As leszek says I think you have a few things confused:

DataNucleus is a JDO/JPA implementation that can run within AppEngine.

AppEngine provides 2 persistence mechanisms, BigTable and VFS (Virtual
File System). You cannot configure your GoogleApp to use an external
RDBMS, nor can you host an RDBMS within your GoogleApp. Also note that
with each DB record, BigTable effectively stores not only the data but
also the metadata for the table. Ie all the column names are stored
alongside the column data, for each record. So a Gigabyte of data will
commonly consume 10GB of space within BigTable.

Using GWT on your client is orthogonal, to the persistence on the
server.

However, if you have a clean JPA (non-Hibernate specific)
implementation you might have a way continue to use JPA within your
GoogleApp by using a H2 RDBMS implementation running on top of VFS.
See 
http://groups.google.com/group/google-appengine-java/browse_thread/thread/fce7750aad2845ff?hl=en
and
    http://groups.google.com/group/gaevfs/browse_thread/thread/c23b8af5791b3a4

On a side note, Andy (aka Datanucleus) you need to chill dude.
Users are reporting problems with Datanucleus because they are feeling
pain.
Barking at them is not the way to win support and market share for
Datanucleus, quite the opposite.

William


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