The lab rat's guide getting away with oops.

One day when I'm no longer a lab rat, I may consider publishing a little handbook titled "How to cut corners in molecular biology and still get results!" 

Anonymously of course, because I imagine there will be some people who may not believe the materials and methods section of my papers anymore if I do that in my real name. 

Of course, I don't cut corners because I'm lazy. I take my wet work very seriously because I'm not a natural white coated lab rat. These short cuts were discovered by accident, much like most significant scientific discoveries. You think Fleming set out to discover penicillin? He found them in a mouldy petri dish left in a tray! 

For example, yesterday was spent in a haze of preparation my samples for sequencing. I started work at 1pm, purifying my amplified products (60 samples, four genes with one gene split into three parts) and re-amplifying samples that had failed the previous day (Yes. I was in the lab on Easter Sunday too. Clocked in eight hours because I have to deliver results for 3 projects by the end of the week.)

I started at 1pm and only finished at 7pm or so. It took a long time because screw ups at this stage means fucked up results with no chance of troubleshooting later on, so its well worth the effort to JUST MAKE SURE nothing gets pipetted to where it shouldn't be later on and labels are written correctly. At the end of the day, they all look the same so its very important to make sure. No cutting corners here, I'm afraid. 

From 7pm to 9.30pm, I was still preparing my sequencing reaction. Its no joke when you have 120 different samples to sequence and each one needs its own mix of reagents. So this part has to be handled with utmost concentration as well. Volumes are also minute - 5 microlitres! That's 0.005 ml per reaction comprising 0.7 microlit of template, 0.4 microlit of primer and 1 microlit of dye and topped up with water. A drop of water is more than 5 μl. I tend not to wear gloves at this stage though, as chances of contamination is almost nil. At 9.30pm, everything is ready and I pop them in the machine for 3 hours of cycle sequencing. 

So, what is the shortcut, I hear you cry. Well.. that comes much later. 12.30am comes around, and its time to purify my precious products. That takes an hour, using the magnetic plate. At this stage, all gloves are off, literally. I don't see the point in wearing gloves when the sequencing products are already tagged with dye so DNA from my finger nail isn't going to show up. I also reuse pipette tips when aspirating supernatant from my ethanol wash at least 4 times before I throw them away. Z and D thinks its a no no - they change it every time for every single well but I guess I don't care so much about it. As long as you keep your tips away from the sides if the tube, it shouldn't be a problem. I've not had any issues so far. 

So all was hunky dory and at 1.15am, I was done and ready to pop my plate into the sequencer. I had two plates and in case you don't know what they look like, here's a picture. 

Each well with a unique sequencing product suspended in water waiting to be read by the sequencer. Almost done, I thought to myself. Just pop it in, click on "run" and results will be waiting for you when you come in tomorrow! 

 

Guess what then. On my way down the the sequencing lab situated in the next building, I noticed air bubbles at the bottom of some wells in one of my plates. I don't know what I was thinking, but I had this notion that it would disappear if I flicked my plate. I probably wasn't thinking at all because I FLICKED MY SEQUENCING PRODUCTS OUT OF THEIR WELLS AND ONTO THE FLOOR. 

Aaaaaaaaargh! OH SHIT. Fuck. OH NO!!! I'm dreaming!!! Somebody slap me! 

There was no damage control to be had. What was left (luckily it was the plate with 20 samples and not 96) was about 10 microlitres in each well.. hardly enough. I thought of abandoning this plate but decided to just sequence it anyway since I've already prepared them. Went back to the lab and topped up them wells with water and walked very carefully to the sequencing lab where I left them for the night. 

Came in today fully expecting my results to be screwed up for the twenty samples but guess what. EVERYTHING WORKED BEEEYOOOTIFULLY! How cool is that! I'm ridiculously happy today because of this.  Maybe its a testament to the sequencing machine too. Well worth the gajillion dollars it cost the department! Thumbs up!

So yeah. A long anecdote to illustrate the fact that screw ups during experiments aren't as disastrous as they appear to be and the short cut being you can lose 80% of your sequencing sample and things will still be fine. No need to get your knickers in a twist, no need to spend another 6 hours sequencing those lost products. Like the PCR reaction where I accidentally got my reaction volumes mixed up and added way too much water thus diluting everything else, I've discovered that some things do still work even if you make mistakes. 

Either that or I'm very lucky.  Yay me anyway! I'm on track for my data collection this week and am due to hunker down for April writing my papers. And viva. Not so yay, that one. 

Notes from the field - Phuket

Day 3 in Phuket and A has collected about 25 species of Alpheus spp. Or so he says. I don't know man.. they look the same to me. I ask him to teach me how to id but he doesn't want to.. only telling me to attend the shrimp course in Panama sometime in the summer. Where got time and money! 

We've gotten a really nice place in a quiet neighbourhood off Chaofa road, thanks to Z. I'ts like a hotel/hostel, offering fairly good rates. Tai-tan court. Weekly rent for a two bed room costs 2000 baht. We've managed to convince the lady at the counter to throw in an extra mattress in the room for an extra 500 baht so that's 2 500 baht in total for the 3 of us. Pretty reasonable, with FREE! wifi. However, electricity costs 5 baht per unit (whatever 'unit' means) and I will wait till later to check how much it adds up. 

Ate at the chicken place with M last night as A had to stay in to process his shrimps. Mmmm.. chicken place. I wish Z and Applecow were around too.. we would have gone crazy with everything! Have to remember to drop by on Friday night to ta-pow for the girls. 

Rawai beach yesterday and Karon today. The Russians have indeed invaded Phuket. A managed to buy some booties (that actually fit his 45/46 feet) by walking into a dive shop and chatting up a young Russian fler. Now I get the brunt of  A's teasing.. all this talk of going to Chalong Bay and inviting Andre for walks and what not. I think that A is the one interested in him. Mwuahaha. A thinks its much better if everyone thinks he is gay. Less problems.  M took pictures of sagging breasts and rolls of flab of orange westerners today. Perve! 

Am waiting for A to finish up with his shrimp photography. We skipped lunch today. Am heading out for dinner and a nightwalk perhaps.