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[bioontology-support] Feedback

Trish Whetzel whetzel at
Wed May 19 21:51:11 PDT 2010

Interesting. I too am having problems with the text you sent, but the  
text below works fine (text from the first element for nanoparticle on  
the resource page).  I can report this as a bug.  Do you have a  
comment on the priority for this?

Montet et al. reported a detailed synthesis of cRGD-CLIO(Cy5.5) (5).  
Initially, a linear RGD peptide GSSK(FI)GGGCRGDC (IRGD) was obtained  
with the Fmoc method as a C-terminal amide and oxidized via bubbling  
air to yield a disulfide-linked cRGD peptide in 0.1 M ammonium  
bicarbonate. The amino-CLIO nanoparticle was synthesized in several  
steps. The starting material, monocrystalline iron oxide (MION), was  
synthesized by neutralization of ferrous salts, ferric salts, and  
dextran with ammonium hydroxide, followed by ultra-filtration (14).  
The obtained MION was cross-linked in strong base with epichlorohydrin  
and then reacted with ammonia to produce amino-CLIO (CLIO-NH2) (14).  
Finally, CLIO-NH2 was reacted with the N-hydroxysuccinimide ester of  
Cy5.5 (Amersham Biosciences Corp., Piscataway, NJ), followed by  
peptide attachment using disuccinimidyl suberimidate to produce cRGD- 
CLIO(Cy5.5) (5). There were ~250 amines, 8,000 iron atoms, 27  
peptides, and 8 Cy5.5 molecules per CLIO-NH2 nanoparticle.

On May 19, 2010, at 9:37 PM, Nigam Shah wrote:

> and FITC-BCDDDGQMLGNHLAVGQWR (ScrBN-CLIO-Cy5.5, control peptide) was  
> described by Montet et al. (1). In brief, the peptides were  
> synthesized using solid-phase peptide synthesis via 9- 
> fluorenylmethyloxycarbonyl (Fmoc) chemistry. The N-terminus beta- 
> alanine (B) was used to conjugate with FITC and the thiol group of  
> cysteine was utilized to conjugate the peptide with CLIO-Cy5.5  
> nanoparticles. CLIO-NH2 nanoparticles (produced by coating iron  
> oxide nanoparticles with dextran, followed by cross-linking with  
> epichlorohydrin, and then activated by reacting with ammonia (13,  
> 14)) were mixed with Cy5.5 solution to produce 5.1 dyes per  
> nanoparticle. Purified CLIO(NH2)-Cy5.5 was further activated by  
> reacting with succinimidyl iodoacetate. Activated CLIO-Cy5.5 was  
> then conjugated with a BN peptide through cysteine. The size of the  
> nanoparticle was determined to be 35 nm using laser light scattering  
> method, with an average of 50 peptides per iron oxide particle.
> .. is the exact text.
> -nigam.
> On Wed, May 19, 2010 at 9:36 PM, Nigam Shah <nigam at>  
> wrote:
> Anything .. I just took the second element from MICAD that shows up  
> on the "nanoparticle" resource page.
> -nigam.
> On Wed, May 19, 2010 at 9:19 PM, Trish Whetzel  
> <whetzel at> wrote:
> Hi Nigam,
> Can you send the input text?
> Trish
> On May 19, 2010, at 8:31 PM, admin at wrote:
> Name : Nigam Shah
> Email : nigam at
> Comment:
> Annotator is non responsive as of 8:30 PM, pacific time on  
> 5/18/2010. Small amount of text, with just one ontology to annotate  
> with (NPO) .. takes over 5 minutes and no response comes back.
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at

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