Continuation Part 15: Amanda Knox/Raffaele Sollecito

[Chris_Halkides]

degradation of DNA

It's too bad Chris isn't around. I'd bet he would reference some stufdy. My bet is that under the right or wrong conditions DNA might deteriorate in hours, maybe even minutes and in different conditions last thousands of years. I'm sure light, oxygen or countless other elements as well,as other organic material would be contributing factors.

acbytesla,

I am very busy at the moment, but this is very much on the right track. UV light (from the sun, for example) is damaging, and nucleases (enzymes that degrade nucleic acids) are a problem, which is probably why feces are not a good source of DNA. Chapter 3 in Jason Gilder's Ph.D. thesis would be a good place to start.

 

[Bill Williams]

You recall police originally identified the shoeprints as Raf's, in particular, because there was a specific star shaped deformity on the heel (?) which matched his.

As you know, Dad Raf moved heaven and earth to match it with a brand that matched a shoebox in Rudy's apartment. At the trial, the court allowed him that point that the footprints were Rudy's not Raf's.

Now consider this. The court conceded this point on the basis there was plenty more evidence of Raf's presence anyway, and it was established Rudy was there anyway.

What if they were Raf's shoeprints all along?

After all, he did soak his daps in bleach immediately after the crime. In addition, he told police, "The person who committed the murder, must have stolen my trainers."

The random factoid generator just keeps spinning them out.

I'd ask for cites, but there are now 34 people ahead of me making that request of this poster.

 

[acbytesla]

acbytesla,

I am very busy at the moment, but this is very much on the right track. UV light (from the sun, for example) is damaging, and nucleases (enzymes that degrade nucleic acids) are a problem, which is probably why feces are not a good source of DNA. Chapter 3 in Jason Gilder's Ph.D. thesis would be a good place to start.

Thanks Chris. I knew you could provide a reference.

 

[Planigale]

The problem with DNA testing is that in organic matter, DNA is broken down quite quickly by bacteria. Rudy's faeces could not be tested for DNA for this reason, and came from the toilet paper, probably from skin cells.

Hair is dead matter anyway, so unless you can obtain a recently live follicle, it is not unusual to not obtain DNA.

We discussed this some time ago. What should have been done is to do mitochondrial DNA testing on the hair. Whilst genomic typing is likely to be negative unless you have the hair root, mitochondrial DNA typing is more reliable. Unfortunately Stefanoni did not do this. Whilst mitochondrial typing has some limitations in this case since the mother's of the principle suspectsand victims were from different ethnic groups mitochondrial DNA typing would have been informative.

PS the reason that typing DNA from faeces is difficult is not that bacteria breakdown the human DNA just that the huge amount of bacterial DNA makes typing the human DNA difficult. Faeces is almost entirely bacteria and vegetable fibre.

 

[RoseMontague]

There was blood and the greatest DNA forensic scientist in the world couldn't find the needed donors DNA?

Did she use the same methodology on that sample as she did on the knife?

How many pg of material was in the blood sample?

Did she use it all up?

Did she preserve it properly did she use a container made in the USA that caused it to spoil?

I would think that if she didn't preform the same heroic breakthrough science on the blood spot as the knife that that should be a problem for her.

Wonder if it could still be tested. Maybe it's in a garage somewhere.

Maybe so. The really strange thing about this spot of blood on the wood next to the broken window is that according to the SAL reports it was not tested until 4 months later (after AK and RS were charged and well after the theory of the staged break in was part of the prosecution's case).

SAL records for rep. 199 (a presumed blood substance from the wood part of the window in Filomena's room identified with the letter S) tested positive for TMB on 2/28/08, and quantification was run on 3/5/08. As someone has already mentioned, this should have been one of the very first things tested.

 

[Chris_Halkides]

intestinal epithelial cells

Planigale,

Would there be some intestinal epithelial cells on the surface of feces?
EDT
This link has some information.

"An estimated 10 billion cells are shed from the epithelial lining of the human intestine daily; some of these cells survive the digestive processes to be excreted intact into the feces. The presence of these nucleated cells offers another approach to individualization—DNA analysis. Previous advances made in fecal typing have involved mitochondrial DNA, however this type of DNA analysis is not routinely performed in forensic laboratories. Attempts to type nuclear DNA have been problematic due to low DNA yields, and the presence of high amounts of bacteria and PCR amplification inhibitors....However, samples dried for one week did consistently produce the lowest yields of DNA as well as displaying the highest degree of degradation." Given that heme is a known PCR inhibitor, I have to wonder whether or not its breakdown products found in feces are also inhibitors.

Other references
J Forensic Sci. 2005 Jul;50(4):802-8. STR-typing of human DNA from human fecal matter using the QIAGEN QIAamp stool mini kit.
J Forensic Sci. 2003 Sep;48(5):1035-40. Analysis of human fecal material for autosomal and Y chromosome STRs.

 

[bagels]

So what does a guilt believer think of rudy's involvement?

-was he there on a date with meredith?
-did he break in at what happened to be the worst possible time?
-did he come along with amanda and raffaele?

He showed up randomly like the costumed man in the selective attention test posted earlier while Knox and Raffaele were busy stabbing Meredith for 300 euros, and planted his DNA and bloody prints in the appropriate places then quietly vanished from the scene.

 

[Planigale]

It's too bad Chris isn't around. I'd bet he would reference some stufdy. My bet is that under the right or wrong conditions DNA might deteriorate in hours, maybe even minutes and in different conditions last thousands of years. I'm sure light, oxygen or countless other elements as well,as other organic material would be contributing factors.

Ultraviolet.

DNA is very sensitive to UV. Left out in direct sunlight DNA can breakdown in minutes. Obviously this is hugely dependant on the weather and whether the material protects the DNA from UV. Thus DNA has been extracted from neanderthal teeth nx10⁶ years old found in caves. Bacteria tend not to breakdown eukaryotic cells. This is the responsibility of fungi and other eukaryotes.

So as one might expect most of what Vixen sats is untrue.

 

[anglolawyer]

Aren't they trying to extract DNA from mammoth?

 

[Dan O.]

I'm going on record with a prediction that cassation will annul the conviction for calunnia in its motivation report due in June 2015.

I don't know if they can change their own ruling in the motivations report. By the time they get to writing it they may wish they could make the callunia verdict go away. But it may be up to ECHR to make it happen.

 

[Planigale]

Planigale,

Would there be some intestinal epithelial cells on the surface of feces?
EDT
This link has some information.

"An estimated 10 billion cells are shed from the epithelial lining of the human intestine daily; some of these cells survive the digestive processes to be excreted intact into the feces. The presence of these nucleated cells offers another approach to individualization—DNA analysis. Previous advances made in fecal typing have involved mitochondrial DNA, however this type of DNA analysis is not routinely performed in forensic laboratories. Attempts to type nuclear DNA have been problematic due to low DNA yields, and the presence of high amounts of bacteria and PCR amplification inhibitors....However, samples dried for one week did consistently produce the lowest yields of DNA as well as displaying the highest degree of degradation." Given that heme is a known PCR inhibitor, I have to wonder whether or not its breakdown products found in feces are also inhibitors.

Other references
J Forensic Sci. 2005 Jul;50(4):802-8. STR-typing of human DNA from human fecal matter using the QIAGEN QIAamp stool mini kit.
J Forensic Sci. 2003 Sep;48(5):1035-40. Analysis of human fecal material for autosomal and Y chromosome STRs.

Thanks Chris.

You are the biochemist. I think I have reached the limit of my knowledge. Surprisingly little is known about faeces (and it is really a quite fascinating subject). Certainly there may well be inhibitors of PCR amongst the various breakdown products of heme and enzymes in faeces. Faeces will contain lots of epithelials from gut mucosa some in various states of digestion, but little digestion occurs in the colon so colonic epithelials will be intact. Certainly rectal mucosa would be expected to be on the surface of faeces.

 

[anglolawyer]

Thanks Chris.

You are the biochemist. I think I have reached the limit of my knowledge. Surprisingly little is known about faeces (and it is really a quite fascinating subject). Certainly there may well be inhibitors of PCR amongst the various breakdown products of heme and enzymes in faeces. Faeces will contain lots of epithelials from gut mucosa some in various states of digestion, but little digestion occurs in the colon so colonic epithelials will be intact. Certainly rectal mucosa would be expected to be on the surface of faeces.

don't talk crap

 

[Grinder]

don't talk crap

Coming from some sort of lawyer I mean pot kettle

 

[Kauffer]

Maybe so. The really strange thing about this spot of blood on the wood next to the broken window is that according to the SAL reports it was not tested until 4 months later (after AK and RS were charged and well after the theory of the staged break in was part of the prosecution's case).

SAL records for rep. 199 (a presumed blood substance from the wood part of the window in Filomena's room identified with the letter S) tested positive for TMB on 2/28/08, and quantification was run on 3/5/08. As someone has already mentioned, this should have been one of the very first things tested.

So, the interesting thing is why, since it want tested earlier, in November or December, was it tested at all? Was there just a massive queue of samples from this and other cases to get through, or is there another reason?

A reasonable investigator, whatever his or her suspicions might be with regard to the break in, must regard such a sample as a potentially important piece of evidence. If it had typed to any of the suspects it would have been crucial because it would not have supported an innocent explanation.

 

[anglolawyer]

Coming from some sort of lawyer I mean pot kettle

What's the Mata?

 

[Grinder]

What's the Mata?

120 Dalmatians to go

 

[anglolawyer]

120 Dalmatians to go

Wait 'til next season ...

 

[Vixen]

Didn't Rudy's lawyer Biscotti come out of that Dec 7, 2007 interview and say that Rudy Guede didn't name anyone else as an accomplice, because there was no one to name?

I do wonder if he repeated his earlier statement that amanda wasn't there? I also wonder if the prosecution or even Biscotti has any kind of legal or moral obligation to disclose that full interview statement to the defense teams.

All discussion between client and lawyer are legally privileged. 100% protected by law.

 

[Vixen]

The random factoid generator just keeps spinning them out.

I'd ask for cites, but there are now 34 people ahead of me making that request of this poster.

I cited the TIMES. For some reason, you claim to know better.

Bill, you have the same access to resources as me.

 

[Vixen]

Thanks Chris. I knew you could provide a reference.

Please don't forget to report back on Jason's thesis Chapter 3.