Methods Digest, Vol 23, Issue 13

Kristin Hager via methods%40net.bio.net (by khager1 from nd.edu)
Mon Apr 16 12:36:49 EST 2007


Thank you. I have been able to reach Dr. Marck and received the DNA  
strider 1.4. It works great. Thanks, K
------------------------------------------------------------
Kristin M. Hager, PhD
Assistant Professor Biological Sciences
Office Tel./Fax: 574-631-8135/7413
Center for Global Health and Infectious Disease
216 Galvin Life Sciences Building
University of Notre Dame
Notre Dame, IN. 46556-0369 USA

"Chance Favors the Prepared Mind." Louis Pasteur




On Apr 16, 2007, at 1:01 PM, methods-request from oat.bio.indiana.edu wrote:

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> Today's Topics:
>
>    1. Lipase assay? (Yoram Gerchman)
>    2. Re: Quantification of Western Blot Signals on ECL Film
>       (Dr Engelbert Buxbaum)
>    3. Re: DNA Strider 1.4 for OS X? (Bas Jansen) (Yoram Gerchman)
>    4. Re: How to ship? Nitrocellulose memb for Western
>       (Dr Engelbert Buxbaum)
>    5. Re: Lipase assay? (WS)
>    6. qPCR negative controls (Gerardine.Persson from gmail.com)
>    7. Re: DNA Strider 1.4 for OS X? (Bas Jansen) (Ian A. York)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 15 Apr 2007 08:52:22 +0300
> From: Yoram Gerchman <gerchman from research.haifa.ac.il>
> Subject: Lipase assay?
> To: "methods bio.net" <methods from magpie.bio.indiana.edu>
> Message-ID: <1176616342.4621bd968519f from webmail.haifa.ac.il>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Greetings netters
> I am looking for a colorimetric assay of lipase activity  (no  
> radioisotops or
> fluorescence, sorry), a kit is preferred.
> Any ideas welcome.
> Thanks
> Yoram
>
> ---------------------------------------------------------------------- 
> --
> This message was sent using IMP, the Webmail Program of Haifa  
> University
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 15 Apr 2007 15:04:16 -0400
> From: Dr Engelbert Buxbaum <engelbert_buxbaum from hotmail.com>
> Subject: Re: Quantification of Western Blot Signals on ECL Film
> To: methods from net.bio.net
> Message-ID: <58fb70F29foe3U1 from mid.individual.net>
> Content-Type: text/plain; charset=iso-8859-2
>
> WS wrote:
>
>> I want to quantificate signals on X-Ray films obtained by Western
>> Blot / ECL.
>
> If you can show by western that your antibody interacts with only 1
> protein in your sample, quantitation is much easier to perform by dot-
> rather than western blot.
>
> There are 96-well filtration manifolds commercially available,  
> which can
> be used to filter the sample over a high-protein-binding membrane  
> (e.g.
> PVDF). Alternatively, there are also 96-well plates available with
> filters as bottom. For small samples add PBS or similar to the  
> wells, so
> that the sample fills the entire area of the well and you get defined
> spot shapes.
>
> After filtration the blot is developed like a western, using
> peroxidase-conjugated secondary antibodies. After incubation in a
> substrate solution for a few minutes place the membrane in a holder  
> and
> that into a 96-well chemoluminescence counter (I used Berthold and was
> quite satisfied, but other manufacturers make similar instruments).
>
> This type of assay is linear over 5-6 orders of magnitude. If you
> include calibration standards you get absolute concentrations. And  
> with
> 96 samples handled in parallel, even large studies can be performed  
> in a
> timely and economic manner.
>
>
> ------------------------------
>
> Message: 3
> Date: Sun, 15 Apr 2007 21:57:51 +0300
> From: Yoram Gerchman <gerchman from research.haifa.ac.il>
> Subject: Re: DNA Strider 1.4 for OS X? (Bas Jansen)
> To: methods from oat.bio.indiana.edu
> Message-ID: <1176663471.462275afc2260 from webmail.haifa.ac.il>
> Content-Type: text/plain; charset=ISO-8859-1
>
> You can try ApE (Free) - http://www.biology.utah.edu/jorgensen/ 
> wayned/ape/
>> In article <None-F7E733.18305030032007 from geraldo.cc.utexas.edu>,
>>  Joe Doe <None from mail.utexas.edu> wrote:
>>
>>> In article <mailman.527.1175021213.5139.methods from net.bio.net>,
>>>  Kristin Hager <khager1 from nd.edu> wrote:
>>>
>>>> Hi,
>>>> I am looking for DNA strider 1.4.  I have received no email  
>>>> response
>>>> using the email address: marck from jonas.saclay.cea.fr.  Do you have  
>>>> any
>>>> suggestions on how to buy this software? I have used the DNA  
>>>> strider
>>>> program for more than 15 years and would like to continue to do so.
>>>> Best, Kristin Hager
>>>
>>> If you are willing to consider alternatives:  Invitrogen allows free
>>> usage of Vector NTI for academic labs.  You can get 1 Windows and  
>>> 1 Mac
>>> license and each license allows installation on up to 3 machines.  
>>> The
>>> license needs to be renewed on a yearly basis.
>>>
>>> https://catalog.invitrogen.com/index.cfm? 
>>> fuseaction=userGroup.userGroupHo
>>> me
>>
>> One word of caution though:
>> <http://www.invitrogen.com/content.cfm?pageid=11368>.
>>
>> Bas
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> Methods mailing list
>> Methods from net.bio.net
>> http://www.bio.net/biomail/listinfo/methods
>>
>> End of Methods Digest, Vol 23, Issue 12
>> ***************************************
>>
>
>
>
>
> ---------------------------------------------------------------------- 
> --
> This message was sent using IMP, the Webmail Program of Haifa  
> University
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 15 Apr 2007 15:04:22 -0400
> From: Dr Engelbert Buxbaum <engelbert_buxbaum from hotmail.com>
> Subject: Re: How to ship? Nitrocellulose memb for Western
> To: methods from net.bio.net
> Message-ID: <58fb76F2g7dbaU1 from mid.individual.net>
> Content-Type: text/plain; charset=iso-8859-2
>
> Tom Anderson wrote:
>
>> On Thu, 5 Apr 2007, AK wrote:
>>
>>> Hello everyone, I need to ship internationally some nitrocellulose
>>> membranes for Western analysis. I plan to transfer, block with milk,
>>> wash, then place in wet (with azide) plastic bag (sealed), ship with
>>> regular mail.  could you guide me with any tips or advise.
>>
>> For starters, see if you can use PVDF instead. Many postal  
>> services take a
>> dim view of attempts to send explosives by mail.
>
> I tend to aggree. The PVDF membrane can be shipped after blotting and
> drying, that is without blocking.  The recipient does not hydrate the
> membrane but starts directly with detection on the dry membrane, see
> Sadra et al., Anal. Biochem. 278 (2000) 235-7.
>
>
> ------------------------------
>
> Message: 5
> Date: 15 Apr 2007 12:32:52 -0700
> From: "WS" <novalidaddress from nurfuerspam.de>
> Subject: Re: Lipase assay?
> To: methods from net.bio.net
> Message-ID: <1176665572.613201.23590 from w1g2000hsg.googlegroups.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Yoram,
>
> Google finds more than you'll need *^_^*
>
> http://www.google.de/search?q=colorimetric+lipase 
> +assay&ie=utf-8&oe=utf-8&aq=t&rls=org.mozilla:en- 
> US:official&client=firefox-a
>
> Wo
>
>
> On Apr 15, 7:52 am, Yoram Gerchman <gerch... from research.haifa.ac.il>
> wrote:
>> Greetings netters
>> I am looking for a colorimetric assay of lipase activity  (no  
>> radioisotops or
>> fluorescence, sorry), a kit is preferred.
>> Any ideas welcome.
>> Thanks
>> Yoram
>>
>> --------------------------------------------------------------------- 
>> ---
>> This message was sent using IMP, the Webmail Program of Haifa  
>> University
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: 15 Apr 2007 12:51:42 -0700
> From: Gerardine.Persson from gmail.com
> Subject: qPCR negative controls
> To: methods from net.bio.net
> Message-ID: <1176666702.039159.111820 from o5g2000hsb.googlegroups.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> This is a fundamental question about (quantitative realtime) PCR.
>
> Hi group,
> I've been using ABI7000 realtime PCR, mostly with SYBR detection. I've
> always been wondering why I pick up some amplification eventually.
>
> I get amplification of my samples containing template, so far so good.
> They come up at cycle numbers that are around 20-30.
>
> My negative control (PCR with water as "template") also gives
> amplification, although as late as CT 35-45, depending on the primer
> pairs used. But eventually, they all come up.
>
> My questions:
> - What exactly is actually amplified here? I've had many students ask
> me, and I grow tired of answering "I don't know, stop asking"
>
> - Why do the CTs vary widely (standard deviation of ca. 3 opposed to
> <0,5 for normal triplicates) in the negative controls?
>
> Just so this is clear: I'm not looking for a solution to a problem. I
> just want a sound explanation of this phenomenon, which has been
> bugging me for a while! And who knows, maybe my students will learn
> something, too :)
>
> Cheers,
>
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 16 Apr 2007 02:14:29 +0000 (UTC)
> From: iayork from panix.com (Ian A. York)
> Subject: Re: DNA Strider 1.4 for OS X? (Bas Jansen)
> To: methods from net.bio.net
> Message-ID: <evum65$fm0$1 from reader2.panix.com>
>
> In article <mailman.746.1176688593.5139.methods from net.bio.net>,
> Yoram Gerchman  <gerchman from research.haifa.ac.il> wrote:
>> You can try ApE (Free) - http://www.biology.utah.edu/jorgensen/ 
>> wayned/ape/
>
> -- or EnzymeX, also free, and (unlike ApE) being actively maintained: 
> http://mekentosj.com/enzymex/
>
> But as others have pointed out, Dr Marck does answer his email
> (marck from matthieu.saclay.cea.fr) and DNA Strider is still available.
>
> Ian
>
>>> In article <None-F7E733.18305030032007 from geraldo.cc.utexas.edu>,
>>>  Joe Doe <None from mail.utexas.edu> wrote:
>>>
>>>> In article <mailman.527.1175021213.5139.methods from net.bio.net>,
>>>>  Kristin Hager <khager1 from nd.edu> wrote:
>>>>
>>>>> Hi,
>>>>> I am looking for DNA strider 1.4.  I have received no email  
>>>>> response
>>>>> using the email address: marck from jonas.saclay.cea.fr.  Do you  
>>>>> have any
>>>>> suggestions on how to buy this software? I have used the DNA  
>>>>> strider
>>>>> program for more than 15 years and would like to continue to do  
>>>>> so.
>>>>> Best, Kristin Hager
>>>>
>>>> If you are willing to consider alternatives:  Invitrogen allows  
>>>> free
>>>> usage of Vector NTI for academic labs.  You can get 1 Windows  
>>>> and 1 Mac
>>>> license and each license allows installation on up to 3  
>>>> machines. The
>>>> license needs to be renewed on a yearly basis.
>>>>
>>>> https://catalog.invitrogen.com/index.cfm? 
>>>> fuseaction=userGroup.userGroupHo
>>>> me
>>>
>>> One word of caution though:
>>> <http://www.invitrogen.com/content.cfm?pageid=11368>.
>>>
>>> Bas
>>>
>>>
>>> ------------------------------
>>>
>>> _______________________________________________
>>> Methods mailing list
>>> Methods from net.bio.net
>>> http://www.bio.net/biomail/listinfo/methods
>>>
>>> End of Methods Digest, Vol 23, Issue 12
>>> ***************************************
>>>
>>
>>
>>
>>
>> --------------------------------------------------------------------- 
>> ---
>> This message was sent using IMP, the Webmail Program of Haifa  
>> University
>>
>
>
> -- 
>     Ian York   (iayork from panix.com)  <http://www.panix.com/~iayork/>
>     "-but as he was a York, I am rather inclined to suppose him a
>      very respectable Man." -Jane Austen, The History of England
>
>
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>
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> End of Methods Digest, Vol 23, Issue 13
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