HIV hides in gut, evading eradication

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Researchers at UC Davis have made some surprising discoveries about the body’s initial responses to HIV infection. Studying simian immunodeficiency virus (SIV), the team found that specialized cells in the intestine called Paneth cells are early responders to viral invasion and are the source of gut inflammation by producing a cytokine called interleukin-1 beta (IL-1β).

Though aimed at the presence of virus, IL-1β causes breakdown of the gut epithelium that provides a barrier to protect the body against pathogens. Importantly, this occurs prior to the wide spread viral infection and immune cell killing. But in an interesting twist, a beneficial bacterium, Lactobacillus plantarum, helps mitigate the virus-induced inflammatory response and protects gut epithelial barrier. The study was published in the journal PLoS Pathogens.

One of the biggest obstacles to complete viral eradication and immune recovery is the stable HIV reservoir in the gut. There is very little information about the early viral invasion and the establishment of the gut reservoir.

“We want to understand what enables the virus to invade the gut, cause inflammation and kill the immune cells,” said Satya Dandekar, lead author of the study and chair of the Department of Medical Microbiology and Immunology at UC Davis.

“Our study has identified Paneth cells as initial virus sensors in the gut that may induce early gut inflammation, cause tissue damage and help spread the viral infection. Our findings provide potential targets and new biomarkers for intervening or blocking early spread of viral infection,” she said.

In the study, the researchers detected a very small number of SIV infected cells in the gut within initial 2.5 days of viral infection; however, the inflammatory response to the virus was playing havoc with the gut lining. IL-1β was reducing the production of tight-junction proteins, which are crucial to making the intestinal barrier impermeable to pathogens. As a result, the normally cohesive barrier was breaking down.

Digging deeper, the researchers found the inflammatory response through IL-1β production was initiated in Paneth cells, which are known to protect the intestinal stem cells to replenish the epithelial lining. This is the first report of Paneth cell sensing of SIV infection and IL-1β production that links to gut epithelial damage during early viral invasion. In turn, the epithelial breakdown underscores that there’s more to the immune response than immune cells.

“The epithelium is more than a physical barrier,” said first author Lauren Hirao. “It’s providing support to immune cells in their defense against viruses and bacteria.”

The researchers found that addition of a specific probiotic strain, Lactobacillus plantarum, to the gut reversed the damage by rapidly reducing IL-1β, resolving inflammation, and accelerating repair within hours. The study points to interesting possibilities of harnessing synergistic host-microbe interactions to intervene early viral spread and gut inflammation and to mitigate intestinal complications associated with HIV infection.

“Understanding the players in the immune response will be important to develop new therapies,” said Hirao. “Seeing how these events play out can help us find the most opportune moments to intervene.”

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‘Robo Brain’ – Robots Devouring Internet Info

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Robo Brain – a large-scale computational system that learns from publicly available Internet resources – is currently downloading and processing about 1 billion images, 120,000 YouTube videos, and 100 million how-to documents and appliance manuals.

The information is being translated and stored in a robot-friendly format that robots will be able to draw on when they need it.

To serve as helpers in our homes, offices and factories, robots will need to understand how the world works and how the humans around them behave. Robotics researchers have been teaching them these things one at a time: How to find your keys, pour a drink, put away dishes, and when not to interrupt two people having a conversation. This will all come in one package with Robo Brain.

“Our laptops and cell phones have access to all the information we want. If a robot encounters a situation it hasn’t seen before it can query Robo Brain in the cloud,” said Ashutosh Saxena, assistant professor of computer science at Cornell University. Saxena and colleagues at Cornell, Stanford and Brown universities and the University of California, Berkeley, say Robo Brain will process images to pick out the objects in them, and by connecting images and video with text, it will learn to recognize objects and how they are used, along with human language and behavior.

If a robot sees a coffee mug, it can learn from Robo Brain not only that it’s a coffee mug, but also that liquids can be poured into or out of it, that it can be grasped by the handle, and that it must be carried upright when it is full, as opposed to when it is being carried from the dishwasher to the cupboard.

Saxena described the project at the 2014 Robotics: Science and Systems Conference, July 12-16 in Berkeley, and has launched a website for the project at http://robobrain.me

The system employs what computer scientists call “structured deep learning,” where information is stored in many levels of abstraction. An easy chair is a member of the class of chairs, and going up another level, chairs are furniture. Robo Brain knows that chairs are something you can sit on, but that a human can also sit on a stool, a bench or the lawn.

A robot’s computer brain stores what it has learned in a form mathematicians call a Markov model, which can be represented graphically as a set of points connected by lines (formally called nodes and edges). The nodes could represent objects, actions or parts of an image, and each one is assigned a probability – how much you can vary it and still be correct. In searching for knowledge, a robot’s brain makes its own chain and looks for one in the knowledge base that matches within those limits. “The Robo Brain will look like a gigantic, branching graph with abilities for multi-dimensional queries,” said Aditya Jami, a visiting researcher art Cornell, who designed the large-scale database for the brain. Perhaps something that looks like a chart of relationships between Facebook friends, but more on the scale of the Milky Way Galaxy.

Like a human learner, Robo Brain will have teachers, thanks to crowdsourcing. The Robo Brain website will display things the brain has learned, and visitors will be able to make additions and corrections.

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Modeling How Neurons Work May Inform Robotics

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A highly accurate model of how neurons behave when performing complex movements could aid in the design of robotic limbs which behave more realistically.

Multiphoton microscopy of mouse motor neurons – Photo Credit: Zeiss Microscopy via flickr

A newly-developed, highly accurate representation of the way in which neurons behave when performing movements such as reaching could not only enhance understanding of the complex dynamics at work in the brain, but aid in the development of robotic limbs which are capable of more complex and natural movements.

Researchers from the University of Cambridge, working in collaboration with the University of Oxford and the Ecole Polytechnique Fédérale de Lausanne (EPFL), have developed a new model of a neural network, offering a novel theory of how neurons work together when performing complex movements. The results are published in the 18 June edition of the journal Neuron.

While an action such as reaching for a cup of coffee may seem straightforward, the millions of neurons in the brain’s motor cortex must work together to prepare and execute the movement before the coffee ever reaches our lips. When we reach for the much-needed cup of coffee, the neurons spring into action, sending a series of signals from the brain to the hand. These signals are transmitted across synapses – the junctions between neurons.

Determining exactly how the neurons work together to execute these movements is difficult, however. The new theory was inspired by recent experiments carried out at Stanford University, which had uncovered some key aspects of the signals that neurons emit before, during and after the movement. “There is a remarkable synergy in the activity recorded simultaneously in hundreds of neurons,” said Dr Guillaume Hennequin of the University’s Department of Engineering, who led the research. “In contrast, previous models of cortical circuit dynamics predict a lot of redundancy, and therefore poorly explain what happens in the motor cortex during movements.”

Better models of how neurons behave will not only aid in our understanding of the brain, but could also be used to design prosthetic limbs controlled via electrodes implanted in the brain. “Our theory could provide a more accurate guess of how neurons would want to signal both movement intention and execution to the robotic limb,” said Dr Hennequin.

The behaviour of neurons in the motor cortex can be likened to a mousetrap or a spring-loaded box, in which the springs are waiting to be released and are let go once the lid is opened or the mouse takes the bait. As we plan a movement, the ‘neural springs’ are progressively flexed and compressed. When released, they orchestrate a series of neural activity bursts, all of which takes place in the blink of an eye.

The signals transmitted by the synapses in the motor cortex during complex movements can be either excitatory or inhibitory, which are in essence mirror reflections of each other. The signals cancel each other out for the most part, leaving occasional bursts of activity.

Using control theory, a branch of mathematics well-suited to the study of complex interacting systems such as the brain, the researchers devised a model of neural behaviour which achieves a balance between the excitatory and inhibitory synaptic signals. The model can accurately reproduce a range of multidimensional movement patterns.

The researchers found that neurons in the motor cortex might not be wired together with nearly as much randomness as had been previously thought. “Our model shows that the inhibitory synapses might be tuned to stabilise the dynamics of these brain networks,” said Dr Hennequin. “We think that accurate models like these can really aid in the understanding of the incredibly complex dynamics at work in the human brain.”

Future directions for the research include building a more realistic, ‘closed-loop’ model of movement generation in which feedback from the limbs is actively used by the brain to correct for small errors in movement execution. This will expose the new theory to the more thorough scrutiny of physiological and behavioural validation, potentially leading to a more complete mechanistic understanding of complex movements.

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Tumor weaknesses in epigenetics

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Scientists have known for decades that cancer can be caused by genetic mutations, but more recently they have discovered that chemical modifications of a gene can also contribute to cancer. These alterations, known as epigenetic modifications, control whether a gene is turned on or off.

This image shows a DNA molecule that is methylated on both strands on the center cytosine. Photo Credit: Christoph Bock

Analyzing these modifications can provide important clues to the type of tumor a patient has, and how it will respond to different drugs. For example, patients with glioblastoma, a type of brain tumor, respond well to a certain class of drugs known as alkylating agents if the DNA-repair gene MGMT is silenced by epigenetic modification.

A team of MIT chemical engineers has now developed a fast, reliable method to detect this type of modification, known as methylation, which could offer a new way to choose the best treatment for individual patients.

“It’s pretty difficult to analyze these modifications, which is a need that we’re working on addressing. We’re trying to make this analysis easier and cheaper, particularly in patient samples,” says Hadley Sikes, an assistant professor of chemical engineering and the senior author of a paper describing the technique in the journal Analyst.

The paper’s lead author is Brandon Heimer, an MIT graduate student in chemical engineering.

Beyond the genome

After sequencing the human genome, scientists turned to the epigenome — the chemical modifications, including methylation, that alter a gene’s function without changing its DNA sequence.

In some cancers, the MGMT gene is turned off when methyl groups attach to specific locations in the DNA sequence — namely, cytosine bases that are adjacent to guanine bases. When this happens, proteins bind the methylated bases and effectively silence the gene by blocking it from being copied into RNA.

“This very small chemical modification triggers a sequence of events where that gene is no longer expressed,” Sikes says.

Current methods for detecting cytosine methylation work well for large-scale research studies, but are hard to adapt to patient samples, Sikes says. Most techniques require a chemical step called bisulfite conversion: The DNA sample is exposed to bisulfite, which converts unmethylated cytosine to a different base. Sequencing the DNA reveals whether any methylated cytosine was present.

However, this method doesn’t work well with patient samples because you need to know precisely how much methylated DNA is in a sample to calculate how long to expose it to bisulfite, Sikes says.

“When you have limited amounts of samples that are less well defined, it’s a lot harder to run the reaction for the right amount of time. You want to get all of the unmethylated cytosine groups converted, but you can’t run it too long, because then your DNA gets degraded,” she says.

Rapid detection

Sikes’ new approach avoids bisulfite conversion completely. Instead, it relies on a protein called a methyl binding domain (MBD) protein, which is part of cells’ natural machinery for controlling DNA transcription. This protein recognizes methylated DNA and binds to it, helping a cell to determine if the DNA should be transcribed.

The other key component of Sikes’ system is a biochip — a glass slide coated with hundreds of DNA probes that are complementary to sequences from the gene being studied. When a DNA sample is exposed to this chip, any strands that match the target sequences are trapped on the biochip. The researchers then treat the slide with the MBD protein probe. If the probe binds to a trapped DNA molecule, it means that sequence is methylated.

The binding between the DNA and the MBD protein can be detected either by linking the protein to a fluorescent dye or designing it to carry a photosensitive molecule that forms hydrogels when exposed to light.

This technique, which cuts the amount of time required to analyze epigenetic modifications, could be a valuable research tool as well as a diagnostic device for cancer patients, says Andrea Armani, a professor of chemical engineering and materials science at the University of Southern California, who was not part of the research team.

“It’s a really innovative approach,” Armani says. “Not only could it impact diagnostics, but on a broader scale, it could impact our understanding of which epigenetic markers are linked to which diseases.”

The MIT team is now adapting the device to detect methylation of other cancer-linked genes by changing the DNA sequences of the biochip probes. They also hope to create better versions of the MBD protein and to engineer the device to require less DNA. With the current version, doctors would need to do a surgical biopsy to get enough tissue, but the researchers would like to modify it so the test could be done with just a needle biopsy.

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HIV antibodies block infection by reservoir-derived virus

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A laboratory study led by scientists from the National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health (NIH), lends further weight to the potential effectiveness of passive immunotherapy to suppress HIV in the absence of drug treatment.

This is Tae-Wook Chun, Ph.D., staff scientist in the NIAID Laboratory of Immunoregulation and first author of the study.

Passive immunotherapy for HIV is an experimental strategy that involves periodically administering broadly neutralizing HIV-specific antibodies (bNAbs) to control the virus. It would be advantageous to control HIV without antiretroviral drugs because of their cost, the potential for cumulative toxicities from lifelong therapy, and the difficulties some patients have adhering to drug regimens and tolerating certain drugs.

Although bNAbs have proven effective at blocking infection by various strains of HIV in the laboratory, their effect on HIV in humans, and particularly on the virus particles that hide in immune cells (called latent viral reservoirs), has been unknown.

In this study, NIH scientists obtained HIV from the latent reservoirs of 29 infected people in whom antiretroviral therapy fully inhibited viral replication. In the laboratory, the researchers found that several bNAbs — particularly PGT121, VRC01 and VRC03 — effectively blocked HIV from entering the CD4+ T cells obtained from uninfected healthy donors. In addition, the scientists demonstrated in the laboratory that these antibodies could completely block HIV replication in CD4+ T cells obtained from infected individuals receiving antiretroviral therapy.

The researchers conclude that passive immunotherapy involving bNAbs individually or in combination may control HIV in the absence of antiretroviral therapy. A number of clinical trials are already underway or planned to test this hypothesis.

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Travelling by resonance

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How nerve cells within the brain communicate with each other over long distances has puzzled scientists for decades.

The way networks of neurons connect and how individual cells react to incoming pulses in principle makes communication over large distances impossible. Scientists from Germany and France provide now a possible answer how the brain can function nonetheless: by exploiting the powers of resonance.

As Gerald Hahn, Alejandro F. Bujan and colleagues describe in the journal “PLoS Computational Biology”, the ability of networks of neurons to resonate can amplify oscillations in the activity of nerve cells, allowing signals to travel much farther than in the absence of resonance. The team from the cluster of excellence BrainLinks-BrainTools and the Bernstein Center at the University of Freiburg and the UNIC department of the French Centre national de la recherche scientifique in Gif-sur-Yvette created a computer model of networks of nerve cells and analyzed its properties for signal propagation.

Earlier propositions how information travels through the brain had the flaw of being biologically implausible. They either postulated strong connections between distant brain areas for which there was no evidence, or they required a global mechanism setting these distant parts of the brain into linked oscillations. However, nobody could explain how this could actually be implemented.

The simulation study of Hahn and Bujan required neither unrealistic network properties nor the existence of a pacemaker for the brain. Instead, they found that resonance could be the key to long-distance communication in networks with relatively few and weak connections, as it is the case in the brain. Not all nerve cells excite other cells; some inhibit the activity of others. This means that the activity in a network can oscillate around a certain level of activity as a result of the interplay of excitation and inhibition. These networks typically have preferred frequencies at which oscillations are particularly strong, just as a taut string on a violin has a preferred frequency. If the activity tunes into this frequency, pulses propagate much farther. As the scientists point out, the combination of oscillatory signals together with resonance induced amplification may be the only possible form of long distance communication in certain cases. They further suggest that a network’s ability to change its preferred frequency may play a role in the way how information is at times processed differently in the brain.

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Protein glue shows potential for use with biomaterials

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Researchers at the University of Milan in Italy have shown that a synthetic protein called AGMA1 has the potential to promote the adhesion of brain cells in a laboratory setting. This could prove helpful in improving cell adhesiveness to biomaterials.

Representative confocal microscopy pictures of primary mixed coculture neurons-astrocytes grown on AGMA1 (Left) and PLL (Rigt). – Scale bar = 25 μm. Photo Credit: Science and Technology of Advanced Materials

Isolating nerve cells from their original organism and culturing them in the laboratory has long been used as a method to study brain metabolism. It has been challenging, however, to provide brain cell cultures with the necessary “adhesion promoters” that facilitate cell attachment, spreading, growth and morphological development.

Improving cell adhesion to biomaterials is also a major challenge in nerve tissue engineering and is crucial for the development of implanted neural prostheses, such as cochlear implants, and biosensors, such as blood glucose biosensors.

Coating the surfaces of negatively charged cell membranes with positively charged synthetic proteins promotes nerve adhesion and extension in laboratory settings. Most synthetic proteins, however, are toxic to living cells and thus need to be washed off before cell suspensions are spread onto a new plate. They are also unsuitable for applications that are used inside a living organism.

Within the central nervous system, extracellular matrix substances such as collagen and laminin promote the regeneration, differentiation, adhesion and migration of nerve fibers.

A protein sequence found in collagen and laminin has been identified as the minimum sequence that can mediate the adhesion of many cell types, including nerve cells.

AGMA1 is a basic synthetic protein that is biocompatible, water soluble, positively charged, and has a protein sequence similar to that found in collagen and laminin. It is much less toxic to living cells than conventionally used synthetic proteins. AGMA1 is also much easier to prepare on a large scale using relatively low-cost materials. As a result it is much cheaper.

University of Milan scientists tested the potential of AGMA1 to promote the adhesion, proliferation, and differentiation of primary brain cells in the laboratory.

Different primary cell types from rat brain were cultured on AGMA1, and the results compared with those of cells cultured under the same conditions on conventional substrates using other commonly used synthetic proteins. All experimental results showed that the performance of AGMA1 in this respect was comparable to that of conventional substrates.

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Boosting Memory With Electric Current to Brain

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Stimulating a particular region in the brain via non-invasive delivery of electrical current using magnetic pulses, called Transcranial Magnetic Stimulation, improves memory, reports a new Northwestern Medicine® study.

Discovery may help treat memory disorders resulting from stroke, Alzheimer’s and brain injury

The discovery opens a new field of possibilities for treating memory impairments caused by conditions such as stroke, early-stage Alzheimer’s disease, traumatic brain injury, cardiac arrest and the memory problems that occur in healthy aging.

“We show for the first time that you can specifically change memory functions of the brain in adults without surgery or drugs, which have not proven effective,” said senior author Joel Voss, assistant professor of medical social sciences at Northwestern University Feinberg School of Medicine. “This noninvasive stimulation improves the ability to learn new things. It has tremendous potential for treating memory disorders.”

The study was published August 29 in Science.

The study also is the first to demonstrate that remembering events requires a collection of many brain regions to work in concert with a key memory structure called the hippocampus – similar to a symphony orchestra. The electrical stimulation is like giving the brain regions a more talented conductor so they play in closer synchrony.

“It’s like we replaced their normal conductor with Muti,” Voss said, referring to Riccardo Muti, the music director of the renowned Chicago Symphony Orchestra. “The brain regions played together better after the stimulation.”

The approach also has potential for treating mental disorders such as schizophrenia in which these brain regions and the hippocampus are out of sync with each other, affecting memory and cognition.

TMS Boosts Memory

The Northwestern study is the first to show TMS improves memory long after treatment. In the past, TMS has been used in a limited way to temporarily change brain function to improve performance during a test, for example, making someone push a button slightly faster while the brain is being stimulated. The study shows that TMS can be used to improve memory for events at least 24 hours after the stimulation is given.

Finding the Sweet Spot

It isn’t possible to directly stimulate the hippocampus with TMS because it’s too deep in the brain for the magnetic fields to penetrate. So, using an MRI scan, Voss and colleagues identified a superficial brain region a mere centimeter from the surface of the skull with high connectivity to the hippocampus. He wanted to see if directing the stimulation to this spot would in turn stimulate the hippocampus. It did.

“I was astonished to see that it worked so specifically,” Voss said.

When TMS was used to stimulate this spot, regions in the brain involved with the hippocampus became more synchronized with each other, as indicated by data taken while subjects were inside an MRI machine, which records the blood flow in the brain as an indirect measure of neuronal activity.

The more those regions worked together due to the stimulation, the better people were able to learn new information.

How the Study Worked

Scientists recruited 16 healthy adults ages 21 to 40. Each had a detailed anatomical image taken of his or her brain as well as 10 minutes of recording brain activity while lying quietly inside an MRI scanner. Doing this allowed the researchers to identify each person’s network of brain structures that are involved in memory and well connected to the hippocampus. The structures are slightly different in each person and may vary in location by as much as a few centimeters.

“To properly target the stimulation, we had to identify the structures in each person’s brain space because everyone’s brain is different,” Voss said.

Each participant then underwent a memory test, consisting of a set of arbitrary associations between faces and words that they were asked to learn and remember. After establishing their baseline ability to perform on this memory task, participants received brain stimulation 20 minutes a day for five consecutive days.

During the week they also received additional MRI scans and tests of their ability to remember new sets of arbitrary word and face parings to see how their memory changed as a result of the stimulation. Then, at least 24 hours after the final stimulation, they were tested again.

At least one week later, the same experiment was repeated but with a fake placebo stimulation. The order of real stimulation and placebo portions of the study was reversed for half of the participants, and they weren’t told which was which.

Both groups performed better on memory tests as a result of the brain stimulation. It took three days of stimulation before they improved.

“They remembered more face-word pairings after the stimulation than before, which means their learning ability improved,” Voss said. “That didn’t happen for the placebo condition or in another control experiment with additional subjects.”

In addition, the MRI showed the stimulation caused the brain regions to become more synchronized with each other and the hippocampus. The greater the improvement in the synchronicity or connectivity between specific parts of the network, the better the performance on the memory test. “The more certain brain regions worked together because of the stimulation, the more people were able to learn face-word pairings, “ Voss said.

Using TMS to stimulate memory has multiple advantages, noted first author Jane Wang, a postdoctoral fellow in Voss’s lab at Feinberg. “No medication could be as specific as TMS for these memory networks,” Wang said. “There are a lot of different targets and it’s not easy to come up with any one receptor that’s involved in memory.”

The Future

“This opens up a whole new area for treatment studies where we will try to see if we can improve function in people who really need it,“ Voss said.

His current study was with people who had normal memory, in whom he wouldn’t expect to see a big improvement because their brains are already working effectively.

“But for a person with brain damage or a memory disorder, those networks are disrupted so even a small change could translate into gains in their function,” Voss said.

In an upcoming trial, Voss will study the electrical stimulation’s effect on people with early-stage memory loss.

Voss cautioned that years of research are needed to determine whether this approach is safe or effective for patients with Alzheimer’s disease or similar disorders of memory.

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Reprogramming Skin Cells to Mimic Rare Disease

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Johns Hopkins stem cell biologists have found a way to reprogram a patient’s skin cells into cells that mimic and display many biological features of a rare genetic disorder called familial dysautonomia. The process requires growing the skin cells in a bath of proteins and chemical additives while turning on a gene to produce neural crest cells, which give rise to several adult cell types.

Neural crest cells were made from reprogrammed adult skin cells. A single neural crest cell divided many times and these cells (green) were coaxed to become four different types of adult cells, as shown by the presence of cell-specific proteins (red). Clockwise from upper left corner: nerve cells, smooth muscle cells, pigment-producing skin cells and cells that protect and support nerve cells. Photo Credit: Courtesy Cell Press

The researchers say their work substantially expedites the creation of neural crest cells from any patient with a neural crest-related disorder, a tool that lets physicians and scientists study each patient’s disorder at the cellular level.

Previously, the same research team produced customized neural crest cells by first reprogramming patient skin cells into induced pluripotent stem (iPS) cells, which are similar to embryonic stem cells in their ability to become any of a broad array of cell types.

“Now we can circumvent the iPS cells step, saving seven to nine months of time and labor and producing neural crest cells that are more similar to the familial dysautonomia patients’ cells,” says Gabsang Lee, Ph.D., an assistant professor of neurology at the Institute for Cell Engineering and the study’s senior author. A summary of the study was published online in the journal Cell Stem Cell on Aug. 21.

Neural crest cells appear early in human and other animal prenatal development, and they give rise to many important structures, including most of the nervous system (apart from the brain and spinal cord), the bones of the skull and jaws, and pigment-producing skin cells. Dysfunctional neural crest cells cause familial dysautonomia, which is incurable and can affect nerves’ ability to regulate emotions, blood pressure and bowel movements. Less than 500 patients worldwide suffer from familial dysautonomia, but dysfunctional neural crest cells can cause other disorders, such as facial malformations and an inability to feel pain.

The challenge for scientists has been the fact that by the time a person is born, very few neural crest cells remain, making it hard to study how they cause the various disorders.

To make patient-specific neural crest cells, the team began with laboratory-grown skin cells that had been genetically modified to respond to the presence of the chemical doxycycline by glowing green and turning on the gene Sox10, which guides cells toward maturation as a neural crest cell.

Testing various combinations of molecular signals and watching for telltale green cells, the team found a regimen that turned 2 percent of the cells green. That combination involved turning on Sox10 while growing the cells on a layer of two different proteins and giving them three chemical additives to “rewind” their genetic memory and stimulate a protein network important for development.

Analyzing the green cells at the single cell level, the researchers found that they showed gene activity similar to that of other neural crest cells. Moreover, they discovered that 40 percent were “quad-potent,” or able to become the four cell types typically derived from neural crest cells, while 35 percent were “tri-potent” and could become three of the four. The cells also migrated to the appropriate locations in chick embryos when implanted early in development.

The team then applied a modified version of the technique to skin cells from healthy adults and found that the skin cells became neural crests at a rate similar to the team’s previous experiments.

Finally, the investigators used their regimen on skin cells from patients with familial dysautonomia, then compared these familial dysautonomia-neural crest cells to the control neural crest cells made from healthy adults. They identified 412 genes with lower activity levels in the familial dysautonomia-neural crest cells, of which 98 are involved in processing RNA products made from active genes.

According to the authors, this new observation offers insight into what goes wrong in familial dysautonomia.

“It seems as though the neural crest cells created directly from patient skin cells show more of the characteristics of familial dysautonomia than the neural crest cells we created previously from induced pluripotent stem cells,” says Lee. “That means they should be better predictors of what happens in a particular familial dysautonomia patient, and whether or not a potential treatment will work for any given individual.”

The method they devised should also be applicable to skin cells taken from people with any of the other diseases that result from dysfunctional neural crest cells, such as congenital pain disorders and Charcot-Marie-Tooth diseases, Lee says.

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From Nose to Knee: Biongineered Cartilage Regenerates Joints

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Human articular cartilage defects can be treated with nasal septum cells. Researchers at the University and the University Hospital of Basel report that cells taken from the nasal septum are able to adapt to the environment of the knee joint and can thus repair articular cartilage defects.

Articular cartilage replaced: MRI of defect tissue site before (left) and four months after (right) transplantation. Photo Credit: University of Basel, Department of Biomedicine

The nasal cartilage cells’ ability to self-renew and adapt to the joint environment is associated with the expression of so-called HOX genes. The scientific journal Science Translational Medicine has published the research results together with the report of the first treated patients.

Cartilage lesions in joints often appear in older people as a result of degenerative processes. However, they also regularly affect younger people after injuries and accidents. Such defects are difficult to repair and often require complicated surgery and long rehabilitation times. A new treatment option has now been presented by a research team lead by Prof. Ivan Martin, professor for tissue engineering, and Prof. Marcel Jakob, Head of Traumatology, from the Department of Biomedicine at the University and the University Hospital of Basel: Nasal cartilage cells can replace cartilage cells in joints.

Cartilage cells from the nasal septum (nasal chondrocytes) have a distinct capacity to generate a new cartilage tissue after their expansion in culture. In an ongoing clinical study, the researchers have so far taken small biopsies (6 millimeters in diameter) from the nasal septum from seven out of 25 patients below the age of 55 years and then isolated the cartilage cells. They cultured and multiplied the cells and then applied them to a scaffold in order to engineer a cartilage graft the size of 30 x 40 millimeters. A few weeks later they removed the damaged cartilage tissue of the patients’ knees and replaced it with the engineered and tailored tissue from the nose. In a previous clinical study conducted in cooperation with plastic surgeons and using the same method, the researchers from Basel recently already successfully reconstructed nasal wings affected by tumors.

Surprising Adaption

The scientists around first author Dr. Karoliina Pelttari were especially surprised by the fact that in the animal model with goats, the implanted nasal cartilage cells were compatible with the knee joint profile; even though, the two cell types have different origins. During the embryonic development, nasal septum cells develop from the neuroectodermal germ layer, which also forms the nervous system; their self-renewal capacity is attributed to their lack of expression of some homeobox (HOX) genes. In contrast, these HOX genes are expressed in articular cartilage cells that are formed in the mesodermal germ layer of the embryo.

“The findings from the basic research and the preclinical studies on the properties of nasal cartilage cells and the resulting engineered transplants have opened up the possibility to investigate an innovative clinical treatment of cartilage damage”, says Prof. Ivan Martin about the results. It has already previously been shown that the human nasal cells’ capacity to grow and form new cartilage is conserved with age. Meaning, that also older people could benefit from this new method, as well as patients with large cartilage defects. While the primary target of the ongoing clinical study at the University Hospital of Basel is to confirm the safety and feasibility of cartilage grafts engineered from nasal cells when transplanted into joint, the clinical effectiveness assessed until now is highly promising.

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Neuroscientists reverse memories’ emotional associations

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Most memories have some kind of emotion associated with them: Recalling the week you just spent at the beach probably makes you feel happy, while reflecting on being bullied provokes more negative feelings.

A new study from MIT neuroscientists reveals the brain circuit that controls how memories become linked with positive or negative emotions. Furthermore, the researchers found that they could reverse the emotional association of specific memories by manipulating brain cells with optogenetics — a technique that uses light to control neuron activity.

The findings, described in the Aug. 27 issue of Nature, demonstrated that a neuronal circuit connecting the hippocampus and the amygdala plays a critical role in associating emotion with memory. This circuit could offer a target for new drugs to help treat conditions such as post-traumatic stress disorder, the researchers say.

“In the future, one may be able to develop methods that help people to remember positive memories more strongly than negative ones,” says Susumu Tonegawa, the Picower Professor of Biology and Neuroscience, director of the RIKEN-MIT Center for Neural Circuit Genetics at MIT’s Picower Institute for Learning and Memory, and senior author of the paper.

The paper’s lead authors are Roger Redondo, a Howard Hughes Medical Institute postdoc at MIT, and Joshua Kim, a graduate student in MIT’s Department of Biology.

Shifting memories

Memories are made of many elements, which are stored in different parts of the brain. A memory’s context, including information about the location where the event took place, is stored in cells of the hippocampus, while emotions linked to that memory are found in the amygdala.

Previous research has shown that many aspects of memory, including emotional associations, are malleable. Psychotherapists have taken advantage of this to help patients suffering from depression and post-traumatic stress disorder, but the neural circuitry underlying such malleability is not known.

In this study, the researchers set out to explore that malleability with an experimental technique they recently devised that allows them to tag neurons that encode a specific memory, or engram. To achieve this, they label hippocampal cells that are turned on during memory formation with a light-sensitive protein called channelrhodopsin. From that point on, any time those cells are activated with light, the mice recall the memory encoded by that group of cells.

Last year, Tonegawa’s lab used this technique to implant, or “incept,” false memories in mice by reactivating engrams while the mice were undergoing a different experience. In the new study, the researchers wanted to investigate how the context of a memory becomes linked to a particular emotion. First, they used their engram-labeling protocol to tag neurons associated with either a rewarding experience (for male mice, socializing with a female mouse) or an unpleasant experience (a mild electrical shock). In this first set of experiments, the researchers labeled memory cells in a part of the hippocampus called the dentate gyrus.

Two days later, the mice were placed into a large rectangular arena. For three minutes, the researchers recorded which half of the arena the mice naturally preferred. Then, for mice that had received the fear conditioning, the researchers stimulated the labeled cells in the dentate gyrus with light whenever the mice went into the preferred side. The mice soon began avoiding that area, showing that the reactivation of the fear memory had been successful.

The reward memory could also be reactivated: For mice that were reward-conditioned, the researchers stimulated them with light whenever they went into the less-preferred side, and they soon began to spend more time there, recalling the pleasant memory.

A couple of days later, the researchers tried to reverse the mice’s emotional responses. For male mice that had originally received the fear conditioning, they activated the memory cells involved in the fear memory with light for 12 minutes while the mice spent time with female mice. For mice that had initially received the reward conditioning, memory cells were activated while they received mild electric shocks.

Next, the researchers again put the mice in the large two-zone arena. This time, the mice that had originally been conditioned with fear and had avoided the side of the chamber where their hippocampal cells were activated by the laser now began to spend more time in that side when their hippocampal cells were activated, showing that a pleasant association had replaced the fearful one. This reversal also took place in mice that went from reward to fear conditioning.

Altered connections

The researchers then performed the same set of experiments but labeled memory cells in the basolateral amygdala, a region involved in processing emotions. This time, they could not induce a switch by reactivating those cells — the mice continued to behave as they had been conditioned when the memory cells were first labeled.

This suggests that emotional associations, also called valences, are encoded somewhere in the neural circuitry that connects the dentate gyrus to the amygdala, the researchers say. A fearful experience strengthens the connections between the hippocampal engram and fear-encoding cells in the amygdala, but that connection can be weakened later on as new connections are formed between the hippocampus and amygdala cells that encode positive associations.

“That plasticity of the connection between the hippocampus and the amygdala plays a crucial role in the switching of the valence of the memory,” Tonegawa says.

These results indicate that while dentate gyrus cells are neutral with respect to emotion, individual amygdala cells are precommitted to encode fear or reward memory. The researchers are now trying to discover molecular signatures of these two types of amygdala cells. They are also investigating whether reactivating pleasant memories has any effect on depression, in hopes of identifying new targets for drugs to treat depression and post-traumatic stress disorder.

David Anderson, a professor of biology at the California Institute of Technology, says the study makes an important contribution to neuroscientists’ fundamental understanding of the brain and also has potential implications for treating mental illness.

“This is a tour de force of modern molecular-biology-based methods for analyzing processes, such as learning and memory, at the neural-circuitry level. It’s one of the most sophisticated studies of this type that I’ve seen,” he says.

The research was funded by the RIKEN Brain Science Institute, Howard Hughes Medical Institute, and the JPB Foundation.

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DARPA Project Starts Building Human Memory Prosthetics

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The first memory-enhancing devices could be implanted within four years

Lawrence Livermore engineer Vanessa Tolosa holds up a silicon wafer containing micromachined implantable neural devices for use in experimental memory prostheses.

“They’re trying to do 20 years of research in 4 years,” says Michael Kahana in a tone that’s a mixture of excitement and disbelief. Kahana, director of the Computational Memory Lab at the University of Pennsylvania, is mulling over the tall order from the U.S. Defense Advanced Research Projects Agency (DARPA). In the next four years, he and other researchers are charged with understanding the neuroscience of memory and then building a prosthetic memory device that’s ready for implantation in a human brain.

DARPA’s first contracts under its Restoring Active Memory (RAM) program challenge two research groups to construct implants for veterans with traumatic brain injuries that have impaired their memories. Over 270,000 U.S. military service members have suffered such injuries since 2000, according to DARPA, and there are no truly effective drug treatments. This program builds on an earlier DARPA initiative focused on building a memory prosthesis, under which a different group of researchers had dramatic success in improving recall in mice and monkeys.

Kahana’s team will start by searching for biological markers of memory formation and retrieval. For this early research, the test subjects will be hospitalized epilepsy patients who have already had electrodes implanted to allow doctors to study their seizures. Kahana will record the electrical activity in these patients’ brains while they take memory tests.

“The memory is like a search engine,” Kahana says. “In the initial memory encoding, each event has to be tagged. Then in retrieval, you need to be able to search effectively using those tags.” He hopes to find the electric signals associated with these two operations.

Once they’ve found the signals, researchers will try amplifying them using sophisticated neural stimulation devices. Here Kahana is working with the medical device maker Medtronic, in Minneapolis, which has already developed one experimental implant that can both record neural activity and stimulate the brain. Researchers have long wanted such a “closed-loop” device, as it can use real-time signals from the brain to define the stimulation parameters.

Kahana notes that designing such closed-loop systems poses a major engineering challenge. Recording natural neural activity is difficult when stimulation introduces new electrical signals, so the device must have special circuitry that allows it to quickly switch between the two functions. What’s more, the recorded information must be interpreted with blistering speed so it can be translated into a stimulation command. “We need to take analyses that used to occupy a personal computer for several hours and boil them down to a 10-millisecond algorithm,” he says.

In four years’ time, Kahana hopes his team can show that such systems reliably improve memory in patients who are already undergoing brain surgery for epilepsy or Parkinson’s. That, he says, will lay the groundwork for future experiments in which medical researchers can try out the hardware in people with traumatic brain injuries—people who would not normally receive invasive neurosurgery.

The second research team is led by Itzhak Fried, director of the Cognitive Neurophysiology Laboratory at the University of California, Los Angeles. Fried’s team will focus on a part of the brain called the entorhinal cortex, which is the gateway to the hippocampus, the primary brain region associated with memory formation and storage. “Our approach to the RAM program is homing in on this circuit, which is really the golden circuit of memory,” Fried says. In a 2012 experiment, he showed that stimulating the entorhinal regions of patients while they were learning memory tasks improved their performance.

Fried’s group is working with Lawrence Livermore National Laboratory, in California, to develop more closed-loop hardware. At Livermore’s Center for Bioengineering, researchers are leveraging semiconductor manufacturing techniques to make tiny implantable systems. They first print microelectrodes on a polymer that sits atop a silicon wafer, then peel the polymer off and mold it into flexible cylinders about 1 millimeter in diameter. The memory prosthesis will have two of these cylindrical arrays, each studded with up to 64 hair-thin electrodes, which will be capable of both recording the activity of individual neurons and stimulating them. Fried believes his team’s device will be ready for tryout in patients with traumatic brain injuries within the four-year span of the RAM program.

Outside observers say the program’s goals are remarkably ambitious. Yet Steven Hyman, director of psychiatric research at the Broad Institute of MIT and Harvard, applauds its reach. “The kind of hardware that DARPA is interested in developing would be an extraordinary advance for the whole field,” he says. Hyman says DARPA’s funding for device development fills a gap in existing research. Pharmaceutical companies have found few new approaches to treating psychiatric and neurodegenerative disorders in recent years, he notes, and have therefore scaled back drug discovery efforts. “I think that approaches that involve devices and neuromodulation have greater near-term promise,” he says.

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The above story is based on materials provided by IEEE Spectrum, Eliza Strickland. / This article originally appeared in print as “Making a Human Memory Chip.”

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Eye implant developed at Stanford could lead to better glaucoma treatments

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Lowering internal eye pressure is currently the only way to treat glaucoma. A tiny eye implant developed by Stephen Quake’s lab could pair with a smartphone to improve the way doctors measure and lower a patient’s eye pressure.

Bioengineer Stephen Quake and collaborators have developed an eye implant that could help stave off blindness caused by glaucoma.

For the 2.2 million Americans battling glaucoma, the main course of action for staving off blindness involves weekly visits to eye specialists who monitor – and control – increasing pressure within the eye.

Now, a tiny eye implant developed at Stanford could enable patients to take more frequent readings from the comfort of home. Daily or hourly measurements of eye pressure could help doctors tailor more effective treatment plans.

Internal optic pressure (IOP) is the main risk factor associated with glaucoma, which is characterized by a continuous loss of specific retina cells and degradation of the optic nerve fiber. The mechanism linking IOP and the damage is not clear, but in most patients IOP levels correlate with the rate of damage.

Reducing IOP to normal or below-normal levels is currently the only treatment available for glaucoma. This requires repeated measurements of the patient’s IOP until the levels stabilize. The trick with this, though, is that the readings do not always tell the truth.

Like blood pressure, IOP can vary day-to-day and hour-to-hour; it can be affected by other medications, body posture or even a neck-tie that is knotted too tightly. If patients are tested on a low IOP day, the test can give a false impression of the severity of the disease and affect their treatment in a way that can ultimately lead to worse vision.

The new implant was developed as part of a collaboration between Stephen Quake, a professor of bioengineering and of applied physics at Stanford, and ophthalmologist Yossi Mandel of Bar-Ilan University in Israel. It consists of a small tube – one end is open to the fluids that fill the eye; the other end is capped with a small bulb filled with gas. As the IOP increases, intraocular fluid is pushed into the tube; the gas pushes back against this flow.

As IOP fluctuates, the meniscus – the barrier between the fluid and the gas – moves back and forth in the tube. Patients could use a custom smartphone app or a wearable technology, such as Google Glass, to snap a photo of the instrument at any time, providing a critical wealth of data that could steer treatment. For instance, in one previous study, researchers found that 24-hour IOP monitoring resulted in a change in treatment in up to 80 percent of patients.

The implant is currently designed to fit inside a standard intraocular lens prosthetic, which many glaucoma patients often get when they have cataract surgery, but the scientists are investigating ways to implant it on its own.

“For me, the charm of this is the simplicity of the device,” Quake said. “Glaucoma is a substantial issue in human health. It’s critical to catch things before they go off the rails, because once you go off, you can go blind. If patients could monitor themselves frequently, you might see an improvement in treatments.”

Remarkably, the implant won’t distort vision. When subjected to the vision test used by the U.S. Air Force, the device caused nearly no optical distortion, the researchers said.

Before they can test the device in humans, however, the scientists say they need to re-engineer the device with materials that will increase the life of the device inside the human eye. Because of the implant’s simple design, they expect this will be relatively achievable.

“I believe that only a few years are needed before clinical trials can be conducted,” said Mandel, head of the Ophthalmic Science and Engineering Laboratory at Bar-Ilan University, who collaborated on developing the implant.

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Sorting cells with sound waves

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Acoustic device that separates tumor cells from blood cells could help assess cancer’s spread.

Photo Credit: Illustration Christine Daniloff/MIT

Researchers from MIT, Pennsylvania State University, and Carnegie Mellon University have devised a new way to separate cells by exposing them to sound waves as they flow through a tiny channel. Their device, about the size of a dime, could be used to detect the extremely rare tumor cells that circulate in cancer patients’ blood, helping doctors predict whether a tumor is going to spread.

Separating cells with sound offers a gentler alternative to existing cell-sorting technologies, which require tagging the cells with chemicals or exposing them to stronger mechanical forces that may damage them.

“Acoustic pressure is very mild and much smaller in terms of forces and disturbance to the cell. This is a most gentle way to separate cells, and there’s no artificial labeling necessary,” says Ming Dao, a principal research scientist in MIT’s Department of Materials Science and Engineering and one of the senior authors of the paper, which appears this week in the Proceedings of the National Academy of Sciences.

Subra Suresh, president of Carnegie Mellon, the Vannevar Bush Professor of Engineering Emeritus, and a former dean of engineering at MIT, and Tony Jun Huang, a professor of engineering science and mechanics at Penn State, are also senior authors of the paper. Lead authors are MIT postdoc Xiaoyun Ding and Zhangli Peng, a former MIT postdoc who is now an assistant professor at the University of Notre Dame.

The researchers have filed for a patent on the device, the technology of which they have demonstrated can be used to separate rare circulating cancer cells from white blood cells.

To sort cells using sound waves, scientists have previously built microfluidic devices with two acoustic transducers, which produce sound waves on either side of a microchannel. When the two waves meet, they combine to form a standing wave (a wave that remains in constant position). This wave produces a pressure node, or line of low pressure, running parallel to the direction of cell flow. Cells that encounter this node are pushed to the side of the channel; the distance of cell movement depends on their size and other properties such as compressibility.

However, these existing devices are inefficient: Because there is only one pressure node, cells can be pushed aside only short distances.

The new device overcomes that obstacle by tilting the sound waves so they run across the microchannel at an angle — meaning that each cell encounters several pressure nodes as it flows through the channel. Each time it encounters a node, the pressure guides the cell a little further off center, making it easier to capture cells of different sizes by the time they reach the end of the channel.

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Microchip reveals how tumor cells transition to invasion

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A microscopic obstacle course of carefully spaced pillars enables researchers to observe cancer cells directly as they break away from a tumor mass and move more rapidly across the microchip. The device could be useful for testing cancer drugs and further research on the mechanics of metastasis.

Benign cancer cells that had been induced to become malignant made their way slowly around microscopic obstacles. About 16 percent of the cells moved much more rapidly across the microchip.

Photo Credit: Ian Y. Wong/Brown University

Using a microengineered device that acts as an obstacle course for cells, researchers have shed new light on a cellular metamorphosis thought to play a role in tumor cell invasion throughout the body.

The epithelial-mesenchymal transition (EMT) is a process in which epithelial cells, which tend to stick together within a tissue, change into mesenchymal cells, which can disperse and migrate individually. EMT is a beneficial process in developing embryos, allowing cells to travel throughout the embryo and establish specialized tissues. But recently it has been suggested that EMT might also play a role in cancer metastasis, allowing cancer cells to escape from tumor masses and colonize distant organs.

For this study, published in the journal Nature Materials, the researchers were able to image cancer cells that had undergone EMT as they migrated across a device that mimics the tissue surrounding a tumor.

“People are really interested in how EMT works and how it might be associated with tumor spread, but nobody has been able to see how it happens,” said lead author Ian Y. Wong, assistant professor in the Brown School of Engineering and the Center for Biomedical Engineering, who performed the research as a postdoctoral fellow at Massachusetts General Hospital. “We’ve been able to image these cells in a biomimetic system and carefully measure how they move.”

The experiments showed that the cells displayed two modes of motion. A majority plod along together in a collectively advancing group, while a few cells break off from the front, covering larger distances more quickly.

“In the context of cell migration, EMT upgrades cancer cells from an economy model to a fast sports car,” Wong said. “Our technology enabled us to track the motion of thousands of ‘cars’ simultaneously, revealing that many sports cars get stuck in traffic jams with the economy cars, but that some sports cars break out of traffic and make their way aggressively to distant locations.”

Armed with an understanding of how EMT cancer cells migrate, the researchers hope they can use this same device for preliminary testing of drugs aimed at inhibiting that migration. The work is part of a larger effort to understand the underpinnings of cancer metastasis, which is responsible for nine out of 10 cancer-related deaths.

‘Obstacle course for cells’

To get this new view of how cancer cells move, the researchers borrowed microelectronics processing techniques to pattern miniaturized features on silicon wafers, which were then replicated in a rubber-like plastic called PDMS. The device consists of a small plate, about a half-millimeter square, covered in an array of microscopic pillars. The pillars, each about 10 micrometers in diameter and spaced about 10 micrometers apart, leave just enough space for the cells to weave their way through. Using microscopes and time-lapse photography, the researchers can watch cells as they travel across the plate.

“It’s basically an obstacle course for cells,” Wong said. “We can track individual cells, and because the size and spacing of these pillars is highly controlled, we can start to do statistical analysis and categorize these cells based on how they move.”

For their experiments, the researchers started with a line of benign cancer cells that were epithelial, as identified by specific proteins they express. They then applied a chemical that induced the cells to become malignant and mesenchymal. The transition was confirmed by looking for proteins associated with the mesenchymal cell type. Once all the cells had converted, they were set free on the obstacle course.

The study showed that about 84 percent of the cells stayed together and slowly advanced across the plate. The other 16 percent sped off the front and quickly made it all the way across the device. To the researchers’ surprise, they found that the cells that stayed with the group started to once again express the epithelial proteins, indicating that they had reverted back to the epithelial cell type.

“That was a remarkable result,” Wong said. “Based on these results, an interesting therapeutic strategy might be to develop drugs that downgrade mesenchymal sports cars back to epithelial economy models in order to keep them stuck in traffic, rather than aggressively invading surrounding tissues.”

As for the technology that made these findings possible, the researchers are hopeful that it can be used for further research and drug testing.

“We envision that this technology will be widely applicable for preclinical testing of anti-migration drugs against many different cancer cell lines or patient samples,” Wong said.

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New research sheds light on how children’s brains memorize facts

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As children shift from counting on their fingers to remembering math facts, the hippocampus and its functional circuits support the brain’s construction of adultlike ways of using memory.

As children learn basic arithmetic, they gradually switch from solving problems by counting on their fingers to pulling facts from memory. The shift comes more easily for some kids than for others, but no one knows why.

Now, new brain-imaging research gives the first evidence drawn from a longitudinal study to explain how the brain reorganizes itself as children learn math facts. A precisely orchestrated group of brain changes, many involving the memory center known as the hippocampus, are essential to the transformation, according to a study from the Stanford University School of Medicine.

The results, published online Aug. 17 in Nature Neuroscience, explain brain reorganization during normal development of cognitive skills and will serve as a point of comparison for future studies of what goes awry in the brains of children with learning disabilities.

“We wanted to understand how children acquire new knowledge, and determine why some children learn to retrieve facts from memory better than others,” said Vinod Menon, PhD, the Rachael L. and Walter F. Nichols, MD, Professor and professor of psychiatry and behavioral sciences, and the senior author of the study. “This work provides insight into the dynamic changes that occur over the course of cognitive development in each child.”

The study also adds to prior research into the differences between how children’s and adults’ brains solve math problems. Children use certain brain regions, including the hippocampus and the prefrontal cortex, very differently from adults when the two groups are solving the same types of math problems, the study showed.

“It was surprising to us that the hippocampal and prefrontal contributions to memory-based problem-solving during childhood don’t look anything like what we would have expected for the adult brain,” said postdoctoral scholar Shaozheng Qin, PhD, who is the paper’s lead author.

Charting the shifting strategy

In the study, 28 children solved simple math problems while receiving two functional magnetic resonance imaging brain scans; the scans were done about 1.2 years apart. The researchers also scanned 20 adolescents and 20 adults at a single time point. At the start of the study, the children were ages 7-9. The adolescents were 14-17 and the adults were 19-22. The participants had normal IQs. Because the study examined normal math learning, potential participants with math-related learning disabilities and attention deficit hyperactivity disorder were excluded. The children and adolescents were studying math in school; the researchers did not provide any math instruction.

During the study, as the children aged from an average of 8.2 to 9.4 years, they became faster and more accurate at solving math problems, and relied more on retrieving math facts from memory and less on counting. As these shifts in strategy took place, the researchers saw several changes in the children’s brains. The hippocampus, a region with many roles in shaping new memories, was activated more in children’s brains after one year. Regions involved in counting, including parts of the prefrontal and parietal cortex, were activated less.

The scientists also saw changes in the degree to which the hippocampus was connected to other parts of children’s brains, with several parts of the prefrontal, anterior temporal cortex and parietal cortex more strongly connected to the hippocampus after one year. Crucially, the stronger these connections, the greater was each individual child’s ability to retrieve math facts from memory, a finding that suggests a starting point for future studies of math-learning disabilities.

Although children were using their hippocampus more after a year, adolescents and adults made minimal use of their hippocampus while solving math problems. Instead, they pulled math facts from well-developed information stores in the neocortex.

Memory scaffold

“What this means is that the hippocampus is providing a scaffold for learning and consolidating facts into long-term memory in children,” said Menon, who is also the Rachel L. and Walter F. Nichols, MD, Professor at the medical school. Children’s brains are building a schema for mathematical knowledge. The hippocampus helps support other parts of the brain as adultlike neural connections for solving math problems are being constructed. “In adults this scaffold is not needed because memory for math facts has most likely been consolidated into the neocortex,” he said. Interestingly, the research also showed that, although the adult hippocampus is not as strongly engaged as in children, it seems to keep a backup copy of the math information that adults usually draw from the neocortex.

The researchers compared the level of variation in patterns of brain activity as children, adolescents and adults correctly solved math problems. The brain’s activity patterns were more stable in adolescents and adults than in children, suggesting that as the brain gets better at solving math problems its activity becomes more consistent.

The next step, Menon said, is to compare the new findings about normal math learning to what happens in children with math-learning disabilities.

“In children with math-learning disabilities, we know that the ability to retrieve facts fluently is a basic problem, and remains a bottleneck for them in high school and college,” he said. “Is it that the hippocampus can’t provide a reliable scaffold to build good representations of math facts in other parts of the brain during the early stages of learning, and so the child continues to use inefficient strategies to solve math problems? We want to test this.”

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500 million year reset for the immune system

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A single factor can reset the immune system of mice to a state likely similar to what it was 500 million years ago, when the first vertebrates emerged.

The normal mouse thymus (left) contains only a small fraction of B-cells (red). If the gene FOXN4 is activated, a fish-like thymus with many B-cells develops. This state is likely to have existed about 500 million years ago, at the time when the first vertebrates emerged.

Scientists at the Max Planck Institute of Immunobiology and Epigenetics (MPI-IE) in Freiburg re-activated expression of an ancient gene, which is not normally expressed in the mammalian immune system, and found that the animals developed a fish-like thymus. To the researchers surprise, while the mammalian thymus is utilized exclusively for T cell maturation, the reset thymus produced not only T cells, but also served as a maturation site for B cells – a property normally seen only in the thymus of fish. Thus the model could provide an explanation of how the immune system had developed in the course of evolution. The study has been published in Cell Reports.

The adaptive immune response is unique to vertebrates. One of its core organs is the thymus, which exists in all vertebrate species. Epithelial cells in the thymus control the maturation of T-cells, which later fight degenerated or infected body cells. The gene FOXN1 is responsible for the development of such T-cells in the mammalian thymus. Scientists led by Thomas Boehm, director at the MPI-IE and head of the department for developmental immunology, activated the evolutionary ancestor of FOXN1, called FOXN4, in the thymic epithelial cells of mice. FOXN4 is present in all vertebrates, but appears to play only a role in the maturation of immune cells of jawed fish, such as cat sharks and zebra fish.

“The simultanuous expression of FOXN4 and FOXN1 in the mouse led to a thymus that showed properties as in fish,” said first author Jeremy Swann. Together with earlier results this suggests that the development and function of thymic tissue was originally intitiated by FOXN4. Due to an evolutionary gene duplication, which led to FOXN1, transiently both genes, and finally only FOXN1 were active in the thymus.

To the researchers surprise not only T-cells developed in the thymus of the mice, but also B-cells. Mature B-cells are responsible for antibody production. In mammals, they normally do not mature in the thymus, but in other organs, such as the bone marrow.

“Our studies suggest a plausible scenario for the transition of a bipotent lymphopoietic tissue to a lymphoid organ supporting primarily T cell development,” said Boehm. Since B- and T-cell progenitors can not yet be distinguished, it remains unclear whether the B-cell development is based on the migration of dedicated B-cell precursors to the thymus, or to maturation from a shared T/B progenitor in the thymus itself. Comparative studies often suggest that the origin of a particular evolutionary innovation must have occurred in an extinct species. „Here, the re-creation and functional analysis of presumed ancestral stages could provide essential insights into the course of such developments,” explained Boehm the study approach.

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Researchers Write Languages to Design Synthetic Living Systems

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Researchers at Virginia Tech and the Massachusetts Institute of Technology have used a computer-aided design tool to create genetic languages to guide the design of biological systems.

Researchers with the Virginia Bioinformatics Institute work to create genetic languages to design biological systems, including, front row, Neil Adames, Celine Menezo, Jean Peccoud, Amanda Wilson, Logan Schuck, and, back row, Heather LaFrance, Chris Overend, David Ball, and Gang Fang. Photo Credit: Virginia Tech

Known as GenoCAD, the open-source software was developed by researchers at the Virginia Bioinformatics Institute at Virginia Tech to help synthetic biologists capture biological rules to engineer organisms that produce useful products or health-care solutions from inexpensive, renewable materials.

GenoCAD helps researchers in the design of protein expression vectors, artificial gene networks, and other genetic constructs, essentially combining engineering approaches with biology.

Synthetic biologists have an increasingly large library of naturally derived and synthetic parts at their disposal to design and build living systems. These parts are the words of a DNA language and the “grammar” a set of design rules governing the language.

It has to be expressive enough to allow scientists to generate a broad range of constructs, but it has to be focused enough to limit the possibilities of designing faulty constructs.

MIT’s Oliver Purcell, a postdoctoral associate, and Timothy Lu, an associate professor in the Department of Electrical Engineering and Computer Science, have developed a language detailed in ACS Synthetic Biology describing how to design a broad range of synthetic transcription factors for animals, plants, and other organisms with cells that contain a nucleus.

Meanwhile, Sakiko Okumoto, an assistant professor of plant pathology, physiology, and weed science at the Virginia Tech College of Agriculture and Life Sciences, and Amanda Wilson, a software engineer with the Synthetic Biology Group at the Virginia Bioinformatics Institute, developed a language describing design rules for expressing genes in the chloroplast of microalgae Their work was published in the Jan. 15 issue of Bioinformatics.

“Just like software engineers need different languages like HTML, SQL, or Java to develop different kinds of software applications, synthetic biologists need languages for different biological applications,” said Jean Peccoud, an associate professor at the Virginia Bioinformatics Institute, and principal investigator of the GenoCAD project. “From its inception, we envisioned GenoCAD as a framework allowing users to capture their expertise of a particular domain in languages that they could use themselves or share with others.”

The researchers said encapsulating current knowledge by defining standards will become increasingly important as the number and complexity of components engineered by synthetic biologists increases.

They propose that grammars are a first step toward the standardization of a broad range of synthetic genetic parts that could be combined to develop innovative products.

“Developing a grammar in GenoCAD is a little like writing a review paper,” Purcell said. “You start with the headings and you progressively dig deeper in the details. At the end of the process, you have a much better appreciation for what you know and what you don’t know about a particular domain.”

Lu added, “Our group has a recognized expertise in synthetic transcription factors. We hope that this work will help a broad range of scientists use our results in their own projects.”

“GenoCAD exemplifies the kind of cyberinfrastructure the institute is known for,” said Dennis Dean, the director of the Virginia Bioinformatics Institute. “This type of portal can enable collaborations across disciplines and institutions to foster a team approach to today’s most pressing scientific challenges.”

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The above story is based on materials provided by Virginia Bioinformatics Institute.

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Study finds crucial step in DNA repair

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cientists at Washington State University have identified a crucial step in DNA repair that could lead to targeted gene therapy for hereditary diseases such as “children of the moon” and a common form of colon cancer. Such disorders are caused by faulty DNA repair systems that increase the risk for cancer and other conditions.

Smerdon, left, and Mao in their lab in the WSU School of Molecular Biosciences. Photos Credits: Becky Phillips, WSU University Communications

The findings are published in this week’s Proceedings of the National Academy of Sciences. The study was funded by the National Institute of Environmental Health Sciences. Regents Professor Michael Smerdon and post-doctoral researcher Peng Mao found that when DNA is damaged, a specific protein must first be “unbuckled” to allow easy access for the DNA “repair crew.” Without this unbuckling, entry to the damaged site is hampered by the compact arrangement of genes and protein in chromosomes called chromatin. Smerdon and Mao’s finding is one of the first to document details of how this repair process takes place in chromatin.

Daily demands for DNA repair

Each human cell sustains a range of assaults that can create up to 100,000 DNA injuries every day, said Smerdon. The cells must repair this damage by continually—and quickly—producing replacement DNA and proteins. Like a tiny locomotive, an enzyme called RNA polymerase runs up and down the DNA copying genetic information.

When it comes to a gene whose protein is needed by the cell, it stops and unwinds the double-stranded DNA, copies one strand and sends it off to machinery to manufacture the new protein. And all is well. But when DNA is damaged by UV radiation or harmful substances, it forms an impenetrable mass that stalls the RNA polymerase, said Smerdon.

Like a boulder on the railroad tracks, the lifeless lump blocks all protein production from that gene. Unless quickly repaired, the cell could die. In healthy people, an enzyme repair crew travels along with the RNA polymerase and instantly rushes in to excise the damage and clear the tracks. This is called transcription-coupled repair, or TCR, an aspect of one of four known DNA repair systems. Smerdon said that even a partial deficiency in any of the repair systems could lead to life-threatening disorders.

Children of the moon

Smerdon’s laboratory studies repair deficiency diseases like xeroderma pigmentosum or XP, first identified as a possible hereditary disorder in 1874. Known as children of the moon, XP patients lack the enzymes to cut out damaged DNA and are so sensitive to UV light that even fluorescent lights can blister their skin. Their skin cancer rates are 2,000 times higher than in people without the disorder. They can safely venture outside only at night.

Smerdon and his colleagues also study Cockayne Syndrome, a TCR deficiency disease that causes extreme sun sensitivity, nervous system degeneration and premature aging. Other DNA repair deficits can cause a range of diseases such as leukemia, breast cancer and hereditary non-polyposis colorectal cancer, a common cause of colon cancer in Western nations.

Loosening the belt

Using yeast and human cells, Smerdon, Mao and their team discovered that there are two steps to the normal TCR repair process and that a protein in the chromatin, called H2B, is critically involved in the first step.

To help the repair enzymes gain entry to heavily shielded DNA, H2B first unbuckles a smaller protein. Like loosening your belt after a big dinner, this allows the strands of DNA to relax and move apart. As the strands open, the repair crew has room to come in and clear the damage. This unbuckling of the smaller protein, ubiquitin, is saddled with a jawbreaker term called deubiquitylation, but Smerdon and Mao say it makes DNA repair more efficient and that without it repair would be next to impossible.

Their finding sets the stage for future investigations into the largely uncharted arena of DNA repair in chromatin. The goal is to better understand how this process works in humans.

Gene therapy

“Even at a basic fundamental level, I have not lost sight of what you hope this research could ultimately do in terms of human health,” said Smerdon. “One of the treatments under development is targeted gene therapy,” he said. “If a patient has a mutation in a specific gene, it would be a way of giving them a normal copy to try to correct that gene. Though it has been done successfully in some diseases, it is still being investigated in repair deficit cases.”

Mao speculates that in the future, people with DNA repair problems might be given a drug that could boost the activity of repair enzymes. But there are no clinical trials at this point.

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The above story is based on materials provided by Washington State University, Becky Phillips.

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