【科普】从拉登之死到DNA鉴定
2011-05-05 20:00:36   来源：   作者：  评论：0 点击：

DNA鉴定是一个非常熟悉的名词，特别是对于从事医学以及生命科学的人员。

但实际上你对DNA鉴定，又了解多少呢？

拉登的死，让DNA鉴定之说又火了一把。

这是两篇在Nature上的报道。

让我们离DNA鉴定更近一些，更加感性一些。

第一篇：How DNA may have confirmed bin Laden's death

The US government has said that DNA samples from family members of Osama bin Laden were used to positively identify his body with "99.9 percent" certainty. How would this work, and how can the government be so certain?
Modern forensic techniques analyze short tandem repeats — pieces of DNA that are copied different numbers of times in different individuals on the chromosomes that contain an individual’s genetic code. Christie Wilcox blogs about how polymerase chain reaction and genetic sequencing are used to count the number of tandem repeats in a genome. It’s then easy to compare the tandem repeat profile between two individuals to find out whether their DNA profiles match.
Chad Nusbaum of the Broad Institute of MIT and Harvard in Cambridge, Mass., estimates that this process would take five or six hours, or even faster in a lab using proprietary technology dedicated to forensic identification. This would have given military analysts time to perform a DNA analysis after the U.S. raid on Monday morning in Pakistan, and deliver results to President Obama by the time of his announcement on Sunday night in Washington, DC.
The equipment necessary for such a DNA analysis could have been located on a ship or at a base near the site of the raid, for instance, at Bagram Airfield in Afghanistan.
But how can the government be so certain that the man it has killed is bin Laden?

The strongest possible match would be made by comparing a sample taken from the putative bin Laden body to previously collected samples of his own DNA.
“My guess is maybe they had samples of bin Laden’s that could have been around for a while,” says Robert Shaler, who directed the DNA identification efforts for victims of the September 11, 2001 terrorist attacks on the World Trade Center in New York City. Shaler points out that his team was provided with DNA profiles of some of the hijackers involved in the 9/11 attacks to identify their remains in the World Trade Center rubble, and that a sample of bin Laden’s own DNA could have been collected by military or intelligence agents from places that bin Laden had lived or visited.
Samples also could have been collected from any of bin Laden’s living siblings or children, either with or without their knowledge, by obtaining discarded material bearing their DNA, such as beverage cups or dental floss, says David Kaye, a lawyer at Pennsylvania State University.
Bin Laden reportedly has no full siblings, as he was the only child born to his mother and father. However, his mother remarried after she and bin Laden's father divorced, so bin Laden reportedly has three half-brothers and one half-sister born to her, as well as dozens of half-brothers and half-sisters also born to his father. He also is said to have fathered as many as 26 children.
“Bin Laden’s relatives might have cooperated, or even if they didn’t, agencies might have obtained DNA samples surreptitiously — it’s a well known practice in law enforcement now,” says Kaye, who last year published a book, The Double Helix and the Law of Evidence, on genetic forensic evidence in the criminal justice system.
For instance, DNA collected from a discarded slice of pizza was used to identify the man charged last year with the so-called “Grim Sleeper” murders in California. DNA taken from the alleged killer's son was also used in that case.
The strength of a match made between bin Laden’s putative DNA and that of his relatives would depend on how many related DNA samples are available for comparison, and how closely they are related to bin Laden, says Allison Williams Dobson, a lawyer and molecular biologist who works with the Center for Genomics and Society at the University of North Carolina Chapel Hill.
“The more siblings and children you have samples from, the easier and more certain it would be,” Williams Dobson says.
It is likely that sequencing of DNA from mitochondria — organelles in the cell that are passed down from mother to child — could have been used to confirm that the man killed in Afghanistan was a sibling to bin Laden's half-sisters and brothers, or was the son of bin Laden's mother, who is still living. Since mitochondria are passed down from mother to child, they can establish with near certainty that two individuals are siblings, says Mary-Claire King of the University of Washington, who pioneered the use of mitochondrial DNA to identify victims of mass killings and homicides in the 1990s.
"Mitochondrial DNA sequencing would be the most certain way, by far, of identifying two people as full siblings,” King said.
Short tandem repeat analysis could also be conducted on the y-chromosome, which is passed down from father to son. Such an analysis could be used to link the putative bin Laden to any of his known half-brothers or sons, further strengthening the evidence that it was indeed he who was killed in the Navy raid in Pakistan.
If it is true that bin Laden was the only son born to his mother and father, a combination of y chromosome and mitochondrial DNA markers could yield a strong match to bin Laden himself, because none of his half-brothers would have inherited the same combination of y chromosome and mitochondrial DNA markers that he has.
Short tandem repeat analysis could also have been conducted on nuclear chromosomal DNA from many bin Laden siblings and children, further cementing the case that the killed man is Osama bin Laden himself.
“If they have the right samples, the identification is virtually certain,” Shaler says.
In addition, news reports have also mentioned other identification techniques, such as facial analysis, that would complement the DNA analysis.
Whatever DNA evidence does exist, Williams Dobson points out, the U.S. government must feel very confident about it.
“They must be quite sure it is him, because if they are wrong, we will have a video from him circulating pretty soon, showing that he is actually alive,” she says.
Posted by Erika Check Hayden on May 02, 2011

第二篇：具体化的
How do you ID a dead Osama anyway?
Posted on: May 1, 2011 9:13 PM, by Christie Wilcox

Osama Bin Laden is dead. At least, that's what we've been told, and I tend to believe such things.
But how do they know[/i] it's him? Well, they have the visual evidence and the body, for one. But to be certain it's not a look-a-like, the government has taken steps above and beyond to make sure they've got who they think they have: DNA analysis.
Now, I'm not entirely sure what DNA analysis has been done, but I can say this for certain - whatever method they used could be completed in a matter of hours given a lab ready to go and focused solely on this. Using commonplace PCR methods - which, for the record, is what I use in my lab every day - Bin Laden could easily be ID'd faster than you'd think. Heck, I can get DNA from a fish and turn it into sequences or genotypes in 24 hours, so I think the US government can work faster than me when time is of the essence. Allow let me explainhow[/i] they could do it so quickly.

Step 1. Extract DNA
If they've got his body, then they've got enough DNA to run a billion or two genetic tests. It takes extremely little DNA to run genetic tests - on the order of single cells. So having even a 1 mm square piece of flesh would provide more DNA than they would even have use for. Extraction takes very little time. All you need to do it place the cells/tissue in some kind of solution that will break up the cell's membranes, thus liberating the DNA from the nucleus without damaging the DNA too much. There are hundreds of extraction kits and protocols. I don't know what the gov't extraction policy is, but the Arkansas State Crime Lab just uses sodium hydroxide and hydrochloric acid to extract DNA from their samples (which, btw, is how I get DNA from my fish samples, too). For example, this is their protocol for buccal punches (a.k.a. cheek tissue):

Place 52 μl of 0.01 M NAOH in each well with 2.0 mm of tissue.
Incubate samples at 65°C for 10 minutes.
Add 10 μl of 0.1 M Tris HCl (pH 7.3).
Mix.
Let stand for 5 minutes.
Samples are now ready for amplification

TOTAL TIME: 15 min

Step 2: Amplify Identifying DNA Sequences
Once you have DNA, you're ready to ID your suspect. While there have been a few methods used in the past, the onset of Polymerase Chain Reaction, or PCR technology, has made looking at parts of a genome pretty darn quick and easy.

The namesake of PCR, polymerase, is a very special enzyme that cells use to duplicate DNA. Polymerases are found in all creatures because we all must, at some point, have cells divide to grow and reproduce. When our cells divide, we have to make two copies of our genome - one for each new cell. To do this, our cells unwind the DNA, spread apart the two matching strands, then use each as templates to make two new strands. Polymerases are the enzymes that actually do that - they attach to single strands of DNA and grab matching nucleotides to create the other half of the strand.
PCR was invented in the 1980s and takes advantage of how our DNA reacts to temperature. At lower temperatures, like in our bodies, DNA sticks to it's complementary half and forms a tight helix. But as you turn up the heat, our DNA denatures - that is, it unwinds and each half of the helix separates. We can't use our own cell's polymerases for PCR because they can't stand that kind of heat. Instead, we've borrowed an enzyme from a particularly heat-tolerant bacteria to do the job for us.
PCR uses multiple cycles of heating and cooling to create thousands to millions of copies of a single piece of DNA. But how do we copy just what we want? Well, it turns out that polymerases need a little help getting started. They require a short sequence of RNA to tell them where to attach, called a primer[/i]. Because we can design this primer to match any unique sequence in the genome, we can target where the polymerase will attach, and voila. You've just picked your little chunk of genome to amplify over and over and over again. The total process doesn't take all that long - you heat it up for a bit, run it through a set of temperature cycles, and then you're good to go. The Arkansas protocol, for example, takes just about two and a half hours.
In the case of DNA fingerprinting, a set of very special genome regions called Short Tandem Repeats (or STRs) are used. These are non-coding sections that vary a lot between people. To be certain of ID, 13 separate regions, called loci, are compared between people. The chance that two people who are not twins would be the exact same across all 13 different loci is approximately 1 in 575 trillion[/i].
The best part of PCR is that you can attach things to those primers to make the new DNA really easy to find. For example, the AmpF?STR? Identifiler ? PCR Amplification Kit used by Arkansas has the primers for 15 different STR loci all tagged with fluorescent dyes. That means once you're done with the PCR, you're just a hop skip and a jump away from a full genetic ID.
TOTAL TIME: 3 hours, tops.
Step 3: Genotyping
Once you have your DNA amplified, you need to find out what it looks like. In the case of STRs, you're looking for how many repeats are in each DNA chunk. In other words, you're looking to see how long they are. Because they're each flagged with a fluorescent dye, the sequence in and of itself doesn't matter, just the size. Some people just run this out on a gel, which is what we see in our classic TV fingerprinting:



But nowadays, more and more labs are shifting to genotyping analysis with the help of automated machines. Determining the size of fluorescent labeled DNA sequences is the job of specialized machines like the ABI 3130xl Genetic Analyzer. It can take a sample of DNA and tell you how much DNA you have at what sizes in what colors. The output looks something like this:

The pattern of peaks are the person's "DNA Fingerprint". All you gotta do then is line them up with the peaks of your target person, and it's either a match or it's not.

TOTAL TIME: 1 hour, maybe less.

So how long did it take to get Bin Laden's fingerprint? Well, with the three steps here, justunder 5 hours. And for all I know, the FBI has a faster way of doing it - I wouldn't exactly be shocked. That, and some are reporting he actually died last week sometime, and they've been waiting for the DNA confirmation - which also, frankly, wouldn't shock me.

Of course, to ID Bin Laden in this way, they would have to have some Bin Laden DNA lying around to compare it to. I don't know if they had some from some inside source, or not.What they do have is brain tissue from Bin Laden's sister, who died in the US. They can[/i]compare his genetic signature to hers and determine if they are related - which is as close as you can get to guaranteeing it's Bin Laden without a sample of his actual DNA from prior to his death.