NS/ Silent synapses are abundant in the adult brain
Neuroscience biweekly vol. 72, 23rd November — 7th December
TL;DR
- MIT neuroscientists discovered that the adult brain contains millions of ‘silent synapses’ — immature connections between neurons that remain inactive until they’re recruited to help form new memories.
- Researchers developed a new type of holographic microscope. It is said that the new microscope can achieve “see-through” the intact skull, and is capable of high-resolution 3D imaging of the neural network within a living mouse brain without removing the skull.
- A team of engineers at UC Santa Cruz has developed a new method for remote automation of the growth of cerebral organoids — miniature, three-dimensional models of brain tissue grown from stem cells. Cerebral organoids allow researchers to study and engineer key functions of the human brain with a level of accuracy not possible with other models. This has implications for understanding brain development and the effects of pharmaceutical drugs for treating cancer or other diseases.
- Neuroscientists have discovered that a specific type of brain cell could be a key player in making you feel the negative impacts of stress. More than 70% of adults will experience at least one traumatic experience, such as a life-threatening illness or accident, violent assault, or natural disaster, in their lifetimes and nearly a third will experience four or more, according to global data.
- A research team has discovered the underlying neural mechanism that allows us to feel empathy. The group’s study on mice hinted that empathy is induced by the synchronized neural oscillations in the right hemisphere of the brain, which allows the animals to perceive and share each other’s fear.
- LMU researchers demonstrate in a zebrafish model that two proteins prevent scar formation in the brain, thereby improving the ability of the tissue to regenerate.
- Researchers have discovered that removal of cilia from the brain’s striatum region impaired time perception and judgment, revealing possible new therapeutic targets for mental and neurological conditions including schizophrenia, Parkinson’s and Huntington’s diseases, autism spectrum disorder, and Tourette syndrome.
- A new study published by researchers at the University of Bath demonstrates the positive impact learning to play a musical instrument has on the brain’s ability to process sights and sounds, and shows how it can also help to lift a blue mood.
- Ketamine, an established anesthetic, and increasingly popular antidepressant, dramatically reorganizes activity in the brain, as if a switch had been flipped on its active circuits, according to a new study by Penn Medicine researchers. In a Nature Neuroscience paper released this month, the team described starkly changed neuronal activity patterns in the cerebral cortex of animal models after ketamine administration — observing normally active neurons that were silenced and another set that was normally quiet suddenly springing to action. This ketamine-induced activity switch in key brain regions tied to depression may impact our understanding of ketamine’s treatment effects and future research in the field of neuropsychiatry.
- Could the underproduction of poorly understood immune cells contribute to Alzheimer’s disease and other forms of cognitive decline? A Rutgers study in Nature Immunology suggests it may — and that increasing these cells could reverse the damage.
- ‘Nature Neuroscience’ December issue is out.
- And more!
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Latest news and research
Filopodia are a structural substrate for silent synapses in adult neocortex
by Vardalaki, D., Chung, K. & Harnett, M.T. in Nature
MIT neuroscientists have discovered that the adult brain contains millions of “silent synapses” — immature connections between neurons that remain inactive until they’re recruited to help form new memories.
Until now, it was believed that silent synapses were present only during early development when they help the brain learn the new information that it’s exposed to early in life. However, a new MIT study revealed that in adult mice, about 30 percent of all synapses in the brain’s cortex are silent.
The existence of these silent synapses may help to explain how the adult brain is able to continually form new memories and learn new things without having to modify existing conventional synapses, the researchers say.
“These silent synapses are looking for new connections, and when important new information is presented, connections between the relevant neurons are strengthened. This lets the brain create new memories without overwriting the important memories stored in mature synapses, which are harder to change,” says Dimitra Vardalaki, an MIT graduate student and the lead author of the new study.
Mark Harnett, an associate professor of brain and cognitive sciences, is the senior author of the paper, which appears in Nature. Kwanghun Chung, an associate professor of chemical engineering at MIT, is also an author.
When scientists first discovered silent synapses decades ago, they were seen primarily in the brains of young mice and other animals. During early development, these synapses are believed to help the brain acquire the massive amounts of information that babies need to learn about their environment and how to interact with it. In mice, these synapses were believed to disappear by about 12 days of age (equivalent to the first months of human life).
However, some neuroscientists have proposed that silent synapses may persist into adulthood and help with the formation of new memories. Evidence for this has been seen in animal models of addiction, which is thought to be largely a disorder of aberrant learning.
Theoretical work in the field from Stefano Fusi and Larry Abbott of Columbia University has also proposed that neurons must display a wide range of different plasticity mechanisms to explain how brains can both efficiently learn new things and retain them in long-term memory. In this scenario, some synapses must be established or modified easily, to form new memories, while others must remain much more stable, to preserve long-term memories.
In the new study, the MIT team did not set out specifically to look for silent synapses. Instead, they were following up on an intriguing finding from a previous study in Harnett’s lab. In that paper, the researchers showed that within a single neuron, dendrites — antenna-like extensions that protrude from neurons — can process synaptic input in different ways, depending on their location.
As part of that study, the researchers tried to measure neurotransmitter receptors in different dendritic branches, to see if that would help to account for the differences in their behavior. To do that, they used a technique called eMAP (epitope-preserving Magnified Analysis of the Proteome), developed by Chung. Using this technique, researchers can physically expand a tissue sample and then label specific proteins in the sample, making it possible to obtain super-high-resolution images.
While they were doing that imaging, they made a surprising discovery. “The first thing we saw, which was super bizarre and we didn’t expect, was that there were filopodia everywhere,” Harnett says.
Filopodia, thin membrane protrusions that extend from dendrites, have been seen before, but neuroscientists didn’t know exactly what they do. That’s partly because filopodia are so tiny that they are difficult to see using traditional imaging techniques.
After making this observation, the MIT team set out to try to find filopodia in other parts of the adult brain, using the eMAP technique. To their surprise, they found filopodia in the mouse visual cortex and other parts of the brain, at a level 10 times higher than previously seen. They also found that filopodia had neurotransmitter receptors called NMDA receptors, but no AMPA receptors.
A typical active synapse has both of these types of receptors, which bind the neurotransmitter glutamate. NMDA receptors normally require cooperation with AMPA receptors to pass signals because NMDA receptors are blocked by magnesium ions at the normal resting potential of neurons. Thus, when AMPA receptors are not present, synapses that have only NMDA receptors cannot pass along an electric current and are referred to as “silent.”
To investigate whether these filopodia might be silent synapses, the researchers used a modified version of an experimental technique known as patch clamping. This allowed them to monitor the electrical activity generated at individual filopodia as they tried to stimulate them by mimicking the release of the neurotransmitter glutamate from a neighboring neuron.
Using this technique, the researchers found that glutamate would not generate any electrical signal in the filopodium receiving the input, unless the NMDA receptors were experimentally unblocked. This offers strong support for the theory the filopodia represent silent synapses within the brain, the researchers say.
The researchers also showed that they could “unsilence” these synapses by combining glutamate release with an electrical current coming from the body of the neuron. This combined stimulation leads to accumulation of AMPA receptors in the silent synapse, allowing it to form a strong connection with the nearby axon that is releasing glutamate.
The researchers found that converting silent synapses into active synapses was much easier than altering mature synapses.
“If you start with an already functional synapse, that plasticity protocol doesn’t work,” Harnett says. “The synapses in the adult brain have a much higher threshold, presumably because you want those memories to be pretty resilient. You don’t want them constantly being overwritten. Filopodia, on the other hand, can be captured to form new memories.”
The findings offer support for the theory proposed by Abbott and Fusi that the adult brain includes highly plastic synapses that can be recruited to form new memories, the researchers say.
“This paper is, as far as I know, the first real evidence that this is how it actually works in a mammalian brain,” Harnett says. “Filopodia allow a memory system to be both flexible and robust. You need flexibility to acquire new information, but you also need stability to retain the important information.”
The researchers are now looking for evidence of these silent synapses in human brain tissue. They also hope to study whether the number or function of these synapses is affected by factors such as aging or neurodegenerative disease.
“It’s entirely possible that by changing the amount of flexibility you’ve got in a memory system, it could become much harder to change your behaviors and habits or incorporate new information,” Harnett says. “You could also imagine finding some of the molecular players that are involved in filopodia and trying to manipulate some of those things to try to restore flexible memory as we age.”
Ventral tegmental area glutamate neurons mediate nonassociative consequences of stress
by Dillon J. McGovern, Annie Ly, Koy L. Ecton, David T. Huynh, Emily D. Prévost, Shamira C. Gonzalez, Connor J. McNulty, Andrew R. Rau, Shane T. Hentges, Tanya L. Daigle, Bosiljka Tasic, Michael V. Baratta, David H. Root in Molecular Psychiatry
More than 70% of adults will experience at least one traumatic experience, such as a life-threatening illness or accident, violent assault, or natural disaster, in their lifetimes and nearly a third will experience four or more, according to global data.
While some people who have suffered trauma fully recover, others struggle to find lasting relief.
Researchers found that inescapable stressors impact behavior and the brain differently than stressors that can be controlled, contributing to more generalized and enduring anxiety-like behavior. The study, conducted in mice, also implicates a specific type of brain cell, glutamate cells in the “ventral tegmental area (VTA),” as a key player underlying the impact of stressors.
“Understanding how stressful experiences shape our brain is critical in order for us to develop new treatments and therapies that can counteract these changes,” said co-senior author Michael Baratta, an assistant professor of behavioral neuroscience at CU Boulder. “This study reveals that a little-known population of cells in the brain’s reward center is critical in generating the negative consequences of exposure to stress.”
Traumatic experiences, the authors note, can lead to a broad range of negative consequences. Some people experience “associative” responses, meaning that thoughts, feelings or external reminders like people, places or things related to the original trauma can prompt anxiety and fear. For instance, a war veteran might flinch at the sound of a car backfiring or fireworks crackling.
Others experience “non-associative” responses, a general aversion to stimuli — including those unrelated to the initial trauma. These kinds of responses can permeate many aspects of life and be harder to treat.
Scientists theorize that associative and non-associative responses to stress may be driven by distinct circuits in the brain. But gold-standard treatments like exposure therapy and cognitive behavioral therapy tend to only address associative responses.
To better address trauma-related disorders like post-traumatic stress disorder or PTSD, which impacts 8% of U.S. adults, many believe both circuits must be targeted, said Baratta.
To explore this, he and co-senior author David Root, assistant professor of behavioral neuroscience, set out to explore what circumstances, circuits and cells in the brain might drive those hard-to-treat, non-associative responses to trauma.
First, they exposed one group of mice to a stressor that they could easily escape and another to an identical stressor in duration and intensity but with no ability to escape. Behaviorally, the differences were profound. The mice exposed to an inescapable stressor showed more effects on non-associative behavior: Males were less social and less willing to explore and exhibited exaggerated fear; females exhibited general anxiety-like behavior. Meanwhile, mice exposed to a controllable stressor showed little or no effect the next day.
“Having control over some aspect of negative life events has long been associated with resilience in humans,” said Root, noting that animal experiments help scientists better understand the underlying neurobiology at play.
Next, the research team targeted a brain region called the ventral tegmental area (VTA), often referred to as the brain’s reward center due to its rich fabric of reward-associated dopamine-producing cells.
Through laboratory experiments, they found that stress activated a different kind of cells in the VTA known as vesicular glutamate transporter 2 neurons (VGluT2), which produce the chemical messenger glutamate, among other messengers.
When they used cutting-edge molecular tools to temporarily silence a subset of those cells before a stressful event, no negative consequences occurred.
“The mice continued to be social, explore new environments and were very resistant to future stressors,” said Root. “It’s almost as if the animal didn’t experience any stress the day before.”
The study confirms that stress-induced activation of glutamate neurons is required for the development of the more intractable behavioral consequences of trauma. It also suggests that by silencing those cells, the brain can be made more resilient to stress.
But the authors caution that the development of a “magic pill” or “stress vaccine” is a long way off. Notably, both controllable and uncontrollable stress-activated glutamate neurons.
“That tells us that they are part of a grander circuit and many more cell types and brain regions are participating in this process,” said Root.
The researchers envision a day when soldiers or emergency room doctors could be given a treatment prophylactically to reduce the activity of such cells before they’re exposed to a major stressor, or even after a traumatic event has occurred, to fend off lingering health effects.
“Understanding which neural circuits and cell types contribute to both associative and nonassociative consequences following stress is a critical step toward developing targeted therapeutics to ameliorate mental health disorders that can result from trauma,” said Root.
Hemispherically lateralized rhythmic oscillations in the cingulate-amygdala circuit drive affective empathy in mice
by Seong-Wook Kim, Minsoo Kim, Jinhee Baek, Charles-Francois Latchoumane, Gireesh Gangadharan, Yongwoo Yoon, Duk-Soo Kim, Jin Hyung Lee, Hee-Sup Shin in Neuron
A research team led by Dr. SHIN Hee-Sup at the Center for Cognition and Sociality (CCS) within the Institute for Basic Science (IBS) in Daejeon, South Korea has discovered the underlying neural mechanism that allows us to feel empathy. The group’s study on mice hinted that empathy is induced by the synchronized neural oscillations in the right hemisphere of the brain, which allows the animals to perceive and share each other’s fear.
Empathy is the ability that allows us to perceive and understand another individual’s emotions, such as joy, sadness, or fear. It is an essential function for human sociality, and its impairment has been observed in numerous psychiatric and neurological disorders such as autism, schizophrenia, and Alzheimer’s disease. The precise mechanisms within the brain that form the basis of empathy have not been identified, and few studies have been conducted on uncovering its origins.
This capacity to sense the feelings of others is not unique to humans, and its biological mechanisms are shared with other mammals including rodents. ‘Observational fear’, which is a rodent model for emotional contagion, is the basic form of affective empathy. This model has been well-established and is frequently used for studying the neurobiology of empathy. During the observational fear experiment, a “demonstrator” mouse is given an electric shock, while an “observer” mouse watches from behind a transparent screen. When witnessing another animal receiving a shock, the observer mouse displays an immediate fear response, as demonstrated by its freezing behavior. The observer mouse is also known to be able to recall the experience at a later time.
The CCS-IBS team led by Dr. SHIN Hee-Sup combined this observational fear model with optogenetic experiments to explore the origin of empathy. Notably, this study showed that the synchronized brain rhythms within multiple brain areas are essential for triggering empathy. In particular, the synchronization between the anterior cingulate cortex (ACC) and basolateral amygdala (BLA) is unique to empathic fear by indirect exposure to others’ distress, not to fear by first-hand experience.
First, they showed that the reciprocal circuit between the ACC-BLA in the right hemisphere is essential for observational freezing behavior. When they optogenetically inhibited the ACC-BLA circuits only in the right brain, mice showed reduced observational freezing. On the other hand, the mice were unaffected when only the left side was inhibited.
Furthermore, the researchers recorded electroencephalogram (EEG) in the ACC and BLA. As a result, they found that brain rhythms with the range of 5–7 Hz selectively increased in the ACC and BLA at the specific moment within the observer mice at the time they showed empathic freezing behavior. On the other hand, the demonstrator mice which experienced the electric shock first hand showed increase in the lower 3–5 Hz range only within the BLA but not in the ACC.
Dr. Shin, states, “Synchronous neural oscillations within the networks could allow enhanced communications among multiple brain areas for various cognitive and emotional functions. However, their causal relationship has rarely been demonstrated.”
To test the causal relationship between 5–7 Hz rhythms and empathic behavior, the team performed an experiment called ‘closed-loop manipulations’, which involves using optogenetics to inhibit specific neural functions and monitoring the brain waves using EEG. Through the closed-loop experiment, they could selectively disrupt 5–7 Hz rhythms in the ACC-BLA circuit, resulting in significant impairment of observational fear-induced freezing during the conditioning sessions. These results indicate that 5–7 Hz rhythms in the ACC-BLA circuit are causally involved in empathic behaviors.
As such, the researchers hypothesized that hippocampal theta (4–12 Hz) rhythms may tune the synchronized activities within the ACC-BLA circuit. It has been suggested that hippocampal theta rhythm provides an oscillatory framework that synchronizes activities between different brain areas. They selectively modulated the lower range of hippocampal theta by optogenetic manipulations during observational fear. Following the changes in hippocampal theta power, 5–7 Hz rhythm in the ACC-BLA circuits and empathic responses were bi-directionally modulated.
This study strongly indicates that hippocampal-dependent 5–7 Hz synchronized oscillations in the ACC-BLA specifically drive empathic responses in mice.
Dr. Hee-Sup Shin remarked, “Considering the universality of observational fear across mammals, it is reasonable to suppose a similar neural signature critical for affective empathy may be found in humans and could be used to identify empathy dysfunction in humans with psychiatric disorders involving severe social deficits.” He added, “At the moment, we do not know how hippocampal theta rhythms control the ACC-BLA rhythms. Future studies should address how multiple brain regions are simultaneously mobilized during observational fear.”
Ketamine triggers a switch in excitatory neuronal activity across neocortex
by Joseph Cichon, Andrzej Z. Wasilczuk, Loren L. Looger, Diego Contreras, Max B. Kelz, Alex Proekt in Nature Neuroscience
Ketamine, an established anesthetic and increasingly popular antidepressant, dramatically reorganizes activity in the brain, as if a switch had been flipped on its active circuits, according to a new study by Penn Medicine researchers. In a Nature Neuroscience paper released this month, the team described starkly changed neuronal activity patterns in the cerebral cortex of animal models after ketamine administration — observing normally active neurons that were silenced and another set that were normally quiet suddenly springing to action. This ketamine-induced activity switch in key brain regions tied to depression may impact our understanding of ketamine’s treatment effects and future research in the field of neuropsychiatry.
“Our surprising results reveal two distinct populations of cortical neurons, one engaged in normal awake brain function, the other linked to the ketamine-induced brain state,” said the co-lead and co-senior author Joseph Cichon, MD, PhD, an assistant professor of Anesthesiology and Critical Care and Neuroscience in the Perelman School of Medicine at the University of Pennsylvania. “It’s possible that this new network induced by ketamine enables dreams, hypnosis, or some type of unconscious state. And if that is determined to be true, this could also signal that it is the place where ketamine’s therapeutic effects take place.”
Anesthesiologists routinely deliver anesthetic drugs before surgeries to reversibly alter activity in the brain so that it enters its unconscious state. Since its synthesis in the 1960s, ketamine has been a mainstay in anesthesia practice because of its reliable physiological effects and safety profile. One of ketamine’s signature characteristics is that it maintains some activity states across the surface of the brain (the cortex). This contrasts with most anesthetics, which work by totally suppressing brain activity. It is these preserved neuronal activities that are thought to be important for ketamine’s antidepressant effects in key brain areas related to depression. But, to date, how ketamine exerts these clinical effects remains mysterious.
In their new study, the researchers analyzed mouse behaviors before and after they were administered ketamine, comparing them to control mice who received placebo saline. One key observation was that that given ketamine, within minutes of injection, exhibited behavioral changes consistent with what is seen in humans on the drug, including reduced mobility, and impaired responses to sensory stimuli, which are collectively termed “dissociation.”
“We were hoping to pinpoint exactly what parts of the brain circuit ketamine affects when it’s administered so that we might open the door to better study of it and, down the road, more beneficial therapeutic use of it,” said co-lead and co-senior author Alex Proekt, MD, PhD, an associate professor of Anesthesiology and Critical Care at Penn.
Two-photon microscopy was used to image cortical brain tissue before and after ketamine treatment. By following individual neurons and their activity, they found that ketamine turned on silent cells and turned off previously active neurons.
The neuronal activity observed was traced to ketamine’s ability to block the activity of synaptic receptors — the junction between neurons — called NMDA receptors and ion channels called HCN channels. The researchers found that they could recreate ketamine’s effects without the medications by simply inhibiting these specific receptors and channels in the cortex. The scientists showed that ketamine weakens several sets of inhibitory cortical neurons that normally suppress other neurons. This allowed the normally quiet neurons, the ones usually being suppressed when ketamine wasn’t present, to become active.
The study showed that this dropout in inhibition was necessary for the activity switch in excitatory neurons — the neurons forming communication highways, and the main target of commonly prescribed antidepressant medications. More work will need to be undertaken to determine whether the ketamine-driven effects in excitatory and inhibitory neurons are the ones behind ketamine’s rapid antidepressant effects.
“While our study directly pertains to basic neuroscience, it does point at the greater potential of ketamine as a quick-acting antidepressant, among other applications,” said co-author Max Kelz, MD, PhD,a distinguished professor of Anesthesiology and vice chair of research in Anesthesiology and Critical Care. “Further research is needed to fully explore this, but the neuronal switch we found also underlies dissociated, hallucinatory states caused by some psychiatric illnesses.”
An RCT study showing few weeks of music lessons enhance audio-visual temporal processing
by Yuqing Che, Crescent Jicol, Chris Ashwin, Karin Petrini in Scientific Reports
A new study published by researchers at the University of Bath demonstrates the positive impact learning to play a musical instrument has on the brain’s ability to process sights and sounds, and shows how it can also help to lift a blue mood.
Publishing their findings in the academic journal Nature Scientific Reports, the team behind the study shows how beginners who undertook piano lessons for just one hour a week over 11 weeks reported significant improvements in recognizing audio-visual changes in the environment and reported less depression, stress and anxiety.
In the randomized control study, 31 adults were assigned into either music training, music listening, or a control group. Individuals with no prior musical experiences or training were instructed to complete weekly one-hour sessions. Whilst the intervention groups played music, the control groups either listened to music or used the time to complete homework.
The researchers found that within just a few weeks of starting lessons, people’s ability to process multisensory information — i.e., sight and sound — was enhanced. Improved ‘multisensory process’ has benefits for almost every activity we participate in — from driving a car and crossing a road, to finding someone in a crowd or watching TV.
These multisensory improvements extended beyond musical abilities. With musical training, people’s audio-visual processing became more accurate across other tasks. Those who received piano lessons showed greater accuracy in tests where participants were asked to determine whether sound and vision ‘events’ occurred at the same time.
This was true both for simple displays presenting flashes and beeps, and for more complex displays showing a person talking. Such fine-tuning of individuals’ cognitive abilities was not present for the music-listening group (where participants listened to the same music as played by the music group), or for the non-music group (where members studied or read).
In addition, the findings went beyond improvements in cognitive abilities, showing that participants also had reduced depression, anxiety and stress scores after the training compared to before it. The authors suggest that music training could be beneficial for people with mental health difficulties, and further research is currently underway to test this.
Cognitive psychologist and music specialist Dr Karin Petrini from the University of Bath’s Department of Psychology, explained:
“We know that playing and listening to music often brings joy to our lives, but with this study we were interested in learning more about the direct effects a short period of music learning can have on our cognitive abilities.
“Learning to play an instrument like the piano is a complex task: it requires a musician to read a score, generate movements and monitor the auditory and tactile feedback to adjust their further actions. In scientific terms, the process couples visual with auditory cues and results in a multisensory training for individuals.
“The findings from our study suggest that this has a significant, positive impact on how the brain processes audio-visual information even in adulthood when brain plasticity is reduced.”
Cilia in the Striatum Mediate Timing-Dependent Functions
by Wedad Alhassen, Sammy Alhassen, Jiaqi Chen, Roudabeh Vakil Monfared, Amal Alachkar in Molecular Neurobiology
Researchers at the University of California, Irvine have discovered that removal of cilia from the brain’s striatum region impaired time perception and judgment, revealing possible new therapeutic targets for mental and neurological conditions including schizophrenia, Parkinson’s and Huntington’s diseases, autism spectrum disorder, and Tourette syndrome.
The striatum processes and integrates new environmental sensory information and coordinates the time sequence of motor responses. A common feature across specific mental and neurological disorders is a profound decline in patients’ ability to adjust to variations in their surroundings and accurately estimate the timing and termination of voluntary actions.
The study, recently published online in the journal Molecular Neurobiology, uncovered the first evidence of the important role cilia plays in timing-dependent dysfunction.
“Our findings may revolutionize our understanding of brain functions and mental disorders in the context of the critical task performed by these previously unappreciated organelles in the brain’s ‘central clock’ function,” said Amal Alachkar, Ph.D., corresponding author and professor of teaching in UCI’s Department of Pharmaceutical Sciences. “Our results may open new avenues for effective intervention through cilia-targeted therapies for treatment.”
The striatum is part of the brain’s circuitry that performs central clock processes, essential in controlling executive functions such as motor coordination, learning, planning and decision-making, as well as working memory and attention. Cilia protrude from the brain cell surfaces like antennae, working as a signaling hub that senses and transmits signals to generate appropriate reactions.
To examine their physiological role, the researchers removed cilia from the striatum in mice using conditional gene manipulation technology. These rodents were not able to learn new motor tasks, showed repetitive motor behavior and exhibited delays in decision-making. They were also deficient in rapidly recalling information about their location and orientation in space and in their ability to filter irrelevant environmental sensory information. However, the mice maintained habitual or already learned motor skills and long-term memories.
“Successful performance of working memory, attention, decision-making and executive function requires accurate and precise timing judgment, usually within a millisecond to a minute,” Alachkar said. “When that capacity is impaired, it means losing the ability to quickly adjust behavior in response to changes in external stimuli and failing to sustain appropriate, goal-oriented motor responses. Our ongoing work is aimed at understanding the mechanisms by which cilia regulate time perception and developing targeted therapies to improve behavioral deficits.”
Through-skull brain imaging in vivo at visible wavelengths via dimensionality reduction adaptive-optical microscopy
by Jo Y, Lee YR, Hong JH, et al. in Science Advances
Researchers led by Associate Director CHOI Wonshik of the Center for Molecular Spectroscopy and Dynamics within the Institute for Basic Science, Professor KIM Moonseok of The Catholic University of Korea, and Professor CHOI Myunghwan of Seoul National University developed a new type of holographic microscope. It is said that the new microscope can achieve “see through” the intact skull, and is capable of high-resolution 3D imaging of the neural network within a living mouse brain without removing the skull.
In order to scrutinize the internal features of a living organism using light, it is necessary to A) deliver sufficient light energy to the sample and B) accurately measure the signal reflected from the target tissue. However, in living tissues, multiple scattering effects and severe aberration tend to occur when light hits the cells, which makes it difficult to obtain sharp images.
In complex structures such as living tissue, light undergoes multiple scattering, which causes the photons to randomly change their direction several times as they travel through the tissue. Because of this process, much of the image information carried by the light becomes ruined. However, even if it is a very small amount of reflected light, it is possible to observe the features located relatively deep within the tissues by correcting the wavefront distortion of the light that was reflected from the target to be observed. However, the above-mentioned multiple scattering effects interfere with this correction process. Therefore, in order to obtain a high-resolution deep-tissue image, it is important to remove the multiple-scattered waves and increase the ratio of the single-scattered waves.
All the way back in 2019, for the first time the IBS researchers developed a high-speed time-resolved holographic microscope that can eliminate multiple scattering and simultaneously measure the amplitude and phase of light. They used this microscope to observe the neural network of live fish without incisional surgery. However, in the case of a mouse which has a thicker skull than that of a fish, it was not possible to obtain a neural network image of the brain without removing or thinning the skull, due to severe light distortion and multiple scattering occurring when the light travels through the bone structure.
The research team managed to quantitatively analyze the interaction between light and matter, which allowed them to further improve their previous microscope. In this recent study, they reported the successful development of a super-depth, three-dimensional time-resolved holographic microscope that allows for the observation of tissues to a greater depth than ever before.
Specifically, the researchers devised a method to preferentially select single-scattered waves by taking advantage of the fact that they have similar reflection waveforms even when light is input from various angles. This is done by a complex algorithm and a numerical operation that analyzes the eigenmode of a medium (a unique wave that delivers light energy into a medium), which allows the finding of a resonance mode that maximizes constructive interference (interference that occurs when waves of the same phase overlap) between wavefronts of light. This enabled the new microscope to focus more than 80 times of light energy on the neural fibers than before, while selectively removing unnecessary signals. This allowed the ratio of single-scattered waves versus multiple-scattered waves to be increased by several orders of magnitude.
The research team went on the demonstration of this new technology by observing the mouse brain. The microscope was able to correct the wavefront distortion even at a depth that was previously impossible using existing technology. The new microscope succeeded in obtaining a high-resolution image of the mouse brain’s neural network under the skull. This was all achieved in the visible wavelength without removing the mouse skull and without requiring a fluorescent label.
Professor KIM Moonseok and Dr. JO Yonghyeon, who have developed the foundation of the holographic microscope, said, “When we first observed the optical resonance of complex media, our work received great attention from academia. From basic principles to practical application of observing the neural network beneath the mouse skull, we have opened a new way for brain neuroimaging convergent technology by combining the efforts of talented people in physics, life, and brain science.”
Associate Director CHOI Wonshik said, “For a long time, our Center has developed super-depth bioimaging technology that applies physical principles. It is expected that our present finding will greatly contribute to the development of biomedical interdisciplinary research including neuroscience and the industry of precision metrology.”
TDP-43 condensates and lipid droplets regulate the reactivity of microglia and regeneration after traumatic brain injury
by Alessandro Zambusi, Klara Tereza Novoselc, Saskia Hutten, Sofia Kalpazidou, Christina Koupourtidou, Rico Schieweck, Sven Aschenbroich, Lara Silva, Ayse Seda Yazgili, Frauke van Bebber, Bettina Schmid, Gabriel Möller, Clara Tritscher, Christian Stigloher, Claire Delbridge, Swetlana Sirko, Zeynep Irem Günes, Sabine Liebscher, Jürgen Schlegel, Hananeh Aliee, Fabian Theis, Silke Meiners, Michael Kiebler, Dorothee Dormann, Jovica Ninkovic in Nature Neuroscience
LMU researchers demonstrate in a zebrafish model that two proteins prevent scar formation in the brain, thereby improving the ability of tissue to regenerate.
Whereas cells regularly renew themselves in most endogenous tissues, the number of nerve cells in the human brain and spinal cord remains constant. Although nerve cells can regenerate in the brains of adult mammals, as LMU scientist Professor Magdalena Götz has previously shown, young neurons in brain injury patients are unable to integrate into existing neural networks and survive, outside of two specific areas of the brain. This appears to be due to glial cells, which form the supporting tissue in the brain. Microglia in particular trigger inflammations and lead to scars that isolate the injured site from the healthy brain, but on the long run prevent proper incorporation of new neurons to the circuitry. How the body regulates such mechanisms was previously unknown.
Now a team led by LMU cell biologist Prof. Jovica Ninkovic has demonstrated in Nature Neuroscience that reducing the reactivity of microglia is crucial to preventing chronic inflammations and tissue scars and thus to improving regeneration capability.
In contrast to mammals, the central nervous system (CNS) of zebrafish has exceptional regenerative powers. In the case of injury, neural stem cells generate long-lived neurons, among other responses. Furthermore, CNS injuries prompt merely transitory reactivity of glial cells in zebrafish, which facilitates the integration of nerve cells into injured regions of the tissue.
“The idea was to tease out the differences between zebrafish and mammals so as to understand which signaling pathways in the human brain inhibit regeneration — and how we might be able to intervene,” says Ninkovic.
The scientists deliberately inflicted CNS lesions in zebrafish, prompting the activation of microglia. At the same time, the researchers found an accumulation of lipid droplets and TDP-43 condensates in the lesions. To date, the protein TDP-43 has been primarily associated with neurodegenerative diseases.
Granulin also played an important role in the zebrafish model. This protein contributed to the removal of the lipid droplets and TDP-43 condensates, whereupon the microglia transitioned from their activated to their resting form. The unscarred regeneration of the injury was the outcome. Zebrafish with experimentally induced granulin deficiency, by contrast, exhibited poor regeneration of the injury similar to what we see in mammals.
“We suspect therefore that granulin plays an important role in the regeneration of nerves in zebrafish,” says Ninkovic.
To further pursue the comparison between humans and zebrafish, Ninkovic’s team investigated material from patients who had died of brain injuries. Here, too, there was a correlation between the extent of microglia activation and the accumulation of lipid droplets and TDP-43 condensates. The corresponding signaling pathways in human tissue were therefore comparable with those in zebrafish.
The LMU researcher sees “potential for novel therapeutic applications in humans.” As the next step, he is planning to investigate whether known low-molecular-weight compounds are suitable for inhibiting signaling pathways of microglia activation, thereby promoting the healing of neural lesions. Zebrafish models will be used again in this pre-clinical phase.
Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoids
by Spencer T. Seiler, Gary L. Mantalas, John Selberg, Sergio Cordero, Sebastian Torres-Montoya, Pierre V. Baudin, Victoria T. Ly, Finn Amend, Liam Tran, Ryan N. Hoffman, Marco Rolandi, Richard E. Green, David Haussler, Sofie R. Salama, Mircea Teodorescu in Scientific Reports
A team of engineers at UC Santa Cruz has developed a new method for remote automation of the growth of cerebral organoids — miniature, three-dimensional models of brain tissue grown from stem cells. Cerebral organoids allow researchers to study and engineer key functions of the human brain with a level of accuracy not possible with other models. This has implications for understanding brain development and the effects of pharmaceutical drugs for treating cancer or other diseases.
In a new study published in the journal Nature Scientific Reports, researchers from the UCSC Braingeneers group detail their automated, internet-connected microfluidics system, called “Autoculture.” The system precisely delivers feeding liquid to individual cerebral organoids in order to optimize their growth without the need for human interference with the tissue culture.
Cerebral organoids require a high level of expertise and consistency to maintain the precise conditions for cell growth over weeks or months. Using an automated system, as demonstrated in this study, can eliminate disturbance to cell culture growth caused by human interference or error, provide more robust results, and allow more scientists access to opportunities to conduct research with human brain models.
Autoculture also addresses variation that arises in organoid growth due to “batch effect” issues, where organoids grown at different times or at different labs under similar conditions may vary just because of the complexity of their growth. Using this uniform, automated system can reduce variation and allow researchers to better compare and validate their results.
“One of the big challenges is that these cultures are not very reproducible, and in part it’s not surprising because these are months-long experiments. You have to change media every couple of days and try to treat these cultures uniformly, which is extremely challenging,” said Sofie Salama, an acting professor of molecular, cellular and developmental biology at UCSC and an author on the study.
Autoculture uses a microfluidic chip designed by the researchers, spearheaded by Associate Professor of Electrical and Computer Engineering Mircea Teodorescu and Biomolecular Engineering Ph.D. student Spencer Seiler. Their novel chips, created from a unique bi-layer mold, have tiny wells and channels for delivering minute amounts of liquid to the organoid, which allow the scientists to have a high level of control over nutrient concentrations and byproducts. Overall, the system uses mostly off-the-shelf, low-cost components, making it accessible and modular.
“A novel and important feature of this machine is that on one hand, it streamlines the process and makes sure that everything is very consistent,” Teodorescu said. “On the other hand, it’s very modular because the system is controlled by the computer, so there are different parts of the chip that are interchangeable and have their own advantages — it’s very much a modern agent.”
Because the system delivers a non-stop flow of liquid to the organoids, it more closely resembles the real conditions of the brain, which is constantly fed nutrients through the blood.
Unlike other methods for organoid growth which grow the cultures together in one dish, the Autoculture system contains a culture plate with 24 individual wells, so each well can be its own experiment in which cultures can be grown independently and fed liquids at varying, programmable concentrations and times. An in-incubator imaging system lets the researchers constantly remotely monitor organoid growth and morphology.
“The prize of the system is that every organoid has its own, personal micro-environment for which fluid flows in and out of,” Seiler said. “Now we’ve separated them — this would be too laborious to do by hand, but it’s fine for a machine.”
Additionally, a unique feature of the system is that feeding media for each individual culture can be pulled out for analysis at any point during an experiment. This allows researchers to non-invasively measure data such as pH and glucose levels which can be important for monitoring cell growth.
The microfluidics system is connected to the internet to allow scientists to remotely operate and retrieve real-time data from the system at any point, without disrupting the culture. Another paper from the Braingeneers group, published in the journal Internet of Things, shows how the Autoculture system is one example of the power of extending the internet-of-things to enable remote-controlled experiments — a need that the pandemic made more urgent.
When measuring their cerebral organoids, the researchers found that the stem cells grown using the Autoculture system not only differentiated into various cell types normally, but actually looked healthier than those grown using standard methods. RNA sequencing found lower levels of glycolytic and endoplasmic reticulum stress, showing a first promising set of data for addressing cellular stress identified in a Nature paper by collaborating researchers at UCSF, evidence that the group plans to expand on in ongoing research.
This research provides an important platform for the ongoing work within the UCSC Live Cell Genomics Center. It is aligned with the center’s mission to apply lessons from the computer revolution to life sciences and is part of a larger drive toward automation of wet labs to make experiments more robust and reproducible.
Mucosal-associated invariant T cells restrict reactive oxidative damage and preserve meningeal barrier integrity and cognitive function
by Yuanyue Zhang, Jacob T. Bailey, En Xu, Kunal Singh, Marieke Lavaert, Verena M. Link, Shanti D’Souza, Alex Hafiz, Jian Cao, Gaoyuan Cao, Derek B. Sant’Angelo, Wei Sun, Yasmine Belkaid, Avinash Bhandoola, Dorian B. McGavern, Qi Yang in Nature Immunology
Could the underproduction of poorly understood immune cells contribute to Alzheimer’s disease and other forms of cognitive decline? A Rutgers study in Nature Immunology suggests it may — and that increasing these cells could reverse the damage.
Rutgers researchers deactivated the gene that produces mucosal-associated invariant T cells (MAITs) in mice and compared the cognitive function of normal and MAIT cell-deficient mice. Initially, the two groups performed identically, but as the mice grew into middle age, the genetically altered mice struggled to form new memories.
Researchers then injected the genetically altered mice with MAITs, and their performance in learning and memory-intensive tasks such as swimming through a water maze returned to normal.
The study authors believe this is the first work to link MAITs to cognitive function and hope to follow it up with research that compares MAIT numbers in healthy humans and those with cognitive diseases such as Alzheimer’s.
“The MAIT cells that protect the brain are located in the meninges, but they are also present in blood, so a simple blood test should let us compare levels in healthy subjects and those with Alzheimer’s disease and other cognitive disorders,” said Qi Yang, senior author of the study and associate professor at the Child Health Institute of New Jersey at Rutgers Robert Wood Johnson Medical School.
MAIT cells, which were discovered in the 1990s, were already known to be the most abundant innate-like T cells in humans and to be particularly numerous in the liver and skin. The Rutgers study was the first to detect these cells, which are not fully understood when it comes to fighting disease, in the meninges, the membrane layers that cover the brain.
MAITs nested in the meninges appear to protect against cognitive decline by creating antioxidant molecules that combat toxic byproducts of energy production called reactive oxidative species. Without MAITs, the reactive oxidative species accumulate in the meninges and cause meningeal barrier leakage. When the meningeal barrier leaks, potentially toxic substances enter and inflame the brain. This accumulation eventually disrupts brain and cognitive function.
Genetic alteration prevented the experimental mice from producing any MAIT cells, but humans can probably increase MAIT cell production by altering their diets or making other lifestyle changes, said Yuanyue Zhang, the lead author of the study and a postdoctoral researcher at the Child Health Institute of New Jersey.
“MAIT cell production is connected to the bacteria in your gut microbiome,” Zhang said. “People who grew up in relatively sterile environments or took antibiotics frequently make fewer of them than people who grew up in more rural areas, where there is more exposure to beneficial bacteria. But everyone may improve their microbiota by changing their diet or living environment. This is just one more reason to pursue a natural and healthy lifestyle.”
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