BIONUMERICS applications

Bacterial community fingerprinting refers to a number of cultivation-independent methods that are used to measure biodiversity in environmental samples or to profile microbial community structures, e.g. in response to experimental conditions.

In marker assisted breeding, successful cross-over is assisted and facilitated by genetic markers. A commonly used DNA marker technology is Amplified Fragment Length Polymorphism (AFLP) analysis, where selectively amplified whole genome restriction fragments are separated via electrophoresis into a complex band profile. The occurrence of specific bands can be linked to the presence of particular phenotypic traits. In diploid organisms however, a phenotypic trait can be homozygous or heterozygous, which in theory will result in marker bands that can have double or single intensities.

The BIONUMERICS SARS-CoV-2 plugin tool facilitates the processing and analysis of SARS-CoV-2 genomic sequences, whether downloaded from a public data repository or generated locally.

Variable-Number Tandem Repeats (VNTR's) are well known for their high mutation rate and are therefore widely used for subtyping. Some VNTR's, however, exhibit polymorphism in their individual repeat sequences. By sequencing the polymorphic repeat region, each new repeat variant determined can be assigned a unique repeat code. The repeat succession for a given strain in turn, determines that strain's VNTR type.

Multi Locus VNTR Analysis (MLVA) is a molecular typing method to subtype microbial isolates based upon the Variable copy Numbers of Tandem Repeats (VNTR). A VNTR typically exhibits a large range of copy numbers, even among highly related bacterial strains. For a selected set of tandem repeats, copy number analysis reveals insights about the relationships at a micro-evolutionary level.

The TaqMan® SNP genotyping technology utilizes the 5’ nuclease activity of Taq polymerase to generate a fluorescent signal during PCR. For each SNP, the assay uses two TaqMan® probes that differ in sequence only at the SNP site, with one probe complementary to the wild-type allele and the other to the variant allele. The technique utilizes the FRET technology whereby a 5’ reporter dye and a 3’ quencher dye are covalently linked to the wild-type and variant allele probes.

The spa typing technique uses the sequence of a polymorphic VNTR in the 3' coding region of the S. aureus-specific staphylococcal protein A (spa). Each new base composition of the polymorphic repeat found in a strain is assigned a unique repeat code. The repeat succession for a given strain determines its spa type.

Multilocus sequence typing (MLST) is a technique whereby a number of housekeeping genes (loci) are sequenced, usually in part. In a typical MLST approach, recombination is expected to occur with a much higher frequency than point mutations. Therefore, one does not look at the total sequence similarity between strains. Instead, each sequence for a given locus is screened for identity with already known sequences for that locus. If the sequence is different, it is considered to be a new allele and is assigned a unique (arbitrary) allele number.

Inter-Simple Sequence Repeat Polymerase Chain Reaction (ISSR-PCR) is a reproducible and relatively inexpensive DNA fingerprinting method for animals, plants, fungi and bacteria. It is based on the amplification of genomic regions between microsatellite loci. Running this versatile typing method on an automated DNA sizing system such as the QIAxcel Advanced System reduces the number of manipulations required as well as the time to result. Raw data files from the QIAxcel Advanced System ScreenGel® software can be imported as densitometric curve files or peak table files in BIONUMERICS with the QIAxcel plugin.