Hi Deborah:

    Hmmm ... sounds like an MPTP/neuroprotection experiment. :-)   What 
I do is notch the cortex (I cut a V out of the cortex with a razor 
blade) on the (animal's) right side. This works for me but if you cut 
far into the brain stem the cortex may separate during staining and then 
you have to match sections, not fun. You could also use a 25 gauge hypo 
needle to punch a hole on the right side in the region of the superior 
colliculus, or far enough dorsal to avoid the SNpc. I have found that 
examining free-floating sections against a black background allows one 
to see a great deal of detail.  Perhaps a bit of  india ink in the hypo 
might work?
    The clinical lab people on this list use india ink or a commercially 
available indelible marking pen to mark tissue so they can orient it for 
sectioning, that sounds like a good thing to try. I'm sure someone will 
provide the name of that device.  "Sharpie" ink might work but it is 
soluble in alcohols and xylene.
    Have fun counting all those cells!

Geoff

deborah.mills@syngenta.com wrote:

>I am sectioning Para formaldehyde fixed, sucrose cryoprotected mouse brain
>tissue on the microtome to then perform free floating tyrosine hydroxylase
>IHC with a cresyl violet counterstain to count CV+/TH- neurons in the SNpc
>region.  Before sectioning I need to mark the tissue so I can load them all
>onto slides in the same orientation.  I have tried puncturing the tissue
>with various sizes of needle and have found it difficult to get a hole large
>enough to be visible to the eye yet small enough to avoid the SNpc and avoid
>the sections breaking apart during the staining process.  Is there a dye I
>could puncture with that wouldn't spread to the rest of the tissue or
>interfere with my IHC?  Any other suggestions?
>
>Many thanks in advance.
>
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>  
>

-- 
--
**********************************************
Geoff McAuliffe, Ph.D.
Neuroscience and Cell Biology
Robert Wood Johnson Medical School
675 Hoes Lane, Piscataway, NJ 08854
voice: (732)-235-4583; fax: -4029 
mcauliff@umdnj.edu
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