RNA science

Running an Agilent RNA gel for Affymetrix work with a soundtrack by System of a Down (Science).

The nanochip separates RNA by size.
HOW: It is a bit like dropping a piece of flat paper and a piece of screwed up paper - air resistance will make the bigger thing fall more slowly.
In this case there is an electrical pull instead of gravity, and there is a semi-solid gel instead of air for resistance, but the idea is the same.
Why separate it by size ?
Because this alows you to look at the types of RNA in a sample, you can see how good it is (structurally, not morally). If it is undamaged, you can use it to decode all of the information (RNA) in a sample.

Category:

Howto & Style

Tags:

• agilent
• RNA
• gel
• affymetrix
• system
• ofa
• down
• science

[animateclay]

Is it possible to decode sections of DNA so you can write your own DNA code and know the outcome in a living organism? I heard you can engineer your own ribosomes which is coded in the same way as RNA to do splicing. But it seems like there should be a way to create organisms like you make a web page using HTML if you know all the different outcomes of each section of code.

[seantobiasmay]

Yes, getting the 'sequence' of DNA is the first step. After that there are various computational (normally bootstrapped from previous examples) and experimental ways to 'decode' the function. Writing your own DNA code has become very easy and understanding the way that it will perform in an organism has become much easier over time as we have 'decoded' more genes and organisms. This is the basis for GM technology including concepts like gene therapy.

[seantobiasmay]

HTML is not a bad analogy for GM, although perhaps XML takes you a little bit closer. Perl/CGI would add different levels of indirection and finally, obfuscated perl might be an analogy for the cryptic ways that DNA/RNA/Proteins work :).

Seriously, there are many similarities between programming and developmental genetics including concepts like recursion, decision trees, subroutines etc...

Languages like logo and forth are also analogous in concept to some processes in development.

[maleysnemesis]

So, what is the function of the nanochip? What's Qiagen? What are you even doing? How can you you do advanced RNA research but allow skips on the audio file?

[seantobiasmay]

Qiagen - well spotted, it appears only briefly - it is a company that makes kits for pulling the RNA out of living organisms. This video wasn't about that bit.

Q: How can we do advanced RNA research and allow skips ?

A1: The audio file was like that when I added it - I have often wondered if that one semi-beat was intentional.

A2: Can everyone who codes in obfuscated Perl, fly a 747 ? They're unconnected.

A3: I used to be a brain surgeon, now I'm a Pharmer, none of it is rocket science...

[maleysnemesis]

Sorry! I meant to make the last question sound playful...woops!

[seantobiasmay]

Me too (in my answers) - your other queries are answered in the improved description... thanks for commenting BTW....

[citanon]

How much is the benchtop bioanalyzer?

[catalifornian]

setting up a gel in 3-5 minutes, not bad! We love our bioanalyzer!

For those in the dark the bioanalyzer replaces slab gels for the analysis of RNA, DNA, proteins and even can do cytometry