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After more than a decade, ChIP-seq may be quantitative after all

For more than a decade, scientists studying epigenetics have used a powerful method called ChIP-seq to map changes in proteins and other critical regulatory factors across the genome. While ChIP-seq provides invaluable insights into the underpinnings of health and disease, it also faces a frustrating challenge: its results are often viewed as qualitative rather than quantitative, making interpretation difficult.

But, it turns out, ChIP-seq may have been quantitative all along, according to a recent report selected as an Editors’ Pick by and featured on the cover of the Journal of Biological Chemistry.

“ChIP-seq is the backbone of epigenetics research. Our findings challenge the belief that additional steps are required to make it quantitative,” said Brad Dickson, Ph.D., a staff scientist at Van Andel Institute and the study’s corresponding author. “Our new approach provides a way to quantify results, thereby making ChIP-seq more precise, while leaving standard protocols untouched.”

Previous attempts to quantify ChIP-seq results have led to additional steps being added to the protocol, including the use of “spike-ins,” which are additives designed to normalize ChIP-seq results and reveal histone changes that otherwise may be obscured. These extra steps increase the complexity of experiments while also adding variables that could interfere with reproducibility. Importantly, the study also identifies a sensitivity issue in spike-in normalization that has not previously been discussed.

Using a predictive physical model, Dickson and his colleagues developed a novel approach called the sans-spike-in method for Quantitative ChIP-sequencing, or siQ-ChIP. It allows researchers to follow the standard ChIP-seq protocol, eliminating the need for spike-ins, and also outlines a set of common measurements that should be reported for all ChIP-seq experiments to ensure reproducibility as well as quantification.

By leveraging the binding reaction at the immunoprecipitation step, siQ-ChIP defines a physical scale for sequencing results that allows comparison between experiments. The quantitative scale is based on the binding isotherm of the immunoprecipitation products.

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Cosmic flashes come in all different sizes

By studying the site of a spectacular stellar explosion seen in April 2020, a Chalmers-led team of scientists have used four European radio telescopes to confirm that astronomy’s most exciting puzzle is about to be solved. Fast radio bursts, unpredictable millisecond-long radio signals seen at huge distances across the universe, are generated by extreme stars called magnetars — and are astonishingly diverse in brightness.

For over a decade, the phenomenon known as fast radio bursts has excited and mystified astronomers. These extraordinarily bright but extremely brief flashes of radio waves — lasting only milliseconds — reach Earth from galaxies billions of light years away.

In April 2020, one of the bursts was for the first time detected from within our galaxy, the Milky Way, by radio telescopes CHIME and STARE2. The unexpected flare was traced to a previously-known source only 25 000 light years from Earth in the constellation of Vulpecula, the Fox, and scientists all over the world coordinated their efforts to follow up the discovery.

In May, a team of scientists led by Franz Kirsten (Chalmers) pointed four of Europe’s best radio telescopes towards the source, known as SGR 1935+2154. Their results are published today in a paper in the journal Nature Astronomy

“We didn’t know what to expect. Our radio telescopes had only rarely been able to see fast radio bursts, and this source seemed to be doing something completely new. We were hoping to be surprised!,” said Mark Snelders, team member from the Anton Pannekoek Institute for Astronomy, University of Amsterdam.

The radio telescopes, one dish each in the Netherlands and Poland and two at Onsala Space Observatory in Sweden, monitored the source every night for more than four weeks after the discovery of the first flash, a total of 522 hours of observation.

On the evening of May 24, the team got the surprise they were looking for. At 23:19 local time, the Westerbork telescope in the Netherlands, the only one of the group on duty, caught a dramatic and unexpected signal: two short bursts, each one millisecond long but 1.4 seconds apart.

Kenzie Nimmo, astronomer at Anton Pannekoek Institute for Astronomy and ASTRON, is a member of the team.

“We clearly saw two bursts, extremely close in time. Like the flash seen from the same source on April 28, this looked just like the fast radio bursts we’d been seeing from the distant universe, only dimmer. The two bursts we detected on May 24 were even fainter than that,” she said.

This was new, strong evidence connecting fast radio bursts with magnetars, the scientists thought. Like more distant sources of fast radio bursts, SGR 1935+2154 seemed to be producing bursts at random intervals, and over a huge brightness range.

“The brightest flashes from this magnetar are at least ten million times as bright as the faintest ones. We asked ourselves, could that also be true for fast radio burst sources outside our galaxy? If so, then the universe’s magnetars are creating beams of radio waves that could be criss-crossing the cosmos all the time — and many of these could be within the reach of modest-sized telescopes like ours,” said team member Jason Hessels (Anton Pannekoek Institute for Astronomy and ASTRON, Netherlands).

Neutron stars are the tiny, extremely dense remnants left behind when a short-lived star of more than eight times the mass of the Sun explodes as a supernova. For 50 years, astronomers have studied pulsars, neutron stars which with clock-like regularity send out pulses of radio waves and other radiation. All pulsars are believed to have strong magnetic fields, but the magnetars are the strongest known magnets in the universe, each with a magnetic field hundreds of trillions of times stronger than the Sun’s.

In the future, the team aims to keep the radio telescopes monitoring SGR 1935+2154 and other nearby magnetars, in the hope of pinning down how these extreme stars actually make their brief blasts of radiation.

Scientists have presented many ideas for how fast radio bursts are generated. Franz Kirsten, astronomer at Onsala Space Observatory, Chalmers, who led the project, expects the rapid pace in understanding the physics behind fast radio bursts to continue.

“The fireworks from this amazing, nearby magnetar have given us exciting clues about how fast radio bursts might be generated. The bursts we detected on May 24 could indicate a dramatic disturbance in the star’s magnetosphere, close to its surface. Other possible explanations, like shock waves further out from the magnetar, seem less likely, but I’d be delighted to be proved wrong. Whatever the answers, we can expect new measurements and new surprises in the months and years to come,” he said.

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Researcher analyzes the use of solar energy at US airports

By studying 488 public airports in the United States, University of Colorado Denver School of Public Affairs researcher Serena Kim, PhD, found that 20% of them have adopted solar photovoltaic (PV), commonly known as solar panels, over the last decade. Solar photovoltaic (PV) is the conversion of light into electricity using semiconducting materials that exhibit the photovoltaic effect.

While studying institutional arrangements as a factor that contributes to airport solar PV deployment, Kim found that airports operated by general-purpose governments (cities, states, or counties) have deployed solar panels more than special-purpose governments (port or airport authorities) as of 2020. Kim discovered that airports involved in professional organizations are more likely to deploy solar panels, but this relationship is contingent on airport governance. Airport solar deployment increases by airports’ professional organization membership, but with a higher rate for special-purpose airports than general-purpose airports.

According to Kim, airports provide an ideal venue for studying how institutional arrangements shape renewable energy deployment due to the notable differences between the general-purpose and special-purpose airports. The biggest difference between these two types of airports is how each selects its board members. More than 80% of general-purpose board members are elected, while only 7% of special-purpose airport board members are elected.

“Airport board members, directors, and managers’ leadership, and their interactions with other airport professionals can promote renewable energy transitions at airports,” said Kim.

Colorado Connection

One of the airports studied was Denver International Airport (DIA, as state residents know it, although the official abbreviation is DEN). Since 2008, DIA has become one of the largest solar projects in the U.S., installing 42,614 solar panels on a total of 56 acres.

According to airport officials interviewed for the study, DIA has been successful in rolling out solar energy because of support from the city government, airport leadership, and its electricity provider, Xcel Energy. Being at the forefront of on-site solar energy at airports, DIA has built an economically and environmentally sustainable energy management system. While reducing the airport’s carbon footprint by operating 10 megawatts (MW) solar facilities, DIA pays less than the average electricity cost for the energy generated from the solar arrays built after 2012. Excess electricity is sold back to the utility under the Xcel Solar Rewards program. All contracts go through the city council approval process, and the aviation department works closely with the city government’s sustainability department.

“DIA’s solar energy project is an example of successful collaborative partnerships,” said Kim. “All solar arrays at DIA are developed by public-private partnerships. Private solar companies own and operate the solar systems, and DIA executes power purchase agreements with the private solar companies. Xcel Energy plays a key role in the partnership as they offer rebates to offset the construction costs, purchase excess energy, and retain renewable energy certificates.”

Other airports involved in this study include Minneapolis-St. Paul International Airport, Tallahassee International Airport, and Orlando International Airport.

Next Steps for Policymakers

According to Kim’s research findings, on-site solar deployment potentials are shaped by utilities’ engagement and interest in renewable energy development. Airport solar energy is more likely to appear in the service area of investor-owned utilities, which have greater resources and expertise to invest in renewable energy.

“Accessing clean, reliable, and affordable energy is integral to resilient, sustainable, and equitable futures,” said Kim. “Policymakers who wish to facilitate on-site solar use should consider strategies for addressing resource and information gaps across investor-owned utilities, municipal utilities, and rural electric cooperatives.”

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Europe’s largest Solar Telescope GREGOR unveils magnetic details of the Sun

The Sun is our star and has a profound influence on our planet, life, and civilization. By studying the magnetism on the Sun, we can understand its influence on Earth and minimize damage of satellites and technological infrastructure. The GREGOR telescope allows scientists to resolve details as small as 50 km on the Sun, which is a tiny fraction of the solar diameter of 1.4 million km. This is as if one saw a needle on a soccer field perfectly sharp from a distance of one kilometer.

“This was a very exciting, but also extremely challenging project. In only one year we completely redesigned the optics, mechanics, and electronics to achieve the best possible image quality.” said Dr. Lucia Kleint, who led the project and the German solar telescopes on Tenerife. A major technical breakthrough was achieved by the project team in March this year, during the lockdown, when they were stranded at the observatory and set up the optical laboratory from the ground up. Unfortunately, snow storms prevented solar observations. When Spain reopened in July, the team immediately flew back and obtained the highest resolution images of the Sun ever taken by a European telescope.

Prof. Dr. Svetlana Berdyugina, professor at the Albert-Ludwig University of Freiburg and Director of the Leibniz Institute for Solar Physics (KIS), is very happy about the outstanding results: “The project was rather risky because such telescope upgrades usually take years, but the great team work and meticulous planning have led to this success. Now we have a powerful instrument to solve puzzles on the Sun.” The new optics of the telescope will allow scientists to study magnetic fields, convection, turbulence, solar eruptions, and sunspots in great detail. First light images obtained in July 2020 reveal astonishing details of sunspot evolution and intricate structures in solar plasma.

Telescope optics are very complex systems of mirrors, lenses, glass cubes, filters and further optical elements. If only one element is not perfect, for example due to fabrication issues, the performance of the whole system suffers. This is similar to wearing glasses with the wrong prescription, resulting in a blurry vision. Unlike for glasses, it is however very challenging to detect which elements in a telescope may be causing issues. The GREGOR team found several of those issues and calculated optics models to solve them. For example, astigmatism is one of such optical problems, which affects 30-60% people’s vision, but also complex telescopes. At GREGOR this was corrected by replacing two elements with so-called off-axis parabolic mirrors, which had to be polished to 6 nm precision, about 1/10000 of the diameter of a hair. Combined with several further enhancements the redesign led to the sharp vision of the telescope. A technical description of the redesign was recently published by the Astronomy & Astrophysics journal in a recent article led by Dr. L. Kleint.

European researchers have access to observations with the GREGOR telescope through national programs and a program funded by the European commission. New scientific observations are starting in September 2020.

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How galaxies die: New insights into the quenching of star formation

Astronomers studying galaxy evolution have long struggled to understand what causes star formation to shut down in massive galaxies. Although many theories have been proposed to explain this process, known as “quenching,” there is still no consensus on a satisfactory model.

Now, an international team led by Sandra Faber, professor emerita of astronomy and astrophysics at UC Santa Cruz, has proposed a new model that successfully explains a wide range of observations about galaxy structure, supermassive black holes, and the quenching of star formation. The researchers presented their findings in a paper published July 1 in the Astrophysical Journal.

The model supports one of the leading ideas about quenching which attributes it to black hole “feedback,” the energy released into a galaxy and its surroundings from a central supermassive black hole as matter falls into the black hole and feeds its growth. This energetic feedback heats, ejects, or otherwise disrupts the galaxy’s gas supply, preventing the infall of gas from the galaxy’s halo to feed star formation.

“The idea is that in star-forming galaxies, the central black hole is like a parasite that ultimately grows and kills the host,” Faber explained. “That’s been said before, but we haven’t had clear rules to say when a black hole is big enough to shut down star formation in its host galaxy, and now we have quantitative rules that actually work to explain our observations.”

The basic idea involves the relationship between the mass of the stars in a galaxy (stellar mass), how spread out those stars are (the galaxy’s radius), and the mass of the central black hole. For star-forming galaxies with a given stellar mass, the density of stars in the center of the galaxy correlates with the radius of the galaxy so that galaxies with bigger radii have lower central stellar densities. Assuming that the mass of the central black hole scales with the central stellar density, star-forming galaxies with larger radii (at a given stellar mass) will have lower black-hole masses.

What that means, Faber explained, is that larger galaxies (those with larger radii for a given stellar mass) have to evolve further and build up a higher stellar mass before their central black holes can grow large enough to quench star formation. Thus, small-radius galaxies quench at lower masses than large-radius galaxies.

“That is the new insight, that if galaxies with large radii have smaller black holes at a given stellar mass, and if black hole feedback is important for quenching, then large-radius galaxies have to evolve further,” she said. “If you put together all these assumptions, amazingly, you can reproduce a large number of observed trends in the structural properties of galaxies.”

This explains, for example, why more massive quenched galaxies have higher central stellar densities, larger radii, and larger central black holes.

Based on this model, the researchers concluded that quenching begins when the total energy emitted from the black hole is approximately four times the gravitational binding energy of the gas in the galactic halo. The binding energy refers to the gravitational force that holds the gas within the halo of dark matter enveloping the galaxy. Quenching is complete when the total energy emitted from the black hole is twenty times the binding energy of the gas in the galactic halo.

Faber emphasized that the model does not yet explain in detail the physical mechanisms involved in the quenching of star formation. “The key physical processes that this simple theory evokes are not yet understood,” she said. “The virtue of this, though, is that having simple rules for each step in the process challenges theorists to come up with physical mechanisms that explain each step.”

Astronomers are accustomed to thinking in terms of diagrams that plot the relations between different properties of galaxies and show how they change over time. These diagrams reveal the dramatic differences in structure between star-forming and quenched galaxies and the sharp boundaries between them. Because star formation emits a lot of light at the blue end of the color spectrum, astronomers refer to “blue” star-forming galaxies, “red” quiescent galaxies, and the “green valley” as the transition between them. Which stage a galaxy is in is revealed by its star formation rate.

One of the study’s conclusions is that the growth rate of black holes must change as galaxies evolve from one stage to the next. The observational evidence suggests that most of the black hole growth occurs in the green valley when galaxies are beginning to quench.

“The black hole seems to be unleashed just as star formation slows down,” Faber said. “This was a revelation, because it explains why black hole masses in star-forming galaxies follow one scaling law, while black holes in quenched galaxies follow another scaling law. That makes sense if black hole mass grows rapidly while in the green valley.”

Faber and her collaborators have been discussing these issues for many years. Since 2010, Faber has co-led a major Hubble Space Telescope galaxy survey program (CANDELS, the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey), which produced the data used in this study. In analyzing the CANDELS data, she has worked closely with a team led by Joel Primack, UCSC professor emeritus of physics, which developed the Bolshoi cosmological simulation of the evolution of the dark matter halos in which galaxies form. These halos provide the scaffolding on which the theory builds the early star-forming phase of galaxy evolution before quenching.

The central ideas in the paper emerged from analyses of CANDELS data and first struck Faber about four years ago. “It suddenly leaped out at me, and I realized if we put all these things together — if galaxies had a simple trajectory in radius versus mass, and if black hole energy needs to overcome halo binding energy — it can explain all these slanted boundaries in the structural diagrams of galaxies,” she said.

At the time, Faber was making frequent trips to China, where she has been involved in research collaborations and other activities. She was a visiting professor at Shanghai Normal University, where she met first author Zhu Chen. Chen came to UC Santa Cruz in 2017 as a visiting researcher and began working with Faber to develop these ideas about galaxy quenching.

“She is mathematically very good, better than me, and she did all of the calculations for this paper,” Faber said.

Faber also credited her longtime collaborator David Koo, UCSC professor emeritus of astronomy and astrophysics, for first focusing attention on the central densities of galaxies as a key to the growth of central black holes.

Among the puzzles explained by this new model is a striking difference between our Milky Way galaxy and its very similar neighbor Andromeda. “The Milky Way and Andromeda have almost the same stellar mass, but Andromeda’s black hole is almost 50 times bigger than the Milky Way’s,” Faber said. “The idea that black holes grow a lot in the green valley goes a long way toward explaining this mystery. The Milky Way is just entering the green valley and its black hole is still small, whereas Andromeda is just exiting so its black hole has grown much bigger, and it is also more quenched than the Milky Way.”

In addition to Faber, Chen, Koo, and Primack, the coauthors of the paper include researchers at some two dozen institutions in seven countries. This work was funded by grants from NASA and the National Science Foundation.

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Experimentally identifying effective theories in many-body systems

One goal of science is to find physical descriptions of nature by studying how basic system components interact with one another. For complex many-body systems, effective theories are frequently used to this end. They allow describing the interactions without having to observe a system on the smallest of scales. Physicists at Heidelberg University have now developed a new method that makes it possible to identify such theories experimentally with the aid of so-called quantum simulators. The results of the research effort, led by Prof. Dr Markus Oberthaler (experimental physics) and Prof. Dr Jürgen Berges (theoretical physics), were published in the journal Nature Physics.

Deriving predictions about physical phenomena at the level of individual particles from a microscopic description is practically impossible for large systems. This applies not only to quantum mechanical many-body systems, but also to classical physics, such as when heated water in a cooking pot needs to be described at the level of the individual water molecules. But if a system is observed on large scales, like water waves in a pot, new properties can become relevant under certain preconditions. To describe such physics efficiently, effective theories are used. “Our research aimed to identify these theories in experiments with the help of quantum simulators,” explains Torsten Zache, the primary author of the theoretical portion of the study. Quantum simulators are used to modify many-body systems more simply and to calculate their properties.

The Heidelberg physicists recently demonstrated their newly developed method in an experiment on ultracold rubidium atoms, which are captured in an optical trap and brought out of equilibrium. “In the scenario we prepared, the atoms behave like tiny magnets whose orientation we are able to precisely read out using new processes,” according to Maximilian Prüfer, the primary author on the experimental side of the study. To determine the effective interactions of these “magnets,” the experiment has to be repeated several thousand times, which requires extreme stability.

“The underlying theoretical concepts allow us to interpret the experimental results in a completely new way and thereby gain insights through experiments into areas that have thus far been inaccessible through theory,” points out Prof. Oberthaler. “In turn, this can tell us about new types of theoretical approaches to successfully describe the relevant physical laws in complex many-body systems,” states Prof. Berges. The approach used by the Heidelberg physicists is transferrable to a number of other systems, thus opening groundbreaking territory for quantum simulations. Jürgen Berges and Markus Oberthaler are confident that this new way of identifying effective theories will make it possible to answer fundamental questions in physics.

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Eclipse data illuminate mysteries of Sun’s corona

Researchers at the University of Hawaiʻi Institute for Astronomy (IfA) have been hard at work studying the solar corona, the outermost atmosphere of the sun that expands into interplanetary space. The properties of the solar corona are a consequence of the Sun’s complex magnetic field, which is produced in the solar interior and extends outward into space.

IfA graduate student Benjamin Boe conducted a new study that used total solar eclipse observations to measure the shape of the coronal magnetic field with higher spatial resolution and over a larger area than ever before. The results were published in the Astrophysical Journal on June 3.

The corona is most easily seen during a total solar eclipse — when the moon is directly between the Earth and Sun, blocking sunlight. Significant technological advances in recent decades have shifted a majority of analysis to space-based observations at wavelengths of light not accessible from the ground, or to large ground-based telescopes such as the Daniel K. Inouye Solar Telescope on Maui. Despite these advances, some aspects of the corona can only be studied during total solar eclipses.

Boe was advised by UH Mānoa Astronomy Professor Shadia Habbal, a coronal research expert. Habbal has led a group of eclipse chasers, the Solar Wind Sherpas making scientific observations during solar eclipses for more than 20 years. These observations have led to breakthroughs in unveiling some of the secrets of the physical processes defining the corona.

“The corona has been observed with total solar eclipses for well over a century, but never before had eclipse images been used to quantify its magnetic field structure,” explained Boe. “I knew it would be possible to extract a lot more information by applying modern image processing techniques to solar eclipse data.”

Boe traced the pattern of the distribution of magnetic field lines in the corona, using an automatic tracing method applied to images of the corona taken during 14 eclipses the past two decades. This data provided the chance to study changes in the corona over two 11-year magnetic cycles of the Sun.

Boe found that there were very fine-scale structures throughout the corona. Higher resolution images showed smaller-scale structures, implying that the corona is even more structured than what was previously reported. To quantify these changes, Boe measured the magnetic field angle relative to the Sun’s surface.

During periods of minimum solar activity, the corona’s field emanated almost straight out of the Sun near the equator and poles, while it came out at a variety of angles at mid-latitudes. During periods of maximum, the coronal magnetic field was far less organized and more radial.

“We knew there would be changes over the solar cycle but we never expected how extended and structured the coronal field would be,” Boe explained. “Future models will have to explain these features in order to fully understand the coronal magnetic field.”

These results challenge the current assumptions used in coronal modeling, which often assume that the coronal magnetic field is radial beyond 2.5 solar radii. Instead, this work found that the coronal field was often non-radial to at least 4 solar radii.

This work has further implications in other areas of solar research — including the formation of the solar wind, which impacts the Earth’s magnetic field and can have effects on the ground, such as power outages.

“These results are of particular interest for solar wind formation. It indicates that the leading ideas for how to model the formation of the solar wind are not complete, and so our ability to predict and defend against space weather can be improved,” Boe said.

Boe is already planning to be part of his team’s next eclipse expeditions. The next one is slated for South America in December 2020.

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Exploring the use of ‘stretchable’ words in social media

An investigation of Twitter messages reveals new insights and tools for studying how people use stretched words, such as “duuuuude,” “heyyyyy,” or “noooooooo.” Tyler Gray and colleagues at the University of Vermont in Burlington present these findings in the open-access journal PLOS ONE on May 27, 2020.

In spoken and written language, stretched words can modify the meaning of a word. For instance, “suuuuure” can imply sarcasm, while “yeeessss” may indicate excitement. Stretched words are rare in formal writing, but the rise of social media has opened up new opportunities to study them.

Gray and colleagues have now completed the most comprehensive study to date of “stretchable” words in social media. They developed a new, more thorough strategy for identifying stretched words in tweets and used it to analyze a randomly selected dataset of about 10 percent of all tweets generated between September 2008 and December 2016 — totaling about 100 billion tweets.

The researchers identified thousands of “stretchable” words in the tweets, including “ha” (e.g., “hahaha” or “haaahaha”), “awesome” (e.g., “awesssssommmmmeeeeee”) and “goal) (e.g., ggggoooooaaaaallllll).

They also identified two key ways of measuring the characteristics of stretchable words: balance and stretch. Balance refers to the degree to which different letters tend to be repeated. For instance, “ha” has a high degree of balance because when it is stretched, the “h” and the “a” tend to be repeated just about equally. “Goal” is less balanced, with “o” repeated more than any other letter in the word.

Stretch refers to how long a word tends to be stretched. For instance, short words or sounds like “ha” have a high degree of stretch because people often repeat them many times (e.g., “hahahahahahahaha”). Meanwhile, regular words like “infinity” have lower stretch, often with just one letter repeated: “infinityyyy.”

For this analysis, the researchers developed various tools and methods that could be used in future research of stretchable words, such as investigations of mis-typings and misspellings. The tools could also be applied to improve natural language processing, search engines, and spam filters

The authors add: “We were able to comprehensively collect and count stretched words like ‘gooooooaaaalll’ and ‘hahahaha’, and map them across the two dimensions of overall stretchiness and balance of stretch, while developing new tools that will also aid in their continued linguistic study, and in other areas, such as language processing, augmenting dictionaries, improving search engines, analyzing the construction of sequences, and more.”

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NASA’s Curiosity rover finds clues to chilly ancient Mars buried in rocks

By studying the chemical elements on Mars today — including carbon and oxygen — scientists can work backwards to piece together the history of a planet that once had the conditions necessary to support life.

Weaving this story, element by element, from roughly 140 million miles (225 million kilometers) away is a painstaking process. But scientists aren’t the type to be easily deterred. Orbiters and rovers at Mars have confirmed that the planet once had liquid water, thanks to clues that include dry riverbeds, ancient shorelines, and salty surface chemistry. Using NASA’s Curiosity Rover, scientists have found evidence for long-lived lakes. They’ve also dug up organic compounds, or life’s chemical building blocks. The combination of liquid water and organic compounds compels scientists to keep searching Mars for signs of past — or present — life.

Despite the tantalizing evidence found so far, scientists’ understanding of Martian history is still unfolding, with several major questions open for debate. For one, was the ancient Martian atmosphere thick enough to keep the planet warm, and thus wet, for the amount of time necessary to sprout and nurture life? And the organic compounds: are they signs of life — or of chemistry that happens when Martian rocks interact with water and sunlight?

In a recent Nature Astronomy report on a multi-year experiment conducted in the chemistry lab inside Curiosity’s belly, called Sample Analysis at Mars (SAM), a team of scientists offers some insights to help answer these questions. The team found that certain minerals in rocks at Gale Crater may have formed in an ice-covered lake. These minerals may have formed during a cold stage sandwiched between warmer periods, or after Mars lost most of its atmosphere and began to turn permanently cold.

Gale is a crater the size of Connecticut and Rhode Island combined. It was selected as Curiosity’s 2012 landing site because it had signs of past water, including clay minerals that might help trap and preserve ancient organic molecules. Indeed, while exploring the base of a mountain in the center of the crater, called Mount Sharp, Curiosity found a layer of sediments 1,000 feet (304 meters) thick that was deposited as mud in ancient lakes. To form that much sediment an incredible amount of water would have flowed down into those lakes for millions to tens of millions of warm and humid years, some scientists say. But some geological features in the crater also hint at a past that included cold, icy conditions.

“At some point, Mars’ surface environment must have experienced a transition from being warm and humid to being cold and dry, as it is now, but exactly when and how that occurred is still a mystery,” says Heather Franz, a NASA geochemist based at NASA’s Goddard Space Flight Center in Greenbelt, Maryland.

Franz, who led the SAM study, notes that factors such as changes in Mars’ obliquity and the amount of volcanic activity could have caused the Martian climate to alternate between warm and cold over time. This idea is supported by chemical and mineralogical changes in Martian rocks showing that some layers formed in colder environments and others formed in warmer ones.

In any case, says Franz, the array of data collected by Curiosity so far suggests that the team is seeing evidence for Martian climate change recorded in rocks.

Carbon and oxygen star in the Martian climate story

Franz’s team found evidence for a cold ancient environment after the SAM lab extracted the gases carbon dioxide, or CO2, and oxygen from 13 dust and rock samples. Curiosity collected these samples over the course of five Earth years (Earth years vs. Mars years).

CO2 is a molecule of one carbon atom bonded with two oxygen atoms, with carbon serving as a key witness in the case of the mysterious Martian climate. In fact, this simple yet versatile element is as critical as water in the search for life elsewhere. On Earth, carbon flows continuously through the air, water, and surface in a well-understood cycle that hinges on life. For example, plants absorb carbon from the atmosphere in the form of CO2. In return, they produce oxygen, which humans and most other life forms use for respiration in a process that ends with the release of carbon back into the air, again via CO2, or into the Earth’s crust as life forms die and are buried.

Scientists are finding there’s also a carbon cycle on Mars and they’re working to understand it. With little water or abundant surface life on the Red Planet for at least the past 3 billion years, the carbon cycle is much different than Earth’s.

“Nevertheless, the carbon cycling is still happening and is still important because it’s not only helping reveal information about Mars’ ancient climate,” says Paul Mahaffy, principal investigator on SAM and director of the Solar System Exploration Division at NASA Goddard. “It’s also showing us that Mars is a dynamic planet that’s circulating elements that are the buildings blocks of life as we know it.”

The gases build a case for a chilly period

After Curiosity fed rock and dust samples into SAM, the lab heated each one to nearly 1,650 degrees Fahrenheit (900 degrees Celsius) to liberate the gases inside. By looking at the oven temperatures that released the CO2 and oxygen, scientists could tell what kind of minerals the gases were coming from. This type of information helps them understand how carbon is cycling on Mars.

Various studies have suggested that Mars’ ancient atmosphere, containing mostly CO2, may have been thicker than Earth’s is today. Most of it has been lost to space, but some may be stored in rocks at the planet’s surface, particularly in the form of carbonates, which are minerals made of carbon and oxygen. On Earth, carbonates are produced when CO2 from the air is absorbed in the oceans and other bodies of water and then mineralized into rocks. Scientists think the same process happened on Mars and that it could help explain what happened to some of the Martian atmosphere.

Yet, missions to Mars haven’t found enough carbonates in the surface to support a thick atmosphere.

Nonetheless, the few carbonates that SAM did detect revealed something interesting about the Martian climate through the isotopes of carbon and oxygen stored in them. Isotopes are versions of each element that have different masses. Because different chemical processes, from rock formation to biological activity, use these isotopes in different proportions, the ratios of heavy to light isotopes in a rock provide scientists with clues to how the rock formed.

In some of the carbonates SAM found, scientists noticed that the oxygen isotopes were lighter than those in the Martian atmosphere. This suggests that the carbonates did not form long ago simply from atmospheric CO2 absorbed into a lake. If they had, the oxygen isotopes in the rocks would have been slightly heavier than the ones in the air.

While it’s possible that the carbonates formed very early in Mars’ history, when the atmospheric composition was a bit different than it is today, Franz and her colleagues suggest that the carbonates more likely formed in a freezing lake. In this scenario, the ice could have sucked up heavy oxygen isotopes and left the lightest ones to form carbonates later. Other Curiosity scientists have also presented evidence suggesting that ice-covered lakes could have existed in Gale Crater.

So where is all the carbon?

The low abundance of carbonates on Mars is puzzling, scientists say. If there aren’t many of these minerals at Gale Crater, perhaps the early atmosphere was thinner than predicted. Or maybe something else is storing the missing atmospheric carbon.

Based on their analysis, Franz and her colleagues suggest that some carbon could be sequestered in other minerals, such as oxalates, which store carbon and oxygen in a different structure than carbonates. Their hypothesis is based on the temperatures at which CO2 was released from some samples inside SAM — too low for carbonates, but just right for oxalates — and on the different carbon and oxygen isotope ratios than the scientists saw in the carbonates.

A model of a carbonate molecule next to an oxalate molecule

Oxalates are the most common type of organic mineral produced by plants on Earth. But oxalates also can be produced without biology. One way is through the interaction of atmospheric CO2 with surface minerals, water, and sunlight, in a process known as abiotic photosynthesis. This type of chemistry is hard to find on Earth because there’s abundant life here, but Franz’s team hopes to create abiotic photosynthesis in the lab to figure out if it actually could be responsible for the carbon chemistry they’re seeing in Gale Crater.

On Earth, abiotic photosynthesis may have paved the way for photosynthesis among some of the first microscopic life forms, which is why finding it on other planets interests astrobiologists.

Even if it turns out that abiotic photosynthesis locked some carbon from the atmosphere into rocks at Gale Crater, Franz and her colleagues would like to study soil and dust from different parts of Mars to understand if their results from Gale Crater reflect a global picture. They may one day get a chance to do so. NASA’s Perseverance Mars rover, due to launch to Mars between July and August 2020, plans to pack up samples in Jezero Crater for possible return to labs on Earth.

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Astronomers detect biggest explosion in the history of the Universe

Scientists studying a distant galaxy cluster have discovered the biggest explosion seen in the Universe since the Big Bang.

The blast came from a supermassive black hole at the centre of a galaxy hundreds of millions of light-years away.

It released five times more energy than the previous record holder.

Professor Melanie Johnston-Hollitt, from the Curtin University node of the International Centre for Radio Astronomy Research, said the event was extraordinarily energetic.

“We’ve seen outbursts in the centres of galaxies before but this one is really, really massive,” she said.

“And we don’t know why it’s so big.

“But it happened very slowly — like an explosion in slow motion that took place over hundreds of millions of years.”

The explosion occurred in the Ophiuchus galaxy cluster, about 390 million light-years from Earth.

It was so powerful it punched a cavity in the cluster plasma — the super-hot gas surrounding the black hole.

Lead author of the study Dr Simona Giacintucci, from the Naval Research Laboratory in the United States, said the blast was similar to the 1980 eruption of Mount St. Helens, which ripped the top off the mountain.

“The difference is that you could fit 15 Milky Way galaxies in a row into the crater this eruption punched into the cluster’s hot gas,” she said.

Professor Johnston-Hollitt said the cavity in the cluster plasma had been seen previously with X-ray telescopes.

But scientists initially dismissed the idea that it could have been caused by an energetic outburst, because it would have been too big.

“People were sceptical because the size of outburst,” she said. “But it really is that. The Universe is a weird place.”

The researchers only realised what they had discovered when they looked at the Ophiuchus galaxy cluster with radio telescopes.

“The radio data fit inside the X-rays like a hand in a glove,” said co-author Dr Maxim Markevitch, from NASA’s Goddard Space Flight Center.

“This is the clincher that tells us an eruption of unprecedented size occurred here.”

The discovery was made using four telescopes; NASA’s Chandra X-ray Observatory, ESA’s XMM-Newton, the Murchison Widefield Array (MWA) in Western Australia and the Giant Metrewave Radio Telescope (GMRT) in India.

Professor Johnston-Hollitt, who is the director of the MWA and an expert in galaxy clusters, likened the finding to discovering the first dinosaur bones.

“It’s a bit like archaeology,” she said.

“We’ve been given the tools to dig deeper with low frequency radio telescopes so we should be able to find more outbursts like this now.”

The finding underscores the importance of studying the Universe at different wavelengths, Professor Johnston-Hollitt said.

“Going back and doing a multi-wavelength study has really made the difference here,” she said.

Professor Johnston-Hollitt said the finding is likely to be the first of many.

“We made this discovery with Phase 1 of the MWA, when the telescope had 2048 antennas pointed towards the sky,” she said.

“We’re soon going to be gathering observations with 4096 antennas, which should be ten times more sensitive.”

“I think that’s pretty exciting.”

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