Classification: UNCLASSIFIED
Caveats: NONE

Are you sure about the vericons? From Sartorius, I know the vivacons. We
tested those and they are heavily contaminated for mito.
Please, let us know if these are really different items and if they are
clean(er).
Thank you
odile

-----Original Message-----
From: Ancient DNA List [mailto:[log in to unmask]] On Behalf Of
Palmer, Sarah
Sent: Wednesday, July 15, 2009 1:23 PM
To: [log in to unmask]
Subject: Centricon alternative

Dear all,

As many of you will know by now, Millipore ceased making centricon
filtration units which many of us used. I have tried the Millipore
alternatives and found them not fit for purpose as I loose too much
product in the process. Today I met Peter Wright from Sartorius Stedim
Biotech, who I believe used to supply the centricons to Millipore and
they have a product (called vericons) which is designed for DNA
concentration. This was news to me so thought it may be to others too. I
will be trialing some samples soon, but the amplicon filters are the
same and the units which I have seen are almost identical to the old
centricons, futhermore Peter informed me that Satorius Stedim have a 2mL
unit to fit into microfuges in development also. If you are also
interested in trying these products please find details attached and
Peter's contact details below. I'm sure if he cannot help you himself he
will be able to point you in the right direction.

Email: [log in to unmask] Mobile: +44 7710 075872 Fax:
+44 1372 726171 Phone: +44 1372 737159 Sartorius Stedim UK Limited
Longmead Business Centre, Blenheim Road, Epsom Surrey, KT19 9QQ

Sincerely,
Sarah Palmer

Archaeogenomics lab
Warwick HRI
Wellesbourne
Warwickshire
CV359EF

+44 (0)2476 575145
[log in to unmask]



-----Original Message-----
From: Ancient DNA List on behalf of Eveline Altena
Sent: Tue 7/14/2009 2:41 PM
To: [log in to unmask]
Subject: Re: mtDNA in teeth (UNCLASSIFIED)

Dear people,

I want to thank you for your help in trying to solve my strange case.
Although I don't think I solved it I sure did learn a lot from your
comments. I hope I can help you guys out some time.

Best wishes,

Eveline Altena

-----Original Message-----
From: Ancient DNA List [mailto:[log in to unmask]
<blockedmailto:[log in to unmask]> ] On Behalf Of Loreille,
Odile CONTR
Sent: woensdag 8 juli 2009 17:33
To: [log in to unmask]
Subject: Re: mtDNA in teeth (UNCLASSIFIED)

Classification: UNCLASSIFIED
Caveats: NONE

If the teeth got + quants with Quantifiler, then they HAVE to work with
mito.


-----Original Message-----
From: Ancient DNA List [mailto:[log in to unmask]
<blockedmailto:[log in to unmask]> ] On Behalf Of Carney
Matheson
Sent: Wednesday, July 08, 2009 9:57 AM
To: [log in to unmask]
Subject: Re: mtDNA in teeth

Dear Evaline,
I agree with Wera, I would not expect inhibitors in the teeth to be
greater than that in the bone. Different tissue will have different
numbers of mitochondria and different mitochondria do have different
numbers of the mitochondrial genome but I do not expect this to be a
significant issue as many if not all other researchers have extracted
from teeth very successfully compared to bone. And if it was an issue
others would have noticed it.

Do you observe fragmentation in the STR profile?

That is the larger STR are not amplified or have a weaker PFU values?

Have you tried shorter fragments of approximately 100bp?

Are there metals associated with the burials?

You quantified all the samples and did they all have DNA based on those
results?

Did the bone and teeth that gave no result have quantifiable DNA?

Are the samples that amplified and the samples that failed have
different degrees of preservation or taphonomy?

Carney


Dr. Carney Matheson
Associate Professor
Department of Anthropology
Department of Biology
Paleo-DNA Laboratory
Lakehead University
955 Oliver Rd.
Thunder Bay
P7B 5E1, ON, Canada

School of Social Science (Adjunct)
University of Queensland
St Lucia, 4072, QLD, Australia




-----Original Message-----
From: Ancient DNA List [mailto:[log in to unmask]
<blockedmailto:[log in to unmask]> ] On Behalf Of Schmerer, Wera
M. (Dr)
Sent: July 8, 2009 9:24 AM
To: [log in to unmask]
Subject: Re: mtDNA in teeth

Dear Evaline and Mike,

Generally, I would not expect a significant content of inhibitory
substances in tooth material, especially not if the tooth in question
was sitting in the alveola until analyzed and thus was "protected" by
the surrounding bone.
When comparing extracts from tooth and bone, excavated from soil
burrials after hundreds or thousands of years, tooth extracts will
generally have significantly lower inhibitor concentrations than bone
extracts from the same skeleton.

Wera

-----Original Message-----
From: Ancient DNA List [mailto:[log in to unmask]
<blockedmailto:[log in to unmask]> ] On Behalf Of George M
Taylor
Sent: 08 July 2009 13:11
To: [log in to unmask]
Subject: Re: mtDNA in teeth

Dear Evaline,

Another factor to consider may be PCR inhibition. We have done some work
recently that shows that different PCR targets may be inhibited to
different extents by the same extract. Could it be that the inhibitor
profile is different in teeth and this is causing problems with the
particular mtDNA primers or amplicon targetted?

Mike





Dr. G.M.Taylor,
Windeyer Institute UCL,
46, Cleveland Street,
London W1T4JF.


> Dear Odile, Wera and Carney,
>
>
>
> Thank you for your response to my mail. Your answers are very helpful.
>
>
>
> To give you a bit better idea about my samples I'll explain a bit more

> about them. Currently I'm working on an archaeological project where I

> have three bone samples and nine teeth from the late medievals. Three 
> of the teeth and one bone sample give no result at all. But four teeth

> give both autosomal STRs and mtDNA sequences, two teeth give only 
> autosomal STRs and the other two bone samples only give mtDNA 
> sequences. I sequenced only the first half of HVR1 in two overlapping 
> fragments, with maximum fragment length of 154 bp (including primers).
>
> So it is not that I only get mt for bones and auto STRs from teeth, 
> but I was still a bit surprised with the result I got from this
project.
> Perhaps it is just a stochastic effect, but I heard from other people 
> to that they suspect that there might be more mtDNA in bone then in
teeth.
> But the explanation that nuclear DNA is better protected then mtDNA 
> also makes sense.
>
>
>
> So, again thanks for your help!
>
>
>
> Best regards,
>
>
>
> Eveline
>
> ________________________________
>
> From: Ancient DNA List [mailto:[log in to unmask] 
> <blockedmailto:[log in to unmask]> ] On Behalf Of Carney 
> Matheson
> Sent: dinsdag 7 juli 2009 15:50
> To: [log in to unmask]
> Subject: Re: mtDNA in teeth
>
>
>
> Dear Evelina,
>
> I have experienced this once.
>
> The occasion for which I experienced this was when an individual was 
> burnt and submerged in petroleum for a while. I suspected that the 
> recovery of mtDNA in this case was affected by the hydrocarbons that 
> were present and permeated the bones. The tooth root canal was exposed

> to hydrocarbons as we tested and identified their presence. However we

> did not work on the bone from this individual to compare the results.
>
>
>
> So in addition to Odile's and Wera's methodological comments maybe the

> taphonomy of the sample may explain the differential preservation.
>
>
>
> Remember that the nuclear DNA is somewhat protected by the histone 
> proteins to between 145-200bp while the mtDNA is fairly exposed with 
> only the possibility of the nucleoids (A DNA associated protein found 
> in the mitochondria) for protection. However the nucleoids are not 
> spaced the same way as the histones. Therefore the protection from the

> nuceloids does not provide specific fragment sizes, thus the 
> fragmentation can be random. There has been some research published on

> the protection of nucleoids to X-ray's and Hydrogen peroxide amongst 
> other agents.
>
>
>
> Carney Matheson
>
>
>
>
>
> Dr. Carney Matheson
>
> Associate Professor
>
> Department of Anthropology
>
> Department of Biology
>
> Paleo-DNA Laboratory
>
> Lakehead University
>
> 955 Oliver Rd.
>
> Thunder Bay
>
> P7B 5E1, ON, Canada
>
>
>
> School of Social Science (Adjunct)
>
> University of Queensland
>
> St Lucia, 4072, QLD, Australia
>
>
>
>
>
>
>
>
>
>
>
> From: Ancient DNA List [mailto:[log in to unmask] 
> <blockedmailto:[log in to unmask]> ] On Behalf Of Eveline 
> Altena
> Sent: July 6, 2009 6:24 AM
> To: [log in to unmask]
> Subject: mtDNA in teeth
>
>
>
> Dear colleagues,
>
>
>
> At our lab we have the idea from experiences with both forensic and 
> archeological human samples that there is much less mtDNA present in 
> teeth then in bone. We think so because sometimes we can get nuclear 
> DNA from teeth but no mtDNA (or we get mtDNA from bones but no nuclear
DNA).
> Even though we use very sensitive multiplex PCR kits for forensic 
> cases (eg Powerplex16 form Promega).
>
>
>
> I have heard from two other labs that they have the same experiences, 
> but I am not aware of articles that have tested this or where this is 
> discussed. Does anyone know of such an article or does anyone have the

> same experiences?
>
> Best regards,
>
>
>
> Eveline Altena
>
>
>
> PhD student ancient human DNA research
>
> Forensic Laboratory for DNA Research
>
> Leiden University Medical Center
>
> PO Box 9600
>
> 2300 RC Leiden
>
> The Netherlands
>
> phone: +31 (0)71 526 9540
>
> fax: +31 (0)71 526 8278
>
>
>
>
--
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Classification: UNCLASSIFIED
Caveats: NONE





Classification: UNCLASSIFIED
Caveats: NONE