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!

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

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

It's been almost a year since my last post!

Wow, time has gone by quite fast since my last post... school, school, and more school... someday, just maybe, I will get that Nobel prize. To be honest it's pretty much the only competition that I have ever felt like I truly want to win...

School is going well, I really love learning, but keeping focus is tough. Is it so bad that I love to learn not only about chemistry in the lab, but also the simple joys of chemistry in the kitchen? I spent most of the evening Friday making pizza for a party with friends later that night, it was quite tasty, and my first time using millet flour. Saturday I cleaned up the apartment, mainly the kitchen and my room, and later spent a good while with Juliet making dinner. It was nice, the simple beauty and joy of cooking, something that is hard to accomplish with the pressure of school and society... I relish these moments. Cooking in this sense is not just a means to feed oneself, it is human ability coming to fruition.

SDR>>:
GNU Radio>>:
echolink
HDTV
Route tx/rx to skype

tired, making progress?

http://lwn.net/Articles/267672/
http://lists.freedesktop.org/archives/xorg/2008-February/032906.html
http://fiire.com/fiire-chief.php
http://people.freedesktop.org/~whot/Xi/
http://linux.conf.au/programme/presentations
http://www.rowetel.com/ucasterisk/ip04.html
http://www.rowetel.com/ucasterisk/store.html
http://idahopcug.apcug.org/linuxSIG.html
http://www.digipedia.pl/man/teleport.1.html

hack VNC--- have small docked button on the side of your screen(room-client), when you click and hold it either encapsulates the whole screen into VNC-server and then dragging the button starts up a viewer on the (room-server) and continuing to drag now drags the viewer.

Or, click the side button, then click a window title bar, somehow use xInput (linux) or windows API (java robot class) to get the window dimensions, and open a viewer on the (room-server) that is sized only around the window.

using something like the java robot class, there should be a way to say over the network "open a vnc client with these dimensions, around this part of the (room-client)'s screen and create a new pointer on (room-server) that is **still being clicked mouse-down** dragging the vnc contents around.

VNC on the (room-client) side should make the window disappear, put it behind everything, maybe some fake desktop space somehow that isn't viewable on the screen.

Today's shit

Design of an algal/biotic fuel source:
Needs an "ignition key" that would be easy to produce, cheap, abundant/easily recyclable, but not readily/immediately available in natural settings to avoid the outbreak of a modified organism.

The supply of energy for CO₂ anabolism is common to all photosynthetic organisms which exhibit photosynthesis. Energy conversion, ATP synthesis and the production of both CO₂ and hydrogen on the other hand, are not unique to photosynthetic organisms, but occur in all types of microorganisms, and are in fact similar to the respiratory processes which occur in mitochondria of higher organisms.

Two types of photosynthesis are distinguishable on the basis of source of the electrons used as energy carriers. In plants such as green algae, and cyanobacteria (blue-green algae), water is the electron source, while in photosynthetic bacteria, organic or sulfur compounds provide electron sources.

Then there are some bacteria that produce hydrogen directly, but currently their overall sunlight to combustion efficiency is about 7%:
http://www.fao.org/docrep/w7241e/w7241e06.htm#2.2.2%20bacterial%20photosynthesis

I want a really nice microscope. I want a really high-quality, cheap way to make a quick high-resolution, high magnification digital image of a large area of cell culture for computer vision analysis and automatic cell counting.

A possible means to achieve this using optics would be a CNC like platform which moved the viewing stage about a matrix. If this could be performed fast enough you could consistently monitor a biological culture. Along with oxygen, CO2 levels, pH, maybe the resistance/electrical conductivity (could that tell me the ionic concentration/ionic charge).

Or maybe a prism or something; fiber optics maybe, dunno about the resolution ceiling for that, or fiber diameter floor...

auto cell counter:
http://www.blackwell-synergy.com/doi/abs/10.1111/j.1550-7408.1974.tb03697.x

http://en.wikipedia.org/wiki/Essential_nutrient

http://en.wikipedia.org/wiki/Avitaminosis

http://en.wikipedia.org/wiki/Strong_inference

http://en.wikipedia.org/wiki/Entropy

Gooood photosynthesis page:
http://www.fao.org/docrep/w7241e/w7241e06.htm

http://en.wikipedia.org/wiki/Transpirational_pull

http://en.wikipedia.org/wiki/Osmotic_pressure

http://en.wikipedia.org/wiki/Flash_point

http://en.wikipedia.org/wiki/Apoptosis

http://en.wikipedia.org/wiki/Cellular_respiration

http://en.wikipedia.org/wiki/Catabolism

http://en.wikipedia.org/wiki/Crista

http://en.wikipedia.org/wiki/Brown_adipose_tissue

http://www.springerlink.com/content/u1uh281174pj0l84/

DNA Sense
http://en.wikipedia.org/wiki/Sense_(molecular_biology)

PCR "discoverer"
http://en.wikipedia.org/wiki/Kary_Mullis
--seems like this guy is the George Hotz of PCR!

http://en.wikipedia.org/wiki/Microinjection

cross-regulation of transcription factors, a conserved cell differentiation system:
http://books.google.com/books?id=bh2cOAKHU_kC&pg=PA16&lpg=PA16&dq=ectopic+ey+expression+fly+frog&source=web&ots=qSQng7L5VD&sig=hirQBQasnI90eqFQ_thI-l2sA3A#PPA17,M1

Use nitrogenase as our friend somehow???
http://en.wikipedia.org/wiki/Nitrogenase

Rhodobacter sphaeroides
http://www.hgsc.bcm.tmc.edu/projects/microbial/Rsphaeroides/

Techniques that seem wasteful/innefficient:
http://www.journalarchive.jst.go.jp/english/jnlabstract_en.php?cdjournal=bbb1961&cdvol=50&noissue=11&startpage=2837

Food stuff:

Soybean content before/after fermentation
http://www.blackwell-synergy.com/doi/abs/10.1111/j.1365-2621.1967.tb00837.x