Do-It-Yourself Neuroscience

By Moheb CostandiNovember 28, 2011

Traditionally, scientific research was the preserve of the wealthy and today the situation is not much different—while researchers need not be rich, almost all of them work in institutional laboratories using equipment that can be very expensive.

Recently, however, a do-it-yourself biology movement has emerged, and a symposium held at the 41^st annual meeting of the Society for Neuroscience in Washington, DC, earlier this month described several innovative projects aimed at minimizing the cost of brain research and making it accessible to everyone.

“If astronomy were like neuroscience, you’d need a Ph.D. to look through a telescope,” says Tim Marzullo, who chaired the symposium. “It’s ridiculous—the technology for recording nervous impulses is 90 years old and there’s no reason why it can’t be brought into schools.”

Marzullo and his colleague Greg Gage are doing just that. Three years ago, they founded Backyard Brains, a small company that manufactures neuroscience kits out of cheap off-the-shelf electronics purchased from outlets such as Radio Shack and distributes them to high schools and colleges, with the help of grant funding from the National Institutes of Health.

“I come from a family of teachers,” says Marzullo. “Backyard Brains came out of my love of neuroscience, education and building things. We see ourselves as part of a broader movement of DIY hackers who are trying to build just-good-enough versions of gear to reduce the barrier to entry.”

Michael Pollan Calls for Open Source Genetic Engineering

Try this at home by Daniel Grushkin

The next big scientific breakthrough may come from a garage, not a lab, with do-it-yourself biologists popping up everywhere. Genetic tinkerer Daniel Grushkin has a message for the curious: go ahead, try this at home. 

In the scientific journals, we’ve been labeled biotech hobbyists, citizen scientists, even biohackers.

Last December, seven of us opened the first community lab, called Genspace. Though it’s a fully functional lab, it has a decidedly hacked-together aesthetic. We built it in a Brooklyn, N.Y., warehouse that was converted into a workspace for architects and designers. At the center of the floor sits a glass cube made of found objects. The walls are created from windows and sliding glass doors saved from demo sites. The lab benches are stainless steel tables salvaged from industrial kitchens. Most of the equipment was donated by a biotech company that downsized during the economic crisis.

We incorporated Genspace as a nonprofit to serve as a shared lab, a nursery for biotech tinkerers. Our members include an entrepreneur with great ideas but a miniscule budget, an artist employing single-celled organisms for an experimental design palette, a molecular biologist with a penchant for mentorship, and folks like me, who want to learn by creating novel organisms.

DIY Bio: Growing Movement takes On Aging

Article by H+ Magazine



A movement is growing quietly, steadily, and with great speed. In basements, attics, garages, and living rooms, amateurs and professionals alike are moving steadily towards disparate though unified goals. They come home from work or school and transform into biologists: do-it-yourself biologists, to be exact.

DIYbiology (“DIYbio”) is a homegrown synthesis of software, hardware, and wetware. In the tradition of homebrew computing and in the spirit of the Make space (best typified by o‘Reilly‘s Make Magazine), these DIYers hack much more than software and electronics. These biohackers build their own laboratory equipment, write their own code (computer and genetic) and design their own biological systems. They engineer tissue, purify proteins, extract nucleic acids and alter the genome itself. Whereas typical laboratory experiments can run from tens-of-thousands to millions of dollars, many DIYers knowledge of these fields is so complete that the best among them design and conduct their own experiments at stunningly low costs. With adequate knowledge and ingenuity, DIYbiologists can build equipment and run experiments on a hobbyist‘s budget. As the movement evolves, cooperatives are also springing up where hobbyists are pooling resources and creating “hacker spaces” and clubs to further reduce costs, share knowledge and boost morale.

The Pearl Gel Box and Creative Commons

Open Hardware for Molecular Biology Experiments

Sure it takes years of training to become a world class biologist, but now you can have fun with their equipment without slaving away in academia. Pearl Biotech is selling an electrophoresis gel box, an instrument used in the separation and characterization of DNA online. Electrophoresis is a safe procedure that is useful to molecular biologists but can be enjoyed by anyone. It’s a standard experiment in high school labs. The Pearl Gel Box is an open hardware device which means that anyone is free to build or adapt it as along as they share their modifications in a similar manner. Pearl Biotech sells a fully assembled version for $200. By providing a cheap entry level tool for genetics Pearl is helping generate interest in the field and supporting the do it yourself community.

Programmable cells: Interfacing natural and engineered gene networks

Article From Proceedings of the National Academy of Sciences of the United States of America.

(Full-text available)

Abstract:

Novel cellular behaviors and characteristics can be obtained by coupling engineered gene networks to the cell's natural regulatory circuitry through appropriately designed input and output interfaces. Here, we demonstrate how an engineered genetic circuit can be used to construct cells that respond to biological signals in a predetermined and programmable fashion. We employ a modular design strategy to create Escherichia coli strains where a genetic toggle switch is interfaced with: (i) the SOS signaling pathway responding to DNA damage, and (ii) a transgenic quorum sensing signaling pathway from Vibrio fischeri. The genetic toggle switch endows these strains with binary response dynamics and an epigenetic inheritance that supports a persistent phenotypic alteration in response to transient signals. These features are exploited to engineer cells that form biofilms in response to DNA-damaging agents and cells that activate protein synthesis when the cell population reaches a critical density. Our work represents a step toward the development of “plug-and-play” genetic circuitry that can be used to create cells with programmable behaviors.

Here is a fine discussion of the above article from an Openwetware blog.

Imaging brain electric signals with genetically targeted voltage-sensitive fluorescent proteins

Nature Methods

 

7,

 

643–649

 

(2010)

 

doi:10.1038/nmeth.1479

Received

 

23 December 2009

 

Accepted

 

07 June 2010

 

Published online

 

11 July 2010

(Must subscribe to view full article)

Abstract:
Cortical information processing relies on synaptic interactions between diverse classes of neurons with distinct electrophysiological and connection properties. Uncovering the operational principles of these elaborate circuits requires the probing of electrical activity from selected populations of defined neurons. Here we show that genetically encoded voltage-sensitive fluorescent proteins (VSFPs) provide an optical voltage report from targeted neurons in culture, acute brain slices and living mice. By expressing VSFPs in pyramidal cells of mouse somatosensory cortex, we also demonstrate that these probes can report cortical electrical responses to single sensory stimuli in vivo. These protein-based voltage probes will facilitate the analysis of cortical circuits in genetically defined cell populations and are hence a valuable addition to the optogenetic toolbox.

Clarifying brain structure, literally

Nature Methods

 

8,

 

793

 

(2011)

 

doi:10.1038/nmeth.1720

Published online

 

29 September 2011

A fluorescence-compatible tissue-clearing reagent enables light microscopy–based imaging deep in the mouse brain.

In The Invisible Man, a science fiction novella by Herbert G. Wells, the protagonist is a scientist who finds a way to make the human body invisible by changing its refractive index to prevent the bending and reflection of light. In a recent report, Atsushi Miyawaki and his colleagues at RIKEN described the development of a tissue-clearing reagent with similar effects, bridging the gap between science and fiction and enabling fluorescence-based imaging of biological tissues at unprecedented depth and subcellular resolution.

High-resolution microscopy methods and fluorescence-based labeling techniques have enabled the three-dimensional imaging and reconstruction of defined cellular populations in a variety of biological tissues. However, axial resolution and imaging depth are often limited by the intrinsic opacity of biological specimens. For example, in visualizing the mammalian brain, light microscopy–based advances have been confined to the few hundred micrometers under the organ's surface. Alternatively, mechanical sectioning or insertion of minuscule endoscopes can be used to access deeper structures, but such approaches are inevitably laborious, invasive or of limited perspective.

Neuroscience Experiments

In the "Experiments" page of Backyard Brains are a series of nine increasingly complex experiments - from listening to action potentials to learning the basics of neuropharmacology and neuroprosthesis.

"Backyard Brains wiki page, [is] an open-source experimental how-to's for teachers and amateurs alike."

The page also lists the materials you will need to perform the experiments.

Synthetic biology: new engineering rules for an emerging discipline

From the Caltech Synthetic Biology Journal Club papers, I found this Nature Review:

Abstract
Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.

My Smartphone Is A Microscope. What Can Yours Do?

From NPR:

I lied. My smartphone isn't a microscope — yet. But there are some smart physicists who want to make that transformation possible very soon, if not for you and me at first, then for doctors who don't have easy access to laboratories.

There are a lot of ways to trick out your smartphone. And if you're an eager Apple fan, the brand-new iPhone 4S will come with fancy apps that use its increasingly sophisticated camera to scan and image the world. A smartphone camera lens can measure objects, help translate words, and even tell you whether your potato chips have been caught in a food safety recall.

But Sebastian Wachsmann-Hogiu and colleagues at the Center for Biophotonics, Science and Technology at the University of California, Davis say a smartphone's camera lens can also serve as a microscope and a spectrometer, which both could be pretty handy for looking at blood samples.

A few years ago, Wachsmann-Hogiu was thinking about creating tools to help doctors do tests right at the site where they're caring for patients, something called "point-of-care testing."

He'd heard about bioengineer Daniel Fletcher's work developing a low-tech mobile microscope called CellScope. But Wachsmann-Hogiu was interested in making something even simpler. And he noticed that when water droplets formed on the top of his iPhone camera, they magnified the image. So he took a tiny lens — just 1 millimeter in diameter — and attached it to the phone to try to get a similar effect.