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RFE Chemical Taxonomy

Characteristic Pattern and Chemotaxonomic Key for 1-D Gel Banding Patterns

In chemical taxonomic identification ("chemotaxonomy") the comparison of characteristic gel banding patterns from biochemical analyses are used to demonstrate species similarity (or non-similarity).

Summary: For each band in the gel pattern, the position distribution (and area distribution) based on same-specimen replicates constitutes a smart bin defining a characteristic peak. The multiplicity of characteristic peaks is that specimen's characteristic pattern. If that characteristic pattern matches the characteristic pattern of another specimen of the same species ("same species" determined via a reference method), and if the characteristic pattern does not match the characteristic pattern of a specimen from a legitimate different species, then the characteristic pattern of the first specimen may be identified by a chemotaxonomic key for that specimen. A chemotaxonomic key is the characteristic pattern or portion of the characteristic pattern for a species that discriminates that species from another species.

Full Definition and Terms: Depending on the experimental arrangement, an electrophoresis experiment in 1 dimension can generate a gel banding pattern of 2 or more bands. Through densitometry of this visual gel banding pattern, a numerical (digital) representation of the gel banding pattern can be formed. Each gel band is converted through densitometry and subsequent peak finding and integration into a densitometric peak. Each densitometric peak has a given position (relative to some landmark within the lane, such as the arbitrary start of the densitogram, or perhaps a well position (initial point of migration)). A pattern is defined as 2 or more (a "multiplicity of") peaks of given position and area (or height). The digital information of the peaks positions and areas (heights) is the digital pattern for a solitary lane's gel banding pattern from a solitary specimen.

Electrophoretic patterns from many "within-gel" and "between-gel" lanes of the same specimen will show electrophoretic variation on a peak-by-peak basis. The variation may have systematic components of change along the axis of migration and may have random components of change along the axis between lane replicates of the specimen. Migration position normalization uses internal standard peaks (in the same lane as the banding pattern) or external standard peaks (in an external lane) to adjust the gel banding patterns of a specimen relative to these standards. With or without migration position normalization, the like-peaks of a solitary specimen between lanes ("within-gel" and/or "between-gel") can be collected in a distribution of peak positions, areas, and heights for the specific like peaks for each band in the pattern. The practice of collecting like peaks in such a position-area distribution is called binning, and the process of binning can take on many forms:

  1. fixed-window binning on axis of migration
  2. variable-window binning on the axis of migration
  3. fixed-window binning-window on peak maximum
  4. variable-window binning-window on peak

With several specimen replicates and using variable-window binning, window on peak, the peak distribution per be peak can called a smart bin (because the peak's variation has been learned through replication) with an average and standard deviation associated with both position and area (or height). Other distributional values could be used (e.g. percentile values). In cases of extreme uncertainty in peak position, summed peak features may be created.

Each peak smart bin corresponding to a specimen gel banding pattern band, replicated, is a characteristic peak. The multiplicity of characteristic peaks is that specimen's characteristic pattern. If that characteristic pattern matches the characteristic pattern of another specimen of the same species ("same species" determined via a reference method), and if the characteristic pattern does not match the characteristic pattern of a specimen from a legitimate different species, then the characteristic pattern of the first specimen may be identified by a chemotaxonomic key for that specimen. A chemotaxonomic key is the characteristic pattern or portion of the characteristic pattern for a species that discriminates that species from another species.

These concepts may be applied to patterns from various types of electrophoretic analyses of prokaryotic and eukaryotic systems. The important point is replication of specimen patterns to account for components of electrophoretic variation to adjust for these components when declaring levels of match between two specimens of interest. The concepts may also be applied to capillary electrophoresis and chromatography using retention time (migration time) normalization and binning.