Phenotype MicroArrays for Microbial Cells

A Breakthrough in Technology

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. 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.

Phenotype MicroArray technology enables researchers to evaluate nearly 2000 phenotypes of a microbial cell in a single experiment. Through comprehensive and precise quantitation of phenotypes, researchers are able to obtain an unbiased perspective of the effect on cells of genetic differences, environmental change, and exposure to drugs and chemicals. You can:

• Correlate genotypes with phenotypes

• Determine a cell's metabolic and chemical sensitivity properties

• Discover new targets for antimicrobial compounds

• Optimize cell lines and culture conditions in bioprocess development

• Characterize cell phenotypes for taxonomic or epidemiological studies

Important Applications of PM technology fall into three broad categories:

1. Testing Cell Lines Exposed to Drugs or Other Chemicals

2. Testing Cell Lines with Genetic Differences

3. Direct Testing of Cell Lines

Phenotype MicroArrays for Microbial Cells

Phenotype MicroArray Technology is now available for applications with nearly all important species of bacteria and fungi. Simple protocols are available for testing nearly 2000 cellular phenotypes simultaneously.

Uses with microbial cells

Determine gene functions

• Compare gene knock-out mutants to wild types

• Compare naturally-isolated strains with different genetic backgrounds

Identify novel antimicrobial targets by finding genes unique to pathogenic Micro Organisms

• Find phenotypes present in pathogenic but not in non-pathogenic strains

• Find phenotypes present in pathogenic microbes but not in host cells (animal or plant)

Test antimicrobial targets and drug leads by comparative phenotyping

• Determine MOA of drug leads

• Compare phenotypic changes caused by target gene knockout versus drug addition

Bioprocess improvement

• Compare and analyze different generations of production strains

• QC fingerprint production strains

• Scan 2000 culture conditions simultaneously to optimize the growth medium for product yield

General cell characterization

• Determine metabolic properties of any microbe

• Determine drug/chemical sensitivities

Available tests for microbial cells

To view the tests in the PM sets, click on the map links below.

PM-1 to PM-10:   Metabolic tests for bacteria and fungi

PM-11 to PM-20: Chemical sensitivity tests for bacteria

PM-21 to PM-25: Chemical sensitivity tests for fungi

Drug Discovery Using PMs

The Drug Discovery Process

PMs can be applied at multiple stages in the drug discovery process, providing researchers with better information to help make better decisions. With PMs the entire process becomes faster and more efficient.

The current drug discovery and development process is long and expensive. Just consider:

• Only one compound of 10,000 makes it to market

• It can take upwards of 15 years and $800 million to commercialize a single drug

The challenge for drug companies is three-fold: reduce product development costs… decrease time to market… and increase the probability of success for the most promising leads. Biolog's PM technology can assist with these three challenges — and more.

The genomic revolution has delivered massive amounts of data about life's molecular components, moving the bottleneck in drug discovery downstream by giving drug discovery organizations more qualified targets and leads than ever before. However, there remains a barrier in going from molecular data to understanding what really happens in living cells. PMs provide the needed technology to complement molecular genomics and cross that barrier (see diagram below).

Just as genomics and proteomics have made it possible to measure levels of sounds of genes and proteins all at once, Biolog's new PM technology can quantitatively measure thousands of cellular phenotypes in one analysis. This provides the technological transition over the barrier from molecular to cellular analysis.

Impact on the Drug Discovery Process

Continuing innovations in genomics and analytical technologies have made it particularly difficult for pharmaceutical and biotechnology organizations to determine the optimum approach to employ in the drug discovery process. Biolog has demonstrated that Phenotype MicroArray technology has the ability to deliver significant benefits at multiple stages in the drug discovery process:

Target Identification:

• Permits direct cellular assay of gene function

• Complements genetic and molecular methods and extends existing gene expression data

• Provides analysis of genetic mutations

Lead Validation:

• Identifies metabolic pathways and may include enzyme specific targeting

Lead Identification:

• Allows efficient evaluation of drug leads

Lead Optimization:

• Allows direct observation of a drug's primary and secondary effects at the cellular level

• Reduces need for expensive, slow animal / plant models

The result of using PM technology? More promising druggable leads and a reduction in failure rates. PMs help drug companies to choose the right drug leads for animal and human testing, saving time and money by lowering the opportunity cost associated with bad decisions.

Brochure on Using PM Technology in Drug Discovery

Click Here to view the document providing an overview of PM technology applied to drug discovery

Mechanism of Action (MOA) of Antimicrobials

Click Here to view the document on Using PM Technology in Antimicrobial MOA Studies

Structure Activity Relationship (SAR) Analysis

Click Here to view a document on Using PM Technology to Guide SAR Studies

How PM Technology Works

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.

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.

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).

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