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How can I run Ubuntu 16.04 from a USB stick and retain the changes that I have made to the set up. Given that every time I close down my system Ubuntu removes the changes that I have made to the USB stick.

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If you want to save changes to a Live Ubuntu install, the install needs to be Persistent.

You can save up to 4GB of changes if you use UNetbootin to install Ubuntu to a USB stick.

You can save unlimited changes to a persistent install made with mkusb.

Startup Disk Creator that comes with Ubuntu no longer makes persistent installs.

It is also possible to do a Full install to USB, the same as to an internal HDD. It is recommended that you disable the internal drive before proceeding with this so as not to mess up the internal drive or install the boot loader in the wrong place. It also ensures a clean grub menu on the USB drive.

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Here's a howto for persistent LiveUsb There's also a wiki page about it, though maybe not up to date.

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