Caterpillars see using their skin

Possibly my favourite science story of 2019 – scientists at the University of Liverpool conduct 3 experiments to show that caterpillars of the peppered moth see using their skin. Live interview with BBC Radio Oxford.

Image credit: Arjen van’t Hof, University of Liverpool

The Naked Science of a DNA test

I had my genes sequenced by 23andMe in the name of science… and of course I had to ask about the ‘maths’ behind the results.

Nowadays, a lot of companies offer online ancestry tests, or tests to quantify your risk of inheriting some life-changing diseases. But how seriously should we take their results? Izzie Clarke and Tom Crawford spoke to Garrett Hellenthal from UCL and Julianna Cintron from 23andMe in order to find out…

Tom – Fill the tube with saliva to the black wavy line… shall we just crack on?

Izzie – Okay! You get the idea. But in order for companies to analyse our genetic information, all we have to do is spit into a test tube and send it off to the lab. Tom sent his to a company called 23&Me to find out about his health and physical traits, and I wanted to explore my family history. So, how does a bit of my saliva reveal so much about my ancestry?

Garrett Hellenthal from University College London’s Genetics Institute…

  • Saliva contains your genetic code in a series of cells which can be extracted and identified via a series of genetic markers that define your unique DNA sequence.
  • They look at about 500,000 different pieces of genetic code and compare them to the codes of people in the company database to determine who you share matching DNA patterns with.
  • Izzie found out that she is 30% Irish, 24% Western European, 15% Great Britain and 15% Scandinavian.

Izzie – But what about health and physical appearance? Let’s take a look at Tom’s results…

Tom – I think most of them are correct for me like I should likely have lighter eyes, and I have blue eyes. It says likely little upper back hair, and I can fortunately report I have minimal upper back hair. I was also pleased to see that I’m likely not to have a bald spot; I really hope that one’s true.

Izzie – In addition to appearance, Tom’s test was able to look at specific parts of his genetic code and explain the likelihood of there being a change called a ‘variant’, which could possibly lead to a life-changing illness.

Julianna – My name is Julianna Cintron and I’m a produce specialist on the customer care team at 23andMe.

  • There are some traits that are more influenced by genes than others, for example if you have two copies of the gene associated with having red hair then you are much more likely to have red hair.

Tom – Just with you mentioning there this idea of it’s to do with the confidence in something, or there’s a probability. We’re using phrases like more likely, it’s not sort of fixed. In my result I was told that I have a particular variant which leads me to be at a higher risk of Alzheimer’s disease and I was just wondering what exactly does this mean? Does this mean I will get Alzheimer’s; does this just mean I’m above average likely; how does this result actually relate to the risk factor?

  • The e4 variant is known to impact your risk of developing Alzheimer’s and having one copy of the variant puts you at a slightly increased risk of developing Alzheimer’s by a certain age. Having two copies increases the risk further.
  • Most of the genetic risks are actually relatively small, much less than say smoking or unhealthy lifestyles in general.
  • The most important thing is to use the results as ‘one piece of the puzzle’ and not as a diagnosis that you will or will not get a certain disease.

You can listen to the full interview with the Naked Scientists here.

Plankton change genes to combat climate change

2016 was another record-breaker in terms of global temperatures, and it’s part of a longer-term trend which has seen 15 of the hottest years on record since 2001. One victim of this warming is the Artic. The sea ice is steadily retreating, which means that the habitats for species that live there are also radically altering. So are these organisms equipped to cope with the change? Thomas Mock, from the University of East Anglia, has been studying one marine species which use a genetic trick to adapt, as he explains…

Thomas – With our study we have provided first isights into the evolution adaptation of phytoplankton which are little plants floating in the ocean and we selected to sequence one of their genomes. It was a diatome, they prefer to live in nutrient rich and cold water and therefore their natural home are the polar oceans like the Southern Ocean and the Arctic Ocean. In polar oceans they are the base of the entire food web, including fish, birds and mammals like the polar bears and whales. So if their diversity changes according to global warming, which is a significant concern, then the entire food web might change with consequences for human societies.

Tom – You said that you’d looked at the genome of these phytoplankton – is that DNA sequencing?

Thomas – Yes, what we did is we selected one keystone species and we sequenced its DNA. And what we found is that they are very very different to anything that was sequenced before, at least form the marine system.

Tom – And those differences, are they because of the cold and variable environment?

Thomas – Yes that’s what we think. The variability of the polar oceans has basically caused or shaped the genomes of these organisms. What we’ve found is that the adaptation basically boils down to how they use their alleles. Alleles are basically different versions of the same gene. So in our genome we have two versions of each gene. One is derived from the mother and the other is derived from the father. They can be different from each other which impacts how we look. So I can give you an example, for instance the gene for eye colour has an allele for brown and for blue eyes. People can have two for brown, two for blue or a mix of both alleles. And this mix of alleles is basically what we found in our polar diatome genome, but not only for a small number of genes, but for 25% of all genes in the genome. These different versions are used under different environmental conditions.

Tom – So the phytoplankton are in some sense switching on the genes that help them to survive given the current environment?

Thomas – Yes that’s right – they switch on different versions of the same genes in different ways and this makes them able to cope with changing environmental conditions.

Tom – Could you give an example of one of these particular alleles that you found specifically in the phytoplankton?

Thomas – One group of genes we found is the group of antifreeze proteins. And they are expressed, they are used whenever temperatures drop below the freezing point of seawater. These creatures live between the ice crystals – this very very extreme habitat with high salinities and very low temperatures and they can cope in these extreme conditions very well because they have very different types of these antifreeze proteins.

Tom – I’m putting myself in the shoes of one of these phytoplankton. If I’m happily floating about in the sea and then suddenly the sea freezes and I become trapped in sea ice, would I then suddenly switch on this particular version of this protein to allow me to survive.

Thomas – Yeah that’s correct and this is what we actually tested in the laboratory. We simulated sea ice formation and then we looked at how all of the different genes in the genome are expressed.

Tom – Now that we now this, ultimately how is this going to help us, what does this actually mean going forwards?

Thomas – We hope that we can make predictions better about polar organisms cope with global warming. We have global warming and the most threatened ecosystems are polar ecosystems because they are the most sensitive – we see a retreat of sea ice and so on. What we didn’t know so far is how these organisms cope. What are the mechanisms that underpin how they can cope? And with our study we can say that they have a very broad tool set. To me it doesn’t seem to be all doom and gloom, they are very resilient to be honest. With our study we can say that they are very well equipped to cope with global warming and potentially also loss of sea ice.

You can listen to the full interview for the Naked Scientists here.

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