GENE COPY ANALYSIS
Microorganisms can contain more than one copy of a gene, cassette or operon. This is a phenomenon that occurs especially in fungi. The gene copy number can affect the production levels of the corresponding proteins and is therefore an essential parameter for production strain optimization. BaseClear offers a special gene copy number determination service, based on next-generation sequencing.
INSERTION CASSETTE ANALYSIS
When new genes or gene cassettes are introduced into the genome of a microorganism, it is crucial to verify the final results of this modification. Three different questions need to be answered:
- Is the cassette correctly inserted?
- How many copies of the insertion cassette are incorporated into the genome?
- Has the incorporation of the insertion cassette resulted in modification or damage of any other genes in the genome?
Using next-generation sequencing on the modified genome, BaseClear can answer these three questions. If you only need to obtain an answer to the first question, we can analyse the DNA with Sanger sequencing.
GENOME COMPARISON AND SNP ANALYSIS
When working with microorganisms, for example as a production strain, it is important to check the strain for the presence of mutations. The most common type of mutations are SNPs (single nucleotide polymorphisms). BaseClear offers the possibility to check the complete genome by re-sequencing the strain and analysing the data via comparative genomics. We can also analyse the genome partially using Sanger sequencing.
GENE EXPRESSION ANALYSIS
Microorganisms can only be applied as food ingredient or production strain when they are sufficiently stable and able to function optimally under the desired conditions. Probiotic bacteria, for example, often need to be able to withstand the gastric acid and bile salts that are present in the stomach and intestines. Fermentation production strains should function optimally under the desired conditions. To investigate and optimize these characteristics, it is necessary to find out which genes are expressed in a given physiological background. Such information can be obtained via transcriptome sequencing and gene expression analysis. BaseClear offers a complete solution to determine the gene expression. This also allows for the discovery of novel exons and alternative splicing.