Advanced Phenotypic Analysis


Phenotype MicroArrays for Microbial Cells


How PM's Work

Phenotype MicroArrays (PMs) represent the third major technology, alongside DNA Microarrays and Proteomic Technologies, that is needed in the genomic era of research and drug development (Figure 1). Just as DNA Microarrays and Proteomic Technologies have made it possible to assay the level of thousands of genes or proteins all at once, Phenotype MicroArrays make it possible to quantitatively measure thousands of cellular phenotypes all at once. Many publications demonstrate the power of this technology in enabling new discoveries and in generating new hypothesis.

Figure 1

DNA Microarrays and Proteomic Technologies allow scientists to detect genes or proteins that are coregulated and whose patterns of change correlate with something important such as a disease state. However there is no assurance that these changes are really significant to the cell. Phenotype MicroArrays are a complementary technology providing the needed information at the cellular level ... and much more.

Phenotype MicroArrays provide comprehensive cellular profiles that can be used to identify gene function, validate drug targets, and streamline lead validation, optimization, and toxicology studies. After a genetic change or exposure to a drug lead, the researcher can directly evaluate the cellular response to that change.

Phenotype MicroArray technology is a breakthrough platform technology. It is an integrated system of cellular assays, instrumentation, and bioinformatic software for high-throughput screening (HTS) of cells.The technology and the testing process are shown Figure 2. Biolog preconfigures a wide range of phenotypic tests into sets of arrays. Each well of the array is designed to test a different phenotype. The scientist simply inoculates a standardized cell suspension into the wells of the MicroArray, thereby testing thousands of phenotypes at once. The MicroArray is then incubated, typically for 24 hours.

Figure 2
PMs use Biolog's patented redox chemistry, employing cell respiration as a universal reporter. If the phenotype is strongly "positive" in a well, the cells respire actively, reducing a tetrazolium dye and forming a strong color (Figure 2, left). If it is weakly positive or negative, respiration is slowed or stopped, and less color or no color is formed. The redox assay provides for both amplification and precise quantitation of phenotypes.Incubation and recording of phenotypic data is performed by the patented OmniLog instrument (Figure 2, middle) which captures a digital image of the MicroArray several times each hour and stores the quantitative color change values into computer files. The computer files can be displayed to the scientist in the form of kinetic graphs. Thousands of phenotypes are monitored simultaneously by the OmniLog and up to 450,000 data points can be generated in one 24-hour run. To compare the phenotypes of two cell lines, one is recorded as a red tracing and one as a green tracing (Figure 2, right). These graphs can then be overlaid by the bioinformatic software to detect differences. Areas of overlap (i.e. no change) are colored yellow, whereas differences are highlighted as patches of red or green (Figure 2, right and Figure 3).
Figure 3
Phenotype MicroArrays can monitor, either directly or indirectly, most known aspects of cell function. The range of phenotypes includes:
  • Cell surface structure and transport functions
  • Catabolism of carbon, nitrogen, phosphorus, and sulfur
  • Biosynthesis of small molecules
  • Synthesis and function of macromolecules and cellular machinery
  • Cellular respiratory functions
  • Stress and repair functions
  • Other cellular properties

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