Tell me, Flies, tell me, sweet little Flies

I've had this song stuck in my head all day. Simply replace "lies" for "flies" and the song in its entirety is worryingly apt for my research. Give it a go and then I'll give you some context.

I finally managed to delete a gene using CRISPR! So I've been waiting 11 days to see what the homozygous mutants look like.

13 days later (because the food isn't so great) and...

They look absolutely fine.

Bugger. I'll have to wait a few days to see whether they are fertile and a few more until they possibly drop dead or start behaving oddly. Chances are they don't have anything wrong with them which means I'll have to start poking around a little more.

There are several options - a sensible one is to do some genetic interactions with candidate genes (that have a phenotype when mutated) obtained from an interactome I obtained. The caveat there is that it's an interactome for the human protein and not the fly one. Ideally make a mutant phenotype better/worse when adding my mutation to the mix.

Another option is to look a lot closer. Based on expression data there seems to be an enrichment in hemocytes (sort of fly macrophages) and the Central Nervous System. Given I share lab space with experts on hemocyte function and behaviour it seems like it's worth a quick look in that direction. The central nervous system I can delve into with simple things like "is there a difference in size/appearance" but I'd also probably hope to see things go wrong with the flies as they get older.

Anyway, there's a bit of work to be done yet until I find a solid lead. Now I have the mutant I may as well at least establish that it conclusively does nothing before moving on.

So yeah - no, no, no you can't disguise. Tell me Flies.

Science Songs

I have to give a lab meeting tomorrow so quick and easy song it is.

I picked this one because a scientist needs to keep their eyes wide open to spot/connect/interpret potential results. They should also be sceptical and demand to see things with their own eyes every now and then!

Science Music

I may have used this one before (Every post is exactly the same) but this is another song that comes to mind in a repetitive screen.

Screened 130 of the 450 potential mutant fly lines now. Out of the 6 different deletions I've got one.  As cruel fate would have it, it's in the gene that lies within the intron of my gene of interest. So I potentially have a control mutant for my non-existent mutant of interest. I guess I can't get too pessimistic until I hit the half way mark. As it is the long weekend out of the country will provide a much needed break as there's no way I can nip into work to do "a few DNA prep/PCRS" while away.

Science Music

This song definitely sums up the last couple of weeks at work.

I guess it's the downside of screening. I'm essentially going in the morning and collecting virgin* flies from 350 crosses, crossing these flies to other stocks, having lunch and then repeating the process in the afternoon. Over and Over again.

I guess it serves me right for picking a gene on the X chromosome. This means I have to go for the "maiden" female flies as there's the possibility the mutation may be lethal which isn't so great if you're a male and only have the one X chromosome to play with . It also means that all the males from the crosses are potentially ones where the deletion hasn't occurred so there's no point in using them at all. I was planning on doing some courtesy PCR on the males in the sense that if there is a deletion I'd know it isn't lethal. I haven't really had the time though.  I'll probably wish I made the time if it turns out it is a viable mutation and I could have just picked a bunch of males from each line ONCE rather than twice a day for a week. Let's not think of that though.

Next week, I can at least change the repetition of virgin collecting (not as fun and/or sinister as it sounds) with serial fly squashing (essentially as sinister as it sounds) and PCRs.
I have another mutagenesis screen on the go too but fortunately that one isn't on the X chromosome so it will be an absolute breeze by comparison. Unless it's not.

*Just in case you think I'm some kind of kinky drosophilist I should point out that flies use internal fertilisation to reproduce (like most people do) and not externally by the female dumping a load of eggs and then the male does his manly duties over said laid eggs. For this reason, when doing crosses you need females that haven't mated with their brothers (flies are cool with Game of Thrones plotlines) or you will wind up with progeny you don't really want.
They do it doggy style in answer to your inevitable follow-up question. In terms of "how do you know they are virgins" - you can do it based on time or you can check if they have a black spot on their belly. If they have a spot they are still virgin. It's definitely a talking point at interviews if you put that one on your CV.

Science Songs

Since getting back from holiday I've been having a nightmare getting a certain type of PCR to work. The most recent head scratching moment was to get a round of PCR that worked perfectly. I immediately ran the same PCR with the same reagents and settings but with the DNA samples I wanted to check. Nothing worked - not even the positive controls that had worked 3 hours earlier.
When an experiment can't be repeated with the same conditions there's only a few explanations;
a) there's something you aren't accounting for so it isn't the "same"
b) you are the variable
c) you are switching universes in between experiments
d) there are science goblins messing with your mind

All of these options reminded me of this song

The chorus is

"There are monsters here
And as you scream it makes no sense
It makes no sense
It makes no sense at all "

That pretty much sums up the last 2 weeks of work for me.

Science Songs

 One transformant from my test plate and twelve from my negative control. I'll miniprep it anyway.

Listening to the lyrics of verse 1 and chorus more carefully, I 'm thinking this song should be a science anthem!

Mutant Fail

This song pretty much sums up the discovery I made on Friday.

Basically the Drosophila mutant I have (and have been performing various experiments with) is still being expressed, Which isn't great news when you've been assuming it is a null mutant (a mutation with no expression of functional protein).
The mutant is missing the first two exons and has lost it's original start (ATG) site but annoyingly it has chosen to pick up an alternate start site. This gets more tricky as there are two that are close together

ATGCCATGGGC...

If it has picked the first one then I should still be ok as it is out of frame has 8 nonsense amino acids and then hits a STOP codon. The problem is that the second one is in frame and would happily make the remainder of the protein that contains at least one domain that is vital to its function.
The unfortunate thing is that I have no way of telling which start site is being used without an antibody (which I don't have). If anyone knows of a way to do so - I'm all ears. The best I can come up with is to clone the mutant cDNA into a GFP vector and see what is expressed. Not a great experiment as the only thing it can confirm is whether a truncated protein is being produced,

Ultimately I need to make a genuine null mutant which is what my priority has to be. Somewhat worrying with 11 months left on my contract but I may as well get on with it.

In an attempt to see a positive in this revelation - it may at least explain the lack of a phenotype in the mutant I have been using. Maybe the real deal will have a phenotype that rewards the mutant making!

Science Songs

Inspired by this morning's wasted journey into the lab. Looking at the lyrics closely I can't help but wonder if Trent Reznor worked in research at some stage.

"it didn't turn out the way you wanted it to
but it didn't turn out the way you wanted it to
it didn't turn out quite the way that you wanted it

now you know
this is what it feels like"

Dance your PhD

An important aspect of Science is communication. We tend to do it via papers, presentations and posters but what about the medium of dance? Well here is a selection of brave and inventive souls who have tried to dance their PhDs. I'll let them explain themselves but a good effort and remember you can vote for your favourite.
I'm pleased this didn't exist while I was writing my PhD because while I can't dance to save myself it would have been just the kind of distraction from actual writing I needed. Not sure how I'd choreograph the role of Cdc2 kinase in acentrosomal spindle formation. Maybe after a lot of drinks at a science-related party we'd find out?

Science Songs

By all accounts this was an intentional play on words by the band. "Selfish Jean" by Travis.

Science Songs

This song popped up on my mp3 player and I'd never considered the relevance to science. It definitely feels like a song about a project that isn't working!

These Wooden Ideas by Idlewild;

"I bet you don't know how to sell Conviction" - those talks are always the toughest...

An Anthem for Bad Results

A colleague of mine got the results back from a pet project he was hoping to expand upon when he has his own lab. They weren't very promising and he pronounced "The dream is over".

I instantly wanted to say "Hey now, don't dream it's over" which resulted in this song being stuck in my head for the rest of the day.

As it turned out he got some more results in the afternoon that meant the dream wasn't over. A happy ending.

If I wasn't so self-conscious of my atrocious singing I think I'd be tempted to break out into this whenever a colleague is feeling defeated. Although they may think I'm taking the piss, which I might be.

Science Songs

Finished for Christmas!  Working with flies always makes for a tricky wind-down as you need to time things properly for coming back. It's a frustrating week though when you can only do immediate things, so I'm happy to be done.
I think this song is quite apt.

Science Songs (mature content)

The following rant contains immature content so for those who blush easily at the discussion of sex and related bodily functions should read on at their own risk. This article also contains terrible pop music so for those with impeccable taste, please don't click on the video.


X-factor winning "little Mix" try their hand at a song about d-d-d-DNA (maybe a misplaced reference to Sanger's dd DNA sequencing?). Anyway I'll let you enjoy the song/video before trying to dissect the lyrics.

And now to look at the lyrics; First verse is just fluff - nothing to do with biology other than being horny. Snide comments are in brackets and not to be confused with bizarre background pop echo lyrics.

"It's the blue in his eyes that helps me see the future  [true on the eyes - not so much seeing the future]
Fingerprints that leave me covered for days, yeah yeah  [I guess there might be DNA from the grooves?]
Now I don't have any first degree  [that's becoming self-evident]
But I know, what he does to me
No need to work it out, it's so familiar  [this isn't a very scientific attitude]"

" And my heart won't beat again
If I can't feel him in my veins  [I have no idea what kinky kind of things they are getting up to - or they may just be sharing needles]
No need to question, I already know  [again with the anti-science stance]"

" He's from a different strain
That science can't explain"
 [Again, I'm sure with the right kind of experimentation and samples, science probably could eventually explain this. Not that it would be a good use of research funding. ]




My favourite lyric by far is this one though;


"It's simple genetic
I'm the x to his y"

Let's ignore the dropping of the "s" (this is maybe how the cool kids use the word) but consider the genetic(s) of the statement. So, the girl is the guy's mum? That's just sick. A pop song about incest. Game of Thrones and Boardwalk Empire have really become a trend setters. The lyrics tend to fit the "pop song innuendo" a lot better if the "DNA" they are referring to is sperm. This may also let them off the hook for the incest line in that she's maybe singing about making a baby, which is possibly connecting with their target audience.

" It's in his dna
And he just takes my breath away
B-b-breath away
I feel it every day, and that's what makes a man"

and "Contaminates my lips"  [she should have read the COSHH form and at least had safety glasses on]

Laying it on a bit thick there? (innuendo intended)

In summary, while it's nice that biological terms are so well known they can be used as the basis of a pop song, it's clear they don't know much about how the things actually work. Or they do but prefer nonsense pop lyrics over substance, which is fair enough. Or they are trying to make the next generation comfortable with the idea of incest.

Science songs

This is the official London olympics song by Muse. Pretty scary in that it sounds like it should be the national anthem of some "300" style nation that has ordered Queen to compose at gunpoint. The reason I'm including the song is because for some unknown reason they have people chanting "somites" throughout it. I heard a lot about somites in relation to Zebrafish. If I ever hear any other talks about somites this song will play in my head.

"SOMITE, SOMITE, SOMITE!!!"

Edit: For some reason Youtube will only let you watch the video through their website. I'm sure you know how to click on it though.

Science Songs

My PhD was in spindle formation and how the centrosome isn't essential, so you can forgive me for thinking this songs has the lyrics "End of the Centriole. It's nothing special"  You'd have to work on the subject to appreciate it, I guess...

Science Songs

I'm sure this song was supposed to be about losing a girl but I was listening to it yesterday and it reminds me a lot of science and getting a PhD or paper. Bear with me and listen carefully...

Science Songs: RIP Adam Yauch

I was wanting to post this one a while back but due to EMI policing their copyright it's impossible to get the song off the net (well, without very intensive searching). Sadly Adam Yauch, of the Beastie boys passed away to cancer yesterday. Everyone should like at least one Beastie Boys track as they had a huge range. But they had a song called "the sounds of science (and an entire anthology bearing the name) which fits this feature perfectly. I urge you to track it down on Spotify or something, Until then we'll have to make do with the lyrics.

Science Songs

"Chemistry" by Semisonic. There are a lot of Biologists who would agree with the chorus "it's all about chemistry".

Science song

This is another "on the nose" science song, where it's hard not to notice the lyrics. That said, I initially thought the chorus was "karaoke girl" so it shows how much attention I pay.
So here it is; "Biological" by Air.