Scientists have long pondered just what the brain’s tree of cell types looks like. Now, an international collaboration led by Dr. Andreas Tolias from Baylor College of Medicine, Dr. Philipp Berens from the University of Tübingen in Germany and Dr. Rickard Sandberg from the Karolinska Institute in Stockholm, Sweden, has published an article in Nature that provides one of the most detailed and complete characterizations of the diversity of neural types in the brain so far.

Uncovering the shape of the tree of cortical cell types with Patch-seq

Neuroscientists mostly use three fundamental features to describe neurons: their anatomy, or how they look under a microscope; their physiology, or how they respond when stimulated; and, more recently, the genes they express, which are known as their transcriptome.

For this study, the research team used an experimentally challenging technique that they developed several years ago, called Patch-seq. This technique allowed them to collect a large multimodal database including genetic, anatomical and physiological information from single cells in the mouse motor cortex.

“Gathering all these three fundamental features from the same set of neurons was the key that enabled us to get a much deeper understanding of how neurons in the motor cortex are related to each other and a clearer view of how the tree of cell types looks like,” said co-first author Dr. Federico Scala, postdoctoral associate in Tolias lab at Baylor.

Dr. Dmitry Kobak, also co-first author and a research scientist in Berens lab, described that while the broad genetic families of neurons had distinct anatomical and physiological properties, within each family the neurons exhibited extensive anatomical and physiological diversity. Importantly, all the three basic neuronal characteristics (anatomy, physiology and transcriptome) were correlated, which enabled the team to find interesting links between them.

“Our data supports the view that the tree of cortical cell types may look more like a banana tree with few big leaves rather than an olive tree with many small ones. This view provides a simpler model to describe the diversity of neurons we find in the brain. We believe that this simpler view will lead to a more principled understanding of why we have so many cell types in the brain to begin with and what they are used for,” said Tolias, Brown Foundation Endowed Chair of Neuroscience and director of the Center for Neuroscience and Artificial Intelligence at Baylor.

In this metaphor, neurons follow a hierarchy consisting of distinct, non-overlapping branches at the level of families, the large leaves of the banana tree. Within each family, neurons show continuous changes in their genetic, anatomical and physiological features, and all three features within a family are correlated. In parallel, work published simultaneously in Cell, scientists from the Allen Institute of Brain Science in Seattle obtained very similar results from mouse visual cortex underscoring that this view of cell types may be a general building principle of brain circuits.

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Materials provided by Baylor College of Medicine. Original written by Graciela Gutierrez. Note: Content may be edited for style and length.

Smoking emits reactive chemicals that remain in the air (so-called secondhand smoke) or deposit onto surfaces, including walls, windows, clothing and upholstery (thirdhand smoke). Unlike the secondhand variety, thirdhand smoke lingers long after a person stops smoking. Nicotine is semi-volatile and reacts with other chemicals on surfaces, producing new compounds that, if volatile, can also become airborne. Because cannabis smoke is chemically distinct from tobacco smoke, Aaron Wylie and Jonathan Abbatt wanted to characterize the compounds formed when THC, by itself or in cannabis smoke, on surfaces reacts with ozone in the air.

The researchers coated glass and cotton cloth, to simulate windows and clothing, with a THC solution. Then, they exposed the surfaces to concentrations of ozone that could exist in indoor air. In their analysis, they found that over time, the amount of THC on glass and cotton decreased, while the quantities of three THC oxidation products increased. In other experiments, the team used a smoking machine to deposit cannabis smoke onto cotton. Upon exposure to ozone, the same three compounds formed at roughly the same rate as observed for the THC-coated cloth. Because of the low volatility of THC and its oxidation products, the compounds are unlikely to be emitted to the air where they could be inhaled in as large amounts as nicotine, the researchers say. They say that somebody could still be exposed to THC and its derivatives, whose health effects are unknown, if they, for example, lick their fingers after touching a surface contaminated by cannabis smoke.

The authors acknowledge funding from the Chemistry of Indoor Environments program at the Alfred P. Sloan Foundation.

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The team’s work, described Dec. 2 in Nature, represents the first demonstration that it may be possible to safely reprogram complex tissues, such as the nerve cells of the eye, to an earlier age.

In addition to resetting the cells’ aging clock, the researchers successfully reversed vision loss in animals with a condition mimicking human glaucoma, a leading cause of blindness around the world.

The achievement represents the first successful attempt to reverse glaucoma-induced vision loss, rather than merely stem its progression, the team said. If replicated through further studies, the approach could pave the way for therapies to promote tissue repair across various organs and reverse aging and age-related diseases in humans.

“Our study demonstrates that it’s possible to safely reverse the age of complex tissues such as the retina and restore its youthful biological function,” said senior author David Sinclair, professor of genetics in the Blavatnik Institute at Harvard Medical School, co-director of the Paul F. Glenn Center for Biology of Aging Research at HMS and an expert on aging.

Sinclair and colleagues caution that the findings remain to be replicated in further studies, including in different animal models, before any human experiments. Nonetheless, they add, the results offer a proof of concept and a pathway to designing treatments for a range of age-related human diseases.

“If affirmed through further studies, these findings could be transformative for the care of age-related vision diseases like glaucoma and to the fields of biology and medical therapeutics for disease at large,” Sinclair said.

For their work, the team used an adeno-associated virus (AAV) as a vehicle to deliver into the retinas of mice three youth-restoring genes — Oct4, Sox2 and Klf4 — that are normally switched on during embryonic development. The three genes, together with a fourth one, which was not used in this work, are collectively known as Yamanaka factors.

The treatment had multiple beneficial effects on the eye. First, it promoted nerve regeneration following optic-nerve injury in mice with damaged optic nerves. Second, it reversed vision loss in animals with a condition mimicking human glaucoma. And third, it reversed vision loss in aging animals without glaucoma.

The team’s approach is based on a new theory about why we age. Most cells in the body contain the same DNA molecules but have widely diverse functions. To achieve this degree of specialization, these cells must read only genes specific to their type. This regulatory function is the purview of the epigenome, a system of turning genes on and off in specific patterns without altering the basic underlying DNA sequence of the gene.

This theory postulates that changes to the epigenome over time cause cells to read the wrong genes and malfunction — giving rise to diseases of aging. One of the most important changes to the epigenome is DNA methylation, a process by which methyl groups are tacked onto DNA. Patterns of DNA methylation are laid down during embryonic development to produce the various cell types. Over time, youthful patterns of DNA methylation are lost, and genes inside cells that should be switched on get turned off and vice versa, resulting in impaired cellular function. Some of these DNA methylation changes are predictable and have been used to determine the biologic age of a cell or tissue.

Yet, whether DNA methylation drives age-related changes inside cells has remained unclear. In the current study, the researchers hypothesized that if DNA methylation does, indeed, control aging, then erasing some of its footprints might reverse the age of cells inside living organisms and restore them to their earlier, more youthful state.

Past work had achieved this feat in cells grown in laboratory dishes but fell short of demonstrating the effect in living organisms.

The new findings demonstrate that the approach could be used in animals as well.

Overcoming an important hurdle

Lead study author, Yuancheng Lu, research fellow in genetics at HMS and a former doctoral student in Sinclair’s lab, developed a gene therapy that could safely reverse the age of cells in a living animal.

Lu’s work builds on the Nobel Prize winning discovery of Shinya Yamanaka, who identified the four transcription factors, Oct4, Sox2, Klf4, c-Myc, that could erase epigenetics markers on cells and return these cells to their primitive embryonic state from which they can develop into any other type of cell.

Subsequent studies, however, showed two important setbacks. First, when used in adult mice, the four Yamanaka factors could also induce tumor growth, rendering the approach unsafe. Second, the factors could reset the cellular state to the most primitive cell state, thus completely erasing a cell’s identity.

Lu and colleagues circumvented these hurdles by slightly modifying the approach. They dropped the gene c-Myc and delivered only the remaining three Yamanaka genes, Oct4, Sox2 and Klf4. The modified approach successfully reversed cellular aging without fueling tumor growth or losing their identity.

Gene therapy applied to optic nerve regeneration

In the current study, the researchers targeted cells in the central nervous system because it is the first part of body affected by aging. After birth, the ability of the central nervous system to regenerate declines rapidly.

To test whether the regenerative capacity of young animals could be imparted to adult mice, the researchers delivered the modified three-gene combination via an AAV into retinal ganglion cells of adult mice with optic nerve injury.

For the work, Lu and Sinclair partnered with Zhigang He, HMS professor of neurology and of ophthalmology at Boston Children’s Hospital, who studies optic nerve and spinal cord neuro-regeneration.

The treatment resulted in a two-fold increase in the number of surviving retinal ganglion cells after the injury and a five-fold increase in nerve regrowth.

“At the beginning of this project, many of our colleagues said our approach would fail or would be too dangerous to ever be used,” said Lu. “Our results suggest this method is safe and could potentially revolutionize the treatment of the eye and many other organs affected by aging.”

Reversal of glaucoma and age-related vision loss

Following the encouraging findings in mice with optic nerve injuries, the team partnered with colleagues at Schepens Eye Research Institute of Massachusetts Eye and Ear Bruce Ksander, HMS associate professor of ophthalmology, and Meredith Gregory-Ksander, HMS assistant professor of ophthalmology. They planned two sets of experiments: one to test whether the three-gene cocktail could restore vision loss due to glaucoma and another to see whether the approach could reverse vision loss stemming from normal aging.

In a mouse model of glaucoma, the treatment led to increased nerve cell electrical activity and a notable increase in visual acuity, as measured by the animals’ ability to see moving vertical lines on a screen. Remarkably, it did so after the glaucoma-induced vision loss had already occurred.

“Regaining visual function after the injury occurred has rarely been demonstrated by scientists,” Ksander said. “This new approach, which successfully reverses multiple causes of vision loss in mice without the need for a retinal transplant, represents a new treatment modality in regenerative medicine.”

The treatment worked similarly well in elderly, 12-month-old mice with diminishing vision due to normal aging. Following treatment of the elderly mice, the gene expression patterns and electrical signals of the optic nerve cells were similar to young mice, and vision was restored. When the researchers analyzed molecular changes in treated cells, they found reversed patterns of DNA methylation — an observation suggesting that DNA methylation is not a mere marker or a bystander in the aging process, but rather an active agent driving it.

“What this tells us is the clock doesn’t just represent time — it is time,” said Sinclair. “If you wind the hands of the clock back, time also goes backward.”

The researchers said that if their findings are confirmed in further animal work, they could initiate clinical trials within two years to test the efficacy of the approach in people with glaucoma. Thus far, the findings are encouraging, researchers said. In the current study, a one-year, whole-body treatment of mice with the three-gene approach showed no negative side effects.

At a time when the incidence and social costs of dementia and Alzheimer’s disease in particular continue to rise, this breakthrough is very timely as it could enable the detection of the disease much earlier than current approaches. The findings are also important for the testing of therapies against this devastating disease.

Alzheimer’s disease is characterized by two pathological changes in brain tissue. One is a protein called tau while the other involves the amyloid beta peptide. Both can form clumps of aggregates that progressively accumulate in specific areas of the brain. For tau, individual units of the protein can aggregate into finely-ordered fibrillar structures facilitated by a biochemical process called phosphorylation. Throughout the disease process, amyloid beta and phosphorylated tau (p-tau) are released from the brain into cerebrospinal fluid; the amount of the released proteins are used as reliable surrogate markers for clinical diagnoses of Alzheimer’s disease.

Normally, amyloid beta levels in cerebrospinal fluid become abnormal several years before p-tau. The current clinical tests for p-tau become abnormal when memory failings develop. This makes it difficult to identify people with the disease at the very early stages before it is too late. How can we, therefore, reliably detect these sub-threshold disease changes?

To address these challenges, the scientists discovered that there are specific forms of p-tau that undergo very minute increases in cerebrospinal fluid and blood in people with emerging Alzheimer pathology. Consequently, the researchers developed highly sensitive techniques to measure these biological markers that precede clinical signs by several years.

In the first study, conducted in the Alfa parent cohort study at the Barcelona Beta Research Centre (BBRC), with the support of “la Caixa” Foundation, about a third of the 381 people evaluated had brain evidence of Alzheimer pathology but without any cognitive problems, meaning that these changes could not be detected in the clinic by memory assessments. Remarkably, the new p-tau markers correctly identified these emerging abnormalities measured in cerebrospinal fluid and regular blood samples.

Subsequent studies performed in Gothenburg, Paris and Ljubljana revealed that these new markers continue to increase from the preclinical stage through the onset of cognitive problems to the late dementia stages. For this reason, progressive increases in p-tau could provide insights into the biological and clinical development of Alzheimer’s disease. The studies are now published in the leading journals EMBO Molecular Medicine and Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association.

Kaj Blennow, professor of neurochemistry at the University of Gothenburg, who directed the work said “A possible way to improve the chances of future therapies is to test them on people in the very early stages of the disease with elusive biological changes but lacking clinical symptoms including memory failings. Candidate drug trials have not been too successful.” He added that: “The practical challenge, however, is that these very tiny initial changes are incredibly difficult to measure reliably. This compromises our chances to identify and recruit preclinical AD patients for clinical trials.”

Dr. Thomas Karikari, an assistant professor at the University of Gothenburg, who co-led the discovery commented: “The remarkable findings reported in these publications show that the new highly sensitive tools capture the earliest Alzheimer disease changes in the brain in clinically normal people. These tools therefore have the potential to advance population screening and clinical trials.”

According to Dr. Marc Suárez-Calvet, neurologist and ERC researcher at BBRC, “the biomarker detected in blood may change clinical practice in the coming years, since it will improve the diagnosis of patients with Alzheimer’s disease, both in its asymptomatic and symptomatic phases.”

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Materials provided by University of Gothenburg. Note: Content may be edited for style and length.

A new study — published today [Wednesday 2 December 2020] in the international journal Pain from researchers at the universities of Bath (UK) and Calgary (Canada) — analysed how characters’ experiences of pain were depicted across different media aimed at 4 to 6-year olds.

The team behind the research were interested in assessing what painful incidents characters were subject to, as well as how they and others around them responded.

Their analysis looked at 10 family movies from 2009 onwards (Despicable Me 2, The Secret Life of Pets, Toy Story 3 & 4, Incredibles 2, Inside Out, Up, Zootopia, Frozen and Finding Dory), as well as popular kids’ TV programmes (Sofia the First, Shimmer and Shine, Paw Patrol, Octonauts, Peppa Pig, Daniel Tiger’s Neighbourhood).

These programmes were chosen to represent either girl-focused, boy-focused or gender-neutral TV series (dependent on the key characters).

Over the 10 movies and six TV series (which equated to over 52 hours of film / TV), the researchers identified:

• 454 painful incidents — a mean of 8.66 incidents of pain per hour.
• Violent pain or injury being the most common type of pain depicted (occurring in over two-thirds of instances — 79%).
• Boy characters much more likely to experience severe pain in comparison with girl characters (according to facial expressions).
• Examples of everyday pain (i.e. a character falling over or bumping their knee), being much less common, represented in only 20% of incidents.
• A general lack of empathy from other characters in responding to pain: 75% of painful instances were seen by others, yet in 41% of cases those witnessing it did not respond or where they did they were generally not empathetic.

Researchers say this work matters because what children watch on TV shapes and models their behaviours. They want producers to use their influence to re-think how pain is portrayed in order to better equip young people to cope with common, everyday pain which they are more likely to experience but is often forgotten and misunderstood. Indeed, how children’s pain is often sidelined was a topic highlighted in a recent and significant Lancet Commission report, also authored by pain researchers from the University of Bath.

Dr Abbie Jordan of the Department of Psychology and Centre for Pain Research at the University of Bath explained: “How children experience, model, understand and manage pain has real lasting consequences for them as individuals but also for all of us across wider society. Pain, in particular chronic pain, can have hugely debilitating effects on the lives of children and young people right through into adulthood.

“Part of the challenge in this is how we talk about pain. We know children spend increasing amounts of time watching these influential programmes and films and that what they depict feeds through to their understanding and awareness of an issue. When it comes to pain, as we see from this study, the picture presented by these media is not reflective of children’s common experiences, instead focusing much more on extreme and violent pain.

“Our assessment is that these programmes could do much more to help children understand pain by modelling it in different ways and crucially by showing more empathy when characters experience pain. That’s important for how children interact with others when one of them experiences pain, such as when a friend might fall over in the playground or when they go to the doctors for routine vaccinations.”

Lead researcher, Dr Melanie Noel, Associate Professor of Clinical Psychology from the University of Calgary said: “We examined shows and movies that millions of young children in North America and beyond are watching. The findings were, frankly, shocking.

“It is undoubtable that the media is a powerful force in how children learn about the world. The way pain is unrealistically portrayed is teaching young children that pain is not worthy of help or empathy from others, and that it will be experienced and responded to differently if you are a boy or a girl. We have a responsibility to change these societal narratives about pain.”

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Materials provided by University of Bath. Note: Content may be edited for style and length.

In a healthy person, the body absorbs calcium to maintain strong bones and perform other important functions like helping muscles move and nerves carry messages between the brain and body parts. Vitamin D is critical for this calcium absorption from the intestine and for the function of the intestine.

The study, published in the journal Molecular and Cellular Biology, highlights the importance of the distal segments of the intestine — including the colon — in vitamin D regulation of calcium and bone calcification. Previously, this regulation was thought to only occur in the proximal intestine, the first section of the intestine immediately beyond the stomach.

From the study, researchers also learned that a transporter of manganese — an essential element that plays a role in many cellular processes — was one of the genes most induced by vitamin D in both the proximal and distal intestine.

The study’s lead author, Sylvia Christakos, a professor in the Department of Microbiology, Biochemistry and Molecular Genetics at Rutgers New Jersey Medical School, says these findings suggest that vitamin D plays other roles as well. “The findings suggest that vitamin D may have a role not only in calcium absorption, but also in the cellular regulation of other essential ions and in the function of intestinal stem cells,” she said.

This research may lead to new strategies that can compensate for calcium malabsorption and increase the efficacy of intestinal calcium uptake to minimize bone loss due to bariatric surgery, small bowel resection or reduced calcium absorption after menopause or due to aging.

Co-authors include Michael Verzi, Department of Genetics, Rutgers University; Noah Shroyer, Baylor College of Medicine; and James Fleet, Purdue University.

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Materials provided by Rutgers University. Original written by Patti Verbanas. Note: Content may be edited for style and length.

The researchers envision their hybrid optical-acoustic system one day being used to conduct drone-based biological marine surveys from the air, carry out large-scale aerial searches of sunken ships and planes, and map the ocean depths with a similar speed and level of detail as Earth’s landscapes. Their “Photoacoustic Airborne Sonar System” is detailed in a recent study published in the journal IEEE Access.

“Airborne and spaceborne radar and laser-based, or LIDAR, systems have been able to map Earth’s landscapes for decades. Radar signals are even able to penetrate cloud coverage and canopy coverage. However, seawater is much too absorptive for imaging into the water,” said study leader Amin Arbabian, an associate professor of electrical engineering in Stanford’s School of Engineering. “Our goal is to develop a more robust system which can image even through murky water.”

Subhead: Energy loss

Oceans cover about 70 percent of the Earth’s surface, yet only a small fraction of their depths have been subjected to high-resolution imaging and mapping.

The main barrier has to do with physics: Sound waves, for example, cannot pass from air into water or vice versa without losing most — more than 99.9 percent — of their energy through reflection against the other medium. A system that tries to see underwater using soundwaves traveling from air into water and back into air is subjected to this energy loss twice — resulting in a 99.9999 percent energy reduction.

Similarly, electromagnetic radiation — an umbrella term that includes light, microwave and radar signals — also loses energy when passing from one physical medium into another, although the mechanism is different than for sound. “Light also loses some energy from reflection, but the bulk of the energy loss is due to absorption by the water,” explained study first author Aidan Fitzpatrick, a Stanford graduate student in electrical engineering. Incidentally, this absorption is also the reason why sunlight can’t penetrate to the ocean depth and why your smartphone — which relies on cellular signals, a form of electromagnetic radiation — can’t receive calls underwater.

The upshot of all of this is that oceans can’t be mapped from the air and from space in the same way that the land can. To date, most underwater mapping has been achieved by attaching sonar systems to ships that trawl a given region of interest. But this technique is slow and costly, and inefficient for covering large areas.

Subhead: An invisible jigsaw puzzle

Enter the Photoacoustic Airborne Sonar System (PASS), which combines light and sound to break through the air-water interface. The idea for it stemmed from another project that used microwaves to perform “non-contact” imaging and characterization of underground plant roots. Some of PASS’s instruments were initially designed for that purpose in collaboration with the lab of Stanford electrical engineering professor Butrus Khuri-Yakub.

At its heart, PASS plays to the individual strengths of light and sound. “If we can use light in the air, where light travels well, and sound in the water, where sound travels well, we can get the best of both worlds,” Fitzpatrick said.

To do this, the system first fires a laser from the air that gets absorbed at the water surface. When the laser is absorbed, it generates ultrasound waves that propagate down through the water column and reflect off underwater objects before racing back toward the surface.

The returning sound waves are still sapped of most of their energy when they breach the water surface, but by generating the sound waves underwater with lasers, the researchers can prevent the energy loss from happening twice.

“We have developed a system that is sensitive enough to compensate for a loss of this magnitude and still allow for signal detection and imaging,” Arbabian said.

The reflected ultrasound waves are recorded by instruments called transducers. Software is then used to piece the acoustic signals back together like an invisible jigsaw puzzle and reconstruct a three-dimensional image of the submerged feature or object.

“Similar to how light refracts or ‘bends’ when it passes through water or any medium denser than air, ultrasound also refracts,” Arbabian explained. “Our image reconstruction algorithms correct for this bending that occurs when the ultrasound waves pass from the water into the air.”

Subhead: Drone ocean surveys

Conventional sonar systems can penetrate to depths of hundreds to thousands of meters, and the researchers expect their system will eventually be able to reach similar depths.

To date, PASS has only been tested in the lab in a container the size of a large fish tank. “Current experiments use static water but we are currently working toward dealing with water waves,” Fitzpatrick said. “This is a challenging but we think feasible problem.”

The next step, the researchers say, will be to conduct tests in a larger setting and, eventually, an open-water environment.

“Our vision for this technology is on-board a helicopter or drone,” Fitzpatrick said. “We expect the system to be able to fly at tens of meters above the water.”

See video: https://youtu.be/2YyAnxQkeuk