New Meaning for the Term ‘Computer Bug’

Researchers in the US have created ‘living computers’ by using genetically altered bacteria. The findings of this research demonstrate that computing in living cells is feasible. It also opens the doors to a number of potential applications including data storage and as a tool in manipulating genes for genetic engineering.

The research team was from the biology and mathematics departments of Davidson College, North Carolina and Missouri Western State University, Missouri, USA. They achieved execution of DNA-based computation in living cells by engineering Escherichia coli to address a classic mathematical puzzle called the Burnt Pancake Problem (BPP).

The BPP is solved by sorting a stack of distinct objects (pancakes) into proper order and orientation using the minimum number of manipulations. The pancakes are of different sizes, each of which has a golden and a burnt side. The largest pancake must be on the bottom and all pancakes golden side up. Each manipulation reverses the order and orientation of one or more adjacent objects in the stack.

A system was designed that uses site-specific DNA recombination to mediate inversions of genetic elements that represent pancakes within plasmid DNA. Inversions (or “flips”) of the DNA fragment pancakes were driven by genes added from the Salmonella typhimurium Hin/hix DNA recombinase system. The system used sorts DNA segments by inversions to produce different permutations of a promoter and a tetracycline resistance coding region; E. coli cells become antibiotic resistant when the segments are properly sorted. The time required to reach the mathematical solution reflects the minimum number of flips needed to solve the burnt pancake problem.

It is believed the system has the potential to be scaled up to larger and more complex problems and by exploiting the infinitesimally tiny scale of DNA and bacteria, ‘living computers’ could carry out complex parallel processing problems that would otherwise utilise very large and expensive electronic computing systems. Since bacteria multiply naturally and have their own repair mechanisms, ‘living computers’ could be less expensive and require less space compared with conventional devices. Additionally, ‘living computers’ could evolve through DNA mutations to solve new problems.

For further reading:
http://www.jbioleng.org/content/pdf/1754-1611-2-8.pdf
http://www.sciencedaily.com/releases/2008/05/080520090551.htm
http://www.itnews.com.au/News/NewsStory.aspx?story=76534

Malcolm Keth (41751819)

Cloned sniffer dogs

The Korea Customs Service reported that seven cloned puppies named Toppy ("Tomorrow's puppy") were born in late 2007 to three surrogate mothers under a state-funded project. Lee Byung-Chun who managed to clone the Toppies played a key role in cloning a three year old Afghan Hound. The cost of cloning the Toppies was approximately 301,205 dollar. Lee Byung-Chun used the nuclei of somatic cells from a sniffer Golden Retriever, Chase, to clone the puppies. The project manager Lim Jae-Yong said that it would be easier to train sniffer cloned dogs than ordinary canines. The Toppies have passed the first round of tests for behavourial patterns and genetic qualities, and they will report for duty in June this year after completing a second round of tests.

Indeed, successful cloning of dogs show that the use of genetics in technology is essential. However, with regards to the issue of cloning humans and other organisms, ethical issues are always involved.

Reference: http://news.yahoo.com/s/afp/20080421/hl_afp/healthskoreacloningdogs_080421171230

Artificial Letters Added to Life's Alphabet

US researchers have created two artificial DNA bases, or 'letters', that can actually be accurately and efficiently replicated by a natural enzyme. Eventually, the researchers say, they may be able to add these two artificial building blocks to the four natural genetic bases that comprise DNA, opening up doors to widely different kinds of genetic engineering.

This unnatural but functioning new base pair is the result of nearly a decade of researcher by chemical biologist Floyd Romesberg, from the Scripps Reseach Institue, California, US.

Romesberg borrowed some tricks from drug development companies and, with the help of graduate student Aaron Leconte, used these to synthesis 3600 potential candidates for the artificial bases to see if they would be treated normally by a polymerase enzyme.Two different methods of screening both turned up the same pair of molecules, called dSICS and dMM02. A minor chemical alteration was made on the dSICS, due to its greater readiness to pair with itself rather than its intended partner, finally making an unnatural base pair, d5SICS and dMM02, that efficiently replicated without the need of an unnatural polymerase.

The molecular pair that worked surprised Romesberg. "We got it and said, 'Wow!' It would have been very difficult to have designed that pair rationally."

In the near future it is expected that these bases will be used to synthesize DNA with new and unnatural properties. These could include highly specific primers for DNA amplification; tags for materials, such as explosives, that could be detected without the risk of contamination from natural DNA; and building novel DNA-based nanomaterials.

Further Readings:
-http://www.newscientist.com/channel/life/genetics/dn13252-artificial-letters-added-to-lifes-alphabet.html

Blog post by Bethany Reid (41807444)