Beta
×

Welcome to the Slashdot Beta site -- learn more here. Use the link in the footer or click here to return to the Classic version of Slashdot.

Thank you!

Before you choose to head back to the Classic look of the site, we'd appreciate it if you share your thoughts on the Beta; your feedback is what drives our ongoing development.

Beta is different and we value you taking the time to try it out. Please take a look at the changes we've made in Beta and  learn more about it. Thanks for reading, and for making the site better!

Human Genome Contaminated With Mycoplasma DNA

timothy posted more than 3 years ago | from the beer-goggles-to-the-nth-degree dept.

Science 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."

cancel ×

123 comments

Sorry! There are no comments related to the filter you selected.

huh??? (0)

Anonymous Coward | more than 3 years ago | (#36545730)

why do i feel like im getting punk'd??

Re:huh??? (0)

Anonymous Coward | more than 3 years ago | (#36545894)

You've been X Punk'd! We were kidding!

Re:huh??? (0)

Anonymous Coward | more than 3 years ago | (#36545896)

I think I speak for us all when I say

"um... what the fuck?"

Intelligent design... (2, Funny)

Anonymous Coward | more than 3 years ago | (#36545732)

...clearly uses DRM.

Re:Intelligent design... (1)

NoNonAlphaCharsHere (2201864) | more than 3 years ago | (#36546028)

There's NOTHING intelligent about DRM.

Re:Intelligent design... (1)

Anonymous Coward | more than 3 years ago | (#36546460)

S'all right, there's nothing intelligent about intelligent design, either.

in silico (1)

taktoa (1995544) | more than 3 years ago | (#36545744)

Haven't heard that one before...

Re:in silico (0)

canajin56 (660655) | more than 3 years ago | (#36545878)

That's because it's stupid.

Re:in silico (0)

Anonymous Coward | more than 3 years ago | (#36546436)

Not as stupid as you.

Re:in silico (0)

Anonymous Coward | more than 3 years ago | (#36546336)

In Silico has been a standard term for a long time now in biology. You do experiments in vitro (literally in glass but often now in plastic using isolated biological components), in vivo (in an organism), so you have to have something to say when you do an experiment computationally. Though I agree with the below about the evolution part being stupid. Replication isn't dependent on the gene arrays so once filtered it's gone.

Re:in silico (4, Informative)

stillnotelf (1476907) | more than 3 years ago | (#36546376)

Experiments done in a cell are in vivo (life); experiments done in a test tube are in vitro (glass); experiments done in a computer are in silico (silicon computer chips). In silico is used to describe computational modeling experiments (think FoldIt or Rosetta@Home), or manipulation and searching of large DNA/RNA/protein sequence databases. You'd expect it to apply to stuff like weather modeling or nuclear physics, but there the analogy to vivo/vitro is lost so I believe those fields don't use the term.

Except... (0)

Anonymous Coward | more than 3 years ago | (#36550402)

Except that glass is made from silicon.

Re:in silico (0)

Anonymous Coward | more than 3 years ago | (#36551310)

In silico experiments are simply simulations of a real paper

Re:in silico (0)

Anonymous Coward | more than 3 years ago | (#36547690)

See an interesting use of the term in "ISC'11 Keynote Simulating the Brain – The Next Decisive Years", for example. Brain simulation in silico, leading to a conclusion that the German researchers think the Terminator is an operating manual.. ;)

Re:in silico (1)

lennier (44736) | more than 3 years ago | (#36547786)

Haven't heard that one before...

Not an Australian [wikipedia.org] then, eh mate?

Wow that's a relief! (0)

Anonymous Coward | more than 3 years ago | (#36545760)

My doctor has been insisting I have a genetic defect because I lack the gene for flagella.

Re:Wow that's a relief! (0)

Anonymous Coward | more than 3 years ago | (#36545902)

This is really unfortunate if you intend to reproduce, as all Eukaryots pass through flagellum stage at a point of the life cycle.

Re:Wow that's a relief! (1)

ColdWetDog (752185) | more than 3 years ago | (#36546036)

This is really unfortunate if you intend to reproduce, as all Eukaryots pass through flagellum stage at a point of the life cycle.

Just exactly where did you go to school? Have you considered trying it again?

A sperm has a flagellum (1)

tepples (727027) | more than 3 years ago | (#36546166)

All humans save three have passed through flagellum stage. Their names were Adam, Eve, and Jesus.

Re:A sperm has a flagellum (0)

Anonymous Coward | more than 3 years ago | (#36546232)

And Spock, the second time.

Oh wait, he was only half-human. I see what you did there.

Re:Wow that's a relief! (1)

bcmm (768152) | more than 3 years ago | (#36546172)

This is Slashdot. You almost certainly have flagella.

Re:Wow that's a relief! (1)

jweller13 (1148823) | more than 3 years ago | (#36546870)

Try self flagellation

And if they could clone humans using this DNA.. (1)

cyberchondriac (456626) | more than 3 years ago | (#36545802)

would they wind up with Swamp Thing?

Re:And if they could clone humans using this DNA.. (2)

lennier (44736) | more than 3 years ago | (#36547806)

Swamp Thing
You make my heart sing
You make everything
Squelchy

Re:And if they could clone humans using this DNA.. (0)

Anonymous Coward | more than 3 years ago | (#36548474)

Swamp Thing I think I love you... But I want to know for sure

That's not good (2)

YodasEvilTwin (2014446) | more than 3 years ago | (#36545810)

I wonder exactly how far medicine has been set back by this. Researchers trying to investigate genetic or genetically-influenced diseases cannot be happy. They've unwittingly been missing information, and treating false information as valid, for a long time.

Re:That's not good (2)

jd (1658) | more than 3 years ago | (#36547080)

That's a good point, as most companies rely on multiple studies to verify if a mutation applies or not. There is no test to see if the studies are using the same hardware, as far as I know, which means that identical results can be a result of identical database errors.

It also creates problems for things like the 1000 Genomes Project. How many of the thousands (they're already well over the 1000 mark) will have to be retested in order to be able to reliably subtract out the contamination?

It's not limited to genetic disease, however. Archaeological DNA results will be of questionable value. How do you know what is actually Neandertal or Denisovian DNA? And with the volume of material being extremely limited (we have one fingerbone for Denisovian DNA and a handful of teeth as the source for Neandertal data), retesting isn't really a serious option. From a scientific perspective, this is the more serious problem as finding people with Parkinson's or with Alzheimer's is easier than finding new Neandertal remains. It'll also be important to subtract out the duplicated errors from the DNA that appears to be in common between species, so all claims of a genetic link between humans and Neandertals (for example) have to be put on hold until the scientists can confirm how much of the contamination is being falsely read as duplication.

Re:That's not good (1)

RDW (41497) | more than 3 years ago | (#36549970)

'I wonder exactly how far medicine has been set back by this.'

No measurable distance. The summary is rather misleading and the arXiv article isn't exactly clear, either. The previous letter they reference (and co-author) is clearer:

http://www.biotechniques.com/BiotechniquesJournal/2009/December/Letter-to-the-editor-Unexpected-presence-of-mycoplasma-probes-on-human-microarrays/biotechniques-181035.html?service=print [biotechniques.com]

Basically a couple of tiny fragments have been found in the public DNA sequence databases that were misclassified as human, presumably because they were derived from cDNA 'libraries' constructed from cells contaminated with mycoplasma. These sequences are NOT part of the reference human genome sequence. They exist only as small independent files supposedly representing fragments of genes expressed in human cells:

http://www.ncbi.nlm.nih.gov/nuccore/af241217 [nih.gov]
http://www.ncbi.nlm.nih.gov/nucest/DA466599 [nih.gov]

but really mapping to mycoplasma sequences. Unfortunately a commercial provider used one of these files in the (semi-automated) design of a microarray. A probe for a sequence like this (one of many thousands on the array) would generally be harmless, since it does not detect a human sequence. Rather embarrasingly, it did appear to give a positive result in some publicly available data sets from researchers who used the array. This suggests that the cells used by these researchers were also contaminated with mycoplasma. So the problem isn't so much an insidious 'in silico' contamination of databases by bug sequences, but rather the actual contamination of cell cultures by mycoplasma, which suggests sloppy lab technique and a lack of routine testing.

Data vs executable (5, Insightful)

Dan East (318230) | more than 3 years ago | (#36545842)

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.

Re:Data vs executable (1)

x6060 (672364) | more than 3 years ago | (#36545900)

Its not that easy though. Bacteria, viruses, and your DNA will accumulate mutations. It can happen on a cell by cell level. Thats some of the cause for some cancers.

Re:Data vs executable (0)

Anonymous Coward | more than 3 years ago | (#36545918)

I agree completely... this is an attempt by the original poster or the article to sound more important than it really is... and advertising or eye-ball enhancing word/phrase. In other words, bogus.

Not that the problem is an issue, just not the kind of issue we're being lead to believe.

Mod Parent Up (1)

Anonymous Coward | more than 3 years ago | (#36545924)

This was my first thought when reading the summary - there is no source of feedback to make the data filtering mechanisms loop into the evolutionary design of the bacteria involved unless - and this incredibly out there - everyone starts applying methods to kill the bacteria only based on the amount of corrupt data they scan in - then *maybe* it would be possible for those bacteria with lesser differences to make their way into the system while the rest die out, but that is incredibly unlikely given their otherwise blind nature to the whole process and the fact it would impose evolutionary constraints in direct contradiction to what makes them able to survive - not absolutely impossible, but detracting from the actual story here with such nonsensical hype would be like suggesting the same evolutionary arms race in the same situation because darth vador were to rise out of the earth's molten core to proclaim dominance over the moon, leaving some new bacteria behind on his way - it doesn't make any fucking sense.

Re:Data vs executable (3, Informative)

Richard Dick Head (803293) | more than 3 years ago | (#36546322)

The topic is not about "vestigial" DNA.

TFA talks about bacteria being mixed in with human samples accidentally, then sequenced. The bacterial DNA shows up with the human DNA, and the bacterial DNA is being documented as human.

Re:Data vs executable (1)

Ruke (857276) | more than 3 years ago | (#36546328)

Exactly; the "fitter," undetected DNA has no opportunity to reproduce and pass on it's trats; we're simply culling members from a static population as they present themselves. You could argue that the population isn't exactly static: new genes are being sequenced and inserted into the database; therefore "fitter" DNA will squirm its way into the databases more frequently. However, we definitely won't be seeing any "evolutionary" arms race - the database entries have no affect on the biological populations of bacteria living in labs, so there is no pressure to be any more or less undetectable.

Re:Data vs executable (1)

Krackbaby (123197) | more than 3 years ago | (#36547092)

Is it really static? You assume researchers aren't going to try to use this raw data to generate any actual end product. I wouldn't make that assumption.

See Craig Venter's latest attempts at synthetic life, "Mycoplasma laboratorium".

Re:Data vs executable (0)

Anonymous Coward | more than 3 years ago | (#36548228)

Let us imagine we take a DNA sample in the lab.

Assume these mycobacteria live on the dna

we have created protocols to eliminate them - but they might try to evolve techniques to bypass our methods and protocols.

here's where it gets to be a stretch, but is reasonable.

we judge the success of our prevention protocols on the levels of corruption or infection of the dna data. so in order to survive and thrive the live mycobacteria must bypass our protocols - one way might be to mask the degree of infection or corruption they create on the data.

maybe they will find that they can mimic a good dna readout on some gene so it looks like you don't have a propensity for cancer!...but you actually do.

Antivirus *and* Antibacterial? (4, Funny)

teebob21 (947095) | more than 3 years ago | (#36545876)

At first I was relieved that this was a bacteria infecting silicon. Now I'm concerned: When will Avast release an Antibacterial beta? I'm still running Windows, folks! I know I'm vulnerable to this!!!

Re:Antivirus *and* Antibacterial? (2)

lennier (44736) | more than 3 years ago | (#36547874)

When will Avast release an Antibacterial beta?

Well, since a computer virus just injects code into an already-existing hardware processor, I guess a computer bacteria would have to carry around its own little itsy-bitsy mini-PC on little ambulatory robot legs, eat power from sockets where they can find it, and reproduce by splitting down the middle into two extra widdle bran-new baby mini-PCs.

Truly an insidious force. They'd infect the entire world through their sheer power of cuteness.

In silico? (0)

Anonymous Coward | more than 3 years ago | (#36545904)

So is this term to be applied both virtually and physically? While it's defined as something via computer simulation, it's also being stated that the mold is physically showing up on the chips. Is this then a concern for labs on a chip, or for that matter, any current fabrication processes? Or did I misinterpret the concept?

Re:In silico? (4, Informative)

NoNonAlphaCharsHere (2201864) | more than 3 years ago | (#36546128)

No, they're not saying that the mold itself is appearing in the chips, just that the mold's DNA is. Therefore, the presence (or absence) of the mold in a sample would skew the results when using these chips. And yes, saying that the DNA appears "in silico" is perfectly valid here - whether you care for the term or not.

Re:In silico? (1)

treeves (963993) | more than 3 years ago | (#36548670)

Bacterium, not mold. Mycoplasma is genus name of this particular bacterium.

No (1)

kilraid (645166) | more than 3 years ago | (#36545910)

No resources are freed for any future generations of database contaminants to breed on by filtering. And, the notion of evolution would also require changes to the contaminants, which don't really happen. So by all means, filter. It will leave harder-to-detect contaminants there, but they won't become more numerous.

Proof title please (1)

Anonymous Coward | more than 3 years ago | (#36545914)

Is the human genome contaminated or is it the published sequence that is contaminated?

If only the latter, fix the title.

Re:Proof title please (4, Interesting)

stillnotelf (1476907) | more than 3 years ago | (#36546392)

The human genome is surely highly contaminated, just not with mycoplasma. Endogenous retroviruses, retrotransposons, repetitive elements galore, on the other hand...

Re:Proof title please (0)

Anonymous Coward | more than 3 years ago | (#36547116)

The difference here is that this contaminant is not actually part of our genome, but has been introduced between sample retrieval and sequencing.

Is the submitter brain fryed ? (4, Insightful)

JonySuede (1908576) | more than 3 years ago | (#36546046)

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

Re:Is the submitter brain fryed ? (-1)

Anonymous Coward | more than 3 years ago | (#36546194)

You don't get it, do you.

This is the case of a gene, that continued to duplicate and spread after translation to information introduction into a memetic system Essentially, an infectious memetic organism that used to be an organic one.

Of COURSE the evolution won't happen in the static data, you twit. The point the author was trying to make: as we keep sequencing genes and turning them into memes, we will naturally select for those extra-organismous sequences that are best adapted to replicating in our databases.

Re:Is the submitter brain fryed ? (0)

Anonymous Coward | more than 3 years ago | (#36546276)

If we copy the DNA on a harddrive, and a copy error is made, is that evolution?

Re:Is the submitter brain fryed ? (1)

Ruke (857276) | more than 3 years ago | (#36546446)

So what you're saying is that, once we start cleaning garbage data out of the database, we will skip over data that is harder to detect more often than we will skip over data that is easier to detect? I'm not quite sure that this counts as "evolution"; evolution implies adaptation to the environment, and there is no indication that any change or adaptation is going to occur here at all.

It's kind of like saying that buttons are evolving to populate photographs of my lawn; I'm more likely to bend over and pick up a red button than a green one because it's easier to see, and there is a kind of duplication in the distribution of photographs, but the buttons themselves are completely static.

Re:Is the submitter brain fryed ? (1)

pz (113803) | more than 3 years ago | (#36546442)

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

The original poster was engaging in self-indulgent free association.

Re:Is the submitter brain fryed ? (1)

lennier (44736) | more than 3 years ago | (#36547926)

static data don't evolve

Nothing in the real world is truly static over time. You think your /etc config files are static data? Ever done a series of in-place system upgrades?

Re:Is the submitter brain fryed ? (1)

snowgirl (978879) | more than 3 years ago | (#36548376)

static data don't evolve

Nothing in the real world is truly static over time. You think your /etc config files are static data? Ever done a series of in-place system upgrades?

I installed my router, and then applied the system immutable flag to all of my /etc directory. So, my /etc data has been static for 10 years! ...

and has been hacked 42 times...

Re:Is the submitter brain fryed ? (1)

JonySuede (1908576) | more than 3 years ago | (#36549108)

well the pictures of Lenna [wikipedia.org] taken years ago sure did not change. Some things are to be considered static at the human scale.

Grateful Dead, Saratoga PAC (0)

Anonymous Coward | more than 3 years ago | (#36546078)

I'm still enjoying my mycoplasma infection, almost 30 years later.

Why not repeat the genome sequencing? (2)

quax (19371) | more than 3 years ago | (#36546102)

My understanding is that nowadays new high speed sequencing machine can get an entire human genome processed in a couple of month.

So I would think that after a couple of independent runs one should be able to flush out the non-human DNA assuming the same bacteria contamination is not ever present?

Obviously this is not a cheap endeavor but given that there is quite a bit of commercial interest in using correct human genome data this seems to me to be a worthwhile investment.

I find it puzzling that the abstract of the article does not allude to this.

Re:Why not repeat the genome sequencing? (0)

Anonymous Coward | more than 3 years ago | (#36546696)

Most of the genome sequencing techniques use published genomes as a basis for comparison. The 1000-genome project and others are trying to add to the published genomes in order to alleviate errors that could be sample-dependent, but if the techniques used don't account for mycoplasma contamination then all the samples will be affected.

On another note, what is no evolutionary advantage to mycoplasma to be in the database of human DNA? I can't see any reason that mycoplasma would survive better if it was included in the database, so its evolution would not be affected by filtering those genes out of the published sequences. That means the filter would be an effective mechanism so long as it does not accidentally filter out real human genes. Because of the numbers we're dealing with and the probability of mistakes, it is not unreasonable to believe that any filter for mycoplasma will either erroneously remove human genes or not filter all mycoplasma genes.

Re:Why not repeat the genome sequencing? (2)

juggledean (792527) | more than 3 years ago | (#36546784)

From the abstract

"We ... suggest there is a need to clean up genomic databases but fear current tools will be inadequate to catch genes which have jumped the silicon barrier. "

http://arxiv.org/abs/1106.4192 [arxiv.org]

Re:Why not repeat the genome sequencing? (1)

quax (19371) | more than 3 years ago | (#36551580)

I read this as cleaning up an already corrupted database. Hence my question why you don't go back to the source? Preferably repeatedly and independently to have a better statistic in separating "noise" i.e. Mycoplasma from "signal" i.e. human genome.

Re:Why not repeat the genome sequencing? (0)

Anonymous Coward | more than 3 years ago | (#36550144)

Mod parent up. Whenever your data is corrupt, you go back to the source to get new data. This is how science works - proof by continuous experimentation.

Furthermore, TFA is misleading. The problem is not the capability of genetic codes to jump through data files. There are simply mycoplasma present in real tissue/ cell samples from time to time. (i.e. It's not an electronic problem; it's a biological problem.) It is easy to repair: Cleanliness in the lab, careful processing of samples, and frequent use of antimycotics where applicable...

Next topic: Is it still okay to make beer in the lab?

No feedback mechanism (3, Insightful)

Vornzog (409419) | more than 3 years ago | (#36546114)

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?

Re:No feedback mechanism (1)

wikdwarlock (570969) | more than 3 years ago | (#36546952)

The "will be rejected" part, I think, is where the issue comes in. Rejected based on what? Comparison to a known good database is demonstrably suspect and is in fact the main point of TFA. If I can find 90% of the non-human DNA corruption in the database and delete it, that now cleaned database becomes the standard. The other 10% of non-human DNA that wasn't caught in the database is now even more vetted, more certified, and less easily detected and deleted by the same database scanning algorithm. Thus, a new and better (i.e. evolved) algorithm is created and some new percentage of the non-human data is cleaned out, but the stuff that's left this time is even more well hidden (i.e. evolved, more similar to human DNA) and suspected more to be authentically human.

If there's ever use of the data, transcribing it back into actual viable DNA molecules, these newly manufactured DNA could presumably be checked in molecular biology labs for purity/accuracy and picked up by their already happily-infecting-the-lab cousins and the loop is closed. Now granted, the chances are that such a mutation for digital resilience is unlikely to be beneficial in the wider universe where the bacteria lives, but it's a numbers game and it could be helpful or neutral. Or, if the digital scanning algorithms are based on techniques inspired by nature (perhaps the bacteria is attacked by a virus and using that virus' DNA as a search pattern could improve algorithm performance), the bacterial DNA can beat the digital implementation and have a successful mutation that need only get transcribed into actual viable DNA and infect a lab somewhere and the loop is closed again.

Re:No feedback mechanism (1)

drooling-dog (189103) | more than 3 years ago | (#36547556)

The "will be rejected" part, I think, is where the issue comes in. Rejected based on what?

Ummm, maybe on known viral/bacterial/mycoplasmal sequences? It's pretty much routine when you're assembling a genome, and it's not hard to screen a database retrospectively as new contaminating genomes are discovered.

As for sequence data mutating and evolving in silico in genome databases (if that's what people are saying here; I can't be sure), well... That might be a good plot for a SciFi novel, but not one that would seem credible to any biologist.

Best to wait (1)

Anonymous Coward | more than 3 years ago | (#36546130)

For genome 3.1.

Um what (0)

Anonymous Coward | more than 3 years ago | (#36546158)

They're keeping the database in the form of actual DNA? Why not digitize it?

Don't see how Natural Selection applies here (0)

Anonymous Coward | more than 3 years ago | (#36546170)

Its not like the Data in the databases is going to reproduce.

Re:Don't see how Natural Selection applies here (0)

Anonymous Coward | more than 3 years ago | (#36546246)

Don't copy that floppy!

Re:Don't see how Natural Selection applies here (1)

AlamedaStone (114462) | more than 3 years ago | (#36551094)

Well *I* laughed.

Misidentification (1)

Caerdwyn (829058) | more than 3 years ago | (#36546248)

So to what extent does this "epidemic of mycoplasma contamination" increase the potential for false-positives on DNA matching tests, such as used in criminal investigation or paternity cases? Does a given lab or lab-equipment manufacturer have a common strain of contamination which increases the number of "always match" markers above the threshhold defined for claiming a match?

Re:Misidentification (1)

stillnotelf (1476907) | more than 3 years ago | (#36546448)

This has little to no relevance for DNA matching tests. Those tests do not match specific sequences, they usually match lengths of repeats in repetitive elements - elements that are unlikely to have been drawn from mycoplasma (because they don't have them!) http://en.wikipedia.org/wiki/DNA_profiling [wikipedia.org]

Re:Misidentification (1)

Caerdwyn (829058) | more than 3 years ago | (#36547168)

Ok, thanks. Here in the San Francisco Bay Area lately there has been scandal after scandal concerning sloppy forensics lab operation, theft of evidence, and police departments conspiring to hide histories of police officer misconduct form defense teams. This would have been just one more nail in the coffin.

Nature is teh ninja haxoarz (1)

theCat (36907) | more than 3 years ago | (#36546278)

Who knew?

The Immortal HeLa cell (3, Interesting)

Latinhypercube (935707) | more than 3 years ago | (#36546364)

This is EXACTLY what happened in 70s-80s with Henrietta Lacks IMMORTAL 'HeLa' cell. http://en.wikipedia.org/wiki/HeLa [wikipedia.org]
Her cells were the first Human cells to grow outside the human body.
In fact they were so successful, that unbeknown to scientists ALL OVER THE WORLD, her cells had TAKEN OVER all of the cells in their labratories GLOBALLY.
There is an amazing BBC documentary on this by Adam Curtis called "Modern Times: The Way of All Flesh"
wiki quote " Contamination: Because of their adaptation to growth in tissue culture plates, HeLa cells are sometimes difficult to control. They have proven to be a persistent laboratory "weed" that contaminates other cell cultures in the same laboratory, interfering with biological research and forcing researchers to declare many results invalid. The degree of HeLa cell contamination among other cell types is unknown because few researchers test the identity or purity of already-established cell lines. It has been demonstrated that a substantial fraction of in vitro cell lines — approximately 10%, maybe 20% — are contaminated with HeLa cells"
Almost created a COLD WAR incident:
wiki quote:-"The USSR and the USA had begun to cooperate in the war on cancer launched by President Richard Nixon only to find that the exchanged cells were contaminated by HeLa"

Re:The Immortal HeLa cell / Jurassic Park (2)

retroworks (652802) | more than 3 years ago | (#36548502)

And it is EXACTLY what happened in JURASSIC PARK! The frog cells allowed some of the female dinosaurs to mutate into MALE Dinosaurs! We COULD be looking at RAPTORS who live in SILICA, and WE will ALL be typing in ALL CAPS out of sheer FEAR!

...and the results are in... (1)

erroneus (253617) | more than 3 years ago | (#36546366)

In the case of little Jeffery, Mycoplasma, you ARE the father!

Re:...and the results are in... (2)

lennier (44736) | more than 3 years ago | (#36547960)

In the case of little Jeffery, Mycoplasma, you ARE the father!

Join me, and together we can rule the upper right nasal cavity!

Noooo! I'll never exchange plasmids with you! E Coli, why didn't you tell me?

erroneus makes blackmail threats? (0)

Anonymous Coward | more than 3 years ago | (#36550868)

http://slashdot.org/comments.pl?sid=2261720&cid=36545928 [slashdot.org] Is it because you trolled someone http://slashdot.org/comments.pl?sid=2253808&threshold=-1&commentsort=0&mode=thread&pid=36521452 [slashdot.org] and they shot you down on every so called point you tried to make and they did it with documented facts anyone could see? I saw you run like a whipped dog 10 times there in fact, and for starting trouble with others you threaten blackmail Very intelligent (not).

Evolution (1)

Hylandr (813770) | more than 3 years ago | (#36546508)

So it would seem Evolution is favoring hackers, that breed well...

- Dan.

Summary is contaminated with random science jargon (5, Insightful)

Anonymous Coward | more than 3 years ago | (#36546596)

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.

So it really doesn't matter anyway... (0)

Anonymous Coward | more than 3 years ago | (#36548040)

Human DNA.... microbial DNA.... it's all just a soup of the same 4 damn chemicals anyway.

Robotiv overlords (0)

Anonymous Coward | more than 3 years ago | (#36546628)

So file could win against out robotic overlords afterall! So H. G. Wells was right after all.

horrible language (5, Informative)

Taibhsear (1286214) | more than 3 years ago | (#36546642)

This article was horribly written. They go between using terms with their literal meaning and using terms in metaphorical creative language but do not differentiate between the two using context at all. It's an incredibly confusing read. Actual ancestral human DNA is not contaminated with actual mycoplasma DNA sequences.

Here's what I gather is going on:
Researchers took a sample of human DNA and sequenced it, while doing so the sample was contaminated with DNA from mycoplasma (possibly from bacteria in the lab or on the researchers themselves). While sequencing it, the data is assumed to be a representation of pure human DNA (which would be incorrect). Other researchers then use this data set as a reference to compare other human DNA samples they sequenced themselves. They use this to test gene expression and so forth. So if their DNA samples show gene expression for mycoplasma they would incorrectly think it was normal human gene expression. What they did is use software to strip the mycoplasma DNA data from the original data set (that had both human and mycoplasma DNA sequences) to only use the actual human DNA data as a reference. The biological contamination was first in the original sample that was tested, and then the contamination referred to elsewhere is computational data "contamination." This is the software they are referring to as antivirus software and virtual immune system (which isn't antivirus software or similar to a biological immune system, it's DNA data filtering software).

These people really need to think about what they're trying to say before puking up jargon salad on the readers' brains.

Re:horrible language (1)

drooling-dog (189103) | more than 3 years ago | (#36547872)

It seems as if the metaphors (e.g., "virus") that computational science has borrowed from biology have come around full-circle, with the result that concepts from different fields are getting conflated with one another in bizarre ways. The reasoning seems to be: If data (in the form of a computer program) can replicate and spread to other machines, then perhaps DNA sequence data in genomic databases can perform similar biological feats like mutation, evolution, and transmission. This seems inane enough that it's likely me who is missing something, but it's a "something" that I should have been able to get from the article.

Re:horrible language (0)

Anonymous Coward | more than 3 years ago | (#36550794)

What they are not considering is that if the contamination comes from petri dishes or any container in silicon, its probably a good idea to use that material everywhere so the contamination is never abnormal and you avoid the expensive antivirus analysis.

venter (0)

Anonymous Coward | more than 3 years ago | (#36546830)

it was all contaminated with Craig Venter's DNA to start with!

Mindless drivel (4, Interesting)

Iron (III) Chloride (922186) | more than 3 years ago | (#36546862)

I don't want to be excessively harsh but the summary was seriously a bunch of drivel. In silico either means it's data on the computer, or that you are simulating a biological process computationally. But as other posters have mentioned, unless you are purposely simulating evolution, mycoplasma sequences in your human databases isn't going to cause any "arms race." Yes, it seriously screws with validity, but that's a completely different issue.

This is a generalization, and no offense to fellow Slashdotters, but in my experience most of the computer scientists that I've met have a really crappy understanding of even basic biology. CS concepts don't directly translate to biology ones.

Re:Mindless drivel (0)

Anonymous Coward | more than 3 years ago | (#36547164)

Yes. It was complete drivel. I thought it had to be a joke at first. But my calender says 23rd of June. Not 1st of April.

Re:Mindless drivel (0)

Anonymous Coward | more than 3 years ago | (#36548816)

I've worked on more of the human genome sequence than most people who are alive- I agree that this is mindless drivel "published" outside of it's discipline. Ncbi didn't even start ecoli filtering until a few years ago. Transposons of all kinds are rampant in all sequencing projects, we still don't know enough to make sure they aren't present. We have biological contaminants (things that live with whatever you are sequencing), laboratory contaminants (things that are introduced during sample processing amplification, detection) and computational contaminants (introduced during data analyses and assembly).

It's really pretty freaking complicated to do any of this. While ngs stuff has introduced new ways of doing QC it has also forced projects to occur at a rate where QC isn't feasible - so expect more not less!

Re:Mindless drivel (1)

poopdeville (841677) | more than 3 years ago | (#36548830)

I don't want to be excessively harsh but the summary was seriously a bunch of drivel. In silico either means it's data on the computer, or that you are simulating a biological process computationally. But as other posters have mentioned, unless you are purposely simulating evolution, mycoplasma sequences in your human databases isn't going to cause any "arms race." Yes, it seriously screws with validity, but that's a completely different issue.

You're still missing the point.

Methods to screen out junk contamination will all miss something. The data representation of a genome is reproduced, as a cost (and time) saving measure. In other words, the contamination that survives the screening process will "survive" as a silicon representation.

This is a problem in the long term, since we will presumably be using the genomic data to eradicate diseases. So our use of contaminated data will select for diseases which cannot be screened.

Fungi? (1)

jweller13 (1148823) | more than 3 years ago | (#36546892)

Myco means fungi right?

Re:Fungi? (1)

treeves (963993) | more than 3 years ago | (#36550350)

Yes. But this is about bacteria that happens to have the genus name Mycoplasma, not fungi.

trigger evolutionary arms race? (1)

hierophanta (1345511) | more than 3 years ago | (#36547216)

i believe the evolutionary arms race was triggered a long time ago (possibly in a galaxy far far away) /. is so full of tripe today its making me question my patronage

Funny, guys. (1)

imric (6240) | more than 3 years ago | (#36547238)

Were these the patented sequences?

Parasite Eve? (0)

Anonymous Coward | more than 3 years ago | (#36547258)

Am I the only person who read this and thought Parasite Eve? The Game or the Japanese film, either way. Human genome contaminated with mycoplasma = mitochondria taking over the body's genetics (causing spontaneous combustion among other things.)

I did read the article and they're just talking about mycoplasma contamination that winds up being replicated into databases (eg taking over the human genome.)

Someone else mentioned the serious nature of the problem, in that DNA databases can false-positive if the match with both samples contaminated with the mycoplasma.

Why are we sequencing from cell culture? (0)

Anonymous Coward | more than 3 years ago | (#36547376)

An actual, working molecular biologist here. Just left the lab, actually. Why the bloody hell are they sequencing from tissue culture? Buccal cells collected and purified or buffy coat derived from whole blood seems to be a more robust method of acquiring gDNA to sequence. I addition, why the f@&$ are they not testing for mycoplasma contamination? PCR primers and probes are widely available in the literature for testing for presence or absence, or just buy a bloody kit from the likes of Sigma or Ambion or Applied Biosystems or Invitrogen or Bio-Rad. It's easy to perform and should be a standard qc procedure wether you're working in commercial r&d or academia. The lack of a simple test that may compromise years of work (not to mention derivative works, too) can be chalked up to pure and simple laziness. As a scientist, all I have is my integrity- nothing else matters to me. To ruin years of data and derivative cell lines that have been passaged to other labs disgusts me, and anyone who isn't routinely testing in research that's meant for publication or production should be ashamed of themselves.

Move along - the genome data is NOT contaminated. (0)

Anonymous Coward | more than 3 years ago | (#36547732)

I went ahead and read the original article: More Mouldy Data: Virtual Infection of the Human Genome

The authors found two tiny submissions in GenBank that appear to be of mycoplasma origin, but mislabeled as Homo Sapiens: http://www.ncbi.nlm.nih.gov/nuccore/AF241217 and http://www.ncbi.nlm.nih.gov/nucest/DA466599

Having BLASTed the above sequneces against the Human Genome assemblies, all hits are noise (e.g. Poly-T stretch in the first sequence).

Kids, when a daddy loves a mommy very much... (0)

Anonymous Coward | more than 3 years ago | (#36547974)

OK...so let me make sure I got this straight.

The germ that causes walking pneumonia is infecting computer database information, and inserting its DNA into the digital record of the human genome sequences. This corrupted information is in turn being forwarded erroneously to scientists around the globe...
Will you crackheads please call Bill Nye before you post any more garbled "Bachelor of Arts and I read this scary medical story in Reader's Digest-last minute term paper idea garbage."
Trust you guys to get anything remotely related to biologic transfer of genetic material correct...sheesh

This makes very little sense (1)

rnaiguy (1304181) | more than 3 years ago | (#36550104)

When you assemble a genome, you assemble the sequences into chromosomes based on overlap with other sequences. This contamination should not match up properly, or be assemble into its own "chromosome".

The whole "evolution" thing is the biggest sensationalist bullshit I've ever heard. Ignore it.

As was mentioned in another comment, it seems like the summary is misleading on the "contamination" actually being in the genome sequence.

sequence != expression (1)

neurogeneticist (1631367) | more than 3 years ago | (#36550152)

The use of terms for sequence data and expression data are not interchangeable. The U133 microarray is for RNA, yes RNA, expression data. RNA microarrays quantify the fold change difference in expression between different subjects. DNA microarrays identify polymorphisms or repeats or the like. While arrays like the U133 rely on sequence level data to create the array, this is not the same as saying that sequence-level data is contaminated. Bottom line, the fact that this is not the cover article for Nature|Genetics this month tells you a lot of the story. Unless you are some sort of conspiracy theorist, or want to get swept up in the usual slashdot "sky is falling" imperative.

This is not new (0)

Anonymous Coward | more than 3 years ago | (#36550452)

This has been known for a long time. Bacteria and viruses fly around in the air. Anybody's who's sifted through genomic reads knows this. There's a noise level in all this high throughput genomics.

Load More Comments
Slashdot Login

Need an Account?

Forgot your password?