'Fettuccine' may be most obvious sign of life on Mars, researchers report

Travertine terraces in Mammoth Hot Springs, Yellowstone National Park

A rover scanning the surface of Mars for evidence of life might want to check for rocks that look like pasta, researchers report in the journal Astrobiology.

The bacterium that controls the formation of such rocks on Earth is ancient and thrives in harsh environments that are similar to conditions on Mars, said University of Illinois geology professor Bruce Fouke, who led the new, NASA-funded study.

"It has an unusual name, Sulfurihydrogenibium yellowstonense," he said. "We just call it 'Sulfuri.'"

The bacterium belongs to a lineage that evolved prior to the oxygenation of Earth roughly 2.35 billion years ago, Fouke said. It can survive in extremely hot, fast-flowing water bubbling up from underground hot springs. It can withstand exposure to ultraviolet light and survives only in environments with extremely low oxygen levels, using sulfur and carbon dioxide as energy sources.

"Taken together, these traits make it a prime candidate for colonizing Mars and other planets," Fouke said.

And because it catalyzes the formation of crystalline rock formations that look like layers of pasta, it would be a relatively easy life form to detect on other planets, he said.

The unique shape and structure of rocks associated with Sulfuri result from its unusual lifestyle, Fouke said. In fast-flowing water, Sulfuri bacteria latch on to one another "and hang on for dear life," he said.

"They form tightly wound cables that wave like a flag that is fixed on one end," he said. The waving cables keep other microbes from attaching. Sulfuri also defends itself by oozing a slippery mucus.

"These Sulfuri cables look amazingly like fettuccine pasta, while further downstream they look more like capellini pasta," Fouke said. The researchers used sterilized pasta forks to collect their samples from Mammoth Hot Springs in Yellowstone National Park.

The team analyzed the microbial genomes, evaluated which genes were being actively translated into proteins and deciphered the organism's metabolic needs, Fouke said.

The team also looked at Sulfuri's rock-building capabilities, finding that proteins on the bacterial surface speed up the rate at which calcium carbonate -- also called travertine -- crystallizes in and around the cables "1 billion times faster than in any other natural environment on Earth," Fouke said. The result is the deposition of broad swaths of hardened rock with an undulating, filamentous texture.

"This should be an easy form of fossilized life for a rover to detect on other planets," Fouke said.

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Early humans deliberately recycled flint to create tiny, sharp tools

Flint.

A new Tel Aviv University study finds that prehistoric humans "recycled" discarded or broken flint tools 400,000 years ago to create small, sharp utensils with specific functions. These recycled tools were then used with great precision and accuracy to perform specific tasks involved in the processing of animal products and vegetal materials.

The site of Qesem Cave, located just outside Tel Aviv, was discovered during a road construction project in 2000. It has since offered up countless insights into life in the region hundreds of thousands of years ago.

In collaboration with Prof. Cristina Lemorini of Sapienza University of Rome, the research was led jointly by postdoctoral fellow Dr. Flavia Venditti in collaboration with Profs. Ran Barkai and Avi Gopher. All three are members of TAU's Department of Archaeology and Ancient Near Eastern Cultures. It was published on April 11 in the Journal of Human Evolution.

In recent years, archaeologists working in caves in Spain and North Africa and digs in Italy and Israel have unearthed evidence that prehistoric people recycled objects they used in daily life. Just as we recycle materials such as paper and plastic to manufacture new items today, early hominids collected discarded or broken tools made of flint to create new utensils for specific purposes hundreds of thousands of years ago.

"Recycling was a way of life for these people," Prof. Barkai says. "It has long been a part of human evolution and culture. Now, for the first time, we are discovering the specific uses of the recycled 'tool kit' at Qesem Cave."

Exceptional conditions in the cave allowed for the immaculate preservation of the materials, including micro residue on the surface of the flint tools.

"We used microscopic and chemical analyses to discover that these small and sharp recycled tools were specifically produced to process animal resources like meat, hide, fat and bones," Venditti explains. "We also found evidence of plant and tuber processing, which demonstrated that they were also part of the hominids' diet and subsistence strategies."

According to the study, signs of use were found on the outer edges of the tiny objects, indicating targeted cutting activities related to the consumption of food: butchery activities and tuber, hide and bone processing. The researchers used two different and independent spectroscopic chemical techniques: Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy coupled with energy dispersive X-ray spectroscopy (SEM-EDX).

"The meticulous analysis we conducted allowed us to demonstrate that the small recycled flakes were used in tandem with other types of utensils. They therefore constituted a larger, more diversified tool kit in which each tool was designed for specific objectives," Venditti says.

She adds, "The research also demonstrates that the Qesem inhabitants practiced various activities in different parts of the cave: The fireplace and the area surrounding it were eventually a central area of activity devoted to the consumption of the hunted animal and collected vegetal resources, while the so-called 'shelf area' was used to process animal and vegetal materials to obtain different by-products."

"This research highlights two debated topics in the field of Paleolithic archaeology: the meaning of recycling and the functional role of small tools," Prof. Barkai observes. "The data from the unique, well-preserved and investigated Qesem Cave serve to enrich the discussion of these phenomena in the scientific community."

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Did ancient supernovae prompt human ancestors to walk upright?

Supernova illustration.

Did ancient supernovae induce proto-humans to walk on two legs, eventually resulting in Homo sapiens with hands free to build cathedrals, design rockets and snap iPhone selfies?

A paper published today in the Journal of Geology makes the case: Supernovae bombarded Earth with cosmic energy starting as many as 8 million years ago, with a peak some 2.6 million years ago, initiating an avalanche of electrons in the lower atmosphere and setting off a chain of events that feasibly ended with bipedal hominins such as Homo habilis, dubbed "handy man."

The authors believe atmospheric ionization probably triggered an enormous upsurge in cloud-to-ground lightning strikes that ignited forest fires around the globe. These infernos could be one reason ancestors of Homo sapiens developed bipedalism -- to adapt in savannas that replaced torched forests in northeast Africa.

"It is thought there was already some tendency for hominins to walk on two legs, even before this event," said lead author Adrian Melott, professor emeritus of physics & astronomy at the University of Kansas. "But they were mainly adapted for climbing around in trees. After this conversion to savanna, they would much more often have to walk from one tree to another across the grassland, and so they become better at walking upright. They could see over the tops of grass and watch for predators. It's thought this conversion to savanna contributed to bipedalism as it became more and more dominant in human ancestors."

Based on a "telltale" layer of iron-60 deposits lining the world's sea beds, astronomers have high confidence supernovae exploded in Earth's immediate cosmic neighborhood -- between 100 and only 50 parsecs (163 light years) away -- during the transition from the Pliocene Epoch to the Ice Age.

"We calculated the ionization of the atmosphere from cosmic rays which would come from a supernova about as far away as the iron-60 deposits indicate," Melott said. "It appears that this was the closest one in a much longer series. We contend it would increase the ionization of the lower atmosphere by 50-fold. Usually, you don't get lower-atmosphere ionization because cosmic rays don't penetrate that far, but the more energetic ones from supernovae come right down to the surface -- so there would be a lot of electrons being knocked out of the atmosphere."

According to Melott and co-author Brian Thomas of Washburn University, ionization in the lower atmosphere meant an abundance of electrons would form more pathways for lightning strikes.

"The bottom mile or so of atmosphere gets affected in ways it normally never does," Melott said. "When high-energy cosmic rays hit atoms and molecules in the atmosphere, they knock electrons out of them -- so these electrons are running around loose instead of bound to atoms. Ordinarily, in the lightning process, there's a buildup of voltage between clouds or the clouds and the ground -- but current can't flow because not enough electrons are around to carry it. So, it has to build up high voltage before electrons start moving. Once they're moving, electrons knock more electrons out of more atoms, and it builds to a lightning bolt. But with this ionization, that process can get started a lot more easily, so there would be a lot more lightning bolts."

The KU researcher said the probability that this lightning spike touched off a worldwide upsurge in wildfires is supported by the discovery of carbon deposits found in soils that correspond with the timing of the cosmic-ray bombardment.

"The observation is that there's a lot more charcoal and soot in the world starting a few million years ago," Melott said. "It's all over the place, and nobody has any explanation for why it would have happened all over the world in different climate zones. This could be an explanation. That increase in fires is thought to have stimulated the transition from woodland to savanna in a lot of places -- where you had forests, now you had mostly open grassland with shrubby things here and there. That's thought to be related to human evolution in northeast Africa. Specifically, in the Great Rift Valley where you get all these hominin fossils."

Melott said no such event is likely to occur again anytime soon. The nearest star capable of exploding into a supernova in the next million years is Betelgeuse, some 200 parsecs (652 light years) from Earth.

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Comet inspires chemistry for making breathable oxygen on Mars

Oxygen element in periodic table.

Science fiction stories are chock full of terraforming schemes and oxygen generators for a very good reason -- we humans need molecular oxygen (O2) to breathe, and space is essentially devoid of it. Even on other planets with thick atmospheres, O2 is hard to come by.

So, when we explore space, we need to bring our own oxygen supply. That is not ideal because a lot of energy is needed to hoist things into space atop a rocket, and once the supply runs out, it is gone.

One place molecular oxygen does appear outside of Earth is in the wisps of gas streaming off comets. The source of that oxygen remained a mystery until two years ago when Konstantinos P. Giapis, a professor of chemical engineering at Caltech, and his postdoctoral fellow Yunxi Yao, proposed the existence of a new chemical process that could account for its production. Giapis, along with Tom Miller, professor of chemistry, have now demonstrated a new reaction for generating oxygen that Giapis says could help humans explore the universe and perhaps even fight climate change at home. More fundamentally though, he says the reaction represents a new kind of chemistry discovered by studying comets.

Most chemical reactions require energy, which is typically provided as heat. Giapis's research shows that some unusual reactions can occur by providing kinetic energy. When water molecules are shot like extremely tiny bullets onto surfaces containing oxygen, such as sand or rust, the water molecule can rip off that oxygen to produce molecular oxygen. This reaction occurs on comets when water molecules vaporize from the surface and are then accelerated by the solar wind until they crash back into the comet at high speed.

Comets, however, also emit carbon dioxide (CO2). Giapis and Yao wanted to test if CO2 could also produce molecular oxygen in collisions with the comet surface. When they found O2 in the stream of gases coming off the comet, they wanted to confirm that the reaction was similar to water's reaction. They designed an experiment to crash CO2 onto the inert surface of gold foil, which cannot be oxidized and should not produce molecular oxygen. Nonetheless, O2 continued to be emitted from the gold surface. This meant that both atoms of oxygen come from the same CO2 molecule, effectively splitting it in an extraordinary manner.

"At the time we thought it would be impossible to combine the two oxygen atoms of a CO2 molecule together because CO2 is a linear molecule, and you would have to bend the molecule severely for it to work," Giapis says. "You're doing something really drastic to the molecule."

To understand the mechanism of how CO2 breaks down to molecular oxygen, Giapis approached Miller and his postdoctoral fellow Philip Shushkov, who designed computer simulations of the entire process. Understanding the reaction posed a significant challenge because of the possible formation of excited molecules. These molecules have so much energy that their constituent atoms vibrate and rotate around to an enormous degree. All that motion makes simulating the reaction in a computer more difficult because the atoms within the molecules move in complex ways.

"In general, excited molecules can lead to unusual chemistry, so we started with that," Miller says. "But, to our surprise, the excited state did not create molecular oxygen. Instead, the molecule decomposed into other products. Ultimately, we found that a severely bent CO2 can also form without exciting the molecule, and that could produce O2."

The apparatus Giapis designed to perform the reaction works like a particle accelerator, turning the CO2 molecules into ions by giving them a charge and then accelerating them using an electric field, albeit at much lower energies than are found in a particle accelerator. However, he adds that such a device is not necessary for the reaction to occur.

"You could throw a stone with enough velocity at some CO2 and achieve the same thing," he says. "It would need to be traveling about as fast as a comet or asteroid travels through space."

That could explain the presence of small amounts of oxygen that have been observed high in the Martian atmosphere. There has been speculation that the oxygen is being generated by ultraviolet light from the sun striking CO2, but Giapis believes the oxygen is also generated by high-speed dust particles colliding with CO2 molecules.

He hopes that a variation of his reactor could be used to do the same thing at more useful scales -- perhaps one day serving as a source of breathable air for astronauts on Mars or being used to combat climate change by pulling CO2, a greenhouse gas, out of Earth's atmosphere and turning it into oxygen. He acknowledges, however, that both of those applications are a long way off because the current version of the reactor has a low yield, creating only one to two oxygen molecules for every 100 CO2 molecules shot through the accelerator.

"Is it a final device? No. Is it a device that can solve the problem with Mars? No. But it is a device that can do something that is very hard," he says. "We are doing some crazy things with this reactor."

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Climate change affects the genetic diversity of a species

Marmot family.

What effects does climate change have on the genetic diversity of living organisms? In a study led by Charité -- Universitätsmedizin Berlin, an international team of researchers studied the genome of the alpine marmot, an ice-age remnant that now lives in large numbers in the high altitude Alpine meadow. Results were unexpected: the species was found to be the least genetically diverse of any wild mammal studied to date. An explanation was found in the marmots genetic past. The alpine marmot has lost its genetic diversity during ice-age related climate events and been unable to recover its diversity since. Results from this study have been published in the journal Current Biology.

A large rodent from the squirrel family, the alpine marmot lives in the high-altitude mountainous terrain found beyond the tree line. An international team of researchers has now successfully deciphered the animal's genome and found the individual animals tested to be genetically very similar. In fact, the animal's genetic diversity is lower than that of any other wild mammal whose genome has been genetically sequenced. "We were very surprised by this finding. Low genetic diversity is primarily found among highly endangered species such as, for instance, the mountain gorilla. Population numbers for the alpine marmot, however, are in the hundreds of thousands, which is why the species is not considered to be at risk," explains Prof. Dr. Markus Ralser, the Director of Charité's Institute of Biochemistry and the investigator with overall responsibility for the study, which was co-led by the Francis Crick Institute.

As the alpine marmot's low genetic diversity could not be explained by the animal's current living and breeding habits, the researchers used computer-based analysis to reconstruct the marmot's genetic past. After combining the results of comprehensive genetic analyses with data from fossil records, the researchers came to the conclusion that the alpine marmot lost its genetic diversity as a result of multiple climate-related adaptations during the last ice age. One of these adaptations occurred during the animal's colonization of the Pleistocene steppe at the beginning of the last ice age (between 110,000 and 115,000 years ago). A second occurred when the Pleistocene steppe disappeared again towards the end of the ice age (between 10,000 and 15,000 years ago). Since then, marmots have inhabited the high-altitude grasslands of the Alps, where temperatures are similar to those of the Pleistocene steppe habitat. The researchers found evidence to suggest that the marmot's adaptation to the colder temperatures of the Pleistocene steppe resulted in longer generation time and a decrease in the rate of genetic mutations. These developments meant that the animals were unable to effectively regenerate their genetic diversity. Overall results suggest that the rate of genome evolution is exceptionally low in alpine marmots.

Commenting on the significance of their results, Prof. Ralser says: "Our study shows that climate change can have extremely long-term effects on the genetic diversity of a species. This had not previously been shown in such clear detail. When a species displays very little genetic diversity, this can be due to climate events which occurred many thousands of years ago," He adds: "It is remarkable that the alpine marmot managed to survive for thousands of years despite its low genetic diversity." After all, a lack of genetic variation can mean a reduced ability to adapt to change, rendering the affected species more susceptible to both diseases and altered environmental conditions -- including changes in the local climate."

Summarizing the study's findings, Prof. Ralser explains: "We should take the results of the study seriously, as we can see similar warnings from the past. In the 19th century, the passenger pigeon was one of the most abundant species of land birds in the Northern Hemisphere, yet, it was completely wiped out within just a few years. It is possible that low genetic diversity played a role in this." Outlining his plans for further research, he adds: "An important next step would be to study other animals more closely which, like the alpine marmot, managed to survive the ice age. These animals might be trapped in a similar state of low genetic diversity. Currently, estimates of a particular species' extinction risk are primarily based on the number of animals capable of breeding. We ought to reconsider whether this should be the only criterion we use."

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GRACE data contributes to understanding of climate change

The University of Texas at Austin team that led a twin satellite system launched in 2002 to take detailed measurements of the Earth, called the Gravity Recovery and Climate Experiment (GRACE), reports in the most recent issue of the journal Nature Climate Change on the contributions that their nearly two decades of data have made to our understanding of global climate patterns.

Among the many contributions that GRACE has made:

• GRACE recorded three times the mass of ice lost in the polar and mountainous regions since first beginning measurements -- a consequence of global warming.
• GRACE enabled a measure of the quantity of heat added to the ocean and the location for said heat that remains stored in the ocean. GRACE has provided detailed observations, confirming that the majority of the warming occurs in the upper 2,000 meters of the oceans.
• GRACE has observed that of the 37 largest land-based aquifers, 13 have undergone critical mass loss. This loss, due to both a climate-related effect and an anthropogenic (human-induced) effect, documents the reduced availability of clean, fresh water supplies for human consumption.
• The information gathered from GRACE provides vital data for the federal agency United States Drought Monitor and has shed light on the causes of drought and aquifer depletion in places worldwide, from India to California.

Intended to last just five years in orbit for a limited, experimental mission to measure small changes in the Earth's gravitational fields, GRACE operated for more than 15 years and has provided unprecedented insight into our global water resources, from more accurate measurements of polar ice loss to a better view of the ocean currents, and the rise in global sea levels. The mission was a collaboration between NASA and the German Aerospace Centre and was led by researchers in the Center for Space Research (CSR) in UT's Cockrell School of Engineering.

UT's Texas Advanced Computing Center (TACC) has played a critical role in this international project over the last 15 years, according to Byron Tapley, the Clare Cockrell Williams Centennial Chair Emeritus in the Department of Aerospace Engineering and Engineering Mechanics who established the Center for Space Research at UT in 1981 and who served as principal investigator of the GRACE mission.

"As the demand for the GRACE science deliverables have grown, TACC's ability to support these demands have grown. It has been a seamless transition to a much richer reporting environment," he said.

By measuring changes in mass that cause deviations in the strength of gravity's pull on the Earth's various systems -- water systems, ice sheets, atmosphere, land movements, and more -- the satellites can measure small changes in the Earth system interactions.

"By monitoring the physical components of the Earth's dynamical system as a whole, GRACE provides a time variable and holistic overview of how our oceans, atmosphere and land surface topography interact," Tapley said.

The data system for the mission is highly distributed and requires significant data storage and computation through an internationally distributed network. Although the final data products for the CSR solutions are generated at TACC, there is considerable effort in Germany by the Geophysics Center in Potsdam and the NASA Jet Propulsion Laboratory (JPL) in Pasadena, California. The final CSR analysis at TACC starts with a data downlink from the satellites to a raw data collection center in Germany. The data is then transmitted to JPL where the primary measurements are converted into the geophysical measurements consisting of GPS, accelerometer, attitude quaternions, and the high accuracy intersatellite ranging measurements collected by each satellite during a month-long observation span.

"The collection of information from this international community are brought together by the fundamental computing capability and the operational philosophy at TACC to undergo the challenging data analysis required to obtain the paradigm-shifting view of the Earth's interactions," Tapley said.

Despite being a risky venture operating on minimal funding, the GRACE mission surpassed all expectations and continues to provide a critical set of measurements.

"The concept of using the changing gravimetric patterns on Earth as a means to understanding major changes in the Earth system interactions had been proposed before," Tapley said. "But we were the first to make it happen at a measurement level that supported the needs of the diverse Earth-science community."

One of the remarkable benefits of working with TACC, according to Tapley, is the ability to pose questions whose solutions would have not been feasible prior to TACC and to find the capability to answer the questions.

"As an example, when we began the GRACE mission, our capability was looking at gravity models that were characterized by approximately 5,000 model parameters, whose solution was obtained at approximately yearly analysis intervals. The satellite-only GRACE models today are based on approximately 33,000 parameters that we have the ability to determine at a daily interval. In the final re-analysis of the GRACE data, we're looking to expand this parameterization to 4,000,000 parameters for the mean model. The interaction with TACC has always been in the context of: 'If the answer to a meaningful question requires extensive computations, let's find a way to satisfy that requirement,'" Tapley said.

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New causes of autism found in 'junk' DNA

DNA illustration.

Leveraging artificial intelligence techniques, researchers have demonstrated that mutations in so-called 'junk' DNA can cause autism. The study, published May 27 in Nature Genetics, is the first to functionally link such mutations to the neurodevelopmental condition.

The research was led by Olga Troyanskaya in collaboration with Robert Darnell. Troyanskaya is deputy director for genomics at the Flatiron Institute's Center for Computational Biology (CCB) in New York City and a professor of computer science at Princeton University. Darnell is the Robert and Harriet Heilbrunn Professor of Cancer Biology at Rockefeller University and an investigator at the Howard Hughes Medical Institute.

Their team used machine learning to analyze the whole genomes of 1,790 individuals with autism and their unaffected parents and siblings. These individuals had no family history of autism, meaning the genetic cause of their condition was probably spontaneous mutations rather than inherited mutations.

The analysis predicted the ramifications of genetic mutations in parts of the genome that do not encode proteins, regions often mischaracterized as 'junk' DNA. The number of autism cases linked to the noncoding mutations was comparable to the number of cases linked to protein-coding mutations that disable gene function.

The implications of the work extend beyond autism, Troyanskaya says. "This is the first clear demonstration of non-inherited, noncoding mutations causing any complex human disease or disorder."

Scientists can apply the same techniques used in the new study to explore the role noncoding mutations play in diseases such as cancer and heart disease, says study co-author Jian Zhou of CCB and Princeton. "This enables a new perspective on the cause of not just autism, but many human diseases."

Only 1 to 2 percent of the human genome is made up of genes that encode the blueprints for making proteins. Those proteins carry out tasks throughout our bodies, such as regulating blood sugar levels, fighting infections and sending communications between cells. The other 98 percent of our genome isn't genetic dead weight, though. The noncoding regions help regulate when and where genes make proteins.

Mutations in protein-coding regions account for at most 30 percent of autism cases in individuals without a family history of autism. Evidence suggested that autism-causing mutations must happen elsewhere in the genome as well.

Uncovering which noncoding mutations may cause autism is tricky. A single individual may have dozens of noncoding mutations, most of which will be unique to the individual. This make the traditional approach of identifying common mutations among affected populations nonviable.

Troyanskaya and her colleagues took a new approach. They trained a machine learning model to predict how a given sequence would affect gene expression.

"This is a shift in thinking about genetic studies that we're introducing with this analysis," says Chandra Theesfeld, a research scientist in Troyanskaya's lab at Princeton. "In addition to scientists studying shared genetic mutations across large groups of individuals, here we're applying a set of smart, sophisticated tools that tell us what any specific mutation is going to do, even those that are rare or never observed before."

The researchers studied the genetic basis of autism by applying the machine learning model to a treasure trove of genetic data called the Simons Simplex Collection. The Simons Foundation, the Flatiron Institute's parent organization, produced and maintains the repository. The Simons Simplex Collection contains the whole genomes of nearly 2,000 'quartets' made up of a child with autism, an unaffected sibling and their unaffected parents.

These foursomes had no previous family history of autism, meaning that non-inherited mutations were probably responsible for the affected child's condition. (Such mutations occur spontaneously in sperm and egg cells as well as in embryos.)

The researchers used their model to predict the impact of non-inherited, noncoding mutations in each child with autism. They then compared those predictions with the effects of the same, unmutated strand in the child's unaffected sibling.

"The design of the Simons Simplex Collection is what allowed us to do this study," says Zhou. "The unaffected siblings are a built-in control."

Noncoding mutations in many of the children with autism altered gene regulation, the analysis suggested. Moreover, the results suggested that the mutations affected gene expression in the brain and genes already linked to autism, such as those responsible for neuron migration and development. "This is consistent with how autism most likely manifests in the brain," says study co-author Christopher Park, a research scientist at CCB. "It's not just the number of mutations occurring, but what kind of mutations are occurring."

The researchers tested the effects of some of the noncoding mutations in laboratory experiments. They inserted predicted high-impact mutations found in children with autism into cells and observed the resulting changes in gene expression. These changes affirmed the model's predictions.

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Scientists uncover a trove of genes that could hold key to how humans evolved

DNA sequence illustration

Researchers at the Donnelly Centre in Toronto have found that dozens of genes, previously thought to have similar roles across different organisms, are in fact unique to humans and could help explain how our species came to exist.

These genes code for a class of proteins known as transcription factors, or TFs, which control gene activity. TFs recognize specific snippets of the DNA code called motifs, and use them as landing sites to bind the DNA and turn genes on or off.

Previous research had suggested that TFs which look similar across different organisms also bind similar motifs, even in species as diverse as fruit flies and humans. But a new study from Professor Timothy Hughes' lab, at the Donnelly Centre for Cellular and Biomolecular Research, shows that this is not always the case.

Writing in the journal Nature Genetics, the researchers describe a new computational method which allowed them to more accurately predict motif sequences each TF binds in many different species. The findings reveal that some sub-classes of TFs are much more functionally diverse than previously thought.

"Even between closely related species there's a non-negligible portion of TFs that are likely to bind new sequences," says Sam Lambert, former graduate student in Hughes' lab who did most of the work on the paper and has since moved to the University of Cambridge for a postdoctoral stint.

"This means they are likely to have novel functions by regulating different genes, which may be important for species differences," he says.

Even between chimps and humans, whose genomes are 99 per cent identical, there are dozens of TFs which recognize diverse motifs between the two species in a way that would affect expression of hundreds of different genes.

"We think these molecular differences could be driving some of the differences between chimps and humans," says Lambert, who won the Jennifer Dorrington Graduate Research Award for outstanding doctoral research at U of T's Faculty of Medicine.

To reanalyze motif sequences, Lambert developed new software which looks for structural similarities between the TFs' DNA binding regions that relate to their ability to bind the same or different DNA motifs. If two TFs, from different species, have a similar composition of amino-acids, building blocks of proteins, they probably bind similar motifs. But unlike older methods, which compare these regions as a whole, Lambert's automatically assigns greater value to those amino-acids -- a fraction of the entire region -- which directly contact the DNA. In this case, two TFs may look similar overall, but if they differ in the position of these key amino-acids, they are more likely to bind different motifs. When Lambert compared all TFs across different species and matched to all available motif sequence data, he found that many human TFs recognize different sequences -- and therefore regulate different genes -- than versions of the same proteins in other animals.

The finding contradicts earlier research, which stated that almost all of human and fruit fly TFs bind the same motif sequences, and is a call for caution to scientists hoping to draw insights about human TFs by only studying their counterparts in simpler organisms.

"There is this idea that has persevered, which is that the TFs bind almost identical motifs between humans and fruit flies," says Hughes, who is also a professor in U of T's Department of Molecular Genetics and Fellow of the Canadian Institute for Advanced Research. "And while there are many examples where these proteins are functionally conserved, this is by no means to the extent that has been accepted."

As for TFs that have unique human roles, these belong to the rapidly evolving class of so-called C2H2 zinc finger TFs, named for zinc ion-containing finger-like protrusions, with which they bind the DNA.

Their role remains an open question but it is known that organisms with more diverse TFs also have more cell types, which can come together in novel ways to build more complicated bodies.

Hughes is excited about a tantalizing possibility that some of these zinc finger TFs could be responsible for the unique features of human physiology and anatomy -- our immune system and the brain, which are the most complex among animals. Another concerns sexual dimorphism: countless visible, and often less obvious, differences between sexes that guide mate selection -- decisions that have an immediate impact on reproductive success, and can also have profound impact on physiology in the long term. The peacock's tail or facial hair in men are classic examples of such features.

"Almost nobody in human genetics studies the molecular basis of sexual dimorphism, yet these are features that all human beings see in each other and that we are all fascinated with," says Hughes. "I'm tempted to spend the last half of my career working on this, if I can figure out how to do it!"

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On Mars, sands shift to a different drum

Illustration of sand dunes on Mars

Wind has shaped the face of Mars for millennia, but its exact role in piling up sand dunes, carving out rocky escarpments or filling impact craters has eluded scientists until now.

In the most detailed analysis of how sands move around on Mars, a team of planetary scientists led by Matthew Chojnacki at the University of Arizona Lunar and Planetary Lab set out to uncover the conditions that govern sand movement on Mars and how they differ from those on Earth.

The results, published in the current issue of the journal Geology, reveal that processes not involved in controlling sand movement on Earth play major roles on Mars, especially large-scale features on the landscape and differences in landform surface temperature.

"Because there are large sand dunes found in distinct regions of Mars, those are good places to look for changes," said Chojnacki, associate staff scientist at the UA and lead author of the paper, "Boundary conditions controls on the high-sand-flux regions of Mars." "If you don't have sand moving around, that means the surface is just sitting there, getting bombarded by ultraviolet and gamma radiation that would destroy complex molecules and any ancient Martian biosignatures."

Compared to Earth's atmosphere, the Martian atmosphere is so thin its average pressure on the surface is a mere 0.6 percent of our planet's air pressure at sea level. Consequently, sediments on the Martian surface move more slowly than their Earthly counterparts.

The Martian dunes observed in this study ranged from 6 to 400 feet tall and were found to creep along at a fairly uniform average speed of two feet per Earth year. For comparison, some of the faster terrestrial sand dunes on Earth, such as those in North Africa, migrate at 100 feet per year.

"On Mars, there simply is not enough wind energy to move a substantial amount of material around on the surface," Chojnacki said. "It might take two years on Mars to see the same movement you'd typically see in a season on Earth."

Planetary geologists had been debating whether the sand dunes on the red planet were relics from a distant past, when the atmosphere was much thicker, or whether drifting sands still reshape the planet's face today, and if so, to what degree.

"We wanted to know: Is the movement of sand uniform across the planet, or is it enhanced in some regions over others?" Chojnacki said. "We measured the rate and volume at which dunes are moving on Mars."

The team used images taken by the HiRISE camera aboard NASA's Mars Reconnaissance Orbiter, which has been surveying Earth's next-door neighbor since 2006. HiRISE, which stands for High Resolution Imaging Science Experiment, is led by the UA's Lunar and Planetary Laboratory and has captured about three percent of the Martian surface in stunning detail.

The researchers mapped sand volumes, dune migration rates and heights for 54 dune fields, encompassing 495 individual dunes.

"This work could not have been done without HiRISE," said Chojnacki, who is a member of the HiRISE team. "The data did not come just from the images, but was derived through our photogrammetry lab that I co-manage with Sarah Sutton. We have a small army of undergraduate students who work part time and build these digital terrain models that provide fine-scale topography."

Across Mars, the survey found active, wind-shaped beds of sand and dust in structural fossae -- craters, canyons, rifts and cracks -- as well as volcanic remnants, polar basins and plains surrounding craters.

In the study's most surprising finding, the researchers discovered that the largest movements of sand in terms of volume and speed are restricted to three distinct regions: Syrtis Major, a dark spot larger than Arizona that sits directly west of the vast Isidis basin; Hellespontus Montes, a mountain range about two-thirds the length of the Cascades; and North Polar Erg, a sea of sand lapping around the north polar ice cap. All three areas are set apart from other parts of Mars by conditions not known to affect terrestrial dunes: stark transitions in topography and surface temperatures.

"Those are not factors you would find in terrestrial geology," Chojnacki said. "On Earth, the factors at work are different from Mars. For example, ground water near the surface or plants growing in the area retard dune sand movement."

On a smaller scale, basins filled with bright dust were found to have higher rates of sand movement, as well.

"A bright basin reflects the sunlight and heats up the air above much more quickly than the surrounding areas, where the ground is dark," Chojnacki said, "so the air will move up the basin toward the basin rim, driving the wind, and with it, the sand."

Read more at Science Daily

Mites and ticks are close relatives, new research shows

Mite illustration.

Scientists from the University of Bristol and the Natural History Museum in London have reconstructed the evolutionary history of the chelicerates, the mega-diverse group of 110,000 arthropods that includes spiders, scorpions, mites and ticks.

They found, for the first time, genomic evidence that mites and ticks do not constitute two distantly related lineages, rather they are part of the same evolutionary line. This now makes them the most diverse group of chelicerates, changing our perspective on their biodiversity.

Arthropoda, or jointed-legged animals, make up the majority of animal biodiversity. They both pollinate (bees) and destroy our crops (locusts), are major food sources (shrimps and crabs), and are vectors of serious diseases like malaria and Lyme disease (mosquitoes and ticks).

Arthropods are ancient and fossils show that they have been around for more than 500 million years. The secret of their evolutionary success, which is reflected in their outstanding species diversity, is still unknown. To clarify what makes arthropod so successful we first need to understand how the different arthropod lineages relate to each other.

Co-author of the study, Professor Davide Pisani, from the University of Bristol's School of Earth Sciences and Biological Sciences, said: "Finding that mites and ticks constitute a single evolutionary lineage is really important for our understanding of how biodiversity is distributed within Chelicerata.

"Spiders, with more than 48,000 described species, have long been considered the most biodiverse chelicerate lineage, but 42,000 mite and 12,000 tick species have been described. So, if mites and ticks are a single evolutionary entity rather than two distantly related ones, they are more diverse than the spiders."

Dr Greg Edgecombe of the Natural History Museum London added: "Because of their anatomical similarities it has long been suspected that mites and ticks form a natural evolutionary group, which has been named Acari. However, not all anatomists agreed, and genomic data never found any support for this idea before."

Lead author, Dr Jesus Lozano Fernandez, from Bristol's School of Biological Sciences, said: "Spiders are iconic terrestrial animals that have always been part of the human imagination and folklore, representing mythological and cultural symbols, as well as often being objects of inner fears or admiration.

"Spiders have long been considered the most biodiverse chelicerate lineage, but our findings show that Acari is, in fact, bigger."

In order to come up with their findings, the researchers used an almost even representation of mites and ticks (10 and 11 species, respectively), the most complete species-level sampling at the genomic level for these groups so far.

Dr Lozano-Fernandez added: "Regardless of the methods we used, our results converge on the same answer -- mites and ticks really do form a natural group. Evolutionary trees like the one we've reconstructed provide us with the background information we need to interpret processes of genomic change.

Read more at Science Daily