Catherine Zandonella

Genome-wide search reveals new genes involved in long-term memory (Neuron)

Posted on January 22, 2015January 22, 2015 by Catherine Zandonella

By Catherine Zandonella, Office of the Dean for Research

Whole genome expression data reveals new genes involved in long-term memory formation in worms. (Image source: Murphy lab)

A new study has identified genes involved in long-term memory in the worm as part of research aimed at finding ways to retain cognitive abilities during aging.

The study, which was published in the journal Neuron, identified more than 750 genes involved in long-term memory, including many that had not been found previously and that could serve as targets for future research, said senior author Coleen Murphy, an associate professor of molecular biology and the Lewis-Sigler Institute for Integrative Genomics at Princeton University.

“We want to know, are there ways to extend memory?” Murphy said. “And eventually, we would like to ask, are there compounds that could maintain memory with age?”

Long-term memory training in worms (left) led to induction of the transcription factor CREB in AIM neurons (shown by arrows in right). CREB-induced genes were shown to be involved in forming long-term memories in worm neurons. (Image source: Murphy lab)

The newly pinpointed genes are “turned on” by a molecule known as CREB (cAMP-response element-binding protein), a factor known to be required for long-term memory in many organisms, including worms and mice.

“There is a pretty direct relationship between CREB and long-term memory,” Murphy said, “and many organisms lose CREB as they age.” By studying the CREB-activated genes involved in long-term memory, the researchers hope to better understand why some organisms lose their long-term memories as they age.

To identify the genes, the researchers first instilled long-term memories in the worms by training them to associate meal-time with a butterscotch smell. Trained worms were able to remember that the butterscotch smell means dinner for about 16 hours, a significant amount of time for the worm.

The researchers then scanned the genomes of both trained worms and non-trained worms, looking for genes turned on by CREB.

The researchers detected 757 CREB-activated genes in the long-term memory-trained worms, and showed that these genes were turned on primarily in worm cells called the AIM interneurons.

They also found CREB-activated genes in non-trained worms, but the genes were not turned on in AIM interneurons and were not involved in long-term memory. CREB turns on genes involved in other biological functions such as growth, immune response, and metabolism. Throughout the worm, the researchers noted distinct non-memory (or “basal”) genes in addition to the memory-related genes.

The next step, said Murphy, is to find out what these newly recognized long-term memory genes do when they are activated by CREB. For example, the activated genes may strengthen connections between neurons.

Worms are a perfect system in which to explore that question, Murphy said. The worm Caenorhabditis elegans has only 302 neurons, whereas a typical mammalian brain contains billions of the cells.

“Worms use the same molecular machinery that higher organisms, including mammals, use to carry out long-term memory,” said Murphy. “We hope that other researchers will take our list and look at the genes to see whether they are important in more complex organisms.”

Murphy said that future work will involve exploring CREB’s role in long-term memory as well as reproduction in worms as they age.

The team included co-first-authors Postdoctoral Research Associate Vanisha Lakhina, Postdoctoral Research Associate Rachel Arey, and Associate Research Scholar Rachel Kaletsky of the Lewis-Sigler Institute for Integrative Genomics. Additional research was performed by Amanda Kauffman, who earned her Ph.D. in Molecular Biology in 2010; Geneva Stein, who earned her Ph.D. in Molecular Biology in 2014; William Keyes, a laboratory assistant in the Department of Molecular Biology; and Daniel Xu, who earned his B.A. in Molecular Biology in 2014.

Funding for the research was provided by the National Institutes of Health and the Paul F. Glenn Laboratory for Aging Research at Princeton University.

Read the abstract

Citation: Vanisha Lakhina, Rachel N. Arey, Rachel Kaletsky, Amanda Kauffman, Geneva Stein, William Keyes, Daniel Xu, and Coleen T. Murphy. Genome-wide Functional Analysis of CREB/Long-Term Memory-Dependent Transcription Reveals Distinct Basal and Memory Gene Expression Programs, Neuron (2015), http://dx.doi.org/10.1016/j.neuron.2014.12.029.

Dirty pool: Soil’s large carbon stores could be freed by increased CO2, plant growth (Nature Climate Change)

Posted on December 22, 2014 by Catherine Zandonella

By Morgan Kelly, Office of Communications

Soil carbon — Researchers based at Princeton University report that an increase in human-made carbon dioxide in the atmosphere could initiate a chain reaction between plants and microorganisms that would unsettle one of the largest carbon reservoirs on the planet — soil. The researchers developed the first computer model to show at a global scale the complex interaction between carbon, plants and soil. The model projected changes (above) in global soil carbon as a result of root-soil interactions, with blue indicating a greater loss of soil carbon to the atmosphere. (Image by Benjamin Sulman, Princeton Environmental Institute)

An increase in human-made carbon dioxide in the atmosphere could initiate a chain reaction between plants and microorganisms that would unsettle one of the largest carbon reservoirs on the planet — soil.

Researchers based at Princeton University report in the journal Nature Climate Change that the carbon in soil — which contains twice the amount of carbon in all plants and Earth’s atmosphere combined — could become increasingly volatile as people add more carbon dioxide to the atmosphere, largely because of increased plant growth. The researchers developed the first computer model to show at a global scale the complex interaction between carbon, plants and soil, which includes numerous bacteria, fungi, minerals and carbon compounds that respond in complex ways to temperature, moisture and the carbon that plants contribute to soil.

Although a greenhouse gas and pollutant, carbon dioxide also supports plant growth. As trees and other vegetation flourish in a carbon dioxide-rich future, their roots could stimulate microbial activity in soil that in turn accelerates the decomposition of soil carbon and its release into the atmosphere as carbon dioxide, the researchers found.

This effect counters current key projections regarding Earth’s future carbon cycle, particularly that greater plant growth could offset carbon dioxide emissions as flora take up more of the gas, said first author Benjamin Sulman, who conducted the modeling work as a postdoctoral researcher at the Princeton Environmental Institute.

“You should not count on getting more carbon storage in the soil just because tree growth is increasing,” said Sulman, who is now a postdoctoral researcher at Indiana University.

On the other hand, microbial activity initiated by root growth could lock carbon onto mineral particles and protect it from decomposition, which would increase long-term storage of carbon in soils, the researchers report.

Whether carbon emissions from soil rise or fall, the researchers’ model depicts an intricate soil-carbon system that contrasts starkly with existing models that portray soil as a simple carbon repository, Sulman said. An oversimplified perception of the soil carbon cycle has left scientists with a glaring uncertainty as to whether soil would help mitigate future carbon dioxide levels — or make them worse, Sulman said.

“The goal was to take that very simple model and add some of the most important missing processes,” Sulman said. “The main interactions between roots and soil are important and shouldn’t be ignored. Root growth and activity are such important drivers of what goes on in the soil, and knowing what the roots are doing could be an important part of understanding what the soil will be doing.”

The researchers’ soil-carbon cycle model has been integrated into the global land model used for climate simulations by the National Oceanic and Atmospheric Administration’s (NOAA) Geophysical Fluid Dynamics Laboratory (GFDL) located on Princeton’s Forrestal Campus.

Read the abstract

Benjamin N. Sulman, Richard P. Phillips, A. Christopher Oishi, Elena Shevliakova, and Stephen W. Pacala. 2014. Microbe-driven turnover offsets mineral-mediated storage of soil carbon under elevated CO₂. Nature Climate Change. Article published in December 2014 print edition. DOI: 10.1038/nclimate2436

The work was supported by grants from NOAA (grant no. NA08OAR4320752); the U.S. Department of Agriculture (grant no. 2011-67003-30373); and Princeton’s Carbon Mitigation Initiative sponsored by BP.

Computational clues into the structure of a promising energy conversion catalyst (J. Physical Chemistry Letters)

Posted on December 18, 2014December 19, 2014 by Catherine Zandonella

Mosaic structure — Representation of the mosaic texture of β-NiOOH and its possible structures.

By Tien Nguyen, Department of Chemistry

Hydrogen fuel is a promising source of clean energy that can be produced by splitting water into hydrogen and oxygen gas with the help of a catalyst, a material that can speed up the process. Although most known catalysts are inefficient, one called iron-doped nickel oxide is promising but not well understood.

Now researchers at Princeton University have reported new insights into the structure of an active component of the nickel oxide catalyst, known as β-NiOOH, using theoretical calculations. Led by Annabella Selloni, professor of chemistry at Princeton, the findings were published in The Journal of Physical Chemistry Letters on October 28.

“Understanding the structure is the basis for any further study of the material’s properties. If you don’t know the material’s structure you can’t know what it’s doing,” Selloni said. Nickel oxide’s exact structure has been difficult to determine experimentally because it is constantly changing during the reaction.

The research team took a theoretical approach and employed a “genetic algorithm” to search for the structure. Genetic algorithms operate under a set of parameters that draw inspiration from evolution by creating generation after generation of structures to arrive at the most “fit” or most likely candidates.

Taking the results of the genetic algorithm search in combination with computational techniques known as hybrid density functional theory calculations—which estimate a molecule’s electronic structure—co-author Ye-Fei Li, a former postdoctoral researcher at Princeton who is now at Fudan University, and Selloni were able to identify structures of nickel oxide that supported existing observations.

One such observation is the material’s mosaic texture, composed of tiny grain-like microstructures. The researchers propose that these microstructures are stable tunnel structures that relieve stress between layers. Another observed feature is the doubling of the distance between layers made of the same material, referred to as its c axis periodicity, which represents the alternating layers of Ni(OH)₂ and NiO₂formed during the reaction.

Armed with a better understanding of the material’s structure, the scientists hope to further map out its activity in the reaction. “I’m interested in the microscopic mechanisms, what are the electrons and atoms doing?” Selloni said.

Read the abstract

Li, Ye-Fei and Annabella Selloni. “Mosaic Texture and Double c-Axis Periodicity of β–NiOOH: Insights from First-Principles and Genetic Algorithm Calculations.” J. Phys. Chem. Lett. 2014, 5, 3981.

This work was supported by the US Department of Energy, Division of Chemical Sciences, Geosciences and Biosciences under award DE-FG0212ER16286.

Caught in the act: Video system for mapping behaviors (Royal Society: Interface)

Posted on December 12, 2014December 18, 2014 by Catherine Zandonella

By Catherine Zandonella, Office of the Dean for Research

Studies of animal behavior have come a long way from the days when scientists followed their subjects around with pen and notepad. But although cameras have replaced clipboards, evaluating the resulting videos is still a cumbersome process.

To make that job easier and more comprehensive, researchers at Princeton have built a computerized system that analyzes videos to reveal what animals do, how often and for how long, and then generates an easy-to-understand map of the behaviors.

By looking at the map, the researchers can tell what sorts of movements the animal did without having to spend time watching the video. They used the system to track the behavior of fruit flies (Drosophila melanogaster) and found that it accurately detected behaviors such as grooming a leg or waggling a wing.

Map that indicates the type of movements of a fly. — Princeton researchers have developed a computerized system for evaluating animal behavior. A video system records an animal, in this case a fruit fly, for one hour. Then a computer program analyzes the video to create a map of the behaviors. The map can reveal, for example, the differences in movements between male and female fruit flies. (Image source: Joshua Shaevitz)

The researchers’ goal was a system that could create accurate records of behaviors for use in studies of the mechanisms behind those behaviors – in other words, the genes and brain circuits that govern movements. Knowing which genes and neural circuits govern behavior will help answer basic scientific questions and could shed light on the mechanisms behind conditions such as autism.

Described in the journal The Royal Society Interface, the system was built for monitoring Drosophila flies, which are commonly used in studies of genes, but the researchers say that the system can also analyze the movements of other creatures, including worms, mice and humans.

The new system is a significant advance over current approaches because it takes note of all the animal’s activities, not just behaviors that seem important to researchers, said Joshua Shaevitz, associate professor of physics and the Lewis-Sigler Institute for Integrative Genomics, who led the study. “We don’t know which behaviors are important to a fruit fly, or a mouse,” he said. “Instead, we ask the computer to find behaviors that are frequently repeated, which tend to be the ones that are worth studying.”

Researchers need reliable ways to catalog behaviors in studies of how genes and neural pathways control behavior. A common experiment involves deleting a gene in an organism such as a fruit fly or worm to look for any resulting loss of function or change in the organism’s behavior. But without reliable behavioral data, researchers cannot make firm conclusions about the role of the deleted gene.

With the new system, a high-speed camera records the animal for a given period of time, and the computer sorts the resulting video frames. For the current study, the researchers recorded individual fruit flies for a period of one hour, resulting in an enormous amount of data. The challenge was how to sort the frames and translate the images into data that could be evaluated.

“We have to figure out how the body parts of the fly are positioned in relation to each other at each point in time, and then find a way to tell how those body parts are moving, while keeping the amount of data manageable using the available computing power,” said Gordon Berman, an associate research scholar in the Lewis-Sigler Institute for Integrative Genomics. “Then you have to project the information into some form that allows you to understand the data.”

The researchers accomplished this goal by writing a computer program that converts the information about a fly’s position and movements into mathematical descriptions that are then grouped according to their similarities. The computer places these groupings on a two-dimensional map, so that different regions of the map represent different types of movements.

A computerized system for evaluating animal behavior. — Individual fruit flies were filmed for about one hour, resulting in over 300,000 video frames. Then, a computer program converts the fly’s position in each frame into mathematical descriptions that represent movements. The computer then groups the movements on a map, so that one region of the map represents leg movements while another represents wing movements, and so on. By looking at the map, the researchers can tell what sorts of movements the fly did, such as grooming its front leg, grooming its head, or waggling its wing. (Image source: Joshua Shaevitz)

To verify that the system worked, the researchers collected data from 50 male and 50 female flies. They identified hundreds of behaviors, including ones that had never been documented and others that were consistent with findings from human observers. For example, some of the findings consistent with previous observations were that male fruit flies kick out their legs when grooming, whereas females don’t, and that young females are more active than young males. “Males and females do things slightly differently, and we can pick up on that right away,” said Shaevitz.

Male fruit flies kick out with their legs when grooming:

whereas females do not:

The team is now expanding the capabilities of the method, Shaevitz said. “The technique that we have developed can also be used to study patterns of behavior in humans,” Shaevitz said. “There are several conditions that are diagnosed on the basis of behavior, such as autism. Having a more quantitative way of measuring behavior could improve the accuracy of diagnoses.”

The study co-authors included William Bialek, Princeton’s John Archibald Wheeler/Battelle Professor in Physics and the Lewis-Sigler Institute for Integrative Genomics, and Daniel Choi, a graduate student working with Shaevitz.

The work was funded through awards from the National Institutes of Health (GM098090, GM071508), the National Science Foundation (PHY 0957573, PHY 1066293), the Pew Charitable Trusts, the Swartz Foundation and the Alfred P. Sloan Foundation.

Read the abstract

Gordon J. Berman, Daniel M. Choi, William Bialek, Joshua W. Shaevitz. Mapping the stereotyped behaviour of freely moving fruit flies. The Journal of the Royal Society Interface (2014). DOI: 10.1098/rsif.2014.0672 Published online 20 August 2014 http://rsif.royalsocietypublishing.org/content/11/99/20140672

Quantum mechanical calculations reveal the hidden states of enzyme active sites (Nature Chemistry)

Posted on November 21, 2014 by Catherine Zandonella

[2Fe–2S] cluster in front of a leaf. (Image by C. Todd Reichart) — Researchers at Princeton University have reported the first direct observation of the electronic states of iron-sulfur clusters, common to many enzyme active sites. Iron-sulfur cluster in front of a leaf. (Image by C. Todd Reichart)

By Tien Nguyen, Department of Chemistry

Enzymes carry out fundamental biological processes such as photosynthesis, nitrogen fixation and respiration, with the help of clusters of metal atoms as “active” sites. But scientists lack basic information about their function because the states thought to be critical to their chemical abilities cannot be experimentally observed.

Now, researchers at Princeton University have reported the first direct observation of the electronic states of iron-sulfur clusters, common to many enzyme active sites. Published on August 31 in the journal Nature Chemistry, the states were revealed by computing the complicated quantum mechanical behavior of the electrons in the clusters.

“These complexes were thought of as impossible to model, due to the complexity of the quantum mechanics,” said Garnet Chan, the A. Barton Hepburn Professor of Chemistry and corresponding author on the paper.

In these systems, the electrons interact strongly with each other, their movements resembling a complicated dance. To reduce the complexity, the researchers drew on a new understanding, gained from fundamental work in quantum information theory, that the motion of the electrons had a special pattern.

“At first glance, the electrons appear to move in a complicated way, but eventually you realize that they only care about what their immediate neighbors are doing, similar to being in a crowded room. This restriction on their behavior leads to important simplifications: the calculations become very difficult rather than impossible — it’s just on the edge of what can be done,” Chan said.

Using their new method, Chan and coworkers found that iron-sulfur clusters possess an order of magnitude more accessible electronic states than previously reported. The researchers suggested that this unusual richness might explain their ubiquity in biological processes.

This finding, that there are many more available electronic states than previously thought, presents many different chemical possibilities. What if these clusters simultaneously used a combination of mechanisms, instead of the accepted chemical idea that there is one distinct electronic pathway, Chan wondered. To test that idea and learn more about the clusters’ behavior, the researchers plan to extend their calculations to observe a chemical transformation in action.

“If you want to understand why iron-sulfur clusters are a ubiquitous biological motif and how we can create even better synthetic analogs, then you need to know what the electrons are doing,” Chan said. “Now we’ve caught a first glimpse as to what they are getting up to.”

Read the abstract.

Sharma, S.; Sivalingam, K.; Neese, F.; Chan, K.-L. G. “Low-energy spectrum of iron sulfur clusters directly from many-particle quantum mechanics.” Nat. Chem. 2014, 6, 927.

This work was supported by the US National Science Foundation (CHE-1265277) and used software developed with the support of OCI-1265278. F.N. and K.S acknowledge financial support from the Max Planck Society, the University of Bonn and the SFB 813 “Chemistry at Spin Centers.”

Genetic tweak gave yellow fever mosquitoes a nose for human odor (Nature)

Posted on November 12, 2014 by Catherine Zandonella

-By Morgan Kelly, Office of Communications

2014_11_12_Mosquito1 One of the world’s deadliest mosquitoes sustains its taste for human blood thanks in part to a genetic tweak that makes it more sensitive to human odor, according to new research.

Researchers report in the journal Nature that the yellow fever mosquito contains a version of an odor-detecting gene in its antennae that is highly attuned to sulcatone, a compound prevalent in human odor. The researchers found that the gene, AaegOr4, is more abundant and more sensitive in the human-preferring “domestic” form of the yellow fever mosquito than in its ancestral “forest” form that prefers the blood of non-human animals.

The research provides a rare glimpse at the genetic changes that cause behaviors to evolve, explained first author Carolyn “Lindy” McBride, an assistant professor in Princeton University’s Department of Ecology and Evolutionary Biology and the Princeton Neuroscience Institute who conducted the work as a postdoctoral researcher at the Rockefeller University. Uncovering the genetic basis of changes in behavior can help us understand the neural pathways that carry out that behavior, McBride said.

The research also could help in developing better ways to stem the yellow fever mosquito’s appetite for humans, McBride said. The yellow fever mosquito is found in tropical and subtropical areas worldwide and is the principal carrier of yellow fever, the measles-like dengue fever, and the painful infection known as chikungunya. Yellow fever annually kills tens of thousands of people worldwide, primarily in Africa, while dengue fever infects hundreds of millions. The research also suggests a possible genetic root for human preference in other mosquitoes, such as malaria mosquitoes, although that species is genetically very different from the yellow fever mosquito.

“The more we know about the genes and compounds that help mosquitoes target us, the better chance we have of manipulating their response to our odor” McBride said, adding that scent is not the only driver of mosquito behavior, but it is a predominant factor.

The researchers first conducted a three-part series of experiments to establish the domestic yellow fever mosquito’s preference for human scent. Forest and domestic mosquitoes were put into a large cage and allowed to bite either a guinea pig or a researcher’s arm. Then the mosquitoes were allowed to choose between streams of air that had passed over a guinea pig or human arm. Finally, to rule out general mosquito attractants such as exhaled carbon dioxide, mosquitoes were allowed to choose between the scent of nylon sleeves that had been in contact with a human or a guinea pig.

In all three cases, the domestic form of the yellow fever mosquito showed a strong preference for human scent, while the forest form primarily chose the guinea pig. Although domestic mosquitoes would sometimes go for the guinea pig, it happened very rarely, McBride said.

McBride and colleagues then decided to look for differences in the mosquitoes’ antennae, which are equivalent to a human’s nose. They interbred domestic and forest mosquitoes, then interbred their offspring to create a second hybrid generation. The genomes of these second-generation hybrids were so completely reshuffled that when the researchers compared the antennae of the human- and guinea pig-preferring individuals they expected to see only genetic differences linked directly to behavior, McBride said.

The researchers found 14 genes that differed between human- and guinea pig-preferring hybrids — two of them were the odorant receptors Or4 and Or103. Choosing to follow up on Or4, the researchers implanted the gene into fruit-fly neurons. They found that the neurons exhibited a burst of activity when exposed to sulcatone, but no change when exposed to guinea pig odors. McBride plans to further study Or103 and other genes that could be linked to host preference at Princeton.

Gene expression — A comparison of domestic and forest form antennae found that two odorant-receptor genes, Or4 and Or103, are more “expressed,” or abundant, in the human-preferring domestic mosquitoes (top bar) than in the forest form that feeds primarily on non-human animals (bottom bar). The color scale indicates the level of gene expression with purple standing for the least amount and red for the most. The numbers to the left of the colored bars represent three different colonies of each mosquito form. The slanted line under each gene’s name points to the level of expression of that gene in each colony. (Image courtesy of Carolyn McBride, Department of Ecology and Evolutionary Biology and the Princeton Neuroscience Institute)

This work provides insight into how the domestic form of the yellow fever mosquito evolved from its animal-loving ancestor into a human-biting specialist, McBride said. “At least one of the things that happened is a retuning of the ways odors are detected by the antennae,” she said. “We don’t yet know whether there are also differences in how odor information is interpreted by the brain.”

This work was supported in part by the National Institutes of Health (NIDCD grant no. DC012069; NIAID grant no. HHSN272200900039C; and NCATS CTSA award no. 5UL1TR000043); the Swedish Research Council and the Swedish University of Agricultural Science’s Insect Chemical Ecology, Ethology and Evolution initiative; and the Howard Hughes Medical Institute.

Read the abstract.

Carolyn S. McBride, Felix Baier, Aman B. Omondi, Sarabeth A. Spitzer, Joel Lutomiah, Rosemary Sang, Rickard Ignell, and Leslie B. Vosshall. 2014. Evolution of mosquito preference for humans linked to an odorant receptor. Nature. Article published in print Nov. 13, 2014. DOI: nature13964.3d

European satellite could discover thousands of planets in Earth’s galaxy (arXiv)

Posted on November 5, 2014November 6, 2014 by Catherine Zandonella

By Morgan Kelly, Office of Communications

Celestial Sphere — Princeton University and Lund University researchers project that the recently launched European satellite Gaia could discover tens of thousands of planets during its five-year mission. In this image, the colored portions indicate the number of observations Gaia would make of a particular part of the sky during its mission; the scale at the bottom indicates the number of observations from zero (purple) to 200 (red). The total number of observations of any part of the sky ranges from about 60 at low ecliptic latitudes to about 80 at high ecliptic latitudes, with a maximum of about 150-200 at intermediate latitudes. From these many different observations of each star, the highly accurate Gaia measurements will reveal the tiny star motion, or “wobble,” that results from any orbiting planet. (Image by Lennart Lindegren, Lund University)

A recently launched European satellite could reveal tens of thousands of new planets within the next few years, and provide scientists with a far better understanding of the number, variety and distribution of planets in our galaxy, according to research published today.

Researchers from Princeton University and Lund University in Sweden calculated that the observational satellite Gaia could detect as many as 21,000 exoplanets, or planets outside of Earth’s solar system, during its five-year mission. If extended to 10 years, Gaia could detect as many as 70,000 exoplanets, the researchers report. The researchers’ assessment is accepted in the Astrophysical Journal and was published Nov. 6 in advance-of-print on arXiv, a preprint database run by Cornell University.

Exoplanets will be an important “by-product” of Gaia’s mission, explained first author Michael Perryman, who made the assessment while serving as Princeton’s Bohdan Paczyński Visiting Fellow in the Department of Astrophysical Sciences. Built and operated by the European Space Agency (ESA) and launched in December 2013, Gaia will capture the motion, physical characteristics and distance from Earth — and one another — of roughly 1 billion objects, mostly stars, in the Milky Way galaxy with unprecedented precision. The presence of an exoplanet will be determined by how its star “wobbles” as a result of the planet’s orbit around it.

More important than the numbers of predicted discoveries are the kinds of planets that the researchers expect Gaia to detect, many of which — such as planets with multi-year orbits that pass directly, or transit, in front of their star as seen from Earth — are currently difficult to find, Perryman said. The satellite’s instruments could reveal objects that are considered rare in the Milky Way, such as an estimated 25 to 50 Jupiter-sized planets that orbit faint, low-mass stars known as red dwarfs. Unique planets and systems — such as planets that orbit in the opposite direction of their companions — can inspire years of research, he said.

Transit Distances — One of the main objectives of the Gaia mission is to establish the currently uncertain distance from Earth to various stars using high-precision triangulation, which would allow a much better understanding of the properties of the stars and the planets orbiting them. Of the 1,163 confirmed transiting planets, which pass directly in front of their stars as seen from Earth, there are 644 distinct host stars; less than 200 have accurately known distances from Earth. This image shows the distances from Earth (center) to the stars (black dots) of transiting exoplanets. The inner dashed circle has a radius of 100 parsecs (about 326 light years) with the middle and outer circles corresponding to 500 parsecs (1,630 light years) and 1,000 parsecs (3,260 light years), respectively. The cluster of points to the lower right represents the transiting planets discovered by NASA’s Kepler satellite. For each star, the straight lines extending from the circle indicate the current uncertainty of its distance from Earth. (Image by Michael Perryman)

“It’s not just about the numbers. Each of these planets will be conveying some very specific details, and many will be highly interesting in their own way,” Perryman said. “If you look at the planets that have been discovered until now, they occupy very specific regions of discovery space. Gaia will not only discover a whole list of planets, but in an area that has not been thoroughly explored so far.”

Ultimately, a comprehensive census allows scientists to more accurately determine how many planets and planetary systems exist, the detailed properties of those planets, and how they are positioned throughout the galaxy, Perryman said.

Perryman worked with Joel Hartman, an associate research scholar in Princeton’s astrophysical sciences department, Gáspár Bakos, an associate professor of astrophysical sciences, and Lennart Lindegren, a professor of astronomy at Lund University. Gaia is based on a satellite proposal led by Lindegren and Perryman that was submitted to the ESA in 1993.

Research on exoplanets has increased dramatically in the 15 years since Gaia was accepted by the ESA in 2000. The new estimate is based on a highly detailed model of how stars and planets are positioned in the Milky Way; more accurate details of Gaia’s measurement and data-analysis capabilities; and current estimates of exoplanet distributions, particularly those derived from NASA’s Kepler satellite, which has identified nearly 1,000 confirmed planets and more than 3,000 candidates. Crucial to conducting the assessment is the much-improved knowledge that now exists about distant planets, Perryman said, such as the types of stars that exoplanets orbit.

The first exoplanet was detected in 1995. Nearly 1,900 have since been discovered. Bakos, who focuses much of his research on exoplanets, launched and oversees HATNet (Hungarian-made Automated Telescope Network) and HATSouth, planet-hunting networks of fully automated, small-scale telescopes installed on four continents that scan the sky every night for planets as they transit in front of their parent star. The projects have discovered more than 50 planets since 1999.

“Our assessment will help prepare exoplanet researchers for what to expect from Gaia,” Perryman said. “We’re going to be adding potentially 20,000 new planets in a completely new area of discovery space. It’s anyone’s guess how the field will develop as a result.”

This work was partly supported by the National Science Foundation (grant no. 1108686) and NASA (grant no. NNX13AJ15G).

Read the article.

Michael Perryman, Joel Hartman, Gáspár Bakos and Lennart Lindegren. 2014. Astrometric exoplanet detection with Gaia. Astrophysical Journal. Article first published to the arXiv preprint database: Nov. 6, 2014.

When less is more: Death in moderation boosts population density in nature (Trends in Ecology and Evolution)

Posted on November 4, 2014November 4, 2014 by Catherine Zandonella

A study by Princeton researchers and European colleagues found that the positive effect that mortality can have on populations depends on the size and developmental stage of the creatures that die. The finding could aid the management of wildlife and fish such as the Atlantic cod (Image source: NOAA). — A study by Princeton researchers and European colleagues found that the positive effect that mortality can have on populations depends on the size and developmental stage of the creatures that die. The finding could aid the management of wildlife and fish such as Atlantic cod (Image source: NOAA).

By Morgan Kelly, Office of Communications

In nature, the right amount of death at the right time might actually help boost a species’ population density, according to new research that could help in understanding animal populations, pest control and managing fish and wildlife stocks.

In a paper in the journal Trends in Ecology and Evolution, a Princeton University researcher and European colleagues conclude that the kind of positive population effect an overall species experiences from a loss of individuals, or mortality, depends on the size and developmental stage of the creatures that die.

If many juveniles perish, more adults are freed up to reproduce, but if more adults die, the number of juveniles that mature will increase because density dependence is relaxed, explained co-author Anieke van Leeuwen, a postdoctoral researcher in Princeton’s Department of Ecology and Evolutionary Biology. Van Leeuwen worked with first author Arne Schröder, a postdoctoral research fellow at the Leibniz-Institute of Freshwater Ecology and Inland Fisheries in Berlin, and Tom Cameron, a lecturer in aquatic community ecology at the University of Essex in the United Kingdom.

This dynamic wherein the loss of individuals in one developmental stage translates to more robust individuals in another stage can be important to managing wildlife, pests or resource stocks, van Leeuwen said. For instance, targeting the adults of an invasive insect could have a counterproductive effect of making more food available to growing larvae, she said.

“It doesn’t matter which developmental stage you target, if you impose mortality on one you will get overcompensation on the opposite end of the size range,” van Leeuwen said. “This effect can be especially advantageous in situations where we want to manage resources we want to harvest. Knowing that there are potential effects that result in an increase in that segment of the population we want to encourage is highly relevant.”

At a certain point, of course, mortality becomes too high and the species as a whole declines, the researchers report.

The researchers compared existing theoretical and experimental work on the effect of mortality on population density to resolve various inconsistencies between the two. Existing mathematical models have predicted this phenomenon, and laboratory and field studies have shown that the effect holds true for a variety of animal species.

Many ecological theories and models, however, have ignored differences in body size and development, and predicted that a modest amount of mortality would result in an increase in the total number of individuals, the researchers wrote. On the other hand, experiments have predominantly shown — along with certain models — that mortality has a positive effect within certain life stages or size classes. The researchers concluded that the overlap of experimental and theoretical data indicates that the benefit of mortality is likely divided by developmental stage. In addition, the number of species in which the phenomenon has been observed makes it commonplace in the natural world.

This work was supported by the Journal of Experimental Biology; the Swedish Research Council and the Leibniz-Institute of Freshwater Ecology and Inland Fisheries; the University of Leeds, the National Environment Research Council (grant no. NE/C510467/1) and the European Commission Intra-European Fellowship (FANTISIZE, #275873); and the National Science Foundation (grant no. 1115838).

Read the abstract.

Citation: Schröder, Arne, Anieke van Leeuwen, Thomas C. Cameron. 2014. When less is more: Positive population-level effects of mortality. Trends in Ecology and Evolution. Published in November 2014 edition: Vol. 29, issue 11, pp. 614–624. DOI: 10.1016/j.tree.2014.08.006

Scientists use plasma shaping to control turbulence in stellarators (Phys. Rev. Lett.)

Posted on October 10, 2014 by Catherine Zandonella

By John Greenwald, Princeton Plasma Physics Laboratory

Stellerator — Magnetic field strength in a turbulence-optimized stellarator design. Regions with the highest strength are shown in yellow. (Source: PPPL)

Researchers at the U.S. Department of Energy’s Princeton Plasma Physics Laboratory (PPPL) and the Max Planck Institute of Plasma Physics in Germany have devised a new method for minimizing turbulen

ce in bumpy donut-shaped experimental fusion facilities called stellarators. This week in Physical Review Letters, these authors describe an advanced application of the method that could help physicists overcome a major barrier to the production of fusion energy in such devices, and could also apply to their more widely used symmetrical donut-shaped cousins called tokamaks. This work was supported by the DOE Office of Science.

Turbulence allows the hot, charged plasma gas that fuels fusion reactions to escape from the magnetic fields that confine the gas in stellarators and tokamaks. This turbulent transport occurs at comparable levels in both devices, and has long been recognized as a challenge for both in producing fusion power economically.

“Confinement bears directly on the cost of fusion energy,” said physicist Harry Mynick, a PPPL coauthor of the paper, “and we’re finding how to reshape the plasma to enhance confinement.”

The new method uses two types of advanced computer codes that have only recently become available. The authors modified these codes to address turbulent transport, evolving the starting design of a fusion device into one with reduced levels of turbulence. The current paper applies the new method to the Wendelstein 7-X stellarator, soon to be the world’s largest when construction is completed in Greifswald, Germany.

Results of the new method, which has also been successfully applied to the design of smaller stellarators and tokamaks, suggest how reshaping the plasma in a fusion device could produce much better confinement. Equivalently, improved plasma shaping could produce comparable confinement with reduced magnetic field strength or reduced facility size, with corresponding reductions in the cost of construction and operation.

The simulations further suggest that a troublesome characteristic called “stiffness” could occur in reactor-sized stellarators. Stiffness, the tendency for heat to rapidly escape as the plasma temperature gradient rises above a threshold, has been observed in tokamaks but less so in stellarators. The possibility that stiffness might be present in reactor-sized stellarators, wrote the authors, could stimulate efforts “toward further optimizing stellarator magnetic fields for reduced turbulence.”

PPPL, on Princeton University’s Forrestal Campus in Plainsboro, New Jersey, is devoted to creating new knowledge about the physics of plasmas — ultra-hot, charged gases — and to developing practical solutions for the creation of fusion energy. Fusion takes place when atomic nuclei fuse and release a burst of energy. This compares with the fission reactions in today’s nuclear power plants, which operate by splitting atoms apart.

Results of PPPL research have ranged from a portable nuclear materials detector for anti-terrorist use to universally employed computer codes for analyzing and predicting the outcome of fusion experiments. The laboratory is managed by the University for the U.S. Department of Energy’s Office of Science, which is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time.

Read the abstract.

Xanthopoulos, P.; Mynick, H.E.; Helander, P.; Turkin, Y.; Plunk, G.G.; Jenko, F.; Görler, T.; Told, D.; Bird, T.; J.H.E. Controlling turbulence in present and future stellarators. Article published in Physical Review Letters on Oct. 7, 2014.

Unstoppable magnetoresistance (Nature)

Posted on October 9, 2014October 10, 2014 by Catherine Zandonella

Mazhar Ali (left) and Steven Flynn (right), co-authors on the Nature paper. Photo by C. Todd Reichert. — Mazhar Ali (left) and Steven Flynn (right), co-authors on the Nature paper. Photo by C. Todd Reichart.

by Tien Nguyen, Department of Chemistry

Mazhar Ali, a fifth-year graduate student in the laboratory of Robert Cava, the Russell Wellman Moore Professor of Chemistry at Princeton University, has spent his academic career discovering new superconductors, materials coveted for their ability to let electrons flow without resistance. While testing his latest candidate, the semimetal tungsten ditelluride (WTe₂), he noticed a peculiar result.

Ali applied a magnetic field to a sample of WTe₂, one way to kill superconductivity if present, and saw that its resistance doubled. Intrigued, Ali worked with Jun Xiong, a student in the laboratory of Nai Phuan Ong, the Eugene Higgins Professor of Physics at Princeton, to re-measure the material’s magnetoresistance, which is the change in resistance as a material is exposed to stronger magnetic fields.

“He noticed the magnetoresistance kept going up and up and up—that never happens.” said Cava. The researchers then exposed WTe₂ to a 60-tesla magnetic field, close to the strongest magnetic field mankind can create, and observed a magnetoresistance of 13 million percent. The material’s magnetoresistance displayed unlimited growth, making it the only known material without a saturation point. The results were published online on September 14 in the journal Nature.

Crystal structure of WTe2 (Source: Nature)

Electronic information storage is dependent on the use of magnetic fields to switch between distinct resistivity values that correlate to either a one or a zero. The larger the magnetoresistance, the smaller the magnetic field needed to change from one state to another, Ali said. Today’s devices use layered materials with so-called “giant magnetoresistance,” with changes in resistance of 20,000 to 30,000 percent when a magnetic field is applied. “Colossal magnetoresistance” is close to 100,000 percent, so for a magnetoresistance percentage in the millions, the researchers hoped to coin a new term.

Their original choice was “ludicrous” magnetoresistance, which was inspired by “ludicrous speed,” the fictional form of fast-travel used in the comedy “Spaceballs.” They even included an acknowledgement to director Mel Brooks. After other lab members vetoed “ludicrous,” the researchers considered “titanic” before Nature editors ultimately steered them towards the term “large magnetoresistance.”

Terminology aside, the fact remained that the magnetoresistance values were extraordinarily high, a phenomenon that might be understood through the structure of WTe₂. To look at the structure with an electron microscope, the research team turned to Jing Tao, a researcher at Brookhaven National Laboratory.

“Jing is a great microscopist. They have unique capabilities at Brookhaven,” Cava said. “One is that they can measure diffraction at 10 Kelvin (-441 °F). Not too many people on Earth can do that, but Jing can.”

Electron microscopy experiments revealed the presence of tungsten dimers, paired tungsten atoms, arranged in chains responsible for the key distortion from the classic octahedral structure type. The research team proposed that WTe₂ owes its lack of saturation to the nearly perfect balance of electrons and electron holes, which are empty docks for traveling electrons. Because of its structure, WTe₂ only exhibits magnetoresistance when the magnetic field is applied in a certain direction. This could be very useful in scanners, where multiple WTe₂ devices could be used to detect the position of magnetic fields, Ali said.

“Aside from making devices from WTe₂, the question to ask yourself as a scientist is: How can it be perfectly balanced, is there something more profound,” Cava said.

Read the abstract.

Ali, M. N.; Xiong, J.; Flynn, S.; Tao, J.; Gibson, Q. D.; Schoop, L. M.; Haldolaarachchige, N.; Hirschberger, M.; Ong, N. P.; Cava, R. J. “Large, non-saturating magnetoresistance in WTe₂.” Nature. Published online September 14. 514, 205–208 (09 October 2014).

This research was supported by the Army Research Office, grants W911NF-12-1-0461 and W911NF-11-1-0379, and the NSF MRSEC Program Grant DMR-0819860. This work was supported by the US Department of Energy’s Basic Energy Sciences (DOE BES) project “Science at 100 Tesla.” The electron microscopy study at Brookhaven National Laboratory was supported by the DOE BES, by the Materials Sciences and Engineering Division under contract DE-AC02-98CH10886, and through the use of the Center for Functional Nanomaterials.

Author: Catherine Zandonella

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