Rare embryo discovery gives hints on how dinosaurs reproduced

Sometime in the Late Jurassic era, a dinosaur nest was hit by a fatal tragedy and its eggs never hatched. Whatever killed the baby dinos - perhaps a hungry predator or a flood - was a stroke of luck for the team of paleontologists who, about 150 million years later, stumbled on the crushed eggs and embryo remains in the Lourinhã geological formation, in Portugal.  

“Most of the time what happens is that you find eggs without embryos, to find them together is really a matter of chance,” says Ricardo Araújo, lead author in the recent Scientific Reports study describing the Lourinhã fossils.

 

Lourinhã geological formation (Credit: wikipedia commons)

Findings of fossilised eggs with embryos are extremely rare - no more than a handful have ever been found. But without embryos it is virtually impossible to link an egg to a specific dinosaur species. So although many dinosaur eggs have been discovered all around the world, sadly we still know little about how dinosaurs reproduced and looked after their babies.

Araújo and colleagues at the Museum of Lourinhã didn’t immediately realise the importance of their fossil discovery; it wasn’t until they prepared the specimens in the lab that they saw tiny teeth and bones amongst the broken eggshells. “That’s when the good news really happened,” Araújo says.

The dinosaur baby teeth had nothing cute about them - they were long, pointy and sharp. Together with other bone features, the shape of the fossilised teeth gave away their identity: they belonged to Torvosaurus, the top meat-eating predator of the Late Jurassic era.

Sketch of the anterior part of the embryonic maxilla, showing the sharp teeth.
(Credit: Museu da Lourinhã)

Torvosaurus is an older, or 'primitive', dinosaur of the theropod family, which includes large carnivorous predators like the famous Tyrannosaurus and also modern birds. Even though Torvosaurus lived (and was extinct) well before Tyrannosaurus was around, it looked a lot like its cousin- it had huge jaws and walked on two legs, but it had longer and stronger arms. Torvosaurus was also nearly as big as Tyrannosaurus, measuring up to 11 meters and weighing about two tons.

Partial fossils of adult Torvosaurus have been found in North America and in the Lourinhã formation, but no embryos had ever been discovered. Up until now that is. The new specimens are the oldest theropod embryos found to date.

"Before we had examples of eggs and embryos of very advanced theropod dinosaurs, but we didn’t know anything at all of what was happening at the base of the family tree," says Araújo “[…] this finding is one of the oldest in the world, and it’s certainly the oldest for theropod dinosaurs,” he adds.

So what do these new fossils tell us about how primitive theropods lived?

By using a bunch of high tech methods, like high-power electron microscopy, the Lourinhã researchers looked in extreme detail at the microstructure of the eggshell pieces. They found that Torvosaurus’ eggs had a single structural layer, in contrast to advanced theropods that have more complex eggshells with two or even three layers (including modern birds, which are technically living dinosaurs).

It was known that primitive dinosaurs from other families had single-layered eggs, but theropods were the missing piece in the puzzle. “Now we have the evidence that eggshells of primitive dinosaurs only have one structural layer,” Araújo says. It appears that eggshell complexity increased throughout dinosaur egg evolution. But this isn’t all.

Torvosaurus is a basal or 'primitive' member of the theropod dinosaur family (Credit: Vladimir Bondar
& GEAL - CIID - Museu da Lourinhã)

The Torvosaurus’ eggshells have another interesting (and strange) feature- they have huge pores, or holes. Bird, reptile and dinosaur eggshells have pores so gases can be exchanged between the inside and the outside of the egg, so the embryos can breath. As a rule of thumb, eggs with larger pores are laid in a moist substrate, while eggs with smaller pores are incubated in nests exposed to air.

The Torvosaurus eggshells have large pores that “interconnect in a network towards the top of the eggshells,” explains Araújo “this is really different from what was found to date”. The eggshell pore size suggests that Torvosaurus buried their eggs, just like most modern reptiles. 

Another indication that Torvosaurus’ eggs were buried is the fact that the fossilised eggshells and embryos are exceptionally well preserved. "The eggshells are nearly exactly the same as they were 150 million years ago," says Araújo. Being underground would have protected the fossils from bacteria and atmospheric erosion.

“Dinosaur embryos are very rare and also challenging to identify,” says David Varricchio, a paleontologist from Montana State University “This study provides an important addition to our understanding on dinosaur reproduction.”

The Lourinhã formation is very rich in Late Jurassic fossils; it has many dinosaur nests and footprints, and countless invertebrate fossils. Araújo notes “There have been more discoveries and […] they will give further insights into dinosaurs and other types of vertebrates from 150 million years ago in Portugal. Finding other eggshells and embryo associations from other groups of dinosaurs would be really helpful to complete the picture.”

Reference:

Araújo R., Castanhinha R., Martins R.M.S., Mateus O., Hendrickx C., Beckmann F., Schell N. & Alves L.C. (2013). Filling the gaps of dinosaur eggshell phylogeny: Late Jurassic Theropod clutch with embryos from Portugal, Scientific Reports, 3 DOI: 10.1038/srep01924

This article was publish in Lab Times on the 13-08-2013. You can read it here.

The strange virus from the sewage

Viruses can infect all types of organisms. Unable to multiply on their own, viruses parasitise animals, plants, bacteria and even other viruses, in order to propagate. Bacteria-killing viruses, called bacteriophages or simply phages, are the most abundant and diverse organisms on the planet. It is estimated that there are over 100 million different phages, but only about 0.0002% of phage genomes have been sequenced. 

Sewage-polluted waters, like some lakes and ponds, are a sample haven for virologists- they are filled with organic material on which bacteria thrive; and where there are bacteria, there are bacteriophages. It was in one of these bacteria broths, about 200km northwest of Vilnius, in Lithuania, that a research team led by Rolandas Meskys and Laura Kaliniene found Rak2, a phage unlike any other.

 

Water contaminated with sewage is a sample-haven for virologists. 

(Credit: Flickr/eutrophication&hypoxia)

Merciless lifestyle
Bacteriophages latch on to bacteria and then transfer their genetic material into them. In a matter of minutes, the bacterial cellular machines replicate and translate the phage genes into viral proteins, which assemble into hundreds of new viral particles. Merciless to their host, the new phages burst the bacterium to free themselves and move on to infect other victims.

Despite the phages' tiny size - about 100 times smaller than bacteria - with the help of high-power electron microscopes (EM), scientists can see them in quite some detail. The most abundant types of phage are by far the Caudovirales, or tailed phages, which have a maraca shape, with a head (containing the genetic information) and, as the name suggests, a tail. The phage tail is a versatile lethal weapon. First, it recognises the right bacteria host by protein matching, like a barcode reading machine. Second, it works as an anchor, firmly attaching the phage to the bacterial surface. And finally, the phage tail acts as a syringe, by piercing the bacterial cell wall and pushing viral DNA through it.

It was the shape of the Rak2 phage that first intrigued Meskys and his colleagues at the University of Vilnius. "The morphology of this phage is amazing," he says. Detailed EM images revealed that Rak2 is a tailed virus from the Myoviridae family, which typically have a contractile tail with six fibres at the end. But Rak2’s tail is very special. “The EM shows that the tail fibres contain spikes, this is only known in a few phages,” explains Meskys. Rak2’s tail structure, with its spiky fibres, resembles the tails of some myoviruses, but other features, like the absence of prongs and the intricate pattern of the spikes, set Rak2 aside from any other known phages.

 

Typical myovirus bacteriophage (Credit: wikipedia)

A giant phage

The other unusual thing about Rak2 is its genome- it’s huge. With about 534 predicted genes, Rak2 is the fourth largest myovirus sequenced to date, and the largest phage known to infect Klebsiella sp. bacteria, Rak2’s only host. But size isn’t everything; Rak2’s genome is truly unique. About half of its genes don’t have any similarity to other viral genes, and a significant proportion of its predicted proteins have an unknown function. The 117 genes that do encode for well-described proteins, such as tail or DNA repair proteins, show similarities to genes of different phage families, but also to some bacterial genes. Meskys says “Philogenetic analysis shows that this phage is quite mosaic, some parts [of the genome] are more similar to the Myoviridae group and other parts to the Podoviridae group, maybe there was some horizontal transfer of genes.”

Horizontal gene transfer occurs when genes ‘jump’ from one species to another. For instance, different bacteria strains can exchange antibiotic-resistance genes between them in a process called conjugation- the closest thing bacteria have to sex. Viruses can exchange genes between them and also with their host. Instead of killing their host cell, some viruses, including phages, insert their DNA into the host’s genome so it replicates with its DNA. When the viral DNA leaves the host’s genome, it can carry along some chunks of it, or, more often, it can leave some of its own DNA behind. Because several viruses can invade the same host, genes from one virus might end up in another virus’ genome. It is estimated that a whopping 8% of the human genome is made of viral DNA, and it seems that most species, from bacteria, to mammals and plants, carry viral genes in their genome. Bacteriophages are experts in this kind of inter-species gene mixing, and Rak2 appears to have an extreme mishmash genome.

EM images of Rak2 phages (Credit: PLoS ONE/Rolandas Meskys)

An alternative to antibiotics?

Meskys plans to continue working on this phage. He would like to understand the function of its unique proteins predicted by sequence analysis. “We found a gene that predicts a huge protein with no functional homology in any other phage. What is this protein doing?” he asks. There are also potential applications for Rak2. Historically, phages have been used in medicine to treat bacterial infections, such as dysentery and cholera, but with the discovery of antibiotics this approach was mostly abandoned. Now, with the dangerous rise in antibiotic-resistance bacteria strains, phage therapy is coming back in vogue.

There are many advantages for using phage therapy. Unlike antibiotics, phages target specific bacteria strains, so the ‘friendly’ bacteria in our guts are left unharmed. If bacteria become resistant to a phage, it can quickly change to overcome the new resistance, while new antibiotics take over ten years to be developed. Besides, new phages targeting multi-resistant bacteria can easily be identified in sewage samples. 

Another key difference between using antibiotics and phage therapy is that, in contrast to antibiotics, which normally just prevent bacteria from multiplying, phages actually destroy bacteria. And they do it with finesse- at low dosage (phage dose is increased ‘naturally’ by replication in the bacteria) and with negligible toxicity for the human patient. 

A number of pharmaceutical companies are also developing phages for other applications, such as veterinary, agriculture, food control and drug delivery, just to name a few. “If we could identify which type of tail spikes are involved in the recognition of a specific bacteria strain, […] maybe we will be able to change the spike proteins so that the phage attacks other bacteria that are more important for medicine or food,” Meskys says.

A productive department

Meskys currently runs a research department at the Institute of Biochemistry of the University of Vilnius, the country’s capital. With six research groups working on several aspects of bacteriophage diversity and biocatalysis, the department operates as a huge lab. “If we have a particular problem to solve, we can involve different members of the department to solve it.” Meskys has a strong creative input in the department’s research and plays an essential part in getting intra-departmental collaborations going. “I am involved in all research groups […] I need someone to implement my crazy ideas,” he jokes. 

A biochemistry graduate, Meskys began his research career as a PhD student in Valdas Laurinavicius’s lab at the Institute of Biochemistry, where he later established himself as an independent researcher and finally was promoted to head of department in 2002. Despite having spent his entire career in Lithuania, Meskys started multiple international collaborations and has, in several instances, been invited to teach or visit labs in other countries. There are fruitful relations established in the department with local and foreign biotech companies. “We are cooperating in the screening for new enzymes for chemical synthesis, diagnostics, food processing etc. Our expertise is in development of new screening technologies,” he says.

Laura Kaliniene, lead author of the Rak2 study, holding a phage plate.

Research in Lithuania

The main source of research funding in Lithuania is the Lithuanian Research Council (LRC). Like many research institutions in Europe, the LRC gives priority to applied research. Most research grants are allocated to projects with potential industrial applications, or to groups with high number of publications and patent submissions. “There is pressure to show that you are achieving something,” says Meskys, but there are also smaller grants for projects “where you can do what you want,” but the competition is high.

Despite Lithuania’s fast growing economy, rising unemployment and low salaries continue pushing highly skilled Lithuanians abroad. "We are losing the bright and intelligent people, emigration is a huge problem for Lithuania.” Meskys adds that there is a ‘narrow market’ in research in Lithuania, so students prefer to do their PhDs in countries like the UK, Denmark or the USA. But there is some world-leading research in Lithuania, especially in the fields of biochemistry and laser technology (a certain type of laser produced in Lithuania accounts for 80% of the world market), and the number of biotech start-ups is on the rise; for example, Fermentas, which was bought by Thermo-Fisher in 2010, was originally a Lithuanian company. “Some research fields are well established, Vilnius University is more than 400 years old, […] in some specialities there are long traditions.”

Reference:

Šimoliūnas E., Kaliniene L., Truncaitė L., Zajančkauskaitė A., Staniulis J., Kaupinis A., Ger M., Valius M., Meškys R. & van Raaij M.J. & (2013). Klebsiella Phage vB_KleM-RaK2 — A Giant Singleton Virus of the Family Myoviridae, PLoS ONE, 8 (4) e60717. DOI: 10.1371/journal.pone.0060717.s003

This is a modified version of my article published in Lab Times on 5-07-13. You can read it here.

Why don't men understand women?

Men might have found themselves an excuse not to listen to women. New research suggests that men have twice more difficulty reading emotions in women than in men. This may not sound surprising, but evidence that men have trouble understanding women is, at best, scarce.

Being able to guess someone else’s thoughts, feelings and intentions is an instinctive social skill that develops in early childhood. We might take it for granted, but people who struggle or are unable to read other people, like people with autism spectrum disorders, have serious problems in communicating and interacting socially. This important ‘mindreading’ trait, so far thought to be unique to our species, recruits a complex brain network. Different, but partially overlapping, brain regions are activated when we perceive mental states like beliefs, intentions or desires (mentalizing) and when we ‘feel’ the emotions of another person (empathy).

In a new PLoSONE study, Boris Schiffer’s research group at the University of Duisburg-Essen, Germany, investigates whether there are differences in neural activation when men recognise emotions in women when compared to men.

The researchers asked 22 healthy adult men to do a modified version of the ‘Reading the Mind in the Eyes’ (RME) test while their brain activity was measured using functional magnetic resonance imaging (fMRI). The RME test has been used in countless studies to measure mentalizing and empathy (you can take the test here). In this study, each participant had to guess what either a man or a woman in a photo was thinking or feeling from looking only at his or her eyes. For each of the 36 pairs of eyes, there was a choice of two mental states, for instance ‘terrified’ or ‘upset’. The participants performed better in the test when the eyes belonged to men, suggesting that men have greater difficulty in recognising mental states in women than in their own gender. But the question is… why? The fMRI readings shed some light into this.

Schiffer and colleagues predicted that recognising mental states in male or female eyes would activate brain areas involved in mentalizing and empathy, and this is what they found. But there was more. Some areas were more active when the participants were guessing emotions in men, and others when they were recognising emotions in women. It isn't clear what these results mean though. As these differently activated brain regions have in one way or another previously been involved in memory, the authors speculate that they are recruited to retrieve either autobiographical emotional memories (when the participants look at male eyes) or memories of past encounters with women (when they look at female eyes). But this doesn’t explain why men have more difficulty in perceiving women’s emotions. There was, however, another clue in the fMRI readings. Just looking at male eyes, without having to do any particular task, activated the amygdala, which is a brain region associated with processing of emotions and empathy.

The authors suggest that when men respond to their own gender, emotion and empathy brain networks are recruited (because men can more easily relate to other men), and this might enhance their ability to perceive mental states. A few studies support this idea. For instance, one study showed that men are better than women at recognising angry faces in men. Schiffer and colleagues further speculate that in evolutionary terms, ‘it makes more sense’, they claim, that we should be better at mentalizing about people that are most similar to us. This would have been particularly important for men in the ‘ancient times’, the authors add, as men were hunting and fighting for territory and it was advantageous for them to predict the intentions of their male rivals. But while this is an attractive hypothesis, it remains rather speculative.

And what about women? The main lingering question from this research is perhaps whether women are also better at reading mental states in individuals of their own gender. According to the authors, the prediction is that they should. So men should not be too quick to blame their gender for not understanding the opposite sex- this may backfire.

Reference:

Schiffer B., Pawliczek C., Müller B.W., Gizewski E.R., Walter H. & Krueger F. (2013). Why Don't Men Understand Women? Altered Neural Networks for Reading the Language of Male and Female Eyes, PLoS ONE, 8 (4) e60278. DOI: 10.1371/journal.pone.0060278.g003

This article was published in Lab Times on 15-05-2013. You can read it here.

Multi-tasking pigments

Carotenoids are organic pigments that play contrasting roles during photosynthesis in absorbing light energy and protecting plants from excess of light. Roberto Bassi’s research group now reveals that carotenoids have yet a new trick up their sleeve.

Plants and other photosynthetic organisms live in a catch-22 situation. “Plants produce oxygen but are also poisoned by oxygen,” says Roberto Bassi, an Italian plant physiologist who has been passionate about photosynthesis since his graduate degree at the Padua University Botanical Garden. Bassi’s research group at Verona University played a pivotal role in understanding the dual function of carotenoid pigments in absorbing light energy and protecting the photosynthetic machinery against light-induced damage by oxygen. Now his team has identified a new unexpected function for carotenoids in controlling the production of photosynthetic proteins. 

Carotenoids are organic pigments made by plants, algae, fungi and cyanobacteria that are found in all organisms (animals obtain them from food). Besides their fundamental roles in photosynthesis, carotenoids can act as plant hormones, vitamins, odours, colours (in fruits, flowers and bird feathers, for instance) and, in the eye retina, photo-protection. There are two types of carotenoids: carotenes, which give carrots their orange colour, and their oxygenated offshoots, the yellow xanthophylls. In plant leaves, carotenoids are normally masked by chlorophyll, but they put on a show in autumn as chlorophyll gets degraded and their striking orange and yellow colours are revealed.

In autumn, chlorophyll gets degraded and the yellow and orange colours of carotenoids are exposed.
(Credit: wikipediacommons)

Poisoned by light

Over the past 20 years, studies of plants and algae lacking each of the four main xanthophylls showed they have specific functions in photo-protection. Photosynthesis generates a waste product without which we couldn’t live: oxygen (O₂). But in the presence of excessive light, toxic forms of oxygen, called reactive oxygen species (ROS), are produced. Photosynthetic organisms have come up with clever ways of protecting themselves against photo-damage induced by ROS. Some plants can simply turn their leaves to minimise light absorption, but most invest in dissipating excess photons and getting rid of ROS. 

Xanthophylls protect the photosynthetic apparatus from photo-damage by scavenging ROS, by preventing its formation or by converting the excess light energy into heat. They are mostly found in the so-called ‘antenna’ protein-pigment structures, which absorb and transfer light energy to the photosynthetic reaction centres. And this is where the magic happens: light energy is converted into chemical energy, used to make organic matter from carbon dioxide removed from the atmosphere.

Without each of the xanthophylls, plants become photosensitive but are still able to grow. However, a new study led by Bassi and his colleague Luca Dall'Osto shows that simultaneously removing all four xanthophylls, but not carotenes, has dramatic effects for plants. “If you avoid the synthesis of xanthophylls the plant is not viable anymore,” Bassi says “It’s something really new and was completely unexpected.” The researchers blocked the synthesis of all xanthophylls in Arabidopsis thaliana, a weed widely used in research, by using a combination of genetic mutations they called nox (for ‘no xanthophylls’). They found that, in addition to their role in light absorption and photo-protection, xanthophylls are essential for plant development- the nox plants simply couldn’t grow. But this didn’t make sense. Previous studies showed that removing each xanthophyll at the time, or removing the antenna proteins to which they bind to, doesn’t affect plant growth. So why do these nox plants have such severe developmental defects?

Plants without xanthophylls (right panel) can be 'forced' to grow on a suger-rich medium, but they have severe growth defects and white leaves because they lack photosynthetic complexes. Left: normal plants. (Credit: Luca Dall'Osto)

A function at the core

To try and understand this, the researchers rolled up their sleeves and plunged into some serious biochemistry. When they analysed the proteins in the two photosynthetic reaction centres - photosystems I (PSI) and II (PSII) - they faced yet another surprise: the PSI core proteins had nearly completely vanished in the nox plants. This was strange because xanthophylls bind mainly PSII antenna proteins, which were mostly unaffected, but not PSI. “It was so surprising that we spent two years repeating the experiments to be sure we didn’t make a mistake,” Bassi recalls.

Chloroplasts, the home of photosynthesis, contain about 120 genes encoding for proteins of the photosynthetic machinery. Bassi and colleagues found that xanthophylls are important for the translation of some of this genetic information into PSI core proteins, such as the PsaA/PsaB unit, within chloroplasts. It was known that without the PsaA/PsaB central unit the PSI super-structure can’t assemble properly and eventually gets degraded, and this is exactly what the researchers see in the nox plants.

The absence of a functional PSI reaction centre in plants lacking xanthophylls explains their developmental defects, but it remains unclear why this pigment acts specifically on the synthesis of certain PSI core proteins. It is also difficult to imagine how xanthophylls, which are embedded in the chloroplast membranes, can act on the cell protein factories, the ribosomes, dispersed inside the chloroplast. Bassi believes that xanthophylls are chopped into smaller molecules that leave the membrane and interact with ribosomes to control the production of PSI core proteins, and his team is currently searching for these molecules. “There is some evidence that products from cleavage of other carotenoids are involved in development, now we know that products of carotenoids are needed for translation of genes,” he explains.

Roberto Bassi's research team. (Credit: Luca Dall'Osto)

An enlightened career

While part of Bassi’s team continues investigating carotenoids in Arabidopsis, the rest studies photosynthesis using his favourite model system: Chlamydomonas reinhardtii. This single-cell green alga is used in photosynthesis research because it grows faster than plants but their photosynthetic machineries are nearly identical. After a first postdoc in Copenhagen isolating antenna proteins from barley, Bassi reckoned that biochemistry would only take him so far in his research, so he spent the next years learning biophysics with Pierre Joliot in Paris and then molecular biology with Jean David Rochaix in Geneva, both experts and pioneers in Chlamydomonas photosynthesis research. Bassi then returned to Italy to set up his own lab to study photosynthesis in algae at Padua University, but finding little support there for his research he decided to leave and finally settled at Verona University. The idea of working with algae was not appreciated by the Italian research funding agencies, however, so eventually he was forced to switch model system from algae to plants.

Science funding in Italy: a political tragedy

“The funding situation for science in Italy is extremely bad and we live with money from Europe,” Bassi says. His team of 15 people currently runs on three European grants and some funding from the private sector. For over a decade, under the government of former Prime Minister Silvio Berlusconi, public research funding and university recruitments in Italy lacked transparency and a clear strategy. With the election of a new government in 2011, Italian scientists were hopeful the situation would improve, but because of the global economical crisis and the country’s huge public debt, Italy’s modest science budget suffered further cuts as part of the government’s austerity plan. As a result, despite recent reforms in the public science funding system, Italian research continues to rely considerably on European grants. Increasingly aware of this grim situation, thousands of Italian researchers leave the country every year with little expectations of going back. Did Bassi ever feel tempted to move abroad? In 2002 he took the plunge and moved to France to set up a lab in Marseille, but after three years he had to return to Verona for personal reasons.

Algae photo-bioreactor
(Credit: kaibara87/everystockphoto)

From algae to biofuels

In recent years the Italian government began to show some interest in the production of biofuels from algae, so after a hiatus of many years Bassi could work with Chlamydomonas again. “I like the field of bioenergy because the applied research and the basic research are very much the same thing,” he says. His team studies photosynthesis while trying to improve the efficiency of biofuel production in algae. Biofuels made from plants, such as corn or soybean, while initially regarded as a good alternative to fossil fuels like petrol, in reality cause great damage to the economy. The problem is that these crops take up a lot of land that would otherwise be used for agriculture, leading to food price inflation in the long run. Bassi’s team is part of the Sunbiopath international research consortium funded by the European Union, which aims at optimising biofuel production by photosynthetic algae for commercialisation. His team has already succeeded in genetically engineering algae strains that use light energy more efficiently, making them grow faster and thus generate more biofuel. The researchers are now trying to expand these results to the industrial scale. “I think this is a promising accomplishment and I’m very positive we could produce biofuels from algae.”

Reference:

Dall'Osto L., Piques M., Ronzani M., Molesini B., Alboresi A., Cazzaniga S. & Bassi R. (2013). The Arabidopsis nox Mutant Lacking Carotene Hydroxylase Activity Reveals a Critical Role for Xanthophylls in Photosystem I Biogenesis, The Plant Cell, 25 (2) 591-608. DOI: 10.1105/tpc.112.108621 

This article was published in Lab Times on 3-05-13. You can read it here.

Kidneys grown in the lab work in animals

Researchers from the Massachusetts General Hospital in the US have grown rat kidneys in the laboratory that produced urine when transplanted into living animals. This is an important step towards the production of customised organs for transplantation into people with kidney failure, which could replace donor organ transplants. 

Bioengineered rat kidney.
(Credit: Ott Lab, Massachusetts General Hospital)  

Patients with kidney failure can be treated with dialysis, but can only be cured with a kidney transplant. About 15,000 people are waiting for a donor kidney in the Eurotransplant region, but only 7,000 kidney transplants take place each year. Patients may wait up to five years for a donor kidney and many lose their lives during that time.

A few research groups have attempted to make artificial kidneys, and some are trying to genetically modify pigs so their kidneys can be used in human transplants, but Harald Ott and his team take a different approach: they hope to grow kidneys in the laboratory using the patient’s own cells. This would put an end to donor organ shortage and immune rejection problems. “If this works, there wouldn’t be any need for immunosuppression or dialysis anymore, it would be a revolution,” says Raymond Vanholder, a nephrologist at the Ghent University Hospital in Belgium and president of the European Renal Association-European Dialysis and Transplant Association (ERA-EDTA). After a transplant patients need to take immunosuppressant drugs throughout their entire lives. And despite these treatments, which can have severe side-affects, many organ recipients will have an acute rejection or lose kidney function within 10 years.

A recipe to make kidneys

In a new Nature Medicine study, Ott and colleagues describe how they successfully 'bioengineered' and transplanted rat kidneys into living animals. They started by taking kidneys from dead rats and stripping them of cells using a detergent commonly used in household cleaning products. This leaves an intact kidney-shaped protein scaffold, complete with all the complex microscopic vascular and tubular kidney structures.

Bioengineered rat kidney in bioreactor incubator. 
(Credit: Ott Lab, Massachusetts General Hospital)

Next the researchers coated the kidney ‘skeletons’ with new cells by pushing them through the kidney main artery and the ureter (a tube that takes urine to the bladder). In these rat kidney prototypes, they used kidney cells from a newborn rat and human umbilical cord cells to make blood vessels. Getting the cells to stick to the kidney scaffolds was the trickiest step (if too much pressure was applied the scaffolds exploded), but after a few days in an incubator the cells rearranged into three-dimensional tissues that looked like kidney structures under the microscope. The different rat kidney cell types seemed to be at the right place. This was very promising, and indeed, after 12 days, when blood was passed through the kidneys they started producing urine. Further tests showed that these bioengineered kidneys partially restored most kidney functions, like filtering the blood and producing urine.

Could these kidneys work in living animals? When the team transplanted the regenerated kidneys into living rats that had one of their kidneys removed, the new kidneys immediately filled with the rats’ blood, without clot formation or bleeding, and produced urine.

Customised organs on demand

Bioengineered kidneys made ‘on demand’ with the patient’s own cells would make organ waiting lists and immune rejections a thing of the past, and this would completely change the lives of patients with kidney failure. But unfortunately this scenario is still a long way down the line. Vanholder says “I think this is very beautiful research […] but it has to be confirmed independently by other studies, and before it can be used in the human clinical situation it will take many years.”

Pig kidneys being stripped of cells. 
(Credit: Ott Lab, Massachusetts General Hospital)

Many challenges remain ahead. In Ott’s rat regenerated kidneys, a small percentage of kidney cells attached to the wrong place in the kidney scaffold, and the kidneys functioned poorly when compared to normal kidneys. Ott believes this is due to the immaturity of the cells implanted on the scaffold, and that using other cell types and letting them mature for longer may improve kidney function. Another challenge will be to scale up the cell coating method to larger organs like human kidneys. The team has already succeeded in making pig and human kidney scaffolds, but coating them with new cells is a more complicated step.

Ott’s group previously used these techniques to make hearts and lungs, and other groups are currently trying to develop livers in similar ways. So could this technology replace donor organ transplants in the future? Vanholder answers “It’s unlikely that this research will emanate in a real application very soon […] but if it works it will be a fantastic thing, it may solve a lot of problems, like the need for dialysis and the shortage of donor organs for transplant.”

Reference:

Song J.J., Guyette J.P., Gilpin S.E., Gonzalez G., Vacanti J.P. & Ott H.C. (2013). Regeneration and experimental orthotopic transplantation of a bioengineered kidney, Nature Medicine, DOI: 10.1038/nm.3154

This article was published in The Munich Eye on  18-04-13.

Excuse me, that's my hand! (... but is it really?)

About 15 years ago, a one-page Nature study shook the scientific community. Researchers from the University of Pittsburg showed with a simple experiment that people could feel that a fake rubber hand was in fact their own- they called it the ‘rubber hand illusion’. It goes like this: place a fake hand on a table in front of you and your own hand just next to it. Then block your hand from your view, stare at the fake hand, and get someone to stroke both hands in the same way for a few minutes. Now close your eyes and point at your hand. Most people will point at the fake hand, and so should you.

Credit: melodi2/everystockphoto

Since this intriguing discovery, neuroscientists have been trying to understand how the brain combines visual, touch and position information to create the feeling of body ownership, or in another words, the awareness that our body parts belong to ourselves. A new study led by Anna Berti’s team at the University of Turin now shows that the embodiment of an alien limb, like someone else’s hand, can be so deeply rooted in our neural circuits that it affects motor control.

When we try to perform a different motor task with each hand at the same time, let's say drawing a circle with one hand and a straight line with the other, both hands somehow get it wrong. In this circle-line example, we would end up with two oval doodles, because one hand’s task interfered with the other. This is called ‘bimanual coupling’ effect, and it happens because our brains find it hard to cope with different motor directives simultaneously (it is possible, but it requires a lot of practice).

Berti and colleagues explored this idea to ask whether believing that an alien hand doing something is our own (in this case, it was the researcher’s hand), could affect how our own real hand performs a task. So they asked volunteers to draw lines and circles in different experimental set ups. As expected, when healthy subjects watched an alien hand draw circles, they could draw straight lines with their own hand as well as if the alien hand wasn’t there because they knew it didn’t belong to them.

What happens to people who are convinced the alien hand is their own? To answer this question, Berti’s team tested brain-damaged people with the left side of their body paralysed and who also suffered from asomatoagnosia. Patients with this rare condition can deny, forget, ignore or misperceive their paralysed limbs. The patients in this study were convinced that the alien hand drawing circles was their own, as if they had a spontaneous rubber hand illusion, and this interfered with their motor control- they couldn’t draw a straight line with their healthy hand. These patients’ brains fully integrated the alien hand into their sensory and motor neural circuits.

As weird as it may sound, our body self-awareness is a mental representation created by the brain, which can be tricked so convincingly that someone else’s hand, or even a rubber hand, can completely replace our own.

Reference:

Garbarini F., Pia L., Piedimonte A., Rabuffetti M., Gindri P. & Berti A. (2013). Embodiment of an alien hand interferes with intact-hand movements, Current Biology, 23 (2) R57-R58. DOI: 10.1016/j.cub.2012.12.003

This article was published in Lab Times on 2-03-2013. You can read it here.