A day in the life of

Labelling tiny plastic tubes and doing a lot of washing up – that’s how I summed up the daily grind of the lab bioscientist in my last post. Now that I’m back in a lab coat and safety glasses on a daily basis, let’s see how accurate my memory of the lab was with an account of what I got up to at work today.

Today, started slowly. In general, I’m very much a morning person. I work best in the morning. It’s when my concentration levels are greatest and when I think most clearly. But this morning, I was glum, sluggish and possibly even a tiny bit grumpy.  The uncharacteristic lapse in my sunny disposition was mostly the product of having been unwelcomingly awoken at 5:30 am by a bird of unascertained species singing outside my window, in what was frankly, a very accurate mimic of an alarm clock. Sadly it lacked any accurate mimic of a snooze button. Sigh. Adding insult to injury, I then rose to find that the house had NO COFFEE. Hardship, after hardship. So, yes, today’s scientific endeavours started slowly.

Having made it to work, I settled down at my computer to enjoy a much-needed large Flat White and to check my emails. I checked in on a protein crystallography forum, skimmed the contents of this week’s volume of Nature and monitored the alerts I’ve set up to inform me of new papers published in my field. And yes, I emailed my mum and checked my Facebook account. Slowly, I told you. I started slowly.

Caffeine levels restored I ventured out of the office into the lab itself to process four litres of bacterial cultures that I had left growing overnight. Suspensions of bacteria are used routinely in the biological sciences as a means of producing large quantities of DNA or protein.  It’s routine – and pretty damn gross if you choose to think too carefully about it.  The bacteria of choice are given a liquid support medium (consisting of salts, amino acids, glucose, metal ions, and everything else they need to grow happily) and allowed to multiply in heated incubators, which shake the flasks of culture to keep them aerated.

My main task was the thoroughly enjoyable job of harvesting the bacteria from the liquid culture, as only the former is of use. Over time if the flask was left stationary, the bacterial cells would just settle to the bottom (think of a fine sediment at the bottom of your wine glass) but to speed up the process, we use a centrifuge (see the Absolute Source of All Human Knowledge for more information) to achieve the same effect. After centrifuging the suspension of bugs in liquid at 6000g, we are left with a neat pellet of cells at the bottom of the bottle and can easily decant off the unwanted culture. “Pellet” is a bit misleading. It is actually more of a sludge of the consistency of cocoa butter – but with an aroma not of body lotion, but of, well, a sludge of bacteria. This bug-sludge is transferred using a spatula (similar to the kitchen kind, but it’s not advised to share them for this purpose) to a clean 50 mL tube, (which once meticulously labeled) is stored in a -80 degrees Celsius freezer. Next came an hour of washing: rinsing flasks and centrifuge bottles, decontaminating spatulas and my bench top, cleaning up spills and splashes etc and somehow lightly burning the skin on two knuckles off my right hand with bleach. I’m still not sure how I did that.

At some point in the middle of this cutting-edge work and self-mutilation, I got a horrible, sinking feeling in my tummy as it dawned on me that I had incubated the cultures for 24 hours at the wrong temperature. D’oh! Cue much gnashing of teeth, personal admonishment and frantic reasoning about whether it mattered or not. Two hours and a lot of detective work later (which involved the labeling of 16 plastic tubes, a lot of pipetting and SDS-PAGE, it seems that I may have just gotten away with it. Scientific work can be a lot about salvage operations.

Back in the safety of the office, I tackled some data from a thermal shift assay that I did last week. Two hours later, much of which was spent trying to remember how to get Excel to calculate and graphically plot 95% confidence limits, I was buried under 25 separate graphs and was somewhat confuddled as to what any of them really meant. I couldn’t be sure, but I strongly suspected that the results of the experiment were inconclusive. Seriously.

So a day involving some mindless prepping and washing, an unintended salvage operation to detect the outcome of setting up cultures mindlessly and analysis of a lot of data that frankly didn’t make a lot of sense.

It seems my memory served me well. Still, it’s good to be back.

by róisín