All -- I would be really interested in peoples' answers to Odile's 
question about centricons.  We're using our stock up quickly and are 
trying to figure out what to substitute in for them.

best,

Rika

Quoting "Loreille, Odile CONTR" <[log in to unmask]>:

> No apology necessary Susannah. Everybody has its own preferences when it
> comes to Molecular Biology. If "no BSA" works fine for your
> applications, then everything is fine, and you should keep it that way.
>
> I think that the people who need it the most are people who need to
> fight against high amounts of Humic Acids. BSA is great because it is
> much cheaper than other reagents like the T4.
>
> I agree though that people should try to mention it more often in their
> publications. We are so used to our good old protocols that we tend to
> skip more and more the M&M part. Or maybe it's the journal's fault.
> Nowadays, the shorter, the better, sometimes it's a pity. Especially for
> people who recently started working with degraded DNA.
>
> Now, I'm on a roll people. I have a last question for the Centricon
> lovers.
> As you probably know, Millipore stopped making/selling centricons.
> What are you using instead? Ultra-4? Vivacons? What is your experience.
> For those who work with human DNA, did you detect contamination
> problems?
> I really like the ultra-4 but I start thinking they might be slightly
> contaminated with very small human DNA fragments.
>
>
>
>
>
>
> -----Original Message-----
> From: Ancient DNA List [mailto:[log in to unmask]] On Behalf Of
> Susannah Baldry
> Sent: Wednesday, October 29, 2008 5:41 PM
> To: [log in to unmask]
> Subject: Re: BSA
>
> I apologise, I didn't mean to make it sound like a UK "consensus"! Just
> a consensus of the people still in the office at 5pm! I should clarify
> that our team works primarily with modern DNA and we do not have any
> trouble with our reactions omitting BSA. I believe the high-throughput
> sequencing teams do use BSA as part of the commercial kit; I am not sure
> why it is required in their chemistries but not our small-scale
> experiments. I suppose modern samples are more simply cleaned than aDNA
> so inhibitive compounds are not such an issue.
>
> However I stick by my original statement, that if a paper details the
> contents of a PCR reaction and does not mention BSA, then BSA should not
> need to be assumed!
>
> Susannah
>
>
> Frederika Kaestle <[log in to unmask]> wrote:
>> Actually, we still use BSA a lot in the US in our ancient DNA work.
> In
>> the past (when I was in grad school in David Glenn Smith's lab), we
> did
>> some in-house experiments and found it does help with problematic
>> extracts that seem to inhibit enzyme (Taq) activity due to coextracted
>
>> compounds.  Since it's no too expensive, we just add it to all our
> aDNA
>> reactions (unless we're working with ancient bovids, in which case we
>> use Rabbit Serum Albumin). We haven't had a problem with it becoming
>> contaminated, although in my lab our stock is aliquoted into very
> small
>> volumes.  But if the consensus in the UK is that it's a waste of time
>> and money, I'd love to see some research showing that.
>>
>> best,
>>
>> Rika
>>
>> Dr. Frederika Kaestle
>> Departments of Anthropology and Biology
>> Indiana University, Bloomington
>> USA
>>
>> Susannah Baldry wrote:
>> > Dear Odile,
>> >
>> > I am not sure which protocols in the past used BSA in the PCR mix,
> but
>> > (after throwing your question at my office colleagues) we agree it
> is
>> > not common now - except for some commercial enzyme kits for arrays
> and
>> > sequencing. In the latter case you would be following manufacturer's
>
>> > protocols which would be exhaustive. If a published paper specifies
>> > the contents of the PCR reaction it should be complete & repeatable,
>
>> > so you will be safe following their protocol as described.
>> >
>> > Good luck with your experiments,
>> >
>> > Kind regards,
>> >
>> > Susannah Baldry
>> >
>> >
>> > Odile Loreille wrote:
>> >> Hi everyone,
>> >>
>> >> I'm back with a second question. Reading the latest aDNA papers, I
>> >> noticed that many PCR protocols don't mention BSA anymore.
>> >> I was wondering if you, aDNA specialists, omitted this information
>> >> because you believed that the presence and amount of BSA isn't
> worth
>> >> mentioning  or if you truly stopped using it in your
> amplifications.
>> >>
>> >> If you want your response to be private, please simply write to
>> >> [log in to unmask]
>> >>
>> >> Thank you very much
>> >>
>> >> Odile
>> >>
>> >
>> >
>> >
>