It is fully equipped with the state of the art instruments for doing molecular ecology including 7 PCR machines, one qPCR instrument (Mx3000) and in house access to an 454 instrument for automated sequencing and genotyping. We have weekly lab meetings for the approximately 20 people associated to the lab for discussions of practical and scientific issues. Jane Jönsson is employed as a technician to maintain the lab and the scientific projects are jointly coordinated by Staffan Bensch, Bengt Hansson, Dennis Hasselquist, Lars Råberg and Helena Westerdahl. They work with a diverse set of organisms including birds, mammals, fish, insects and pathogens. Some of the projects are included within the CAnMove program.
DNA sequencing is a method for determining the precise order of the nucleotide bases - adenine, guanine, cytosine, and thymine - in a molecule of DNA. In automated sequencing machines the four bases are recognized e.g. by four different coloured dyes and displayed in an electropherogram as peaks of different colors that can be read directly by a computer. Knowledge of DNA sequencing technology has made it possible to determine, characterize and map the complete set of chromosomes – genomes - of many animals, plants, and microbes.
PCR - Polymerase Chain Reaction
PCR is used to amplify a specific region of a DNA strand. Starting with tiny amounts of a particular sequence, PCR generates millions of identical copies of the fragment of interest. The invention of the PCR technique resulted in a revolution for evolutionary biologists interested in genetic questions. Suddenly there was a fast, robust and relatively inexpensive technique to get hold of genetic information from small samples of e.g. skin, blood or faeces which allow us to extract DNA of the animal.
Similar technique regardless of taxonomy
The great advantage with PCR based molecular studies of DNA is that, once DNA is extracted and purified, the techniques are very similar regardless of the taxonomy of the study organisms. For example, microsatellite typing of birds is no different than performing it on samples taken from other organisms like trees, wasps or humans, given that you have a protocol available for these species.
Protocols are predefined procedural definitions used to standardize a laboratory method to ensure successful replication of results by other researchers. In addition to detailed procedures and lists of required equipment and instruments, protocols often include information on safety precautions, the calculation of results and reporting standards, including statistical analysis and rules for predefining and documenting excluded data to avoid bias.
The method is to the determine antibodies produced in response to a viral infection or an autoimmune disease or to determine other disease-related or physiological active substances. Photo: Jane Jönsson
Lund now has a new-generation sequencing machine called 454. This can provide opportunities for multidimensional examinations of transcriptomes (the expressed part of the genome) in which high-throughput expression data are obtained at a single-base resoultion.
One molecular method that is often used to reveal genetic population structure is to characterise populations at several microsatellite sites (loci) across the genome. Microsatellites are neutral markers of short repeated regions that are dispersed at several thousand loci inside the genome.
Another technique that can be used to generate an anonymous multilocous genetic profile to describe and characterise population substructure is amplified fragment length polymorphism (AFLP). This method is based on selective PCR amplification of restriction fragments from a total DNA digest, and allows you to generate a large number of genetic markers on the whole genome level quite rapidly. This way you can detect differences in fragment length that are caused by mutations that create or abolish restriction enzyme cutting sites.