatever your interests in improving the story are… Once upon a time there was a beautiful girl named Cinderella [rewind sound effect]… Once upon a time there was a methodical girl named

Cinderella. She lived with her wicked step-mother and two step-sisters [rewind sound effect]… And three step-sisters [rewind sound effect]… and no step-sisters. [Music]… The Fairy Godmother

touched Cinderella’s feet with the magic wand and lo’, she had beautiful glass slippers [rewind sound effect]… And lo’ she had beautiful concrete slippers.

Well you know in the French version is not glass, it’s a very nice rabbit fur moccasin which I think sounds much more comfortable. Changes like that are going on all the time… [Music]

An example of one change the team has made to the yeast’s code – its sentences if you like – is that they’ve gone through and taken out some of the material that they think isn’t being used,

like formatting the pages to have less blank space. Elsewhere, they’ve taken one type of genetic element – transfer RNA – and tidied it all into one place. That way they can test whether

the yeast was using the code in particular ways in particular places.

Yeast has sixteen chromosomes and we’ve actually made a seventeenth chromosome that we call a neo-chromosome.

This might feel a bit like just tidying up but there are major insights to be learned, says Joel. Whatever they did to the yeast’s genetics, he said, the yeast was pretty robust. Most of the

time it integrated the new sequence without a problem and carried on as if nothing had happened. Their design had another bonus: the researchers added in a mechanism that can reshuffle

portions of the code at random. This is essentially the material that evolution works on – so they could see which cells are fittest under different conditions. They could watch evolution

happening in millions of cells in just a single test tube.

Each doing their own rearrangements, so each changing the copy numbers of different elements in the story and then we can test them, see which one works the best, and then take that strain

as the starting point for further optimization.

The team have the design for the other chromosomes ready and they reckon they might have the full genome synthesized within a year. So, naturally, Joel Bader is thinking about what they

might do next.

I think the next target, because of medical and basic science benefits, will probably be a mammalian target, and the two leading candidates, no doubt, are mouse and human. It’s really a

discussion that involves bio-ethicists and scientists and society to decide what the next target should be.

That was Joel Bader, one of more than two hundred researchers who make up the synthetic yeast project which they refer to as SC 2.0. His group’s paper along with the six other articles, are

available at sciencemag.org. There’s also a News story from Natureon the work. That’s by Amy Maxmen and you can find it at nature.com/news.

Ready for the Research Highlights? You’d better be because here’s Noah Baker.

There could be more rain than snow falling in the Arctic by the end of the century owing to global warming. Right now, rain accounts for about a third of the precipitation in the Arctic.

Climate models suggest that precipitation overall will increase and pretty much all of that increase will be rain. The idea is that as the sea ice retreats, more ocean surface is exposed and

water evaporates off to become precipitation. In warmer temperatures, it falls as rain. Rain can cause more melting of permafrost and sea ice and could have effects on the region’s climate

and ecosystems. The paper is in Nature Climate Change.

About a dozen related beetle species have independently mastered the art of disguise. There’s about forty species of Rove Beetle that disguise themselves as army ants, deceiving their way

into colonies to eat the ants’ young and food supply. According to DNA data from beetles and army ants, the copycat technique has evolved independently at least a dozen times. Evolution can

often seem a bit of a lottery but the fact that so many beetle species happened upon the same strategy over such a long time suggests that evolution can actually be pretty predictable. The

journal Current Biologyhas the paper.

Medicine has given us some pretty good treatments for HIV. Drugs called antiretroviral therapies can suppress the virus to undetectable levels. But the drugs aren’t perfect. HIV is very good

at going to ground and it lies in wait in a few dormant but infected cells. Scientists refer to this tiny group as a reservoir. And it is a tiny group – one in a million immune cells. But

the virus can reactivate if treatment stops so scientists are keen to find ways to kill off the reservoir. They’re now a step closer to that goal, as I found out from immunologist Monsef

Benkirane. In his lab in Montpelier in France, Benkirane and his team have found a way to study these elusive cells and have found a marker that sets them apart from their healthy cousins.

With apologies for the poor connection between London and France, here’s Monsef Benkirane telling me about the type of immune cells that harbour the reservoir.

In the blood there are cells – called CD4 T cells – that can change what we call replication competent viruses. These cells are dormant cells and thus the virus that is inside contained in

these cells, is dormant.

So these cells cannot be targeted by the immune system, and at the same time they are not targeted by the antiretroviral therapy.

And this population of cells – this reservoir – that’s what stands between having a treatment and having a cure for HIV?

Exactly, exactly. The major obstacle to an HIV cure is the reservoir: these cells that contain the dormant virus.

These are a very difficult population of cells to study because you just can’t tell from the outside which have HIV latently in them and which don’t and so actually the first part of the

process was the most difficult – getting the cells next to each other in order to be able to study them.

Yes. The most challenging part was actually to derive an in vitrosimilar model that would recapitulate the features that were reported for the HIV reservoir.

So you wanted to recreate these reservoir cells in the lab to study them and one reason why that was so difficult was that, ironically, it turned out to be tricky to deliberately infect

these cells with HIV. But you found a way to sneak the HIV into these cells. That turned them into these dormant, infected cells and that allowed you to compare their genomes with the

healthy ones. So what was the difference between them in the end?

Well, the difference is that the cells that contained the virus, they expressed some specific genes that healthy cells do not express and one of these genes is actually a gene that encodes

for a protein and this protein is actually expressed at the cell surface of the cell. This is just like slag at the surface of the cell.

So now that you’ve found this new marker, can you act on this new information? Maybe test out trying to exterminate the cells with the marker on them?

Yes, we can because we can use some ligands that bind to this marker at the surface of the cells and kill these cells. If there is any therapeutic objective it would be this one.

If the HIV is latent, quiescent, in the cell, why is it, do you think, the cell has this marker on its surface? What’s it using it for?

This is a beautiful question and I think we have to understand… It is really one of the major questions that we have to answer in the future: why expressing this marker? Why expressing this

signature? What does it mean, functionally? I agree with you – cells do not express a gene just to express a gene. It expresses genes to achieve a function so we have to find it. We have no

clue but this is certainly one of the major objectives that we have. The other thing that is going to be challenging is to ask whether this signature is specific for this virus, okay? What

does it mean? Does that cellular response to the signature constitute a new immune response? I think it’s very important. Is it restricted to HIV or will infection by other viruses lead to

the expression of the signature? I think it’s something that we really need to understand.

That was Monsef Benkirane. The paper and the News and Views article digesting the new finding are available at nature.com/nature and there is also a News story at nature.com/news.

Speaking of news, here’s Richard Van Noorden with his pick of the week. Hi Richard.

Another week, another load of Donald Trump news… This week there’s news from the EPA: the Environmental Protection Agency. The chief has been getting quite a lot of somewhat negative

attention.

We’re focusing on the Environmental Protection Agency and the ways that Trump’s administration and congressional Republicans are beginning what seems like an all-out effort to reshape the

agency on everything from climate change to how it uses scientific data in policy making. This all comes ahead of Trump’s budget request which is on Thursday the 16th March, or it’s

scheduled to be, so if you’re listening it may be out already. And rumors are that Trump will request a large cut to the EPA. Of course that doesn’t mean that it will get through congress,

and he’s clearly looking to reshape the agency.

Most controversially, as you say, the EPA’s head Scott Pruitt said in a media interview last week that he doesn’t believe carbon dioxide is a primary contributor to global warming, which

goes against the longstanding scientific consensus. And this week scientists have reminded him very forcefully that, in fact, the science is very clear on this and one can have one’s

opinions on what to do about it but that basic fact cannot be contested.

But there’s other things going on with the EPA as well. Last week Republicans on the House of Representative’s Science, Space and Technology Committee approved two bills that would – well,

one of them would bar scientists who are currently funded by the EPA from serving on Agency Advisory Committees. This is being spun as a way to give greater representation on the EPA’s

advisory board but people are looking at this and saying well, does this mean greater industry representation? Does this in the end just make it just harder for the EPA to solicit solid

scientific advice? The other bill that the committee put forwards is a bill to require that all scientific data that the EPA uses to justify new regulations be made public. Again, sounds

like a move towards transparency but in practice this bill would just require the agency to make public all kinds of data including health data that the EPA often doesn’t have the legal

right to release. Yogin Kothariwho tracks legislation at the Union of Concerned Scientists in Washington DC says this is really just a way to prevent the agency from doing anything.

Are these kinds of developments – are they surprising or would you say people predicted this?

This has long been expected. Essentially, as David Doniger, the director of the Climate and Clean Air Program at the Natural Resources Defence Council says, what Trump’s administration wants

to do is essentially paralyse the EPA, cut its budget and roll back various environmental regulations. And at the top of that list, two of the landmark Climate regulations developed under

Obama’s administration – one, to reduce emissions from power plants (that is anyway on hold pending a lawsuit) and the other is aggressive fuel efficiency requirements for vehicles. Now,

although a lot of these developments are very worrying for environmentalists and for scientists at the EPA, Doniger says, look it’s going to be a long fight but he says he thinks – maybe he

would say this – that there’s a good chance of blocking some of these moves, at least so that a future administration after Trump’s time in office could – as he puts it – put Humpty Dumpty

back together again.

Yes, the EPA is teetering a bit on the edge of being down-sized, cut, of having its regulations rolled back.

On now to a lighter topic, and yes that is a pun. A glow in the dark frog has been discovered.

This is the first fluorescent frog. It’s a polka dot tree frog in South America. Normally it’s very muted green, yellow and red but if you shine a black light, an ultraviolet light on it, it

gives off a bright blue and green glow. And, weirdly, fluorescents haven’t been seen in amphibians before. It’s very rare in terrestrial animals and this polka dot frog uses molecules to

fluoresce which are totally unlike those found in other animals – actually quite similar to what are seen in plants.

You mention that this isn’t actually unique to terrestrial animals. What other animals do fluoresce?

It has been seen in parrots, and some scorpions and it’s not clear why animals can do this. Maybe communication. Maybe camouflage. Maybe attracting mates, and just for people listening who

are wondering what fluorescence actually means: you need a source of light first, like UV light, and then you fluoresce, you give off light in a different colour.

And is this the kind of routine thing that people check? Do they carry around a black light torch to just shine on animals to see whether they fluoresce?

So this discovery was made by herpetologists at the University of Buenos Aires in Argentina and they were actually looking for fluorescence and they did carry a black light with them and

this is how they discovered this. He hopes that some of his colleagues will start carrying UV flashlights in the field because why shouldn’t other frogs fluoresce? Probably just because

people haven’t been looking hard enough for it. Now, what I was quite intrigued by was that we don’t know, unfortunately, much about the polka dot tree frog’s visual system, so we don’t know

if they can see their own fluorescence, but no doubt more study on that.

Surely it would know it’s fluorescent because why would it have developed that ability? Well, maybe it was something to do with a predator or camouflage. But we still don’t know what the

ecological and behavioural function of this is.

This frog isn’t a new discovery, it’s just a new discovery that it glows in the dark.

Exactly. Yeah, the frog is well known and no-one had seen this greenish blue glow because no-one had trained a black light on it.

Richard, thank you very much for shedding light on those two stories.

That’s all for this week. Remember, you can recommend us to someone who may not even have heard of podcasts if you use the hashtag ‘trypod’ on Twitter.

They might enjoy the history of science series we’ve been re-broadcasting which is still available on the RSS feed. The Nature Past Castunlocks the archive and looks at key moments in

science. This week: Arthur Eddington and his quest to test Einstein’s theory of general relativity in the early 1900s.

We’ll be back next week with more of the best research and news. I’m Kerri Smith.