Translation of genes more complex than expected

Illustration of DNA in cell

Researchers from the group of Marvin Tanenbaum at the Hubrecht Institute have shown that translation of the genetic information stored in our DNA is much more complex than previously thought. This discovery was made by developing a type of advanced microscopy that directly visualizes the translation of the genetic code in a living cell. Their study is published in the scientific journal Cell on June 6th.

From gene to protein

Each cell in our body contains the same DNA, yet different cells, like brain cells or muscle cells, have different functions. The differences in cell function depend on which parts of the genetic information (called genes) are active in each cell. The genetic information stored in these genes is translated by specialized translation factories called ribosomes. Ribosomes read the genetic code and assemble proteins based on the information stored in this genetic code analogous to a factory building a machine based on a blueprint. Proteins are the workhorses of our body and perform the functions encoded in our genes. For our cells and organs to function correctly, it is critical that the genetic information stored in our genes is translated accurately to proteins. If the genetic code is translated incorrectly, harmful proteins can be produced, which can lead to neurological diseases such as Huntington's disease.

The 'reading frame' of genes

The genetic code is translated in groups of 3 letters, each resembling a word, which is translated into a single part of the protein. If a ribosome starts translating the code at the wrong position, a shift in the 3-letter-code can occur. For example, the sentence below should read:

"the man saw his new red car"

However, if a ribosome starts translating this sentence one letter too late, the sentence would read:

"hem ans awh isn ewr edc ar"

In the case of the genetic code, this phenomenon is called 'out-of-frame' translation. Sanne Boersma, researcher at the Hubrecht Institute explains: "As illustrated by the example sentence, out-of-frame translation has a big effect on the protein and usually results in a protein that behaves differently and can damage the cell." Until now, it was unclear how the ribosome knows where to start translating the code, and how often the ribosome gets it wrong.

A new method: SunTag and MoonTag

The researchers developed a new method to visualize the decoding of our genetic information in living cells. They were able to label different protein products in different colors and visualize the production of each type of protein using advanced microscopy. Each protein was labeled using a specific label, or tag, called the SunTag and MoonTag, which they could see through the microscope. By combining the MoonTag and the SunTag, the researchers could now see for the first time how often out-of-frame translation takes place.

Read more at Science Daily

Could climate change make Siberia more habitable?

Island in the city of Irkutsk on the Angara River, eastern Siberia, Russia.

Large parts of Asian Russia could become habitable by the late 21st century due to climate change, new research has found.

A study team from the Krasnoyarsk Federal Research Center, Russia, and the National Institute of Aerospace, USA, used current and predicted climate scenarios to examine the climate comfort of Asian Russia and work out the potential for human settlement throughout the 21st century.

They published their results today in Environmental Research Letters.

At 13 million square kilometres Asian Russia -- east of the Urals towards the Pacific -- accounts for 77 per cent of Russia's land area. Its population, however, accounts for just 27 per cent of the country's people and is concentrated along the forest-steppe in the south, with its comfortable climate and fertile soil.

"Previous human migrations have been associated with climate change. As civilisations developed technology that enabled them to adapt, humans became less reliant on the environment, particularly in terms of climate," said the study's lead author Dr Elena Parfenova, from the Krasnoyarsk Federal Research Center.

"We wanted to learn if future changes in climate may lead to the less-hospitable parts of Asian Russia becoming more habitable for humans."

For their analysis, the team used a combination of 20 general circulation models (Coupled Model Intercomparison Project Phase 5) and two CO2 Representative Concentration Pathway scenarios -- RCP 2.6 representing mild climate change and RCP 8.5 representing more extreme changes.

They applied the collective means of January and July temperatures and annual precipitation of the two scenarios to Asian Russia to find their respective effects on three climate indices that are important for human livelihood and well-being: Ecological Landscape Potential (ELP), winter severity, and permafrost coverage.

Dr Parfenova said: "We found increases in temperature of 3.4°C (RCP 2.6) to 9.1°C (RCP 8.5) in mid-winter; increases of 1.9°C (RCP 2.6) to 5.7°C (RCP 8.5) in mid-summer; and increases in precipitation of 60 mm (RCP 2.6) to 140 mm (RCP 8.5).

"Our simulations showed that under RCP8.5, by the 2080s Asian Russia would have a milder climate, with less permafrost coverage, decreasing from the contemporary 65 per cent to 40 per cent of the area by the 2080s."

The researchers also found that even under the RCP 2.6 scenario, the ELP for human sustainability would improve in more than 15 per cent of the area, which could allow for a five-fold increase in the in the capacity of the territory to sustain and become attractive to human populations.

Dr Parfenova concluded: "Asian Russia is currently extremely cold. In a future warmer climate, food security in terms of crop distribution and production capability is likely to become more favourable for people to support settlements.

"However, suitable land development depends on the authorities' social, political and economic policies. Lands with developed infrastructure and high agricultural potential would obviously be populated first.

Read more at Science Daily

Study provides new insight into origin of Canadian Rockies

Banff National Park, Canadian Rockies

The Canadian Rocky Mountains were formed when the North American continent was dragged westward during the closure of an ocean basin off the west coast and collided with a microcontinent over 100 million years ago, according to a new study by University of Alberta scientists.

The research, based on high resolution data of Earth's subsurface at the Alberta-British Columbia (BC) border, favours an interpretation different from the traditional theory of how the Canadian Rocky Mountains formed. The traditional theory, known as the accretion model, suggests that a gradual accumulation of additional matter eventually formed the Canadian Rockies -- unlike the sudden collision event proposed by this research.

"This research provides new evidence that the Canadian section of this mountain range was formed by two continents colliding," said Jeffrey Gu, professor in the Department of Physics and co-author on the study. "The proposed mechanism for mountain building may not apply to other parts of the Rocky Mountains due to highly variable boundary geometries and characteristics from north to south."

The study involved seismic data collected from a dense network of seismic stations in western Alberta and eastern BC, combined with geodynamic calculations and geological observations. The results suggest that an ocean basin off North America's west coast descended beneath the ribbon-shaped microcontinent, dragging North America westward, where it collided with the microcontinent.

"This study highlights how deep Earth images from geophysical methods can help us to understand the evolution of mountains, one of the most magnificent processes of plate tectonics observed at the Earth's surface," said Yunfeng Chen, who conducted this research during his PhD studies under the supervision of Gu. Chen received the Faculty of Science Doctoral Dissertation Award in 2018.

"There are other mountain belts around the world where a similar model may apply," said Claire Currie, associate professor of physics and co-author on the study. "Our data could be important for understanding mountain belts elsewhere, as well as building our understanding of the evolution of western North America."

Alberta and British Columbia communities supported these research efforts by hosting seismic stations on their land. This research is also supported by the Alberta Energy Regulator.

From Science Daily

Exomoons may be home to extra-terrestrial life

Artist's concept of a moon orbiting a ringed planet.

Moons orbiting planets outside our solar system could offer another clue about the pool of worlds that may be home to extra-terrestrial life, according to an astrophysicist at the University of Lincoln.

Exoplanets are planets outside our solar system and up to this point nearly 4,000 have been discovered. Only a small proportion of these are likely to be able to sustain life, existing in what is known as the habitable zone. But some planets, especially large gas giants, may harbour moons which contain liquid water.

Dr Sutton said: "These moons can be internally heated by the gravitational pull of the planet they orbit, which can lead to them having liquid water well outside the normal narrow habitable zone for planets that we are currently trying to find Earth-like planets in. I believe that if we can find them, moons offer a more promising avenue to finding extra-terrestrial life."

This interest has inspired Dr Sutton's latest research, which looked at the possibility of moons orbiting the exoplanet J1407b, analysing whether they may have caused gaps in the planet's ring system.

Because of their size and distance from Earth, exomoons are very difficult to detect. Scientists have to locate them by looking for the effect they have on objects around them, such as planetary rings.

Dr Sutton ran computer simulations to model the rings around J1407b, which are 200 times larger than those around Saturn. Gravitational forces between all particles were calculated and used to update the positions, velocities and accelerations in the computer models of the planet and its ring system. He then added a moon that orbited at various ratios outside of the rings to test whether this caused gaps to form where expected over 100 orbital periods.

Findings revealed that while the orbiting moon did have an effect on the scattering of particles along the ring edge, the expected gaps in the ring structure were unlikely to be caused by the gravitational forces of a currently unseen moon orbiting outside the rings.

From Science Daily

Danger avoidance can be genetically encoded for four generations, say biologists

C. elegans.

Princeton University researchers have discovered that learned behaviors can be inherited for multiple generations in C. elegans, transmitted from parent to progeny via eggs and sperm cells. The paper detailing this finding, by Rebecca Moore, Rachel Kaletsky and Coleen Murphy, appears in the June 13 issue of the journal Cell.

It's well known that an organism's characteristics are encoded in genes that are passed down from parent to progeny through the eggs and sperm of the germline. The inheritance of some traits is determined exclusively by whether the individual receives the dominant or recessive form of an associated gene from each parent. Other heritable traits are influenced both by genetic makeup and by factors such as nutrition, temperature or environmental stress, which can affect the expression levels of related genes. Features whose inheritance isn't driven exclusively by DNA sequence are termed "epigenetic" (the prefix "epi" means "on top of").

An organism's phenotype can change during its lifetime due to epigenetic mechanisms. For example, in the microscopic roundworm Caenorhabditis elegans, starvation or heat stress prompts animals to adapt to these conditions by varying the expression of multiple genes. At the level of the genome, these changes can be made durable by altering how tightly the DNA that encodes a gene is packed, thereby regulating its accessibility to RNA transcription machinery. Alternatively, cells can engage mechanisms that destroy or sequester protein-coding RNA transcripts. When these modifications are made in germ cells, they can be passed down to future generations in a phenomenon is known as transgenerational epigenetic inheritance. Studies have shown that C. elegans adaptations to starvation and heat stress can be inherited for several generations. Might more complex phenotypes, such as behavioral changes, also be passed down in this way?

"In their natural environment, worms come into contact with many different bacterial species. Some of these are nutritious food sources, while others will infect and kill them," said Murphy, a professor in Princeton's Department of Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics. "Worms are initially attracted to the pathogen Pseudomonas aeruginosa, but upon infection, they learn to avoid it. Otherwise they will die within a few days."

Moore and her colleagues investigated whether C. elegans can convey this learned avoidance behavior to their progeny. They found that when mother worms learned to avoid pathogenic P. aeruginosa, their progeny also knew to avoid the bacteria. The natural attraction of offspring to Pseudomonas was overridden even though they had never previously encountered the pathogen. Remarkably, this inherited aversive behavior lasted for four generations, but in the fifth generation the worms were once again attracted to Pseudomonas. In another surprise, the researchers observed that inheritance of learned avoidance was not universal for all pathogenic bacteria; although mother worms could learn to avoid the pathogenic bacterium Serratia marcescens, which is less abundant than Pseudomonas in C. elegans' environment, this aversion was not passed down to offspring. Intrigued, the researchers set out to explore what controls transmission of P. aeruginosa avoidance behavior across generations.

The authors showed that C. elegans mothers must actually become ill from ingesting P. aeruginosa in order to transmit avoidance to future generations; exposure to odors emitted by the pathogen wasn't sufficient to provoke avoidance. Nonetheless, neuronal sensory pathways are important for inherited avoidance, because avoidance behavior in both mothers and their progeny was associated with upregulated expression of several neuronally-associated genes. Among these, elevated expression of the TGF-β ligand daf -7 in mothers was needed for progeny to inherit pathogen aversion. Moore and her colleagues found that daf-7 expression in a certain type of sensory neuron, ASI neurons, correlated strongly with inherited avoidance behavior.

"The process of inheriting this learned avoidance [also] requires the activity of small RNAs called piRNA," Murphy said. piRNAs have been implicated in other transgenerational epigenetic inheritance pathways in C. elegans, where they're thought to silence gene expression and indirectly regulate DNA packing. The researchers found that the piRNA-associated protein PRG-1, while not necessary for C. elegans mothers to learn avoidance of P. aeruginosa, was required for increased daf-7 expression in progeny, and for their inherited avoidance behavior. Whether piRNAs and PRG-1 operate primarily in the mother, the progeny, or both to promote inheritance of avoidance behavior isn't yet known.

Importantly, expression of daf-7 remains elevated in the ASI neurons of progeny for four generations, then returns to basal levels in the fifth generation, which is when the inherited avoidance behavior also disappears. As Murphy points out, although inheritance of avoidance behavior provides a survival advantage, it's also necessary for this avoidance behavior to eventually go away. That's because P. aeruginosa is only pathogenic at high temperatures; at lower temperatures, it's increasingly safe to eat, as are other Pseudomonas species. If the pathogenic threat is temporary, the eventual lapsing of inherited avoidance allows future generations to return to feasting on nutritious Pseudomonas.

Read more at Science Daily

New findings on Earth's magnetic field

Inside the Earth concept illustration.

The huge magnetic field which surrounds the Earth, protecting it from radiation and charged particles from space -- and which many animals even use for orientation purposes -- is changing constantly, which is why geoscientists keep it constantly under surveillance. The old well-known sources of the Earth's magnetic field are the Earth's core -- down to 6,000 kilometres deep down inside the Earth -- and the Earth's crust: in other words, the ground we stand on. The Earth's mantle, on the other hand, stretching from 35 to 2,900 kilometres below the Earth's surface, has so far largely been regarded as "magnetically dead." An international team of researchers from Germany, France, Denmark and the USA has now demonstrated that a form of iron oxide, hematite, can retain its magnetic properties even deep down in the Earth's mantle. This occurs in relatively cold tectonic plates, called slabs, which are found especially beneath the western Pacific Ocean.

"This new knowledge about the Earth's mantle and the strongly magnetic region in the western Pacific could throw new light on any observations of the Earth's magnetic field," says mineral physicist and first author Dr. Ilya Kupenko from the University of Münster (Germany). The new findings could, for example, be relevant for any future observations of the magnetic anomalies on the Earth and on other planets such as Mars. This is because Mars has no longer a dynamo and thus no source enabling a strong magnetic field originating from the core to be built up such as that on Earth. It might, therefore, now be worth taking a more detailed look on its mantle. The study has been published in the "Nature" journal.

Background and methods used:

Deep in the metallic core of the Earth, it is liquid iron alloy that triggers electrical flows. In the outermost crust of the Earth, rocks cause magnetic signal. In the deeper regions of the Earth's interior, however, it was believed that the rocks lose their magnetic properties due to the very high temperatures and pressures.

The researchers now took a closer look at the main potential sources for magnetism in the Earth's mantle: iron oxides, which have a high critical temperature -- i.e. the temperature above which material is no longer magnetic. In the Earth's mantle, iron oxides occur in slabs that are buried from the Earth's crust further into the mantle, as a result of tectonic shifts, a process called subduction. They can reach a depth within the Earth's interior of between 410 and 660 kilometres -- the so-called transition zone between the upper and the lower mantle of the Earth. Previously, however, no one had succeeded in measuring the magnetic properties of the iron oxides at the extreme conditions of pressure and temperature found in this region.

Now the scientists combined two methods. Using a so-called diamond anvil cell, they squeezed micrometric-sized samples of iron oxide hematite between two diamonds, and heated them with lasers to reach pressures of up to 90 gigapascal and temperatures of over 1,000 °C (1,300 K). The researchers combined this method with so-called Mössbauer spectroscopy to probe the magnetic state of the samples by means of synchrotron radiation. This part of the study was carried out at the ESRF synchrotron facility in Grenoble, France, and this made it possible to observe the changes of the magnetic order in iron oxide.

The surprising result was that the hematite remained magnetic up to a temperature of around 925 °C (1,200 K) -- the temperature prevailing in the subducted slabs beneath the western part of Pacific Ocean at the Earth's transition zone depth. "As a result, we are able to demonstrate that the Earth's mantle is not nearly as magnetically 'dead' as has so far been assumed," says Prof. Carmen Sanchez-Valle from the Institute of Mineralogy at Münster University. "These findings might justify other conclusions relating to the Earth's entire magnetic field," she adds.

Relevance for investigations of the Earth's magnetic field and the movement of the poles

By using satellites and studying rocks, researchers observe the Earth's magnetic field, as well as the local and regional changes in magnetic strength. Background: The geomagnetic poles of the Earth -- not to be confused with the geographic poles -- are constantly moving. As a result of this movement they have actually changed positions with each other every 200,000 to 300,000 years in the recent history of the Earth. The last poles flip happened 780,000 years ago, and last decades scientists report acceleration in the movement of the Earth magnetic poles. Flip of magnetic poles would have profound effect on modern human civilisation. Factors which control movements and flip of the magnetic poles, as well as directions they follow during overturn are not understood yet.

One of the poles' routes observed during the flips runs over the western Pacific, corresponding very noticeably to the proposed electromagnetic sources in the Earth's mantle. The researchers are therefore considering the possibility that the magnetic fields observed in the Pacific with the aid of rock records do not represent the migration route of the poles measured on the Earth's surface, but originate from the hitherto unknown electromagnetic source of hematite-containing rocks in the Earth's mantle beneath the West Pacific.

Read more at Science Daily

New global warming model highlights strong impact of social learning

A new climate modeling approach suggests that social processes strongly affect global warming predictions, and mitigation efforts should account for this influence. Thomas Bury of the Universities of Waterloo and Guelph, Canada, and colleagues present these findings in PLOS Computational Biology.

Human behavior influences a wide range of complex systems, including ecosystems, social networks, and the climate. Moreover, these systems impact human behavior, creating a feedback loop. Human behavior is a driver of climate change, but climate models often neglect how climate change in turn affects human behavior.

In an effort to improve climate change predictions, Bury and colleagues developed a mathematical model that captures key features of social and climate systems, while also incorporating how climate change and mitigation efforts impact human behavior. The researchers then used the model to investigate how human behavior might influence climate change dynamics.

Their analysis suggests that the rate at which people learn about climate mitigation strategies via social interactions, such as hearing that a friend bought a hybrid car, strongly influences climate outcomes. Social learning takes time, so plausible values of this rate alone could raise warming predictions by over 1 degree Celsius.

On the contrary, the model suggests that social norms do not protect against rising temperatures. They initially act against adoption of mitigation behaviors, even when such efforts are strongly justified by rising temperatures, and they do not significantly speed the transition to an emission-free world once mitigation becomes the norm.

The researchers also ran the model with different parameters to explore how mitigation efforts could be optimized. "Our socio-climate model indicates that an increase in social media and other campaigns to raise awareness, such as climate marches and international reports, should ideally be followed by governmental and other incentives to reduce carbon emissions," Bury says.

Senior author, Madhur Anand states that "There are pathways for humans to mitigate climate change, but processes driving behavior and norms at the individual and societal level will be essential to all of them, and our longstanding work on coupled human-environment systems applied here to climate change is providing direction in this regard."

The researchers note that their model is relatively simple and future research efforts should assess whether models of a higher complexity produce different forecasts. Collaborating author, Chris Bauch says "Mathematical models that capture social dynamics and their interaction with climate trends will become increasingly used in climate research." Models that accurately capture the interplay between population behavior and climate change could improve predictions and inform mitigation strategies.

From Science Daily

Glacial sediments greased the gears of plate tectonics

Grand Canyon.

Earth's outer layer is composed of giant plates that grind together, sliding past or dipping beneath one another, giving rise to earthquakes and volcanoes. These plates also separate at undersea mountain ridges, where molten rock spreads from the centers of ocean basins.

But this was not always the case. Early in Earth's history, the planet was covered by a single shell dotted with volcanoes -- much like the surface of Venus today. As Earth cooled, this shell began to fold and crack, eventually creating Earth's system of plate tectonics.

According to new research, the transition to plate tectonics started with the help of lubricating sediments, scraped by glaciers from the slopes of Earth's first continents. As these sediments collected along the world's young coastlines, they helped to accelerate the motion of newly formed subduction faults, where a thinner oceanic plate dips beneath a thicker continental plate.

The new study, published June 6, 2019 in the journal Nature, is the first to suggest a role for sediments in the emergence and evolution of global plate tectonics. Michael Brown, a professor of geology at the University of Maryland, co-authored the research paper with Stephan Sobolev, a professor of geodynamics at the GFZ German Research Centre for Geosciences in Potsdam.

The findings suggest that sediment lubrication controls the rate at which Earth's crust grinds and churns. Sobolev and Brown found that two major periods of worldwide glaciation, which resulted in massive deposits of glacier-scrubbed sediment, each likely caused a subsequent boost in the global rate of plate tectonics.

The most recent such episode followed the "snowball Earth" that ended sometime around 635 million years ago, resulting in Earth's modern plate tectonic system.

"Earth hasn't always had plate tectonics and it hasn't always progressed at the same pace," Brown said. "It's gone through at least two periods of acceleration. There's evidence to suggest that tectonics also slowed to a relative crawl for nearly a billion years. In each case, we found a connection with the relative abundance -- or scarcity -- of glacial sediments."

Just as a machine needs grease to keep its parts moving freely, plate tectonics operates more efficiently with lubrication. While it may be hard to confuse the gritty consistency of clay, silt, sand and gravel with a slippery grease, the effect is largely the same at the continental scale, in the ocean trenches where tectonic plates meet.

"The same dynamic exists when drilling Earth's crust. You have to use mud -- a very fine clay mixed with water or oil -- because water or oil alone won't work as well," Brown said. "The mud particles help reduce friction on the drill bit. Our results suggest that tectonic plates also need this type of lubrication to keep moving."

Previous research on the western coast of South America was the first to identify a relationship between sediment lubrication and friction along a subduction fault. Off the coast of northern Chile, a relative lack of sediment in the fault trench creates high friction as the oceanic Nazca plate dips beneath the continental South America plate. This friction helped to push the highest peaks of the central Andes Mountains skyward as the continental plate squashed and deformed.

In contrast, further south there is a higher sediment load in the trench, resulting in less friction. This caused less deformation of the continental plate and, consequently, created smaller mountain peaks. But these findings were limited to one geographic area.

For their study, Sobolev and Brown used a geodynamic model of plate tectonics to simulate the effect of sediment lubrication on the rate of subduction. To verify their hypothesis, they checked for correlations between known periods of widespread glaciation and previously published data that indicate the presence of continental sediment in the oceans and trenches. For this step, Sobolev and Brown relied on two primary lines of evidence: the chemical signature of the influence of continental sediments on the chemistry of the oceans and indicators of sediment contamination in subduction-related volcanoes, much like those that make up today's "ring of fire" around the Pacific Ocean.

According to Sobolev and Brown's analysis, plate tectonics likely emerged on Earth between 3 and 2.5 billion years ago, around the time when Earth's first continents began to form. This time frame also coincides with the planet's first continental glaciation.

A major boost in plate tectonics then occurred between 2.2 to 1.8 billion years ago, following another global ice age that scrubbed massive amounts of sediments into the fault trenches at the edges of the continents.

The next billion years, from 1.75 billion to 750 million years ago, saw a global reduction in the rate of plate tectonics. This stage of Earth's history was so sedate, comparatively speaking, that it earned the nickname "the boring billion" among geologists.

Read more at Science Daily

Hoard of the rings: Unusual rings are a novel type of Bronze Age cereal-based product

Wheat

Strange ring-shaped objects in a Bronze Age hillfort site represent a unique form of cereal-based product, according to a study published June 5, 2019 in the open-access journal PLOS ONE by Andreas G. Heiss of the Austrian Archaeological Institute (ÖAW-ÖAI) and colleagues.

Agricultural practices are well known in the archaeological record, but less understood is how food was produced and prepared by ancient cultures. In this study, Heiss and colleagues describe unusual cereal-derived rings from the Late Bronze Age site of Stillfried an der March in Austria. Between 900-1000BCE, this settlement was a center of grain storage, and archaeological materials have been excavated from around 100 pits interpreted as grain storage pits.

This study focuses on the fragmentary charred remains of three ring-shaped objects, each around three centimeters across. Analysis confirms that they are made of dough derived from barley and wheat. The authors were able to determine that the dough was made from fine quality flour and then most likely shaped from wet cereal mixture and dried without baking. This time-consuming preparation process differs from other foods known from the site, leading the authors to suggest that these cereal rings may not have been made for eating.

These rings also bear a striking resemblance to clay rings interpreted as loom weights found in the same pit and may have been designed to imitate them. The unusual context of these cereal rings and the care that went into making them, suggests they may have been created for some unknown ritual purpose, thus expanding the list of ways the cultures of this time period are known to have used cereal products. Since such remains are scarce, the authors suggest that future studies sample more intensely for similar plant-based products that may typically be overlooked.

Heiss adds: "Prehistoric bakers produced so much more than just bread. A Late Bronze Age "odd" deposit from central European site Stillfried (Austria) yielded dough rings comparable to Italian tarallini, discovered together with a larger number of clay loom weights, likewise ring-shaped -- resulting in new insights into the material culture of food, symbolism, and diversity of dishes."

From Science Daily

Bees can link symbols to numbers, study finds

Bees on honeycomb.

We've learned bees can understand zero and do basic math, and now a new study shows their tiny insect brains may be capable of connecting symbols to numbers.

Researchers have trained honeybees to match a character to a specific quantity, revealing they are able to learn that a symbol represents a numerical amount.

It's a finding that sheds new light on how numerical abilities may have evolved over millennia and even opens new possibilities for communication between humans and other species.

The discovery, from the same Australian-French team that found bees get the concept of zero and can do simple arithmetic, also points to new approaches for bio-inspired computing that can replicate the brain's highly efficient approach to processing.

The RMIT University-led study is published in the Proceedings of the Royal Society B.

Associate Professor Adrian Dyer said while humans were the only species to have developed systems to represent numbers, like the Arabic numerals we use each day, the research shows the concept can be grasped by brains far smaller than ours.

"We take it for granted once we've learned our numbers as children, but being able to recognise what '4' represents actually requires a sophisticated level of cognitive ability," Dyer said.

"Studies have shown primates and birds can also learn to link symbols with numbers, but this is the first time we've seen this in insects.

"Humans have over 86 billion neurons in our brains, bees have less than a million, and we're separated by over 600 million years of evolution.

"But if bees have the capacity to learn something as complex as a human-made symbolic language, this opens up exciting new pathways for future communication across species."

Mini brains, maximum potential: what the bees learned

Studies have shown that a number of non-human animals have been able to learn that symbols can represent numbers, including pigeons, parrots, chimpanzees and monkeys.

Some of their feats have been impressive -- chimpanzees were taught Arabic numbers and could order them correctly, while an African grey parrot called Alex was able to learn the names of numbers and could sum the quantities.

The new study for the first time shows that this complex cognitive capacity is not restricted to vertebrates.

The bee experiment was conducted by Dr Scarlett Howard, formerly a PhD researcher in the Bio Inspired Digital Sensing-Lab (BIDS-Lab) at RMIT and now a fellow at the Research Center on Animal Cognition, University of Toulouse III -- Paul Sabatier, CNRS.

In a Y-shaped maze, individual bees were trained to correctly match a character with a number of elements.

They were then tested on whether they could apply their new knowledge to match the character to various elements of the same quantity (in the same way that '2' can represent two bananas, two trees or two hats).

A second group was trained in the opposite approach, matching a number of elements with a character.

While both could grasp their specific training, the different groups were unable to reverse the association and work out what to do when tested with the opposite (character-to-number or number-to-character).

"This suggests that number processing and understanding of symbols happens in different regions in bee brains, similar to the way separate processing happens in the human brain," Howard said.

"Our results show honeybees are not at the same level as the animals that have been able to learn symbols as numbers and perform complex tasks.

"But the results have implications for what we know about learning, reversing tasks, and how the brain creates connections and associations between concepts.

"Discovering how such complex numerical skills can be grasped by miniature brains will help us understand how mathematical and cultural thinking evolved in humans, and possibly, other animals."

Studying insect brains offers intriguing possibilities for the future design of highly efficient computing systems, Dyer said.

"When we're looking for solutions to complex problems, we often find that nature has already done the job far more elegantly and efficiently," he said.

Read more at Science Daily

First-ever spider glue genes sequenced, paving way to next biomaterials breakthrough

Spider building web.

UMBC postdoctoral fellow Sarah Stellwagen and co-author Rebecca Renberg at the Army Research Lab have published the first-ever complete sequences of two genes that allow spiders to produce glue -- a sticky, modified version of spider silk that keeps a spider's prey stuck in its web. The findings appeared in Genes, Genomes, Genetics.

The innovative method they employed could pave the way for others to sequence more silk and glue genes, which are challenging to sequence because of their length and repetitive structure. Better understanding of these genes could move scientists closer to the next big advance in biomaterials.

Sticky solutions

Spider silk is what spider webs are made of, and it's been touted for years as the next big thing in biomaterials because of its unusual tensile strength combined with its flexibility. There are more than 45,000 known species of spiders, each of which makes between one and seven types of silk. However, despite many partial sequences, less is known about the full genetic structure of spider silk: Only about 20 complete genes have been sequenced. "Twenty pales in comparison to what's out there," Stellwagen says.

Plus, spider silk has proven tough to produce in large amounts. Spiders convert liquid blobs of silk into solid, spindly fibers in a complex process inside their bodies. Scientists can make the liquid, but "we can't replicate the process of going from liquid to solid on a large industrial scale," Stellwagen says.

Spider glue, however, is a liquid both inside and outside the spider. While the glue "does have its own challenges," Stellwagen says, that difference might make spider glue easier to produce in a lab than silk.

Stellwagen sees great potential for spider glue applications as organic pest control. After all, she says, "This stuff evolved to capture insect prey."

For example, farmers could spray the glue along a barn wall to protect their livestock from insects that bite or cause disease, and then could rinse it off without worrying about polluting waterways with dangerous pesticides. They could use glue similarly to protect crops from pests. It could also be applied in areas where mosquito-borne illnesses are prevalent. "It could also just be fun to play with," Stellwagen says.

A "behemoth of a gene"

Before Stellwagen and Renberg's work, which was funded by the Army Research Lab, the longest silk gene sequenced was about 20,000 base pairs. When she started this project, Stellwagen was expecting to sequence the glue genes quickly and then move on, building on what she learned from the sequence. Instead, it took her and Renberg two years just to finalize the sequence.

"It ended up being this behemoth of a gene that's more than twice as large as the previous largest silk gene," Stellwagen says. It was a long, hard road to the day she found Renberg in the lab and said, "I think our gene is 42,000 bases long. I think we finished it." And in the end, it was taking a risk on a cutting-edge technique that finally yielded the complete sequence.

Not only was the gene exceptionally long, but, like spider silk genes, it has many repetitions of the same sequence of bases -- A, T, G, and C -- in the middle. Modern sequencing techniques (called "next generation sequencing") work by generating DNA sequences for all of an organism's genes, but chopped up in little pieces. Then, like solving a puzzle, scientists must match up the overlapping ends of the short sections to determine the entire sequence.

However, if your gene is repetitive, you need a single sequence, or "read," that extends from before the repetitious region to beyond the end to know how many repetitions there are. If your repetitious section is long, as it is in the glue genes Stellwagen and Renberg studied, the chance that you would get the read you need with next-generation methods is slim.

Fortunately, "third-generation" sequencing techniques are now available. Third-generation sequencing produces longer reads, but fewer of them. Only by repeating the experiment several times do you have a chance of getting the reads you need to determine the number of repetitions and finally define the gene's entire sequence. "It's challenging," says Stellwagen. "You're picking a needle from a haystack."

But it worked. After two years of going to the computer and not seeing positive results, Stellwagen and Renberg finally got the reads they needed to define the entire gene's sequence.

Stellwagen is already thinking ahead to what comes next. "Now that we have a protocol for discovering full-length silk genes, what do silks from other species look like?" she asks.

Read more at Science Daily

Is there a limit to human endurance? Science says yes

Marathon runners

From the Ironman triathlon to the Tour de France, some competitions test the limits of even the toughest endurance athletes. Now, a new study of energy expenditure during some of the world's longest, most grueling sporting events suggests that no matter what the activity, everyone hits the same metabolic limit -- a maximum possible level of exertion that humans can sustain in the long term.

When it comes to physical activities lasting days, weeks and months, the researchers found, humans can only burn calories at 2.5 times their resting metabolic rate.

Not even the world's fastest ultra-marathoners managed to surpass that limit, the researchers found.

"This defines the realm of what's possible for humans," said study co-author Herman Pontzer, an associate professor of evolutionary anthropology at Duke University.

Beyond the threshold of 2.5 times a person's resting metabolic rate, researchers found, the body starts to break down its own tissues to make up for the caloric deficit.

One explanation for this limit may be the digestive tract's ability to break down food, said team leaders Pontzer and John Speakman of Scotland's University of Aberdeen and the Chinese Academy of Sciences.

In other words, eating more won't necessarily help someone make Iditarod history. "There's just a limit to how many calories our guts can effectively absorb per day," Pontzer said.

The results will appear online June 5 in the journal Science Advances.

For the study, the team measured daily calories burned by a group of athletes who ran six marathons a week for five months as part of the 2015 Race Across the USA, a 3,000-mile race from California to Washington, D.C. The team also considered other feats of human endurance, including punishing 100-mile trail races and pregnancy.

When they plotted the data over time, they found an L-shaped curve. The athletes' energy expenditure started out relatively high, but inevitably plunged and flattened out at 2.5 times their basal metabolic rate for the remainder of the event.

Co-author Caitlin Thurber analyzed urine samples collected during the first and final legs of Race Across the USA. After 20 weeks of running back-to-back marathons, the athletes were burning 600 fewer calories a day than expected based on their mileage. The findings suggest that the body can "downshift" its metabolism to help stay within sustainable levels.

"It's a great example of constrained energy expenditure, where the body is limited in its ability to maintain extremely high levels of energy expenditure for an extended period of time," Thurber said.

"You can sprint for 100 meters, but you can jog for miles, right? That's also true here," Pontzer said.

All the endurance events followed the same L-shaped curve, whether the athletes were hauling 500-pound sleds across Antarctica for days in sub-freezing temperatures, or cycling the Tour de France in summer. That finding challenges the idea, proposed by previous researchers, that human endurance is linked to the ability to regulate body temperature.

One limiting factor for endurance events, researchers found, lies in the digestive process -- the body's ability to process food and absorb calories and nutrients to fuel bodily processes.

Interestingly, the maximum sustainable energy expenditure found among endurance athletes was only slightly higher than the metabolic rates women sustain during pregnancy. This suggests that the same physiological limits that keep, say, Ironman triathletes from shattering speed records may also constrain other aspects of life too, such as how big babies can grow in the womb.

As far as the researchers know, no one's ever sustained levels beyond this limit. "So I guess it's a challenge to elite endurance athletes," Pontzer said. "Science works when you're proven wrong. Maybe someone will break through that ceiling some day and show us what we're missing."

Read more at Science Daily

Cool, nebulous ring around Milky Way's supermassive black hole

ALMA image of the disk of cool hydrogen gas flowing around the supermassive black hole at the center of our galaxy. The colors represent the motion of the gas relative to Earth: the red portion is moving away, so the radio waves detected by ALMA are slightly stretched, or shifted, to the 'redder' portion of the spectrum; the blue color represents gas moving toward Earth, so the radio waves are slightly scrunched, or shifted, to the 'bluer' portion of the spectrum. Crosshairs indicate location of black hole.

New ALMA observations reveal a never-before-seen disk of cool, interstellar gas wrapped around the supermassive black hole at the center of the Milky Way. This nebulous disk gives astronomers new insights into the workings of accretion: the siphoning of material onto the surface of a black hole. The results are published in the journal Nature.

Through decades of study, astronomers have developed a clearer picture of the chaotic and crowded neighborhood surrounding the supermassive black hole at the center of the Milky Way. Our galactic center is approximately 26,000 light-years from Earth and the supermassive black hole there, known as Sagittarius A* (A "star"), is 4 million times the mass of our Sun.

We now know that this region is brimming with roving stars, interstellar dust clouds, and a large reservoir of both phenomenally hot and comparatively colder gases. These gases are expected to orbit the black hole in a vast accretion disk that extends a few tenths of a light-year from the black hole's event horizon.

Until now, however, astronomers have been able to image only the tenuous, hot portion of this flow of accreting gas, which forms a roughly spherical flow and showed no obvious rotation. Its temperature is estimated to be a blistering 10 million degrees Celsius (18 million degrees Fahrenheit), or about two-thirds the temperature found at the core of our Sun. At this temperature, the gas glows fiercely in X-ray light, allowing it to be studied by space-based X-ray telescopes, down to scale of about a tenth of a light-year from the black hole.

In addition to this hot, glowing gas, previous observations with millimeter-wavelength telescopes have detected a vast store of comparatively cooler hydrogen gas (about 10 thousand degrees Celsius, or 18,000 degrees Fahrenheit) within a few light-years of the black hole. The contribution of this cooler gas to the accretion flow onto the black hole was previously unknown.

Although our galactic center black hole is relatively quiet, the radiation around it is strong enough to cause hydrogen atoms to continually lose and recombine with their electrons. This recombination produces a distinctive millimeter-wavelength signal, which is capable of reaching Earth with very little losses along the way.

With its remarkable sensitivity and powerful ability to see fine details, the Atacama Large Millimeter/submillimeter Array (ALMA) was able to detect this faint radio signal and produce the first-ever image of the cooler gas disk at only about a hundredth of a light-year away (or about 1000 times the distance from the Earth to the Sun) from the supermassive black hole. These observations enabled the astronomers both to map the location and trace the motion of this gas. The researchers estimate that the amount of hydrogen in this cool disk is about one tenth the mass of Jupiter, or one ten-thousandth of the mass of the Sun.

By mapping the shifts in wavelengths of this radio light due to the Doppler effect (light from objects moving toward the Earth is slightly shifted to the "bluer" portion of the spectrum while light from objects moving away is slightly shifted to the "redder" portion), the astronomers could clearly see that the gas is rotating around the black hole. This information will provide new insights into the ways that black holes devour matter and the complex interplay between a black hole and its galactic neighborhood.

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Details of first historically recorded plague pandemic revealed by ancient genomes

Illustration of plague bacteria Yersinia pestis.

An international team of researchers has analyzed human remains from 21 archaeological sites to learn more about the impact and evolution of the plague-causing bacterium Yersinia pestis during the first plague pandemic (541-750 AD). In a study published in PNAS, the researchers reconstructed 8 plague genomes from Britain, Germany, France and Spain and uncovered a previously unknown level of diversity in Y. pestis strains. Additionally, they found the first direct genetic evidence of the Justinianic Plague in the British Isles.

The Justinianic Plague began in 541 in the Eastern Roman Empire, ruled at the time by the Emperor Justinian I, and recurrent outbreaks ravaged Europe and the Mediterranean basin for approximately 200 years. Contemporaneous records describe the extent of the pandemic, estimated to have wiped out up to 25% of the population of the Roman world at the time. Recent genetic studies revealed that the bacterium Yersinia pestis was the cause of the disease, but how it had spread and how the strains that appeared over the course of the pandemic were related to each other was previously unknown.

In the current study, an international team of researchers led by the Max Planck Institute for the Science of Human History analyzed human remains from 21 sites with multiple burials in Austria, Britain, Germany, France and Spain. They were able to reconstruct 8 new Y. pestis genomes, allowing them to compare these strains to previously published ancient and modern genomes. Additionally, the team found the earliest genetic evidence of plague in Britain, from the Anglo-Saxon site of Edix Hill. By using a combination of archaeological dating and the position of this strain of Y. pestis in its evolutionary tree, the researchers concluded that the genome is likely related to an ambiguously described pestilence in the British Isles in 544 AD.

High diversity of Y. pestis strains during the First Pandemic

The researchers found that there was a previously unknown diversity of strains of Y. pestis circulating in Europe between the 6th and 8th centuries AD. The 8 new genomes came from Britain, France, Germany and Spain. "The retrieval of genomes that span a wide geographic and temporal scope gives us the opportunity to assess Y. pestis' microdiversity present in Europe during the First Pandemic," explains co-first author Marcel Keller, PhD student at the Max Planck Institute for the Science of Human History, now working at the University of Tartu. The newly discovered genomes revealed that there were multiple, closely related strains of Y. pestis circulating during the 200 years of the First Pandemic, some possibly at the same times and in the same regions.

Despite the greatly increased number of genomes now available, the researchers were not able to clarify the onset of the Justinianic Plague. "The lineage likely emerged in Central Asia several hundred years before the First Pandemic, but we interpret the current data as insufficient to resolve the origin of the Justinianic Plague as a human epidemic, before it was first reported in Egypt in 541 AD. However, the fact that all genomes belong to the same lineage is indicative of a persistence of plague in Europe or the Mediterranean basin over this time period, instead of multiple reintroductions."

Possible evidence of convergent evolution in strains from two independent historical pandemics

Another interesting finding of the study was that plague genomes appearing towards the end of the First Pandemic showed a big deletion in their genetic code that included two virulence factors. Plague genomes from the late stages of the Second Pandemic some 800-1000 years later show a similar deletion covering the same region of the genomes. "This is a possible example of convergent evolution, meaning that these Y. pestis strains independently evolved similar characteristics. Such changes may reflect an adaptation to a distinct ecological niche in Western Eurasia where the plague was circulating during both pandemics," explains co-first author Maria Spyrou of the Max Planck Institute for the Science of Human History.

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Ear-generated Doppler shifts in bat biosonar

Greater horseshoe bat.

Anybody who has been passed by an ambulance at high speed has experienced a physical effect called the Doppler shift: As the ambulance moves toward the listener, its motion compresses the siren's sound waves and raises the sound pitch. As the ambulance moves away from the listener, the sound waves get dilated and the pitch is lowered. A listener wearing a blindfold could use this Doppler shift pattern to track the motion of the ambulance.

In a paper published by the Proceedings of the National Academy of Sciences, the authors, Rolf Mueller, professor of mechanical engineering in the College of Engineering, and his doctoral student, Xiaoyan Yin, demonstrate that the ears of bats come with a "built-in ambulance" that creates the same physical effect. Yin and Mueller think the study of ear-generated Doppler shifts in bat biosonar could give rise to new sensory principles that could enable small, yet powerful sensors. An example of this type of sensor would be for drones that can operate in dense foliage or autonomous underwater vehicles navigating near complex underwater structures.

"The animals move their ears fast enough so that sound waves that impinge on the ears are transformed by the motion of the ear surfaces and shifted to higher or lower frequencies," said Mueller. "In fact, the bat species studied (horseshoe bats and Old World Roundleaf bats) can move their ears so fast that Doppler shifts of around 350 Hz can be created. This is about seven times larger than the smallest Doppler shift the animals haven been shown to be able to detect."

Doppler shifts have long been known to play an important role in the biosonar system of bats such as the species studied by Mueller and Yin. The bats have the enviable ability to hunt in very dense vegetation, but to accomplish this, they have to solve the problem of how to distinguish a moth, their preferred prey, from hundreds of leaves that surround it.

"The solution these two types of bats have come up with has been to tune in on the Doppler shifts that are produced by the wing beat motion of their prey," Mueller explained. "These 'good Doppler shifts' serve as a unique identifying feature that sets prey apart from static distractors, such as leaves in foliage."

Researchers became aware early on that the bats' own flight motion also produces Doppler shifts that would interfere with the perception of the prey-induced Doppler shifts. In the late 1960s a solution to this conundrum was discovered when it was found that horseshoe bats decrease their emission frequency by an amount that is carefully controlled to exactly eliminate any of the "bad Doppler shifts" caused by the bats' flight velocity.

"Since these groundbreaking discoveries, the general belief in the scientific community has been that the role of Doppler shifts in the biosonar systems of these animals has been completely understood," said Mueller. "Doppler shifts due to prey motions are 'good Doppler shifts' that the animals' entire hearing system is optimized to detect, whereas Doppler shifts due to the bats' own flight motion are 'bad Doppler shifts' that the animals eliminate through feedback control of their emission."

While Mueller and Yin found speculation in the literature of the early 1960s that bats may be producing Doppler shifts with their own ear motions, the idea was never followed up with experimental work.

The work conducted by Mueller and Yin has measured the motion of the ear surfaces carefully using stereo-vision based on high-speed video cameras, and the authors were able to predict how fast surfaces move in different portions of the ear. They also estimated the angle between the directions of the ear motions and the direction the bat has its biosonar pointed in and found that motion speeds and directions were aligned to maximize the Doppler shifts produced.

To show that Doppler-shifted signals entered the ear canal of the biomimetic pinna and would be accessible to bats, the researchers built a flexible silicone replicate of a bat ear that could be made to execute fast motions by pulling on an attached string.

The final piece in the research has been to find possible uses for the ear-generated Doppler shifts.

Read more at Science Daily

Solving the sun's super-heating mystery with Parker Solar Probe

Sun surface illustration.

It's one of the greatest and longest-running mysteries surrounding, quite literally, our sun -- why is its outer atmosphere hotter than its fiery surface?

University of Michigan researchers believe they have the answer, and hope to prove it with help from NASA's Parker Solar Probe.

In roughly two years, the probe will be the first human-made craft to enter the zone surrounding the sun where heating looks fundamentally different that what has previously been seen in space. This will allow them to test their theory that the heating is due to small magnetic waves traveling back and forth within the zone.

Solving the riddle would allow scientists to better understand and predict solar weather, which can pose serious threats to Earth's power grid. And step one is determining where the heating of the sun's outer atmosphere begins and ends -- a puzzle with no shortage of theories.

"Whatever the physics is behind this superheating, it's a puzzle that has been staring us in the eye for 500 years," said Justin Kasper, a U-M professor of climate and space sciences and a principal investigator for the Parker mission. "In just two more years, Parker Solar Probe will finally reveal the answer."

The U-M theory, and how the team will use Parker to test it, is laid out in a paper published June 4 in The Astrophysical Journal Letters.

In this "zone of preferential heating" above the sun's surface, temperatures rise overall. More bizarre still, individual elements are heated to different temperatures, or preferentially. Some heavier ions are superheated until they're 10 times hotter than the hydrogen that is everywhere in this area -- hotter than the core of the sun.

Such high temperatures cause the solar atmosphere to swell to many times the diameter of the sun and they're the reason we see the extended corona during solar eclipses. In that sense, Kasper says, the coronal heating mystery has been visible to astronomers for more than a half millenium, even if the high temperatures were only appreciated within the last century.

This same zone features hydromagnetic "Alfvén waves" moving back and forth between its outermost edge and the sun's surface. At the outermost edge, called the Alfvén point, the solar wind moves faster than the Alfvén speed, and the waves can no longer travel back to the sun.

"When you're below the Alfvén point, you're in this soup of waves," Kasper said. "Charged particles are deflected and accelerated by waves coming from all directions."

In trying to estimate how far from the sun's surface this preferential heating stops, U-M's team examined decades of observations of the solar wind by NASA's Wind spacecraft.

They looked at how much of helium's increased temperature close to the sun was washed out by collisions between ions in the solar wind as they traveled out to Earth. Watching the helium temperature decay allowed them to measure the distance to the outer edge of the zone.

"We take all of the data and treat it as a stopwatch to figure out how much time had elapsed since the wind was superheated," Kasper said. "Since I know how fast that wind is moving, I can convert the information to a distance."

Those calculations put the outer edge of the superheating zone roughly 10 to 50 solar radii from the surface. It was impossible to be more definitive since some values could only be guessed at.

Initially, Kasper didn't think to compare his estimate of the zone's location with the Alfvén point, but he wanted to know if there was a physically meaningful location in space that produced the outer boundary.

After reading that the Alfvén point and other surfaces have been observed to expand and contract with solar activity, Kasper and co-author Kristopher Klein, a former U-M postdoc and new faculty at University of Arizona, reworked their analysis looking at year-to-year changes rather than considering the entire Wind Mission.

"To my shock, the outer boundary of the zone of preferential heating and the Alfvén point moved in lockstep in a totally predictable fashion despite being completely independent calculations," Kasper said. "You overplot them, and they're doing the exact same thing over time."

So does the Alfvén point mark the outer edge of the heating zone? And what exactly is changing under the Alfvén point that superheats heavy ions? We should know in the next couple of years. The Parker Solar Probe lifted off in August 2018 and had its first rendezvous with the sun in November 2018 -- already getting closer to the sun than any other human-made object.

In the coming years, Parker will get even closer with each pass until the probe falls below the Alfvén point. In their paper, Kasper and Klein predict it should enter the zone of preferential heating in 2021 as the boundary expands with increasing solar activity. Then NASA will have information direct from the source to answer all manner of long-standing questions.

"With Parker Solar Probe we will be able to definitively determine through local measurements what processes lead to the acceleration of the solar wind and the preferential heating of certain elements," Klein said. "The predictions in this paper suggest that these processes are operating below the Alfvén surface, a region close to the sun that no spacecraft has visited, meaning that these preferential heating processes have never before been directly measured."

Read more at Science Daily

New research explores the mechanics of how birds flock

Wildlife researchers have long tried to understand why birds fly in flocks and how different types of flocks work. A new study from the University of North Carolina at Chapel Hill explores the mechanics and benefits of the underlying flock structure used by four types of shorebirds. Understanding more about how these birds flock moves researchers a step closer to understanding why they flock.

The study, led by Aaron Corcoran, a postdoctoral researcher studying bat and bird flight and ecology, and biology Professor Tyson Hedrick of UNC-Chapel Hill, appears in the June 4 issue of eLife. The National Science Foundation funded the work.

In the study, the researchers focused on four types of shorebirds that vary in size: dunlin, short-billed dowitcher, American avocet and marbled godwit. Corcoran and Hedrick filmed and analyzed almost 100 hours of video footage to better understand the mechanics of shorebird flocks. They found that the birds fly in a newly defined shape the team named a compound V-formation, which they believe provides an aerodynamic advantage and predator protection.

This compound formation is a blend of two of the most common flock formations. One is a cluster formation, common with pigeons, where a large number of birds fly in a moving three-dimensional cloud with no formal structure. This structure is useful for avoiding predators. The second is a simple V-formation, commonly used by Canada Geese, where a smaller number of birds will line up in a well-defined two-dimensional V-shape.

"A flying bird creates downward-moving air immediately behind it and upward-moving air just beyond its wingspan on the left and right," Hedrick said. "Taking advantage of this upward-moving air is all about positioning, and birds in the simple-V formation and compound-V formation are positioned correctly for aerodynamic advantage."

To better understand the cluster-V formation and its mechanics, Corcoran and Hedrick recorded 18 cluster-like flocks of 100 to 1,000 birds flying over a bird sanctuary and agricultural fields during a migration stopover. The researchers measured the individual bird positions, flight speeds and even flapping frequency using three-dimensional computer reconstructions of the flocks from the video recordings.

"We thought we would find a trend in flock organization related to how large or small the different birds were," Hedrick said. "Instead we saw that regardless of size, all these birds flew in the same formation -- one that might let them get an aerodynamic benefit while flying in large groups, aiding their long-distance migration."

Birds often fly in flocks ranging from very structured V-formations to loose clusters to improve flight efficiency, navigation or for predator avoidance. However, because it is difficult to measure large flocks of moving birds, few studies have measured how birds position themselves in large flocks or how their position affects their flight speed and flapping frequency.

The four types of birds studied in this project live in similar environments, but vary greatly in size, fly at different speeds, and have been evolutionarily separate for 50 million years. The birds mostly flocked with their own species, except for a few occasions where the godwits and dowitchers flew together in a mixed flock.

Read more at Science Daily

New genes out of nothing

One key question in evolutionary biology is how novel genes arise and develop. Swedish researchers now show how new genes and functions that are advantageous to bacteria can be selected from random DNA sequences. The results are presented in the scientific journal mBio.

How do new genes and functional proteins arise and develop? This is one of the most fundamental issues in evolutionary biology. Two different types of mechanism have been proposed: (1) new genes with novel functions arise from existing genes, and (2) new genes and proteins evolve from random DNA sequences with no similarity to existing genes and proteins. In the present study, the researchers explored the latter type of mechanism: evolution of new genes and proteins from randomised DNA sequences -- de novo evolution, as it is called. It is fairly easy to understand that when a gene already exists, it can be modified and acquire a new function. But how does "nothing" turn into a function affording a small advantage that is favoured by natural selection?

The raw material for the experiment was an big library of some 500 million randomised gene sequences, from which peptide sequences with a biological function were identified. In the experiment, random gene sequences were placed on a plasmid and overexpressed. The scientists then investigated whether they could give bacteria a specific, defined property. Were they, for example, able to give the bacteria antibiotic resistance? They identified several short peptides (22-25 amino acids long) that could give the bacteria a high degree of resistance to aminoglycosides, an important class of antibiotics used for severe infections.

"When the project started, we had low expectations. We were amazed when we found peptides able to confer a resistance level 48 times higher," says Dr Michael Knopp, the study's lead author.

Through a combination of genetic and functional experiments, the scientists were able to demonstrate that the peptides cause resistance by attaching themselves to bacterial cell membranes and affecting the proton potential across the membrane. The disruption of the proton potential causes a decrease in antibiotic uptake, rendering the bacteria resistant.

"This study is important because it shows that completely random sequences of amino acids can give rise to new, advantageous functions, and that this process of de novo evolution can be studied experimentally in the laboratory," says Dan I. Andersson, Professor of Medical Bacteriology, who is chiefly responsible for the study.

From Science Daily

A treasure map to understanding the epigenetic causes of disease

DNA illustration.

More than 15 years after scientists first mapped the human genome, most diseases still cannot be predicted based on one's genes, leading researchers to explore epigenetic causes of disease. But the study of epigenetics cannot be approached the same way as genetics, so progress has been slow. Now, researchers at the USDA/ARS Children's Nutrition Research Center at Baylor College of Medicine and Texas Children's Hospital have determined a unique fraction of the genome that scientists should focus on. Their report, which provides a "treasure map" to accelerate research in epigenetics and human disease, was published in Genome Biology.

Epigenetics is a system for molecular marking of DNA -- it tells the different cells in the body which genes to turn on or off in that cell type. But the cell-specific nature of epigenetics makes it challenging to study. Whereas a blood sample can be used to 'genotype' an individual, most epigenetic marks in blood DNA provide no clues about epigenetic dysregulation in other parts of the body, such as the brain or heart.

Dr. Robert A. Waterland, professor of pediatrics -- nutrition and of molecular and human genetics at Baylor, and his team identified special regions of the genome where a blood sample can be used to infer epigenetic regulation throughout the body, allowing scientists to test for epigenetic causes of disease.

To do this, they focused on the most stable form of epigenetic regulation -- DNA methylation. This addition of methyl groups to the DNA molecule occurs in the embryonic state and can impact health for your entire life.

To identify genomic regions in which DNA methylation differs between people but is consistent across different tissues, they profiled DNA methylation throughout the genome in three tissues (thyroid, heart and brain) from each of 10 cadavers.

"Since these tissues each represent a different layer of the early embryo, we're essentially going back in time to events that occurred during early embryonic development," Waterland said. "To map DNA methylation we converted methylation information into a genetic signal, then sequenced the genomes. Our atlas required massive amounts of sequencing data -- 370 times more than were used for the first map of the human genome in 2001."

The nearly 10,000 regions the researchers mapped out, called correlated regions of systemic interindividual variation (CoRSIVs), comprise a previously unrecognized level of molecular individuality in humans.

"Recent studies are already showing that methylation at these regions is associated with a range of human diseases including obesity, cancer, autism, Alzheimer's disease and cleft palate," said Dr. Cristian Coarfa, associate professor of molecular and cell biology at Baylor and co-leader of the project

Waterland believes these findings will transform the study of epigenetics and disease, as researchers will now know where in the genome to look.

"Because epigenetic marking has the power to stably silence or stably activate genes, any disease that has a genetic basis could equally likely have an epigenetic basis," Waterland said. "There is incredible potential for us to understand disease processes from an epigenetic perspective. CoRSIVs are the entryway to that."

Read more at Science Daily

Carbon dioxide levels in atmosphere hit record high in May

Earth.

Atmospheric carbon dioxide continued its rapid rise in 2019, with the average for May peaking at 414.7 parts per million (ppm) at NOAA's Mauna Loa Atmospheric Baseline Observatory.

The measurement is the highest seasonal peak recorded in 61 years of observations on top of Hawaii's largest volcano and the seventh consecutive year of steep global increases in concentrations of carbon dioxide (CO2), according to data published today by NOAA and Scripps Institution of Oceanography. The 2019 peak value was 3.5 ppm higher than the 411.2 ppm peak in May 2018 and marks the second-highest annual jump on record.

Monthly CO2 values at Mauna Loa first breached the 400 ppm threshold in 2014.

"It's critically important to have these accurate, long-term measurements of CO2 in order to understand how quickly fossil fuel pollution is changing our climate," said Pieter Tans, senior scientist with NOAA's Global Monitoring Division. "These are measurements of the real atmosphere. They do not depend on any models, but they help us verify climate model projections, which if anything, have underestimated the rapid pace of climate change being observed."

The concentration of CO2 in the atmosphere increases every year, and the rate of increase is accelerating. The early years at Mauna Loa saw annual increases averaging about 0.7 ppm per year, increasing to about 1.6 ppm per year in the 1980s and 1.5 ppm per year in the 1990s. The growth rate rose to 2.2 ppm per year during the last decade. There is abundant and conclusive evidence that the acceleration is caused by increased emissions, Tans said.

The Mauna Loa data, together with measurements from sampling stations around the world, are collected by NOAA's Global Greenhouse Gas Reference Network and produce a foundational research dataset for international climate science.

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Oldest flaked stone tools point to the repeated invention of stone tools

Ethiopia map.

A new archaeological site discovered by an international and local team of scientists working in Ethiopia shows that the origins of stone tool production are older than 2.58 million years ago. Previously, the oldest evidence for systematic stone tool production and use was 2.58 to 2.55 million years ago.

Analysis by the researchers of early stone age sites, published this week in the Proceedings of the National Academy of Sciences, suggests that stone tools may have been invented many times in many ways before becoming an essential part of the human lineage.

The excavation site, known as Bokol Dora 1 or BD 1, is close to the 2013 discovery of the oldest fossil attributed to our genus Homo discovered at Ledi-Geraru in the Afar region of northeastern Ethiopia. The fossil, a jaw bone, dates to about 2.78 million years ago, some 200,000 years before the then oldest flaked stone tools. The Ledi-Geraru team has been working for the last five years to find out if there is a connection between the origins of our genus and the origins of systematic stone tool manufacture.

A significant step forward in this search was uncovered when Arizona State University geologist Christopher Campisano saw sharp-edged stone tools sticking out of the sediments on a steep, eroded slope.

"At first we found several artifacts lying on the surface, but we didn't know what sediments they were coming from," says Campisano. "But when I peered over the edge of a small cliff, I saw rocks sticking out from the mudstone face. I scaled up from the bottom using my rock hammer and found two nice stone tools starting to weather out."

It took several years to excavate through meters of sediments by hand before exposing an archaeological layer of animal bones and hundreds of small pieces of chipped stone representing the earliest evidence of our direct ancestors making and using stone knives. The site records a wealth of information about how and when humans began to use stone tools.

Preservation of the artifacts comes from originally being buried close to a water source.

"Looking at the sediments under a microscope, we could see that the site was exposed only for a very short time. These tools were dropped by early humans at the edge of a water source and then quickly buried. The site then stayed that way for millions of years," noted geoarchaeologist Vera Aldeias of the Interdisciplinary Center for Archaeology and Behavioral Evolution at the University of Algarve, Portugal.

Kaye Reed, who studies the site's ecology, is director of the Ledi-Geraru Research Project and a research associate with Arizona State University's Institute of Human Origins along with Campisano, notes that the animals found with these tools were similar to those found only a few kilometers away with the earliest Homo fossils.

"The early humans that made these stone tools lived in a totally different habitat than 'Lucy' did," says Reed. "Lucy" is the nickname for an older species of hominin known as Australopithecus afarensis, which was discovered at the site of Hadar, Ethiopia, about 45 kilometers southwest of the new BD 1 site. "The habitat changed from one of shrubland with occasional trees and riverine forests to open grasslands with few trees. Even the fossil giraffes were eating grass!"

In addition to dating a volcanic ash several meters below the site, project geologists analyzed the magnetic signature of the site's sediments. Over the Earth's history, its magnetic polarity has reversed at intervals that can be identified. Other earlier archaeological sites near the age of BD 1 are in "reversed" polarity sediments. The BD 1 site is in "normal" polarity sediments. The reversal from "normal" to "reversed" happened at about 2.58 million years ago, geologists knew that BD 1 was older than all the previously known sites.

The recent discovery of older hammering or "percussive" stone tools in Kenya dated to 3.3 million years ago, described as "Lomekwian," and butchered bones in Ethiopia shows the deep history of our ancestors making and using tools. However, recent discoveries of tools made by chimpanzees and monkeys have challenged "technological ape" ideas of human origins.

Archaeologists working at the BD 1 site wondered how their new stone tool discovery fit into this increasingly complex picture. What they found was that not only were these new tools the oldest artifacts yet ascribed to the "Oldowan," a technology originally named after finds from Olduvai Gorge in Tanzania, but also were distinct from tools made by chimpanzees, monkeys or even earlier human ancestors.

"We expected to see some indication of an evolution from the Lomekwian to these earliest Oldowan tools. Yet when we looked closely at the patterns, there was very little connection to what is known from older archaeological sites or to the tools modern primates are making," said Will Archer of the Max Planck Institute for Evolutionary Anthropology in Leipzig and the University of Cape Town.

The major differences appear to be the ability for our ancestors to systematically chip off smaller sharp-edged tools from larger nodules of stone. Chimpanzees and monkeys generally use tools for percussive activities, to hammer and bash food items like nuts and shellfish, which seems to have been the case with the 3.3 million year old Lomekwian tools as well.

Something changed by 2.6 million years ago, and our ancestors became more accurate and skilled at striking the edge of stones to make tools. The BD 1 artifacts captures this shift.

It appears that this shift in tool making occurred around the same time that our ancestor's teeth began to change. This can be seen in the Homo jaw from Ledi-Geraru. As our ancestors began to process food prior to eating using using stone tools, we start to see a reduction in the size of their teeth. Our technology and biology were intimately intertwined even as early as 2.6 million years ago.

The lack of clear connections with earlier stone tool technology suggests that tool use was invented multiple times in the past.

David Braun, an archaeologist with George Washington University and the lead author on the paper, noted, "Given that primate species throughout the world routinely use stone hammers to forage for new resources, it seems very possible that throughout Africa many different human ancestors found new ways of using stone artifacts to extract resources from their environment. If our hypothesis is correct then we would expect to find some type of continuity in artifact form after 2.6 million years ago, but not prior to this time period. We need to find more sites."

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Downpours of torrential rain more frequent with global warming

The frequency of downpours of heavy rain -- which can lead to flash floods, devastation, and outbreaks of waterborne disease -- has increased across the globe in the past 50 years, research led by the Global Institute for Water Security at the University of Saskatchewan (USask) has found.

The number of extreme downpours increased steadily between 1964 and 2013 -- a period when global warming also intensified, according to research published in the journal Water Resources Research.

The frequency of 'extreme precipitation events' increased in parts of Canada, most of Europe, the Midwest and northeast region of the U.S., northern Australia, western Russia and parts of China, (see maps and graphics).

"By introducing a new approach to analyzing extremes, using thousands of rain records, we reveal a clear increase in the frequency extreme rain events over the recent 50 years when global warming accelerated," said Simon Papalexiou, a hydro-climatologist in USask's College of Engineering, and an expert in hydroclimatic extremes and random processes.

Papalexiou, who led the research, added: "This upward trend is highly unlikely to be explained by natural climatic variability. The probability of this happening is less than 0.3 per cent under the model assumptions used."

The USask study of over 8,700 daily rain records from 100,000 stations monitoring rain worldwide found the frequency of torrential rain between 1964 and 2013 increased as the decades progressed.

Between 2004 and 2013, there were seven per cent more extreme bouts of heavy rain overall than expected globally. In Europe and Asia, there were 8.6 per cent more 'extreme rain events' overall, during this decade.

Global warming can lead to increased precipitation because more heat in the atmosphere leads to more atmospheric water which, in turn, leads to rain.

Torrents of rain not only lead to flooding, but can threaten public health, overwhelming sewage treatment plants and increasing microbial contaminants of water. More than half a million deaths were caused by rain-induced floods between 1980 and 2009.

Heavy rain can also cause landslides, damage crops, collapse buildings and bridges, wreck homes, and lead to chaos on roads and to transport, with huge financial losses.

Co-author Alberto Montanari, professor of hydraulic works and hydrology at the University of Bologna and president of the European Geoscience Union, said:

"Our results are in line with the assumption that the atmosphere retains more water under global warming. The fact that the frequency, rather the magnitude, of extreme precipitation is significantly increasing has relevant implications for climate adaptation. Human systems need to increase their capability to react to frequent shocks."

The researchers screened data for quality and consistency, selecting the most robust and complete records from the 100,000 stations worldwide monitoring precipitation. Regions in South America and Africa were excluded from the study, as records for the study period were not complete or robust.

Papalexiou said planning for more frequent 'extreme' rain should be a priority for governments, local authorities and emergency services.

"If global warming progresses as climate model projections predict, we had better plan strategies for dealing with frequent heavy rain right now," said Papalexiou. "Our study of records from around the globe shows that potentially devastating bouts of extreme rain are increasing decade by decade.

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In hot pursuit of dinosaurs: Tracking extinct species on ancient Earth via biogeography

Dinosaurs illustration.

One researcher at the University of Tokyo is in hot pursuit of dinosaurs, tracking extinct species around ancient Earth. Identifying the movements of extinct species from millions of years ago can provide insights into ancient migration routes, interaction between species, and the movement of continents.

"If we find fossils on different continents from closely related species, then we can guess that at some point there must have been a connection between those continents," said Tai Kubo, Ph.D., a postdoctoral researcher affiliated with the University Museum at the University of Tokyo.

A map of life -- biogeography

Previous studies in biogeography -- the geographic distribution of plants and animals -- had not considered the evolutionary relationships between ancient species. The new method that Kubo designed, called biogeographical network analysis, converts evolutionary relationships into geographical relationships.

For example, cats and dogs are more closely related to each other than to kangaroos. Therefore, a geographical barrier must have separated the ancestors of kangaroos from the ancestors of cats and dogs well before cats and dogs became separate species.

Most fossils are found in just a few hot-spot locations around the world and many ancient species with backbones (vertebrates) are known from just one fossil of that species. These limitations mean that a species' fossils cannot reveal the full area of where it was distributed around the world.

"Including evolutionary relationships allows us to make higher resolution maps for where species may have migrated," said Kubo.

The analysis used details from evolutionary studies, the location of fossil dig sites, and the age of the fossils. Computer simulations calculated the most likely scenarios for the migration of species between continents on the Cretaceous-era Earth, 145 to 66 million years ago.

North and south divide

This new analysis verified what earlier studies suggested: nonavian dinosaurs were divided into a group that lived in the Northern Hemisphere and another that lived in the Southern Hemisphere, and that those two groups could still move back and forth between Europe and Africa during the Early Cretaceous period (145 to 100 million years ago), but became isolated in the Late Cretaceous period (100 to 66 million years ago).

During the Early Cretaceous period, there were three major supercontinents: North America-Europe-Asia, South America-Africa, and Antarctica-India-Australia.

By the Late Cretaceous period, only the North America-Europe-Asia supercontinent remained. The other supercontinents had separated into the continents we know today, although they had not yet drifted to their current locations.

"During the Late Cretaceous period, high sea levels meant that Europe was a series of isolated islands. It makes sense that nonavian dinosaur species differentiated between Africa and Europe during that time," said Kubo.

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