Say hello to this month’s workhorse at ETH: the KingFisher
Dear HealthFerm Citizen Scientists, hello world!
Let me introduce you to one of my favorite collegues in the wetlab: the KingFisher. It’s not a bird and doesn’t even have hands. It’s a robot! The KingFisher is highly skilled and efficient and (nearly) always motivated to extract DNA.
What is DNA extraction?
Each single cell in the human body, but also in plants, fungi and bacteria contains a copy of the respective genome. The genome stores the genetic information of an organism in the form of deoxyribonucleic acid (DNA) molecules. Extracting the DNA means purifying these DNA molecules out of a single cell or removing DNA molecules from millions of cells at the same time and separating them from other molecules such as proteins, carbohydrates or fatty acids.
Why do we extract DNA?
DNA is a sequence of different so called nucleotides. Nucleotides are small molecules that can be stringed together, like letters forming words. These ‘DNA-words’ are further stringed together to scentences, paragraphs and chapters – the genes. Most genes are highly conserved, which means they are very similar not only within a certain species but even across the kingdoms of life! But there are also some parts in the genomes that are highly variable. These variable regions enable researchers to distinguish different organisms from each other based on the genetic code. By extracting the DNA of a cell and decoding these variable regions on the DNA, it is possible to identify the nature of a single cell or identify which different kinds of cells are present in a complex mixture containing multiple species.
Why extracting DNA of sourdough?
Each sourdough contains a complex mixture of different yeasts and bacteria which both contribute to the very unique flavors and textures of sourdough bread or other baked goods with sourdough. What we aim to do within HealhtFerm is to identify each one of these microbes in all the collected sourdough samples! This is done by first extracting the DNA of each sourdough sample and then decoding the extracted DNA sequences to identify the different bacteria and yeasts within your sourdoughs. Once we know the exact microbial composition, we can correlate this data with the recipes you provide and your sensory analyses. This will enable us to find out which microbes lead to interesting properties of a sourdough, for example particularly good nutritional values after fermentation. With this knowledge, we can in the future selectively combine microbes to develop customized sourdoughs that exhibit specific flavor characteristics, promote health, and demonstrate high fermentative activity.
So what does the KingFisher do?
As the name suggests, it does fish. Kingfisher birds are known for their remarkable fishing skills – they are quick and efficient in catching their prey. So is our dear robot friend, efficient and specific in catching DNA. Additionally, our KingFisher robot enables parallel DNA extraction from 96 different sourdoughs at the same time! If this is not amazing!
Figure 1 KingFisher Apex, ThermoFisher Scientific. DNA extraction robot and wet-lab colleague. Good working moral, efficient and reliable (mostly, except in April. Seems like he is adapting to the changing weather, resulting in either some really good extraction runs or complete crashes requiring a restart from the beginning).
- Kingfisher image from Planet Custodian https://www.planetcustodian.com/spectacular-images-of-kingfisher-in-action/6959/
- KingFisher image from ThermoFisher Scientific https://www.thermofisher.com/order/catalog/product/5400910
