Wiring the Brain: How Viruses Can Be Engineered to Trace Neural Connections

The fact that the rabies virus can spread from an infected neuron to other neurons connected to it makes it an almost perfect vector for tracing connections in the brain.

Dr. Kevin Mitchell is a geneticist who studies neural development. In this guest post, he explains how viruses can be used to map connections in the brain.

What's the Big Idea?

It is hard to overstate the complexity of the brain. Not only are there tens of billions of individual nerve cells, or neurons, which make literally trillions ofconnections between each other. The complexity really lies in the fact that there are hundreds or maybe even thousands of different types of neurons, which are arranged in highly-organised patterns, and which connect to each other in very specific ways. Now, a new technique is emerging that enables neuroscientists to trace these kinds of connections by enlisting help from an unlikely source – viruses.

To understand why this approach is so exciting, we need to consider the scope of the problem it can help solve. This begins with individual neurons themselves. Neurons are polarised – they have an end for inputs and an end for outputs. Each of these may be branched to give thousands of independent sites of input and output. For any given neuron, there are other neurons that connect to it (information flows from all those neurons into our subject neuron) and other neurons that it connects to (information flows from our subject neuron out to all these neurons).

But neurons are not all the same. The most obvious and perhaps most important difference between neurons is that some are excitatory and some inhibitory. When an excitatory neuron is activated, it releases neurotransmitter at the connections it makes with its output neurons – this neurotransmitter tends to make those other cells electrically active. The exact opposite happens when an inhibitory cell is activated – it releases a different neurotransmitter onto its target neurons, which makes them less electrically active.

Neurons That Fire Together Wire Together

At any given moment, each single neuron is integrating the incoming information from typically hundreds of excitatory and inhibitory neurons – the balance between these and their precise timing will determine whether it becomes active enough to “fire” a signal to its own output neurons. (Without the inhibitory neurons, any electrical activity would rapidly spread through the entire brain in an epileptic-like firestorm).

There are hundreds of subtypes of excitatory and inhibitory neurons, all with different jobs to do. The way in which these different cell types are interconnected determines the functional properties of each little microcircuit in the brain – the type of information that comes into the system, how it filters and transforms that information, how long a neuron will be active before it's shut off, whether it will fire with a rhythm and at what frequency, etc.

These parameters determine the computations that the circuit can perform. While some of the details of such microcircuits have been worked out, for the most part we remain unblissfully ignorant of this crucial information. But we cannot hope to understand how the brain functions without knowing how the basic units of computation are put together.

How to solve this problem? In looking for ways to map the connections of neurons, scientists are turning to viruses – in particular, those that have evolved to infect neurons and to spread from one to another through the synaptic connections between them. One of these is the deadly rabies virus – a specialist in infecting neurons.

Neural connections in the brain

Rabies is typically transmitted from one infected animal to another through saliva, often via a bite, which releases viral particles that infect peripheral neurons. From there, it spreads backwards into the spinal cord and brain, passing from the initially infected neurons into every neuron that connects to them. This continues in the next neurons, resulting in the rapid spread of infection throughout the enture nervous system. This has a striking effect onthe host – among other symptoms, increasing aggression and attack behaviors, along with salivation, resulting in spread to a new host.

The fact that the virus can spread from an infected neuron to other neuronsconnected to it makes it an almost perfect vector for tracing these connections in the brains of experimental animals. To make it perfect required some modifications.

Modifying the Virus

First, using the tools of molecular biology, researchers have modified the genomeof the rabies virus, so that, as well as its own genes, the virus now carries so-called marker proteins, like the well-known green fluorescent protein from jellyfish. When ultraviolet light is shone on this protein, it fluoresces, giving off avivid green light. Neurons infected with the virus (either directly or via synaptic connections) can thus be beautifully visualised.

A major problem, however, is the rabies virus is too efficient – it continues to spread to all the neurons connected to each of the neurons connected to the first neuron, obscuring the pattern we are interested in. To get around this, the virus had to be crippled by removing one of the genes it needs to spread.

The sequence of the rabies virus genome - which is made from RNA, not DNA - encodes five proteins that are essential for the virus to replicate and be transmitted from one cell to another. When a rabies virus infects a neuron, it starts to express these proteins and replicate its genome. These replicates are packaged into a viral particle, which includes an envelope of host cell membrane studded with viral proteins.

One of these is the rabies glycoprotein, encoded by the G gene. This protein is essential for the viral particle to infect another neuron – it accomplishes this by binding to receptor proteins on the surface ofthese neurons, which leads to it being sucked into the cell (tricksy!).

A Solution: Delete the Genes

Even more tricksy is how scientists have taken advantage of this system to control which cells can be infected and to limit the spread of virus to only one synapse. This involves modifying both the virus and the cells of the host animal (usually a transgenic mouse). First, the G gene can be deleted from the viral genome – these viral particles can infect neurons when the virus is grown ina dish with the G protein added. But after they infect one neuron they cannotspread to others because they can’t make more G protein. The trick is to makethe infected host cell supply that protein – this can be achieved by adding DNA encoding this protein directly into a single cell.

When that single cell is infected, it leads to replication of the virus and transfer to only those cells with directinputs on the primary neuron. Scientists can thus visualise all the inputs ontoa single neuron, and painstakingly reconstruct the connectivity of an entiremicrocircuit.

What's the Significance?

Since the development of these techniques there have been a whole range of further modifications, allowing infection of specific cell types, the tracing of connections in the other direction (to all the output neurons) using different viruses, and the transfer of other cargo proteins to allow all kinds of additional analyses of the functions of these microcircuits.

In combination with tremendous advances in microscopy, these approaches are leading to a resurgence of “descriptive” neuroanatomy – just the kinds of studies that fueled the insights of pioneering neuroscientists like Ramon y Cajal 100 years ago. 

Those insights derived from the application of new technologies forvisualising single neurons. These new techniques take us the next step to see themicrocircuits that make up the computational units of the brain.

A still from the film "We Became Fragments" by Luisa Conlon , Lacy Roberts and Hanna Miller, part of the Global Oneness Project library.

Photo: Luisa Conlon , Lacy Roberts and Hanna Miller / Global Oneness Project
Sponsored by Charles Koch Foundation
  • Stories are at the heart of learning, writes Cleary Vaughan-Lee, Executive Director for the Global Oneness Project. They have always challenged us to think beyond ourselves, expanding our experience and revealing deep truths.
  • Vaughan-Lee explains 6 ways that storytelling can foster empathy and deliver powerful learning experiences.
  • Global Oneness Project is a free library of stories—containing short documentaries, photo essays, and essays—that each contain a companion lesson plan and learning activities for students so they can expand their experience of the world.
Keep reading Show less

Four philosophers who realized they were completely wrong about things

Philosophers like to present their works as if everything before it was wrong. Sometimes, they even say they have ended the need for more philosophy. So, what happens when somebody realizes they were mistaken?

Sartre and Wittgenstein realize they were mistaken. (Getty Images)
Culture & Religion

Sometimes philosophers are wrong and admitting that you could be wrong is a big part of being a real philosopher. While most philosophers make minor adjustments to their arguments to correct for mistakes, others make large shifts in their thinking. Here, we have four philosophers who went back on what they said earlier in often radical ways. 

Keep reading Show less

The history of using the Insurrection Act against Americans

Numerous U.S. Presidents invoked the Insurrection Act to to quell race and labor riots.

The army during riots in Washington, DC, after the assassination of civil rights activist Martin Luther King Jr., April 1968.

Photo by Michael Ochs Archives/Getty Images
Politics & Current Affairs
  • U.S. Presidents have invoked the Insurrection Act on numerous occasions.
  • The controversial law gives the President some power to bring in troops to police the American people.
  • The Act has been used mainly to restore order following race and labor riots.
Keep reading Show less

Experts are already predicting an 'active' 2020 hurricane season

It looks like a busy hurricane season ahead. Probably.

Image source: Shashank Sahay/unsplash
Surprising Science
  • Before the hurricane season even started in 2020, Arthur and Bertha had already blown through, and Cristobal may be brewing right now.
  • Weather forecasters see signs of a rough season ahead, with just a couple of reasons why maybe not.
  • Where's an El Niño when you need one?

Welcome to Hurricane Season 2020. 2020, of course, scoffs at this calendric event much as it has everything else that's normal — meteorologists have already used up the year's A and B storm names before we even got here. And while early storms don't necessarily mean a bruising season ahead, forecasters expect an active season this year. Maybe storms will blow away the murder hornets and 13-year locusts we had planned.

NOAA expects a busy season

According to NOAA's Climate Prediction Center, an agency of the National Weather Service, there's a 60 percent chance that we're embarking upon a season with more storms than normal. There does, however, remain a 30 percent it'll be normal. Better than usual? Unlikely: Just a 10 percent chance.

Where a normal hurricane season has an average of 12 named storms, 6 of which become hurricanes and 3 of which are major hurricanes, the Climate Prediction Center reckons we're on track for 13 to 29 storms, 6 to 10 of which will become hurricanes, and 3 to 6 of these will be category 3, 4, or 5, packing winds of 111 mph or higher.

What has forecasters concerned are two factors in particular.

This year's El Niño ("Little Boy") looks to be more of a La Niña ("Little Girl"). The two conditions are part of what's called the El Niño-Southern Oscillation (ENSO) cycle, which describes temperature fluctuations between the ocean and atmosphere in the east-central Equatorial Pacific. With an El Niño, waters in the Pacific are unusually warm, whereas a La Niña means unusually cool waters. NOAA says that an El Niño can suppress hurricane formation in the Atlantic, and this year that mitigating effect is unlikely to be present.

Second, current conditions in the Atlantic and Caribbean suggest a fertile hurricane environment:

  • The ocean there is warmer than usual.
  • There's reduced vertical wind shear.
  • Atlantic tropical trade winds are weak.
  • There have been strong West African monsoons this year.

Here's NOAA's video laying out their forecast:

But wait.

ArsTechnica spoke to hurricane scientist Phil Klotzbach, who agrees generally with NOAA, saying, "All in all, signs are certainly pointing towards an active season." Still, he notes a couple of signals that contradict that worrying outlook.

First off, Klotzbach notes that the surest sign of a rough hurricane season is when its earliest storms form in the deep tropics south of 25°N and east of the Lesser Antilles. "When you get storm formations here prior to June 1, it's typically a harbinger of an extremely active season." Fortunately, this year's hurricanes Arthur and Bertha, as well as the maybe-imminent Cristobal, formed outside this region. So there's that.

Second, Klotzbach notes that the correlation between early storm activity and a season's number of storms and intensities, is actually slightly negative. So while statistical connections aren't strongly predictive, there's at least some reason to think these early storms may augur an easy season ahead.

Image source: NOAA

Batten down the hatches early

If 2020's taught us anything, it's how to juggle multiple crises at once, and layering an active hurricane season on top of SARS-CoV-2 — not to mention everything else — poses a special challenge. Warns Treasury Secretary Wilbur Ross, "As Americans focus their attention on a safe and healthy reopening of our country, it remains critically important that we also remember to make the necessary preparations for the upcoming hurricane season." If, as many medical experts expect, we're forced back into quarantine by additional coronavirus waves, the oceanic waves slamming against our shores will best be met by storm preparations put in place in a less last-minute fashion than usual.

Ross adds, "Just as in years past, NOAA experts will stay ahead of developing hurricanes and tropical storms and provide the forecasts and warnings we depend on to stay safe."

Let's hope this, at least, can be counted on in this crazy year.

Scroll down to load more…