Friday, September 17, 2010

is it possible to crudely in-vitro translate?

if you had synthetic GFP RNA, could you mix it with a crude cell
extract and see a glow? what about a doing
chromatography/gel-separation on the proteins and mix each one with
the supernatant of a centrifuged cell extract, then mixing with RNA to
look for a glow. in the first case you hope to get lucky, in the
second you would be trying to find the ribosomes, and add in some
amino acids and tRNAs.

To find T7 RNA polymerase from your extract(gotta be in the strain),
you would get this plasmid with a T7 driven GFP:
http://www.addgene.org/pgvec1?f=c&identifier=24387&atqx=(t7%20AND%20gfp)%20AND%20vectype:Bacterial%20Expression&cmd=findpl
(Plasmid 24387: pHL32)

To find normal RNA polymerase from a cell extract, you would get a
"normal" GFP plasmid:
http://www.addgene.org/pgvec1?f=c&identifier=17823&atqx=gfp%20AND%20vectype:Bacterial%20Expression&cmd=findpl
(Plasmid 17823: pBAD*RFPEC2)
http://www.nature.com/nbt/journal/v14/n3/abs/nbt0396-315.html

then feed protein isolates to the plasmid, then feed each of those
samples to your confirmed-to-work translation system, and you find the
glowing sample... that sample had RNA polymerase in it.

So theoretically this logic could yield both a transcription and
translation system, all starting from a GFP RNA, and a GFP DNA.

I can't wait to try this!

Tuesday, February 16, 2010

Get nautilus file manager to edit ID3 tags

So editing ID3 tags isn't integrated into Nautilus, which is pretty stupid since it does display your ID3 tag information... so I searched online and found these nautilus scripts:
http://mundogeek.net/nautilus-scripts/

but the ID3 editing script requires your mp3 files to be in a certain directory format and filename format... so I edited it to just send the filename you wish to edit, to a GUI ID3 tag editor, kid3... all you need to do is copy the python file into your user nautilus extension folder "/home/(your user name)/.nautilus/python-extensions", then install kid3 (using synaptic or apt-get on ubuntu/debian) and restart nautilus (you might need to go to the command prompt and do a killall "nautilus")

Enjoy!

http://www.nathanmccorkle.com/projects/scripts/nautilus/nautilus-tag-music.python

Friday, February 5, 2010

My beating heart

This past Tuesday I dissected a chicken embryo... I extracted the heart and cut it into small pieces. Then I placed a single piece into an individual well of a 6 well cell culture plate, and added some DMEM + antibiotic media. A few of the chunks I added to an enzyme solution called trypsin which digests the extracellular protein scaffold that holds cells together, then I added some of this cell solution to a well in the plate and added the same growth media.

The next day the heart explants (chunks) were still beating:
Beating chick heart explant
Beating chick heart trypsinized cells