opsin

Light Work

Understanding more about the human brain’s estimated 100 billion interconnected nerve cells, or neurons, could help us develop new treatments for disorders such as Parkinson’s disease, autism, schizophrenia and epilepsy. One method of investigating brain activity is to genetically engineer an animal, such as a mouse, so that its neurons produce a light-sensitive protein, opsin. Neuron activity can then be triggered by shining light on the brain, once it’s exposed in the anaesthetised animal. The computer simulation here illustrates a light beam hitting clusters of opsin on a neuron surface. The resulting nerve signals can be detected in connected neurons by inserting tiny probes to measure the electrical and genetic activity inside them. Scientists have recently developed a computer-guided robotic arm to insert the probes with greater accuracy than previously possible.

Written by Mick Warwicker

  • Ed Boyden
  • MIT McGovern Institute and Sputnik Animation

Noninvasive brain control

Optogenetics, a technology that allows scientists to control brain activity by shining light on neurons, relies on light-sensitive proteins that can suppress or stimulate electrical signals within cells. This technique requires a light source to be implanted in the brain, where it can reach the cells to be controlled.

MIT engineers have now developed the first light-sensitive molecule that enables neurons to be silenced noninvasively, using a light source outside the skull. This makes it possible to do long-term studies without an implanted light source. The protein, known as Jaws, also allows a larger volume of tissue to be influenced at once.

This noninvasive approach could pave the way to using optogenetics in human patients to treat epilepsy and other neurological disorders, the researchers say, although much more testing and development is needed. Led by Ed Boyden, an associate professor of biological engineering and brain and cognitive sciences at MIT, the researchers described the protein in the June 29 issue of Nature Neuroscience.

Optogenetics, a technique developed over the past 15 years, has become a common laboratory tool for shutting off or stimulating specific types of neurons in the brain, allowing neuroscientists to learn much more about their functions.

The neurons to be studied must be genetically engineered to produce light-sensitive proteins known as opsins, which are channels or pumps that influence electrical activity by controlling the flow of ions in or out of cells. Researchers then insert a light source, such as an optical fiber, into the brain to control the selected neurons.

Such implants can be difficult to insert, however, and can be incompatible with many kinds of experiments, such as studies of development, during which the brain changes size, or of neurodegenerative disorders, during which the implant can interact with brain physiology. In addition, it is difficult to perform long-term studies of chronic diseases with these implants.

Mining nature’s diversity

To find a better alternative, Boyden, graduate student Amy Chuong, and colleagues turned to the natural world. Many microbes and other organisms use opsins to detect light and react to their environment. Most of the natural opsins now used for optogenetics respond best to blue or green light.

Boyden’s team had previously identified two light-sensitive chloride ion pumps that respond to red light, which can penetrate deeper into living tissue. However, these molecules, found in the bacteria Haloarcula marismortui and Haloarcula vallismortis, did not induce a strong enough photocurrent — an electric current in response to light — to be useful in controlling neuron activity.

Chuong set out to improve the photocurrent by looking for relatives of these proteins and testing their electrical activity. She then engineered one of these relatives by making many different mutants. The result of this screen, Jaws, retained its red-light sensitivity but had a much stronger photocurrent — enough to shut down neural activity.

“This exemplifies how the genomic diversity of the natural world can yield powerful reagents that can be of use in biology and neuroscience,” says Boyden, who is a member of MIT’s Media Lab and the McGovern Institute for Brain Research.

Using this opsin, the researchers were able to shut down neuronal activity in the mouse brain with a light source outside the animal’s head. The suppression occurred as deep as 3 millimeters in the brain, and was just as effective as that of existing silencers that rely on other colors of light delivered via conventional invasive illumination.

A key advantage to this opsin is that it could enable optogenetic studies of animals with larger brains, says Garret Stuber, an assistant professor of psychiatry and cell biology and physiology at the University of North Carolina at Chapel Hill.

“In animals with larger brains, people have had difficulty getting behavior effects with optogenetics, and one possible reason is that not enough of the tissue is being inhibited,” he says. “This could potentially alleviate that.”

Restoring vision

Working with researchers at the Friedrich Miescher Institute for Biomedical Research in Switzerland, the MIT team also tested Jaws’s ability to restore the light sensitivity of retinal cells called cones. In people with a disease called retinitis pigmentosa, cones slowly atrophy, eventually causing blindness.

Friedrich Miescher Institute scientists Botond Roska and Volker Busskamp have previously shown that some vision can be restored in mice by engineering those cone cells to express light-sensitive proteins. In the new paper, Roska and Busskamp tested the Jaws protein in the mouse retina and found that it more closely resembled the eye’s natural opsins and offered a greater range of light sensitivity, making it potentially more useful for treating retinitis pigmentosa.

This type of noninvasive approach to optogenetics could also represent a step toward developing optogenetic treatments for diseases such as epilepsy, which could be controlled by shutting off misfiring neurons that cause seizures, Boyden says. “Since these molecules come from species other than humans, many studies must be done to evaluate their safety and efficacy in the context of treatment,” he says.

Boyden’s lab is working with many other research groups to further test the Jaws opsin for other applications. The team is also seeking new light-sensitive proteins and is working on high-throughput screening approaches that could speed up the development of such proteins.

Let's Go, Rick Steves, and Walking in London: A Review Comparing different travel guides for London

A good guide can be a total vacation save when you’re exploring an unfamiliar place with a time. First time visitors to London have not finished packing up that led to one or two good travel guides in their backpacks. But with so many choices, taking the right book can actually become one of the most frustrating travel planning: rails are some redundant, some compliment one another, some are complete, others are superficial.Let ‘s Go London City guidebooks, Rick Steves’ Great Britain, and Andrew Duncan Walking London are three very different books that have distinct purposes. And while certainly not the only London guides worth checking out, there is a 99% chance that at least one of them suits your individual needs. Let’s Go is probably the hottest business travel literature in the world at this time. They have put out guides that are stylish, economical, and-with a new version published every year, timely and accurate. Their London City Guide is no exception. Within the 350 + pages of the book, you will find heaps of detailed advice on eating, drinking, nightlife, museums and galleries, shopping, transport and accommodation (including hostels, bed & breakfasts, and even living rooms. ) All this information is conveniently organized by district. Within the pages of the guide Let’s Go find one for maps, charts, maps and more maps. lines the streets of London sprawling, casual, old-meets-new can make navigation difficult, but you’ll be fine if you’re carrying the guide Let’s Go: the first 8 and last 31 pages are devoted entirely to the maps. Bottom, Let’s Go has some ‘advertising on its pages, some of which can be intrusive at times. And even more significantly, Let’s Go lacks personality. It ‘full of practical information such as addresses, prices and hours, but it lacks that human touch that can be so comforting for a traveler in an unfamiliar place. This is where the game Rick Steves travel stories personal opinions frankly and historical curiosities to Rick Steves’ Great Britain a perfect companion to (or replacement) Let’s Go guide with a section entitled “Delusions of London, you know this guy is pulling no punches. But what really makes it stand out from Steves travel writer and his drawings. He insists that his readers get a visual representation of everything he writes. His guide is filled with easy to follow, hand-drawn maps of everything from entire regions, cities and districts, right down to floorplans of galleries, museums and castles. -And as you probably guessed from the title-Rick Steves’ Britain does not deal exclusively in London. The book covers all the best that England, Wales and Scotland have to offer. This makes it perfect for travelers who plan to spend time outside of London for part of their journey. Steves also publishes a guide of the city of London-specific, but with 80 + pages of the book in Britain devoted exclusively to London, why bother? My only problem with writing Steves’ is that while he certainly does not bear to throw away money, may not be enough for some budget-oriented travelers (like those on a student budget.) For example, his recommendations to address accommodation almost exclusively with hotels, hostels, giving only a hint. And while people in Let’s Go understand that you’re willing to walk eight miles for a cheap drink, Steves’ readers have to resign themselves to the idea that they are going to pay $ 10 for a beer. Last but by no means least, we strongly recommend checking out Walking London by Andrew Duncan. It ‘s a very special book, not an all-encompassing guide to the city, but a manual step-by-step tour to 30 do-it-yourself walking through the most famous districts of the city. Even if you’re not one of the turns in its entirety, holding a copy of Walking in London stock exchange days is guaranteed not to miss important points of reference, good food, or photo opportunities as you are walking from place to place. Although I do not recommend using London as a tourist guide Walking alone makes it a striking partner for any of the most complete guides or country. If you decide to take it, I support the “Westminster and St. James ‘and’ Bankside and Southwark” missed like two walks. Whatever you decide to go with books, there is an important secret to using them correctly: to study before you go. What better way to ruin a vacation than spending all the time with his face buried in a guidebook.


Farellones
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Opsin

Ivan Villafuerte

Sin Are Acids In The Eyes

This guy was standing on a corner in Greenpoint, Brooklyn preaching about “the DNA of sin.” He told me, “Sin are acids in the eyes called OpSin…which form free radicals causing aging, disease, and death.” I think he also said his church sell anti-aging products. It was a lot to take in…

More photos of Preachers and Super Religious Folk and from the Random Strangers Series.

Octopus-Inspired Camouflage Flashes to Life in Smart Material! (TECHNOLOGY)

     Octopuses and their cephalopod cousins are the undisputed masters of disguise. An octopus can change its color, texture and luminosity faster than you can say “camouflage.”

     So far our lowly human attempts at imitation have been quite crude. But a flashy new smart material might just be our closest step yet.

     The main tool the octopus uses for its visual display is a cell called a chromatophore. These small, pigment-filled sacs expand and contract to create an array of colors and patterns. How does the octopus decide what colors and patterns to make? Recent research suggests that octopuses can also sense light—and possibly even color—through photo-sensitive cells (called opsins) in their skin.

     The idea of a material that can both sense and create visual change is quite appealing to science (and the military). Renowned cephalopod researcher Roger Hanlon, a senior scientist at Woods Hole Marine Biological Laboratory, and John Rogers, a professor of materials science and engineering at the University of Illinois at Urbana-Champaign (whose previous work includes flexible temporary tattoo-like circuits), teamed up with a crew of international researchers to create a changing heat- and light-sensitive sheet of pixels, described earlier this week in Proceedings of the National Academy of Sciences.

Photo sensible nanomaterial, based in octopus skin

More facts and Science in: www.newhorizonshept.tumblr.com

BMC

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How plankton gets jet lagged

A hormone that governs sleep and jet lag in humans may also drive the mass migration of plankton in the ocean, scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, have found. The molecule in question, melatonin, is essential to maintain our daily rhythm, and the European scientists have now discovered that it governs the nightly migration of a plankton species from the surface to deeper waters. The findings, published online today in Cell, indicate that melatonin’s role in controlling daily rhythms probably evolved early in the history of animals, and hold hints to how our sleep patterns may have evolved.

In vertebrates, melatonin is known to play a key role in controlling daily activity patterns – patterns which get thrown out of synch when we fly across time zones, leading to jet lag. But virtually all animals have melatonin. What is its role in other species, and how did it evolve the task of promoting sleep? To find out, Detlev Arendt’s lab at EMBL turned to the marine ragworm Platynereis dumerilii. This worm’s larvae take part in what has been described as the planet’s biggest migration, in terms of biomass: the daily vertical movement of plankton in the ocean. By beating a set of microscopic ‘flippers’ – cilia – arranged in a belt around its midline, the worm larvae are able to migrate toward the sea’s surface every day. They reach the surface at dusk, and then throughout the night they settle back down to deeper waters, where they are sheltered from damaging UV rays at the height of day. 

“We found that a group of multitasking cells in the brains of these larvae that sense light also run an internal clock and make melatonin at night.” says Detlev Arendt, who led the research. “So we think that melatonin is the message these cells produce at night to regulate the activity of other neurons that ultimately drive day-night rhythmic behaviour.”

Maria Antonietta Tosches, a postdoc in Arendt’s lab, discovered a group of specialised motor neurons that respond to melatonin. Using modern molecular sensors, she was able to visualise the activity of these neurons in the larva’s brain, and found that it changes radically from day to night. The night-time production of melatonin drives changes in these neurons’ activity, which in turn cause the larva’s cilia to take long pauses from beating. Thanks to these extended pauses, the larva slowly sinks down. During the day, no melatonin is produced, the cilia pause less, and the larva swims upwards.

“When we exposed the larvae to melatonin during the day, they switched towards night-time behaviour,” says Tosches, “it’s as if they were jet lagged.”

The work strongly suggests that the light-sensing, melatonin-producing cells at the heart of this larva’s nightly migration have evolutionary relatives in the human brain. This implies that the cells that control our rhythms of sleep and wakefulness may have first evolved in the ocean, hundreds of millions of years ago, in response to pressure to move away from the sun.

“Step by step we can elucidate the evolutionary origin of key functions of our brain. The fascinating picture emerges that human biology finds its roots in some deeply conserved, fundamental aspects of ocean ecology that dominated life on Earth since ancient evolutionary times,” Arendt concludes.

A non-visual opsin could help future studies of the brain and central nervous system

In the on-going search for a better understanding of how the brain and central nervous system develop, a potentially powerful new tool could soon be available. Researchers at Lawrence Berkeley National Laboratory (Berkeley Lab) have discovered a light-sensitive opsin protein that plays…
Source: A non-visual opsin could help future studies of the brain and central nervous system

(Image caption: Archer1 fluorescence in a cultured rat hippocampal neuron. By monitoring changes in this fluorescence at up to a thousand frames per second, researchers can track the electrical activity of the cell. Credit: Nicholas Flytzanis, Claire Bedbrook and Viviana Gradinaru/Caltech)

Sensing Neuronal Activity With Light

For years, neuroscientists have been trying to develop tools that would allow them to clearly view the brain’s circuitry in action—from the first moment a neuron fires to the resulting behavior in a whole organism. To get this complete picture, neuroscientists are working to develop a range of new tools to study the brain. Researchers at Caltech have developed one such tool that provides a new way of mapping neural networks in a living organism.

The work—a collaboration between Viviana Gradinaru (BS ‘05), assistant professor of biology and biological engineering, and Frances Arnold, the Dick and Barbara Dickinson Professor of Chemical Engineering, Bioengineering and Biochemistry—was described in two separate papers published this month.

When a neuron is at rest, channels and pumps in the cell membrane maintain a cell-specific balance of positively and negatively charged ions within and outside of the cell resulting in a steady membrane voltage called the cell’s resting potential. However, if a stimulus is detected—for example, a scent or a sound—ions flood through newly open channels causing a change in membrane voltage. This voltage change is often manifested as an action potential—the neuronal impulse that sets circuit activity into motion.

The tool developed by Gradinaru and Arnold detects and serves as a marker of these voltage changes.

"Our overarching goal for this tool was to achieve sensing of neuronal activity with light rather than traditional electrophysiology, but this goal had a few prerequisites," Gradinaru says. "The sensor had to be fast, since action potentials happen in just milliseconds. Also, the sensor had to be very bright so that the signal could be detected with existing microscopy setups. And you need to be able to simultaneously study the multiple neurons that make up a neural network."

The researchers began by optimizing Archaerhodopsin (Arch), a light-sensitive protein from bacteria. In nature, opsins like Arch detect sunlight and initiate the microbes’ movement toward the light so that they can begin photosynthesis. However, researchers can also exploit the light-responsive qualities of opsins for a neuroscience method called optogenetics—in which an organism’s neurons are genetically modified to express these microbial opsins. Then, by simply shining a light on the modified neurons, the researchers can control the activity of the cells as well as their associated behaviors in the organism.

Gradinaru had previously engineered Arch for better tolerance and performance in mammalian cells as a traditional optogenetic tool used to control an organism’s behavior with light. When the modified neurons are exposed to green light, Arch acts as an inhibitor, controlling neuronal activity—and thus the associated behaviors—by preventing the neurons from firing.

However, Gradinaru and Arnold were most interested in another property of Arch: when exposed to red light, the protein acts as a voltage sensor, responding to changes in membrane voltages by producing a flash of light in the presence of an action potential. Although this property could in principle allow Arch to detect the activity of networks of neurons, the light signal marking this neuronal activity was often too dim to see.

To fix this problem, Arnold and her colleagues made the Arch protein brighter using a method called directed evolution—a technique Arnold originally pioneered in the early 1990s. The researchers introduced mutations into the Arch gene, thus encoding millions of variants of the protein. They transferred the mutated genes into E. coli cells, which produced the mutant proteins encoded by the genes. They then screened thousands of the resulting E. coli colonies for the intensities of their fluorescence. The genes for the brightest versions were isolated and subjected to further rounds of mutagenesis and screening until the bacteria produced proteins that were 20 times brighter than the original Arch protein.

A paper describing the process and the bright new protein variants that were created was published in the September 9 issue of the Proceedings of the National Academy of Science.

"This experiment demonstrates how rapidly these remarkable bacterial proteins can evolve in response to new demands. But even more exciting is what they can do in neurons, as Viviana discovered," says Arnold.

In a separate study led by Gradinaru’s graduate students Nicholas Flytzanis and Claire Bedbrook, who is also advised by Arnold, the researchers genetically incorporated the new, brighter Arch variants into rodent neurons in culture to see which of these versions was most sensitive to voltage changes—and therefore would be the best at detecting action potentials. One variant, Archer1, was not only bright and sensitive enough to mark action potentials in mammalian neurons in real time, it could also be used to identify which neurons were synaptically connected—and communicating with one another—in a circuit.

The work is described in a study published on September 15 in the journal Nature Communications.

"What was interesting is that we would see two cells over here light up, but not this one over there—because the first two are synaptically connected," Gradinaru says. "This tool gave us a way to observe a network where the perturbation of one cell affects another."

However, sensing activity in a living organism and correlating this activity with behavior remained the biggest challenge. To accomplish this goal Gradinaru’s team worked with Paul Sternberg, the Thomas Hunt Morgan Professor of Biology, to test Archer1 as a sensor in a living organism—the tiny nematode worm C. elegans. “There are a few reasons why we used the worms here: they are powerful organisms for quick genetic engineering and their tissues are nearly transparent, making it easy to see the fluorescent protein in a living animal,” she says.

After incorporating Archer1 into neurons that were a part of the worm’s olfactory system—a primary source of sensory information for C. elegans—the researchers exposed the worm to an odorant. When the odorant was present, a baseline fluorescent signal was seen, and when the odorant was removed, the researchers could see the circuit of neurons light up, meaning that these particular neurons are repressed in the presence of the stimulus and active in the absence of the stimulus. The experiment was the first time that an Arch variant had been used to observe an active circuit in a living organism.

Gradinaru next hopes to use tools like Archer1 to better understand the complex neuronal networks of mammals, using microbial opsins as sensing and actuating tools in optogenetically modified rodents.

"For the future work it’s useful that this tool is bifunctional. Although Archer1 acts as a voltage sensor under red light, with green light, it’s an inhibitor," she says. "And so now a long-term goal for our optogenetics experiments is to combine the tools with behavior-controlling properties and the tools with voltage-sensing properties. This would allow us to obtain all-optical access to neuronal circuits. But I think there is still a lot of work ahead."

One goal for the future, Gradinaru says, is to make Archer1 even brighter. Although the protein’s fluorescence can be seen through the nearly transparent tissues of the nematode worm, opaque organs such as the mammalian brain are still a challenge. More work, she says, will need to be done before Archer1 could be used to detect voltage changes in the neurons of living, behaving mammals.

And that will require further collaborations with protein engineers and biochemists like Arnold.

"As neuroscientists we often encounter experimental barriers, which open the potential for new methods. We then collaborate to generate tools through chemistry or instrumentation, then we validate them and suggest optimizations, and it just keeps going," she says. "There are a few things that we’d like to be better, and through these many iterations and hard work it can happen."

A non-visual opsin could help future studies of the brain and central nervous system

In the on-going search for a better understanding of how the brain and central nervous system develop, a potentially powerful new tool could soon be available. Researchers at Lawrence Berkeley National Laboratory (Berkeley Lab) have discovered a light-sensitive opsin protein that…
Source:A non-visual opsin could help future studies of the brain and central nervous system

Optogenetic toolkit goes multicolor

Optogenetics is a technique that allows scientists to control neurons’ electrical activity with light by engineering them to express light-sensitive proteins. Within the past decade, it has become a very powerful tool for discovering the functions of different types of cells in the brain.

Most of these light-sensitive proteins, known as opsins, respond to light in the blue-green range. Now, a team led by MIT has discovered an opsin that is sensitive to red light, which allows researchers to independently control the activity of two populations of neurons at once, enabling much more complex studies of brain function.

“If you want to see how two different sets of cells interact, or how two populations of the same cell compete against each other, you need to be able to activate those populations independently,” says Ed Boyden, an associate professor of biological engineering and brain and cognitive sciences at MIT and a senior author of the new study.

The new opsin is one of about 60 light-sensitive proteins found in a screen of 120 species of algae. The study, which appears in the Feb. 9 online edition of Nature Methods, also yielded the fastest opsin, enabling researchers to study neuron activity patterns with millisecond timescale precision.

Boyden and Gane Ka-Shu Wong, a professor of medicine and biological sciences at the University of Alberta, are the paper’s senior authors, and the lead author is MIT postdoc Nathan Klapoetke. Researchers from the Howard Hughes Medical Institute’s Janelia Farm Research Campus, the University of Pennsylvania, the University of Cologne, and the Beijing Genomics Institute also contributed to the study.

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CIRpy - A Python interface for the Chemical Identifier Resolver (CIR)

In the past I have used the ChemSpider API (through ChemSpiPy) to resolve chemical names to structures. Unfortunately this doesn’t work that well for IUPAC names and I found myself wondering whether it was worth setting up a system that would try a number of different resolvers. More specifically, I wanted a system that would first try using OPSIN to match IUPAC names, and if that failed, try a ChemSpider lookup. Just as I was about to start doing this myself, I came across the Chemical Identifier Resolver (CIR) that does exactly that (and much more).

CIR is a web service created by by the CADD Group at the NCI that performs various chemical name to structure conversions. In short, it will (attempt to) resolve the structure of any chemical identifier that you throw at it. Under the hood it uses a combination of OPSIN, ChemSpider and CIR’s own database.

To simplify interacting with CIR through Python, I wrote a simple wrapper called CIRpy that handles constructing url requests and parsing XML responses. It’s available on github here.

Using it is a simple case of copying cirpy.py into a directory on your python path. Here’s an example using the resolve function:

import cirpy

smiles_string = cirpy.resolve('Aspirin','smiles')

There are full details of all available options in the readme.