24 Feb 2013

NewsFLASH: A free ride for Salmonella

Our guts are home to over a 100 trillion bacteria that help digestion, prevent inflammatory bowel disease (IBS) and protect us from invaders, such as harmful bacteria. To keep pathogens at bay without destroying ‘good’ bacteria, there is a subset of specialised cells in the gut epithelium that act as sentinels. These so called ‘M cellsengulf and rapidly transport large particles from the gut lumen to the underlying lymphoid tissue, where they are recognised and sorted by immune cells. This ability to sample foreign agents, much like a police border control, is critical to trigger immune responses against disease-causing pathogens, while maintaining a healthy gut microbe balance. 

Uncooked meat is one of the most common sources of Salmonella infection.
(Credit: everystockphoto.com/VirtualErn)

However, the unique feature of M cells to efficiently carry particules across the gut wall is a double-edged sword, as pathogens such as bacteria and virus can use them as free tickets to enter the bloodstream and invade other regions of the body. In fact, some pathogenic bacteria can even increase the number of M cells to boost their transport across the gut epithelium, but exactly how they do this is not understood. Arvin Mahajan and colleagues from the University of Edinburgh tackled this question by infecting bovine cultured gut epithelial cells with Salmonella, in a recent Cell Host & Microbe study.

Salmonella enterica serovar Thyphimurium (S. Thyphimurium) are pathogenic bacteria found in raw eggs, uncooked meat, some vegetables and reptiles (recent Salmonella outbreaks were linked to pet turtles). S. Thyphimurium infection causes diarrhoea, abdominal cramps, vomiting and fever. Most people clear the infection within a week without needing any treatment, but for young children, older adults and people with weakened immune systems, the infection can sometimes be fatal because it spreads from the gut into vital organs, such as the kidneys or liver. S. Typhimurium can invade different cell types to colonise their host, but they preferentially take a shortcut by making more M cells and hitchhiking on them to cross the gut barrier.

Salmonella Thyphimurium (red) invading cultured human epithelia cells.
(Credit: Wikipedia Commons)

But how do Salmonella induce more M cells? Scientists have long been arguing whether bacteria-induced M cells are newly born cells, or instead come from epithelial cells that somehow change their identity. Mahajan’s team first showed that S. Typhimurium induce  a rise in M cell numbers just 90 minutes after infection, which ruled out the first hypothesis, because cells normally take 3 to 4 days to fully mature. Next, the scientists went on a fishing expedition for the bacterial molecule that causes the cell transformation. They infected the cultured bovine gut cells with S. Typhimurium mutant strains, each lacking a different molecule, and found that the bacterial protein SopB is essential to induce more M cells, and these results were confirmed in the mouse small intestine. Finally, the researchers figured out the chain of cellular events triggered by SopB that causes the epithelial to M cell transformation. 

By showing that with a single virulent factor (SopB) Salmonella transform gut epithelial cells into gateways, Mohajan and colleagues have revealed yet another clever strategy used by pathogenic bacteria to invade and colonise their host.

Tahoun A., Mahajan S., Paxton E., Malterer G., Donaldson D., Wang D., Tan A., Gillespie T., O’Shea M. & Roe A. & (2012). Salmonella Transforms Follicle-Associated Epithelial Cells into M Cells to Promote Intestinal Invasion, Cell Host & Microbe, 12 (5) 645-656. DOI:

A shorter version of this article was published in Lab Times on the 7-02-13. You can read it here.

18 Feb 2013

Changing thymes: plants adapt to climate warming

Before ending up on a dinner plate, thyme plants use ingenious ways to survive extreme cold and severe drought. By sniffing around in the field, scientists discover that wild thyme adapts remarkably quickly to climate change.

In the early 1970s, a research team from the Centre National de la Recherche Scientifique led by Philippe Vernet made a very odd finding. While collecting samples of wild thyme (Thymus vulgaris) from a small basin tucked between hills on the north of Montpellier, in France, the scientists discovered that the plants growing on the hill slopes smelled different from the ones growing inside the basin. At the time, little was know about these different types of thyme, so the team spent the next few years trying to understand how a single thyme species produced plants with different odours.

Wild thyme (Credit: A. Renaux)

There are six types of wild thyme, each with a modification in the genetic chain producing the oil that gives the plant its characteristic smell. This scented oil can have up to six phenol chemical groups attached to it (depending on the genetic modification), which makes slightly different molecules that have, however, very distinct smells, ranging from ‘non-phenolic’ to ‘phenolic’.

Vernet had found that non-phenolic plants grew only inside the basin, while phenolic plants thrived in the surrounding rocky hills, but it wasn’t understood why there was this sharp separation of thyme genetic types over just a few kilometers. In a new study published in PNAS, John Thompson and colleagues from the Centre for Functional and Evolutionary Ecology in Montpellier show that wild thyme adapts to climate change by shifting the frequency of these genetic populations.

Thompson had always suspected that the split distribution of thyme genetic types in the St-Martin de Lourdes basin, where Vernet's study was conducted, was related to climate. In the Mediterranean region of the south of France, temperatures often fall as low as -10˚C, typically in early winter. But in the basin temperatures can drop spectacularly, with historic record lows of around -30˚C, because cold air is trapped by the hills. This creates the weird effect of ‘temperature inversion’, when temperature declines as you go down the hills, rather than when going up. “It can be one to two degrees in the hills, and down in the basin it will be -5˚C, and the colder it is, the bigger the difference” says Thompson.

About ten years ago, as he was setting up some experiments with thyme in this area, Thompson literally smelled something wasn’t right. “We were smelling plants, and I couldn’t find any non-phenolics,” he says “I looked at the map from the original study in 1970, I knew I was in the right place”. The researchers collected thyme samples and sent them to the lab to be analysed. These results confirmed Thompson’s sniffing suspicions: the phenolic plants were now growing inside the basin, where they were completely excluded from 30 years before.

St-Martin de Lourdes basin (Credit: J. Thompson)

Could this be due to a change in climate? Previous studies by the team showed that non-phenolic plants cope well with extreme cold but don’t survive severe drought, so they prefer the deep moister soil of the basin. In contrast, phenolic plants thrive in the typical Mediterranean rocky dry landscape of the hill slopes, but can’t tolerate freezing temperatures.

The researchers dug out old temperature charts from a weather station in St-Martin de Lourdes and looked at the lowest temperatures measured in the past six decades. Even though extreme freezing events below -12˚C had always been sporadic, temperatures in the basin haven’t dropped below that level for over 20 years. Recent milder winters favoured the thyme genetic types sensitive to freezing, and this is why phenolic plants invaded the basin. “Mean values in ecology don’t mean a lot, what is important is the extreme values […] because you get extreme mortality events, and that is what causes natural selection” Thompson explains.

“This study reports compelling evidence that the genetic composition of wild thyme populations is being altered by current climate change” says Sébastien Lavergne, an evolutionary ecologist from the University of Grenoble who was not involved in the study. “More studies like this one are needed to document how strongly human activities are reshaping life on earth”.

Thompson cautiously remarks that local climate changes, such as the rise in winter freezing temperatures in the St-Martin de Lourdes basin, do not necessary reflect a change in climate on the planetary scale, but he suspects this might be the case. “The prediction is the warming up, and one part of warming is that you have less extremes” he says.

This study shows that even long-lived perennial plant species like wild thyme can adapt very rapidly to climate change, which is good news. However, if this adaptation occurs by migration, for instance by spreading of seeds or pollen, then even resilient species may be vulnerable to local extinction. “If humans induce fragmentation of landscape, to the extent that species and their genes can’t move, then they are likely to stop responding to climate change” says Thompson.

Thompson, J., Charpentier, A., Bouguet, G., Charmasson, F., Roset, S., Buatois, B., Vernet, P., & Gouyon, P. (2013). Evolution of a genetic polymorphism with climate change in a Mediterranean landscape Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1215833110

This article was published in Lab Times on 18-02-13. You can read it here.

12 Feb 2013

Scientists find new clues on how bacteria resist antibiotics

New research shows how some bacteria manage to evade a widely used antibiotic by removing it from their protein factories.

The widespread use of antibiotics over the past decades has led to the emergence of resistant bacteria. Since their discovery in the 1930s, antibiotics have been overused in human medicine and in industrial farms as food supplements to promote animal growth. A shocking 80% of antibiotics produced in the USA are used in farms, despite warnings from the World Health Organization of the danger this poses to public health. Antibiotic resistant bacteria can spread from animals to humans through meat, water and soil contamination. A few countries, like European Union member countries and South Korea, have recently restricted the use of antibiotics for clinical purposes, but the number of resistant bacteria strains continues to rise at an alarming rate worldwide, and new antibiotics are needed to gain ground against bacteria.

Understanding the molecular details of antibiotic resistance is crucial for the design of effective drugs. Now, two independent studies describe how bacteria evade tetracyclines, a family of antibiotics that act against a broad range of bacteria involved in diseases such as pneumonia, syphilis, cholera and even some strains of the deadly MRSA superbug.

Industrial animal farm in Florida, USA.
(Credit: Wikipedia Commons)

An attack on the bacterial protein factories
Like many other antibiotics, tetracycline drugs work by targeting the bacteria’s protein factories- the ribosomes- and blocking protein production. This doesn’t kill the bacteria, but it stops them from multiplying, which buys the immune system critical time to fight the infection.

Bacteria have many strategies to escape tetracycline drugs, but the most common is the use of specialised proteins that remove the drug from its target, a process called ribosome protection. To understand how this works, Joachim Frank and colleagues at Columbia University determined the 3D structure of one such protein - Tet(O) - bound to ribosomes using cryo-electron microcopy, a technique where samples are frozen quickly and then analysed with a high-power microscope.

Previous work by the team suggested that Tet(O) acts indirectly by attaching to ribosomes and forcing them to change shape so that tetracycline molecules can't stick to them. In a new study published in Nature Communications, Frank’s team shows not only how Tet(O) pulls this off, but also that, unexpectedly, Tet(O) pushes tetracycline molecules away from ribosomes. This gives bacteria double protection against antibiotics.

MRSA bacteria magnified with a scanning electron microscope.
(Credit: Wikipedia Commons)

A step towards new antibiotics
With their detailed 3D structure, the researchers could predict the attachment sites between Tet(O) and the ribosome, which in theory should be essential for ribosomal protection. To test this, they put Tet(O) proteins with missing bits into bacteria, and checked whether they lost the resistance to tetracycline.

Why is this important? These Tet(O)-ribosome binding regions are very likely to change and adapt to the new generation of tetracycline antibiotics that are currently our last defense against some strains of MRSA. With these molecular details scientists can make a good guess where new resistances might appear, and then “an antibiotic might be designed to have affinity to multiple sites near or around the Tet(O)-ribosome binding site” says Frank.

Daniel Wilson’s team at the University of Munich reports similar findings in a study published recently in PNAS, looking at the interaction of ribosomes with Tet(O)’s sister protein Tet(M). Wilson explains "Our main finding is that the Tet(M) protein directly enters into the tetracycline binding site to dislodge the drug from the ribosome".

Antibiotic resistance: how grim is the future?
Unfortunately, in the race between bacteria and men, bacteria have the upper hand. The genes carrying antibiotic resistance, such as the tet genes encoding for Tet(O) and Tet(M) proteins, can quickly spread between bacteria in mobile DNA elements. To make matters worse, these genes can mutate and create new resistances much faster than effective antibiotics can be made and tested in clinical trials. “New antibiotics are urgently needed to fight the growing and threatening development of multi-resistant bacteria strains” says Knud Nierhaus, an expert on ribosome structure and antibiotic resistance from the Max Plank Institute for Molecular Genetics in Berlin.

What is the best strategy to tackle antibiotic resistance in the future? It is estimated that China uses in its industrial farms about four times the total amount of antibiotics used in the USA, and a new study identified around 150 new antibiotic resistant genes in manure samples from only three Chinese farms. “The most dangerous development, with unpredictable results on the human race, is the indiscriminate use of existing antibiotics, including antibiotics in livestock entering the food chain” says Frank “Regulation of agriculture should be a major part of the strategy, along with targeted drug development.”

Li, W., Atkinson, G., Thakor, N., Allas, U., Lu, C., Chan, K., Tenson, T., Schulten, K., Wilson, K., Hauryliuk, V., & Frank, J. (2013). Mechanism of tetracycline resistance by ribosomal protection protein Tet(O) Nature Communications, 4 DOI: 10.1038/ncomms2470 

Donhofer, A., Franckenberg, S., Wickles, S., Berninghausen, O., Beckmann, R., & Wilson, D. (2012). Structural basis for TetM-mediated tetracycline resistance Proceedings of the National Academy of Sciences, 109 (42), 16900-16905 DOI: 10.1073/pnas.1208037109

This article was published in the Munich Eye on 12-02-13. You can read it here.

8 Feb 2013

A cracking discovery

Michel Milinkovitch is an evolutionary biologist who thinks outside the box. His exciting career recently led to the discovery that crocodile head scales form by physical cracking of the skin.

Not many people can say they’ve had close encounters with a 4-metre long crocodile, a near-extinct Galápagos tortoise and… a yeti. For Michel Milinkovitch, an evolutionary biologist at the University of Geneva, this is just part of the job. A typical day at work could be spent in his lab working with computer scientists, or it could be spent at the zoo studying crocodiles up close, very close. “Once we were working in the croc pit and a male charged,” he says laughing “I just shouted RUN and everyone just dropped everything and ran away. This was a 4-metre animal probably weighing half a ton, it’s like a bus passing in front of you”.

Juvenile Nile crocodile

Milinkovitch’s work on crocodile scale patterning recently made the cover of Science. His team found that crocodile head scales form by physical cracking of the skin, rather than being genetically defined like the scales in the body. In fact, this is the first time this cracking phenomenon has ever been observed in a biological process. “Cracking is something known for physicists but totally unknown for biologists.”

Not scales after all
The dogma was that all keratinised appendages like mammalian hairs and feathers and reptile scales, grow from developmental genetic units. But during a visit to a crocodile farm in France he noticed that, unlike the scales of snakes and lizards, the scale patterns on each side of the crocodile’s head did not mirror each other. “I was very surprised by this topology, which was not very organised. […] It didn’t fit with what we knew about the development of hair, feathers and scales.”

Milinkovitch and his team quantified this by making a high-resolution 3D reconstruction of the heads of 15 young Nile crocodiles, and then performed a mathematical analysis on the scales’ apparent chaotic pattern. He baffled at the results: the data didn’t fit any models used to describe biological processes, but were a perfect match with the statistical signatures of cracking phenomena, like when dried mud cracks.

To get to the bottom of this, the team looked in eggs during embryonic development. They found that the genetic units that give rise to the crocodile body scales never appear in the head. Instead, as the skin became thicker, grooves gradually appeared, grew deeper, longer and interconnected. “How can you grow skin and in the meanwhile make it stiff?” Milinkovitch proposes that the fast growth of the crocodile’s skull causes the thick keratinised skin to crack. When they had a closer look at the embryos, the team found that, where the grooves appear, there is increased cell proliferation, as if the skin heals as it breaks. Milinkovitch plans to focus his future research on the physics of biology, for instance, on understanding how mechanical forces, such as a tissue being pulled, control cell proliferation.

Crocodile head scales form by a physical process similar to how dried mud cracks. 

A smart move
His interest in physics goes a long way back. He had a brief affair with it during his undergraduate degree, but decided to stick with his passion for evolution and pursue a PhD at the Université Libre de Bruxelles (ULB) studying phylogeny using DNA hybridization. A chance encounter with Jeffrey Powell at a conference, however, changed his career path. He moved to the US to do a PhD with Powell at Yale University, where he discovered the power of DNA sequencing, which was booming at the time. He swiftly swapped DNA hybridization for DNA sequencing, a step that would place him at the forefront of the phylogenetics scene “It was the right time and the right place.” This was the start of a productive career that led to his first independent position back at ULB in 1996. In these early years, his lab focused on two rather different areas: conservation biology and phylogeny inference.

Saving the Galápagos tortoises
Milinkovitch used phylogenetic and population genetic approaches to investigate the influence of human factors on the genetic diversity of endangered species. His work helped managing south-American dusky dolphin populations threatened by illegal fishing, as well as Jamaican boas, Komodo dragons, amongst others. But his most remarkable conservation success story is the rescue of a near-extinct Galápagos giant tortoise.

The Galápagos are a group of islands on the Ecuador coast famous for inspiring Charles Darwin’s theory on the mechanisms of evolution. Each of the main 13 islands had a different giant tortoise species, but now only ten remain, mostly because their habitats were destroyed by cattle grazing, or because they were poached by whalers, sealers and pirates, who used them as a long-lasting supply of fresh meat (tortoises can survive months without eating or drinking). In the mid 1960’s there were only 14 tortoises left in Española Island, which were taken to the main island for captive breeding by the Charles Darwin Research Station and Galápagos National Park. Milinkovitch and colleagues joined the breeding program in early 1990s, and for ten years they did molecular genetic analysis of the tortoise offspring. Today, there are nearly 2000 giant tortoises in Española, and a significant proportion of these animals were born in the island. “This is one of the most successful repatriation breeding programs ever” he says enthusiastically “Our work shows that genetics can help, we can identify populations […] and maximize genetic diversity in the offspring”.

Michel Milinkovitch with Galapagos baby tortoises.

Frogs hop ‘out of India’
With the progress of computer and DNA sequencing technologies in the 1990’s, evolutionary biologists developed new methods to study phylogeny. Milinkovitch created various software for phylogeny inference, such as MetaPIGA and MANTiS, and worked out some intriguing phylogenetic trees. Of note is his work on the phylogeny of cetaceans, which revealed a close relationship between whales and artiodactyls like hippos, camels and pigs, and his ‘out-of-India’ theory to explain how frogs radiated from India.

Sixty-five million years ago, when dinosaurs were being wiped out because of a massive asteroid impact on the Yucatán coat of Mexico, colossal volcanism events lasting around 10 thousands years covered nearly half of India in lava, leading to mass extinction. Milinkovitch and his student Franky Bossuyt showed that frogs survived this cataclysm and spread around the world after India collided with Asia during continental drift. This and other phylogenetic studies on frogs planted a seed of curiosity that would later make Milinkovitch shift the main axis of his lab to evolutionary developmental biology (evo-devo).

From phylogeny to evo-devo
A problem arose in his mind when he started working on evo-devo. “If you want to study evolution of spines in mammals, or how scales develop, the mouse is not going to help.” To study the evolution of certain traits like spines or scales he would have to use atypical animal models, and this is quite complicated. He started small colonies of snakes and lizards at ULB, but didn’t feel he had enough support to expand this work. However, this fresh view of using non-model animals caught the eye of the evo-devo science community of the University of Geneva, who invited him to work there. Milinkovitch’s lab moved to Geneva in 2004, where he now runs several unique colonies of reptiles and other exotic mammals to study, for instance, how spines develop in unrelated species such as hedgehogs and tenrecs. Aware that breeding these animals is a mammoth (and costly) task that not many can take on, he opens his colonies to other labs around the world.

Milinkovitch's team on a field trip.

Research in Switzerland
What is research in Switzerland like? It seems that even when it comes to science the cliché stands. “It’s very well organised” Milinkovitch answers. He explains how the peer reviewing process that evaluates grant proposals is well managed and fair in Switzerland “What counts is excellence, nothing more”. Project proposals are judged on their quality, and there is little pressure to do ‘applied research’, in contrast to many funding agencies worldwide. “There is a big difference between encouraging interest in applying basic science and forcing work on applied stuff” he says. Another aspect he praises in Swiss research is the wide support for multidisciplinary projects. The Swiss government has recently established SystemsX, a large public research initiative to advance systems biology research in the country. He admits that multidisciplinarity is what excites him most in his research. He currently has working in his lab people with backgrounds in physics, computer science, engineering, evolutionary and developmental biology. This eclectic combination of expertises is not always easy to manage, he confesses, but it is incredibly prolific, and the recent Science paper on crocodile scale development is a clear example of that. “I think this has been possible here because there are specific grants for multidisciplinarity, but also because terrific students are open to these things”.

Milinkovitch, M., Manukyan, L., Debry, A., Di-Poi, N., Martin, S., Singh, D., Lambert, D., & Zwicker, M. (2012). Crocodile Head Scales Are Not Developmental Units But Emerge from Physical Cracking Science, 339 (6115), 78-81 DOI: 10.1126/science.1226265

Image credits: LANE-Michel Milinkovitch

This article was published in Lab Times on the 7-02-13.