The Neuron – A Hackers Perspective

It’s not too often that you see handkerchiefs around anymore. Today, they’re largely viewed as unsanitary and well… just plain gross. You’ll be quite disappointed to learn that they have absolutely nothing to do with this article other than a couple of similarities they share when compared to your neocortex. If you were to pull the neocortex from your brain and stretch it out on a table, you most likely wouldn’t be able to see that not only is it roughly the size of a large handkerchief; it also shares the same thickness.

The neocortex, or cortex for short, is Latin for “new rind”, or “new bark”, and represents the most recent evolutionary change to the mammalian brain. It envelopes the “old brain” and has several ridges and valleys (called sulci and gyri) that formed from evolution’s mostly successful attempt to stuff as much cortex as possible into our skulls. It has taken on the duties of processing sensory inputs and storing memories, and rightfully so. Draw a one millimeter square on your handkerchief cortex, and it would contain around 100,000 neurons. It has been estimated that the typical human cortex contains some 30 billion total neurons. If we make the conservative guess that each neuron has 1,000 synapses, that would put the total synaptic connections in your cortex at 30 trillion — a number so large that it is literally beyond our ability to comprehend. And apparently enough to store all the memories of a lifetime.

In the theater of your mind, imagine a stretched-out handkerchief lying in front of you. It is… you. It contains everything about you. Every memory that you have is in there. Your best friend’s voice, the smell of your favorite food, the song you heard on the radio this morning, that feeling you get when your kids tell you they love you is all in there. Your cortex, that little insignificant looking handkerchief in front of you, is reading this article at this very moment.

What an amazing machine; a machine that is made possible with a special type of cell – a cell we call a neuron. In this article, we’re going to explore how a neuron works from an electrical vantage point. That is, how electrical signals move from neuron to neuron and create who we are.

A Basic Neuron

Neuron diagram via Enchanted Learning

Despite the amazing feats a human brain performs, the neuron is comparatively simple when observed by itself. Neurons are living cells, however, and have many of the same complexities as other cells – such as a nucleus, mitochondria, ribosomes, and so on. Each one of these cellular parts could be the subject of an entire book. Its simplicity arises from the basic job it does – which is outputting a voltage when the sum of its inputs reaches a certain threshold, which is roughly 55 mV.

Using the image above, let’s examine the three major components of a neuron.

Soma

The soma is the cell body and contains the nucleus and other components of a typical cell. There are different types of neurons whose differing characteristics come from the soma. Its size can range from 4 to over 100 micrometers.

Dendrites

Dendrites protrude from the soma and act as the inputs of the neuron. A typical neuron will have thousands of dendrites, with each connecting to an axon of another neuron. The connection is called a synapse but is not a physical one. There is a gap between the ends of the dendrite and axon called a synaptic cleft. Information is relayed through the gap via neural transmitters, which are chemicals such as dopamine and serotonin.

Axon

Each neuron has only a single axon that extends from the soma, and acts similar to an electrical wire. Each axon will terminate with terminal fibers, forming synapses with as many as 1,000 other neurons. Axons vary in length and can reach a few meters long. The longest axons in the human body run from the bottom of the foot to the spinal cord.

The basic electrical operation of a neuron is to output a voltage spike from its axon when the sum of its input voltages (via its dendrites) crosses a specific threshold. And since axons are connected to dendrites of other neurons, you end up with this vastly complicated neural network.

Since we’re all a bunch of electronic types here, you might be thinking of these ‘voltage spikes’ as a difference of potential. But that’s not how it works. Not in the brain anyway. Let’s take a closer look at how electricity flows from neuron to neuron.

Action Potentials – The Communication Protocol of the Brain

The axon is covered in a myelin sheet which acts as an insulator. There are small breaks in the sheet along the length of the axon which are named after its discoverer, called Nodes of Ranvier. It’s important to note that these nodes are ion channels. In the spaces just outside and inside of the axon membrane exists a concentration of potassium and sodium ions. The ion channels will open and close, creating a local difference in the concentration of sodium and potassium ions.

Diagram via Washington U.

We all should know that an ion is an atom with a charge. In a resting state, the sodium/potassium ion concentration creates a negative 70 mV difference of potential between the outside and inside of the axon membrane, with there being a higher concentration of sodium ions outside and a higher concentration of potassium ions inside. The soma will create an action potential when -55 mV is reached. When this happens, a sodium ion channel will open. This lets positive sodium ions from outside the axon membrane to leak inside, changing the sodium/potassium ion concentration inside the axon, which in turn changes the difference of potential from -55 mV to around +40 mV. This process in known as depolarization.

Graph via Washington U.

One by one, sodium ion channels open along the entire length of the axon. Each one opens only for a short time, and immediately afterward, potassium ion channels open, allowing positive potassium ions to move from inside the axon membrane to the outside. This changes the concentration of sodium/potassium ions and brings the difference of potential back to its resting place of -70 mV in a process known as repolarization. Fro start to finish, the process takes about five milliseconds to complete. The process causes a 110 mV voltage spike to ride down the length of the entire axon, and is called an action potential. This voltage spike will end up in the soma of another neuron. If that particular neuron gets enough of these spikes, it too will create an action potential. This is the basic process of how electrical patterns propagate throughout the cortex.

The mammalian brain, specifically the cortex, is an incredible machine and capable of far more than even our most powerful computers. Understanding how it works will give us a better insight into building intelligent machines. And now that you know the basic electrical properties of a neuron, you’re in a better position to understand artificial neural networks.

Sources

Action Potential in Neurons, via Youtube

On Intelligence, by Jeff Hawkins, ISDN 978-0805078534

Get into Biohacking on the Cheap with this Electrophoresis Rig

If you want to get into electronics, it’s pretty straightforward: read up a little, buy a breadboard and some parts, and go to town. Getting into molecular biology as a hobby, however, presents some challenges. The knowledge is all out there, true, but finding the equipment can be a problem, and what’s out there tends to be fiendishly expensive.

So many would-be biohackers end up making their own equipment, like this DIY gel electrophoresis rig. Electrophoresis sorts macromolecules like DNA or proteins by size using an electric field. For DNA, a slab of agarose gel is immersed in a buffer solution and a current through the tank moves the DNA through the gel. The shorter the DNA fragment, the easier it can wiggle through the pores in the gel, and the faster it migrates down the gel. [abizar]’s first attempt at a DIY gel rig involved a lot of plastic cutting and solvent welding, so he simplified the process by using the little plastic drawers from an old parts cabinet. With nichrome and platinum wires for electrodes for the modified ATX power supply, it’s just the right size and shape for the gel, which is cast in a separate mold. The video below shows the whole build, and while [abizar] doesn’t offer much detail on recipes or techniques, there are plenty of videos online to guide you.

Need more apparatus to deck out your lab? We’ve got you covered there too.

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Microfluidic LEGO Bricks

Years ago, prototyping microfluidic systems was a long, time-intensive task. With inspiration from DIY PCB fabrication techniques, that time is now greatly reduced. However, even with the improvements, it still takes a full day to go from an idea to a tangible implementation. However, progress creeps in this petty pace from day to day, and in accordance, a group of researchers have found a way to use 3D printed molds to create microfluidic LEGO bricks that make microfluidic prototyping child’s play.

For the uninitiated, microfluidics is the study and manipulation of very small volumes of water, usually a millionth of a liter and smaller (nL-pL). Interestingly, the behavior of fluids at small scales differs greatly from its larger scale brethren in many key ways. This difference is due to the larger role surface tension, energy dissipation, and fluidic resistance play when distances and volumes are minimized.

By using 3D printed molds to create microfluidic bricks that fit together like LEGOs, the researchers hope to facilitate medical research. Even though much research relies on precise manipulation of minuscule amounts of liquid, most researchers pipette by hand (or occasionally by robot), introducing a high level of human error. Additionally, rather than needing multiple expensive micropipettes, a DIY biohacker only needs PDMS (a silicon-based chemical already used microfluidics) and 3D printed molds to get started in prototyping biological circuits. However, if you prefer a more, ahem, fluid solution, we’ve got you covered.

[via Adafruit]

Growing Plants on Mars… on Earth

One of the biggest challenges of traveling to Mars is that it’s far away. That might seem obvious, but that comes with its own set of problems when compared to traveling to something relatively close like the Moon. The core issue is weight, and this becomes a big deal when you have to feed several astronauts for months or years. If food could be grown on Mars, however, this would make the trip easier to make. This is exactly the problem that [Clinton] is working on with his Martian terrarium, or “marsarium”.

The first task was to obtain some soil that would be a good analog of Martian soil. Obtaining the real thing was out of the question, as was getting similar dirt from Hawaii. [Clinton] decided to make his own by mixing various compounds from the hardware store in the appropriate amounts. From there he turned to creating the enclosure and filling it with the appropriate atmosphere. Various gas canisters controlled by gas solenoid valves mixed up the analog to Martian atmosphere: 96% dioxide, 2% argon, and 2% nitrogen. The entire experiment was controlled by an Intel Edison with custom circuits for all of the sensors and regulating equipment. Check out the appropriately dramatic video of the process after the break.

While the fern that [Clinton] planted did survive the 30-day experiment in the marsarium, it wasn’t doing too well. There’s an apparent lack of nitrogen in Martian soil which is crucial for plants to survive. Normally this is accomplished when another life form “fixes” nitrogen to the soil, but Mars probably doesn’t have any of that. Future experiments would need something that could do this for the other plants, but [Clinton] notes that he’ll need a larger marsarium for that. And, if you’re not interested in plants or Mars, there are some other interesting ramifications of nitrogen-fixing as well.

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Living High-Altitude Balloon

High-altitude balloons are used to perform experiments in “near space” at 60,000-120,000 ft. (18000-36000m). However, conditions at such altitude are not particularly friendly and balloons have to compete with ultraviolet radiation, bad weather and the troubles of long distance communication. The trick is to send up a live entity to make repairs as needed. A group of students from Stanford University and Brown University repurposed nature in their solution. Enter Bioballoon: a living high-altitude research balloon.

Instead of using inorganic materials, the Stanford-Brown International Genetically Engineered Machine (iGEM) team designed microbes that grow the components required to build various tools and structures with the hope of making sustained space research feasible. Being made of living material, Bioballoon can be grown and re-grown with the same bacteria, lowering the cost of manufacturing and improving repeatability.

Bioballoon is engineered to be modular, with different strains of bacteria satisfying different requirements. One strain of bacteria has been modified to produce hydrogen in order to inflate the balloon while the balloon itself is made of a natural Kevlar-latex mix created by other cells. Additionally, the team is using Melanin, the molecule responsible for skin color and our personal UV protection to introduce native UV resistance into the balloon’s structure. And, while the team won’t be deploying a glider, they’ve designed biological thermometers and small molecule sensors that can be grown on the balloon’s surface. They don’t have any logging functionality yet, but these cellular hacks could amalgamate as a novel scientific instrument: cheap, light and durable.

Living things too organic for your taste? Don’t worry, we’ve got some balloons that won’t grow on you.

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Microfluidics “Frogger” is a Game Changer for DIY Biology

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See those blue and green dots in the GIF? Those aren’t pixels on an LCD display. Those are actual drops of liquid moving across a special PCB. The fact that the droplets are being manipulated to play a microfluidics game of “Frogger” only makes OpenDrop v 2.0 even cooler.

Lab biology is mainly an exercise in liquid handling – transferring a little of solution X into some of solution Y with a pipette. Manual pipetting is tedious, error prone, and very low throughput, but automated liquid handling workstations run into the hundreds of thousands of dollars. This makes [Urs Gaudenz]’s “OpenDrop” microfluidics project a potential game changer for the nascent biohacking movement by offering cheap and easy desktop liquid handling.

Details are scarce on the OpenDrop website as to exactly how this works, but diving into the literature cited reveals that the pads on the PCB are driven to high voltages to attract the droplets. The PCB itself is covered with a hydrophobic film – Saran wrap that has been treated with either peanut oil or Rain-X. Moving the droplets is a simple matter of controlling which pads are charged. Splitting drops is possible, as is combining them – witness the “frog” getting run over by the blue car.

There is a lot of cool work being done in microfluidics, and we’re looking forward to see what comes out of this open effort. We’ve covered other open source efforts in microfluidics before, but this one seems so approachable that it’s sure to capture someone’s imagination.

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Open Microfluidics Instrumentation Playset

Micro-what? Microfluidics! It’s the field of dealing with tiny, tiny bits of fluids, and there are some very interesting applications in engineering, biology, and chemistry. [Martin Fischlechner], [Jonathan West], and [Klaus-Peter Zauner] are academic scientists who were working on microfluidics and made their own apparatus, initially because money was tight. Now they’ve stuck to the DIY approach because they can get custom machinery that simply doesn’t exist.

In addition to their collaboration, and to spread the ideas to other labs, they formed DropletKitchen to help advance the state of the art. And you, budding DIY biohacker, can reap the rewards.

In particular, the group is focused on droplet microfluidics. Keeping a biological or chemical reaction confined to its own tiny droplet is like running it inside its own test-tube, but because of the high rate at which the droplets can be pumped out, literally millions of these test-tubes are available. Want to grow hundreds of thousands of single cells, each in their own environment? Done.

The DropletKitchen kit includes an accurate pump system, along with high-speed camera and flash setups to verify that everything’s working as it should. Everything is open-source, and a lot of it is 3D-printable and written in OpenSCAD so that it’s even easy to modify to fit your exact needs. You just need to bring the science.

This is a professional-grade open source project, and we’re excited to see it when academics take a turn toward the open. Bringing cutting edge processing technologies within reach of the biohacker community is a huge multiplier. We can’t wait to see what comes out of this.