DNA-Analyses and Bioinformatics

Lucas Voges

Every (once) living organism can be identified unambiguously by its biological profile. By studying the sequence of DNA molecules, it is possible, for example, to learn which plant or animal species (or mixture thereof) was used for the production of a writing support. Other questions that can be solved by studying DNA molecules concern sex, breed, genetic diversity and diseases of the biological sources that have been used for producing writing supports. That information can aid to unravel the history of past populations, for example livestock breeding and farming.

Furthermore, DNA molecules are ubiquitously present on each object due to its environment in the form of bacteria, fungi, pests and pollen. The molecular characterization of this so-called environmental DNA can deliver information about biodeterioration as well as an object's storage history. 

Due to the poor molecular preservation state of historic material and in order to reduce the risk of introducing contaminations, all sample preparation experiments take place in a dedicated clean room facility. DNA analysis encompasses four steps starting with sampling the object of concern. Usually, DNA sampling is destructive as the chance of a successful and unambiguous biological identification increases with the amount of sampled DNA molecules. This is especially true for the analysis of DNA molecules retrieved from historic material (ancient DNA, aDNA). The preservation and survival of DNA molecules is highly dependent on the tissue analysed (e.g. bone, textile, parchment), a WAs production method (e.g. boiling, application of chemicals), as well as storage conditions (especially temperature and humidity) and age of an object. However, non-invasive sampling techniques are continuously tested and have been already successfully applied on a palm leaf manuscript dating to the 18th CE (Schulz et al. 2017) as well as mediaeval parchment (Teasdale et al. 2017). In a second step DNA molecules are isolated from unwanted cell material and transferred into so-called DNA libraries. This is followed by analysis through state-of-the-art next generation sequencing (NGS) (MiSec, Illumina; iSeq, Illumina) techniques that read millions of DNA sequences and therefore allow an in-depth insight into a material’s biological composition. Depending on the research question, only specific DNA sequences can be targeted (e.g. to learn about the bacteria or fungi present on a material or the animal or plant used for the production of a material, resulting in more species-specific sequencing data) or a so called shotgun sequencing approach can be conducted, in which all DNA molecules present in an DNA isolate are analysed (leading to more overall data but less species-specific data). In a final step the sequencing data needs to be bioinformatically processed, e.g. to distinguish genuine authentic aDNA molecules from modern contaminants. Data analysis can be challenging due to the degradation of DNA molecules. Specialised bioinformatic tools and workflows are applied to cope with these circumstances. Last but not least, linking and annotating the findings to the manuscripts is a key point in the knowledge exchange.