[3dem] Unrecognised CryoEM contaminant 2

[Sharon G Wolf]

I agree with Reza.
It seems to me that a portion of the particles have burst apart, and that you see a mixture of intact particles, and burst-apart particles.
Sharon

-----Original Message-----
From: 3dem-bounces at ncmir.ucsd.edu [mailto:3dem-bounces at ncmir.ucsd.edu] On Behalf Of rkhayat at ccny.cuny.edu
Sent: Friday, 28 March, 2014 20:00
To: Gabriel Lander; 3dem at ncmir.ucsd.edu
Subject: Re: [3dem] Unrecognised CryoEM contaminant 2

The hobgolins are the same size as the virus particles! 
Perhaps treating the samples with DNase/RNase and seeing if they disappear will test the possibility that they are DNA/RNA and not hobgoblins...


Reza Khayat, PhD
Assistant Professor
The City College of New York
Department of Chemistry, MR-1135
160 Convent Avenue
New York, NY  10031
Tel. (212) 650-6070


---- Original message ----
>Date: Fri, 28 Mar 2014 09:46:59 -0700
>From: 3dem-bounces at ncmir.ucsd.edu (on behalf of Gabriel
Lander <glander at gmail.com>)
>Subject: Re: [3dem] Unrecognised CryoEM contaminant 2
>To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
>
>   It would help if you posted some images of the same
>   sample in negative stain. Is there a possibility
>   that this is condensed RNA? It would be almost
>   invisible in negative stain, but show up very nicely
>   in cryo.
>   Otherwise I'm inclined to say that these are
>   microscopic hobgoblins that have infested your
>   plunging device.
>   On Mar 28, 2014, at 9:42 AM, "Xinghong Dai"
>   <bestdz at gmail.com> wrote:
>
>     Hi Daniel,
>     To me, it looks like phantom caused by too thin
>     ice. Especially black patches around the hole in
>     up-left panel, they look like almost-dry areas.
>     Try to increase the humidity, and wait shorter
>     time before, and after, you blot. Also try shorter
>     blot time.
>     Good luck!
>
>     Best regards,
>
>
>     Xinghong Dai
>
>     *********: 3dem-bounces at ncmir.ucsd.edu [mailto:3dem-
bounces at ncmir.ucsd.edu] ****** Daniel
>     Luque
>     ************: Friday, March 28, 2014 5:52 AM
>     *********: 3dem at ncmir.ucsd.edu
>     ******: [3dem] Unrecognised CryoEM contaminant 2
>
>     Hello
>
>     Before a  couple  of  days waiting  for  the  list
>     moderator approval  to attach  the images  in  the
>     list , I do not have received any response (either
>     positive or negative)  and I  do not  have find  a
>     mail/way for contact. Thus, I have made the images
>     available at our server at:
>
>     http://halley.cnb.csic.es/~virus/3DEM/Example_images.pdf
>
>     Bellow is text of the original question:
>
>     We are doing  CryoEM of viral  particles. When  we
>     check the sample by negative staining, a field  of
>     intact homogeneous  particles without  significant
>     contaminants  is   observed.  However,   when   we
>     visualize the same sample by CryoEM,  additionally
>     to a lower-than expected  number of particles,  we
>     observe an unexpected  contaminant mostly  located
>     in the  holes  (see attached  document  with  some
>     example images). Does  anybody see  this class  of
>     contaminants? Any idea about its origin?
>
>     Thanks in advance!
>
>
>     Daniel Luque
>
>
>
>
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