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Almanac

November 2014
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Centipede’s genes reveal how life evolved on our planet

Centipedes, those many-legged creatures that startle us in our homes and gardens, have been genetically sequenced for the first time. An international team of over 100 scientists today reveals how this humble arthropod’s DNA gave them new insight into how life developed on our planet.
Strigamia maritima, the centipede species genetically sequenced in the study. Credit: Dr. Carlo Brena

Strigamia maritima, the centipede species genetically sequenced in the study.
Credit: Dr. Carlo Brena

Centipedes are members of the arthropods, a group with numerous species including insects, spiders and other animals. Until now, the only class of arthropods not represented by a sequenced genome was the myriapods, which include centipedes and millipedes. For this study, the researchers sequenced the genome of the centipede Strigamia maritima, because its primitive features can help us understand more complex arthropods.

According to Prof. Ariel Chipman, senior co-author of the study and project leader at the Hebrew University of Jerusalem’s Alexander Silberman Institute of Life Science, the genetic data reveal how creatures transitioned from their original dwelling-place in the sea to living on land.

“The use of different evolutionary solutions to similar problems shows that myriapods and insects adapted to dry land independently of each other,” said Chipman. “For example, comparing the centipede and insect genomes shows that they independently evolved different solutions to the same problem shared by all land-dwelling creatures — that of living in dry air.”

According to Chipman, the study found that despite being closely related to insects, the centipede lacks the olfactory gene family used by insects to smell the air, and thus developed its own air-sniffing ability by expanding other gene families not present in insects.

In addition, Chipman said, this specific group of centipedes live underground and have lost their eyes, together with almost all vision genes and genes involved in the body’s internal clock. They maintain enhanced sensory capabilities enabling them to recognize their environment and capture prey.

Published in the latest edition of PLoS Biology, the research is a collaborative effort by over 100 scientists from 50 institutions. Thousands of human-hours went into looking at specific genes in the centipede genome, with each researcher looking at a limited set of genes or at specific structural characteristics to address specific questions.

Other leaders of the international research effort include Dr. Stephen Richards, Baylor College of Medicine; Dr. David Ferrier, University of St. Andrews; and Prof. Michael Akam of Cambridge University. The research paper is titled “The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima.”

While early studies of genomics focused on humans, as sequencing equipment and expertise became more readily available, researchers expanded into animals directly relevant to human wellbeing. In the latest research, genomic sequencing has become more broad-based, investigating the workings of the world around us.

In explaining the purpose of the research, Hebrew University’s Chipman said: “If we have a better understanding of the biological world around us, how it operates, and how it came to be as it is, we will ultimately have a better understanding of ourselves.”

According to Chipman, the research will have applications for other researchers ranging from conservation to dealing with crop pests.

Reference: Chipman, Ariel D.; Ferrier, David E. K.; Brena, Carlo; et al. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima. PLoS Biology, November 25, 2014 DOI: 10.1371/journal.pbio.1002005

Soyuz Launch

The Soyuz rocket is the workhorse for Russian human space missions and has been used for that purpose longer than any other vehicle. In the 1960s it began carrying cosmonauts into space and then to the Soviet Salyut and Mir stations. Together with the US Space Shuttle, it ensures the transport of crews to and from the International Space Station.

To ensure that Soyuz will be able to carry out missions of this type from Europe’s Spaceport, the launch infrastructure has been designed so that it can be smoothly adapted for human spaceflight, should this be decided. The first Soyuz flight was unmanned and started on November 28, 1966.

Released 24/11/2014 2:59 am Copyright ESA–S. Corvaja, 2014 Description The Soyuz TMA-15M spacecraft was launched from Baikonur cosmodrome in Kazakhstan on 23 November 2014 with ESA astronaut Samantha Cristoforetti and her crewmates to the weightless research centre where they will live and work for five months. With Samantha are Russian Soyuz commander Anton Shkaplerov and NASA astronaut Terry Virts. All three are part of the Station’s Expedition 42/43 crew. On this mission, Samantha is flying as an ESA astronaut for Italy’s ASI space agency under a special agreement between ASI and NASA.

Released 24/11/2014 2:59 am
Copyright ESA–S. Corvaja, 2014

FUTURA LAUNCH

ESA astronaut Samantha Cristoforetti is all set for her five-month mission on the International Space Station. She will leave Earth on Sunday from the Baikonur cosmodrome in Kazakhstan with NASA astronaut Terry Virts and Roscosmos cosmonaut Anton Shkaplerov.

Watch the international crew of astronauts board their Soyuz TMA-15M spacecraft strapped to 274 tonnes of rocket propellants, accelerate to 28 800 km/h and dock with the Space Station orbiting Earth in just six hours.

Source: European Space Agency ESA

Molecules that came in handy for first life on Earth

For the first time, chemists have successfully produced amino acid-like molecules that all have the same ‘handedness’, from simple building blocks and in a single test tube. Could this be how life started. On Earth? Or in space, as the Philae lander is currently exploring?

Some molecules are found in two chiral variants that, just like hands, are mirror images of one another. Nature, however, makes use of only one variant; for example, DNA is made of a right-handed helix and the most common sugar — glucose — is also right-handed. Why nature does this, and how it all started, remains an intriguing puzzle. After all, whenever chemists make the same molecules they obtain a mix of both variants.

Softenon

Although the molecules are chemically identical, the biological effect of the two mirror images can differ enormously. Due to different interactions with the molecules in our bodies such as DNA and sugars, this can mean a difference between a toxin and a medicine. Thalidomide (trade name Softenon), originally produced as a mix of both mirror images, is the most dramatic example of this. It is therefore very important for the pharmaceutical industry to produce the correct versions of molecules, and a range of chemical methods have been developed to be able to do this selectively. Even so, this does not explain the preference for just one of the mirror images in the early days of Earth.

Primordial soup

The article in Nature Communications describes how Radboud chemists produced an amino acid-like molecule with a single handedness from a solution of a ketone and an amine. Their method may be similar to the processes that took place in the primordial soup. The feasibility of this scenario was first proposed by the physicist F.C. Frank in 1953, which he coined’spontaneous asymmetric synthesis’.

An article by Kenso Soai in Nature in 1995 described the experimental realization for the first time, but this only worked after addition of a pinch of the left-handed or right-handed product to start with. The Radboud chemists however took it an important step further: they updated Frank’s concept and discovered a spontaneous asymmetric synthesis method which takes place in the absence of left- or right-handed molecules. René Steendam: “The first left-handed amino acids could have been produced in this way, no matter whether this happened on earth or somewhere else in the universe.”

Molecules and Materials

“No one has done this before, no-one has achieved — in a single, simple reaction, in a single beaker with no chirality present — an end situation that is 100 % left-handed or 100 % right-handed” says Elias Vlieg, Professor of Solid State Chemistry. “This really is a fantastic example of how we go about things here in the Institute for Molecules and Materials. The molecules that we used came from Floris Rutjes’ Synthetic Organic Chemistry group, who is René’s other supervisor. There they understand reactions, and we understand crystals.” The researchers applied a method during the reaction that was invented a few years ago at Radboud University allowing crystals to repeatedly dissolve and grow through continuous grinding and stirring. “All this does is accelerate the process, but if you have enough time — as you do during evolution — it will work without using this trick.”

Reference: René R. E. Steendam, Jorge M. M. Verkade, Tim J. B. van Benthem, Hugo Meekes, Willem J. P. van Enckevort, Jan Raap, Floris P. J. T. Rutjes, Elias Vlieg.Emergence of single-molecular chirality from achiral reactants. Nature Communications, 2014; 5: 5543 DOI: 10.1038/ncomms6543

People ate mammoth; Dogs got reindeer

Biogeologists have shown how Gravettian people shared their food 30,000 years ago. Around 30,000 years ago Predmosti was inhabited by people of the pan-European Gravettian culture, who used the bones of more than 1000 mammoths to build their settlement and to ivory sculptures. Did prehistoric people collect this precious raw material from carcasses — easy to spot on the big cold steppe — or were they the direct result of hunting for food?

Předmostí I is an exceptional prehistoric site located near Brno in the Czech Republic. Around 30,000 years ago it was inhabited by people of the pan-European Gravettian culture, who used the bones of more than 1000 mammoths to build their settlement and to ivory sculptures. Did prehistoric people collect this precious raw material from carcasses — easy to spot on the big cold steppe — or were they the direct result of hunting for food? This year-round settlement also yielded a large number of canids remains, some of them with characteristics of Palaeolithic dogs. Were these animals used to help hunt mammoths?

To answer these two questions, Tübingen researcher Hervé Bocherens and his international team carried out an analysis of carbon and nitrogen stable isotopes in human and animal fossil bones from the site. Working with researchers from Brno and Brussels, the researchers were able to test whether the Gravettian people of Předmostí ate mammoth meat and how the “palaeolithic dogs” fit into this subsistence picture.

They found that humans did consume mammoth — and in large quantities. Other carnivores, such as brown bears, wolves and wolverines, also had access to mammoth meat, indicating the high availability of fresh mammoth carcasses, most likely left behind by human hunters. Surprisingly, the dogs did not show a high level of mammoth consumption, but rather consumed essentially reindeer meat that was not the staple food of their owners. A similar situation is observed in traditional populations from northern regions, who often feed their dogs with the food that they do not like. These results also suggest that these early dogs were restrained, and were probably used as transportation helpers.

These new results provide clear evidence that mammoth was a key component of prehistoric life in Europe 30,000 years ago, and that dogs were already there to help

Reference: Hervé Bocherens, Dorothée G. Drucker, Mietje Germonpré, Martina Lázničková-Galetová, Yuichi I. Naito, Christoph Wissing, Jaroslav Brůžek, Martin Oliva.Reconstruction of the Gravettian food-web at Předmostí I using multi-isotopic tracking (13C, 15N, 34S) of bone collagen. Quaternary International, 2014; DOI:10.1016/j.quaint.2014.09.044

Gravity may have saved the universe after the Big Bang, say researchers

Physicists may now be able to explain why the universe did not collapse immediately after the Big Bang. Studies of the Higgs particle — discovered at CERN in 2012 and responsible for giving mass to all particles — have suggested that the production of Higgs particles during the accelerating expansion of the very early universe (inflation) should have led to instability and collapse.
Hubble Ultra-Deep Field image of a region of the observable universe (equivalent sky area size shown in bottom left corner), near the constellation Fornax. Each spot is a galaxy, consisting of billions of stars. The light from the smallest, most red-shifted galaxies originated nearly 14 billion years ago.

Hubble Ultra-Deep Field image of a region of the observable universe (equivalent sky area size shown in bottom left corner), near the constellation Fornax. Each spot is a galaxy, consisting of billions of stars. The light from the smallest, most red-shifted galaxies originated nearly 14 billion years ago.

Studies of the Higgs particle — discovered at CERN in 2012 and responsible for giving mass to all particles — have suggested that the production of Higgs particles during the accelerating expansion of the very early universe (inflation) should have led to instability and collapse.

Scientists have been trying to find out why this didn’t happen, leading to theories that there must be some new physics that will help explain the origins of the universe that has not yet been discovered. Physicists from Imperial College London, and the Universities of Copenhagen and Helsinki, however, believe there is a simpler explanation.

In a new study in Physical Review Letters, the team describe how the spacetime curvature — in effect, gravity — provided the stability needed for the universe to survive expansion in that early period. The team investigated the interaction between the Higgs particles and gravity, taking into account how it would vary with energy.

They show that even a small interaction would have been enough to stabilise the universe against decay.

“The Standard Model of particle physics, which scientists use to explain elementary particles and their interactions, has so far not provided an answer to why the universe did not collapse following the Big Bang,” explains Professor Arttu Rajantie, from the Department of Physics at Imperial College London.

“Our research investigates the last unknown parameter in the Standard Model — the interaction between the Higgs particle and gravity. This parameter cannot be measured in particle accelerator experiments, but it has a big effect on the Higgs instability during inflation. Even a relatively small value is enough to explain the survival of the universe without any new physics!”

The team plan to continue their research using cosmological observations to look at this interaction in more detail and explain what effect it would have had on the development of the early universe. In particular, they will use data from current and future European Space Agency missions measuring cosmic microwave background radiation and gravitational waves.

“Our aim is to measure the interaction between gravity and the Higgs field using cosmological data,” says Professor Rajantie. “If we are able to do that, we will have supplied the last unknown number in the Standard Model of particle physics and be closer to answering fundamental questions about how we are all here.”

Reference: M. Herranen, T. Markkanen, S. Nurmi, A. Rajantie. Spacetime Curvature and the Higgs Stability During Inflation. Physical Review Letters, 2014; 113 (21) DOI:10.1103/PhysRevLett.113.211102

Why lizards have bird breath: Iguanas evolved one-way lungs surprisingly like those of birds

Biologists long assumed that one-way air flow was a special adaptation in birds driven by the intense energy demands of flight. But now scientists have shown that bird-like breathing also developed in green iguanas – reptiles not known for high-capacity aerobic fitness. The finding bolsters the case that unidirectional bird-like flow evolved long before the first birds.
University of Utah scientists have shown that green iguanas have bird-like breathing; air flows in a one-directional loop through their lungs. The discovery bolsters the case that this style of breathing evolved in a common ancestor of lizards, snakes, crocodiles and dinosaurs including birds. Credit: Bob Cieri

University of Utah scientists have shown that green iguanas have bird-like breathing; air flows in a one-directional loop through their lungs. The discovery bolsters the case that this style of breathing evolved in a common ancestor of lizards, snakes, crocodiles and dinosaurs including birds.
Credit: Bob Cieri The finding bolsters the case that unidirectional bird-like flow evolved long before the first birds, arising nearly 300 million years ago in a common ancestor of lizards, snakes, crocodiles and dinosaurs including birds.

“We thought we understood how these lungs work, but in fact most of us were completely wrong,” says Colleen Farmer, an associate professor of biology at the U and lead author of the new study published today in Proceedings of the National Academy of Sciences. “People have made a lot of assumptions about how lungs work in animals such as reptiles and crocodiles but they never actually measured flow,” she says.

In humans and other mammals, lungs have airways with a tree-like branching structure. A main trunk in each lung splits into branches and twigs. Air flows in and out in a tidal fashion. Oxygen and carbon dioxide pass to and from blood in tiny air sacs, called alveoli, at the tips of the smallest airway branches.

In bird lungs, air loops in one direction through a series of tubes lined with blood vessels for gas exchange. Aerodynamic forces act like valves to sustain the one-way flow through cycles of inhalation and exhalation.

“For years, people thought that the design evolved to meet the energetic demands of flight,” Farmer says. “That’s all wrong. Iguanas don’t fly.”

Alligators also have a bird-like pattern of airflow. Farmer and Kent Sanders, a radiologist at the U, revealed that in a 2010 study. It was the first evidence that one-directional lung ventilation might be an innovation pre-dating the origin of birds. Earlier this year, Farmer along with Emma Schachner and Robert Cieri at the U, and James Butler of Harvard University reported that monitor lizards have one-directional airflow through their lungs, too.

Those discoveries left open the possibility that crocs and monitor lizards evolved their bird-like lungs independently, that is, their evolution converged on a design similar to birds. The finding of bird-like lungs in yet another group of reptiles builds a stronger case for an origin in the remote past in a common ancestor.

To make the discovery, Farmer and co-authors Cieri, Schachner and Brent Craven of Pennsylvania State University had to find a way to visualize air moving through iguana lungs. In one set of experiments, they used a surgical scope to look inside the lungs of live iguanas as the lizards inhaled harmless smoke from a theatrical fog machine. They also used probes that measure air speed and volume in dissected lungs. Working from 3-D X-ray imaging of the contours of iguana lungs, Craven made a computer model simulating airflow. The model’s predictions closely matched the patterns observed in real lungs. “It was dead-on with the directions of flow we observed,” Farmer says.

The revelations make clear that scientists have much to learn about the physiology of lungs in species other than mammals. Textbooks generally assert that air moving in and out of lungs flows down a pressure gradient from a point of higher pressure to one of lower pressure, but Farmer says her group’s findings show that in iguana lungs “that’s not what’s going on at all.” The shapes and angles of the lung airways point jets of air that create one-directional flow.

The mechanics aren’t fully known yet, but Farmer says a better understanding could inspire new ways to design devices that circulate or filter blood or other fluids without using mechanical valves. “The geometry of these lungs, it is so weird,” Farmer says, “I don’t think any engineer would dream that up.”

Reference: Robert L. Cieri, Brent A. Craven, Emma R. Schachner, and C. G. Farmer. New insight into the evolution of the vertebrate respiratory system and the discovery of unidirectional airflow in iguana lungs. Proceedings of the National Academy of Sciences, 2014; DOI: 10.1073/pnas.1405088111

How to estimate the magnetic field of an exoplanet

Scientists developed a new method which allows to estimate the magnetic field of a distant exoplanet, i.e., a planet, which is located outside the Solar system and orbits a different star. Moreover, they managed to estimate the value of the magnetic moment of the planet HD 209458b.
Artist's interpretation of Planet HD 209458b. Scientists have now estimated the value of the magnetic moment of the planet HD 209458b. Credit: NASA/ESA/CNRS/Alfred Vidal-Madjar

Artist’s interpretation of Planet HD 209458b. Scientists have now estimated the value of the magnetic moment of the planet HD 209458b.
Credit: NASA/ESA/CNRS/Alfred Vidal-Madjar

In the two decades which passed since the discovery of the first planet outside the Solar system, astronomers have made a great progress in the study of these objects. While 20 years ago a big event was even the discovery of a new planet, nowadays astronomers are able to consider their moons, atmosphere and climate and other characteristics similar to the ones of the planets in the Solar system. One of the important properties of both solid and gaseous planets is their possible magnetic field and its magnitude. On Earth it protects all the living creatures from the dangerous cosmic rays and helps animals to navigate in space.

Kristina Kislyakova of the Space Research Institute of the Austrian Academy of Sciences in Graz together with an international group of physicists for the first time ever was able to estimate the value of the magnetic moment and the shape of the magnetosphere of the exoplanet HD 209458b. Maxim Khodachenko, a researcher at the Department of Radiation and computational methods of the Skobeltsyn Institute of Nuclear Physics of the Lomonosov Moscow State University, is also one of the authors of the article. He also works at the Space Research Institute of the Austrian Academy of Sciences.

Planet HD 209458b (Osiris) is a hot Jupiter, approximately one third larger and lighter than Jupiter. It is a hot gaseous giant orbiting very close to the host star HD 209458. HD 209458b accomplishes one revolution around the host star for only 3.5 Earth days. It has been known to astronomers for a long time and is relatively well studied. In particular, it is the first planet where the atmosphere was detected. Therefore, for many scientists it has become a model object for the development of their hypotheses.

Scientists used the observations of the Hubble Space Telescope of the HD 209458b in the hydrogen Lyman-alpha line at the time of transit, when the planet crosses the stellar disc as seen from Earth. At first, the scientists studied the absorption of the star radiation by the atmosphere of the planet. Afterwards they were able to estimate the shape of the gas cloud surrounding the hot Jupiter, and, based on these results, the size and the configuration of the magnetosphere.

“We modeled the formation of the cloud of hot hydrogen around the planet and showed that only one configuration, which corresponds to specific values of the magnetic moment and the parameters of the stellar wind, allowed us to reproduce the observations,” explained Kristina Kislyakova.

To make the model more accurate, scientists accounted for many factors that define the interaction between the stellar wind and the atmosphere of the planet: so-called charge exchange between the stellar wind and the neutral atmospheric particles and their ionization, gravitational effects, pressure, radiation acceleration, and the spectral line broadening.

At present, scientists believe that the size of the atomic hydrogen envelope is defined by the interaction between the gas outflows from the planet and the incoming stellar wind protons. Similarly to Earth, the interaction of the atmosphere with the stellar wind occurs above the magnetosphere. By knowing the parameters of an atomic hydrogen cloud, one can estimate the size of the magnetosphere by means of a specific model.

Since direct measurements of the magnetic field of exoplanets are currently impossible, the indirect methods are broadly used, for example, using the radio observations. There exist a number of attempts to detect the radio emission from the planet HD 209458b. However, because of the large distances the attempts to detect the radio emission from exoplanets have yet been unsuccessful.

“The planet’s magnetosphere was relatively small beeing only 2.9 planetary radii corresponding to a magnetic moment of only 10% of the magnetic moment of Jupiter,” explained Kislyakova, a graduate of the Lobachevsky State University of Nizhny Novgorod. According to her, it is consistent with the estimates of the effectiveness of the planetary dynamo for this planet.

“This method can be used for every planet, including Earth-like planets, if there exist an extended high energetic hydrogen envelope around them,” summarized Maxim Khodachenko.

Reference: K. G. Kislyakova, M. Holmstrom, H. Lammer, P. Odert, M. L. Khodachenko.Magnetic moment and plasma environment of HD 209458b as determined from Ly  observations. Science, 2014; 346 (6212): 981 DOI:10.1126/science.1257829

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