Regenerative Medicine  

Researchers have develop an algorithm that takes the field of cell reprogramming forward, by helping to pinpoint potential errors and cancerous mutations when cells are changed from one type to another. The technique should help to advance the field of regenerative medicine dramatically.

Researchers from the Duke-NUS Medical School (Duke-NUS), the University of Bristol, Monash University and RIKEN have created an algorithm that can predict the factors required to convert one human cell type to another. The findings were recently published in the journal Nature Genetics, have significant implications for regenerative medicine and lay the groundwork for further research into cell reprogramming.

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Cell types in the body are not fixed; cell type can be reprogrammed, or converted, to become another cell type by the addition of a unique set of cellular factors. This process was established by Shinya Yamanaka, in Nobel prize-winning work involved the reprogramming of fibroblast cells from the skin to induced pluripotent stem cells (iPS).

Theoretically, stem cells can be reprogrammed for use in regenerative medicine techniques. To date the practice has not been perfected though. There are technical and safety concerns in converting cells because of  the accumulation of unpredictable errors, including cancerous mutations in the reprogrammed cells.

Despite this development, determining the unique set of cellular factors that is needed to be manipulated for each cell conversion is a long and costly process that involved much trial and error. As a result, this first step of identifying the key set of cellular factors for cell conversion is the major obstacle researchers and doctors face in the field of cell reprogramming.

The researchers worked for five years to develop a computational algorithm to predict the cellular factors for cell conversions. The algorithm, called Mogrify(1), is able to predict the optimal set of cellular factors required for any given cell conversion.

Mogrify uses a network-based algorithm designed to find transcription factors that impart the most influence on changes in cellular state. This website will allow you to explore possible reprogramming experiments, different collections of transcription factors as well as the look at the changes in the regulatory network.

"One of the first clinical applications that we hope to achieve with this innovative approach would be to reprogram 'defective' cells from patients into 'functioning' healthy cells."

"Mogrify acts like a 'world atlas' for the cell and allows us to map out new territories in cell conversions in humans," explained Dr Rackham, who is from the Systems Genetics of Complex Disease Laboratory at Duke-NUS. "One of the first clinical applications that we hope to achieve with this innovative approach would be to reprogram 'defective' cells from patients into 'functioning' healthy cells, without the intermediate iPS step. These then can be re-implanted into patients, and should, in practice, effectively enable new regenerative medicine techniques."

Associate Professor Enrico Petretto, co-author of the study and head of the Systems Genetics of Complex Disease Laboratory in the Centre for Computational Biology at Duke-NUS, highlighted that since Mogrify is completely data-driven, its robustness and accuracy can only continue to improve as more comprehensive data are collected and input into the framework.

"Mogrify is a game-changing method that leverages big-data and systems-biology; this will inspire new translational applications as the result of the work and expertise here at Duke-NUS," said Assoc Prof Petretto.

Mogrify is available online for other researchers and scientists. The team at Duke-NUS now plan to focus on Mogrify's application in translational medicine. Collaborative efforts between research groups within Duke-NUS are already in place to apply the algorithm to help develop treatments for specific diseases, such as cancer.

SOURCE  EurekAlert

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 Neuroscience  

The film 'Inception' may be getting closer to becoming real. Using optogenetics, researchers have planted false memories into the minds of mice. The work potentially illuminates the mechanisms underlying the human phenomenon of “recalling” experiences that never occurred.

Researchers at the RIKEN-MIT Center for Neural Circuit Genetics and MIT's Picower Institute for Learning and Memory have implanted false memories into mice, potentially illuminating the mechanisms underlying the human phenomenon of "recalling" experiences that never occurred.

In previous work, the researchers had detected a single memory in the brain, genetically tagged the brain cells housing that memory with a light-sensitive protein, and flickered pulses of light to "turn on" the memory at any given moment. The latest work, published in the journal Science, tinkers with that memory to change its contents—in essence, creating a false memory.

This work in mice may lead to new understanding of how and why humans form false memories, and may eventually help physically pinpoint where memories are formed in the brain.

Our memories are stored in assemblies of neurons, called engram-bearing cells, that can be compared to toy building blocks. When we recall a sequence of events, our brains reconstruct the past from these bricks of data, but the very act of accessing a memory modifies and distorts it.

When the influence of external sources is, it's not surprising that memory can be notoriously unreliable, yet inaccurate memories can have dire consequences. For instance, most three-quarters of the first 250 people to be exonerated by DNA evidence in the US were victims of faulty eyewitness testimony.

"Human studies utilizing behavioral and fMRI (functional magnetic resonance imaging) techniques have not been able to delineate the hippocampal subregions and circuits responsible for generating false memories," said study author Susumu Tonegawa, Picower Professor of Biology and Neuroscience and director of the RIKEN-MIT Center for Neural Circuit Genetics.

"Our experiments provide the first animal model in which false and genuine memories can be investigated at the memory engram level."

Dr Tonegawa and his team successfully created a false memory in genetically modified mice by manipulating engram-bearing cells in the hippocampus, a seahorse-shaped part of the brain known to play a role in forming and storing memories of experiences.

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Optogenetics, which are transforming neuroscience, were used to locate and chemically label neurons as well as make them susceptible to activation by blue light transmitted by a fiber optic cable in the mouse brain. With these techniques the researchers were able to identify and chemically label which neurons were involved in forming the initial memory of the first environment, and to reactivate the labeled cells a day later with light.

The researchers zeroed in on the animals' brain cells that represented the safe environment of a setting, Box A, and programmed those cells to respond to pulses of light. Next, they placed the animals in a completely different environment—Box B—and pulsed light into their brains to reactivate the memory of Box A.

They then gave the animals mild foot shocks, creating a negative association between the light-reactivated memory of Box A and the foot shocks, which mice find highly aversive.

When the animals were placed back in Box A—the safe environment in which nothing averse had ever happened—the researchers found that the animals now displayed heightened fear responses. In addition, after placing the animals in yet another new environment while shining light on the hippocampal cells that had been artificially associated with fear, the researchers found they could reactivate the false fear memory at will.

"Humans are highly imaginative animals. Just like our mice, an aversive or appetitive event could be associated with a past experience one may happen to have in mind at that moment, hence a false memory is formed," said Tonegawa.

The results are “really mind-blowing,” says Sheena Josselyn, a neuroscientist at the Hospital for Sick Children in Toronto. “It shows that your memories are really just activities of different cells, and they can take the place of an actual thing that happened by just activating some cells in the brain,” she says. “People have been playing around with this idea for a while, but having a theory and showing it are two different things.”

"Remarkably, the recall of this false memory recruited the same fear centers that natural fear memory recall recruits, such as the amygdala," said Xu Liu, a post-doctoral fellow and co-first author of the study. The recall of this false memory drove an active fear response in associated parts of the brain, making it indistinguishable from a real memory. "In a sense, to the animal, the false memory seems to have felt like a 'real' memory," he said.

These kinds of experiments show us just how reconstructive the process of memory actually is," said Steve Ramirez, a graduate student in the Tonegawa lab and the lead author of the paper. "Memory is not a carbon copy, but rather a reconstruction, of the world we've experienced. Our hope is that, by proposing a neural explanation for how false memories may be generated, down the line we can use this kind of knowledge to inform, say, a courtroom about just how unreliable things like eyewitness testimony can actually be."



SOURCE  RIKEN

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 Connectomics  

Japanese researchers have developed a new sugar and water-based solution that turns tissues transparent in just three days, without disrupting the shape and chemical nature of the samples. Combined with fluorescence microscopy, this technique enabled them to obtain detailed images of a mouse brain at an unprecedented resolution.

Japanese researchers have developed a new sugar and water-based solution that turns tissues transparent in just three days, without disrupting the shape and chemical nature of the samples. Combined with fluorescence microscopy, this technique enabled them to obtain detailed images of a mouse brain at an unprecedented resolution.

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The team from the RIKEN Center for Developmental biology reported their findings in Nature Neuroscience.

Over the past few years, teams in the USA and Japan have reported a number of techniques to make biological samples transparent, that have enabled researchers to look deep down into biological structures like the brain.  One of the recent projects that has gathered a lot of attention is CLARITY, devised by Karl Deisseroth and his team at Stanford.

“However, these clearing techniques have limitations because they induce chemical and morphological damage to the sample and require time-consuming procedures,” explains Dr. Takeshi Imai, who led the Japanese study.

SeeDB, an aqueous fructose solution that Dr. Imai developed with colleagues Drs. Meng-Tsen Ke and Satoshi Fujimoto, overcomes these limitations.

Using SeeDB, the researchers were able to make mouse embryos and brains transparent in just three days, without damaging the fine structures of the samples, or the fluorescent dyes they had injected in them.

They could then visualize the neuronal circuitry inside a mouse brain, at the whole-brain scale, under a customized fluorescence microscope without making mechanical sections through the brain.

They describe the detailed wiring patterns of commissural fibers connecting the right and left hemispheres of the cerebral cortex, in three dimensions, for the first time. They also report that they were able to visualize in three dimensions the wiring of mitral cells in the olfactory bulb, which is involved the detection of smells, at single-fiber resolution.

“Because SeeDB is inexpensive, quick, easy and safe to use, and requires no special equipment, it will prove useful for a broad range of studies, including the study of neuronal circuits in human samples,” explain the authors.



SOURCE  RIKEN

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