Cry analyzer seeks clues to babies’ health

Researchers at Brown University and Women & Infants Hospital have developed a new tool that analyzes the cries of babies, searching for clues to potential health or developmental problems. Slight variations in cries, mostly imperceptible to the human ear, can be a “window into the brain” that could allow for early intervention.

To parents, a baby’s cry is a signal of hunger, pain, or discomfort. But to scientists, subtle acoustic features of a cry, many of them imperceptible to the human ear, can hold important information about a baby’s health.

A team of researchers from Brown University and Women & Infants Hospital of Rhode Island has developed a new computer-based tool to perform finely tuned acoustic analyses of babies’ cries. The team hopes their baby cry analyzer will lead to new ways for researchers and clinicians to use cry in identifying children with neurological problems or developmental disorders.

“There are lots of conditions that might manifest in differences in cry acoustics,” said Stephen Sheinkopf, assistant professor of psychiatry and human behavior at Brown, who helped develop the new tool. “For instance, babies with birth trauma or brain injury as a result of complications in pregnancy or birth or babies who are extremely premature can have ongoing medical effects. Cry analysis can be a noninvasive way to get a measurement of these disruptions in the neurobiological and neurobehavioral systems in very young babies.”

The new analyzer is the result of a two-year collaboration between faculty in Brown’s School of Engineering and hospital-based faculty at Women & Infants Hospital. A paper describing the tool is in press in the Journal of Speech, Language and Hearing Research.

The system operates in two phases. During the first phase, the analyzer separates recorded cries into 12.5-millisecond frames. Each frame is analyzed for several parameters, including frequency characteristics, voicing, and acoustic volume. The second phase uses data from the first to give a broader view of the cry and reduces the number of parameters to those that are most useful. The frames are put back together and characterized either as an utterance — a single “wah” — or silence, the pause between utterances. Longer utterances are separated from shorter ones and the time between utterances is recorded. Pitch, including the contour of pitch over time, and other variables can then be averaged across each utterance.

In the end, the system evaluates for 80 different parameters, each of which could hold clues about a baby’s health.

“It’s a comprehensive tool for getting as much important stuff out of a baby cry that we can,” said Harvey Silverman, professor of engineering and director of Brown’s Laboratory for Engineering Man/Machine Systems.

To understand what important stuff to look for, Silverman and his graduate students Brian Reggiannini and Xiaoxue Li worked closely with Sheinkopf and Barry Lester, director of Brown’s Center for the Study of Children at Risk.

“We looked at them as the experts about the kinds of signals we might want to get,” Silverman said, “and we engineers were the experts on what we might actually be able to implement and methods to do so. So working together worked quite well.”

Lester, who has studied baby cries for years, says this vein of research goes back to the 1960s and a disorder called Cri du chat syndrome.

Cri du chat (cry of the cat) is caused by a genetic anomaly similar to Down syndrome. Babies who have it have a distinct, high-pitched cry. While the Cri du chat is unmistakable even without sensitive machinery, Lester and others wondered whether subtler differences in cry could also be indicators of a child’s health.

“The idea is that cry can be a window into the brain,” Lester said.

If neurological deficits change the way babies are able to control their vocal chords, those tiny differences might manifest themselves in differences in pitch and other acoustic features. Lester has published several papers showing that differences in cry are linked to medical problems stemming from malnutrition, prenatal drug exposure, and other risks.

“Cry is an early warning sign that can be used in the context of looking at the whole baby,” Lester said.

The tools used in those early studies, however, are primitive by today’s standards, Lester said. In early work, recorded cries were converted to spectrograms, visual readouts of pitch changes over time. Research technicians then read and coded each spectrogram by hand. Later systems automated the process somewhat, but the research was still slow and cumbersome.

This new automated analyzer enables researchers to evaluate cries much more quickly and in much greater detail. The Brown team plans to make it available to researchers around the world in the hopes of developing new avenues of cry research.

Sheinkopf, who specializes in developmental disorders, plans to use the tool to look for cry features that might correlate with autism.

“We’ve known for a long time that older individuals with autism produce sounds or vocalizations that are unusual or atypical,” Sheinkopf said. “So vocalizations in babies have been discussed as being useful in developing early identification tools for autism. That’s been a major challenge. How do you find signs of autism in infancy?”

The answer could be encoded in a cry.

“Early detection of developmental disorders is critical,” Lester added. “It can lead to insights into the causes of these disorders and interventions to prevent or reduce the severity of impairment.”

Exposure to Stress Even Before Conception Causes Genetic Changes to Offspring

A female’s exposure to distress even before she conceives causes changes in the expression of a gene linked to the stress mechanism in the body — in the ovum and later in the brains of the offspring from when they are born, according to a new study on rats conducted by the University of Haifa.

“The systemic similarity in many instances between us and mice raises questions about the transgenerational influences in humans as well, for example, the effects of the Second Lebanon War or the security situation in the South on the children of those who went through those difficult experiences,” the researchers said. “If until now we saw evidence only of behavioral effects, now we’ve found proof of effects at the genetic level.”

In previous studies in Prof. Micah Leshem’s lab, it was found that exposing rats to stress before they had even conceived (and even at their “teen” stage) influences the behavior of their offspring. This study, conducted in the lab of Dr. Inna Gaisler-Salomon by PhD student Hiba Zaidan, in cooperation with Prof. Leshem, the researchers sought to examine whether there was an influence on genetic expression.

In the study, which was recently published in the journal Biological Psychiatry, the researchers focused on the gene known as CRF-1, a gene linked to the body’s stress-control system that expresses itself in many places in the brain under stress.

The researchers took female rats that were 45 days old, which is parallel to human adolescence. Some of the rats were exposed to “minor” stress, which included changes in temperature and daily routine for seven days, and compared them to a control group that was not exposed to stress at all. The rats were mated and conceived two weeks later.

In the first part of the study, the researchers examined the ova of the rats that were exposed to stress even before they conceived, and they found that at that stage there was enhanced expression of the CRF-1 gene. For the second part, the researchers examined the brains of newborn rats immediately after birth, before the mother could have any influence on them, and found that even at the neonatal stage, there was enhanced expression of the CRF-1 gene in the brains of the rats born to mothers who had been exposed to stress.

During the third stage, the researchers exposed the offspring – both those whose mothers had been exposed to stress and those whose mothers were not – to stress when they reached adulthood. It emerged that the expression of CRF-1 among the offspring was dependent on three factors: The sex of the offspring, the stress undergone by the mother and the stress to which the offspring were exposed. The female rats whose mothers had been exposed to stress and who themselves underwent a “stressful” behavioral test showed higher levels of CRF-1 than other groups.

“This is the first time that we showed that the genetic response to stress in rats is linked to the experiences their mothers underwent long before they even got pregnant with them,” the researchers said. “We are learning more and more about intergenerational genetic transfer and in light of the findings, and in light of the fact that in today’s reality many women are exposed to stress even before they get pregnant, it’s important to research the degree to which such phenomenon take place in humans.”

(Image: iStockphoto)

Unique Epigenomic Code Identified During Human Brain Development

Changes in the epigenome, including chemical modifications of DNA, can act as an extra layer of information in the genome, and are thought to play a role in learning and memory, as well as in age-related cognitive decline. The results of a new study by scientists at the Salk Institute for Biological Studies show that the landscape of DNA methylation, a particular type of epigenomic modification, is highly dynamic in brain cells during the transition from birth to adulthood, helping to understand how information in the genomes of cells in the brain is controlled from fetal development to adulthood. The brain is much more complex than all other organs in the body and this discovery opens the door to a deeper understanding of how the intricate patterns of connectivity in the brain are formed.

“These results extend our knowledge of the unique role of DNA methylation in brain development and function,” says senior author Joseph R. Ecker, professor and director of Salk’s Genomic Analysis Laboratory and holder of the Salk International Council Chair in Genetics. “They offer a new framework for testing the role of the epigenome in healthy function and in pathological disruptions of neural circuits.”

A healthy brain is the product of a long process of development. The front-most part of our brain, called the frontal cortex, plays a key role in our ability to think, decide and act. The brain accomplishes all of this through the interaction of special cells such as neurons and glia. We know that these cells have distinct functions, but what gives these cells their individual identities? The answer lies in how each cell expresses the information contained in its DNA. Epigenomic modifications, such as DNA methylation, can control which genes are turned on or off without changing letters of the DNA alphabet (A-T-C-G), and thus help distinguish different cell types.

In this new study, published July 4 in Science, the scientists found that the patterns of DNA methylation undergo widespread reconfiguration in the frontal cortex of mouse and human brains during a time of development when synapses, or connections between nerve cells, are growing rapidly. The researchers identified the exact sites of DNA methylation throughout the genome in brains from infants through adults. They found that one form of DNA methylation is present in neurons and glia from birth. Strikingly, a second form of “non-CG” DNA methylation that is almost exclusive to neurons accumulates as the brain matures, becoming the dominant form of methylation in the genome of human neurons. These results help us to understand how the intricate DNA landscape of brain cells develops during the key stages of childhood.

The genetic code in DNA is made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). DNA methylation typically occurs at so-called CpG sites, where C (cytosine) sits next to G (guanine) in the DNA alphabet. About 80 to 90 percent of CpG sites are methylated in human DNA. Salk researchers previously discovered that in human embryonic stem cells and induced pluripotent stem cells, a type of artificially derived stem cell, DNA methylation can also occur when G does not follow C, hence “non-CG methylation.” Originally, they thought that this type of methylation disappeared when stem cells differentiate into specific tissue-types such as lung or fat cells. The current study finds this is not the case in the brain, where non-CG methylation appears after cells differentiate, usually during childhood and adolescence when the brain is maturing.

By sequencing the genomes of mouse and human brain tissue as well as neurons and glia (from the frontal cortex of the brain) during early postnatal, juvenile, adolescent and adult stages, the Salk team found that non-CG methylation accumulates in neurons through early childhood and adolescence, and becomes the dominant form of DNA methylation in mature human neurons. “This shows that the period during which the neural circuits of the brain mature is accompanied by a parallel process of large-scale reconfiguration of the neural epigenome,” says Ecker, who is a Howard Hughes Medical Institute and Gordon and Betty Moore Foundation investigator.

The study provides the first comprehensive maps of how DNA methylation patterns change in the mouse and human brain during development, forming a critical foundation to now explore whether changes in methylation patterns may be linked to human diseases, including psychiatric disorders. Recent studies have demonstrated a possible role for DNA methylation in schizophrenia, depression, suicide and bipolar disorder. “Our work will let us begin to ask more detailed questions about how changes in the epigenome sculpt the complex identities of brain cells through life,” says co-first author Eran Mukamel, from Salk’s Computational Neurobiology Laboratory.

“The human brain has been called the most complex system that we know of in the universe,” says Ryan Lister, co-corresponding author on the new paper, previously a postdoctoral fellow in Ecker’s laboratory at Salk and now a group leader at The University of Western Australia. “So perhaps we shouldn’t be so surprised that this complexity extends to the level of the brain epigenome. These unique features of DNA methylation that emerge during critical phases of brain development suggest the presence of previously unrecognized regulatory processes that may be critically involved in normal brain function and brain disorders.”

At present, there is consensus among neuroscientists that many mental disorders have a neurodevelopmental origin and arise from an interaction between genetic predisposition and environmental influences (for example, early-life stress or drug abuse), the outcome of which is altered activity of brain networks. The building and shaping of these brain networks requires a long maturation process in which central nervous system cell types (neurons and glia) need to fine-tune the way they express their genetic code.

“DNA methylation fulfills this role,” says study co-author Terrence J. Sejnowski, a Howard Hughes Medical Institute Investigator, holder of the Francis Crick Chair and head of Salk’s Computational Neurobiology Laboratory. “We found that patterns of methylation are dynamic during brain development, in particular for non-CG methylation during early childhood and adolescence, which changes the way that we think about normal brain function and dysfunction.”

By disrupting the transcriptional expression of neurons, adds co-corresponding author M. Margarita Behrens, a staff scientist in the Computational Neurobiology Laboratory, “the alterations of these methylation patterns will change the way in which networks are formed, which could, in turn, lead to the appearance of mental disorders later in life.”

Researchers discover a gene’s key role in building the developing brain’s scaffolding

The gene, Arl13b, is necessary for the proper construction of the cerebral cortex. The finding offers new insights on normal brain development and illuminates some of the factors behind Joubert’s syndrome, a rare neurological disorder.

Researchers have pinpointed the role of a gene known as Arl13b in guiding the formation and proper placement of neurons in the early stages of brain development. Mutations in the gene could help explain brain malformations often seen in neurodevelopmental disorders.

The research, led by a team at the University of North Carolina School of Medicine, was published June 30 in the journal Nature Neuroscience.

“We wanted to get a better sense of how the cerebral cortex is constructed,” said senior study author Eva Anton, PhD, a professor in the Department of Cell Biology and Physiology and a member of the UNC Neuroscience Center. “The cells we studied — radial glial cells — provide a scaffolding for the formation of the brain by making neurons and guiding them to where they have to go. This is the first step in the formation of functional neuronal circuitry in the brain. This study gives us new information about the mechanisms involved in that process.”

The researchers became interested in the Arl13b gene because of its expression in a part of the cell called primary cilium and its association with a rare neurological disorder known as Joubert syndrome. The syndrome is characterized by brain malformations and autism like features.

“In addition to helping us understand an important cellular mechanism involved in normal brain development, this study may offer an explanation for some of the malformations seen in Joubert syndrome patients,” said Anton. Although there is no immediate clinical application for these patients, the study does help illuminate the factors behind the disease. “It shows what may have gone wrong in some of those patients that led to the malformations,” said Anton.

The cerebral cortex, the brain’s “gray matter,” is responsible for higher-order functions such as memory and consciousness. Like the scaffolding builders use to move people and materials during construction, radial glial cells provide an instructive matrix to create the basic structural features of the cerebral cortex. Mistakes in the formation and development of radial glial cells can translate into structural problems in the brain as it develops, said Anton.

Both mice and humans have the Arl13b gene. The researchers generated a series of mice with mutations on the Arl13b gene at different developmental stages to track the mutations’ effects on brain development. They discovered that the gene is crucial to the radial glial cells’ ability to sense signals through an appendage called the primary cilium. Without this signaling capability, the radial glia were unable to organize into an instructive scaffold capable of orchestrating the orderly formation of cerebral cortex. “The cilia in these cells play an important role in the initial setup of this scaffolding,” said Anton. “Without a functioning Arl13b gene, the cells were not able to determine polarity and formed haphazardly. As a result, they formed a malformed cerebral cortex with ectopic clusters of neurons, instead of the orderly layers of neurons with appropriate connectivity that would be expected, in the developing brain.

Researchers Find Zinc’s Crucial Pathway to the Brain

A new study helps explain how parts of the brain maintain their delicate balance of zinc, an element required in minute but crucial doses, particularly during embryonic development.

The study, led at the Marine Biological Laboratory (MBL) by Mark Messerli in collaboration with scientists from the University of California, Davis, shows that neural cells require zinc uptake through a membrane transporter referred to as ZIP12. If that route is closed, neuronal sprouting and growth are significantly impaired and is fatal for a developing embryo. Their discovery was published in the Proceedings of the National Academy of Sciences.

“This particular transporter is an essential doorway for many neurons in the central nervous system,” explains Messerli. “You knock out this one gene, this one particular pathway for the uptake of zinc into these cells, and you essentially prevent neuronal outgrowth. That’s lethal to the embryo.”

Previously, scientists thought that zinc could use more than one pathway to enter the cell during early brain development. Some other elements, like calcium, enjoy such luxury of multiple options.

Knocking out ZIP12, affected several critical processes in the brain, the scientists found. For example, frog embryos were unable to develop their neural systems properly. Additionally, neurons had trouble reaching out to connect to other neurons; their extensions were both shorter and fewer in number than normal.

“We were surprised that ZIP12 was required at such an early and critical stage of development,” said Winyoo Chowanadisai, a researcher in nutrition at the University of California at Davis and visiting scientist in the Cellular Dynamics Program at the MBL. Dr. Chowanadisai was the first on the team to realize that ZIP12 is expressed in such abundance in the brain.“This study also reinforces the importance of periconceptional and prenatal nutrition and counseling to promote health during the earliest stages of life.”

ZIP12 is part of a larger family of transporters involved in the movement of metal ions from outside the cell. Other reports showed that simultaneously blocking 3 other transporters in the family – including  ZIP1, 2, and 3 – had no major effects on embryonic development.

Zinc is needed for healthy neural development, helping the brain to learn and remember new information. However, too much zinc can also be problematic.

The research team is investigating the implications of their results on processes like embryonic brain development and wound healing.

“[The result] was not expected,” said Messerli, a physiologist in the MBL’s Bell Center for Regenerative Biology and Tissue Enginering and Cellular Dynamics Program. ““We found that zinc uptake through ZIP12 is a regulatory point for neuronal growth, required for development and possibly required for learning and memory throughout life. We want to elucidate the downstream targets that zinc is affecting. That’s the next exploration.”

Study Shows a Solitary Mutation Can Destroy Critical ‘Window’ of Early Brain Development

Scientists from the Florida campus of The Scripps Research Institute (TSRI) have shown in animal models that brain damage caused by the loss of a single copy of a gene during very early childhood development can cause a lifetime of behavioral and intellectual problems.

The study, published this week in the Journal of Neuroscience, sheds new light on the early development of neural circuits in the cortex, the part of the brain responsible for functions such as sensory perception, planning and decision-making.

The research also pinpoints the mechanism responsible for the disruption of what are known as “windows of plasticity” that contribute to the refinement of the neural connections that broadly shape brain development and the maturing of perception, language, and cognitive abilities.

The key to normal development of these abilities is that the neural connections in the brain cortex—the synapses—mature at the right time.

In an earlier study, the team, led by TSRI Associate Professor Gavin Rumbaugh, found that in mice missing a single copy of the vital gene, certain synapses develop prematurely within the first few weeks after birth. This accelerated maturation dramatically expands the process known as “excitability”—how often brain cells fire—in the hippocampus, a part of the brain critical for memory. The delicate balance between excitability and inhibition is especially critical during early developmental periods. However, it remained a mystery how early maturation of brain circuits could lead to lifelong cognitive and behavioral problems.

The current study shows in mice that the interruption of the synapse-regulating gene known as SYNGAP1—which can cause a devastating form of intellectual disability and increase the risk for developing autism in humans—induces early functional maturation of neural connections in two areas of the cortex. The influence of this disruption is widespread throughout the developing brain and appears to degrade the duration of these critical windows of plasticity.

“In this study, we were able to directly connect early maturation of synapses to the loss of an important plasticity window in the cortex,” Rumbaugh said. “Early maturation of synapses appears to make the brain less plastic at critical times in development. Children with these mutations appear to have brains that were built incorrectly from the ground up.”

The accelerated maturation also appeared to occur surprisingly early in the developing cortex. That, Rumbaugh added, would correspond to the first two years of a child’s life, when the brain is expanding rapidly. “Our goal now is to figure out a way to prevent the damage caused by SYNGAP1 mutations. We would be more likely to help that child if we could intervene very early on—before the mutation has done its damage,” he said.

Scientists discover previously unknown requirement for brain development

Scientists at the Salk Institute for Biological Studies have demonstrated that sensory regions in the brain develop in a fundamentally different way than previously thought, a finding that may yield new insights into visual and neural disorders.

In a paper published June 7, 2013, in Science, Salk researcher Dennis O’Leary and his colleagues have shown that genes alone do not determine how the cerebral cortex grows into separate functional areas. Instead, they show that input from the thalamus, the main switching station in the brain for sensory information, is crucially required.

O’Leary has done pioneering studies in “arealization,” the way in which the neo-cortex, the major region of cerebral cortex, develops specific areas dedicated to particular functions. In a landmark paper published in Science in 2000, he showed that two regulatory genes were critically responsible for the general pattern of the neo-cortex, and has since shown distinct roles for other genes in this process. In this new set of mouse experiments, his laboratory focused on the visual system, and discovered a new, unexpected twist to the story.

"In order to function properly, it is essential that cortical areas are mapped out correctly, and it is this architecture that was thought to be genetically pre-programmed," says O’Leary, holder of the Vincent J. Coates Chair in Molecular Neurobiology at Salk. "To our surprise, we discovered thalamic input plays an essential role far earlier in brain development."

Vision is relayed from the outside world into processing areas within the brain. The relay starts when light hits the retina, a thin strip of cells at the back of the eye that detects color and light levels and encodes the information as electrical and chemical signals. Through retinal ganglion cells, those signals are then sent into the Lateral Geniculate Nucleus (LGN), a structure in thalamus.

In the next important step in the relay, the LGN routes the signals into the primary visual area (V1) in the neo-cortex, a multi-layered structure that is divided into functionally and anatomically distinct areas. V1 begins the process of extracting visual information, which is further carried out by “higher order” visual areas in the neo-cortex that are vitally important to visual perception. Like parts in a machine, the functions of these areas are both individual and integrated. Damage in one tiny area can lead to strange visual disorders in which a person may be able to see a moving ball, and yet not perceive it is in motion.

Current dogma holds that this basic architecture is entirely genetically determined, with environmental input only playing a role later in development. One of the most famous examples of this idea is the Nobel Prize-winning work of visual neuroscientists David Hubel and Torsten Wiesel, which showed that there is a “critical period” of sensitivity in vision. Their finding was commonly interpreted as a warning that without exposure to basic visual stimuli early in life, even an individual with a healthy brain will be unable to see correctly.

Later discoveries in neural plasticity more optimistically suggested that early deprivation can be overcome, and the brain can even sprout new neurons in specific areas. Nevertheless, this still reinforced the idea that environmental influences might modify neural architecture, but only genetics could establish how cortical areas would be laid out.

In their new study, however, O’Leary and the paper’s co-first authors, Shen-Ju Chou and Zoila Babot, post-doctoral researchers in O’Leary’s laboratory, show that genetics only provides a broad field in the neo-cortex for visual areas.

When they created mouse mutants that disconnected the link between thalamus and cortex but only after early cortical development was complete, they found that the primary and higher order visual areas failed to differentiate from one another as they should.

"Our new understanding is that genes only create a rough lay-out of cortical areas," explains O’Leary. "There must be thalamic input to develop the fine differentiation necessary for proper sensory processing."

Essentially, if the brain were a house, genes would determine which areas were bedrooms. Thalamic input provides the details, distinguishing what will be the master bedroom, a child’s bedroom, a guest bedroom and so on. “The size and location of areas within the overall cortex does not change, but without thalamic input from the LGN, the critical differentiation process that creates primary and higher order visual areas does not happen,” says O’Leary.

Given that most sensory modalities—sight, hearing, touch—route through thalamus to cortex, this experiment may suggest why, when someone lacks a sensory modality from birth, that individual has a harder time processing restored sensory input than someone who lost the sense later in life. But in addition, as O’Leary says, “More subtle changes in thalamic input in humans would also likely result in changes to the neo-cortex that could well have a substantial impact on the ability to process vision, or other senses, and lead to abnormal behavior.”

O’Leary says his lab plans to continue to explore the links between how cortical areas in the brain are established and various developmental disorders, such as autism.

(Image: Nucleus Medical Art, Inc.)