By Kevin Kang

A recent article in ScienceDaily reviews a new approach in Synthetic Biology that allows cells to respond to a series of input stimuli and simultaneously remember the order of these stimuli over many generations. As noted by the senior investigator, Timothy Lu from MIT, combining computation with memory creates complex cellular circuits that can perform logic functions and store memories of events by encoding them in their DNA (1,2). In their current work, Dr. Lu and his colleagues created cells that can remember and respond to three different inputs, including chemical signals in a particular order, and in the future may be able to incorporate even more inputs (1,2,3). The cellular machines thus created are referred to as biological “state machines” because they exist in different states depending on the identity and order of inputs that they receive. The state machines rely on enzymes called recombinases. When activated by a specific input, recombinases either delete or invert a particular segment of DNA depending on the orientation of two DNA target sequences known as recognition sites. The segment of DNA between these sites may have recognition sites for other recombinases that respond to different inputs. Flipping or deleting these sites permanently changes what will happen if a second or third recombinase is later activated. Therefore, a cell’s history is determined by sequencing its DNA. In a version of this system with just two inputs, there are five possible states for this circuit: states corresponding to no input, input A alone, input B alone, A followed by B, and B followed by A. Dr. Lu’s team in MIT has designed and built circuits that record up to three inputs, in which sixteen states are possible (1,2).

Besides creating circuits that record events in a cell’s life and then transmit these memories to future generations, the researchers from MIT also placed genes into the array of recombinase binding sites along with genetic regulatory elements. In these circuits, when recombinases rearrange the DNA, the circuits record the information as well as control which genes get turned on and off. Lu’s lab tested this work in bacteria by color coding the identity and order of input stimuli, so input A followed by B would would lead to bacteria fluorescing red and green, but input B followed by A would lead to red and blue fluorescence. Hence, these techniques can be used not only to record the states that the cells experience over time, but also to deploy in state-dependent gene expression programs (1,2).

Researchers have used CRISPR—a revolutionary new genetic engineering technique—to convert cells isolated from mouse connective tissue directly into neuronal cells.

In 2006, Shinya Yamanaka, a professor at the Institute for Frontier Medical Sciences at Kyoto University at the time, discovered how to revert adult connective tissue cells, called fibroblasts, back into immature stem cells that could differentiate into any cell type. These so-called induced pluripotent stem cells won Yamanaka the Nobel Prize in medicine just six years later for their promise in research and medicine.

Since then, researchers have discovered other ways to convert cells between different types. This is mostly done by introducing many extra copies of “master switch” genes that produce proteins that turn on entire genetic networks responsible for producing a particular cell type.

Controlling the minds of others from a distance has long been a favourite science fiction theme – but recent advances in genetics and neuroscience suggest that we might soon have that power for real. Just over a decade ago, the bioengineer Karl Deisseroth and his colleagues at Stanford University published their paper on the optical control of the brain – now known as optogenetics – in which the firing pattern of neurons is controlled by light. To create the system, they retrofitted neurons in mouse brains with genes for a biomolecule called channelrhodopsin, found in algae. Channelrhodopsin uses energy from light to open pathways so that charged ions can flow into cells. The charged ions can alter the electrical activity of neurons, influencing the animal’s behaviour along the way.

Soon researchers were using implants to guide light to channelrhodopsin in specific neurons in the brains of those mice, eliciting behaviour on demand. At the University of California the team of Anatol Kreitzer worked with Deisseroth to disrupt movement, mimicking Parkinson’s disease and even restoring normal movement in a Parkinsonian mouse. Deisseroth and his colleague Luis de Lecea later demonstrated that it was possible to wake up mice by activating a group of neurons in the brain that control arousal and sleep.

But optogenetics has been challenging. Since light does not easily penetrate dense fatty brain tissue, researchers must implant a fibre-optic cable to bring light into the brain. This limitation led to the development of another, less intrusive technique known as DREADD (designer receptors exclusively activated by designer drugs). In this case, a receptor normally activated by the neurotransmitter acetylcholine is modified to respond to a designer drug not normally found in the body. When the designer drug is delivered, neurons can be manipulated and behaviour changed over a number of hours. The major drawback here: the slow course of drug administration compared with the rapid changes in brain activity that occur during most tasks.