22 Sep 2017

How kangaroos avoid dehydration with their nose

Red kangaroos are the Conor McGregor of kangaroos, and it’s not because of their hair colour. They are tough, really tough. Unlike grey kangaroos, which typically seek shade in woodlands and mostly depend on human-built water holes, red kangaroos don’t shy away from living in the driest, hottest deserts.

To cool down their bodies and avoid overheating (and death), kangaroos may pant, sweat and even lick themselves. But all these strategies to lower body temperature come with a price: they use up body water. And when you’re living in a place where water is a rare commodity, licking yourself profusely might not always be the best idea… So how do red kangaroos manage to avoid overheating and save body water at the same time?

To answer this question, Dale Nelson, Gavin Prideaux, and Natalie Warburton from Flinders and Murdoch Universities decided to take a close look at the red kangaroo’s nose. Yes, the nose.

Red Kangaroo (Macropus rufus).

Mammals have complex noses with narrow, curled spongy bones that work as an air conditioning system. These so-called turbinate bones are lined with thin blood vessels that make a temperature gradient along the nasal cavity—from cooler near the exterior to warmer internally. As we inhale, the incoming air is quickly warmed as it travels down the nasal passages, and when we exhale, warm air coming from the lungs is cooled, which saves body heat. Turbinate bones have another function though, and this is where red kangaroos come back into the story.

In the late 1970s, a few research teams noticed that desert mammals have extravagantly long turbinate bones. Camels, for example, have very long, convoluted turbinate bones that swirl round and round like a corkscrew. This scrolled shape increases the nasal surface area to about 1000 cm2, which is over six times the nasal surface area of humans. But what’s the advantage of having such extreme noses in the desert?

Scientists back then suspected it must have something to do with saving body water, and they were right. It turns out that in these animals the water vapour in exhaled air condenses as it contacts the cooler nasal surface, turning into liquid water. For example, giraffes may save up to 3 liters of water a day by condensation in the nose. But as impressive as this may sound, how this water is reabsorbed into the body has remained a mystery for over three decades.

Now, Nelson, Warburton, and Prideaux add the first piece to this puzzle in a new study published in the Journal of Zoology.

During work on fossil kangaroos at Flinders University, the team started wondering how the many shapes of noses in different species of kangaroos and wallabies might be related to their environment and behaviour. They were especially intrigued by the bulging noses of red kangaroos.

“Red kangaroos are the most adapted to the very hot, arid conditions of the Australian outback”, says Warburton. “Previous studies had described some aspects of nasal morphology in kangaroos, but we still didn’t really understand how these related to the biology of the animals in the wild.”

They set off to examine the internal bones and tissues of these animals expecting to find very long, coiled turbinate bones, like in other desert mammals, but they discovered something that “has never been found before”, Warburton says.

Digital images from CT-scans, the same technology used in hospitals to image internal body structures, revealed a pocket of bone within the floor of the nasal cavity.  This small hole in the bone was unusual, so the researchers used histological techniques to look carefully at the tissues lining it. To their surprise, they found that the bone pocket was filled with lymphatic vessels.

Lymph vessels are responsible for returning fluid from tissues into the circulating blood, so this pocket could be used to reabsorb the water condensed in the nose into the body.

“The condensation of water vapour from air as animals breathe out is known to […] conserve water in arid environments, but this is the first time that a possible mechanism for the reabsorption of that condensed water has been found in the nose of any mammal”, says Warburton.

Kidneys are the main site of water reabsorption in the body, and this is why in hot days we need to visit the WC less often. Desert mammals including kangaroos have special kidneys that produce very concentrated urine, which helps to save body water.

Nelson and colleagues may have discovered a new mechanism of water reabsorption in the nose that helps explain how desert mammals cope with the harsh conditions of their environment, but “further physiological testing is necessary to see if this is what is really going on”, Warburton claims.

In the future the team also plans to look at fossils of kangaroos to try and understand how extinct species adapted to changes in their environment.

“Through understanding how animals interacted with the environment in the past, we are able to better predict how they might adapt to environmental changes in the future”, Warburton concludes.

Nelson, D. P., N. M. Warburton, and G. J. Prideaux. "The anterior nasal region in the Red Kangaroo (Macropus rufus) suggests adaptation for thermoregulation and water conservation." Journal of Zoology (2017).

18 Jul 2017

Why life got so big

About 570 million years ago, large, frond-like creatures suddenly invaded the ocean floors. For over a billion years, the Earth’s oceans were filled with bacteria and microscopic algae, but during the Ediacaran period, from 635 to 541 million years ago, larger multicellular organisms began crowding the seas.

Fossil imprints from the Ediacaran derive from soft-bodied organisms resembling modern-day sea anemones (Cyclomedusa), annelid worms (Dickinsonia) and sea pens (rangeomorphs such as Charnia). Among these bizarre creatures, the rangeomorphs are the most abundant in the fossil record—and also some of the largest.

Artist impression of rengeomorphs (credit: Jennifer Hoyal Cuthill.)

Rangeomorphs were unlike any creature on Earth today. Some were as small as a coin, while others could grow up to 2 meters high. They looked like ferns, with branches spreading out from a central stem, but they likely fed by filtering nutrients from the water, similar to corals. Because rangeomorphs were so different from any known life form, paleontologists still don’t agree whether they were primitive animals related to soft corals, some sort of weird fungus or even a new (now extinct) kingdom of life, the Vendobiota.

These ocean dwellers eventually disappeared after the Cambrian explosion, some 541 million years ago, when fast-moving predators emerged (and probably ate them).

Changes in ocean chemistry

Based on the chemical signature of ancient seawater left on rocks, geochemists think there was a sharp rise in ocean oxygen levels soon after the end of the Gaskiers glaciation, about 580 million years ago. These changes in the ocean chemistry could explain the appearance of larger and more complex marine organisms—more food, bigger bodies. However, even though this may seem quite obvious, it’s actually quite difficult to demonstrate.

Jennifer Hoyal Cuthill and Simon Conway Morris, from the University of Cambridge (UK) and Tokyo Institute of Technology (Japan), used an original approach to tackle this problem.

“We wanted to see whether the increase in body size could point to a rise in oxygen, since the type of growth can tells us whether the animals have nutrients available or not”, says Hoyal Cuthill.

They suspected that Ediacaran organisms were large because they had a ‘nutrient-dependent’ type of growth, rather than an evolutionarily new genetic makeup.

‘Seeing’ extinct creatures grow

Many organisms can’t grow beyond a certain size, regardless of how much they eat. Humans for example, will (unfortunately) just get fatter, not taller, because they are genetically programmed to reach a specific maximum height. But for some organisms nutrient availability can affect body size. This type of nutrient-dependent growth is quite common in invertebrates and plants. Some plants will grow almost indefinitely, as long as there are nutrients (and light) available in the environment.

But how do you measure growth in organisms that lived nearly 600 million years ago?

This is where rangeomorph fossils come in handy.

Hoyal Cuthill and Conway Morris had previously worked with several rangeomorph specimens to study the unusual body plan of these animals. During this research it dawned on them that the rangeomorphs’ complex fractal branching shape, with larger older branches at the bottom and smaller younger branches on top, was the key for testing the nutrient-dependent growth hypothesis.

“It’s like looking back at your childhood photographs and comparing your height through your old photos up to the present day”, says Hoyal Cuthill. “We were inferring the history of growth of a rangeomorph by looking at parts of the structure of different ages”.

The researchers could basically “see” in a single fossil specimen how the animals were growing during their lifetime, by comparing the relative size and shape of younger and older branches.

A unique rangeomorph fossil

Fossil of Charnia (Jennifer Hoyal Cuthill)
The new study focuses on an exquisitely preserved specimen of Avalofractus abaculus, one of the last fossils removed from the Trepassey Formation, in Newfoundland (Canada), before strict restrictions were imposed to protect the site (currently called Mistaken Point Ecological Reserve). Hoyal Cuthill obtained a high-resolution cast from the Royal Ontario Museum and scanned it by CT- microtomography, a technique which uses x-rays to make detailed digital 3D reconstructions.

Two other specimens (Charnia masoni and an undescribed specimen from the South Australian Museum) were also analysed based on digital photographs.

Mathematical and computer models comparing the surface area and the volume of younger and older branches showed that growth gradually slowed down as rangeomorphs got bigger, which is exactly what happens in modern organisms with nutrient-dependent growth.

 “… You’re getting less nutrients as you get larger, so you cannot sustain the same rate of growth, and it slows down”, Hoyal Cuthill explains.

But there was more. Nutrient availability can also affect body shape, which is technically called ecophenotypic plasticity. Hoyal Cuthill and Conway Morris also found that rangeomorphs could rapidly change shape to access higher levels of oxygen in the seawater above them, by growing into a long, tapered shape.

Nutrient-dependent growth provides a mechanism to explain why changes in ocean chemistry caused the appearance of these large organisms in the Ediacaran, some 30 million years before the Cambrian explosion.

Hoyal Cuthill next wants to investigate whether rangeomorphs really are animals, and to which modern groups are they related to.

“Rangeomorphs are quite mysterious and were only relatively recently discovered and identified as Precambrian organisms”, she says. “This is an exciting time and many researchers are looking at the biota of the Ediacaran and finding new fascinating things”.

Reference: Hoyal Cuthill, Jennifer F., and Simon Conway Morris. "Nutrient-dependent growth underpinned the Ediacaran transition to large body size." Nature Ecology and Evolution (2017). DOI: 10.1038/s41559-017-0222-7

This article was published originally as a guest post in the PLOS Paleo Community blog with the title "Why Precambrian life got so big" on the 18-07-2017. You can read it here. 

20 Apr 2015

Miracle fat-burning hormone doesn't exist after all

Scientists are humans, and as such, they can sometimes get carried away when they make a breakthrough discovery. Because of this premature excitement, they may lose attention to detail, over-interpret results, or cut corners to speed up that much-desired Nature publication. The discovery of irisin, or ‘exercise hormone’, is one such example. Once thought to be a promising exercise-free solution for obesity and diabetes, irisin has now been shown to be no more than a random blood protein detected by flawed reagents.

Irisin was first discovered in 2012 by Bruce Spiegelman and colleagues at Harvard Medical School (US). In a Nature article, the researchers reported that after exercise muscle cells release a fragment of a pre-hormone-like protein called FNDC5 into the bloodstream, where it travels to adipose cells to trigger the conversion of white fat into calorie-burning brown fat. They concluded that this small molecule is a “newly identified hormone”, which they named irisin, after the Greek messenger goddess Iris.

Whereas white fat stores energy, brown fat is converted to heat—that’s how hibernating animals and newborn babies stay warm. So, unless you starve or exercise a lot, your white fat will remain stubbornly lodged on your hips, while brown fat burns calories. Unfortunately for most of us though, only about 10% of our adipose tissue consists of brown fat-producing cells. And this is why the discovery of irisin was so exciting. What if we could take an irisin pill to turn our white fat into brown fat? Could we burn calories while lying comfortably on the couch eating ice cream? 

It is no surprise then that in just three years over 170 studies were published on irisin. It didn’t take that long though for someone to question the Spiegelman study. Harold Erickson from Duke University (US) first voiced his concerns about irisin in 2013, and recently he showed that the commercial antibodies most widely used to detect irisin are unspecific—instead of irisin, they detect cross-reaction blood proteins, basically unknown random proteins.

Antibodies are proteins produced by immune cells that stick to specific bits of other proteins, and they’re used by scientists to detect their proteins of interest. In the original irisin paper, Spiegelman’s team identified irisin with a polyclonal antibody produced by Abcam that should in theory attach to the tail of FNDC5. But irisin is a fragment of FNDC5 that is chopped from the other end of the protein, so this antibody couldn’t possibly detect it, Erickson argued back in 2013. Spiegelman replied to this by saying that Abcam had not correctly annotated the antibody in their catalogue.

Erickson also noticed that none of the commercially available irisin antibodies had been properly tested by the companies that made them. But despite this worrying observation, several research groups continued to use them, and what’s worse, without attempting to verify their specificity for irisin. And there was more.

A few months after Erickson published these findings, Juergen Eckel and colleagues at the German Diabetes Centre (Dusseldorf, German) found that the human FNDC5 gene has an unusual START codon (the bit of DNA that is translated into the first ‘letter’ of a protein). This weird (and rare) codon is associated with very inefficient protein production. In the case of FNDC5, only about 1% of normal FNDC5 protein levels are produced by human cells, Eckel showed. At such low amounts, it would be highly unlikely that irisin had a physiological role in humans.

Over the years contradictory data from dozens of studies that relied on dodgy reagents cast doubts on whether irisin really exists or is a miracle fat-burning hormone, but that wasn’t enough to dissuade most researchers from working on it. Could this be about to change?

In their new study, Erickson's team and colleagues from three other research groups tested four commercial irisin antibodies used in over 80 studies. They employed a technique called ‘western blotting’, which separates proteins by size. To be sure they were looking at the right thing, the researchers synthesised irisin molecules and then compared them side-by-side with the proteins detected by the commercial antibodies. They tested several tissue samples from humans and other animals, including blood serum from horses after strenuous exercise. None of the antibodies detected a protein with the predicted size for irisin, and even more worrying, they didn’t detect synthesised irisin. However, the antibodies reacted with many other proteins of the wrong size. This shows that all previously published studies based on assays using these antibodies “were reporting unknown cross-reacting proteins”, the authors claim in the study.

The question now was… does irisin exist at all?  

To answer this question, the team looked for irisin in human blood serum using a sensitive technique that detects tiny amounts of molecules without the use of antibodies, called mass spectrometry. They were able to identify a molecule corresponding to FNDC5 or irisin, which is the “first mass spectrometry identification of an irisin peptide at the correct size, and might be considered as supporting the existence of irisin in human serum”, the authors say in the study. However, the very low amounts of irisin detected “makes a physiological role for irisin very unlikely”, they add. According to Erickson and colleagues, the exercise hormone is a myth.

These new findings are bad news for irisin researchers and food lovers, but they’re very good news for science. They show than even though human nature might at times corrupt scientific discoveries (voluntarily or involuntarily), science infallibly corrects itself, and we can therefore trust the scientific process.

Albrecht E., Bernd Thiede, Torgeir Holen, Tomoo Ohashi, Lisa Schering, Sindre Lee, Julia Brenmoehl, Selina Thomas, Christian A. Drevon & Harold P. Erickson & (2015). Irisin – a myth rather than an exercise-inducible myokine, Scientific Reports, 5 8889. DOI: http://dx.doi.org/10.1038/srep08889

An edited version of this article was published in Lab Times on the 17-04-2015. You can read it here

27 Mar 2015

The genetics of musical talent: an interview with Irma Järvelä

Would Mozart have become a great composer had his family not encouraged his musical career? Irma Järvelä is a clinical geneticist at the University of Helsinki, Finland, who investigates the molecular genetics of musical traits. After devoting 25 years of her career to the identification of genes and mutations involved in human diseases, she now works in close collaboration with bioinformaticians and music educators to study the influence of genes and the cultural environment in music perception and production. 

What got you interested in studying the genetics of musical talent?
Järvelä: We were studying a lot of things that affect human diseases and I found that it’s also important to understand how the human normal brain functions. This could be helpful to understand the diseases in more detail. In genetics we have genes and then we have environmental effects. […] Our genes do not always tolerate our environment—when you think of carcinogenics, for example—and this kind of crosstalk between genes and the environment is also present in music. […] I was interested in this interaction between the environment and studying music, or listening to music.

Your research shows that several genes involved in inner-ear development and auditory neurocognitive processes are linked to musical aptitude. Does this mean musical talent is innate?
Järvelä: Yes, our recent study points to the genes that are associated strongly with an innate, or inborn, musical aptitude. It was already known before that newborns are interested in very complex musical patterns already at the age of a couple of days, and from research studying human brain function in musicians and non musicians, there is evidence that music is a biological trait. In our study we identify the regions in the human genome that are strongly associated with the ability to perceive and listen to sounds and structures in music.

So do ‘musical geniuses’ really exist? Would Mozart have become a great composer if his family hadn’t encouraged his musical training?
Järvelä: Mozart is a typical example of a talented composer whose family was musical. There are a lot of families in our days that have several professional musicians, so part of the musical talent is explained by the genes but of course also to exposure to music. It’s like an allergy; the risk for an allergy is only expressed when the pollen is coming, so you need this environmental trigger. And music is an excellent environmental trigger. Children who have an ability for music have to be exposed to music, otherwise we don’t know whether they can become musicians. So a rich musical environment is of course needed.

Is it possible to compensate for the lack of genetic musical ability with musical training?
Järvelä: I think it can be compensated to some extended but never fully. […] Some researchers have claimed (and I agree) that children first of all inherit the ability to perceive music and hear music. And if the parents are also very musical and good teachers, that is the ideal setting for the transmission of both the genes and the perfect environment.

Are there also examples of musically talented people that don’t come from a family of musicians?
Järvelä: We have a couple of cases in our family collection, which consists of 800 people in Finland, where the parents are not very interested in music but the child is very talented. Also vice versa, we also have cases where the parents are professional musicians, but the children are not at all interested, or their musical scores are moderate or low.

How do you explain these exceptions?
Järvelä: I think it’s possible that these cases are explained by a novel mutation, because the human genome is supposed to have de novo mutations quite frequently. But we cannot say anything concerning just a couple of cases, this kind of studies are not reliable. We would need more cases.

In a recent study you show that listening to classical music affects gene expression in musically experienced, but not inexperienced, individuals. How do you explain this?
Järvelä: Yes, this is true. We had a group of participants who were professional musicians or experienced listeners [of classical music], and in the other group the participants told us they were not so interested in music. The participants were not informed which music they came to listen […]. Some people would come out and say “yeah, I know this music, this was nice”, and of course those who had no musical experience didn’t know what was played. […] If you think about it people always choose what they like. We saw an effect in people who knew the music, or who were used to listening to classical music.

Do you see this effect on gene expression with any type of music?
Järvelä: I don’t know because this is the first study and you have to start somewhere. This was with classical music but I agree that we should study other genres like jazz or hip hop, or whatever other type of music. I would suggest that jazz would be the next one because imagination, improvisation and creativity in jazz are more prominent and we might get some different effect. I think there might be shared effects and non-shared effects.

Have you thought of studying other ethnicities, maybe semi-isolated tribes, which have a completely different type of music and culture?
Järvelä: It would be nice but it’s easier said than done. I suspect they would have different genetic profiles because of the long distance in genetics, and also the cultural effects are different. It would be extremely interesting to compare these different natural surroundings and it might be that that is the most true effect of music. I think the basic similarities are there, because the human inner ear is very well conserved in evolution. 

What other questions would you like to address in the future?
Järvelä: We are currently studying the genes for creativity in music, and this will hopefully be published this year. This week we have just published a paper on the genetic profiles of professional musicians, just before and after they played a fabulous symphonette at a concert. […] Then we want to look at the different musical genres, and gene regulation and evolution of music.

Oikkonen J., P Onkamo, L Ukkola-Vuoti, P Raijas, K Karma, V J Vieland & I Järvelä (2014). A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neurocognitive functions, Molecular Psychiatry, 20 (2) 275-282. DOI: http://dx.doi.org/10.1038/mp.2014.8

Kanduri C., Minna Ahvenainen, Anju K. Philips, Liisa Ukkola-Vuoti, Harri Lähdesmäki & Irma Järvelä (2015). The effect of listening to music on human transcriptome, PeerJ, 3 e830. DOI: http://dx.doi.org/10.7717/peerj.830 

Kanduri C., Minna Ahvenainen, Anju K. Philips, Harri Lähdesmäki & Irma Järvelä (2015). The effect of music performance on the transcriptome of professional musicians, Scientific Reports, 5 9506. DOI: http://dx.doi.org/10.1038/srep09506

An edited version of this interview was published in Lab Times on the 27-03-2015. You can read it here.

17 Mar 2015

Hippos are (almost) definitely whales, not pigs

Hippos are strange mammals. They lack hairs and sweat glands, and have an unusually thick skin. The only other mammals that share these features with hippos are whales, but they look nothing alike, except they’re also huge and live in water. Coincidence?

Traditionally hippos were included in the Suidae (pigs) branch of the mammalian evolutionary tree, but molecular data unambiguously shows that they're closely related to cetaceans (whales, dolphins and porpoises). This not only sounds unlikely (hippos look much more like pigs than whales), but it's also quite difficult to testthere is simply not enough fossil evidenceSo the origin of hippos has remained something of a mystery. Now, a new fossil discovery by a team of French and Kenyan palaeontologists may have tipped the balance of the hippo evolutionary history.

Common hippo showing off its mandibles.
Fossils of hippo are rare. Every now and then a tooth pops up, but bones are nearly impossible to find. “To make a comparison between whales and hippos we need to find their ancestors. We had the whale ancestor but until now the hippo ancestor was unknown,” says Fabrice Lihoreau, a palaeontologist at the University of Montpellier, in France.

In 2005, Lihoreau and colleagues discovered a mandible with teeth of unusual morphology in the paleontological collection of the National Museum of Kenya, in Nairobi. Lihoreau is an expert on anthracotheres, a diverse group of semi-aquatic herbivorous mammals that lived in Africa from around two to 40 million years ago. For some time palaeontologists had suspected that anthracotheres could be the ancestor of hippos. “We published many studies suggesting hippo is related to anthracotheres, and not to pigs. This new discovery not only supports that, but it tells us precisely to which lineage of anthracotheres hippos originated from,” Lihoreau explains.

The newly found teeth have morphological features of both anthracotheres and hippos. They belonged to a large herbivorous mammal that thrived in Lokona, Kenya, around 28 million years ago. The discovery of this new hippo-like anthracothere, named Epirigenys lokonensis for ‘hippo’ (Epiri) and ‘origin’ (genys), shows that hippos are definitely not pigs—they originated from an old lineage of antrachotheres, the bothriodontines. And not only that, Lihoreau says, “we added a bit more to the history of mammals in saying that hippos are African, they were born in Africa.”

Evolutionary transition of the upper molar from an anthracothere (left),
Epirigenys (middle) and a primitive hippo (right). 
Many African mammals (rhinos, elephants, giraffes…) originated in Eurasia and then migrated to Africa in two large waves of migration, around 35 and 20 million years ago. Because the oldest fossils of a ‘true’ hippo are about 16 millions years old, palaeontologists have assumed they crossed into Africa on a land bridge during the second wave of migration. But Epirigenys lived 28 million years ago, so hippos must have originated from their anthracotheres ancestor in Africa. This also explains why fossils of hippo ancestors hadn’t been found before: palaeontologists were looking in the wrong place.

But are hippos whales? The discovery of Epirigenys doesn’t prove that hippos and whales came from the same ancestor, but it makes any different scenario rather unlikely. “This study is very important because now we have a hippo ancestor. And we know that the ancestors of hippos are from South-East Asia, and the ancestors of whales are also from South-East Asia, from the same period”, Lihoreau says.

Phylogenetic relationships between hippos, anthracotheres and cetaceans.
Lihoreau and colleagues are now going to focus on searching for the ancestor of anthracotheres in South-East Asia, to then compare it with the ancestor of whales, which is well known. If the team gets lucky, they might find their  holy grailthe common ancestor of hippos and whales.

Jonathan Geisler, a palaeontologist at the New York Institute of Technology who studies the evolution of dolphins and whales says “About 15 years ago there was a big gap between the age of the earliest hippos and the oldest whales. These authors, and their collaborators, have been steadily filling in this gap through the discovery of new fossils, as well as detailed studies that have moved known fossil species into this gap.”

Many questions remain unresolved. Lihoreau suspects that hippo ancestors hopped into Africa around 30 million years ago alone and… swimming. “This is somewhat speculative but certainly seems possible,” says Geisler. “There is evidence to suggest some anthracotheres were semi-aquatic, and were able to make this crossing.” This hypothesis implies that the hippo-whale ancestor already lacked hairs and sweat glands, which would have “constrained the evolution of the hippo group to get into water”, Lihoreau says. His team is going to collaborate with geologists and geochemists to try and figure out in what sort of environment hippo ancestors were living. This should help us understand what shaped the evolution of hippos towards their semi-aquatic lifestyle, which is very rarely seen for herbivorous mammals (capivaras and beavers are the only other exceptions).

Lihoreau F., Fredrick Kyalo Manthi & Stéphane Ducrocq (2015). Hippos stem from the longest sequence of terrestrial cetartiodactyl evolution in Africa, Nature Communications, 6 6264. DOI: http://dx.doi.org/10.1038/ncomms7264

An edited version of this article was published in Lab Times on the 17-03-2015. You can read it here.

25 Feb 2015

Should mice be used to study the human gut microbiome?

In recent years, the trillions of bacteria living in our guts have risen from obscurity to stardom. Hyped press releases claim that probiotics and faecal transplants might one day treat almost everything, from bowel inflictions to obesity. These studies often involve mice, but are these rodents really a suitable model for microbiome research?

The gut microbiome has been associated with an ever-growing list of diseases, including obesity, diabetes and even mental disorders such as anxiety and autism. Much like the Human Genome Project around 15 years ago, the booming microbiome research field has promised to deliver new revolutionary treatments, some as simple as eating a yogurt. Perhaps inevitably though, history repeats itself. After a few years of frantic microbiome sequencing and many new biotech start-ups, microbiome researchers are now having to face the hard questions: are the changes in the gut microbiome associated with certain diseases a cause, or a consequence, of the disease? How on earth can bacteria in the gut affect other parts of the body, such as the brain? What are the molecular mechanisms behind all this?

E. coli bacteria thrive in the gut.

Studies in humans can at most reveal correlations between the microbiome composition and a given disease. For example: Bob is obese and happens to have a microbiome with lots of bacteria X, but John, who is slim, doesn’t. This suggests that bacteria X cause obesity, yet, there’s also a good chance that in fact it’s the other way round: obesity might somehow promote growth of bacteria X. Or maybe this type of bacteria thrives on Bob’s diet, or it simply prefers the unique environment of his gut.

It is virtually impossible, and unethical, to perform experiments in humans to explore causal hypotheses (does bacteria X cause obesity?) and control for confounding factors like diet and genetic background. Microbiome researchers have to use the next best thing: mice. There are, however, growing concerns within the scientific community that more often than not, data from mouse can’t be extrapolated to humans for clinical purposes. Or at least, not easily.

In a new study, Jeroen Raes and colleagues at the KULeuven University, in Belgium, carefully compared the human and mouse gut microbiomes to assess the strengths and pitfalls of this model system for studying microbiome-related diseases.

“Microbiome research, notably its association to inflammatory diseases, relies heavily on mouse models […]. It is essential to know the qualities and limitations of each model to choose the correct one to test specific hypotheses”, says Sara Vieira-Silva, one of the authors conducting the study.

Can mice recapitulate the human gut microbiome?
Mice are great for biomedical research. They share most of our genes, and have similar anatomy and physiology. With the many available genetic tools, scientists can easily and quickly discover the function of literally any gene in the mouse genome, and recapitulate human disease in a controlled experimental set up. So where’s the catch? The problem is that although mice and humans share many similarities, there are also many differences.

Rae’s team performed comprehensive statistical analyses for all gut microbiomes from mice and humans published to date. These new data tell us what types of bacteria live in the gut in various scenarios (disease, diet, genetic background…), as well as their relative abundance. The team first compared the gut microbiomes of healthy humans and mice. And the differences start here.

Human and mouse guts have predominantly two ‘families’ of bacteria—Bacteroidetes and Firmicutes—but within these groups, 85% of bacteria species found in mice are not present in humans. And the bacteria found in both? It appears their abundance in the gut also varies between mice and humans; when you’ve got a lot of a certain bacteria in mouse, you may find very little of it in humans, and vice versa. The authors stress that many of these differences could simply be a result of technical limitations, like methodology or interference from external factors (diet, age, etc).

Mouse models of disease
There are over 60 mouse models of Inflammatory Bowel Disease (IBD), but none fully recapitulates the disease. Even so, the changes in the gut microbiome of patients with IBD (when compared to healthy people) are similar to those observed in IBD mouse models. For example, there is a significant reduction in bacterial diversity in both IBD patients and IBD mouse models. However, some specific bacteria species will be more (or less) abundant in mouse but not in IBD patients. The same goes for obesity models. Overall, mice fed on high-fat diet, and also leptin-deficient mice, which cannot control their appetite, recapitulate the microbiome changes observed in obese people. But there are many discrepancies in the data, again likely due to external factors that are difficult to control, at least in human studies.

The conclusion? Well, mice are not people. Raes and colleagues warn microbiome researchers that extreme care should be taken when trying to extrapolate findings in mouse to humans. They should also make bigger efforts to standardise their protocols for animal handling and data analysis, and to share mouse models to eliminate any genetic variability that might skew the data.

“Most limitations of murine [mouse] models for fundamental microbiome research can be overcome by methodical study design and statistical testing: either eliminating or keeping track of possible confounders (e.g. diet variation, genetic background) and testing for their influence on the results”, says Vieira-Silva.

Nevertheless, the authors conclude, when it comes to understanding the causes and molecular mechanisms behind human disease, mouse models seem to fit the bill. “Although the mouse microbiota composition is not identical to the human's, most mechanisms of microbiota-host interaction will be shared between mice and humans” concludes Vieira-Silva. “Mice models allow us to study these mechanisms with direct controlled experiments, towards the ultimate aim of providing therapeutic solutions.”


Nguyen T.L.A., A. Liston & J. Raes (2015). How informative is the mouse for human gut microbiota research?, Disease Models , 8 (1) 1-16. DOI: http://dx.doi.org/10.1242/dmm.017400

And edited version of this article was published in Lab Times on the 24-02-2015. You can read it here.

5 Feb 2015

'One fossil can overturn anything' Interview with Jenny Clack

Now happily living on land, our Devonian ancestors tried many ways to get out of the murky waters. Jenny Clack has been studying the water-to-land transition of vertebrates for many decades. Her discoveries broke dogmas and rewrote textbooks. 

Jenny Clack's passion for palaeontology began at a young age, but unlike most children, Clack found dinosaurs “rather boring” and was instead fascinated with weird older creatures from the Devonian era, over 360 million years ago. After completing an undergraduate degree in vertebrate palaeontology, Clack worked for about seven years as a display technician at the Birmingham City Museum, until she finally had the opportunity to do a PhD with Alec Panchen at the University of Newcastle upon Tyne (UK). Clack’s talent quickly got noticed, and during her PhD she was offered a position as an assistant curator at the Museum of Zoology of the University of Cambridge (UK). At Cambridge, Clack had an insight that would transform her career and her life. During an arduous field trip to Greenland in 1987, she found spectacular remains of Acanthostega, a tetrapode (four-legged vertebrate) that would overturn decades-old theories. Clack was the first woman in her field to become a fellow of the Royal Society, won numerous distinguished awards and is currently a professor and curator of vertebrate palaeontology at the Museum of Zoology of the University of Cambridge.

When did you know you wanted to be a palaeontologist?
Clack: I was always interested in natural history generally, and as quite a young child, from the age of seven or so, I collected plants and fossils. And certainly by the age of ten I was interested in palaeontology and rocks, and I used to borrow books from the library. I would read geology books and books on fossils and natural history instead of what my teachers would want me to do, which was to read novels, of course. Throughout school, I was always interested in natural history and decided that I wanted to do zoology degree, and went to the University of Newcastle upon Tyne. One of the reasons for choosing Newcastle was because it had a programme in palaeontology as part of the zoology degree. It was just the idea of these ancient creatures... I was always interested in the earliest stuff, rather than dinosaurs. I had a series of volumes of a children encyclopaedia that had sections on various periods from the Palaeozoic, and they were really my inspiration. I wanted to know about the very old fishes and early animals, like the amphibians that were described in those days. When I got the opportunity to study at university then obviously I decided that’s where I wanted to go. But it wasn’t straightforward by any means.

What was it like for a little girl back in the 1960s to pursue an academic career? 
Clack:  It was more that the teachers obviously knew that I was interested in that kind of thing. I remember one of the teachers in junior school identifying me as an “academic type”, even though I had no idea what that meant at the time. Certainly, my parents always encouraged me to do whatever it was I wanted to do. They took me on holidays to places where I mind find fossils and other elements of natural history. […] My career has been a bit of a complicated path because I didn’t go into palaeontology professionally after my degree. I did a Museums Study course, and then worked seven years in the City Museum in Birmingham. And it was only when I had the opportunity to do a PhD that my career really started.

How did you eventually get into academia?
Clack: It was partly encouraged by the museum itself because they allowed people to do three weeks of private studies per year and my mentor-boss at the time was very supportive of this. So, I got back in touch with my old mentor, Alec Panchen, in Newcastle and asked him whether he had any projects I could work on, and in fact he did. He directed me to a specimen in a museum in Bradford that was a Carboniferous tetrapode. To cut the long story short, I took that specimen to his lab and worked on it for the three weeks, during which time I found that there was quite a lot more to the specimen than anybody had realised. And then Panchen said I could probably get a PhD from that material; he applied for grants and got it.

Was it at this time that you decided to focus your career on the fish-to-tetrapode transition?
Clack: I was interested in the same sort of field that Panchen was, which was Carboniferous tetrapodes, so it was a natural expectation that I would study something of that nature. And indeed, the PhD started that ball rolling. While I was still doing my PhD, I applied for a job as an assistant curator at the Museum of Zoology of the University of Cambridge and much to my surprise they offered it to me. This would not happen today. There is no way someone who hasn’t finished their PhD, has got no published papers and has no reputation would get that kind of job. Now, you would have to have a postdoc, at least. I had the museum qualifications and the research background that they were interested in. I fit the bill I guess [laughs]. And it wasn’t until some years later that the opportunity to look at the Devonian material came about. 
After I had finished my PhD in 1984, I wondered what on earth am I going to do next? I didn’t have any very clear ideas. My colleague Andrew Miller said something will come up and indeed it did! It turned up in a drawer in the Earth Science Department across the road. This was a drawer full of Devonian material from Greenland that a former student there had collected without realising what it was, or its potential importance. And from there we got the expedition to go to Greenland in 1987 and collected more of this material, which turned out to be extremely important. A very lucky break indeed.

Fossil remains of Acanthostega.

What exactly did we learn about the water-to-land transition from your discoveries of Acanthostega?
Clack: There were two major discoveries. The first one was about the story we had been told that, as soon as these creatures came onto land, they developed the capacity to hear air-born sound. And it became clear from the work I had done in my PhD, and the work on Acanthostega, that this couldn’t possibly be the case. The story of the origin of terrestrial hearing became much more complicated and it was corroborated by people from other palaeontology groups. But probably the most widely known discovery was that Acanthostega had eight digits in each limb. That was a real surprise. It took a little while for people to believe that this was the case because the dogma was that there were five digits in primitive tetrapods. And here we had an animal with eight digits on each limb! 
We then discovered that a Devonian tetrapod that had been known for decades called Icthyostega had in fact seven digits on its hind limb, and this complemented what we had known about a Russian animal from the Devonian, which has got six digits. All of a sudden it became a pattern of multiple digits in the earliest tetrapods with limbs. This changed the idea of how limbs evolved and what they evolved for. If you look at the old books from the 1940s, for instance, you get an idea of what they thought a proto-tetrapode looked like, and basically it looked like a fish that has got legs with five digits on, and it’s making forays onto the land. But actually our work suggests that the animals already had limbs with digits before they ever came out of the water. So, it kind of turns the story upside down.

Is it the number of digits alone that tells us that, or some other features as well?
Clack: Acanthostega had a number of primitive features. One of those was the proportion of [the bones in] the forearm, of the radius to ulna to each other. In most tetrapods, the ulna is longer than the radius, and that’s true to almost all tetrapods, and most fossil ones as well. But in the fish, from what tetrapods were supposed to evolve, it’s the other way round: the radius is much longer than the ulna. And that was the condition in Acanthostega. It seemed to us that the limb elements of Acanthostega were showing us what the primitive condition was like for limbs in general. Also, the fact that the digits were variable in number through these early tetratpods, suggested that the function of the digits in the limbs was quite different from what we assumed. It’s a paddle basically.

You also discovered new features in Icthyostega
Clack: We discovered that Icthyostega is a really enigmatic animal. We’ve known this more or less since it was discovered, and the more we found out about it, the weirder it looked. It’s got some features in which some limbs elements, like the humerus, are more primitive than that of Acanthostega, and yet other aspects of the anatomy of Icthyosthega suggest it was more terrestrial than Acanthostega. Acanthostega seems to be almost certainly entirely aquatic, but Icthyostega has a really robust front limb that looks as though it could at least raise the front body off the ground, whereas the hind limb is a paddle and points backwards towards the animal’s tail. 
We worked out how this animal could move using information from synchroton CT scans of the limbs and reconstruction software that can help you find out how the limbs actually worked in 3D. It turns out that Icthyostega didn’t walk in a conventional manner. It looks as though one of the possible modes that it used would be a source of crunching motion, with the two front limbs together and the hind limbs acting as breaks or supports, but not actually producing any power on land. They were used to propel the animal in water, so for walking or for moving on land it used its front limbs, sort of pulling it along. And in the water it used its hind limbs as paddles for propulsion.

How did the first terrestrial animal walked?
Clack: We don’t really have enough information to be sure about that, but people now have been using the same sort of software and techniques to look at Acanthostega in the same way. But being very much aquatic, it’s obviously not going to be comparable in terms of what it was doing. The implication is that there were lots of different experiments going on in locomotion and we have only looked at the tip of the iceberg, in terms of the information that we’ve got, which is so limited. For example, in 2011, scientists published some track ways that were found in Poland that pre-date the Devonian tetrapods we had found by about 15 millions years. We don’t know what made those track ways, but we know it was made by an animal walking supported by water and using its limbs in an alternated fashion […]. So there were some animals around at this early stage that were using this pattern of locomotion, but we don’t know what they looked like because we don’t have any body fossils for them. 

What does it take for a palaeontologist to take on an ambitious expedition like your expedition to Greenland?
Clack: Again it was a series of lucky breaks. The material from Greenland at the time belonged to the Danish government. The material from Icthyostega, for example, was all in Copenhagen. I got in touch with the then curator of the Geological Museum in Copenhagen and told him about the material I had found in the Earth Sciences Department. And the quality and amount of that material convinced him that there was a lot more to be found. So he got in touch with the authorities in Denmark and the Greenland Geological Survey (as it was called then) and they happened that year to be setting up a 3-year project in the very area that we wanted to go. We managed to jump on the bandwagon, their expedition, using their facilities and transport arrangements, to get our expedition together. And the funding came to a large extent from our museum in Cambridge, and a certain amount also from Copenhagen and the Karlsberg Foundation. That’s how it was funded. We did try the Research Council in the UK but they weren’t interested.

Have there been other findings throughout your career that got you as excited as when you found Acanthostega?
Clack: Well actually, the project that I’m working on now which is now half way through. The Tw:eed Project is a consortium looking at what happened at the end of the Devonian. As the story goes… Devonian was the age of fishes, and at the end of the Devonian, quite a lot of them got wiped out, there was a mass extinction. The cause of it isn’t clear, but it seems to have been something climatic. The period after that, for 15 to 20 million years, was an almost complete blank in the fossil record, certainly for tetrapods but also for almost everything else as well. [...] The problem was that after that period of 20 million years, when we begin to pick up fossils of tetrapods again, they were extremely diverse. There was a huge variety of tetrapod forms, from small ones the size of a mouse, to other ones that were three or four meters long. So how did they get there? What happened after the end of the Devonian that allowed them to do that? We knew nothing about how these things became properly terrestrial. And it all happened in that gap. 
This gap was first identified by an American palaeontologist called Al Romer, so it’s called Romer’s gap. There were a few specimens from the period of this gap known from Nova Scotia, although nothing formal had been published on those. And I published a paper in the early 2000s on a complete specimen of a tetrapod from the middle of this gap that had been found in Dumbarton, in Scotland. In subsequent years, some of my colleagues have been looking at the appropriate sorts of sediments in the borders region in Northumberland, in Scotland, for the rocks of this age. They found some material, and it’s that material that we are beginning to work on, and we’re also finding a lot more. We have found numerous fossils of tetrapods, several new sharks, new lungfishes, all sorts of things. We’re beginning to get a handle on how terrestrial features or adaptations in tetrapods could have arisen.

So it is possible to find fossils from the Romer’s gap...
Clack: Yes, that’s right. Our idea is that this particular formation called the Ballagan Formation, which has been known for many years and was described as the Scottish cement stone series, is not commercially viable. There’s no coal and no decent limestone. In the 19th century a lot of the carboniferous fossils were found by miners, and that’s how we knew they were there. But because nobody has been looking for commercially viable rocks, nobody has found anything, and because nobody has found anything, nobody has looked. It’s a sort of self-fulfilling prophecy until you get somebody with the determination to say, well they got to be there. And indeed, it turns out that they were.

Do you think that a multidisciplinary approach is important for palaeontology, or is it just a trend?
Clack: This seems to be increasingly the case, yes. […] In the 1970s and 1980s or earlier, palaeontologists tended to work by themselves, just looking and describing the animals. They were doing some fieldwork to find new stuff too, but definitely that was “one person, one fossil” kind of thing. But now collaboration is the key word because different people have different skills, and with all the new techniques that are coming forward you need collaborations to get all those skills together. And certainly I’ve collaborated with people from the Royal Veterinary College for example, and people from the synchroton facility in Grenoble. You just can’t work by yourself anymore, and this particular project was really perfect for this kind of collaborative effort.

How has the development of modern instrumentation (isotope analysis, computer modelling, X-ray computed tomography) changed the field?
Clack: Now we can think of asking and answering questions that would have seemed impossible 10 or 15 years ago. We can ask new questions about how things work, what that might mean, and how the animals developed. And, of course, you’ve got geologists on one side, and then you’ve got technicians, and people doing developmental biology on modern creatures to look at how things could relate to what the fossil record is finding. These collaborations are increasingly common. Developmental biologists and Evo-Devo people are constantly coming to us and asking what we see in the fossil record, and how could this fit with what they’re finding. It’s really encouraging. […] Quite a few people are interested in compiling large databases and then interrogating them; what fossils came from this region, how many species are there in these various time slots and what does the phylogeny tells us. That’s all very well but one fossil can overturn any of that. You still need the data and that’s why it’s so encouraging also that more people are going out and finding new stuff all the time, finding new localities and new areas of the world to explore. And at some of the localities people thought were wiped out, they go back and find new material there, so there’s a wealth of stuff. And of course, communication is so much easier than it used to be.

What is the palaeontology of the future?
Clack: Oh, who knows? If you look at the Society of Vertebrate Palaeontology website, they have their programme for their annual meeting which was in Berlin this year, and the diversity of talks is just stunning, where do we go from here? Well, I think we still need to be fuelled by new material, but that new material can overturn anything that I said! 50 years ago we thought we knew everything about fossils and Palaeozoic vertebrates… no we don’t know, it has been completely overturned since then and there’s no doubt it will be overturned again in the next 50 years.

How can we change the way scientists are perceived by the public? 
Clack: The media like to portrait science as rather esoteric, let's say. BBC tries to do a good job, but I think they have very stereotyped ideas about science and they think the public can’t cope with uncertainties. The message needs to get across that science is about questions and not about answers, and that’s hard to communicate. 

What do you love the most about being a palaeontologist?
Clack: Solving the puzzle, interpreting difficult material, and I think it’s probably one of the things I’m best at. I also quite enjoy writing the papers. I don’t find writing difficult, as I know some people do.

What big exciting questions remain out there for palaeontology, and which ones would you really like to see answered?
Clack: In terms of vertebrates, some of the big questions now are: what’s the origin of vertebrates? How do we get limbs from fins? How do you get fins in the first place? How do you get jaws and teeth, where are they coming form? That’s the sort of thing we can relate to modern developmental genetics as well. Where we can find links with other disciplines it’s really important. If you look at the limb bones of the carboniferous animals, in many cases they’re quite different from those of modern forms. How do we get terrestrially capable limbs? Which bits have to be modified so that you can bear weight? What muscles do you attach and how do they develop?

How would you explain to someone in one sentence that it is important to fund and encourage more palaeontology research?
Clack: It’s a bit like learning History, you know what use is History? What use is the Arts? People don’t seem to ask those questions, but what use is Palaeontology? Oh, that’s no use is it? Well it’s a cultural exercise, it expands the mind, it tells us where we came from and it puts us in our place. It’s all part of the evolutionary story. It’s not like a biomedical science where you want to help people, or invent some kid of drug or something, it’s mind expanding blue skies, learning about the world.

What is the fossil of your dreams?
Clack: I would like a sequence of strata with exceptionally well-preserved soft tissue representations of Devonian forms so that we could find out what sort of reproductive strategy they used. It’s what we call a Lagerstätten, like the Burgess Shale where we can actually see soft tissue preservation of early tetrapods. 


Pierce S.E. & John R. Hutchinson (2012). Three-dimensional limb joint mobility in the early tetrapod Ichthyostega, Nature, DOI: http://dx.doi.org/10.1038/nature11124

Clack J.A. (2002). An early tetrapod from ‘Romer's Gap’, Nature, 418 (6893) 72-76. DOI: http://dx.doi.org/10.1038/nature00824 

Image credits: Museum of Zoology, University of Cambridge. Portrait, Chris Green, Department of Zoology, University of Cambridge.

An edited version of this interview was published in Lab Times in print on the 24-11-2014.