(Image caption: In brain cancer cells, the protein PARC plays a key role in long-term cell survival. In both images, the red represents the protein cytochrome c, which is released when mitochondria are damaged and trigger apoptosis – cell suicide. At left, injured brain cancer cells exhibit little cytochrome c; they use the protein PARC to degrade the released cytochrome c, allowing the cancer cells to survive. At right, when researchers reduced PARC, cytochrome c accumulated, allowing apoptosis to carry on)

Neurons, brain cancer cells require the same little-known protein for long-term survival

Researchers at the UNC School of Medicine have discovered that the protein PARC/CUL9 helps neurons and brain cancer cells override the biochemical mechanisms that lead to cell death in most other cells. In neurons, long-term survival allows for proper brain function as we age. In brain cancer cells, though, long-term survival contributes to tumor growth and the spread of the disease.

These results, published in the journal Science Signaling, not only identify a previously unknown mechanism used by neurons for their much-needed survival, but show that brain cancer cells hijack the same mechanism for their own survival.

The discovery will lead to new investigations of brain cancer treatments and provides insight into Parkinson’s disease, including a potential new research tool for scientists.

“PARC is very similar to Parkin, a protein that’s mutated in Parkinson’s disease,” said Mohanish Deshmukh, PhD, a professor of cell biology and physiology and senior author of the Science Signaling paper. “We think they might work in tandem to protect neurons.”

If so, researchers can investigate the interplay between these proteins to create better drugs to treat the second-most prevalent neurodegenerative disease after Alzheimer’s disease.

Vivian Gama, PhD, a postdoctoral fellow in Deshmukh’s lab, led the experiments in cell cultures and animal models. First, she used external stimuli to promote the damage of mitochondria – the energy sources for cells. In most cell types, when mitochondria are damaged, they release a protein called cytochrome c, which triggers a cascade of biochemical steps that end in cell death – a process known as apoptosis.

Working with neurons, though, Gama found that the protein PARC/CUL9 blocked this process; it degraded cytochrome c, halted apoptosis, and allowed for long-term cell survival. “In this setting, we want PARC to do that because we want neurons to survive as long as possible,” said Gama, first author of the Science Signaling paper.

Deshmukh, a member of the UNC Neuroscience Center and the UNC Lineberger Comprehensive Cancer Center, said, “In Parkinson’s disease, we know that Parkin targets damaged mitochondria for degradation. However, exactly what happens to the proteins, such as cytochrome c, that are released from the damaged mitochondria has been unknown. Now, we think PARC plays a role in this process.”

Deshmukh and Gama’s work could lead to an alternative way to study Parkinson’s disease. Other researchers have created mouse models that lack the Parkin gene, but Gama said these models don’t have many of the hallmark symptoms that human patients have, making the model less than desirable for researchers. “Our hypothesis is that in the absence of Parkin, PARC still does the job,” Gama said, “as it may allow cells to survive.”

Gama and Deshmukh are now creating a model that lacks both the Parkin and PARC genes.

They will also investigate PARC as a target for cancer treatment.

“We tested several cancer cell lines and found that PARC degrades cytochrome c in medulloblastoma, a cancer of the central nervous system and in neuroblastoma, a cancer of the peripheral nervous system,” Gama said. “Not all cytochrome c is degraded; there are likely other factors involved. But PARC is an important player.”

When Gama and colleagues triggered the apoptotic process in brain cancer cells, they found that PARC allowed the cells to survive. When PARC was inhibited, the cells were more vulnerable to stress and damage, which means they could be more vulnerable to compounds aimed at destroying them.

Deshmukh said, “We show that brain cancer cells co-opt PARC to bypass apoptosis in the same way that neurons do and for the exact same purpose.”

Virtual Finger Enables Scientists to Navigate and Analyze 3D Images of Complex Biological Structures

Researchers have pioneered a revolutionary new way to digitally navigate three-dimensional images. The new technology, called Virtual Finger, allows scientists to move through digital images of small structures like neurons and synapses using the flat surface of their computer screens. Virtual Finger’s unique technology makes 3D imaging studies orders of magnitude more efficient, saving time, money and resources at an unprecedented level across many areas of experimental biology. The software and its applications are profiled in this week’s issue of the journal Nature Communications.

Most other image analysis software works by dividing a three-dimensional image into a series of thin slices, each of which can be viewed like a flat image on a computer screen. To study three-dimensional structures, scientists sift through the slices one at a time: a technique that is increasingly challenging with the advent of big data. “Looking through 3D image data one flat slice at a time is simply not efficient, especially when we are dealing with terabytes of data,” explains Hanchuan Peng, Associate Investigator at the Allen Institute for Brain Science. “This is similar to looking through a glass window and seeing objects outside, but not being able to manipulate them because of the physical barrier.”

In sharp contrast, Virtual Finger allows scientists to digitally reach into three-dimensional images of small objects like single cells to access the information they need much more quickly and intuitively. “When you move your cursor along the flat screen of your computer, our software recognizes whether you are pointing to an object that is near, far, or somewhere in between, and allows you to analyze it in depth without having to sift through many two-dimensional images to reach it,” explains Peng.

Scientists at the Allen Institute are already using Virtual Finger to improve their detection of spikes from individual cells, and to better model the morphological structures of neurons. But Virtual Finger promises to be a game-changer for many biological experiments and methods of data analysis, even beyond neuroscience. In their Nature Communications article, the collaborative group of scientists describes how the technology has already been applied to perform three-dimensional microsurgery in order to knock out single cells, study the developing lung, and create a map of all the neural connections in the fly brain.

“Using Virtual Finger could make data collection and analysis ten to 100 times faster, depending on the experiment,” says Peng. “The software allows us to navigate large amounts of biological data in the same way that Google Earth allows you to navigate the world. It truly is a revolutionary technology for many different applications within biological science,” says Peng.

Hanchuan Peng began developing Virtual Finger while at the Howard Hughes Medical Institute’s Janelia Research Campus and continued development at the Allen Institute for Brain Science.

Dodging dots helps explain brain circuitry

A neuroscience study provides new insight into the primal brain circuits involved in collision avoidance, and perhaps a more general model of how neurons can participate in networks to process information and act on it.

In the study, Brown University neuroscientists tracked the cell-by-cell progress of neural signals from the eyes through the brains of tadpoles as they saw and reacted to stimuli including an apparently approaching black circle. In so doing, the researchers were able to gain a novel understanding of how individual cells contribute in a broader network that distinguishes impending collisions.

The basic circuitry involved is present in a wide variety of animals, including people, which is no surprise given how fundamental collision avoidance is across animal behavior.

“Imagine yourself walking in a forest while keeping a conversation with your friend,” said Arseny Khakhalin, neuroscience postdoctoral scholar at Brown and lead author of the study in the European Journal of Neuroscience. “You can totally keep the conversation going, and at the same time avoid tree trunks and shrubs without even thinking about them consciously. That’s because you have a whole region in your brain that is dedicated, among other things, to this task.”

Turning tail

To learn how collision avoidance works, Khakhalin studied the task using tadpoles as a model organism, because as senior author and neuroscience professor Carlos Aizenman put it, they are “sufficiently complex to produce interesting behavior, but have nervous systems sufficiently simple to address in an integrated experimental approach.”

They started with the avoidance behavior. With tadpoles in a dish atop a screen, they projected digital black dots, representing virtual objects, of varying widths, at varying speeds and angles of approach. They also just flashed dots in place. The tadpoles would flee approaching dots as long as they reached a certain threshold angular size, but rarely reacted to the dots that merely blinked onto the scene but weren’t moving toward them. The response confirmed that tadpoles can distinguish approaching rather than merely proximate visual stimuli.

The researchers then sought to determine how the tadpoles process different stimuli. To do that they held the tadpoles in place while presenting a variety of simple animations via a fiber optic cable held next to an eye. The animations included a flashed circle, an apparently approaching circle (it became larger and larger), and a couple of “in between” animations, such as a circle that was faded in, rather than simply flashed into being.

While the tadpoles watched the animations, the researchers tracked their tail movements with a high-speed camera (to determine if the tadpoles were executing a fleeing maneuver) and recorded electrical signals along the visual processing circuitry: at the optic nerve leading from the retina to the brain’s optic tectum region, at “excitatory” and “inhibitory” synaptic inputs of neurons in the optic tectum, and at the outputs of the tectal neurons.

What the scientists found was that the tectum, rather than the retina, appears to be where the tadpoles determine that something is approaching rather than merely present. How did they know? The strongest difference between responses to the apparently approaching circle, versus responses to other stimuli, such as flashed or faded circles, was detected at the stage of output from tectal neurons.

Moreover, the difference in activity related to approaching vs. flashed circles increased as the signal propagated from the optic nerve, through tectum input, and to tectum output.

“The tectum is the first place that responded to approaching stimuli not just differently, but stronger,” Khakhalin said.

Inhibition moderates the conversation

An implication of the experiments was that when individual neurons in the tectum are uniquely activated by an apparently approaching stimulus, they collectively generate a signal to send to downstream parts of the brain that can get the tail moving to avoid the collision.

That’s indeed what excitatory neurons do, but the researchers wanted to know what role the inhibitory neurons were playing, especially because the balance of inhibitory and excitatory activity in the tectum varied with different stimuli.

To find out, they chemically blocked inhibitory neurons in the tectum in some tadpoles, chemically enhanced their activity in others and left still other tadpoles unaltered as controls. They found that when they altered the degree of inhibition in either direction, the output selectivity for an oncoming stimulus was lost. When inhibition was blocked, the individual excitatory cells lost their selectivity, too. When inhibition was enhanced, the individual excitatory cells retained their selectivity but could not project a signal collectively.

Khakhalin said the evidence seems to support the idea of inhibitory cells as facilitators of network function. They were not necessarily responsible for making the tectum selective. Instead, their ability to moderate excitation allowed the network of cells to function so that an organized signal from the individual excitatory neurons could emerge from the tectum.

The team was able to use these findings to create a conceptual model of the collision stimulus circuitry.

Khakhalin’s hypothesis of how it works is that inhibitory/excitatory balance allows the tectum to build up a necessary degree of excitement about the stimulus of interest (e.g. something has been getting bigger) while still allowing enough “calm” to consider the next moment wave of input (it just got bigger again).

Aizenman said the paper illustrates broader approach that his lab is applying to fundamental neuroscience questions.

“It is part of a greater project to be able to take an entire behavior and break it down into all of its neuronal components, to build a model in which we can understand how activity in single neurons and in the connections between them can all synergize to produce a behavior,” he said.

Fruit fly research may reveal what happens in female brains during courtship and mating

What are the complex processes in the brain involved with choosing a mate, and are these processes different in females versus males? It’s difficult to study such questions in people, but researchers are finding clues in fruit flies that might be relevant to humans and other animals. Three different studies on the topic are being published in the Cell Press journals Neuron (1, 2) and Current Biology.

Work over the past 100 years has largely focused on the overt courtship behaviors that male flies direct toward females. However, the female ultimately decides whether to reject the male or copulate with him. How does the female make this decision? In one Neuron paper, researchers report that they have identified two small groups of neurons in the female brain that function to modulate whether she will mate or not with a male based on his distinct pheromones and courtship song. In this paper, a team led by Dr. Bruce Baker of the Howard Hughes Medical Institute’s Janelia Farm Research Campus in Virginia also reports that these neurons are genetically distinct from the previously identified neurons that function to drive the elaborate courtship ritual with which a male woos a female. “An understanding of the neural mechanisms underlying how sensory information elicits appropriate sexual behaviors can be used as a point of comparison for how similar sexual behavior circuits are structured and function in other species,” says Dr. Baker.

In the Current Biology study, Dr. Leslie Vosshall of The Rockefeller University in New York City and her team found that a small group of neurons in the abdominal nerve cord and reproductive tract—called Abdominal-B neurons—is necessary for the female to pause her movement and interact with a courting male. When the neurons are inactivated, the female ignores the male and keeps moving, but when the neurons are activated, the female spontaneously pauses. “Sexual courtship is a duet—the male and female send signals back and forth until they reach the point that copulation proceeds,” says Dr. Jennifer Bussell, the lead author of the study. “Pausing to interact with a male, rather than avoiding him, is a crucial step in any female’s behavior leading to copulation. Tying a group of neurons to this particular response to males will allow us to dissect in detail how female mating circuitry functions.”

In another Neuron paper, researchers studied the effects of a small protein called sex peptide that is transferred along with sperm from males to females and is detected by sensory neurons in the uterus. Sex peptide changes the female’s behavior so that she is reluctant to mate again for about10 days. The investigators traced the neuronal pathway that is modulated when the uterus’s sensory neurons detect sex peptide. “Thanks to our work, we think the sex peptide signal goes to a region of the fly’s brain that is the homolog of the hypothalamus, which has been know for many years to be central in controlling sexual receptivity in vertebrates,” explains co-lead author Dr. Mark Palfreyman of the Research Institute of Molecular Pathology in Vienna, Austria. This region of the brain links the nervous system to the endocrine, or hormonal, system. “Of course, these models will still need to be tested and our work only provides an initial glimpse, but our study opens the possibility that analogous neuroendocrine systems control sexual receptivity from flies to vertebrates,” adds senior author Dr. Barry Dickson, who was also a co-author on the Current Biology paper published by Dr. Vosshall.

(Image caption: The light grey coil on the left is a conventional, commercially available TMS coil. The black coil on the right is the new, innovative version designed to fit a smaller non-human primate’s cranium and work with the neural monitoring device. Credit: Photo courtesy of Warren Grill.)

Watching Individual Neurons Respond to Magnetic Therapy

Engineers and neuroscientists at Duke University have developed a method to measure the response of an individual neuron to transcranial magnetic stimulation (TMS) of the brain. The advance will help researchers understand the underlying physiological effects of TMS — a procedure used to treat psychiatric disorders — and optimize its use as a therapeutic treatment.

TMS uses magnetic fields created by electric currents running through a wire coil to induce neural activity in the brain. With the flip of a switch, researchers can cause a hand to move or influence behavior. The technique has long been used in conjunction with other treatments in the hopes of improving treatment for conditions including depression and substance abuse.

While studies have demonstrated the efficacy of TMS, the technique’s physiological mechanisms have long been lost in a “black box.” Researchers know what goes into the treatment and the results that come out, but do not understand what’s happening in between.

Part of the reason for this mystery lies in the difficulty of measuring neural responses during the procedure; the comparatively tiny activity of a single neuron is lost in the tidal wave of current being generated by TMS. But the new study demonstrates a way to remove the proverbial haystack.

The results were published online June 29 in Nature Neuroscience.

“Nobody really knows what TMS is doing inside the brain, and given that lack of information, it has been very hard to interpret the outcomes of studies or to make therapies more effective,” said Warren Grill, professor of biomedical engineering, electrical and computer engineering, and neurobiology at Duke. “We set out to try to understand what’s happening inside that black box by recording activity from single neurons during the delivery of TMS in a non-human primate. Conceptually, it was a very simple goal. But technically, it turned out to be very challenging.”

First, Grill and his colleagues in the Duke Institute for Brain Sciences (DIBS) engineered new hardware that could separate the TMS current from the neural response, which is thousands of times smaller. Once that was achieved, however, they discovered that their recording instrument was doing more than simply recording.

The TMS magnetic field was creating an electric current through the electrode measuring the neuron, raising the possibility that this current, instead of the TMS, was causing the neural response. The team had to characterize this current and make it small enough to ignore.

Finally, the researchers had to account for vibrations caused by the large current passing through the TMS device’s small coil of wire — a design problem in and of itself, because the typical TMS coil is too large for a non-human primate’s head. Because the coil is physically connected to the skull, the vibration was jostling the measurement electrode.

The researchers were able to compensate for each artifact, however, and see for the first time into the black box of TMS. They successfully recorded the action potentials of an individual neuron moments after TMS pulses and observed changes in its activity that significantly differed from activity following placebo treatments.

Grill worked with Angel Peterchev, assistant professor in psychiatry and behavioral science, biomedical engineering, and electrical and computer engineering, on the design of the coil. The team also included Michael Platt, director of DIBS and professor of neurobiology, and Mark Sommer, a professor of biomedical engineering.

They demonstrated that the technique could be recreated in different labs. “So, any modern lab working with non-human primates and electrophysiology can use this same approach in their studies,” said Grill.

The researchers hope that many others will take their method and use it to reveal the effects TMS has on neurons. Once a basic understanding is gained of how TMS interacts with neurons on an individual scale, its effects could be amplified and the therapeutic benefits of TMS increased.

“Studies with TMS have all been empirical,” said Grill. “You could look at the effects and change the coil, frequency, duration or many other variables. Now we can begin to understand the physiological effects of TMS and carefully craft protocols rather than relying on trial and error. I think that is where the real power of this research is going to come from.”

Controlling movement with light

For the first time, MIT neuroscientists have shown they can control muscle movement by applying optogenetics — a technique that allows scientists to control neurons’ electrical impulses with light — to the spinal cords of animals that are awake and alert.  

Led by MIT Institute Professor Emilio Bizzi, the researchers studied mice in which a light-sensitive protein that promotes neural activity was inserted into a subset of spinal neurons. When the researchers shone blue light on the animals’ spinal cords, their hind legs were completely but reversibly immobilized. The findings, described in the June 25 issue of PLoS One, offer a new approach to studying the complex spinal circuits that coordinate movement and sensory processing, the researchers say.

In this study, Bizzi and Vittorio Caggiano, a postdoc at MIT’s McGovern Institute for Brain Research, used optogenetics to explore the function of inhibitory interneurons, which form circuits with many other neurons in the spinal cord. These circuits execute commands from the brain, with additional input from sensory information from the limbs.

Previously, neuroscientists have used electrical stimulation or pharmacological intervention to control neurons’ activity and try to tease out their function. Those approaches have revealed a great deal of information about spinal control, but they do not offer precise enough control to study specific subsets of neurons.

Optogenetics, on the other hand, allows scientists to control specific types of neurons by genetically programming them to express light-sensitive proteins. These proteins, called opsins, act as ion channels or pumps that regulate neurons’ electrical activity. Some opsins suppress activity when light shines on them, while others stimulate it.

“With optogenetics, you are attacking a system of cells that have certain characteristics similar to each other. It’s a big shift in terms of our ability to understand how the system works,” says Bizzi, who is a member of MIT’s McGovern Institute.

Muscle control

Inhibitory neurons in the spinal cord suppress muscle contractions, which is critical for maintaining balance and for coordinating movement. For example, when you raise an apple to your mouth, the biceps contract while the triceps relax. Inhibitory neurons are also thought to be involved in the state of muscle inhibition that occurs during the rapid eye movement (REM) stage of sleep.

To study the function of inhibitory neurons in more detail, the researchers used mice developed by Guoping Feng, the Poitras Professor of Neuroscience at MIT, in which all inhibitory spinal neurons were engineered to express an opsin called channelrhodopsin 2. This opsin stimulates neural activity when exposed to blue light. They then shone light at different points along the spine to observe the effects of neuron activation.

When inhibitory neurons in a small section of the thoracic spine were activated in freely moving mice, all hind-leg movement ceased. This suggests that inhibitory neurons in the thoracic spine relay the inhibition all the way to the end of the spine, Caggiano says. The researchers also found that activating inhibitory neurons had no effect on the transmission of sensory information from the limbs to the brain, or on normal reflexes.

“The spinal location where we found this complete suppression was completely new,” Caggiano says. “It has not been shown by any other scientists that there is this front-to-back suppression that affects only motor behavior without affecting sensory behavior.”

“It’s a compelling use of optogenetics that raises a lot of very interesting questions,” says Simon Giszter, a professor of neurobiology and anatomy at Drexel University who was not part of the research team. Among those questions is whether this mechanism behaves as a global “kill switch,” or if the inhibitory neurons form modules that allow for more selective suppression of movement patterns.

Now that they have demonstrated the usefulness of optogenetics for this type of study, the MIT team hopes to explore the roles of other types of spinal cord neurons. They also plan to investigate how input from the brain influences these spinal circuits.

“There’s huge interest in trying to extend these studies and dissect these circuits because we tackled only the inhibitory system in a very global way,” Caggiano says. “Further studies will highlight the contribution of single populations of neurons in the spinal cord for the control of limbs and control of movement.”

Equations reveal the rebellious rhythms at the heart of nature

From the beating of our hearts to the proper functioning of our brains, many systems in nature depend on collections of ‘oscillators’; perfectly-coordinated, rhythmic systems working together in flux, like the cardiac muscle cells in the heart.

Unless they act together, not much happens. But when they do, powerful changes occur. Cooperation between neurons results in brain waves and cognition, synchronized contractions of cardiac cells cause the whole heart to contract and pump the blood around the body. Lasers would not function without all the atomic oscillators acting in unison. Soldiers even have to break step when they reach a bridge in case oscillations caused by their marching feet cause the bridge to collapse.

But sometimes those oscillations go wrong.

Writing in the journal Nature Communications, scientists at Lancaster University report the possibility of “glassy states” and a “super-relaxation” phenomenon, which might appear in the networks of tiny oscillators within the brain, heart and other oscillating entities.

To uncover these phenomena, they took a new approach to the solution of a set of equations proposed by the Japanese scientist Yoshiki Kuramoto in the 1970s. His theory showed it was possible in principle to predict the properties of a system as a whole from a knowledge of how oscillators interacted with each other on an individual basis.

Therefore, by looking at how the microscopic cardiac muscle cells interact we should be able to deduce whether the heart as a whole organ will contract properly and pump the blood round. Similarly, by looking at how the microscopic neurons in the brain interact, we might be able to understand the origins of whole-brain phenomena like thoughts, or dreams, or amnesia, or epileptic fits.  

Physicists Dmytro Iatsenko, Professor Peter McClintock, and Professor Aneta Stefanovska have reported a far more general solution of the Kuramoto equations than anyone has achieved previously, with some quite unexpected results.

One surprise is that the oscillators can form “glassy” states, where they adjust the tempos of their rhythms but otherwise remain uncoordinated with each other, thus giving birth to some kind of “synchronous disorder” rather like the disordered molecular structure of window glass. Furthermore and even more astonishingly, under certain circumstances the oscillators can behave in a totally independent manner despite being tightly coupled together, the phenomenon the authors call “super-relaxation”.

These results raise intriguing questions. For example, what does it mean if the neurons of your brain get into a glassy state?

Dmytro Iatsenko, the PhD student who solved the equations, admitted the results posed more questions than they answered.

“It is not fully clear yet what it might mean if, for example, this happened in the human body, but if the neurons in the brain could get into a “glassy state” there might be some strong connection with states of the mind, or possibly with disease.”

Lead scientist Professor Aneta Stefanovska said: “With populations of oscillators, the exact moment when something happens is far more important than the strength of the individual event. This new work reveals exotic changes that can happen to large-scale oscillations as a result of alterations in the relationships between the microscopic oscillators. Because oscillations occur in myriads of systems in nature and engineering, these results have broad applicability.”

Professor Peter McClintock said: “The outcome of the work opens doors to many new investigations, and will bring enhanced understanding to several seemingly quite different areas of science.”

Modelling how neurons work together