Bacteria Become 'Genomic Tape Recorders.

MIT engineers have transformed the genome of E. coli into a long-term storage device for memory. They envision that this stable, erasable, and easy-to-retrieve memory will be well suited for applications such as sensor for environmental and medical monitoring. The methods used in this study require a large number of genetic regulatory elements, limiting the amount of information that can be stored. Earl methods were also limited to digital memory; they can record all or nothing memories. Lu, an associate professor of engineering and computer science and biological engineering, with a graduate student (Fahim Farzadfard) set out to create a system for storing analog memory, which can reveal how much exposure there was, of how long it lasted. To achieve this method, they designed a “genomic tape recorder” that lets them write new information into any bacterial DNA sequence. 

The MIT researchers engineered cells to produce a recombinase enzyme that can insert DNA or a specific sequence of single-stranded DNA into a target site to program E. coli bacteria to store memory. However, this DNA is produced only when activated by a predetermined molecule or another type of input. Once DNA is produced, the recominase will insert the DNA into the cell’s genome at a specific preprogrammed site. The memory will be stored for the lifetime of the bacterial population and is passed on from generation to generation once an exposure is recorded.

In the MIT study, researchers either inserted DNA into a nonfunctional part of the genome, sequencing the genome will reveal whether the memory is stored in a particular cell or targeted the sequences to change a gene where the new DNA sequence turned on an antibiotic resistance gene, allowing the MIT researchers to determine how many cells had gotten the memory sequence by adding antibiotics to the cells and observing how many survived. The MIT researchers also measured the proportion of cells in the population that have the new DNA sequence, researchers can determine how much exposure there was and how long it lasted by using a system to detect light, a lactose metabolite called IPTG, and an antibiotic derivative called aTc. This could be tailored to many other molecules or even signals produced by the cell.

The information can also be erased by stimulating the cells to incorporate a different piece of DNA in the same spot. This process was currently deemed no very efficient, but MIT researchers are working to improve this.

Environmental applications for this research include monitoring the ocean for carbon dioxide levels, acidity, or pollutants. Also, the bacteria could potentially be designed to live in human digestive tract to monitor dietary intake or detect inflammation for irritable bowel disease. These engineered bacteria could also be used as biological computers which could be particularly useful in types of computation that require a lot of parallel processing.

Another possible application is engineering brain cells of living animals or human cells grown in a petri dish to allow researchers to track whether a certain disease marker is expressed or whether a neuron is active at a certain time.

This study is innovating and due to billions of bacteria in a test tube, the scientists can start leveraging more of the bacteria population for memory storage and for computing. The only down fall to this study is that it has the potential to be slow but it would also have the potential to be energy efficient.



Article: http://www.sciencedaily.com/releases/2014/11/141113142006.htm