Author Topic: The Defence Will State Their Case  (Read 125191 times)

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Offline [...]

Re: The Defence Will State Their Case
« Reply #1995 on: October 10, 2018, 02:13:27 PM »
May I ask, where is the source which suggests low copy techniques were used to establish a DNA profile in this case?


Quote
LGC Forensics provides key evidence in Jo Yeates investigation
14 NOV 2011
Tags:  Biological, Forensic
LGC Forensics' analysis provides key evidence in Joanna Yeates investigation
LGC Forensics, the UK's largest independent provider of forensic services, successfully used a range of advanced forensic techniques, including LGC’s proprietary DNA enhancement method, DNASenCE, to link Vincent Tabak to the 2010 murder of Joanna Yeates.

Joanna disappeared after walking to her home in Bristol on 17 December 2010 and her body was finally found on Christmas Day in a country lane a few miles from her home. Working closely with Avon & Somerset Police, LGC Forensics was instrumental in obtaining a DNA profile from evidence found at the crime scene and in linking this with a range of supporting forensic evidence, including from Tabak’s car. The crucial evidence was provided by the work to refine the DNA procedures in order to enhance the DNA samples – which were inhibited, possibly by the unusually high levels of salt at the location of the body, because of a recent snow fall. 

Teamwork played a vital role in this case and LGC Forensics set up an internal focus group of forensic scientists who carried out the technical DNA examinations, as well as interpretation, peer review, and quality review. The group analysed a number of items taken from Joanna’s flat and submitted by Police for analysis as well as further evidence from the area where Joanna’s body was found. The scientists used a combination of analytical tools including exacting DNA enhancement work and fibre analysis, and consideration was also given for recovery of hair, ecology and biological samples. 

Steve Allen, Managing Director of LGC Forensics, said: “The successful use of painstaking forensic analysis in this case is a positive result for the Yeates family and for Avon & Somerset Police. We always welcome the opportunity to contribute our skills and expertise to important investigations such as this one, and we are pleased that the very detailed and thorough work of our forensic scientists helped bring resolution to this case.”


https://www.lgcgroup.com/about-us/media-room/latest-news/2011/lgc-forensics-provides-key-evidence-in-jo-yeates-i/#.W736ERNKii4



Offline justsaying

Re: The Defence Will State Their Case
« Reply #1998 on: October 10, 2018, 04:59:12 PM »
From what I have read and what I understand, is that low copy DNA and DNAsense are two different things, there are certainly different definitions for them both. It seems quite gobbledygook to me but as far as I can see, low copy builds up a profile from a minute source whereas DNAsense was used in this case to clean up the DNA strands which were contaminated by salt.

I do not see anywhere in which it is claimed that low copy techniques were used. Low copy DNA, as I have read it, is quite controversial. I think, perhaps, in this case (I could be wrong) there was an ample amount of DNA to test but it needed further forensics to remove the contamination caused by the snow.

The crucial evidence was provided by the work to refine the DNA procedures in order to enhance the DNA samples – which were inhibited, possibly by the unusually high levels of salt at the location of the body, because of a recent snow fall. 
« Last Edit: October 10, 2018, 05:11:13 PM by justsaying »

Offline Baz

Re: The Defence Will State Their Case
« Reply #1999 on: October 10, 2018, 05:01:28 PM »

Offline justsaying

Re: The Defence Will State Their Case
« Reply #2000 on: October 10, 2018, 05:04:18 PM »
What evidence was found in the his car? I don't remember ever reading about evidence being found in his car.

I believe it was a spot of the victims blood.
« Last Edit: October 10, 2018, 05:08:44 PM by justsaying »

Offline [...]

Re: The Defence Will State Their Case
« Reply #2001 on: October 10, 2018, 05:53:16 PM »
From what I have read and what I understand, is that low copy DNA and DNAsense are two different things, there are certainly different definitions for them both. It seems quite gobbledygook to me but as far as I can see, low copy builds up a profile from a minute source whereas DNAsense was used in this case to clean up the DNA strands which were contaminated by salt.

I do not see anywhere in which it is claimed that low copy techniques were used. Low copy DNA, as I have read it, is quite controversial. I think, perhaps, in this case (I could be wrong) there was an ample amount of DNA to test but it needed further forensics to remove the contamination caused by the snow.

The crucial evidence was provided by the work to refine the DNA procedures in order to enhance the DNA samples – which were inhibited, possibly by the unusually high levels of salt at the location of the body, because of a recent snow fall.

I was under the impression that the DNASense was the technique used to amplify the low copy DNA.. `but i may be wrong...

DNA components... ?

Quote
"Eventually, we found something," Lennen says. "On swabs and tapes from her breasts, and tapes from three areas of her jeans. There were DNA components that matched one of the suspects, Vincent Tabak." But there wasn't enough, of enough quality, to evaluate – perhaps because of the high salt levels where the body was found, following heavy snowfall.

https://www.theguardian.com/science/2012/jan/17/csi-oxford-lgc-forensics

Offline justsaying

Re: The Defence Will State Their Case
« Reply #2002 on: October 10, 2018, 06:04:57 PM »
I was under the impression that the DNASense was the technique used to amplify the low copy DNA.. `but i may be wrong...

DNA components... ?

https://www.theguardian.com/science/2012/jan/17/csi-oxford-lgc-forensics

It speaks of the quality not quantity...

If you take a look on wiki, they are completely separate and different definitions of both DNA techniques.

https://en.wikipedia.org/wiki/Low_copy_number

https://en.wikipedia.org/wiki/Sense_(molecular_biology)

https://www.lgcgroup.com/our-science/molecular-biology-science-cluster/#.W74zIPZFzIU

« Last Edit: October 10, 2018, 06:13:52 PM by justsaying »

Offline [...]

Re: The Defence Will State Their Case
« Reply #2003 on: October 10, 2018, 06:22:31 PM »
It speaks of the quality not quantity...

If you take a look on wiki, they are completely separate and different definitions of both DNA techniques.

https://en.wikipedia.org/wiki/Low_copy_number

https://en.wikipedia.org/wiki/Sense_(molecular_biology)

https://www.lgcgroup.com/our-science/molecular-biology-science-cluster/#.W74zIPZFzIU


The low copy comes directly from DCI Phil Jones...

Quote
The Joanna Yates murder inquiry
166. Detective Chief Inspector Philip Jones of Avon and Somerset Constabulary told
the Inquiry that the Daily Mail called the Constabulary Communications Department
during the investigation and said that low copy DNA was found on Joanna Yates
body. This was true and either came from the police or other agencies which had
tested the DNA. The leak investigation was still ongoing when he gave evidence. He
stated that this leak damaged morale of the police and damaged trust2°°.

Am I Missing something??  Low Copy DNA is useless....

http://webarchive.nationalarchives.gov.uk/20140122194510/http://www.levesoninquiry.org.uk/wp-content/uploads/2012/10/Submission-from-Core-Participant-Victims-Module-2.pdf

Offline [...]

Re: The Defence Will State Their Case
« Reply #2004 on: October 10, 2018, 06:31:33 PM »
So did LGC know how to amplify the Low Copy DNA??

Quote
The increased sensitivity of LCN also increases the risks posed by contamination of samples in the laboratory. Since LCN aims to amplify levels of DNA as low as 100 picograms, even breathing on a sample may contaminate it substantially enough to render the final profile unusable[citation needed]. Contamination is particularly problematic before the sample has undergone amplification because both the suspect's and the contaminator's DNA will be amplified, resulting in a mixed profile. Moreover, the small amounts of DNA that LCN aims to amplify also increase the probability of PCR artifacts appearing on profiles such as stochastic effects.

Is that what was meant by the mixed DNA??


https://en.wikipedia.org/wiki/Low_copy_number


Offline justsaying

Re: The Defence Will State Their Case
« Reply #2005 on: October 10, 2018, 06:40:22 PM »

The low copy comes directly from DCI Phil Jones...

Am I Missing something??  Low Copy DNA is useless....

http://webarchive.nationalarchives.gov.uk/20140122194510/http://www.levesoninquiry.org.uk/wp-content/uploads/2012/10/Submission-from-Core-Participant-Victims-Module-2.pdf

I think they have confused "LCN" with DNASenSE… These are two different techniques for DNA profiling. I would trust what the scientist says rather than the Leveson enquiry... I would assume if the techniques were exactly the same then there wouldn't be the need for entirely different definition of both.

https://www.theguardian.com/science/2012/jan/17/csi-oxford-lgc-forensics

So the team deployed an LGC technique known as DNA SenCE, which purifies, concentrates and enhances otherwise unusable DNA:

https://en.wikipedia.org/wiki/Low_copy_number

LCN is an extension of Second Generation Multiplex Plus (SGM Plus) profiling technique. It is a more sensitive technique because it involves a greater amount of copying via polymerase chain reaction (PCR) from a smaller amount of starting material, meaning that a profile can be obtained from only a few cells, which may be as small as a millionth the size of a grain of salt, and amount to just a few cells of skin or sweat left from a fingerprint.

https://en.wikipedia.org/wiki/Sense_(molecular_biology)#DNA_sense
DNA sense
Molecular biologists call a single strand of DNA sense (or positive (+)) if an RNA version of the same sequence is translated or translatable into protein. Its complementary strand is called antisense (or negative (-) sense). Sometimes the phrases coding strand (for sense) and template strand (for antisense) are encountered; however, protein coding and non-coding RNAs can be transcribed from the sense strand. Additionally, the terms "sense" and "antisense" are relative to the RNA transcript in question and not to the DNA strand as a whole. In other words, either DNA strand can serve as the sense or antisense strand for a particular RNA transcript. In some cases, RNA transcripts can be transcribed in both directions (i.e. on either strand) from a common promoter region, or be transcribed from within introns on either strand (see "ambisense" below).


Offline justsaying

Re: The Defence Will State Their Case
« Reply #2006 on: October 10, 2018, 06:43:52 PM »
I assume, again I could be wrong, that DNA strands are found in what is called sense DNA. Whereas it is much smaller than a strand in LCN.

It was DNA sense not LCN which was used in this case, as verified by the forensic scientists.

LCN = as small as a millionth the size of a grain of salt

DNA Sense = Molecular biologists call a single strand of DNA sense

Also, from what I understand, LCN techniques could not be said to be a billion to one match, whereas it could be said using the DNASenSe technique - hence the allegation that the DNA match in this case was a billion to one.
« Last Edit: October 10, 2018, 06:51:59 PM by justsaying »

Offline [...]

Re: The Defence Will State Their Case
« Reply #2007 on: October 10, 2018, 07:23:02 PM »
I assume, again I could be wrong, that DNA strands are found in what is called sense DNA. Whereas it is much smaller than a strand in LCN.

It was DNA sense not LCN which was used in this case, as verified by the forensic scientists.

LCN = as small as a millionth the size of a grain of salt

DNA Sense = Molecular biologists call a single strand of DNA sense

Also, from what I understand, LCN techniques could not be said to be a billion to one match, whereas it could be said using the DNASenSe technique - hence the allegation that the DNA match in this case was a billion to one.

So how did they apparently tie it to Dr Vincent Tabak?? Is it possible to have had the same result with another person?? Depending on + or - ??

Quote
Molecular biologists call a single strand of DNA sense (or positive (+)) if an RNA version of the same sequence is translated or translatable into protein. Its complementary strand is called antisense (or negative (-) sense). Sometimes the phrases coding strand (for sense) and template strand (for antisense) are encountered; however, protein coding and non-coding RNAs can be transcribed from the sense strand. Additionally, the terms "sense" and "antisense" are relative to the RNA transcript in question and not to the DNA strand as a whole. In other words, either DNA strand can serve as the sense or antisense strand for a particular RNA transcript. In some cases, RNA transcripts can be transcribed in both directions (i.e. on either strand) from a common promoter region, or be transcribed from within introns on either strand (see "ambisense" below).[1][2][3]

Antisense DNA
The two complementary strands of double-stranded DNA (dsDNA) are usually differentiated as the "sense" strand and the "antisense" strand. The DNA sense strand looks like the messenger RNA (mRNA) and can be used to read the expected protein code; for example, ATG in the sense DNA may correspond to an AUG codon in the mRNA, encoding the amino acid methionine.

However, the DNA sense strand itself is not used to make protein by the cell. It is the DNA antisense strand which serves as the source for the protein code, because, with bases complementary to the DNA sense strand, it is used as a template for the mRNA. Since transcription results in an RNA product complementary to the DNA template strand, the mRNA is complementary to the DNA antisense strand. The mRNA is what is used for translation (protein synthesis).

Hence, a base triplet 3'-TAC-5' in the DNA antisense strand can be used as a template which will result in an 5'-AUG-3' base triplet in mRNA (AUG is the codon for methionine, the start codon). The DNA sense strand will have the triplet ATG, which looks just like AUG but will not be used to make methionine because it will not be used to make mRNA. The DNA sense strand is called a "sense" strand not because it will be used to make protein (it won't be), but because it has a sequence that looks like the protein codon sequence.

In biology and research, short antisense molecules can interact with complementary strands of nucleic acids, modifying expression of genes. See the section on "antisense oligonucleotides" below.


Example with double-stranded DNA
DNA strand 1: antisense strand (transcribed to)→ RNA strand (sense)

DNA strand 2: sense strand

Some regions within a double strand of DNA code for genes, which are usually instructions specifying the order of amino acids in a protein along with regulatory sequences, splicing sites, noncoding introns, and other complicating details. For a cell to use this information, one strand of the DNA serves as a template for the synthesis of a complementary strand of RNA. The template DNA strand is called the transcribed strand with antisense sequence and the mRNA transcript is said to be sense sequence (the complement of antisense). Because the DNA is double-stranded, the strand complementary to the antisense sequence is called the non-transcribed strand and has the same sense sequence as the mRNA transcript (though T bases in DNA are substituted with U bases in RNA).

A note on the confusion between "sense" and "antisense" strands: The strand names actually depend on which direction you are writing the sequence that contains the information for proteins (the "sense" information), not on which strand is on the top or bottom (that is arbitrary). The only real biological information that is important for labeling strands is the location of the 5' phosphate group and the 3' hydroxyl group because these ends determine the direction of transcription and translation. A sequence 5' CGCTAT 3' is equivalent to a sequence written 3' TATCGC 5' as long as the 5' and 3' ends are noted. If the ends are not labeled, convention is to assume that the sequence is written from left to right in the 5' to 3' direction. Watson strand refers to 5' to 3' top strand (5' → 3'), whereas Crick strand refers to 5' to 3' bottom strand (3' ← 5').[4] Both Watson and Crick strands can be either sense or antisense strands depending on the gene whose sequences are displayed in the genome sequence database. For example, YEL021W, an alias of URA3 gene used in NCBI database, defines that this gene is located on the 21st open reading frame (ORF) from the centromere of the left arm (L) of Yeast (Y) chromosome number V (E), and that the expression coding strand is Watson strand (W). YKL074C defines the 74th ORF to the left of the centromere of chromosome XI and denotes coding strand from the Crick strand (C). Another confusing term referring to "Plus" and "Minus" strand is also widely used. Whether the strand is sense (positive) or antisense (negative), the default query sequence in NCBI BLAST alignment is "Plus" strand.

Antisense RNA
Main article: Antisense RNA
Antisense RNA is an RNA transcript that is complementary to endogenous mRNA. In other words, it is a non-coding strand complementary to the coding sequence of RNA; this is similar to negative-sense viral RNA. Introducing a transgene coding for antisense RNA is a technique used to block expression of a gene of interest. Radioactively-labelled antisense RNA can be used to show the level of transcription of genes in various cell types. Some alternative antisense structural types are being experimentally applied as antisense therapy, with at least one antisense therapy approved for use in humans.[citation needed]

When mRNA forms a duplex with a complementary antisense RNA sequence, translation is blocked. This process is related to RNA interference.

Antisense nucleic acid molecules have been used experimentally to bind to mRNA and prevent expression of specific genes. Antisense therapies are also in development; in the USA, the Food and Drug Administration (FDA) has approved phosphorothioate antisense oligos fomivirsen (Vitravene) and mipomersen (Kynamro)[5] for human therapeutic use.

Cells can produce antisense RNA molecules naturally, called microRNA, which interact with complementary mRNA molecules and inhibit their expression.

RNA sense in viruses
In virology, the genome of an RNA virus can be said to be either positive-sense, also known as a "plus-strand", or negative-sense, also known as a "minus-strand". In most cases, the terms sense and strand are used interchangeably, making such terms as positive-strand equivalent to positive-sense, and plus-strand equivalent to plus-sense. Whether a virus genome is positive-sense or negative-sense can be used as a basis for classifying viruses.

Positive-sense
Positive-sense (5' to 3') viral RNA signifies that a particular viral RNA sequence may be directly translated into the desired viral proteins. Therefore, in positive-sense RNA viruses, the viral RNA genome can be considered viral mRNA, and can be immediately translated by the host cell. Unlike negative-sense RNA, positive-sense RNA is of the same sense as mRNA. Some viruses (e.g., Coronaviridae) have positive-sense genomes that can act as mRNA and be used directly to synthesize proteins without the help of a complementary RNA intermediate. Because of this, these viruses do not need to have an RNA polymerase packaged into the virion.

Negative-sense
Negative-sense (3' to 5') viral RNA is complementary to the viral mRNA and thus from it a positive-sense RNA must be produced by an RNA-dependent RNA polymerase prior to translation. Negative-sense RNA (like DNA) has a nucleotide sequence complementary to the mRNA that it encodes. Like DNA, this RNA cannot be translated into protein directly. Instead, it must first be transcribed into a positive-sense RNA that acts as an mRNA. Some viruses (Influenza, for example) have negative-sense genomes and so must carry an RNA polymerase inside the virion.

Antisense oligonucleotides
Gene silencing can be achieved by introducing into cells a short "antisense oligonucleotide" that is complementary to an RNA target. This experiment was first done by Zamecnik and Stephenson in 1978[6] and continues to be a useful approach, both for laboratory experiments and potentially for clinical applications (antisense therapy).[7]

If the antisense oligonucleotide contains a stretch of DNA or a DNA mimic (phosphorothioate DNA, 2'F-ANA, or others) it can recruit RNase H to degrade the target RNA. This makes the mechanism of gene silencing catalytic. Double-stranded RNA can also act as a catalytic, enzyme-dependent antisense agent through the RNAi/siRNA pathway, involving target mRNA recognition through sense-antisense strand pairing followed by target mRNA degradation by the RNA-induced silencing complex (RISC). The R1 plasmid hok/sok system provides yet another example of an enzyme-dependent antisense regulation process through enzymatic degradation of the resulting RNA duplex.

Other antisense mechanisms are not enzyme-dependent, but involve steric blocking of their target RNA (e.g. to prevent translation or induce alternative splicing). Steric blocking antisense mechanisms often use oligonucleotides that are heavily modified. Since there is no need for RNase H recognition, this can include chemistries such as 2'-O-alkyl, peptide nucleic acid (PNA), locked nucleic acid (LNA), and Morpholino oligomers.


I am at a loss understanding that.... So how did Clegg decide that what the forensics stated was accurate?? Remember he was completely flummoxed by the idea of an ear print being able to identify someone... So how did he manage to understand Molecular Biology??? He cannot (imo) have had anyone at anytime check anything to do with the DNA....

Clegg didn't verify any of this with these expert witness's??  Having them explain how Dr Vincent Tabak's DNA was a match?? 


https://en.wikipedia.org/wiki/Sense_(molecular_biology)

Edit.... If breath can give you a DNA recording, then wasn't it possible that the DNA sample of Dr Vincent Tabak came from something that belonged to CJ??  They would have been in close contact...

And the Forensically tested CJ's clothes etc.....

Or am I mistaken??


Offline justsaying

Re: The Defence Will State Their Case
« Reply #2008 on: October 10, 2018, 07:49:23 PM »
So how did they apparently tie it to Dr Vincent Tabak?? Is it possible to have had the same result with another person?? Depending on + or - ??


I honestly do not know - but it being said to be one in a billion, the chances of it being someone else's DNA are slim.

Quote
I am at a loss understanding that.... So how did Clegg decide that what the forensics stated was accurate?? Remember he was completely flummoxed by the idea of an ear print being able to identify someone... So how did he manage to understand Molecular Biology??? He cannot (imo) have had anyone at anytime check anything to do with the DNA....

Clegg didn't verify any of this with these expert witness's??  Having them explain how Dr Vincent Tabak's DNA was a match??

I do not know if he will have requested tests of his own, taking into account that it was not disputed that Tabak had in fact touched her body whilst killing/moving her.  I would assume that the experts did take the stand though. I would also assume that if he did not admit to killing her then the defence would have had to hire its own experts.

Quote
https://en.wikipedia.org/wiki/Sense_(molecular_biology)

Edit.... If breath can give you a DNA recording, then wasn't it possible that the DNA sample of Dr Vincent Tabak came from something that belonged to CJ??  They would have been in close contact...

And the Forensically tested CJ's clothes etc.....

Or am I mistaken??

I think you're mistaken. If you compare where the DNA was found to what Tabak stated, then it is fair to say he himself put the DNA on her, as opposed to innocent transfer. He said he carried her under her knees, which is where his DNA was found on her. DNA was found on her breast but not on her top. It points to the DNA being left there by Tabak himself.

Offline justsaying

Re: The Defence Will State Their Case
« Reply #2009 on: October 10, 2018, 07:53:23 PM »
Also Nine, if CJ had transferred Tabaks DNA to the victim, then both profiles would have been found. As it were,  only Tabaks was found on her body/clothes.