Study reveals mechanism behind enzyme that tags unneeded DNA (Nature Chem. Bio.)

Designer chromatin experiments
Graphical representation of designer chromatin experiments. Image courtesy of the Muir lab.

By Tien Nguyen, Department of Chemistry

Researchers have discovered the two-step process that activates an essential human enzyme, called Suv39h1, which is responsible for organizing large portions of the DNA found in every living cell.

For any particular cell, such as a skin or brain cell, much of this genetic information is extraneous and must be packed away to allow sufficient space and resources for more important genes. Failure to properly pack DNA jeopardizes the stability of chromosomes and can result in severe diseases. Suv39h1 is one of the main enzymes that chemically mark the irrelevant regions of DNA to be compacted by cellular machinery, but little is known about how it installs its tag.

Now, scientists at Princeton have used ‘designer chromatin’ templates – highly customized replicas of cellular DNA and histone proteins, the scaffolding proteins around which DNA is wrapped – to reveal new details about Suv39h1’s mechanism. The researchers investigated how Suv39h1 employs a positive feedback loop to chemically tag thousands of adjacent histones, thus signaling the cell to stow away these underlying, unnecessary DNA sequences. The work was published in in the journal Nature Chemical Biology.

“One of the things that has always fascinated me about feedback loops is that they’re super dangerous. If you make a mistake once, you end up getting reinforcement through the feedback loop,” said Manuel Müller, a postdoctoral researcher in the Muir lab and lead author on the study. “So how does Suv39h1 keep itself in check?”

Suv39h1 had been known to possess two distinct parts, but the new research revealed how they work together in order to ‘switch on’ the enzyme. One part of the enzyme, known as the chromodomain, is constantly exposed and seeks out specific chemical tags, known as a methyl groups, located at predetermined sites on histones. When the chromodomain finds these groups in the genome, it locks onto the spot and allows the other part, the enzymatic core, to install more methyl tags at adjacent histones.

“The second, anchoring step wasn’t really known before. It provides an extra level of control and allows the process to be extremely fine-tuned,” Müller said. A similar mechanism may be employed by many other enzymes operating on chromatin, given that they contain similar components of a feedback loop.

To understand how the enzyme carries out this process, the researchers synthesized complex chromatin templates that were three times larger than previously reported models. They divided the template into three blocks that could each be manipulated in various ways. For example, a block could be prepared with the chemical tag present, absent or mutated such that tagging can’t occur. “The different blocks should signal to the enzyme either start here or feel free to spread here or absolutely stop here,” said Glen Liszczak, a co-author and postdoctoral researcher in the Muir lab.

By rearranging the various domains, the research team observed where the enzyme spread its mark across the genome. They found that Suv39h1 preferred to spread across small distances, but that it could reach sequences further along if chromatin folding decreased the physical distance in space.

“We’ve learned something new about this enzyme, something that we couldn’t have without the pinpoint precision that the designer chromatin offers,” Liszczak said. “There are a lot of questions that our lab has been interested in that we can now start to answer.”

The research was funded by the Swiss National Science Foundation (postdoctoral fellowships) and the US National Institutes of Health (R01-GM107047).

Read the abstract or full article.

Müller, M. M.; Fierz, B.; Bittova, L.; Liszczak, G.; Muir, T. W. “A two-state activation mechanism controls the histone methyltransferase Suv39h1.” Nature Chem. Bio. Available online January 25, 2016.

 

Antibiotic’s killer strategy revealed (PNAS)

Marine algae
Satellite image of a E. huxleyi marine algae bloom. (Image: NASA)

By Tien Nguyen, Department of Chemistry

Using a special profiling technique, scientists at Princeton have determined the mechanism of action of a potent antibiotic, known as tropodithietic acid (TDA), leading them to uncover its hidden ability as a potential anticancer agent.

TDA is produced by marine bacteria belonging to the roseobacter family, which exist in a unique symbiosis with microscopic algae. The algae provide food for the bacteria, and the bacteria provide protection from the many pathogens of the open ocean.

“This molecule keeps everything out,” said Mohammad Seyedsayamdost, an assistant professor of chemistry at Princeton and corresponding author on the study published in the Proceedings of the National Academy of Science. “How could something so small be so broad spectrum? That’s what got us interested,” he said.

In collaboration with researchers in the laboratory of Zemer Gitai, an associate professor of molecular biology at Princeton, the team used a laboratory technique referred to as bacterial cytological profiling to investigate the mode of action of TDA. This method involves destroying bacterial cells with the antibiotic in the presence of a set of dyes, and then visually assessing the aftermath. “The key assumption is that dead cells that look the same probably died by the same mechanism,” he said.

marine algae
Scanning electron microscope image of E. huxleyi (Image credit. M. Seyedsayamdost)

The team used three dyes to evaluate 13 different features of the deceased cells, such as cell membrane thickness and nucleoid area, comprising TDA’s cytological profile. By comparing to profiles of known drugs, the researchers found a match with a class of compounds called polyethers, which possess anticancer activity.

Given their similar profiles, Seyedsayamdost and coworkers hypothesized that TDA might exhibit anticancer properties as well, and indeed observed its strong anticancer activity in a screen against 60 different cancer cell lines. “The strength of this profiling technique is that it tells you how to repurpose molecules,” Seyedsayamdost said.

The researchers were surprised by the compounds’ shared mode of action because unlike the small sized TDA, polyether compounds are quite large. But through different chemical reactions, they are both able to cause chemical disruptions in the cell membrane that render the bacterium unable to produce the energy needed to perform critical tasks, such as cell division and making proteins.

In addition to TDA’s killing mechanism, the researchers were interested in understanding the mechanism by which a bacterial strain could become resistant to the antibiotic. Particularly, they wondered how the marine roseobacter kept itself safe from the deadly antibiotic weapon that it produced.

The research team approached the task by probing the genes in roseobacter that synthesize TDA as well as the surrounding genes. They identified three nearby genes responsible for transport in and out of the cell, and upon transferring these specific genes to E. coli, were able to produce an elusive TDA resistant bacterial strain.

“We often look at natural products as black boxes,” said Seyedsayamdost, “but these molecules have evolved for millennia to fulfill a certain function. By linking the unusual structural features of TDA to its mode of action, we have begun to explain why TDA looks the way it does.”

Read the abstract:

Wilson, M. Z.; Wang, R.; Gitai, Z.; Seyedsayamdost, M. R. “Tropodithietic Acid: Mode of Action and Mechanism of Resistance.” Proc. Natl. Acad. Sci. 2016, Published online on January 22, 2016.

This work was supported by grants from the National Institutes of Health (GM 098299 and 1DPOD004389).

Fruit flies adjust their courtship song based on distance (Neuron)


A fly runs on an air-supported ball. The audio traces of the fly’s courtship song are shown.

Article courtesy of Joseph Caputo, Cell Press

Outside of humans, the ability to adjust the intensity of acoustic signals with distance has only been identified in songbirds. Research published February 3 in Neuron now demonstrates that the male fruit fly also displays this complex behavior during courtship, adjusting the amplitude of his song depending on how far away he is from a female. Studying this process in the fruit fly can help shed light on the building blocks for social interactions across the animal kingdom.

Mala Murthy, of Princeton University, and her colleagues have revealed an unanticipated level of control in insect acoustic communication by analyzing each stage of the neuronal pathway underlying male fruit flies’ ability to adjust their courtship song—from the visual cues that help estimate distance to the signals that pass through nervous system and cause changes in muscle activity that drive softer or louder song. The complexity is remarkable considering that the fruit fly has only 100,000 neurons, one-millionth that of a human brain.

During courtship, males chase females, extending and vibrating one wing at a time to produce a courtship song. Songs, which consist primarily of two modes: sine and pulse, are extremely quiet and must be recorded on sensitive microphones, then amplified more than 1 million times in order to be heard by humans. When amplified, the sine song sounds like the whine of an approaching mosquito, while the pulse song is more akin to a cat’s purr.

“Females listen to many minutes of male song before deciding whether to accept him,” says Murthy, of the Princeton Neuroscience Institute and Department of Molecular Biology. “There is thus enormous evolutionary pressure for males to optimize their song to match the female’s preference while simultaneously minimizing the energetic cost of singing for long periods of time.” Adjusting the amplitude of song to compensate for female distance allows males to conserve energy and thereby court for longer periods of time and better compete with other males.

“While the precise neural mechanisms underlying the generation and patterning of fly song may be distinct from humans or even songbirds, the fundamental problem is the same: how can a neural network produce such a complex and dynamic signal?” Murthy says. “For this reason, we anticipate that similar neural mechanisms will be employed in all systems, and the genetic model system of the fruit fly is an ideal starting point from which to dissect them.”

The researchers were funded by the Howard Hughes Medical Institute, the DAAD (German Academic Exchange Foundation), the Alfred P. Sloan Foundation, the Human Frontiers Science Program, a National Science Foundation CAREER award, a NIH New Innovator Award, the NSF BRAIN Initiative, an EAGER award, the McKnight Foundation, and the Klingenstein-Simons Foundation.

Read the abstract

Philip Coen, Marjorie Xie, Jan Clemens and Mala Murthy. Sensorimotor Transformations Underlying Variability in Song Intensity during Drosophila Courtship. Neuron. Vol. 89, Issue 3, p629–644, 3 February 2016.

 

‘Radiolabeling’ lets scientists track the breakdown of drugs (Nature)

Graduate student Renyuan Pony Yu
Renyuan Pony Yu, a graduate student working with Princeton Professor Paul Chirik, has discovered a new way to radiolabel compounds for use in drug development.

By Tien Nguyen, Department of Chemistry

A new method for labeling molecules with radioactive elements could let chemists more easily track how drugs under development are metabolized in the body.

Chemists consider thousands of compounds in the search for a new drug, and a candidate’s metabolism is a key factor that must be evaluated carefully and quickly. Researchers at Princeton University and pharmaceutical company Merck & Co., Inc. report in the journal Nature that scientists can selectively replace hydrogen atoms in molecules with tritium atoms — a radioactive form of hydrogen that possesses two extra neutrons — to “radiolabel” compounds. This technique can be done in a single step while preserving the biological properties of the parent compound.

While current state-of-the-art techniques are quite reliable, they only work when dissolved in specific solvents, ones that aren’t always capable of dissolving the drug compound of interest. The researchers’ method, however, used an iron-based catalyst that is tolerant to a wider variety of solvents, and it labels the molecules at the opposite positions as compared to existing methods.

“The fact that you can access other positions is what makes this reaction really special,” said corresponding author Paul Chirik, the Edwards S. Sanford Professor of Chemistry at Princeton. Previous methods only incorporate radioactive tritium atoms into the molecule directly next to an atom or a group of atoms called a directing group. The new iron-catalyzed method does not require a directing group, and instead places tritium at whatever positions in the molecules are the least crowded.

“Radiolabeled compounds help medicinal chemists get a better picture of what actually happens to the drug by showing how the drug is metabolized and cleared,” said David Hesk, a collaborator at Merck and co-author on the work. By rapidly assessing the compounds’ metabolism early on, scientists can shorten the time it takes to develop and bring a drug to market. “Having another labeling reaction is very powerful because it gives radiochemists another tool in the toolbox,” he said.

This unique reactivity was actually discovered unexpectedly. Renyuan Pony Yu, a graduate student in the Chirik lab, had originally set out to use their iron catalyst for a different reaction that they were collaborating on with Merck. To study the iron catalyst’s capabilities, Yu subjected it to a technique called proton nuclear magnetic resonance spectroscopy (NMR), which allows chemists to deduce the positions of hydrogen atoms in molecules.

“We started seeing this beautiful, very systematic pattern of signals in the NMR, but we didn’t really know what they were,” said Yu, who is first author on the new study. Particularly puzzling was the fact that the pattern of signals would disappear over time.

The researchers turned to Istvan Pelczer, Director of the NMR Facility at Princeton chemistry and co-author on the work, who developed a special technique that helped them analyze the signals with much greater confidence. Using this method, they realized that the iron catalyst was reacting with the liquid solvent used to dissolve the NMR sample. The solvent’s deuterium atoms, another form of hydrogen that has one extra neutron and is not radioactive, were replacing the hydrogen atoms.

It wasn’t until Yu presented his findings to Matt Tudge, the Princeton authors’ collaborator at Merck, that the catalyst’s potential to introduce tritium atoms into radiolabeled molecules was recognized. “This is a classic example where you really need both partners,” Chirik said. “We were the catalyst experts, but they were the applications experts.”

Though tritium-labeled compounds are used mostly in metabolism studies, they can also be helpful at the very outset of a drug-discovery project to identify a biological target that the potential drugs can be tested against. The biological target could be an enzyme or protein associated with a certain disease. For example, statins are a well-known class of cholesterol-lowering drugs that target a specific enzyme in the body called HMG-CoA reductase.

To explore the scope of the reaction, Yu first optimized the reaction to incorporate deuterium atoms, which is commonly accepted as a model system for tritium. He found that the iron catalyst was surprisingly robust and successfully labeled many different types of compounds, including some from Merck’s library of past drug candidates.

“It was a very exciting project for me because I got to work with real drugs that are fully functionalized and useful,” Yu said. One of their test substrates was Claritin, which Yu bought from a local store; he extracted its active ingredient back in the lab.

Finally, Yu traveled to Merck’s campus in Rahway, where he received radioactivity training — Chirik’s laboratory isn’t equipped to handle radioactivity — and performed the reactions using tritium gas. The reactions were run in a special apparatus that looks like a steel-lined box and releases radioactive tritium gas. The apparatus can capture any unspent gas to limit the amount of radioactive waste produced.

Chemists take care to handle radioactive compounds and waste very carefully, but tritium’s radioactivity is so weak that the particles it emits cannot penetrate simple glassware. For this reason, tritium-labeled compounds can’t be used in any human imaging studies such as PET scans, which require radiolabeled compounds that emit high-energy particles.

This past summer, Yu presented the preliminary results of the iron-catalyzed reaction at the 2015 International Isotope Society Symposia to researchers in the radiolabeling and pharmaceutical community. They were very excited about the research and eager to use the catalyst in their own studies, Yu said.

But the major challenge for the researchers is that the iron catalyst is extremely air and moisture sensitive, and it can only be handled inside a glovebox, a special chamber in which oxygen and water vapor have been excluded. The Chirik group is working to develop a more stable catalyst that can be made commercially available, and have recently entered into a partnership with Green Center Canada, a company that helps bring academic research to market.

In the meantime, the Chirik group has found that the iron catalyst can replace hydrogen atoms with other groups besides deuterium and tritium atoms and is extending this chemistry into many other projects in the lab.

“This project is always going to be a special one for me because it’s kind of a pivot point for the type of chemistry that our group can do,” Chirik said, “and there’s this really cool application.”

Read the abstract.

Yu, R. P.; Hesk, D.; Rivera, N.; Pelczer, I.; Chirik, P. J. “Iron-Catalyzed Tritiation of Pharmaceuticals.” Nature, 2016, DOI: 10.1038/nature16464.

This work was supported by Merck & Co. and Princeton University’s Intellectual Property Accelerator Fund.

In rainforests, battle for sunlight shapes forest structure (Science)

New finding helps explain rainforests’ influence on global climate

Rainforest photo
Rainforests around the globe have a remarkably consistent pattern of tree sizes. Now researchers have found that the reason for this structure has to do with the competition for sunlight after a large tree falls and leaves an opening in the canopy. Image credit: Caroline Farrior

By Catherine Zandonella, Office of the Dean for Research

Despite their diversity, the structure of most tropical rainforests is highly predictable. Scientists have described the various sizes of the trees by a simple mathematical relationship called a power law.

In a new study using data from a rainforest in Panama, researchers determined that competition for sunlight is the underlying cause of this common structure, which is observed in rainforests around the globe despite differences in plant species and geography. The new finding can be used in climate simulations to predict how rainforests absorb excess carbon dioxide from the atmosphere.

The study, conducted by researchers at Princeton University, the National Institute for Mathematical and Biological Synthesis, the Smithsonian Tropical Research Institute and collaborating institutions, was published Jan. 8 in the journal Science. The investigation was supported in large part by the National Science Foundation.

Diagram of rainforest trees
After a large tree falls, many small individuals are able to grow due to an increase in available sunlight (T=1). Once they have grown to touch one another (T=2), they begin to overtop one another and leave individuals behind in the understory (T=3). Image courtesy of Caroline Farrior.

The researchers found that the rainforest structure stems from what happens after a tall tree falls and creates a gap in the canopy. The gap enables sunlight to reach the forest floor and fuel the rapid growth of small trees. Over time, the trees’ crowns grow to fill the gap until the point where not all of the trees can fit in the sunlit patch. Some will be left behind in the shade of their competitors.

“This process of moving from fast growth in the sun to slow growth in the shade sets up this characteristic size structure that is common across tropical rainforests, despite the differences in their environments,” said Caroline Farrior, first author of the study who is a postdoctoral fellow at the National Institute for Mathematical and Biological Synthesis and will soon be an assistant professor of integrative biology at the University of Texas-Austin.

Farrior, who earned her Ph.D. in ecology and evolutionary biology from Princeton University in 2012, completed most of the work as a postdoctoral researcher in the Princeton Environmental Institute with co-author Stephen Pacala, Princeton’s Frederick D. Petrie Professor in Ecology and Evolutionary Biology.

(View a video interview with Dr. Farrior courtesy of the National Institute for Mathematical and Biological Synthesis.)

“Rainforests store about twice as much carbon as other forests,” Pacala said. “About half of that is due to huge trees, but the other half is all that stuff in the middle. It is not possible to build an accurate climate model without getting that right.”

To gain an understanding of how rainforests grow, Farrior and colleagues analyzed decades of tree census data from a 50-hectare plot on Barro Colorado Island in the Panama Canal. From these data, they identified the mechanism most important in driving the observed size structure in tropical rainforests.

“With this new understanding of tropical forests, we can go on to build better models, we can make more accurate estimates of the carbon storage that’s currently in tropical forests, and we can go on to more accurately predict the pace of climate change in the future,” Farrior said.

The research included work by Stephanie Bohlman, an assistant professor at the University of Florida and a research associate at the Smithsonian Tropical Research Institute (STRI), and Stephen Hubbell, a staff scientist at STRI.

The study was supported by Princeton’s Carbon Mitigation Initiative and the National Institute for Mathematical and Biological Synthesis (NSF grant no. DBI-1300426) at the University of Tennessee-Knoxville. The Barro Colorado Island forest dynamics research project was founded by Stephen Hubbell, Robin Foster and Richard Condit of STRI.

The study, “Dominance of the suppressed: Power-law size structure in tropical forests,” by Caroline Farrior, Stephanie Bohlman, Stephen Hubbell and Stephen Pacala, appeared in the journal Science on Jan. 8, 2016.

PPPL physicists simulate innovative method for starting up tokamaks without using a solenoid (Nuclear Fusion)

Francesca Poli
PPPL Scientist Francesca Poli. Photo Credit: Elle Starkman / PPPL Office of Communications. PPPL, located on Princeton University’s Forrestal Campus and managed by the University, is devoted to developing practical solutions for the creation of sustainable energy from fusion and to creating new knowledge about the physics of ultra-hot, charged gases known as plasmas.

By Raphael Rosen, PPPL Office of Communications

Scientists at the U.S. Department of Energy’s Princeton Plasma Physics Laboratory (PPPL) have produced self-consistent computer simulations that capture the evolution of an electric current inside fusion plasma without using a central electromagnet, or solenoid.

The computer simulations of the process, known as non-inductive current ramp-up, were performed using TRANSP, the gold-standard code developed at PPPL. The results were published in October 2015 in the journal Nuclear Fusion. The research was supported by the DOE Office of Science.

In traditional donut-shaped tokamaks, a large solenoid runs down the center of the reactor. By varying the electrical current in the solenoid scientists induce a current in the plasma. This current starts up the plasma and creates a second magnetic field that completes the forces that hold the hot, charged gas together.

But spherical tokamaks, a compact variety of fusion reactor that produces high plasma pressure with relatively low magnetic fields, have little room for solenoids. Spherical tokamaks look like cored apples and have a smaller central hole for the solenoid than conventional tokamaks do. Physicists, therefore, have been trying to find alternative methods for producing the current that starts the plasma and completes the magnetic field in spherical tokamaks.

One such method is known as coaxial helicity injection (CHI). During CHI, researchers switch on an electric coil that runs beneath the tokamak. Above this coil is a gap that opens into the tokamak’s vacuum vessel and circles the tokamak’s floor. The switched-on electrical current produces a magnetic field that connects metal plates on either side of the gap.

Researchers next puff gas through the gap and discharge a spark across the two plates. This process causes magnetic reconnection — the process by which the magnetic fields snap apart and reconnect. This reconnection creates a magnetic bubble that fills the tokamak and produces the vital electric current that starts up the plasma and completes the magnetic field.

This current must be nurtured and fed. According to lead author Francesca Poli, the new computer simulations show that the current can best be sustained by injecting high-harmonic radio-frequency waves (HHFWs) and neutral beams into the plasma.

HHFW’s are radio-frequency waves that can heat both electrons and ions. The neutral beams, which consist of streams of hydrogen atoms, become charged when they enter the plasma and interact with the ions. The combination of the HHFWs and neutral beams increases the current from 300 kiloamps to 1 mega amp.

But neither HHFWs nor neutral beams can be used at the start of the process, when the plasma is relatively cool and not very dense. Poli found that HHFWs would be more effective if the plasma were first heated by electron cyclotron waves, which transfer energy to the electrons that circle the magnetic field lines.

“With no electron cyclotron waves you would have to pump in four megawatts of HHFW power to create 400 kiloamps of current,” she said. “With these waves you can get the same amount of current by pumping in only one megawatt of power.

“All of this is important because it’s hard to control the plasma at the start-up,” she added. “So the faster you can control the plasma, the better.”

PPPL is managed by Princeton University for the U.S. Department of Energy’s Office of Science.

Read the abstract.

F.M. Poli, R.G. Andre, N. Bertelli, S.P. Gerhardt, D. Mueller and G. Taylor. “Simulations towards the achievement of non-inductive current ramp-up and sustainment in the National Spherical Torus Experiment Upgrade.” Nuclear Fusion. Published October 30, 2015. DOI: 10.1088/0029-5515/55/12/123011

Genes for age-related cognitive decline found in adult worm neurons (Nature)

By Staff

Research image
A research team from Princeton University led by Coleen Murphy, professor of Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics, has developed a new method for isolating neurons from adult C. elegans worms. The first panel shows worms containing neurons labeled with green fluorescent protein (GFP). Using rapid, chilled chemomechanical disruption, the neuron cells were extracted and purified, then sorted using fluorescence-activated cell sorting (FACS).

Researchers from Princeton University have identified genes important for age-related cognitive declines in memory in adult worm neurons, which had not been studied previously. The research, published in the journal Nature, could eventually point the way toward therapies to extend life and enhance health in aging human populations.

“The newly discovered genes regulate enhanced short-term memory as well as the ability to repair damaged neurons, two factors that play an important role in healthy aging,” said Coleen Murphy, a professor of Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics, director of the Glenn Center for Quantitative Aging Research at Princeton, and senior author on the study. “Identifying the individual factors involved in neuron health in the worm is the first step to understanding human neuronal decline with age.”

The small soil-dwelling roundworm, Caenorhabditis elegans, contains genes that determine the rate of aging and overall health during aging. Mutations in one of these genetic pathways, the insulin/IGF-1 signaling (IIS) pathway, can double worm lifespan. Similar mutations in humans have been found in long-lived humans.

But studying the IIS mutation in adult worm neurons was difficult because the adults have a thick, durable covering that protects the neurons.

Using a new technique they developed to break up the tough outer covering, researchers at Princeton succeeded in isolating adult neurons, which enabled the detection of the new set of genes regulated by the insulin/IGF-1 signaling pathway.

“Our technique enabled us to study gene expression in adult neurons, which are the cells that govern cognitive aspects such as memory and nerve-regeneration,” said Murphy, whose research on aging is funded in part by the National Institutes of Health. “Prior to this work, researchers were only able to examine gene regulation either using adult worms or individual tissues from young worms.”

The work allowed co-first authors Rachel Kaletsky and Vanisha Lakhina to explore why long-lived IIS mutants maintain memory and neuron-regeneration abilities with age. Until now, the known targets of the insulin longevity pathway were located mostly in the intestine and skin of the worm rather than the neurons. Kaletsky is a postdoctoral research fellow and Lakhina is a postdoctoral research associate in the Lewis-Sigler Institute.

Kaletsky worked out the new way to isolate neurons from adult worms, and with Lakhina, proceeded to profile the gene activity in adult C. elegans neurons for the first time. They discovered that the IIS mutant worms express genes that keep neurons working longer, and that these genes are completely different from the previously known longevity targets. They also discovered a new factor that is responsible for nerve cell (axon) regeneration in adult worms, which could have implications for human traumatic brain injury.

“Kaletsky and Lakhina developed a new technique that is going to be used by the entire worm community, so it really opens up new avenues of research even beyond the discoveries we describe in the paper,” Murphy said.

One of the newly identified genes, fkh-9, regulates both enhanced memory and neuronal regeneration in IIS mutants. Previous studies have detected only one other gene that regulates neuronal regeneration in the mutants, demonstrating the power of the technique to identify new gene regulators. The researchers also found that fkh-9 gene expression is required for long lifespan in many IIS mutants, but it did not play that role in neurons, suggesting the gene governs multiple outcomes in the worm.

Murphy’s lab is now working to understand how fkh-9 works to influence memory, axon regeneration, and lifespan. The gene codes for a protein, FKH-9, that acts as a transcription factor, meaning it controls the expression of other genes and is likely part of a larger regulatory network. FKH-9 also appears to regulate different processes in different tissues: It is required in neurons for memory and axon repair, but not for lifespan. Murphy’s group is working to figure out how FKH-9 acts in distinct tissues to regulate such different processes.

The study provides a more complete picture of how IIS mutants control gene expression in different tissues to promote healthy aging, Murphy said.

“fkh-9 is likely only one of the exciting genes that will emerge from using this technique,” Murphy said. “By identifying the suite of IIS-regulated neuronal genes, there are many candidates for follow-up, only a fraction of which have been characterized in any great detail,” she said.

Other contributors to the study included Rachel Arey, a postdoctoral research fellow; former graduate students April Williams and Jessica Landis; and Jasmine Ashraf, a research specialist in the Lewis-Sigler Institute.

Additional funding for the study was provided by the Keck Foundation, the Ruth L. Kirschstein National Research Service Awards, the National Science Foundation and the New Jersey Commission on Brain Injury Research.

Read the abstract.

The article, The C. elegans adult neuronal IIS/FOXO transcriptome reveals adult phenotype regulators, by Rachel Kaletsky, Vanisha Lakhina, Rachel Arey, April Williams, Jessica Landis, Jasmine Ashraf and Coleen T. Murphy, was published in the journal Nature online ahead of print on December 14, 2015. doi:10.1038/nature16483.

Using powerful computers, physicists uncover mechanism that stabilizes plasma (Physical Review Letters)

Virtual plasma
A cross-section of the virtual plasma showing where the magnetic field lines intersect the plane. The central section has field lines that rotate exactly once. Image Credit: Stephen Jardin, PPPL.

By Raphael Rosen, Princeton Plasma Physics Laboratory Communications

A team of physicists led by Stephen Jardin of the U.S. Department of Energy’s Princeton Plasma Physics Laboratory (PPPL) has discovered a mechanism that prevents the electrical current flowing through fusion plasma from repeatedly peaking and crashing. This behavior is known as a “sawtooth cycle” and can cause instabilities within the plasma’s core. The results have been published online in Physical Review Letters. The research was supported by the DOE Office of Science.

The team, which included scientists from General Atomics and the Max Planck Institute for Plasma Physics, performed calculations on the Edison computer at the National Energy Research Scientific Computing Center, a division of the Lawrence Berkeley National Laboratory. Using M3D-C1, a program they developed that creates three-dimensional simulations of fusion plasmas, the team found that under certain conditions a helix-shaped whirlpool of plasma forms around the center of the tokamak. The swirling plasma acts like a dynamo — a moving fluid that creates electric and magnetic fields. Together these fields prevent the current flowing through plasma from peaking and crashing.

The researchers found two specific conditions under which the plasma behaves like a dynamo. First, the magnetic lines that circle the plasma must rotate exactly once, both the long way and the short way around the doughnut-shaped configuration, so an electron or ion following a magnetic field line would end up exactly where it began. Second, the pressure in the center of the plasma must be significantly greater than at the edge, creating a gradient between the two sections. This gradient combines with the rotating magnetic field lines to create spinning rolls of plasma that swirl around the tokamak and gives rise to the dynamo that maintains equilibrium and produces stability.

This dynamo behavior arises only under certain conditions. Both the electrical current running through the plasma and the pressure that the plasma’s electrons and ions exert on their neighbors must be in a range that is “not too large and not too small,” said Jardin. In addition, the speed at which the conditions for the fusion reaction are established must be “not too fast and not too slow.”

Jardin stressed that once a range of conditions like pressure and current are set, the dynamo phenomenon occurs all by itself. “We don’t have to do anything else from the outside,” he noted. “It’s something like when you drain your bathtub and a whirlpool forms over the drain by itself. But because a plasma is more complicated than water, the whirlpool that forms in the tokamak needs to also generate the voltage to sustain itself.”

During the simulations the scientists were able to virtually add new diagnostics, or probes, to the computer code. “These diagnostics were able to measure the helical velocity fields, electric potential, and magnetic fields to clarify how the dynamo forms and persists,” said Jardin. The persistence produces the “voltage in the center of the discharge that keeps the plasma current from peaking.”

Physicists have indirectly observed what they believe to be the dynamo behavior on the DIII-D National Fusion Facility that General Atomics operates for the Department of Energy in San Diego and on the ASDEX Upgrade in Garching, Germany. They hope to learn to create these conditions on demand, especially in ITER, the huge multinational fusion machine being constructed in France to demonstrate the practicality of fusion power. “Now that we understand it better, we think that computer simulations will show us under what conditions this will occur in ITER,” said Jardin. “That will be the focus of our research in the near future.”

Learning how to create these conditions will be particularly important for ITER, which will produce helium nuclei that could amplify the sawtooth disruptions. If large enough, these disruptions could cause other instabilities that could halt the fusion process. Preventing the cycle from starting would therefore be highly beneficial for the ITER experiment.

Read the abstract.

S.C. Jardin, N. Ferraro, and I. Krebs. “Self-Organized Stationary States of Tokamaks.” Physical Review Letters. Published November 17, 2015. DOI: http://dx.doi.org/10.1103/PhysRevLett.115.215001

This article is courtesy of the Princeton Plasma Physics Laboratory.

Warm nights could flood the atmosphere with carbon under climate change (PNAS)

Photo courtesy of William Anderegg, Princeton University
Amazonian tropical rainforest near Manaus, Brazil. Photo courtesy of William Anderegg, Princeton University.

By Morgan Kelly, Office of Communications

The warming effects of climate change usually conjure up ideas of parched and barren landscapes broiling under a blazing sun, its heat amplified by greenhouse gases. But a study led by Princeton University researchers suggests that hotter nights may actually wield much greater influence over the planet’s atmosphere as global temperatures rise — and could eventually lead to more carbon flooding the atmosphere.

Since measurements began in 1959, nighttime temperatures in the tropics have had a strong influence over year-to-year shifts in the land’s carbon-storage capacity, or “sink,” the researchers report in the journal Proceedings of the National Academy of Sciences. Earth’s ecosystems absorb about 25% of the excess carbon from the atmosphere, and tropical forests account for about one-third of land-based plant productivity.

During the past 50 years, the land-based carbon sink’s “interannual variability” has grown by 50 to 100 percent, the researchers found. The researchers used climate- and satellite-imaging data to determine which of various climate factors — including rainfall, drought and daytime temperatures — had the most effect on the carbon sink’s swings. They found the strongest association with variations in tropical nighttime temperatures, which have risen by about 0.6 degrees Celsius since 1959.

First author William Anderegg, an associate research scholar in the Princeton Environmental Institute, explained that he and his colleagues determined that warm nighttime temperatures lead plants to put more carbon into the atmosphere through a process known as respiration.

Just as people are more active on warm nights, so too are plants. Although plants take up carbon dioxide from the atmosphere, they also internally consume sugars to stay alive. That process, known as respiration, produces carbon dioxide. Plants step up respiration in warm weather, Anderegg said. The researchers found that yearly variations in the carbon sink strongly correlated with variations in plant respiration.

“When you heat up a system, biological processes tend to increase,” Anderegg said. “At hotter temperatures, plant respiration rates go up and this is what’s happening during hot nights. Plants lose a lot more carbon than they would during cooler nights.”

Previous research has shown that nighttime temperatures have risen significantly faster as a result of climate change than daytime temperatures, Anderegg said. This means that in future climate scenarios respiration rates could increase to the point that the land is putting more carbon into the atmosphere than it’s taking out, “which would be disastrous,” he said.

Of course, plants consume carbon dioxide as a part of photosynthesis, during which they convert sunlight into energy. Photosynthesis also is sensitive to rises in temperature, but it occurs only during the day, whereas respiration occurs at all hours and thus is more sensitive to nighttime warming, Anderegg said.

“Nighttime temperatures have been increasing faster than daytime temperatures and will continue to rise faster,” Anderegg said. “This suggests that tropical ecosystems might be more vulnerable to climate change than previously thought, risking crossing the threshold from a carbon sink to a carbon source. But there’s certainly potential for plants to acclimate their respiration rates and that’s an area that needs future study.”

This research was supported by the National Science Foundation MacroSystems Biology Grant (EF-1340270), RAPID Grant (DEB-1249256) and EAGER Grant (1550932); and a National Oceanic and Atmospheric Administration (NOAA) Climate and Global Change postdoctoral fellowship administered by the University Corporation of Atmospheric Research.

William R. L. Anderegg, Ashley P. Ballantyne, W. Kolby Smith, Joseph Majkut, Sam Rabin, Claudie Beaulieu, Richard Birdsey, John P. Dunne, Richard A. Houghton, Ranga B. Myneni, Yude Pan, Jorge L. Sarmiento, Nathan Serota, Elena Shevliakova, Pieter Tan and Stephen W. Pacala. “Tropical nighttime warming as a dominant driver of variability in the terrestrial carbon sink.” Proceedings of the National Academy of Sciences, published online in-advance of print Dec. 7, 2015. DOI: 10.1073/pnas.1521479112.

 

PPPL physicists propose new plasma-based method to treat radioactive waste (Journal of Hazardous Materials)

Caption: Securing a shipment of mixed, low-level waste from Hanford for treatment and disposal. Credit: U.S. Department of Energy
Caption: Securing a shipment of mixed, low-level waste from Hanford for treatment and disposal. Credit: U.S. Department of Energy

By Raphael Rosen, Princeton Plasma Physics Laboratory Communications

Physicists at the U.S. Department of Energy’s (DOE) Princeton Plasma Physics Laboratory (PPPL) are proposing a new way to process nuclear waste that uses a plasma-based centrifuge. Known as plasma mass filtering, the new mass separation techniques would supplement chemical techniques. It is hoped that this combined approach would reduce both the cost of nuclear waste disposal and the amount of byproducts produced during the process. This work was supported by PPPL’s Laboratory Directed Research and Development Program.

“The safe disposal of nuclear waste is a colossal problem,” said Renaud Gueroult, staff physicist at PPPL and lead author of the paper that appeared in the Journal of Hazardous Materials in October. “One solution might be to supplement existing chemical separation techniques with plasma separation techniques, which could be economically attractive, ideally leading to a reevaluation of how nuclear waste is processed.”

The immediate motivation for safe disposal is the radioactive waste stored currently at the Hanford Site, a facility in Washington State that produced plutonium for nuclear weapons during the Cold War. The volume of this waste originally totaled 54 million gallons and was stored in 177 underground tanks.

In 2000, Hanford engineers began building machinery that would encase the radioactive waste in glass. The method, known as “vitrification,” had been used at another Cold War-era nuclear production facility since 1996. A multibillion-dollar vitrification plant is currently under construction at the Hanford site.

To reduce the cost of high-level waste vitrification and disposal, it may be advantageous to reduce the number of high-level glass canisters by packing more waste into each glass canister. To reduce the volume to be vitrified, it would be advantageous to separate the nonradioactive waste, like aluminum and iron, out of the waste, leaving less waste to be vitrified. However, in its 2014 report, the DOE Task Force on Technology Development for Environmental Management argued that, “without the development of new technology, it is not clear that the cleanup can be completed satisfactorily or at any reasonable cost.”

The high-throughput, plasma-based, mass separation techniques advanced at PPPL offer the possibility of reducing the volume of waste that needs to be immobilized in glass. “The interesting thing about our ideas on mass separation is that it is a form of magnetic confinement, so it fits well within the Laboratory’s culture,” said physicist Nat Fisch, co-author of the paper and director of the Princeton University Program in Plasma Physics. “To be more precise, it is ‘differential magnetic confinement’ in that some species are confined while others are lost quickly, which is what makes it a high-throughput mass filter.”

How would a plasma-based mass filter system work? The method begins by atomizing and ionizing the hazardous waste and injecting it into the rotating filter so the individual elements can be influenced by electric and magnetic fields. The filter then separates the lighter elements from the heavier ones by using centrifugal and magnetic forces. The lighter elements are typically less radioactive than the heavier ones and often do not need to be vitrified. Processing of the high-level waste therefore would need fewer high-level glass canisters overall, while the less radioactive material could be immobilized in less costly wasteform (e.g., concrete, bitumen).

The new technique would also be more widely applicable than traditional chemical-based methods since it would depend less on the nuclear waste’s chemical composition. While “the waste’s composition would influence the performance of the plasma mass filter in some ways, the effect would most likely be less than that associated with chemical techniques,” said Gueroult.

Gueroult points out why savings by plasma techniques can be important. “For only about $10 a kilogram in energy cost, solid waste can be ionized. In its ionized form, the waste can then be separated into heavy and light components. Because the waste is atomized, the separation proceeds only on the basis of atomic mass, without regard to the chemistry. Since the total cost of chemical-based techniques can be $2,000 per kilogram of the vitrified waste, as explained in the Journal of Hazardous Materials paper, it stands to reason that even if several plasma-based steps are needed to achieve pure enough separation, there is in principle plenty of room to cut the overall costs. That is the point of our recent paper. It is also why we are excited about our plasma-based methods.”

Fisch notes that “our original ideas grew out of the thesis of Abe Fetterman, who began by considering centrifugal mirror confinement for nuclear fusion, but then realized the potential for mass separation. Now the key role on this project is being played by Renaud, who has developed the concept substantially further.”

According to Fisch, the current developments are a variation and refinement of a plasma-based mass separation system first advanced by a private company called Archimedes Technology Group. That company, started by the late Dr. Tihiro Ohkawa, a fusion pioneer, raised private capital to advance a plasma-based centrifuge concept to clean up the legacy waste at Hanford, but ceased operation in 2006 after failing to receive federal funding.

Now an updated understanding of the complexity of the Hanford problem, combined with an increased appreciation of new ideas, has led to renewed federal interest in waste-treatment solutions. Completion of the main waste processing operations, which was in 2002 projected for 2028, has slipped by 20 years over the last 13 years, and the total cleanup cost is now estimated by the Department of Energy to be greater than 250 billion dollars, according to the DOE Office of Inspector General, Office of Audits and Inspections. DOE, which has the responsibility of cleaning up the legacy nuclear waste at Hanford and other sites, conducted a Basic Research Needs Workshop on nuclear waste cleanup in July that both Fisch and Gueroult attended. The report of that workshop, which is expected to highlight new approaches to the cleanup problem, is due out this fall.

PPPL, on Princeton University’s Forrestal Campus in Plainsboro, N.J., 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. 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 largest single 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. For more information, please visit science.energy.gov.

Read the abstract.

Renaud Gueroult, David T. Hobbs, Nathaniel J. Fisch. “Plasma filtering techniques for nuclear waste remediation.” Journal of Hazardous Materials, published October 2015. doi:10.1016/j.jhazmat.2015.04.058.