Human Genome Contaminated With Mycoplasma DNA 123
KentuckyFC writes "The published human genome is contaminated with DNA sequences from mycoplasma bacteria, according to bioinformatics researchers who blame an epidemic of mycoplasma contamination in molecular biology labs around the world. The researchers say they've also found mycoplasma DNA in two commercially available human DNA chips made by biotech companies for measuring levels of human gene expression. So anybody using these chips to measure human gene expression is also unknowingly measuring mycoplasma gene expression too. The mycoplasma genes are clearly successful in reproducing themselves in silico raising the possibility that we're seeing the beginnings of an entirely new kind of landscape of infection. One option to combat this kind of virtual infection is to protect databases with the genomic version of antivirus software, a kind of virtual immune system. But this in itself could make things worse by triggering an evolutionary arms race that selects genes most capable of beating the safeguards."
Data vs executable (Score:5, Insightful)
But this in itself could make things worse by triggering an evolutionary arms race that selects genes most capable of beating the safeguards.
Why is the word "evolutionary" used here? We're talking about static data that is not "executed" - it does not reproduce, it is only copied verbatim. Invalid data that bypasses filters ("antivirus software") is simply that - corrupt, invalid data that does not belong, but at least there will be less of it after filtering. That doesn't make the data somehow more powerful or adaptive - the filter merely missed it. The key fact is the data does not get to modify itself in an iterative fashion in order to survive or improve.
Is the submitter brain fryed ? (Score:5, Insightful)
that part is nonsensical:
The mycoplasma genes are clearly successful in reproducing themselves in silico raising the possibility that we're seeing the beginnings of an entirely new kind of landscape of infection. One option to combat this kind of virtual infection is to protect databases with the genomic version of antivirus software, a kind of virtual immune system. But this in itself could make things worse by triggering an evolutionary arms race that selects genes most capable of beating the safeguards.
static data don't evolve
No feedback mechanism (Score:4, Insightful)
How in the world will setting filters on a database put a bacteria in a lab half way around the world at an evolutionary disadvantage? The bacteria will still grow, contaminate the sample, and get sequenced, but the sequence will be rejected. There is no feedback mechanism here, no selective pressure.
Genome sequence assembly is pretty far removed from the milieu in which a bacteria must make it's way. And inadvertently including bacterial sequences on a gene expression chip is sloppy science, but hardly news.
Traditional computer viruses are the only things that truly 'reproduce' in silico. Memes are your next best option, but the 'net is just a carrier - they have to infect a human host to reproduce. Stay away from 4chan if you want to avoid infection...
But bacteria? In silico? Where are we going with this strained analogy, anyway?
Summary is contaminated with random science jargon (Score:5, Insightful)
As a career microbiologist and bioinformatics geek, the complete and utter scientific inaccuracy of this summary made me want to cry.
The mycoplasma genes are clearly successful in reproducing themselves in silico raising the possibility that we're seeing the beginnings of an entirely new kind of landscape of infection. One option to combat this kind of virtual infection is to protect databases with the genomic version of antivirus software, a kind of virtual immune system. But this in itself could make things worse by triggering an evolutionary arms race that selects genes most capable of beating the safeguards
Mycoplasma is a common contaminant of many human cell culture lines. It is often present in low counts, and is a relatively slow growing organism. This is a problem, because many of the immortal cell lines are passed serially, meaning that the mycoplasma propagates right along with it. Most labs that perform cell culture now do routine PCR testing for mycoplasma markers as a quality control measure.
When it comes to sequencing, and in particular, high-throughput next generation sequencing (Illumina/454/SOLiD/PacBio/whatever), you are shotgun sequencing all of the DNA in a given sample extract. This means that if you had a bunch of human cells, that happenned to be contaminated with low counts of mycoplasma, those mycoplasma sequences would be present to some extent in your final sequencing project. Whether this would factor into the final assembly, or just get thrown out depends on the quality control, experience of the bioinformatics team and assembly software pipeline. I am willing to be that most issues with mycoplasma contamination were during the "formative" years of high-throughput sequencing, but may have lingered in databases. These databases would in turn might used by commercial companies that build microarrays or other high-density tools, so it's feasible that some mycoplasma sequence carried over.
Is this relevant? Probably not. On a microarray, it would most likely be wasted space (eg: always negative during gene expression studies... unless the patient had a mycoplasma infection or something). Furthermore, a simple analysis of the sequence would help to rule out sequences that were clearly prokaryotic.
"In silico" does not mean what you think it means. In fact, this whole bit about in-silico replication and arms races is complete and utter nonsense. In-silico biology usually refers to biocomputing. Eg: analyzing, manipulating and simulating gene/protein sequences, expression, signalling cascades, and the like on a computer system. It does not apply to mycoplasma sequences running around all nambly pambly causing infections that would require some sort of anti-virus software. What they might be alluding to is the fact that a lot of shotgun sequencing libraries are run, as needed, through a vector screen, which is designed to pull out irrelevant sequences that may have been necessarily introduced during cloning or sequencing. Plasmids, cosmids, whatever. These algorithms may need better tuning to do a better job of ruling out mycoplasma in human sequences, but there's no danger of these mycoplasma sequencing replicating and taking over the world.
Unless you happen to be William Gibson.