I hope you remembered to shower

By Andrew Farrer

A fairly common statement, perhaps, but at ACAD remembering to shower is not just about the risk of offending your workmate’s sense of smell, not showering could ruin a project and destroy precious samples. Contamination is a major risk for any DNA analysis but is particularly true for highly degraded DNA specimens, such as ancient DNA or forensic samples. Even small amounts of modern DNA entering your sample can be disastrous for a project. In order to overcome this, ACAD has a purpose-built ancient-DNA lab, self-contained and kept hyper-clean, especially for the analysis of highly degraded DNA. Even entering the lab correctly is quite a mammoth task! Here is a brief outline of just what you have to go through to get into this lab and the reasons why. Also, just to be clear, we all shower even if we aren’t going into the lab, it’s South Australia, it’s hot!

DNA degrades naturally over time. It breaks apart and its sequence alters. Different conditions have differing effects. For example, being water-logged is bad, while being frozen is good; the constant environment of caves is good but the changing conditions of a hillside, not so much. Time also contributes; even in good conditions DNA will degrade significantly over thousands of years. So, when you want to get native-DNA out of any material you have to consider the conditions the DNA has been exposed to and for how long. The more damaged the DNA the more easily it can be swamped by contamination, so the more careful you have to be.

Contaminant-DNA is DNA from a source other than the material you’re targeting. Once contamination occurs it is very difficult to remove this unwanted DNA. At worst it obscures the native-DNA completely, producing a completely wrong result. For most modern samples the level of degradation isn’t very large and there are high quantities of native-DNA still remaining. This means a high level of contamination would be required to mask the native DNA. As such, wearing lab coats and gloves, and using regular cleaning protocols (e.g. bleaching work surfaces) should be more than sufficient to prevent contamination. However, samples that have been badly damaged and only contain very small amounts of native-DNA need to be treated even more carefully.

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Our lab building (centre). A serene location, on the outside.

ACAD’s ancient DNA lab is situated in the Adelaide Botanic Gardens, separated from all other molecular biology labs by a 20 minute stroll through park lands (it’s not all bad, this lab work). Now the rules: you cannot have entered other DNA labs beforehand (ACAD’s or otherwise), you must also have very recently showered and be wearing freshly laundered clothes. Pollen, animal hair or human DNA can build up quickly on fabrics so fresh clothes are worn to minimise contamination entering the building. As you cannot guarantee that these clothes are still clean after your trip to the lab you have a change of clothes waiting for you. Kept in a special locker, these clothes are only ever worn in the lab and have to be full length in both leg and sleeve (they’re basically pyjamas, no glamour here).

Now dressed as your 5-year-old self’s attempt at Superman (minus the cape), you enter the first of two lab entry-rooms. Now it’s really serious. Nothing can be touched in these rooms by bare skin and no skin can be exposed in the lab. First step: two pairs of latex gloves. The first pair is a base layer and won’t be removed until you exit the lab. The outer pair is discarded once you have put on a full body suit, clean foot covers and a surgical face-mask (covering your nose and mouth, no breathing on the samples!). A new outer pair of gloves is required before moving to the second entry room.

Behind door number two you collect and clean your visor. The visor keeps your whole face covered, preventing you from contaminating samples with skin cells or hair from the small amount of your face still exposed. You also get some fetching, white rubber boots to wear. These are cleaned with bleach each time you use the lab. Now you discard the outer pair of gloves again, replacing them with sterile surgical gloves (which are longer, sealing the suit cuffs). These surgical gloves are your in-lab base layer; you wear another pair over the top for each and every different activity. Now you can enter the actual lab, you only walked into the building 20 minutes ago! Wait though, you can’t start working with the samples yet. Now you have to clean the workspace and equipment. You keep cleaning too, almost continuously while you work. This prevents cross-contamination (when DNA from one sample gets transferred to another sample). Cross-contamination makes as much of a mess as non-sample contamination.

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A colleague, suited up and ready to work. No body part is exposed and no surface is left uncleaned by the time you get to open that tube.

This all may seem excessive but the aim of it is to make sure the only DNA present in the reaction tube is that of the material you are working on. All other sources have been removed. The utmost care and attention is needed to make sure no mistakes are made (a dose of paranoia may not go amiss either). The results of ancient DNA work can lead to amazing insights, aiding in answering questions such as where did we come from and how did we get here? However, it can be a long and arduous task to get there. Oh, and heaven help you if you need the toilet. The only way out is the equally pain-staking de-suiting process…

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