(Image Caption: A New Technique Called Magnified Analysis Of Proteome (MAP), Developed At MIT, Allows

(Image Caption: A New Technique Called Magnified Analysis Of Proteome (MAP), Developed At MIT, Allows

(Image caption: A new technique called magnified analysis of proteome (MAP), developed at MIT, allows researchers to peer at molecules within cells or take a wider view of the long-range connections between neurons. Credit: Courtesy of the researchers)

Imaging the brain at multiple size scales

MIT researchers have developed a new technique for imaging brain tissue at multiple scales, allowing them to peer at molecules within cells or take a wider view of the long-range connections between neurons.

This technique, known as magnified analysis of proteome (MAP), should help scientists in their ongoing efforts to chart the connectivity and functions of neurons in the human brain, says Kwanghun Chung, the Samuel A. Goldblith Assistant Professor in the Departments of Chemical Engineering and Brain and Cognitive Sciences, and a member of MIT’s Institute for Medical Engineering and Science (IMES) and Picower Institute for Learning and Memory.

“We use a chemical process to make the whole brain size-adjustable, while preserving pretty much everything. We preserve the proteome (the collection of proteins found in a biological sample), we preserve nanoscopic details, and we also preserve brain-wide connectivity,” says Chung, the senior author of a paper describing the method in the July 25 issue of Nature Biotechnology.

The researchers also showed that the technique is applicable to other organs such as the heart, lungs, liver, and kidneys.

The paper’s lead authors are postdoc Taeyun Ku, graduate student Justin Swaney, and visiting scholar Jeong-Yoon Park.

Multiscale imaging

The new MAP technique builds on a tissue transformation method known as CLARITY, which Chung developed as a postdoc at Stanford University. CLARITY preserves cells and molecules in brain tissue and makes them transparent so the molecules inside the cell can be imaged in 3-D. In the new study, Chung sought a way to image the brain at multiple scales, within the same tissue sample.

“There is no effective technology that allows you to obtain this multilevel detail, from brain region connectivity all the way down to subcellular details, plus molecular information,” he says.

To achieve that, the researchers developed a method to reversibly expand tissue samples in a way that preserves nearly all of the proteins within the cells. Those proteins can then be labeled with fluorescent molecules and imaged.

The technique relies on flooding the brain tissue with acrylamide polymers, which can form a dense gel. In this case, the gel is 10 times denser than the one used for the CLARITY technique, which gives the sample much more stability. This stability allows the researchers to denature and dissociate the proteins inside the cells without destroying the structural integrity of the tissue sample.

Before denaturing the proteins, the researchers attach them to the gel using formaldehyde, as Chung did in the CLARITY method. Once the proteins are attached and denatured, the gel expands the tissue sample to four or five times its original size.

“It is reversible and you can do it many times,” Chung says. “You can then use off-the-shelf molecular markers like antibodies to label and visualize the distribution of all these preserved biomolecules.”

There are hundreds of thousands of commercially available antibodies that can be used to fluorescently tag specific proteins. In this study, the researchers imaged neuronal structures such as axons and synapses by labeling proteins found in those structures, and they also labeled proteins that allow them to distinguish neurons from glial cells.

“We can use these antibodies to visualize any target structures or molecules,” Chung says. “We can visualize different neuron types and their projections to see their connectivity. We can also visualize signaling molecules or functionally important proteins.”

High resolution

Once the tissue is expanded, the researchers can use any of several common microscopes to obtain images with a resolution as high as 60 nanometers — much better than the usual 200 to 250-nanometer limit of light microscopes, which are constrained by the wavelength of visible light. The researchers also demonstrated that this approach works with relatively large tissue samples, up to 2 millimeters thick.

“This is, as far as I know, the first demonstration of super-resolution proteomic imaging of millimeter-scale samples,” Chung says.

“This is an exciting advance for brain mapping, a technique that reveals the molecular and connectional architecture of the brain with unprecedented detail,” says Sebastian Seung, a professor of computer science at the Princeton Neuroscience Institute, who was not involved in the research.

Currently, efforts to map the connections of the human brain rely on electron microscopy, but Chung and colleagues demonstrated that the higher-resolution MAP imaging technique can trace those connections more accurately.

Chung’s lab is now working on speeding up the imaging and the image processing, which is challenging because there is so much data generated from imaging the expanded tissue samples.

“It’s already easier than other techniques because the process is really simple and you can use off-the-shelf molecular markers, but we are trying to make it even simpler,” Chung says.

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8 years ago

Ad Astra, John Glenn (1921-2016)

An astronaut. 

A pilot. 

A husband. 

A father. 

A United States Senator.

An American hero. 

An original.

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John Glenn (1921-2016) was all those things and more. When he rocketed into space on Feb. 20, 1962, to become the first American to orbit Earth, the flight set the nation on course to meet ever-more ambitious goals.

The life and career of Senator Glenn eclipses those of many. In spite of his accomplishments, he was a humble and gracious man (and 4-term U.S. senator).

During Glenn’s first flight, a scheduled 30-minute test to determine whether Glenn could fly the capsule manually became a matter of life and death when the automatic system malfunctioned after the first orbit.

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“I went to manual control and continued in that mode during the second and third orbits, and during re-entry,” Glenn recalled later.  “The malfunction just forced me to prove very rapidly what had been planned over a longer period of time.” Another problem seemed even more serious – telemetry indicated the spacecraft’s heat shield was loose. It seemed possible that Glenn and the spacecraft would be incinerated on re-entry.  Glenn left the retrorocket pack in place to steady the heat shield during re-entry. “It made for a very spectacular re-entry from where I was sitting,” he said. Big chunks of the burning material came flying by the window.

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He wasn’t sure whether the flaming debris was the rocket pack or the heat shield breaking up. “Fortunately,” he told an interviewer,“ it was the rocket pack – or I wouldn’t be answering these questions.”

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In the words of President Obama, who awarded him the Presidential Medal of Freedom in 2012: “When John Glenn blasted off from Cape Canaveral atop an Atlas rocket in 1962, he lifted the hopes of a nation. And when his Friendship 7 spacecraft splashed down a few hours later, the first American to orbit the Earth reminded us that with courage and a spirit of discovery there’s no limit to the heights we can reach together. With John’s passing, our nation has lost an icon and Michelle and I have lost a friend. John spent his life breaking barriers, from defending our freedom as a decorated Marine Corps fighter pilot in World War II and Korea, to setting a transcontinental speed record … The last of America’s first astronauts has left us, but propelled by their example we know that our future here on Earth compels us to keep reaching for the heavens.  On behalf of a grateful nation, Godspeed, John Glenn.”

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Glenn left the Astronaut Corps in 1964 and resigned from the Marine Corps in 1965. And, after some time in private industry ran for and was elected ti the U.S. Senate in 1974, carrying all 88 counties of Ohio. He was re-elected in 1980 with the largest margin in Ohio history. Ohio returned him to the Senate for a third term in 1986. In 1992 he was elected again, becoming the first popularly elected senator from his state to win four consecutive terms. During his last term he was the ranking member of both the Governmental Affairs Committee and the Subcommittee on Air/Land Forces in the Senate Armed Services Committee. He also served on the Select Committee on Intelligence and the Special Committee on Aging. He was considered one of the Senate’s leading experts on technical and scientific matters, and won wide respect for his work to prevent the spread of weapons of mass destruction.

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In 1998, Glenn flew on the STS-95 Discovery shuttle flight, a 9-day mission during which the crew supported a variety of research payloads including deployment of the Spartan solar-observing spacecraft, the Hubble Space Telescope Orbital Systems Test Platform, and Glenn’s investigations on space flight and the aging process.

NASA Administrator Charlie Bolden remembers, “Senator Glenn’s legacy is one of risk and accomplishment, of history created and duty to country carried out under great pressure with the whole world watching.”

Today, we honor him for all that he stood for and continues to stand for – grace under pressure, humility, ability, strength. 

Godspeed, John Glenn.

7 years ago
The Greatest Gift And Honor Is Having You For A Daughter.
The Greatest Gift And Honor Is Having You For A Daughter.

The greatest gift and honor is having you for a daughter.


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7 years ago

Voyager: The Spacecraft

The twin Voyager 1 and 2 spacecraft are exploring where nothing from Earth has flown before. Continuing their more-than-40-year journey since their 1977 launches, they each are much farther away from Earth and the Sun than Pluto.

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The primary mission was the exploration of Jupiter and Saturn. After making a string of discoveries there – such as active volcanoes on Jupiter’s moon Io and intricacies of Saturn’s rings – the mission was extended. 

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Voyager 2 went on to explore Uranus and Neptune, and is still the only spacecraft to have visited those outer planets. The adventurers’ current mission, the Voyager Interstellar Mission (VIM), will explore the outermost edge of the Sun’s domain. And beyond.

Spacecraft Instruments

‘BUS’ Housing Electronics

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The basic structure of the spacecraft is called the “bus,” which carries the various engineering subsystems and scientific instruments. It is like a large ten-sided box. Each of the ten sides of the bus contains a compartment (a bay) that houses various electronic assemblies.

Cosmic Ray Subsystem (CRS)

Voyager: The Spacecraft

The Cosmic Ray Subsystem (CRS) looks only for very energetic particles in plasma, and has the highest sensitivity of the three particle detectors on the spacecraft. Very energetic particles can often be found in the intense radiation fields surrounding some planets (like Jupiter). Particles with the highest-known energies come from other stars. The CRS looks for both.

High-Gain Antenna (HGA)

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The High-Gain Antenna (HGA) transmits data to Earth on two frequency channels (the downlink). One at about 8.4 gigahertz, is the X-band channel and contains science and engineering data. For comparison, the FM radio band is centered around 100 megahertz.

Imaging Science Subsystem (ISS)

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The Imaging Science Subsystem (ISS) is a modified version of the slow scan vidicon camera designed that were used in the earlier Mariner flights. The ISS consists of two television-type cameras, each with eight filters in a commandable Filter Wheel mounted in front of the vidicons. One has a low resolution 200 mm wide-angle lens, while the other uses a higher resolution 1500 mm narrow-angle lens.

Infrared Interferometer Spectrometer and Radiometer (IRIS)

Voyager: The Spacecraft

The Infrared Interferometer Spectrometer and Radiometer (IRIS) actually acts as three separate instruments. First, it is a very sophisticated thermometer. It can determine the distribution of heat energy a body is emitting, allowing scientists to determine the temperature of that body or substance.

Voyager: The Spacecraft

Second, the IRIS is a device that can determine when certain types of elements or compounds are present in an atmosphere or on a surface.

Third, it uses a separate radiometer to measure the total amount of sunlight reflected by a body at ultraviolet, visible and infrared frequencies.

Low-Energy Charged Particles (LECP)

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The Low-Energy Charged Particles (LECP) looks for particles of higher energy than the Plasma Science instrument, and it overlaps with the Cosmic Ray Subsystem (CRS). It has the broadest energy range of the three sets of particle sensors. 

Voyager: The Spacecraft

The LECP can be imagined as a piece of wood, with the particles of interest playing the role of the bullets. The faster a bullet moves, the deeper it will penetrate the wood. Thus, the depth of penetration measures the speed of the particles. The number of “bullet holes” over time indicates how many particles there are in various places in the solar wind, and at the various outer planets. The orientation of the wood indicates the direction from which the particles came.

Magnetometer (MAG)

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Although the Magnetometer (MAG) can detect some of the effects of the solar wind on the outer planets and moons, its primary job is to measure changes in the Sun’s magnetic field with distance and time, to determine if each of the outer planets has a magnetic field, and how the moons and rings of the outer planets interact with those magnetic fields.

Optical Calibration Target The target plate is a flat rectangle of known color and brightness, fixed to the spacecraft so the instruments on the movable scan platform (cameras, infrared instrument, etc.) can point to a predictable target for calibration purposes.

Photopolarimeter Subsystem (PPS)

Voyager: The Spacecraft

The Photopolarimeter Subsystem (PPS) uses a 0.2 m telescope fitted with filters and polarization analyzers. The experiment is designed to determine the physical properties of particulate matter in the atmospheres of Jupiter, Saturn and the rings of Saturn by measuring the intensity and linear polarization of scattered sunlight at eight wavelengths. 

Voyager: The Spacecraft

The experiment also provided information on the texture and probable composition of the surfaces of the satellites of Jupiter and Saturn.

Planetary Radio Astronomy (PRA) and Plasma Wave Subsystem (PWS)

Voyager: The Spacecraft

Two separate experiments, The Plasma Wave Subsystem and the Planetary Radio Astronomy experiment, share the two long antennas which stretch at right-angles to one another, forming a “V”.

Plasma Science (PLS)

Voyager: The Spacecraft

The Plasma Science (PLS) instrument looks for the lowest-energy particles in plasma. It also has the ability to look for particles moving at particular speeds and, to a limited extent, to determine the direction from which they come. 

Voyager: The Spacecraft

The Plasma Subsystem studies the properties of very hot ionized gases that exist in interplanetary regions. One plasma detector points in the direction of the Earth and the other points at a right angle to the first.

Radioisotope Thermoelectric Generators (RTG)

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Three RTG units, electrically parallel-connected, are the central power sources for the mission module. The RTGs are mounted in tandem (end-to-end) on a deployable boom. The heat source radioisotopic fuel is Plutonium-238 in the form of the oxide Pu02. In the isotopic decay process, alpha particles are released which bombard the inner surface of the container. The energy released is converted to heat and is the source of heat to the thermoelectric converter.

Ultraviolet Spectrometer (UVS)

Voyager: The Spacecraft

The Ultraviolet Spectrometer (UVS) is a very specialized type of light meter that is sensitive to ultraviolet light. It determines when certain atoms or ions are present, or when certain physical processes are going on. 

Voyager: The Spacecraft

The instrument looks for specific colors of ultraviolet light that certain elements and compounds are known to emit.

Learn more about the Voyager 1 and 2 spacecraft HERE.

Make sure to follow us on Tumblr for your regular dose of space: http://nasa.tumblr.com


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8 years ago

Opinion is really the lowest form of human knowledge. It requires no accountability, no understanding. The highest form of knowledge is empathy, for it requires us to suspend our egos and live in another’s world. It requires profound purpose larger than the self kind of understanding.

Plato, The Republic (via fyp-philosophy)

Interesting

7 years ago
Earlier This Year, The Lutetium Project Explored How Microfluidic Circuits Are Made, And Now They Are

Earlier this year, The Lutetium Project explored how microfluidic circuits are made, and now they are back with the conclusion of their microfluidic adventures. This video explores how microfluidic chips are used and how microscale fluid dynamics relates to other topics in the field. Because these techniques allow researchers very fine control over droplets, there are many chemical and biological possibilities for microfluidic experiments, some of which are shown in the video. Microfluidics in medicine are also already more common than you may think. For example, test strips used by diabetic patients to measure their blood glucose levels are microfluidic circuits! (Video and image credit: The Lutetium Project; submitted by Guillaume D.)


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4 years ago

Spinal Stimulators Repurposed to Restore Touch in Lost Limb

Imagine tying your shoes or taking a sip of coffee or cracking an egg but without any feeling in your hand. That’s life for users of even the most advanced prosthetic arms.

Although it’s possible to simulate touch by stimulating the remaining nerves in the stump after an amputation, such a surgery is highly complex and individualized. But according to a new study from the University of Pittsburgh’s Rehab Neural Engineering Labs, spinal cord stimulators commonly used to relieve chronic pain could provide a straightforward and universal method for adding sensory feedback to a prosthetic arm.

For this study, published in eLife, four amputees received spinal stimulators, which, when turned on, create the illusion of sensations in the missing arm.

Spinal Stimulators Repurposed To Restore Touch In Lost Limb

“What’s unique about this work is that we’re using devices that are already implanted in 50,000 people a year for pain — physicians in every major medical center across the country know how to do these surgical procedures — and we get similar results to highly specialized devices and procedures,” said study senior author Lee Fisher, Ph.D., assistant professor of physical medicine and rehabilitation, University of Pittsburgh School of Medicine. 

The strings of implanted spinal electrodes, which Fisher describes as about the size and shape of “fat spaghetti noodles,” run along the spinal cord, where they sit slightly to one side, atop the same nerve roots that would normally transmit sensations from the arm. Since it’s a spinal cord implant, even a person with a shoulder-level amputation can use this device 

Fisher’s team sent electrical pulses through different spots in the implanted electrodes, one at a time, while participants used a tablet to report what they were feeling and where.

All the participants experienced sensations somewhere on their missing arm or hand, and they indicated the extent of the area affected by drawing on a blank human form. Three participants reported feelings localized to a single finger or part of the palm.

“I was pretty surprised at how small the area of these sensations were that people were reporting,” Fisher said. “That’s important because we want to generate sensations only where the prosthetic limb is making contact with objects.”

When asked to describe not just where but how the stimulation felt, all four participants reported feeling natural sensations, such as touch and pressure, though these feelings often were mixed with decidedly artificial sensations, such as tingling, buzzing or prickling.

Although some degree of electrode migration is inevitable in the first few days after the leads are implanted, Fisher’s team found that the electrodes, and the sensations they generated, mostly stayed put across the month-long duration of the experiment. That’s important for the ultimate goal of creating a prosthetic arm that provides sensory feedback to the user. 

“Stability of these devices is really critical,” Fisher said. “If the electrodes are moving around, that’s going to change what a person feels when we stimulate.” 

The next big challenges are to design spinal stimulators that can be fully implanted rather than connecting to a stimulator outside the body and to demonstrate that the sensory feedback can help to improve the control of a prosthetic hand during functional tasks like tying shoes or holding an egg without accidentally crushing it. Shrinking the size of the contacts — the parts of the electrode where current comes out — is another priority. That might allow users to experience even more localized sensations. 

“Our goal here wasn’t to develop the final device that someone would use permanently,” Fisher said. “Mostly we wanted to demonstrate the possibility that something like this could work.”

8 years ago

Perfect

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