The Living Lab: Navigating into cells

How do viruses attach to cells? How do proteins interact and mediate infection? How do molecular machines organize themselves in healthy cells? How do they differ in diseased cells? These are the types of questions National Institutes of Health researchers ask in the recently established Living Lab for Structural Biology, questions they strive to answer through the most sophisticated of imaging techniques.

The Living Lab is an innovative partnership between NIH and FEI, an Oregon-based instrumentation company that manufactures advanced microscopes. FEI brings to the table invaluable assistance in developing and customizing electron microscopes for biological applications. Using that cutting edge technology, scientists in the Living Lab, unencumbered by any pressure to patent or otherwise protect discoveries for commercial purposes, can proceed purely driven by scientific and biomedical puzzles. Success of the Living Lab, which is on the NIH campus in Bethesda, Md., will rest on that collaboration between the government and the private sector—and the idea that answering scientific questions and technical advancement go hand in hand.

“We want to navigate our way into cells and into viruses,” said Sriram Subramaniam, Ph. D., director of the NIH component of the Living Lab. “We would like to be able to describe the function of complex things, such as whole cells or infectious viruses, in terms of their molecular make-up, and try to figure out how they work.”

The Living Lab’s advanced imaging technology allows researchers to tackle previously unanswered questions in structural biology by creating three-dimensional shapes of various molecular machines. Visualizing tiny details is a step toward understanding the molecular origins of disease. “The prospects for studying structures of a broad spectrum of medically relevant complexes at minute resolutions has changed dramatically in recent years with advances in structural biology,” said Subramaniam. “Our goal with the Living Lab is to capture the synergy between all of these methods including the latest advances in cryo-electron microscopy to extend these advances to key scientific challenges in modern structural biology.”

Subramaniam, who earned his doctorate at Stanford University and did post-doctoral work at the Massachusetts Institute of Technology in chemistry and biology, directs the research activities of the Living Lab, in close consultation with other team members from FEI and from the National Institute of Diabetes and Digestive and Kidney Diseases.

Out of Sight, Out of Mind? How the brain codes its surroundings beyond the field of view

Even when they are not directly in sight, we are aware of our surroundings: so it is that when our eyes are fixed on an interesting book, for example, we know that the door is to the right, the bookshelf is to the left and the window is behind us. However, research into the brain has so far concerned itself predominantly with how information from our field of vision is coded in the visual cortex. To date it has not been known how the brain codes our surroundings beyond the field of view from an egocentric perspective (that is, from the point of view of the observer).

In the latest issue of the renowned journal Current Biology, Andreas Schindler und Andreas Bartels, scientists at the Werner Reichardt Center for Integrative Neuroscience (CIN) of the University of Tübingen, present for the first time direct evidence of this kind of spatial information in the brain.

The participants in their study found themselves in the center of a virtual octagonal room, with a unique object in each corner. As the brain’s activity was monitored by means of functional magnetic resonance imaging, the participants stood in front of one corner and looked at its object. Now they were instructed to determine the position of a second randomly chosen object within the room relative to their current perspective (for example, the object behind them). After a few trials the participant turned around so that the next object was brought into the field of view and the task was set up again. The whole procedure was repeated until every object had been looked at once.

The scientists discovered that patterns of activity in the parietal cortex code the participant’s egocentric position, that is, the relative position to his or her surroundings. The spatial information discovered there proved to be independent of the particular object, its absolute position in the room or that of the observer – i.e. it encoded egocentric spatial information of the three-dimensional surroundings. This result turns out to be particularly interesting because damage to the brain in the parietal cortex can lead to serious disruption of egocentric spatial awareness. Hence it is difficult for patients suffering from optical ataxia to carry out coordinated grasping movements. Lesions in the parietal cortex can also lead to a symptom called spatial neglect where patients have difficulties in perceiving their surroundings on the side opposite to the lesion. The brain areas identified in the present study coincided precisely with the areas of brain damage in such patients and provide for the first time insights regarding their function in the healthy brain.

Why Do Age-Related Macular Degeneration Patients Have Trouble Recognizing Faces?

Abnormalities of eye movement and fixation may contribute to difficulty in perceiving and recognizing faces among older adults with age-related macular degeneration (AMD), suggests a study “Abnormal Fixation in Individuals with AMD when Viewing an Image of a Face” appearing in the January issue of Optometry and Vision Science, official journal of the American Academy of Optometry. The journal is published by Lippincott Williams & Wilkins, a part of Wolters Kluwer Health.

Unlike people with normal vision focus, those with AMD don’t focus on “internal features” (the eyes, nose and mouth) when looking at the image of a face, according to the study by William Seiple, PhD, and colleagues of Lighthouse International, New York.

When Viewing Famous Face, AMD Patients Focus on External Features

The researchers used a sophisticated technique called optical coherence tomography/scanning laser ophthalmoscopy (OCT-SLO) to examine the interior of the eye in nine patients with AMD. Age-related macular degeneration is the leading cause of vision loss in older adults. It causes gradual destruction of the macula, leading to blurring and loss of central vision.

Previous studies have suggested that people with AMD have difficulty perceiving faces. To evaluate the possible role of abnormal eye movements, Dr Seiple and colleagues used the OCT-SLO equipment to make microscopic movies of the interior of the eye (fundus, including the retina and macula) as the patients viewed one of the world’s most famous faces: the Mona Lisa.

This technique allowed the researchers to record eye movements and where the patients looked (fixations) while looking at the face. They compared the findings in AMD patients to a control group of subjects with normal vision.

The results showed significant differences in eye movement patterns and fixations between groups. The AMD patients had fewer fixations on the internal features of the Mona Lisa’s face—eyes, nose, and mouth. For controls, an average of 87 percent of fixations were on internal features, compared to only 13 percent on external features. In contrast, for AMD patients, 62 percent of fixations were on internal features while 38 percent were on external features.

The normal controls also tended to make fewer and shorter eye movements (called saccades) than AMD patients. The differences between groups did not appear to be related to the blurring of vision associated with AMD.

Some older adults with AMD report difficulties perceiving faces. While the problem in “processing faces” is certainly related to the overall sensory visual loss, the new evidence suggests that specific patterns of eye movement abnormalities may also play a role.

Dr Seiple and colleagues note that “abnormal scanning patterns when viewing faces” have also been found in other conditions associated with difficulties in face perception, including autism, social phobias, and schizophrenia. The authors discuss the possible mechanisms of the abnormal scanning patterns in AMD, involving the complex interplay between the eyes and brain in governing eye movement and interpreting visual information.

A previous study suggested that drawing attention to specific characteristics—such as the internal facial features—may increase fixations on internal features and improve face perception. Dr Seiple and coauthors conclude, “That report gives hope that eye movement control training and training of allocation of attention could improve face perception and eye scanning behavior in individuals with AMD.”

Cognitive deficits from concussions still present after two months

The ability to focus and switch tasks readily amid distractions was compromised for up to two months following brain concussions suffered by high school athletes, according to a study at the University of Oregon.

Research team members, in an interview, said the discovery suggests that some athletes may need longer recovery periods than current practices dictate to lower the risk of subsequent concussions. Conventional wisdom, said lead author David Howell, a graduate student in the UO Department of Human Physiology, says that typical recovery from concussion takes seven to 10 days.

"The differences we detected may be a matter of milliseconds between a concussed person and a control subject, but as far as brain time goes that difference for a linebacker returning to competition too soon could mean the difference between another injury or successfully preparing to safely tackle an oncoming running back," Howell said.

The findings are based on cognitive exercises used five times over the two months with a pair of sensitive computer-based measuring tools — the attentional network test and the task-switching test. The study focused on the effects of concussions to the frontal region of the brain, which is responsible for working, or short-term, memory and executive function, said Li-Shan Chou, professor of human physiology and director of the UO Motion Analysis Laboratory.

The study was published online ahead of print by Medicine & Science in Sports & Exercise, the official journal of the American College of Sports Medicine.

Detrimental effect of obesity on lesions associated with Alzheimer’s disease

Researchers from Inserm and the Université Lille/Université Lille Nord de France have recently used a neurodegeneration model of Alzheimer’s disease to provide experimental evidence of the relationship between obesity and disorders linked to the tau protein. This research was conducted on mice and is published in the Diabetes review: it corroborates the theory that metabolic anomalies contribute massively to the development of dementia.

In France, more than 860,000 people suffer from Alzheimer’s disease and related disorders, making them the largest cause of age-related loss of intellectual function. Cognitive impairments observed in Alzheimer’s disease result from the accumulation of abnormal tau proteins in nerve cells undergoing degeneration (see the picture below). We know that obesity, a major risk factor in the development of insulin resistance and type 2 diabetes, increases the risk of dementia during the aging process. However, the effects of obesity on ‘Taupathies’ (i.e. tau protein-related disorders), including Alzheimer’s disease, were not clearly understood. In particular, researchers assumed that insulin resistance played a major role in terms of the effects of obesity.

The “Alzheimer & Tauopathies” team from mixed research unit 837 (Inserm/Université Lille 2/Université Lille Nord de France) directed by Dr. Luc Buée, in collaboration with mixed research unit 1011 “Nuclear receptors, cardiovascular diseases and diabetes”, have just demonstrated, in mice, that obese subjects develop aggravated disorders. To achieve this result, young transgenic mice, who develop tau-related neurodegeneration progressively with age, were put on a high-fat diet for five months, leading to progressive obesity.

“At the end of this diet, the obese mice had developed an aggravated disorder both from the point of view of memory and modifications to the Tau protein”, explains David Blum, in charge of research at Inserm.

This study uses a neurodenegeneration model of Alzheimer’s disease to provide experimental evidence of the relationship between obesity and disorders linked to the tau protein. Furthermore, it indicates that insulin resistance is not the aggravating factor, as was suggested in previous studies.

“Our research supports the theory that environmental factors contribute massively to the development of this neurodegenerative disorder” underlines the researcher. “Our work is now focussing on identifying the factors responsible for this aggravation” he adds.

Can Blood Pressure Drugs Reduce the Risk of Dementia?

People taking the blood pressure drugs called beta blockers may be less likely to have changes in the brain that can be signs of Alzheimer’s disease and other types of dementia, according to a study released today that will be presented at the American Academy of Neurology’s 65th Annual Meeting in San Diego, March 16 to 23, 2013. The study involved 774 elderly Japanese-American men who took part in the Honolulu-Asia Aging Study. Autopsies were performed on the men after their death. Of the 774 men, 610 had high blood pressure or were being treated with medication for high blood pressure. Among those who had been treated (about 350), 15 percent received only a beta blocker medication, 18 percent received a beta blocker plus one or more other medications, and the rest of the participants received other blood pressure drugs.

The study found that all types of blood pressure treatments were clearly better than no treatment. However, men who had received beta blockers as their only blood pressure medication had fewer abnormalities in their brains compared to those who had not been treated for their hypertension, or who had received other blood pressure medications. The brains of participants who had received beta blockers plus other medications showed an intermediate reduction in numbers of brain abnormalities.

These included two distinct types of brain lesion: those indicating Alzheimer’s disease, and lesions called microinfarcts, usually attributed to tiny, multiple, unrecognized strokes. Study participants who had taken beta blockers alone or in combination with another blood pressure medication had significantly less shrinkage in their brains.

“With the number of people with Alzheimer’s disease expected to grow significantly as our population ages, it is increasingly important to identify factors that could delay or prevent the disease,” said study author Lon White, MD, of the Pacific Health Research and Education Institute in Honolulu. “These results are exciting, especially since beta blockers are a common treatment for high blood pressure.”

Earlier research has shown that high blood pressure in midlife is a strong risk factor for dementia.

Molecular ‘Two-Way Radio’ Directs Nerve Cell Branching And Connectivity

Working with fruit flies, Johns Hopkins scientists have decoded the activity of protein signals that let certain nerve cells know when and where to branch so that they reach and connect to their correct muscle targets. The proteins’ mammalian counterparts are known to have signaling roles in immunity, nervous system and heart development, and tumor progression, suggesting broad implications for human disease research. A report of the research was published online Nov. 21 in the journal Neuron.

To control muscle movements, fruit flies, like other animals, have a set of nerve cells called motor neurons that connect muscle fibers to the nerve cord, a structure similar to the spinal cord, which in turn connects to the brain. During embryonic development, the nerve cells send wire-like projections, or axons, from the nerve cord structure out to their targets. Initially, multiple axons travel together in a convoy, but as they move forward, some axons must exit the “highway” at specific points to reach particular targets.

In their experiments, the researchers learned that axons travelling together have proteins on their surfaces that act like two-way radios, allowing the axons to communicate with each other and coordinate their travel patterns, thus ensuring that every muscle fiber gets connected to a nerve cell. “When axons fail to branch, or when they branch too early and too often, fruits flies, and presumably other animals, can be left without crucial muscle-nerve connections,” says Alex Kolodkin, Ph.D., a Howard Hughes investigator and professor of neuroscience at the Institute for Basic Biomedical Sciences at the Johns Hopkins University School of Medicine.

At the center of the communications system, Kolodkin says, is a protein called Sema-1a, already known to reside on the surface of motor neuron axons. If a neighboring axon has a different protein, called PlexA, on its surface, it will be repulsed by Sema-1a and will turn away from the axon bundle. So Sema-1a acts as an instructional signal and PlexA as its receptor. In the fruit fly study, the scientists discovered that Sema-1a can also act as a receptor for PlexA. “We used to think that this pair of surface proteins acted as a one-way radio, with information flowing in a single direction,” says Kolodkin. “What we found is that instructional information flows both ways.”

The Johns Hopkins team identified the “two-way” system by knocking out and otherwise manipulating fruit fly genes and then watching what happened to motor neuron branching. In these experiments, the researchers uncovered still other proteins located within the motor axons that Sema-1a interacts with after receiving a PlexA signal. When the gene for a protein called Pebble was deleted, for example, motor axons bunched together and didn’t branch. When the gene for RhoGAPp190 was deleted, motor axons branched too soon and failed to recognize their target muscles.

Through a series of biochemical tests, Kolodkin’s team found that Pebble and RhoGAPp190 both act on a third protein, Rho1. When Rho1 is activated, it collapses the supporting structures within an axon, making it “limp” and unable to continue toward a target. Sema-1a can bind to Pebble or to RhoGAPp190, and subsequently, these proteins can bind to Rho1. Binding to Pebble activates Rho1, causing axons to branch away from each other. However, binding to RhoGAPp190 shuts down Rho1, causing axons to remain bunched together. Thus, says Kolodkin, balance in the amounts of available Pebble and RhoGAPp190 can determine axon behavior, although what determines this balance is still unknown.

“This signaling is complex and we still don’t understand how it’s all controlled, but we’re one step closer now,” says Kolodkin. He notes that “a relative” of the Sema-1a protein in humans has already been implicated in schizophrenia, although details of this protein’s role in disease remain unclear. “Our experiments affirm how important this protein is to study and understand,” adds Kolodkin.

Mechanism of hearing is similar to car battery

University of Iowa biologist Daniel Eberl and his colleagues have shown that one of the mechanisms involved in hearing is similar to the battery in your car.

And if that isn’t interesting enough, the UI scientists advanced their knowledge of human hearing by studying a similar auditory system in fruit flies—and by making use of the fruit fly “love song.”

To see how the mechanism of hearing resembles a battery, you need to know that the auditory system of the fruit fly contains a protein that functions as a sodium/potassium pump, often called the sodium pump for short, and is highly expressed in a specialized support cell called the scolopale cell.

The scolopale cell is important because it wraps around the sensory endings in the fly’s ear and makes a tight extra-cellular cavity or compartment around them called the scolopale space.

“You could think of these compartments as similar to the compartments of a battery that need to be charged up so they can drive electrons through circuits,” says Eberl, whose paper made the cover of the journal Proceedings of the National Academy of Sciences. “In the auditory system, the charge in the scolopale space drives ions, or electrically charged atoms, through membrane channels in the sensory endings that open briefly in response to activation by sounds.

“Our work shows that the sodium pump plays a particularly important role in this cell to help replenish or recharge this compartment with the right ions. The human ear also relies on a compartment called the scala media, which similarly drives ions into the sensory cells of the ear,” he says.

How was the research done? This is where the fruit fly love song comes into play.

Testing whether or not a fruit fly can hear the love song—a sound generated by a vibrating wing—enables Eberl to learn whether electrical recharging is occurring in the fly ear. The fruit fly love song played a role in the research by stimulating the fly to move whenever a sound was emitted and received.

“In these experiments we tested the fly’s hearing by inserting tiny electrodes in the fly’s antenna, then measuring the electrical responses when we play back computer-generated love songs,” he says.

Eberl notes there are many similarities between fruit fly and human mechanisms of hearing. That means his work on the fly model to identify additional new components required for generating the correct ion balance in the ear will help scientists to understand the human process in more detail.

GE Silent Scan turns down the volume on MRI scanners

GE Healthcare has introduced a new data acquisition technology designed to improve patient comfort by largely eliminating the horrible noise generated during an MRI scan. Conventional MRI scanners can generate noise levels in excess of 110 dBA (creating a din that sounds like a cross between a vehicle’s reverse warning horn and a Star Trek phaser) but GE says its new Silent Scan MRI technology can reduce this to just above background noise levels in the exam room.

The noise that MRI scanners produce is related to changes in the magnetic field that allow the slice by slice body scan to be carried out. In recent years, industry efforts to speed up the scanning process have also resulted in louder and louder scans. The designers have attempted to dampen these noises with mufflers and baffles, achieving only limited success.

Silent Scan is achieved through two new developments. First, acoustic noise is essentially eliminated by using a new 3D scanning and reconstruction technique called Silenz. When the Silenz protocol is used in combination with GE’s new high-fidelity MRI gradient and RF system electronics, the MRI scanning noise is largely eliminated at its source.

At the 2012 meeting of the Radiological Society of North America, an MRI system compatible with the Silent Scan technology was linked into a soundproof room. When the MRI system used conventional scanning methods, a staccato, stuttering racket with noise peaks up to 110 dBA was heard. However, when Silent Scan was switched on, the noise level dropped to 76 dBA, just above the background noise of the MRI electronics. This is accomplished without substantial trade-offs in scanning time or image quality, according to Richard Hausmann, president and CEO, GE Healthcare MR. The comparison is shown in this video.

Silent Scan technology has not yet obtained 510k Premarketing Notification clearance from the FDA, so it’s not yet available for sale. GE is presumably hoping for a decision that Silent Scan is “substantially equivalent” to existing MRI scanners, a result that would greatly simplify the new technology’s entry into the diagnostic market.