Wednesday, January 31, 2018

Do Cells Rock Out? Is There a Healing Sound?

Can sound affect how your genes work?

Cells, the fundamental units of life, are equipped with a variety of environmental recognition systems. Aside from substances such as chemical signals, they can recognize and respond to pressure, gravity, temperature, and light. For example, the cells in your eyes reading this sentence are equipped with systems that are specialized to process light.

In a new PLOS ONE study, scientists from Kyoto University's Graduate School of Biostudies have shown that certain 'mechanosensitive' genes are suppressed when subjected to audible sound. Moreover, these effects vary depending on cell type, where some don't show any sensitivity.

"Much research has been done on these specialized cells, but nobody has looked into the cellular response to audible sound," explains Masahiro Kumeta, lead author of the study. "Sound is arguably the most important and ubiquitous environmental information we receive. So that brings up the question -- do cells recognize sound?"

Scientist from Kyoto University shown that certain 'mechanosensitive' genes are suppressed when subjected to audible sound, and these effects vary on cell type.

Credit: Kyoto University/Eiri Ono

The team conducted their experiments by exposing a variety of cells types to different sounds and performed gene expression analyses over time, focusing on genes that are known to react to physical stimuli.

"One such gene we examined helps in bone formation, and is known to be upregulated with low-intensity ultrasound pulses," continues Kumeta. "The other genes were associated with wound healing and the extracellular matrix."

Series of cells were placed in an incubator outfitted with a full-range loudspeaker. After several hours of exposure to sounds with specific frequencies, expression levels of the target genes were analyzed.

The team found that these mechanosensitive genes were suppressed by up to 40% with only one to two hours of exposure. Moreover, after the genes were suppressed, the effects remained for at least four hours.

The response was also dependent on waveforms and decibel levels. When exposing the cells to square or triangle waves, gene suppression was not as significant compared to sine waves on any tested frequency. Additionally, some genes did not show compounded suppression at higher decibels while others were reduced even further. Kumeta says this indicates that sound stimulation induces different responses in the cell.

The results also showed that such stimulations affect cells differently according to cell type. Cells that would eventually become bone or skeletal muscle showed the most suppression, while cells that had already differentiated had almost no response.

"Our research has found that audible sound stimulation leads to specific genetic responses," adds team leader Shige H Yoshimura. "These data also show that at least two mechanisms are involved: transcriptional control and RNA degradation. Both are key players in controlling how much proteins are made in the cell."

The team is planning to continue testing their hypotheses, as well as search for other genes that have been affected, such as ones that may have been upregulated by audio stimulation.

"Further studies using different sounds, cells, and experimental setups are sure to uncover more of this novel relationship between life and sound," continues Kumeta.

"In addition to the cellular level," concludes Yoshimura, "we will also focus on tissue- and organism-level effects to investigate the biological significance of sound response in living systems."

Contacts and sources:
Raymond Kunikane Terhune
Kyoto University

The paper "Cell type-specific suppression of mechanosensitive genes by audible sound stimulation" appeared 31 January 2018 in PLOS ONE with doi: 10.1371/journal.pone.0188764

The Milky Way Outer Halo Is a Graveyard for Cannibalized Dwarf Galaxies

An international team of astronomers led by Giuseppina Battaglia, researcher at the Instituto de Astrofísica de Canarias (IAC), finds signs that the outer halo of the Milky Way contains stellar remains of massive dwarf galaxies that were devoured by our own. The extended stellar haloes are predicted to be an ubiquitous feature around Milky Way-like galaxies and to consist mainly of the shredded stellar component of smaller galactic systems.

Most of the information we have about the Milky Way stellar halo comes from its inner region, which we can observe close to the solar neighborhood. However, for the first time the chemical properties of the external regions of the halo of our galaxy were explored with high resolution spectroscopy in the optical of a sample of 28 red giant stars at large distances from the Sun. 

The method that was used, i.e. a spectroscopic analysis, consists in separating the light of the stars in its different frequencies in order to obtain information on the star’s chemical composition. The analysis of the chemical properties of the stars can provide information on the characteristics of the environment in which they were born.

Credit: Instituto de Astrofísica de Canarias (IAC)

“The abundance of some chemical elements in the stars in the external regions of the Milky Way halo - explains Giuseppina Battaglia, astrophysicist at the IAC and first author of the article - was found to be surprisingly different from the information we had concerning the inner regions of the halo”. 

On the other hand, several similarities were discovered with the chemical composition observed for stars in nearby massive dwarf galaxies, such as Sagittarius and the Large Magellanic Cloud. These signatures tells us that the external regions of the stellar halo might contain the remains of one, or more, massive dwarf galaxy, devoured by the Milky Way.

Stellar haloes are a common component of galaxies like the Milky Way. “The theory explaining the formation of structure and galaxies in the Universe predicts that stellar haloes, and in particular their outer regions, consist mainly of the stellar component of destroyed, smaller galaxies.” G.Battaglia comments “Qualitatively this is in agreement with the observational findings of this study, where we found remnants of cannibalized dwarf galaxies around the Milky Way.”

Our Milky Way galaxy and its small companions are surrounded by a giant halo of million-degree gas (seen in blue in this artists' rendition) that is only visible to X-ray telescopes in space. University of Michigan astronomers discovered that this massive hot halo spins in the same direction as the Milky Way disk and at a comparable speed.
Milky Way surrounded by million-degree gas halo seen in blue
Credits: NASA/CXC/M.Weiss/Ohio State/A Gupta et al

For this study data from about 100 hours of telescope observing time were used, obtained on facilities in both the Northern and Southern hemisphere. Specifically, the team used the Very Large Telescope "Kueyen" (UT2) of the European Southern Observatory in Paranal and the Magellan telescope Clay in Las Campanas, both in Chile, as well as the Hobby Eberly Telescope, in Texas.

Contacts and sources:  
Giuseppina Battaglia
Instituto de Astrofísica de Canarias (IAC),

Article: G. Battaglia et al. What is the Milky Way outer halo made of? High resolution spectroscopy of distant red giants. Astronomy & Astrophysics, 608, A145 (2017) DOI:

Most Detailed Simulation of the Universe to Date A God's Eye View

Every galaxy harbours a supermassive black hole at its center. A new computer model now shows how these gravity monsters influence the large-scale structure of our universe.

The IllustrisTNG project is an ongoing series of large, cosmological magnetohydrodynamical simulations of galaxy formation. TNG aims to illuminate the physical processes that drive galaxy formation: to understand when and how galaxies evolve into the structures that are observed in the night sky, and to make predictions for current and future observational programs.\

Time evolution of the cosmic magnetic field strength. Blue/purple shows regions of low magnetic energy along filaments of the cosmic web, whereas orange and white indicate regions with significant magnetic energy inside halos and galaxies. The displayed region is taken from the TNG100 simulation and is 10 megaparsec wide.

Credit: TheHITSters

The research team includes scientists from the Heidelberg Institute for Theoretical Studies (HITS), Heidelberg University, the Max-Planck-Institutes for Astronomy (MPIA, Heidelberg) and for Astrophysics (MPA, Garching), US universities Harvard and the Massachusetts Institute of Technology (MIT), as well as the Center for Computational Astrophysics in New York. 

Credit: Mark Vogelsberger

The project, "Illustris - The Next Generation" (IllustrisTNG), is the most complete simulation of its kind to date. Based on the basic laws of physics, the simulation shows how our cosmos evolved since the Big Bang. Adding to the predecessor Illustris project, IllustrisTNG includes some of the physical processes which play a crucial role in this evolution for the very first time in such an extensive simulation. First results of the IllustrisTNG project have now been published in three articles in the journal Monthly Notices of the Royal Astronomical Society. 

Visualization of the intensity of shock waves in the cosmic gas (blue) around collapsed dark matter structures (orange/white). Similar to a sonic boom, the gas in these shock waves is accelerated with a jolt when impacting on the cosmic filaments and galaxies.

Credit: IllustrisTNG collaboration

These findings should help to answer fundamental questions in cosmology.

A realistic universe out of the computer

At its intersection points, the cosmic web of gas and dark matter predicted by IllustrisTNG hosts galaxies quite similar to the shape and size of real galaxies. For the first time, hydrodynamical simulations could directly compute the detailed clustering pattern of galaxies in space. Comparison with observational data - including newest large surveys - demonstrate the high degree of realism of IllustrisTNG.

Credit: CfA Press

 In addition, the simulations predict how the cosmic web changes over time, in particular in relation to the underlying "back bone" of the dark matter cosmos. "It is particularly fascinating that we can accurately predict the influence of supermassive black holes on the distribution of matter out to large scales," says principal investigator Prof. Volker Springel (HITS, MPA, Heidelberg University). "This is crucial for reliably interpreting forthcoming cosmological measurements."

TNG100-1: Fullbox composite which combines gas temperature (as the color) and shock mach number (as the brightness). Red indicates 10 million Kelvin gas at the centers of massive galaxy clusters, while bright structures show diffuse gas from the intergalactic medium shock heating at the boundary between cosmic voids and filaments.

Credit: IllustrisTNG collaboration

The most important transformation in the life cycle of galaxies

In another study, Dr. Dylan Nelson (MPA) was able to demonstrate the important impact of black holes on galaxies. Star-forming galaxies shine brightly in the blue light of their young stars until a sudden evolutionary shift ends the star formation, such that the galaxy becomes dominated by old, red stars, and joins a graveyard full of "red and dead" galaxies. "The only physical entity capable of extinguishing the star formation in our large elliptical galaxies are the supermassive black holes at their centers," explains Nelson. "The ultrafast outflows of these gravity traps reach velocities up to 10 percent of the speed of light and affect giant stellar systems that are billions of times larger than the comparably small black hole itself."

Thin slice through the cosmic large-scale structure in the largest simulation of the IllustrisTNG project. The image brightness indicates the mass density and colour visualizes the mean gas temperature of ordinary ("baryonic") matter. The displayed region extends by about 1.2 billion light-years from left to right. The underlying simulation is presently the largest magneto-hydrodynamic simulation of galaxy formation, containing more than 30 billion volume elements and particles.

Credit: IllustrisTNG collaboration

Where the stars sparkle: New findings for the structures of galaxies

IllustrisTNG also improves researchers´ understanding of the hierarchical structure formation of galaxies. Theorists argue that small galaxies should form first, and then merge into ever larger objects, driven by the relentless pull of gravity. The numerous galaxy collisions literally tear some galaxies apart and scatter their stars onto wide orbits around the newly created large galaxies, which should give them a faint background glow of stellar light. These predicted pale stellar halos are very difficult to observe due to their low surface brightness, but IllustrisTNG was able to simulate exactly what astronomers should be looking for in their data.

"Our predictions can now be systematically checked by observers," Dr. Annalisa Pillepich (MPIA) points out, who led a further IllustrisTNG study. "This yields a critical test for the theoretical model of hierarchical galaxy formation."

Astrophysics with a special code and a supercomputer

For the project, the researchers developed a particularly powerful version of their highly parallel moving-mesh code AREPO and used it on the Hazel Hen machine at the High-Performance Computing Center Stuttgart, Germany's fastest mainframe computer, currently ranked nineteenth in the Top500. IllustrisTNG is the largest hydrodynamic simulation project to date for the emergence of cosmic structures. To compute one of the two main simulation runs, over 24,000 processors were used over the course of more than two months to follow the formation of millions of galaxies in a representative region of the universe with nearly one billion light-years on a side. 

Rendering of the gas velocity in a thin slice of 100-kiloparsec thickness (in the viewing direction), centered on the second most massive galaxy cluster in the TNG100 calculation. Where the image is black, the gas is hardly moving, while white regions have velocities which exceed 1,000 kilometers per second. The image contrasts the gas motions in cosmic filaments against the fast, chaotic motions triggered by the deep gravitational potential well and the supermassive black hole sitting at its center.

Credit: IllustrisTNG collaboration

"Thanks to the computing time obtained from the German Gauss Centre for Supercomputing, we have been able to redefine the state of the art in this field," explains Volker Springel. "The new simulations produced more than 500 terabytes of simulation data. Analyzing this huge mountain of data will keep us busy for years to come, and it promises many exciting new insights into different astrophysical processes."

The stellar content of the Universe on the largest scales: a projection of the distribution of stars across a 50 Mpc region of space. Taken from the TNG100-1 simulation at the present day (z=0)

Credit: IllustrisTNG collaboration

Contacts and sources:
Anastasia Greenebaum
Simons Foundation

Dr. Peter Saueressig

Heidelberg Institute for Theoretical Studies (HITS)

Original scientific publications:

V. Springel, R. Pakmor, A. Pillepich, R. Weinberger, D. Nelson, L. Hernquist, M. Vogelsberger, S. Genel, P. Torrey, F. Marinacci, J. Naiman
First results from the IllustrisTNG simulations: matter and galaxy clustering, MNRAS, Feb 1st, 2018 DOI:

D. Nelson, A. Pillepich, V. Springel, R. Weinberger, L. Hernquist, R. Pakmor, S. Genel, P. Torrey, M. Vogelsberger, G. Kauffmann, F. Marinacci, J. Naiman
First results from the IllustrisTNG simulations: the galaxy color bimodality, MNRAS, Feb 1st, 2018 DOI:

A. Pillepich, D. Nelson, L. Hernquist, V. Springel, R. Pakmor, P. Torrey, R. Weinberger, S. Genel, J. Naiman, F. Marinacci, M. Vogelsberger
First results from the IllustrisTNG simulations: the stellar mass content of groups and clusters of galaxies, MNRAS, Feb 1st, 2018

Lethal Weaponry Circa 12,000 B.C.E. Ancient Technology Recreated

Archaeologists are a little like forensic investigators: They scour the remains of past societies, looking for clues in pottery, tools and bones about how people lived, and how they died.

And just as detectives might re-create the scene of a crime, University of Washington archaeologists have re-created the weapons used by hunter-gatherers in the post-Ice Age Arctic some 14,000 years ago. Looking for clues as to how those early people advanced their own technology, researchers also considered what that might tell us about human migration, ancient climates and the fate of some animal species.

In an article published Jan. 31 in the Journal of Archaeological Science, Janice Wood, recent UW anthropology graduate, and Ben Fitzhugh, a UW professor of anthropology, show how they reconstructed prehistoric projectiles and points from ancient sites in what is now Alaska and studied the qualities that would make for a lethal hunting weapon.

In an article published Jan. 31 in the Journal of Archaeological Science, Janice Wood, recent UW anthropology graduate, and Ben Fitzhugh, a UW professor of anthropology, show how they reconstructed prehistoric projectiles and points from ancient sites in what is now Alaska and studied the qualities that would make for a lethal hunting weapon.

The UW team chose to study hunting weapons from the time of the earliest archaeological record in Alaska (around 10,000 to 14,000 years ago), a time that is less understood archaeologically, and when different kinds of projectile points were in use. Team members designed a pair of experiments to test the effectiveness of the different point types. By examining and testing different points in this way, the team has come to a new understanding about the technological choices people made in ancient times.

University of Washington researchers re-created ancient projectile points to test their effectiveness. From left to right: stone, microblade and bone tips.

Credit: Janice Wood

“The hunter-gatherers of 12,000 years ago were more sophisticated than we give them credit for,” Fitzhugh said. “We haven’t thought of hunter-gatherers in the Pleistocene as having that kind of sophistication, but they clearly did for the things that they had to manage in their daily lives, such as hunting game. They had a very comprehensive understanding of different tools, and the best tools for different prey and shot conditions.”

Prior research has focused on the flight ballistics of the hunting weapons in general, and no prior study has looked specifically at the ballistics of tools used in Siberia and the Arctic regions of North America just after the Ice Age. In addition to foraging for plants and berries (when available), nomadic groups hunted caribou, reindeer and other animals for food, typically with spears or darts (thrown from atlatl boards). Without preservation of the wood shafts, these tools are mainly differentiated in the archaeological record by their stone and bone points. But it was not known how effective different kinds of points were in causing lethal injury to prey.

Nor is it known, definitively, whether different types of points were associated with only certain groups of people, or whether with the same groups used certain point types to specialize on particular kinds of game or hunting practices. It is generally accepted that different point types were developed in Africa and Eurasia and brought to Alaska before the end of the Ice Age. These included rudimentary points made of sharpened bone, antler or ivory; more intricate, flaked stone tips popularly familiar as “arrowheads”; and a composite point made of bone or antler with razor blade-like stone microblades embedded around the edges.

The three likely were invented at separate times but remained in use during the same period because each presumably had its own advantages, Wood said. Learning how they functioned informs what we know about prehistoric hunters and the repercussions of their practices.

So Wood traveled to the area around Fairbanks, Alaska, and crafted 30 projectile points, 10 of each kind. She tried to stay as true to the original materials and manufacturing processes as possible, using poplar projectiles, and birch tar as an adhesive to affix the points to the tips of the projectiles. While ancient Alaskans used atlatls (a kind of throwing board), Wood used a maple recurve bow to shoot the arrows for greater control and precision.

For the bone tip, modeled on a 12,000-year-old ivory point from an Alaskan archaeological site, Wood used a multipurpose tool to grind a commercially purchased cow bone;

For the stone tip, she used a hammerstone to strike obsidian into flakes, then shaped them into points modeled on those found at another site in Alaska from 13,000 years ago;

And for the composite microblade tip -- modeled microblade technologies seen in Alaska since at least 13,000 years ago and a rare, preserved grooved antler point from a more recent Alaskan site used more than 8,000 years ago -- Wood used a saw and sandpaper to grind a caribou antler to a point. She then used the multipurpose tool to gouge out a groove around its perimeter, into which she inserted obsidian microblades.

Wood then tested how well each point could penetrate and damage two different targets: blocks of ballistic gelatin (a clear synthetic gelatin meant to mimic animal muscle tissue) and a fresh reindeer carcass, purchased from a local farm. Wood conducted her trials over seven hours on a December day, with an average outdoor temperature of minus 17 degrees Fahrenheit.

In Wood's field trial, the composite microblade points were more effective than simple stone or bone on smaller prey, showing the greatest versatility and ability to cause incapacitating damage no matter where they struck the animal's body. But the stone and bone points had their own strengths: Bone points penetrated deeply but created narrower wounds, suggesting their potential for puncturing and stunning larger prey (such as bison or mammoth); the stone points could have cut wider wounds, especially on large prey (moose or bison), resulting in a quicker kill.

Wood said the findings show that hunters during this period were sophisticated enough to recognize the best point to use, and when. Hunters worked in groups; they needed to complete successful hunts, in the least amount of time, and avoid risk to themselves.

"We have shown how each point has its own performance strengths," she said. Bone points punctured effectively, flaked stone created a greater incision, and the microblade was best for lacerated wounds. "It has to do with the animal itself; animals react differently to different wounds. And it would have been important to these nomadic hunters to bring the animal down efficiently. They were hunting for food."

Weapon use can shed light on the movement of people and animals as humans spread across the globe and how ecosystems changed before, during and after the ice ages.

"The findings of our paper have relevance to the understanding of ballistic properties affecting hunting success anywhere in the world people lived during the 99 percent of human history that falls between the invention of stone tools more than 3 million years ago in Africa and the origins of agriculture," Fitzhugh said.

It could also inform debates on whether human hunting practices directly led to the extinction of some species. The team's findings and other research show that our ancestors were thinking about effectiveness and efficiency, Wood said, which may have influenced which animals they targeted. An animal that was easier to kill may have been targeted more often, which could, along with changing climates, explain why animals such as the horse disappeared from the Arctic. A shot to the lung was lethal for early equines, Wood said, but a caribou could keep going.

"I see this line of research as looking at the capacity of the human brain to come up with innovations that ultimately changed the course of human history," she said. "This reveals the human capacity to invent in extreme circumstances, to figure out a need and a way to meet that need that made it easier to eat and minimized the risk."

Upon completion of the experiment, the bones were sterilized for future study of projectile impact marks.

Contacts and sources:
Kim Eckart
University of Washington

Citation: Wound ballistics: The prey specific implications of penetrating trauma injuries from osseous, flaked stone, and composite inset microblade projectiles during the Pleistocene/Holocene transition, Alaska U.S.A  Janice Wood,  Ben Fitzhugh Journal of Archaeological Science

Tuesday, January 30, 2018

How Do Crystals Grow? Researchers Find a Piece of the Puzzle

 University of California Santa Barbara (UCSB) researchers unlock another piece of the puzzle that is crystal growth.

From Mother Nature to our must-have devices, we’re surrounded by crystals. Those courtesy of the former, such as ice and snow, can form spontaneously and symmetrically. But the silicon-based or gallium nitride crystals found in LEDs and other electronics require a bit of coaxing to attain their ideal shapes and alignments.

At UC Santa Barbara, researchers have now unlocked another piece of the theoretical puzzle that governs the growth of crystals — a development that may save time and energy in the many processes that require crystal formation.

“The way most industrial processes are designed today is by doing an exhaustively large number of experiments to find out how crystals grow and at what rate they grow under different conditions,” said UCSB chemical engineer Michael Doherty, an author of a paper that appears in the Proceedings of the National Academy of Sciences

A cubic salt crystal aggregate

Credit: UCSB

Snowflakes, for instance, form differently as they fall, depending on variable conditions such as temperature and humidity, hence the widely held belief that no two are alike. After determining the optimal conditions for the growth of the crystal of choice, Doherty added, equipment must be designed and calibrated to provide a consistent growing environment.

However, by pooling decades of expertise, Doherty, along with UCSB colleague Baron Peters and former graduate student Mark Joswiak (now at Dow Chemical) have developed a computational method to help predict growth rates for ionic crystals under different circumstances. Using a relatively simple crystal — sodium chloride (NaCl, more familiarly known as table salt) — in water, the researchers laid the groundwork for the analysis of more complex crystals.

Ionic crystals may appear to the naked eye — and even under some magnification — to consist of perfectly smooth and even faces. But look more closely and you’ll often find they actually contain surface features that influence their ability to grow, and the larger shapes that they take.

“There are dislocations and around the dislocations there are spirals, and around the spirals there are edges, and around the edges there are kinks,” Peters said, “and every level requires a theory to describe the number of those features and the rates at which they change.” At the smallest scale, ions in solution cannot readily attach to the growing crystal because water molecules that solvate (interact with) the ions are not readily dislodged, he said. With so many processes occurring at so many scales, it’s easy to see how difficult it can be to predict a crystal’s growth.

“The largest challenge was applying the various techniques and methods to a new problem — examining ion attachment and detachment at surface kink sites, where there is a lack of symmetry coupled with strong ion-water interactions,” Joswiak said. “However, as we encountered problems and found solutions, we gained additional insight on the processes, the role of water molecules and differences between sodium and chloride ions.”

Among their insights: Ion size matters. The researchers found that due to its size, the larger chloride ion (Cl-) prevents water from accessing kink sites during detachment, limiting the overall rate of sodium chloride dissolution in water.

“You have to find a special coordinate system that can reveal those special solvent rearrangements that create an opening for the ion to slip through the solvent cage and lock onto the kink site,” Peters said. “We demonstrated that at least for sodium chloride we can finally give a concrete answer.”

This proof-of-concept development is the result of the Doherty Group’s expertise with crystallization processes coupled with the Peters Group’s expertise in “rare events” — relatively infrequent and short-lived but highly significant phenomena (such as reactions) that fundamentally change the state of the system. Using a method called transition path sampling, the researchers were able to understand the events leading up to the transition state. The strategy and mechanistic insights from the work on sodium chloride provides a blueprint for predicting growth rates in materials synthesis, pharmaceuticals and biomineralization.

Contacts and sources:
Sonia Fernandez
University of California Santa Barbara (UCSB)

Learning the Secrets of Tissue Regeneration: Decoding the Axolotl Ability to Regrow Limbs

The sequencing of the largest genome to date lays the foundation for novel insights into tissue regeneration.

A team of researchers led by scientists in Vienna, Dresden and Heidelberg has decoded the entire genetic information of the Mexican salamander axolotl. The axolotl genome, which is the largest genome ever to be sequenced, will be a powerful tool to study the molecular basis for regrowing limbs and other forms of regeneration.

After being injured, an axolotl can regrow bones, muscles and nerves in the right places. The decoding of the genome of the Mexican axolotl Ambystoma mexicanu will provide researchers with key insights into the process of tissue regeneration.

Credit: © IMP

Salamanders have long served as valuable biological models for developmental, regeneration and evolutionary studies. In particular, the Mexican axolotl Ambystoma mexicanum has received special attention due to its astounding ability to regenerate body-parts. If the cannibalistically inclined animal loses a limb, it will regrow a perfect substitute within weeks, complete with bones, muscles and nerves in the right places. Even more fascinating, the axolotl can repair severed spinal cord and retinal tissue. These qualities and the relative ease in breeding have made it a favourite biological model, cultivated in the lab for more than 150 years.
Studying the evolution of regeneration

One of the largest axolotl-colonies is maintained by the team of Elly Tanaka, now at the Research Institute of Molecular Pathology (IMP) in Vienna. The Tanaka-group that was based at the DFG-Center for Regenerative Therapies Dresden at the TU Dresden and the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) until 2016 is studying the molecular cell biology of limb and spinal cord regeneration and how these mechanisms evolved. Over the years, the team has developed an extensive molecular toolkit for the axolotl, including comprehensive transcriptome data that reveal protein-coding sequences in the animal’s genome. Using these tools, Elly Tanaka and her colleagues were able to identify the cells that initiate regeneration and describe molecular pathways that control the process.

To fully understand regeneration and to find out why it is so limited in most species, scientists need to have access to genome data to study gene regulation and evolution. So far, the axolotl genome had evaded a complete assembly, due to its sheer size: at 32 billion base pairs, it is more than ten times larger than the human genome. The sequence assembly process using existing tools had been confounded by the enormous number of large repetitive sequences in this genome.
The challenge of sequencing the largest genome

An international team of researchers led by Elly Tanaka (IMP), Michael Hiller and Gene Myers (both MPI-CBG), and Siegfried Schloissnig of the Heidelberg Institute for Theoretical Studies (HITS) have now sequenced, assembled, annotated, and analysed the complete axolotl genome, the largest genome ever to be decoded. Using the PacBio-platform, a sequencing technology that produces long reads to span large repetitive regions, a total of 72 435 954 reads were sequenced at the DRESDEN Concept Genome Center, a joint operation between the MPI-CBG and the TU Dresden. Software systems that were co-developed by Gene Myers and Siegfried Schloissnig with his team in Heidelberg were used to assemble the genome from these millions of pieces. The powerful sequencing machines that made this whole project possible were financed by the Klaus Tschira Foundation and the Max Planck Society.

The analysis of the assembled genome discovered several features that seem to point to the uniqueness of the axolotl: The researchers found that several genes that only exist in axolotl and other amphibian species are expressed in regenerating limb tissue. Most strikingly, an essential developmental gene named PAX3 is completely missing from the genome, and its functions have been taken over by another gene termed PAX7. Both genes play key roles in muscle and neural development.

“We now have the map in our hands to investigate how complicated structures such as legs can be re-grown”, says Sergej Nowoshilow, co-first author of the study and a postdoctoral fellow at the IMP. “This is a turning point for the community of scientists working with axolotl, a real milestone in a research adventure that started more than 150 years ago.”

The sequence of the axolotl genome that is now publicly available is a powerful resource for researchers worldwide to study tissue-regeneration.

Contacts and sources:
Dr. Heidemarie Hurtl
Research Institute of Molecular Pathology, Vienna, Austria

Katrin Boes
Max Planck Institute of Molecular Cell Biology and Genetics, 

Citation: The axolotl genome and the evolution of key tissue formation regulators.
Sergej Nowoshilow, Siegfried Schloissnig, Ji-Feng Fei, Andreas Dahl, Andy W.C. Pang, Martin Pippel, Sylke Winkler, Alex R. Hastie, George Young, Juliana G. Roscito, Francisco Falcon, Dunja Knapp, Sean Powell, Alfredo Cruz, Han Cao, Bianca Habermann, Michael Hiller, Elly M. Tanaka, and Eugene W. Myers
Nature; 24 January, 2018 (doi: 10.1038/nature25458)

Science Fiction Becomes Reality: Minuscule Robot Will Swim, Crawl and Jump in Your Body

 In future, tiny robots moving in your body could transport medication specifically to where it is needed.

Tiny robots need not fear obstacle courses in the future: Scientists from the Max Planck Institute for Intelligent Systems in Stuttgart have developed a minuscule, flexible robot that can master a variety of forms of movement. Its magnetic drive allows it to walk, crawl and roll through difficult terrain. Moreover, it can transport small loads and swim on and in liquids.

The millirobot now introduced by the Max Planck researchers in Stuttgart moves over land and water. Jellyfish and caterpillars are just two of the natural role models that inspired the scientists.

Credit: © MPI for Intelligent Systems

The millirobots are characterized by their manoeuvrability. The tiny vehicle, a strip of elastic silicon just four millimetres long, can be used in a variety of locomotion modes, allowing the millirobot to manoeuvre even through a complex environment. Previous microrobots, on the other hand, can only manoeuvre to a limited extent and meet their match especially in difficult terrain.

The researchers from the Stuttgart-based Max Planck Institute for Intelligent Systems found inspiration for the development of the manoeuvrability talent in nature: "When we build robots, we look at the mechanics of the movement of soft-bodied biological organisms, for example, and are inspired by them", says Metin Sitti, Director of the Physical Intelligence Department. "With our millirobot, the result is a mix of several soft creatures such as beetle larvae and caterpillars. However, a spermatozoid and a jellyfish also served as models."'

Initial tests in a dummy stomach and on chicken meat tissue

Through an obstacle course with ease: The millirobot walks, crawls, swims, climbs a step and jumps through a complex environment.
Credit: © MPI for Intelligent Systems

The robot is able to perform the different movements because the scientists have embedded magnetic microparticles in its soft, elastic silicone rubber body, resulting in a precisely defined magnetization profile. This allows the researchers to operate and control it using an external magnetic field. By varying the strength and direction of the magnetic field, they deform the rubber strip in different ways. This allows the millirobot to complete an obstacle course similar to what would be encountered in the human body: it can walk or roll across surfaces, jump across obstacles, crawl through narrow tubes and swim on or in liquids. In addition, it can grasp objects, transport them and deposit them at defined locations.

Sitti's team tested the millirobot in a synthetic surgical stomach model and in chicken meat tissue, where the artificial multi-talent demonstrated excellent results. When the researchers could not observe it directly, they tracked where and how exactly the robot made his way forward using ultrasound imaging. Great challenges still need to be overcome before such a millirobot can be used in patients: for example, it needs to prove that it can be controlled within the human body. However, the researchers are confident that these hurdles can be taken.

The millirobot is intended to transport medication

The silicone rubber strip with embedded magnetic particles forming the body of the very manoeuvrable millirobot is only four millimetres long.

Credit: © MPI for Intelligent Systems

"Our objective is that our millirobot will one day transport medication to where it is needed – similar to a parcel delivery to the front door", says Metin Sitti. "We aim to use it in minimally invasive medical procedures on the patient: either by swallowing the robot or by inserting it into the body through a small opening on the skin. From there, the robot can then move through the digestive tract or the bladder, or on to the heart – we envisage numerous possibilities."

Research on mobile microrobots, which may be deployed in medicine in the future, plays a central role in the Department of Physical Intelligence. The hope of the Max Planck researchers is that cable-free, mobile robots will one day become established in medicine and open up new disease treatment and surgical perspectives, which are not possible at the moment.

With the aid of such millirobots, a surgeon would have direct access and precise control in areas of the body that can only be penetrated using a scalpel today. "Without surgery, it is currently not possible to gain access to many areas of the body. Our objective is to make these regions accessible non-invasively using our soft millirobot to perform diagnosis and therapy," says Metin Sitti.

Special Way of Smelling Is Related to a Hunter-Gatherer Lifestyle.

When it comes to naming colors, most people do so with ease. But, for odors, it’s much harder to find the words.

One notable exception to this rule is found among the Jahai people, a group of hunter-gatherers living in the Malay Peninsula who can name odors just as easily as colors. A new study by Asifa Majid (Radboud University and MPI for Psycholinguistics) and Nicole Kruspe (Lund University) suggests that the Jahai’s special way with smell is related to their hunting and gathering lifestyle.

“There has been a long-standing consensus that ‘smell is the mute sense, the one without words,’ and decades of research with English-speaking participants seemed to confirm this,” says Asifa Majidof Radboud University and MPI for Psycholinguistics. “But, the Jahai of the Malay Peninsula are much better at naming odors than their English-speaking peers. This, of course, raises the question of where this difference originates.”
Credit:  Radboud University

Hunter-Gatherers and horticulturalists

To find out whether it was the Jahai who have an unusually keen ability with odors or whether English speakers are simply lacking, Majid and Nicole Kruspe (Lund University, Sweden) examined two related, but previously unstudied, groups of people in the tropical rainforest of the Malay Peninsula: the hunter-gatherer Semaq Beri and the non-hunter-gatherer Semelai. The Semelai are traditionally farmers, combining shifting rice cultivation with the collection of forest products for trade.

The Semaq Beri and Semelai not only live in a similar environment; they also speak closely related languages. The question was: how easily are they able to name odors? “If ease of olfactory naming is related to cultural practices, then we would expect the Semaq Beri to behave like the Jahai and name odors as easily as they do colors, whereas the Semelai should pattern differently,” the researchers wrote in their recently published study in Current Biology. And, that’s exactly what they found.

Testing color- and odor-abilities

Majid and Kruspe tested the color- and odor-naming abilities of 20 Semaq Beri and 21 Semelai people. Sixteen odors were used: orange, leather, cinnamon, peppermint, banana, lemon, licorice, turpentine, garlic, coffee, apple, clove, pineapple, rose, anise, and fish. For the color task, study participants saw 80 standardised color chips, sampling 20 equally spaced hues at four degrees of brightness. Kruspe tested participants in their native language by simply asking, “What smell is this?” or “What color is this?”

The results were clear. The hunter-gatherer Semaq Beri performed on those tests just like the hunter-gatherer Jahai, naming odors and colors with equal ease.The non-hunter-gatherer Semelai, on the other hand, performed like English speakers. For them, odors were difficult to name. The results suggest that the downgrading in importance of smells relative to other sensory inputs is a recent consequence of cultural adaption, the researchers say. “Hunter-gatherers’ olfaction is superior, while settled peoples’ olfactory cognition is diminished,” Majid says.

They say the findings challenge the notion that differences in neuroarchitecture alone underlie differences in olfaction, suggesting instead that cultural variation may play a more prominent role. They also raise a number of interesting questions: “Do hunter-gatherers in other parts of the world also show the same boost to olfactory naming?” Majid asks. “Are other aspects of olfactory cognition also superior in hunter-gatherers,” for example, the ability to differentiate one odor from another? “Finally, how do these cultural differences interact with the biological infrastructure for smell?” She says it will be important to learn whether these groups of people show underlying genetic differences related to the sense of smell.

This study was funded by The Netherlands Organisation for Scientific Research as well as the Swedish Foundation.

Contacts and sources:
Asifa Majid
Radboud University

Charlotte Horn
Max Planck Institute for Psycholinguistics

Publication: Majid, A., & Kruspe, N. (2018). Hunter-gatherer olfaction is special. Current Biology. DOI: 10.1016/j.cub.2017.12.014

Two Ancient Routes of Settlement for Scandinavia Revealed by Genetics

Analysis of ancient DNA found that Scandinavia was settled by hunter-gatherers via a southern and a northern route, and reveals that agriculture was likely introduced by migrating agriculturalists.

An international team of scientists, led by researchers from the Max Planck Institute for the Science of Human History, analyzed ancient human genomes from 38 northern Europeans dating from approximately 7,500 to 500 BCE. The study, published in Nature Communications, found that Scandinavia was initially settled via a southern and a northern route and that the arrival of agriculture in northern Europe was facilitated by movements of farmers and pastoralists into the region.

Northern Europe could be considered a late bloomer in some aspects of human history: initial settlement by hunter-gatherers occurred only about 11,000 years ago, after the retreat of the lingering ice sheets from the Pleistocene, and while agriculture was already widespread in Central Europe 7,000 years ago, this development reached Southern Scandinavia and the Eastern Baltic only millennia later.

Skull included in this study from Ölsund, Hälsingland, Sweden, dating to around 2,300 BCE, in the ancient DNA laboratory at the Max Planck Institute for the Science of Human History.

Credit: Alissa Mittnik

Several recent studies of ancient human genomes have dealt with the prehistoric population movements that brought new technology and subsistence strategies into Europe, but how they impacted the very north of the continent has still been poorly understood.

For this study, the research team, which included scientists from Lithuania, Latvia, Estonia, Russia and Sweden, assembled genomic data from 38 ancient northern Europeans, from mobile hunter-gatherers of the Mesolithic (approximately 12,000 to 7,000 years ago) and the first Neolithic farmers in southern Sweden (approximately 6,000 to 5,300 years ago) to the metallurgists of the Late Bronze Age in the Eastern Baltic (approximately 1300 to 500 BCE). This allowed the researchers to uncover surprising aspects of the population dynamics of prehistoric northern Europe.

Two routes of settlement for Scandinavia

Previous analysis of ancient human genomes has revealed that two genetically differentiated groups of hunter-gatherers lived in Europe during the Mesolithic: the so-called Western Hunter-Gatherers excavated in locations from Iberia to Hungary, and the so-called Eastern Hunter-Gatherers excavated in Karelia in north-western Russia. Surprisingly, the results of the current study show that Mesolithic hunter-gatherers from Lithuania appear very similar to their Western neighbors, despite their geographic proximity to Russia. The ancestry of contemporary Scandinavian hunter-gatherers, on the other hand, was comprised from both Western and Eastern Hunter-Gatherers.

Map showing locations and timeline of the samples introduced in this study.

Credit: Mittnik et al. The Genetic Prehistory of the Baltic Sea Region. Nature Communications (2018).

"Eastern Hunter-Gatherers were not present on the eastern Baltic coast, but a genetic component from them is present in Scandinavia. This suggests that the people carrying this genetic component took a northern route through Fennoscandia into the southern part of the Scandinavian peninsula. There they genetically mixed with Western Hunter-Gatherers who came from the South, and together they formed the Scandinavian Hunter-Gatherers," explains Johannes Krause, Director of the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History, and senior author of the study.

Agriculture and animal herding - cultural imports by incoming people

Large-scale farming first started in southern Scandinavia around 6,000 years ago, about one millennium after it was already common in Central Europe. In the Eastern Baltic, the inhabitants relied solely on hunting, gathering and fishing for another 1000 years. Although some have argued that the use of the new subsistence strategy was a local development by foragers, possibly adopting the practices of their farming neighbors, the genetic evidence uncovered in the present study tells a different story.

The earliest farmers in Sweden are not descended from Mesolithic Scandinavians, but show a genetic profile similar to that of Central European agriculturalists. Thus it appears that Central Europeans migrated to Scandinavia and brought farming technology with them. These early Scandinavian farmers, like the Central European agriculturalists, inherited a substantial portion of their genes from Anatolian farmers, who first spread into Europe around 8,200 years ago and set in motion the cultural transition to agriculture known as the Neolithic Revolution.

Similarly, a near-total genetic turnover is seen in the Eastern Baltic with the advent of large-scale agro-pastoralism. While they did not mix genetically with Central European or Scandinavian farmers, beginning around 2,900 BCE the individuals in the Eastern Baltic derive large parts of their ancestry from nomadic pastoralists of the Pontic-Caspian steppe.

"Interestingly, we find an increase of local Eastern Baltic hunter-gatherer ancestry in this population at the onset of the Bronze Age," states Alissa Mittnik of the Max Planck Institute for the Science of Human History, lead author of the study. "The local population was not completely replaced but coexisted and eventually mixed with the newcomers."

This study emphasizes the regional differences of cultural transitions and sets the stage for more in-depth studies of later periods in northern European prehistory, such as the Iron Age and Viking Age.

Contacts and sources:
Anne Gibson
Max Planck Institute for the Science of Human History

Citation:  The Genetic Prehistory of the Baltic Sea Region
Alissa Mittnik, Chuan-Chao Wang, Saskia Pfrengle, Mantas Daubaras, Gunita Zarina, Fredrik Hallgren, Raili Allmäe, Valery Khartanovich, Vyacheslav Moiseyev, Mari Torv, Anja Furtwängler, Aida Andrade Valtueña, Michal Feldman, Christos Economou, Markku Oinonen, Andrejs Vasks , Elena Balanovska, David Reich, Rimantas Jankauskas, Wolfgang Haak, Stephan Schiffels and Johannes Krause
Nature Communications

Unexpected Matter Birthing in the Black Hole Wind : New Theory Predicts Origins Of Molecules in Destructive Cosmic Gale

The existence of large numbers of molecules in winds powered by supermassive black holes at the centers of galaxies has puzzled astronomers since they were discovered more than a decade ago. Molecules trace the coldest parts of space, and black holes are the most energetic phenomena in the universe, so finding molecules in black hole winds was like discovering ice in a furnace.

Astronomers questioned how anything could survive the heat of the energetic outflows, but a new theory from researchers in Northwestern University's Center for Interdisciplinary Research and Exploration in Astrophysics (CIERA) predicts that these molecules are not survivors at all, but brand-new molecules, born in the winds with unique properties that enable them to adapt to and thrive in the hostile environment.

The theory, published in the Monthly Notices of the Royal Astronomical Society, is the work of Lindheimer post-doctoral fellow Alexander Richings, who developed the computer code that, for the first time, modeled the detailed chemical processes that occur in interstellar gas accelerated by radiation emitted during the growth of supermassive black holes. Claude-André Faucher-Giguère, who studies galaxy formation and evolution as an assistant professor in Northwestern's Weinberg College of Arts and Sciences, is a co-author.
Black hole wind sweeping away galactic gas
Credit:  ESA

"When a black hole wind sweeps up gas from its host galaxy, the gas is heated to high temperatures, which destroy any existing molecules," Richings said. "By modeling the molecular chemistry in computer simulations of black hole winds, we found that this swept-up gas can subsequently cool and form new molecules."

This theory answers questions raised by previous observations made with several cutting-edge astronomical observatories including the Herschel Space Observatory and the Atacama Large Millimeter Array, a powerful radio telescope located in Chile.

In 2015, astronomers confirmed the existence of energetic outflows from supermassive black holes found at the center of most galaxies. These outflows kill everything in their path, expelling the food - or molecules - that fuel star formation. These winds are also presumed to be responsible for the existence of "red and dead" elliptical galaxies, in which no new stars can form.

Galaxy-scale outflow driven by the central black hole/ 
Credit: ESA

Then, in 2017, astronomers observed rapidly moving new stars forming in the winds - a phenomenon they thought would be impossible given the extreme conditions in black hole-powered outflows.

New stars form from molecular gas, so Richings and Faucher-Giguère's new theory of molecule formation helps explain the formation of new stars in winds. It upholds previous predictions that black hole winds destroy molecules upon first collision but also predicts that new molecules - including hydrogen, carbon monoxide and water - can form in the winds themselves.

Zoomed-in view of the black hole wind at the center of a galaxy/
Credit: ESA

"This is the first time that the molecule formation process has been simulated in full detail, and in our view, it is a very compelling explanation for the observation that molecules are ubiquitous in supermassive black hole winds, which has been one of the major outstanding problems in the field," Faucher-Giguère said.

Richings and Faucher-Giguère predict that the new molecules formed in the winds are warmer and brighter in infrared radiation compared to pre-existing molecules. That theory will be put to the test when NASA launches the James Webb Space Telescope in spring 2019. If the theory is correct, the telescope will be able to map black hole outflows in detail using infrared radiation.

Contacts and sources:
Kayla Stoner
Northwestern University

Surprisingly Complex Organic Molecules Found in Stellar Embryos in Nearby Dwarf Galaxy

The nearby dwarf galaxy known as the Large Magellanic Cloud (LMC) is a chemically primitive place.

Unlike the Milky Way, this semi-spiral collection of a few tens-of-billions of stars lacks our galaxy's rich abundance of heavy elements, like carbon, oxygen, and nitrogen. With such a dearth of heavy elements, astronomers predict that the LMC should contain a comparatively paltry amount of complex carbon-based molecules. Previous observations of the LMC seem to support that view.

New observations with the Atacama Large Millimeter/submillimeter Array (ALMA), however, have uncovered the surprisingly clear chemical "fingerprints" of the complex organic molecules methanol, dimethyl ether, and methyl formate. Though previous observations found hints of methanol in the LMC, the latter two are unprecedented findings and stand as the most complex molecules ever conclusively detected outside of our galaxy.

Astronomers using ALMA have uncovered chemical “fingerprints” of methanol, dimethyl ether, and methyl formate in the Large Magellanic Cloud. The latter two molecules are the largest organic molecules ever conclusively detected outside the Milky Way. The far-infrared image on the left shows the full galaxy. The zoom-in image shows the star-forming region observed by ALMA. It is a combination of mid-infrared data from Spitzer and visible (H-alpha) data from the Blanco 4-meter telescope.
Credit: Credit: NRAO/AUI/NSF; ALMA (ESO/NAOJ/NRAO); Herschel/ESA; NASA/JPL-Caltech; NOAO

Astronomers discovered the molecules' faint millimeter-wavelength "glow" emanating from two dense star-forming embryos in the LMC, regions known as "hot cores." These observations may provide insights into the formation of similarly complex organic molecules early in the history of the universe.

"Even though the Large Magellanic Cloud is one of our nearest galactic companions, we expect it should share some uncanny chemical similarity with distant, young galaxies from the early universe," said Marta Sewiło, an astronomer with NASA's Goddard Space Flight Center in Greenbelt, Maryland, and lead author on a paper appearing in the Astrophysical Journal Letters.

Astronomers refer to this lack of heavy elements as "low metallicity." It takes several generations of star birth and star death to liberally seed a galaxy with heavy elements, which then get taken up in the next generation of stars and become the building blocks of new planets.

"Young, primordial galaxies simply didn't have enough time to become so chemically enriched," said Sewiło. "Dwarf galaxies like the LMC probably retained this same youthful makeup because of their relatively low masses, which severely throttles back the pace of star formation."

"Due to its low metallicity, the LMC offers a window into these early, adolescent galaxies," noted Remy Indebetouw, an astronomer at the National Radio Astronomy Observatory in Charlottesville, Virginia, and coauthor on the study. "Star-formation studies of this galaxy provide a stepping stone to understand star formation in the early universe."

The astronomers focused their study on the N113 Star Formation Region in the LMC, which is one of the galaxy's most massive and gas-rich regions. Earlier observations of this area with NASA's Spitzer Space Telescope and ESA's Herschel Space Observatory revealed a startling concentration of young stellar objects - protostars that have just begun to heat their stellar nurseries, causing them to glow brightly in infrared light. At least a portion of this star formation is due to a domino-like effect, where the formation of massive stars triggers the formation of other stars in the same general vicinity.

Sewiło and her colleagues used ALMA to study several young stellar objects in this region to better understand their chemistry and dynamics. The ALMA data surprisingly revealed the telltale spectral signatures of dimethyl ether and methyl formate, molecules that have never been detected so far from Earth.

Complex organic molecules, those with six or more atoms including carbon, are some of the basic building blocks of molecules that are essential to life on Earth and - presumably - elsewhere in the universe. Though methanol is a relatively simple compound compared to other organic molecules, it nonetheless is essential to the formation of more complex organic molecules, like those that ALMA recently observed, among others.

If these complex molecules can readily form around protostars, it's likely that they would endure and become part of the protoplanetary disks of young star systems. Such molecules were likely delivered to the primitive Earth by comets and meteorites, helping to jumpstart the development of life on our planet.

The astronomers speculate that since complex organic molecules can form in chemically primitive environments like the LMC, it's possible that the chemical framework for life could have emerged relatively early in the history of the universe.

Contacts and sources:
Charles Blue
The National Radio Astronomy Observatory

This research is presented in a paper titled "'The detection of hot cores and complex organic molecules in the Large Magellanic Cloud," by M. Sewiło, et al., which appears in the Astrophysical Journal Letters.

Red Foxes and Coyotes Go Against Wild Instincts as They Move to Urban Environments

Diverging from centuries of established behavioral norms, red fox and coyote have gone against their wild instincts and learned to coexist in the urban environment of Madison and the University of Wisconsin-Madison campus, according to a recently published study in the journal PLOS One.

Lead author Marcus Mueller, a former graduate student in forest and wildlife ecology, and David Drake, his advisor and a professor in the department, found that over a two-year period, red foxes and coyotes they had radio-tagged were coming into close contact with one another. Some even established home ranges that overlapped.

The findings have implications for wildlife managers working to promote co-existence of species and mitigate conflicts between animals and people in urban settings.

A fox wanders through a city street in Madison, Wisconsin.

Photo courtesy of the UW Urban Canid Project

"It gives us a better understanding of the types of habitats foxes and coyotes prefer to use in developed and residential areas," says Mueller, who now owns a wildlife management company in Milwaukee. "This in turn can help us reduce the kinds of problems that can arise when wild animals and people come into contact."

It also shows that these relatives of dogs have been able to carve out a successful niche for themselves in our own yards, parks and alleys, and are finding ways to coexist with each other to take advantage of this new resource-rich real estate.

"We found an instance where a coyote routinely visited a fox den over about a two or three week period," Drake said. "But the fox and kits did not abandon the den, suggesting to us that they didn't feel predation pressure from the coyote."

In another observation from the study, a red fox and a coyote were seen foraging only meters away from one another and each minded their own business. The urban landscape, Drake suspects, is dissolving hostility between these two species and allowing them to move in close together without conflict.

A map showing some of the places where foxes and coyotes roam in Madison, Wisconsin. It was collected from GPS collars placed on the animals by David Drake, professor of forest and wildlife ecology, and his former graduate student, Marcus Mueller,as part of a study of urban canids. Marked in blue are the coyote home ranges, and in red are the fox home ranges. Fox and coyotes show more tendency to overlap in urban settings than in rural ones, according to a new study published by the researchers in Jan. 2018.

Courtesy of David Drake
"We think that this antagonistic relationship between coyotes and fox is breaking down and relaxing in the urban environment because the food is so abundant that they don't have to compete for a limited resource like they do out in the non-urban areas," Drake said.

This study was conducted in Madison, Wisconsin over a 27-square-mile area encompassing the UW-Madison campus, outlying residential neighborhoods, and some commercial and small natural areas. Drake and Mueller, with help from UW-Madison students and interested members of the public, trapped and radio-tagged 11 coyotes and 12 red foxes. The researchers triangulated the animals' positions using a technology called telemetry once a week for five-hour periods at a time between Jan. 2015 and Dec. 2016.

Drake and Mueller classified the spaces the animals traveled through into five categories based on the amount of human development. This allowed them to determine both species' preferences when it came to where to make their homes with respect to people and to each other.

When selecting their home ranges and establishing dens, coyotes preferred areas with a high proportion of natural space, such as the woods of the UW Arboretum and Picnic Point, instead of developed spaces. Conversely, red foxes opted for open and developed spaces to make their homes and generally avoided more natural areas.

Drake and Mueller's study suggests that the propensity for red foxes to avoid natural spaces may be due to the coyote's role as an apex predator (higher on the food chain). Because they are larger than foxes, coyotes get first dibs on where they call home, which is usually wherever they can be isolated and away from people.

However, studies of red fox in London show that even in a landscape devoid of coyotes, foxes still opt to build their cozy dens in more developed areas of the city. This suggests that red fox in Madison would still choose the same territories even in the absence of coyotes, Drake says.

On Madison's west side, the home ranges of the foxes overlap with the coyotes. Drake suspects this is because Owen Park, the conservation space where the coyotes on the west side have made their home, is smaller than the spaces that the UW Arboretum and Picnic Point coyote packs occupy. This leads them to wander outside their territory and into developed areas, where foxes already live.

On Dec. 15, 2015, a group of student veterinarians draw a blood sample from a sedated, 36-pound adult coyote caught at Curtis Prairie at the Arboretum as part of a research effort to study the behavior of growing fox and coyote populations in Madison. Pictured from left to right are veterinarians Miranda Torkelson, Kaylyn Goertz, Holly Hovanec and Melanie Iverson. The UW Urban Canid Project is led by Professor David Drake (kneeling at center).
Credit: Jeff Miller/UW-Madison
Both animals are crepuscular, or stalk about from sundown to sunup, to avoid human activity. But red foxes are less timid and have been known to den in high-traffic areas of the UW-Madison campus.

Because of the growing tide of canids and wildlife moving into the city, Drake established the Urban Canid Project to encourage citizens and campus visitors to record sightings of animals like red foxes and coyotes, which he hopes will one day replace the need for radio-telemetry tracking. This is time intensive for the scientists, who must search for a signal from the animals' collars to locate them and then stay close enough to track their movements.

Drake has also invited over 500 community members over the past four years to come along with his crews when they are live trapping animals in the winter, and gives dozens of presentations around Madison each year.

"We are seeing a lot of coyote and red fox in Madison and we want to find out what's different in the city that these animals can live in seemingly close proximity with each other when they can't do that in rural areas," Drake says

Contacts and sources:
Mason Muerhoff / David Drake
University of Wisconsin-Madison

This study was funded by the Department of Forest and Wildlife Ecology, the UW-Madison Graduate School, the Milwaukee County Parks Department., and private donations to a gift account for this study through the UW Foundation.

Stellar Magnetism: What's Behind the Most Brilliant Lights in the Sky?

Space physicists at University of Wisconsin-Madison have just released unprecedented detail on a bizarre phenomenon that powers the northern lights, solar flares and coronal mass ejections (the biggest explosions in our solar system).

The data on so-called "magnetic reconnection" came from a quartet of new spacecraft that measure radiation and magnetic fields in high Earth orbit.

"We're looking at the best picture yet of magnetic reconnection in space," says Jan Egedal, a professor of physics and senior author of a study in Physical Review Letters. Magnetic reconnection is difficult to describe, but it can be loosely defined as the merger of magnetic fields that releases an astonishing amount of energy.

Top: Electron movement in solar wind parallels magnetic field direction.
Bottom: After magnetic reconnection, the electrons lose their alignment with Earth’s magnetic field. 
Credit: UW-Madison

Magnetic reconnection remains mysterious, especially since it "breaks the standard law" governing charged particles, or plasma, Egedal says.

Egedal and colleagues studied recordings from Oct. 15, 2016, when the Magnetosphere Multiscale satellite passed through the point where the solar wind meets Earth's magnetic field. "Our data clearly show that electrons suddenly cease to follow magnetic fields and zoom off in another direction, corkscrewing and turning. That begs for explanation," Egedal says.

The activity confirmed the theoretical descriptions of magnetic reconnection. But it violated the standard law governing the behavior of plasmas - clouds of charged particles that comprise, for example, the solar wind. "The 'plasma frozen-in law' says electrons and magnetic fields have to move together always, and suddenly that does not apply here," says Egedal. "It's the clearest example ever to be measured in space, and it blew my mind."

"Our equations tell you reconnection cannot happen, but it does," Egedal says, "and our results show us which factors need to be added to the equations. When the law is violated, we can get an explosion. Even in Earth's moderate magnetic field, reconnection from an area just 10 kilometers across can change the motion of plasma thousands of kilometers distant."

In the 1970s, telescopes orbiting above earth's sheltering magnetic field and atmosphere began returning data on X-rays and other non-visible types of radiation. Rather quickly, the age-old image of the sky as a quiet curtain of stars was yanked aside, revealing a zoo of weird objects, powerful beams and cataclysmic explosions.

All of them needed to be explained, and theorists began to focus on magnetic reconnection, which had been sketched out in 1956. By now, magnetic reconnection has been linked to:

  • Black holes, ultra-dense objects with intense gravity that prohibits even light from leaving.
  • Pulsars, which rotate hundreds of times a second and emit piercing beacons of light.
  • Supernovas, which release energy visible across the galaxies when they explode.
  • Active galactic nuclei, super-bright candles that are visible from billions of light years distance.

"Almost everything we know about the universe comes from the light that reaches us," says Cary Forest, also a professor of physics at UW-Madison. "When one of these fantastic space telescopes sees a massive burst of X-rays that lasts just tens of milliseconds coming from an object in a galaxy far away, this giant burst of energy at such a great distance may reflect a massive reconnection event."

Jan Egedal, professor of physics at UW-Madison who lead an exploration of magnetic reconnection, stands beside a chamber used for experiments in that exotic phenomenon. Magnetic reconnection seems to be involved in some of the most violent explosions in the universe; the recent study was the clearest view of the magnetic reconnection ever measured in space. The results "blew my mind," he says.
Credit: David Tenenbaum/UW-Madison

But there's more, Forest adds. "When neutron stars merge and give off X-rays, that's magnetic reconnection. With these advanced orbiting telescopes, just about everything that's interesting, that goes off suddenly, probably has some major reconnection element at its root."

Magnetic reconnection also underlies the auroras at both poles, Egedal says. When reconnection occurs on the sunward side of Earth, as was seen in the recent study, "it changes the magnetic energy in the system. This energy migrates to the night side, and the same thing happens there, accelerating particles to the poles, forming auroras."

This visualization shows the motion of a single electron undergoing magnetic reconnection. As the spacecraft approaches the reconnection region, it detects first high-energy particles, then low-energy particles. 

Credit: NASA

Beyond offering insight into the role of magnetic reconnection in celestial explosions, eruptions and extraordinary emissions of energy, the observations have a practical side in terms of space weather: explosions of charged matter from the sun can damage satellites and even electrical equipment on the ground. After a solar flare in 1989, for example, the entire power system in Quebec went dark after it picked up a pulse of energy from space. "Across the United States from coast to coast, over 200 power grid problems erupted within minutes of the start of the March 13 magnetic storm," NASA wrote.

Today, Forest notes, modern utility systems contain switches to interrupt the loop of conductors that could become antennas that pick up a problematic pulse from the sun.

"If we understand reconnection better, perhaps we can improve space weather forecasts," says Egedal. "We can look at the sun to predict what may happen in two to four days, which is how long the wind from the sun takes to reach Earth."

Contacts and sources:
David Tenenbaum / Jan Egedal
University of Wisconsin-Madison

The Paradox of Language: Simpler Grammar, Larger Vocabulary

Languages have an intriguing paradox. Languages with lots of speakers, such as English and Mandarin, have large vocabularies with relatively simple grammar. Yet the opposite is also true: Languages with fewer speakers have fewer words but complex grammars.

Why does the size of a population of speakers have opposite effects on vocabulary and grammar?

Through computer simulations, a Cornell cognitive scientist and his colleagues have shown that ease of learning may explain the paradox. Their work suggests that language, and other aspects of culture, may become simpler as our world becomes more interconnected.

Pieter Bruegel the Elder - The Tower of Babel (Vienna) 

Credit: - Google Art Project

Their study was published Jan. 24 in the Proceedings of the Royal Society B: Biological Sciences.

“We were able to show that whether something is easy to learn – like words – or hard to learn – like complex grammar – can explain these opposing tendencies,” said co-author Morten Christiansen, professor of psychology and co-director of the Cognitive Science Program.

The researchers hypothesized that words are easier to learn than aspects of morphology or grammar. “You only need a few exposures to a word to learn it, so it’s easier for words to propagate,” he said.

But learning a new grammatical innovation requires a lengthier learning process. And that’s going to happen more readily in a smaller speech community, because each person is likely to interact with a large proportion of the community, he said. “If you have to have multiple exposures to, say, a complex syntactic rule, in smaller communities it’s easier for it to spread and be maintained in the population.”

Conversely, in a large community, like a big city, one person will talk only to a small proportion the population. This means that only a few people might be exposed to that complex grammar rule, making it harder for it to survive, he said.

In their experiment, researchers simulated communities of individuals who were able to communicate with each other, modeled on real-life interactions on a cellphone network.

Each individual had an inventory of conventions that they could exchange with one another. These were either easier or harder to learn. When one individual met another, they could either use a convention already in their inventory, or they could invent a new convention and use that instead.

“What we did was vary the size of the community and ran simulations on the different variations to see what happened,” Christiansen said.

In larger communities the easy-to-learn conventions swamped the conventions that were harder to learn. And in the smaller communities, the more difficult conventions remained.

“If you don’t get enough exposure to more complex patterns, those patterns are likely to disappear, whereas the simpler patterns that are easy to pick up are likely to survive,” he said. “As the population size of a language community increases, the number of hard-to-learn conventions decreased, whereas the number of easy-to-learn conventions increased.”

This mechanism can explain why all sorts of complex cultural conventions emerge in small communities. For example, bebop developed in the intimate jazz world of 1940s New York City, and the Lindy Hop came out of the close-knit community of 1930s Harlem.

The simulations suggest that language, and possibly other aspects of culture, may become simpler as our world becomes increasingly interconnected, he said. “This doesn’t necessarily mean that all culture will become overly simple. But perhaps the mainstream parts will become simpler over time.”

Not all hope is lost for those who want to maintain complex cultural traditions, he said: “People can self-organize into smaller communities to counteract that drive toward simplification.”

His co-authors on the study, “Simpler Grammar, Larger Vocabulary: How Population Size Affects Language,” are Florencia Reali of Universidad de los Andes, Colombia, and Nick Chater of University of Warwick, England.

Contacts and sources:
Susan Kelley 
Cornell University

Silencing Is Golden: Scientists Image Molecules Vital for Gene Regulation

All the trillions of cells in our body share the same genetic information and are derived from a single, fertilized egg. When this initial cell multiplies during fetal development, its daughter cells become more and more specialized. This process, called cell differentiation, gives rise to all the various cell types, such as nerve, muscle, or blood cells, which are diverse in shape and function and make up tissues and organs. How can the same genetic blueprint lead to such diversity? The answer lies in the way that genes are switched on or off during the course of development.

Scientists at Lawrence Berkeley National Laboratory (Berkeley Lab) have been studying the molecules that act at the genetic level to give rise to different types of cells. Some of these molecules are a complex of proteins called the Polycomb Repressive Complex 2 (PRC2) that is involved in “silencing” genes so that they are not “read” by the cellular machinery that decodes genetic information, effectively keeping the genetic information in the “off” state.

Structure of the human Polycomb Repressive Complex 2 (PRC2) bound to cofactors obtained by cryo-electron microscopy. Both cofactors mimic the histone protein tail to stabilize and stimulate the enzymatic activity of PRC2. 
Structure of the human Polycomb Repressive Complex 2 (PRC2) bound to cofactors obtained by cryo-electron microscopy. Both cofactors mimic the histone protein tail to stabilize and stimulate the enzymatic activity of PRC2. (Credit: Vignesh Kasinath)
Credit: Vignesh Kasinath

In two new studies, a team of researchers led by Eva Nogales, senior faculty scientist in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division, has gained insight into the structure of PRC2 and the ways in which it is regulated to affect gene silencing. Their work was reported on January 18 in the journal Science and on January 29 in Nature Structural and Molecular Biology by Eva Nogales and postdoctoral researchers Vignesh Kasinath and Simon Poepsel.

Both publications provide a structural framework to understand PRC2 function, and in the case of the latter, the structures are the first to illustrate how a molecule of this type engages with its substrate. The structural descriptions of human PRC2 with its natural partners in the cell lend important insight into the mechanism by which the PRC2 complex regulates gene expression. This information could provide new possibilities for the development of therapies for cancer.

PRC2 is a gene regulator that is vital for normal development. Genomic DNA is packaged into nucleosomes, which are formed by histone proteins that have DNA wrapped around them. Histone proteins have long polypeptide tails that can be modified by the addition and removal of small chemical groups. These modifications influence the interaction of nucleosomes with each other and other protein complexes in the nucleus. The function of PRC2 in the cell is to make a particular chemical change in one of the histones. The genes in the regions of the genome that have been modified by PRC2 are switched off, or become silenced.

This montage of the full PRC2 with two nucleosomes is based on the superposition of the cryo-EM maps of PRC2 with and without the nucleosomes to show the consistency of the observed nucleosome binding configuration with the full PRC2 structure. 
Credit: Simon Poepsel

“Not surprisingly, elaborate mechanisms have evolved to ensure that PRC2 marks the correct regions for silencing at the right time,” said Nogales, who is also a Howard Hughes Medical Investigator and professor of Biochemistry, Biophysics and Structural Biology at the University of California, Berkeley. Failure of this regulation not only impairs the process of development, but also contributes to the reversal of cell differentiation and the uncontrolled cell growth that are the hallmarks of cancer. “Therefore,” Nogales continued, “gaining insight into how PRC2 function is adjusted both in space and time is crucial to understanding cell development.”

Nogales and her team use structural biology to elucidate how biomolecules, particularly proteins and nucleic acids (DNA, RNA), are organized and combine to form functional biological assemblies. Obtaining detailed insights into their three-dimensional shape will not only help to understand how they function but also how this function is regulated in the cell. These two studies rely on cryo-electron microscopy for imaging the biomolecules, a technique that can see large biomolecules on a very small scale and in multiple conformations. Kasinath and Poepsel, have now solved the structure of PRC2, which provides a framework to understand how this complex is regulated to modify histone proteins.

The first study, published January 18 in Science by Kasinath, Poepsel, Nogales, and coworkers, visualized the architecture of the complete PRC2 in atomic detail. First author Vignesh Kasinath said, “It took three years of work to obtain this high-resolution structure of all the parts, or subunits, that make up a functional PRC2, as well as visualize how additional protein subunits, called cofactors, may help regulate its activity. Remarkably, both cofactors mimic the histone protein tail in their binding to PRC2 suggesting that cofactors and histone tails together work hand-in-hand to regulate PRC2 function. This structural work holds great promise for new drug development to fight PRC2 dysfunction in cancer.”

From left, Simon Poepsel, Eva Noagles, and Vignesh Kasinath were part of a team of scientists that led the research. 

Credit: Basil Greber

This work is complemented by a second studythat presents snapshots of PRC2 binding to the histone proteins that it modifies as a signal for gene silencing. The structures, which have been published in Nature Structural and Molecular Biology on January 29 by Poepsel, Kasinath and Nogales this week, illustrate beautifully the action of this sophisticated complex. “PRC2 can simultaneously engage two nucleosomes,” said Poepsel, first author of this study. 

“Our cryo-EM images help us understand how the complex can recognize the presence of a histone modification in one nucleosome and place the same tag onto a neighboring nucleosome.” This cascade of activity enables PRC2 to spread this modification over the entire neighboring gene loci, thereby marking it for silencing. Nogales added, “The visualization of such interactions is notoriously hard. We have made an important step forward in our general understanding of how gene regulators can bind to and recognize nucleosomes.”

PRC2 is essential to gene regulation and expression in all multicellular organisms. The findings from both studies open up tremendous possibilities for combatting cancer while simultaneously expanding our knowledge of gene regulation at a molecular level. “Because PRC2 is deregulated in cancers, it makes a good target for potential therapeutics,” said Nogales. The fundamental understanding of PRC2 arising from these studies will have broad implications in both plant and animal biology.

This work was funded by the Howard Hughes Medical Institute and Eli Lilly. This research used cryo-electron microscopy (cryo-EM) and made use of the unique resources of the Bay Area Cryo-EM Facility. Image analysis relied on heavy computational work that was carried out at Berkeley Lab’s National Energy Research Scientific Computing Center (NERSC), a DOE Office of Science User Facility. Vignesh Kasinath was supported by a postdoctoral fellowship from Helen Hay Whitney and Simon Poepsel was supported by the Alexander von Humboldt foundation (Germany) as a Feodor-Lynen postdoctoral fellow.

Contacts and sources:
Dan Krotz
Lawrence Berkeley National Laboratory.

Mammals and Birds Have Better Shot Than Reptiles at Surviving Climate Change

Climate change will be a bigger blow to the survival chances of reptiles than birds and mammals predict scientists. 

New research that analyzed more than 270 million years of data on animals shows that mammals and birds – both warm-blooded animals – may have a better chance of evolving and adapting to the Earth’s rapidly changing climate than their cold-blooded peers, reptiles and amphibians.

“We see that mammals and birds are better able to stretch out and extend their habitats, meaning they adapt and shift much easier,” said Jonathan Rolland, a Banting postdoctoral fellow at the biodiversity research centre at UBC and lead author of the study. “This could have a deep impact on extinction rates and what our world looks like in the future.”

By combining data from the current distribution of animals, fossil records and phylogenetic information for 11,465 species, the researchers were able to reconstruct where animals have lived over the past 270 million years and what temperatures they needed to survive in these regions.

Mammals and birds may have a better chance of adapting to climate change. 
File:Egretta thula at Las Gallinas Wildlife Ponds.jpg
Credit: © Frank Schulenburg / CC BY-SA 3.0

The planet’s climate has changed significantly throughout history and the researchers found that these changes have shaped where animals live. For example, the planet was fairly warm and tropical until 40 million years ago, making it an ideal place for many species to live. As the planet cooled, birds and mammals were able to adapt to the colder temperatures so they were able to move into habitats in more northern and southern regions.

 “It’s possible that they will eventually adapt and could move into these regions but it takes longer for them to change.” said Rolland.

Rolland explained that animals that can regulate their body temperatures, known as endotherms, might be better able to survive in these places because they can keep their embryos warm, take care of their offspring and they can migrate or hibernate.

“These strategies help them adapt to cold weather but we rarely see them in the ectotherms or cold-blooded animals,” he said.

Rolland and colleagues argue that studying the past evolution and adaptations of species might provide important clues to understand how current, rapid changes in temperature impact biodiversity on the planet.

The study was a collaboration between scientists at UBC and in Switzerland and Sweden. It was published this week in Nature Ecology.

Contacts and sources:
Chris Balm
University of Faculty of Science British Columbia

Citation: The impact of endothermy on the climatic niche evolution and the distribution of vertebrate diversity.
Jonathan Rolland, Daniele Silvestro, Dolph Schluter, Antoine Guisan, Olivier Broennimann, Nicolas Salamin..  Nature Ecology & Evolution, 2018; DOI: 10.1038/s41559-017-0451-9