Research on largest network of cortical neurons to date published in Nature

Robust network of connections between neurons performing similar tasks shows fundamentals of how brain circuits are wired

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Even the simplest networks of neurons in the brain are composed of millions of connections, and examining these vast networks is critical to understanding how the brain works. An international team of researchers, led by R. Clay Reid, Wei Chung Allen Lee and Vincent Bonin from the Allen Institute for Brain Science, Harvard Medical School and Neuro-Electronics Research Flanders (NERF), respectively, has published the largest network to date of connections between neurons in the cortex, where high-level processing occurs, and have revealed several crucial elements of how networks in the brain are organized. The results are published this week in the journal Nature.

A network of cortical neurons whose connections were traced from a multi-terabyte 3D data set. The data were created by an electron microscope designed and built at Harvard Medical School to collect millions of images in nanoscopic detail, so that every one of the “wires” could be seen, along with the connections between them. Some of the neurons are color-coded according to their activity patterns in the living brain. This is the newest example of functional connectomics, which combines high-throughput functional imaging, at single-cell resolution, with terascale anatomy of the very same neurons. Image credit: Clay Reid, Allen Institute; Wei-Chung Lee, Harvard Medical School; Sam Ingersoll, graphic artist

“This is a culmination of a research program that began almost ten years ago. Brain networks are too large and complex to understand piecemeal, so we used high-throughput techniques to collect huge data sets of brain activity and brain wiring,” says R. Clay Reid, M.D., Ph.D., Senior Investigator at the Allen Institute for Brain Science. “But we are finding that the effort is absolutely worthwhile and that we are learning a tremendous amount about the structure of networks in the brain, and ultimately how the brain’s structure is linked to its function.”

“Although this study is a landmark moment in a substantial chapter of work, it is just the beginning,” says Wei-Chung Lee, Ph.D., Instructor in Neurobiology at Harvard Medicine School and lead author on the paper. “We now have the tools to embark on reverse engineering the brain by discovering relationships between circuit wiring and neuronal and network computations.” 

“For decades, researchers have studied brain activity and wiring in isolation, unable to link the two,” says Vincent Bonin, Principal Investigator at Neuro-Electronics Research Flanders. “What we have achieved is to bridge these two realms with unprecedented detail, linking electrical activity in neurons with the nanoscale synaptic connections they make with one another.”

“We have found some of the first anatomical evidence for modular architecture in a cortical network as well as the structural basis for functionally specific connectivity between neurons,” Lee adds. “The approaches we used allowed us to define the organizational principles of neural circuits. We are now poised to discover cortical connectivity motifs, which may act as building blocks for cerebral network function.”

Lee and Bonin began by identifying neurons in the mouse visual cortex that responded to particular visual stimuli, such as vertical or horizontal bars on a screen. Lee then made ultra-thin slices of brain and captured millions of detailed images of those targeted cells and synapses, which were then reconstructed in three dimensions. Teams of annotators on both coasts of the United States simultaneously traced individual neurons through the 3D stacks of images and located connections between individual neurons.

Analyzing this wealth of data yielded several results, including the first direct structural evidence to support the idea that neurons that do similar tasks are more likely to be connected to each other than neurons that carry out different tasks. Furthermore, those connections are larger, despite the fact that they are tangled with many other neurons that perform entirely different functions.

“Part of what makes this study unique is the combination of functional imaging and detailed microscopy,” says Reid. “The microscopic data is of unprecedented scale and detail. We gain some very powerful knowledge by first learning what function a particular neuron performs, and then seeing how it connects with neurons that do similar or dissimilar things.

“It’s like a symphony orchestra with players sitting in random seats,” Reid adds. “If you listen to only a few nearby musicians, it won’t make sense. By listening to everyone, you will understand the music; it actually becomes simpler. If you then ask who each musician is listening to, you might even figure out how they make the music. There’s no conductor, so the orchestra needs to communicate.”

This combination of methods will also be employed in an IARPA contracted project with the Allen Institute for Brain Science, Baylor College of Medicine, and Princeton University, which seeks to scale these methods to a larger segment of brain tissue. The data of the present study is being made available online for other researchers to investigate.

This work was supported by the National Institutes of Health (R01 EY10115, R01 NS075436 and R21 NS085320); through resources provided by the National Resource for Biomedical Supercomputing at the Pittsburgh Supercomputing Center (P41 RR06009) and the National Center for Multiscale Modeling of Biological Systems (P41 GM103712); the Harvard Medical School Vision Core Grant (P30 EY12196); the Bertarelli Foundation; the Edward R. and Anne G. Lefler Center; the Stanley and Theodora Feldberg Fund; Neuro-Electronics Research Flanders (NERF); and the Allen Institute for Brain Science.

About the Allen Institute for Brain Science

The Allen Institute for Brain Science, a division of the Allen Institute (alleninstitute.org), is an independent, 501(c)(3) nonprofit medical research organization dedicated to accelerating the understanding of how the human brain works in health and disease. Using a big science approach, the Allen Institute generates useful public resources used by researchers and organizations around the globe, drives technological and analytical advances, and discovers fundamental brain properties through integration of experiments, modeling and theory. Launched in 2003 with a seed contribution from founder and philanthropist Paul G. Allen, the Allen Institute is supported by a diversity of government, foundation and private funds to enable its projects. Given the Institute’s achievements, Mr. Allen committed an additional $300 million in 2012 for the first four years of a ten-year plan to further propel and expand the Institute’s scientific programs, bringing his total commitment to date to $500 million. The Allen Institute’s data and tools are publicly available online at brain-map.org.

About Harvard Medical School

HMS has more than 7,500 full-time faculty working in 10 academic departments located at the School’s Boston campus or in hospital-based clinical departments at 15 Harvard-affiliated teaching hospitals and research institutes: Beth Israel Deaconess Medical Center, Boston Children’s Hospital, Brigham and Women’s Hospital, Cambridge Health Alliance, Dana-Farber Cancer Institute, Harvard Pilgrim Health Care Institute, Hebrew SeniorLife, Joslin Diabetes Center, Judge Baker Children’s Center, Massachusetts Eye and Ear/Schepens Eye Research Institute, Massachusetts General Hospital, McLean Hospital, Mount Auburn Hospital, Spaulding Rehabilitation Hospital and VA Boston Healthcare System.

About NERF

Neuro-Electronics Research Flanders (NERF; www.nerf.be) is a neurotechnology research initiative is headquartered in Leuven, Belgium initiated by imec, KU Leuven and VIB to unravel how electrical activity in the brain gives rise to mental function and behaviour. Imec performs world-leading research in nanoelectronics and has offices in Belgium, the Netherlands, Taiwan, USA, China, India and Japan. Its staff of about 2,200 people includes almost 700 industrial residents and guest researchers. In 2014, imec's revenue (P&L) totaled 363 million euro. VIB is a life sciences research institute in Flanders, Belgium. With more than 1470 scientists from over 60 countries, VIB performs basic research into the molecular foundations of life. KU Leuven is one of the oldest and largest research universities in Europe with over 10,000 employees and 55,000 students.

ORIGINAL: Allen Institute

March 28th, 2016

A DNA hard drive has been built that can store data for 1 MILLION years

Image: Philipp Stössel/ETH Zurich

Scientists have found a way to preserve the world's data for millions of years, by storing it on a tiny strand of DNA preserved in glass.

When you think of humanity’s legacy, the most powerful message for us to leave behind for future civilisations would surely be our billions of terabytes of data. But right now the hard drives and discs that we use to store all this information are frustratingly vulnerable, and unlikely to survive more than a couple of hundred years.

Fortunately scientists have built a DNA time capsule that's capable of safely preserving all of our data for more than a million years. And we’re kind of freaking out over how huge the implications are.

Researchers already knew that DNA was ideal for data storage. In theory, just 1 gram of DNA is capable of holding 455 exabytes, which is the equivalent of one billion gigabytes, and more than enough space to store all of Google, Facebook and pretty much everyone else's data.

Storing information on DNA is also surprisingly simple - researchers just need to program the A and C base pairs of DNA as a binary '0', and the T and G as a '1'. But the researchers, led by Robert Grass from ETH Zürich in Switzerland, wanted to find out just how long this data would last.

DNA can definitely be durable - in 2013 scientists managed to sequence genetic code from 700,000-year-old horse bones - but it has to be preserved in pretty specific conditions, otherwise it can change and break down as it's exposed to the environment. So Glass's team decided to try to replicate a fossil, to see if it would help them create a long-lasting DNA hard drive.

"Similar to these bones, we wanted to protect the information-bearing DNA with a synthetic 'fossil' shell," explained Grass in a press release.

In order to do that, the team encoded Switzerland’s Federal Charter of 1921 and The Methods of Mechanical Theorems by Archimedes onto a DNA strand - a total of 83 kilobytes of data. They then encapsulated the DNA into tiny glass spheres, which were around 150 nanometres in diameter.

The researchers compared these glass spheres against other packaging methods by exposing them to temperatures of between 60 and 70 degrees Celsius - conditions that replicated the chemical degradation that would usually occur over hundreds of years, all crammed into a few destructive weeks.

They found that even after this sped-up degradation process, the DNA inside the glass spheres could easily be extracted using a fluoride solution, and the data on it could still be read. In fact, these glass casings seem to work much like fossilised bones.

Based on their results, which have been published in Angewandte Chemie, the team predicts that data stored on DNA could survive over a million years if it was stored in temperatures below -18 degrees Celsius, for example, in a facility like the Svalbard Global Seed Vault, which is also known as the ‘Doomsday Vault’. They say it could last 2,000 years if stored somewhere less secure at 10 degrees Celsius - a similar average temperature to central Europe.

The tricky part of this whole process is that the data stored in DNA needs to be read properly in order for future civilisations to be able to access it. And despite advances in sequencing technology, errors still arise from DNA sequencing.

The team overcame this by embedding a method for correcting any errors within the glass spheres, based on the Reed-Solomon Codes, which help researchers transmit data over long distances. Basically, additional information is attached to the actual data, to help people read it on the other end.

This worked so well that even after the test DNA had been kept in scorching and degrading conditions for a month, the team could still read Switzerland’s Federal Charter and Archimedes’ wise words at the end of the study.

The other major problem, which is not so easy to overcome, is the fact that storing information on DNA is still extremely expensive - it cost around US$1,500 just to encode the 83 kilobytes of data used in this study. Hopefully this cost will go down as we get better at writing information onto DNA. Researchers out there are already storing books onto DNA, and the band OK Go are also writing their new album into genetic information.

The question is, what would Grass store, now that he’s developed this mind-blowing time capsule? The documents in Unesco’s Memory of the World Programme, and… Wikipedia, he says.

“Many entries are described in detail, others less so. This probably provides a good overview of what our society knows, what occupies it and to what extent,” said Grass in the release.

It’s ridiculously cool to think that even if we do wipe ourselves off the face of the Earth, our civilisation might still live on for millennia to come in the form of Wikipedia pages and Facebook updates.

We really are (almost) infinite.

Source: New Scientist


ORIGINAL: Science Alert

FIONA MACDONALD 

17 FEB 2015

Amazing Infographic Shows Where the World's Greenhouse Gases Come From

It’s hard to keep track of all the greenhouse gases that are steadily collecting in the atmosphere – from auto emissions and coal plants to methane emissions from cattle and landfills. Fortunately,Ecofys has created an easy-to-understand infographic that breaks down the source and sector of the world’s largest greenhouse gas emitters.

Photo via Shutterstock

Ecofys‘ infographic shows that many sources of greenhouse gas emissions can be reduced if the world’s governments decide to take energy conservation and renewable energy seriously. One of the biggest culprits is global coal use, which is still strong in the US, China and several developing countries, which utilize it for steel production. If renewable energy funding increases, then clean alternatives like wind and solar power will help to lessen this footprint. Scientists and inventors around the world are also working to mitigate the other major sources, which include deforestation,building emissions, methane waste and fossil fuel-powered transportation.

For a bigger version of the infographic, click here.

+ Ecofys

ORIGINAL: Inhabitat

by Timon Singh

06/11/13