Labrats' Hangout

[Psi Wavefunction]

Thought we might need one!

Here we can talk about all the top secret world-domination-aimed super-virulent/explosive research we do in our ivory tower lab facilities! :twisted:

<secret>

So, what are your favourite things to do with liquid nitrogen?

</secret>

[Gawdzilla Sama]

Chill beer, of course. I used to work in a LOX plant or two. We could freeze all that unneeded water out of a can of beer in under a minute. The resulting "cream" was a really killer.

[Psi Wavefunction]

Chill beer, of course. I used to work in a LOX plant or two. We could freeze all that unneeded water out of a can of beer in under a minute. The resulting "cream" was a really killer.

Thanks for the suggestion!

I mean, your taxpayer dollars will be put to a good use.

[Gawdzilla Sama]

Chill beer, of course. I used to work in a LOX plant or two. We could freeze all that unneeded water out of a can of beer in under a minute. The resulting "cream" was a really killer.

Thanks for the suggestion!

I mean, your taxpayer dollars will be put to a good use.

We were dumping a contaminated tank, and I had a tiny bit of beer in my car. Cause => Effect.

[MedGen]

Pull up a pew and let me bore you with my research! No really my project is fascinating, for me. Noone else seems to think so

[Psi Wavefunction]

Pull up a pew and let me bore you with my research! No really my project is fascinating, for me. Noone else seems to think so

Go on. And then I'll bore y'all with mine! :twisted:

[MedGen]

Well it all starts with a genome-wide association study conducted across a Caucasian population in search for susceptibility variants to rheumatoid arthritis. Several genetic variants and regions are well characterised, and as expected these were associated with the most significant p-values (in the range of 10-26). Several other regions were significantly associated, including some at 6q23. Several independent studies have since confirmed these findings and replicated them in both UK and Northern American cohorts. In addition a second statistically independent variant was found to be associated with protection against RA just 4kbp away from the original variant. The only problem is that they both fall right in the middle of a 400kb gene desert.

The closest genomic element of interest is a putative processed pseudogene of a non-receptor type 2 protein tyrosine phosphatase found on chromosome 12. The nearest genes are a neuronal transcription factor and a downstream molecule involved in TNF signalling (a good candidate gene for RA susceptibility). However, there is no linkage disequilibrium between these variants and either of the other two genes. Again
Additionally a genome-wide study of all protein tyrosine phosphatases detected a transcript from this pseudogene on 6q23. So we have an actively (?) transcribed processed pseudogene.

So is this processed pseudogene somehow responsible? That's my project. So far I've sequenced across the region and genotyped the various SNP's in the region in the CEU HapMap samples (90 of the buggers). I've also correlated specific genetic variants with publicly available expression data for the pseduogenes parent gene, with a statistically significant result.

The stage I'm on now involves detecting the parent gene within specific immune cells. This I've literally just done (i.e. I finished the Westerns on Friday) and there is no doubt the parent gene is actively expressed in monocytes. What is also interesting is that the Ab I used picked up both the endogenous protein, and the specifically phosphorylated version of the protein which points to it actively dephosphorylating in these cell types, very interesting, but not massively surprising.

So the next step is to detect the pseudogene transcript and see if it is also expressed in these cells types. I'm using orientation specific primers for RT-PCR so that we can also get an idea of what the hell is going on. Potentially I could be looking at the generation of an anti-sense RNA which is incorporated into RISC and acts in that fasion. Alternatively the pseudogene could be transcribed in both orientations leading to a duplex formation and the the generation of endogenous siRNA's. At the moment I wouldn't even hazard a guess as to what the mechanism of action (if any) is.

I've only got about 6months left to work out what the hell is going on, but damn it's fucking interesting. It's also kinda novel, what with a potential ncRNA mechanism and all.

[Psi Wavefunction]

How do you put up with all that molecular work? I guess I'll stop whining about having to genotype in-between playing with the scope then

Oh, and aren't we happy this isn't in vogue anymore:



Looks like a hellish way of doing things...

[The Curious Squid]

Well it all starts with a genome-wide association study conducted across a Caucasian population in search for susceptibility variants to rheumatoid arthritis. Several genetic variants and regions are well characterised, and as expected these were associated with the most significant p-values (in the range of 10-26). Several other regions were significantly associated, including some at 6q23. Several independent studies have since confirmed these findings and replicated them in both UK and Northern American cohorts. In addition a second statistically independent variant was found to be associated with protection against RA just 4kbp away from the original variant. The only problem is that they both fall right in the middle of a 400kb gene desert.

The closest genomic element of interest is a putative processed pseudogene of a non-receptor type 2 protein tyrosine phosphatase found on chromosome 12. The nearest genes are a neuronal transcription factor and a downstream molecule involved in TNF signalling (a good candidate gene for RA susceptibility). However, there is no linkage disequilibrium between these variants and either of the other two genes. Again
Additionally a genome-wide study of all protein tyrosine phosphatases detected a transcript from this pseudogene on 6q23. So we have an actively (?) transcribed processed pseudogene.

So is this processed pseudogene somehow responsible? That's my project. So far I've sequenced across the region and genotyped the various SNP's in the region in the CEU HapMap samples (90 of the buggers). I've also correlated specific genetic variants with publicly available expression data for the pseduogenes parent gene, with a statistically significant result.

The stage I'm on now involves detecting the parent gene within specific immune cells. This I've literally just done (i.e. I finished the Westerns on Friday) and there is no doubt the parent gene is actively expressed in monocytes. What is also interesting is that the Ab I used picked up both the endogenous protein, and the specifically phosphorylated version of the protein which points to it actively dephosphorylating in these cell types, very interesting, but not massively surprising.

So the next step is to detect the pseudogene transcript and see if it is also expressed in these cells types. I'm using orientation specific primers for RT-PCR so that we can also get an idea of what the hell is going on. Potentially I could be looking at the generation of an anti-sense RNA which is incorporated into RISC and acts in that fasion. Alternatively the pseudogene could be transcribed in both orientations leading to a duplex formation and the the generation of endogenous siRNA's. At the moment I wouldn't even hazard a guess as to what the mechanism of action (if any) is.

I've only got about 6months left to work out what the hell is going on, but damn it's fucking interesting. It's also kinda novel, what with a potential ncRNA mechanism and all.

English please MedGen

[leo-rcc]

I fell asleep after "genome-wide association study".

[MedGen]

How do you put up with all that molecular work? I guess I'll stop whining about having to genotype in-between playing with the scope then

Oh, and aren't we happy this isn't in vogue anymore:
ckin


Looks like a hellish way of doing things...

It's cos I'm going to be a molecular geneticist.
If I had to set up separate tubes and run them on gels for chain-termination, I would go fucking insane, especially when you've got to sequence 8 fragments in 90 individuals. I think I put through 8 96-well plates for sequencing, in the space of three days.

English please MedGen

I duz scienz, itz reeel gud fun. (Genetics of rheumatoid arthritis )

[Geoff]

Well it all starts with a study conducted across a Caucasian population in search for Several genetic variants and regions are well characterised, and as expected these were associated with the most Several other regions were . Several independent studies have since confirmed these findings and replicated them in both UK and Northern American cohorts. In addition a second statistically independent variant was found to be associated with . The only problem is that they both fall right in the middle of a .

The closest found on chromosome 12. The nearest genes are a . However, there is no between these variants and either of the other two genes. Again
Additionally a .

So is this somehow responsible? That's my project. So far I've sequenced across the region and (90 of the buggers). I've also correlated , with a statistically significant result.

The stage I'm on now involves detecting the parent gene within specific immune cells. This I've literally just done (i.e. I finished the Westerns on Friday) and there is no doubt the parent gene is . What is also interesting is that the version of the protein which points to it actively in these cell types, very interesting, but not massively surprising.

So the next step is to detect the and see if it is also expressed in these cells types. I'm using so that we can also get an idea of what the hell is going on. Potentially I could be looking at the generation of an and acts in that fasion. Alternatively the . At the moment I wouldn't even hazard a guess as to what the mechanism of action (if any) is.

I've only got about 6months left to work out what the hell is going on, but damn it's fucking interesting. It's also kinda novel, what with a potential and all.

That makes much more sense...

[CP]

I'm a lab assistant in training... can I hang out here?

[ScholasticSpastic]

I'm a lab assistant in training... can I hang out here?

Absolutely.

[Psi Wavefunction]

I'm a lab assistant in training... can I hang out here?

I think we're all in training here!

Might be working in TWO labs this summer!



I have soooo much work! Anyone wanna do some work for me? :twisted: Although I'm paid 10h/wk, I work more like 20-30 just because of all the planning and work and such that goes into it... all in the name of a manuscript. I fucking NEED that paper ASAP...

Meanwhile, my coursework...