Bacteria can be used to engineer genetic modifications, thereby providing scientists with a tool to combat many challenges in areas from food production to drug discovery. However, this sophisticated technology can also be used maliciously, raising the threat of engineered pathogens. New research published in the online open access journal Genome Biology shows that computational tools could become a vital resource for detecting rogue genetically engineered bacteria in environmental samples.
Jonathan Allen, Shea Gardner and Tom Slezak of the Lawrence Livermore National Laboratory in California, US, designed new computational tools that identify a set of DNA markers that can distinguish between artificial vector sequences and natural DNA sequences. Natural plasmids and artificial vector sequences have much in common, but these new tools show the potential to achieve high sensitivity and specificity, even when detecting previously unsequenced vectors in microarray-based bioassays.
A new computational genomics tool was developed to compare all available sequenced artificial vectors with available natural sequences, including plasmids and chromosomes, from bacteria and viruses. The tool clusters the artificial vector sequences into different subgroups based on shared sequence; these shared sequences were then compared with the natural plasmid and chromosomal sequence information so as to find regions that are unique to the artificial vectors. Nearly all the artificial vector sequences had one or more unique regions. Short stretches of these unique regions are termed ‘candidate DNA signatures’ and can be used as probes for detecting an artificial vector sequence in the presence of natural sequences using a microarray. Further tests showed that subgroups of candidate DNA signatures are far more likely to match unseen artificial than natural sequences.
The authors say that the next step is to see whether a bioassay design using DNA signatures on microarrays can spot genetically modified DNA in a sample containing a mixture of natural and modified bacteria. The scientific community will need to cooperate with computational experts to sequence and track available vector sequences if DNA signatures are to be used successfully to support detection and deterrence against malicious genetic engineering applications. Scientists would be able to maintain an expanding database of DNA signatures to track all sequenced vectors.
“As with any attempt to counter malicious use of technology, detecting genetic engineering in microbes will be an immense challenge that requires many different tools and continual effort,” says Allen.
Source: BioMed Central
Related stories:
Algorithm finds the network -- for genes or the Internet
Human diseases and social networks seem to have little in common. However, at the crux of these two lies a network, communities within the network, and farther even, substructures of the communities. In a recent paper in
Physical Review E 77:016104 (2008), Weixiong Zhang, Ph.D., Washington University associate professor of computer science and engineering and of genetics, along with his Ph.D. student, Jianhua Ruan, published an algorithm (a recipe of computer instructions) to automatically identify communities and their subtle structures in various networks.
'Telepathic' genes recognize similarities in each other
Genes have the ability to recognise similarities in each other from a distance, without any proteins or other biological molecules aiding the process, according to new research published this week in the
Journal of Physical Chemistry B. This discovery could explain how similar genes find each other and group together in order to perform key processes involved in the evolution of species.
Scientists map imprinted genes in human genome
Scientists at Duke University have created the first map of imprinted genes throughout the human genome, and they say a modern-day Rosetta stone – a form of artificial intelligence called machine learning – was the key to their success.
Scientists compare 12 fruit fly genomes
In one of the first large-scale comparisons of multiple animal genomes, scientists at the Broad Institute of MIT and Harvard, the Computer Science and Artificial Intelligence Laboratory (CSAIL) at MIT, and many collaborating institutions, have analyzed the genomes of twelve species of the fruit fly Drosophila to reveal insights on the evolution of genes and genomes and to discern the functional elements encoded in animal DNA.
Transgenics transformed
A new method of constructing artificial plant chromosomes from small rings of naturally occurring plant DNA can be used to transport multiple genes at once into embryonic plants where they are expressed, duplicated as plant cells divide, and passed on to the next generation -- a long-term goal for those interested in improving agricultural productivity.
New method of selecting DNA for resequencing accelerates discovery of subtle DNA variations
A new technology developed by scientists at Emory University will allow researchers to more easily discover subtle and overlooked genetic variations that may have serious consequences for health and disease. Called Microarray-based Genomic Selection (MGS), the research protocol allows scientists to extract and enrich specific large-sized DNA regions, then compare genetic variation among individuals using DNA resequencing methods.
Disease-free mosquito bred to disease-carrier can have all disease-free progeny
A decade ago, scientists announced the ability to introduce foreign genes into the mosquito genome. A year ago, scientists announced the successful use of an artificial gene that prevented a virus from replicating within mosquitoes. But how does one apply what can be done with a small number of mosquitoes in a lab to the tens of millions of mosquitoes that spread disease worldwide?
Biologists unravel the genetic secrets of black widow spider silk
Biologists at the University of California, Riverside have identified the genes, and determined the DNA sequences, for two key proteins in the “dragline silk” of the black widow spider – an advance that may lead to a variety of new materials for industrial, medical and military uses.