The phenotype microarray approach is a technology for high-throughput phenotyping of cells. A phenotype microarray system enables one to monitor simultaneously the phenotypic reaction of cells to environmental challenges or exogenous compounds in a high-throughput manner. The phenotypic reactions are recorded as either end-point measurements or respiration kinetics similar to growth curves.

Usages

High-throughput phenotypic testing is increasingly important for exploring the biology of

bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...

fungi A fungus (plural, : fungi or funguses) is any member of the group of Eukaryote, eukaryotic organisms that includes microorganisms such as yeasts and Mold (fungus), molds, as well as the more familiar mushrooms. These organisms are classified ...

yeasts Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The first yeast originated hundreds of millions of years ago, and at least 1,500 species are currently recognized. They are estimated to constitut ...

, and animal cell lines such as human cancer cells. Just as

DNA microarrays A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to ...

and

proteomic Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In ...

technologies have made it possible to assay the expression level of thousands of genes or proteins all a once, phenotype microarrays (PMs) make it possible to quantitatively measure thousands of cellular phenotypes simultaneously. The approach also offers potential for testing gene function and improving genome annotation. In contrast to many of the hitherto available molecular high-throughput technologies, phenotypic testing is processed with living cells, thus providing comprehensive information about the performance of entire cells. The major applications of the PM technology are in the fields of

systems biology Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological syst ...

microbial A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...

cell physiology Cell physiology is the biological study of the activities that take place in a cell to keep it alive. The term ''physiology'' refers to normal functions in a living organism. Animal cells, plant cells and microorganism cells show similarities in ...

microbiology Microbiology () is the scientific study of microorganisms, those being unicellular (single cell), multicellular (cell colony), or acellular (lacking cells). Microbiology encompasses numerous sub-disciplines including virology, bacteriology, ...

, and

taxonomy Taxonomy is the practice and science of categorization or classification. A taxonomy (or taxonomical classification) is a scheme of classification, especially a hierarchical classification, in which things are organized into groups or types. ...

, and mammalian

including clinical research such as on

autism The autism spectrum, often referred to as just autism or in the context of a professional diagnosis autism spectrum disorder (ASD) or autism spectrum condition (ASC), is a neurodevelopmental condition (or conditions) characterized by difficulti ...

. Advantages of PMs over standard growth curves are that

cellular respiration Cellular respiration is the process by which biological fuels are oxidised in the presence of an inorganic electron acceptor such as oxygen to produce large amounts of energy, to drive the bulk production of ATP. Cellular respiration may be des ...

can be measured in environmental conditions where cellular replication (growth) may not be possible, and that it is more accurate than

optical density Absorbance is defined as "the logarithm of the ratio of incident to transmitted radiant power through a sample (excluding the effects on cell walls)". Alternatively, for samples which scatter light, absorbance may be defined as "the negative lo ...

, which can vary between different cellular morphologies. In addition, respiration reactions are usually detected much earlier than cellular growth.

Technology

A sole carbon source that can be transported into a cell and metabolized to produce

NADH Nicotinamide adenine dinucleotide (NAD) is a coenzyme central to metabolism. Found in all living cells, NAD is called a dinucleotide because it consists of two nucleotides joined through their phosphate groups. One nucleotide contains an aden ...

engenders a

redox potential Redox potential (also known as oxidation / reduction potential, ''ORP'', ''pe'', ''E_'', or E_) is a measure of the tendency of a chemical species to acquire electrons from or lose electrons to an electrode and thereby be reduced or oxidised respe ...

and flow of electrons to reduce a tetrazolium dye, such as tetrazolium violet, which produces a purple color. The more rapid this metabolic flow, the more quickly purple color forms. The formation of purple color is a positive reaction. interpreted such that the sole carbon source is used as an energy source. A microplate reader and incubation facility are needed to provide the appropriate incubation conditions, and to automatically read the intensity of colour formation during tetrazolium reduction in intervals of, e.g., 15 minutes. The principal idea of retrieving information about the abilities of an organism and its special modes of action when making use of certain energy sources can be equivalently applied to other macro-nutrients such as

nitrogen Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at seve ...

sulfur Sulfur (or sulphur in British English) is a chemical element with the symbol S and atomic number 16. It is abundant, multivalent and nonmetallic. Under normal conditions, sulfur atoms form cyclic octatomic molecules with a chemical formul ...

, or

phosphorus Phosphorus is a chemical element with the symbol P and atomic number 15. Elemental phosphorus exists in two major forms, white phosphorus and red phosphorus, but because it is highly reactive, phosphorus is never found as a free element on Ea ...

and their compounds and derivatives. As an extension, the impact of auxotrophic supplements or

antibiotics An antibiotic is a type of antimicrobial substance active against bacteria. It is the most important type of antibacterial agent for fighting bacterial infections, and antibiotic medications are widely used in the treatment and prevention ...

heavy metals upright=1.2, Crystals of lead.html" ;"title="osmium, a heavy metal nearly twice as dense as lead">osmium, a heavy metal nearly twice as dense as lead Heavy metals are generally defined as metals with relatively high density, densities, atomi ...

or other inhibitory compounds on the respiration behaviour of the cells can be determined.

Data structure

During a positive reaction, the longitudinal kinetics are expected to appear as sigmoidal curves in analogy to typical bacterial growth curves. Comparable to bacterial growth curves, the respiration kinetic curves may provide valuable information coded in the length of the lag phase λ, the respiration rate μ (corresponding to the steepness of the slope), the maximum cell respiration A (corresponding to the maximum value recorded), and the area under the curve (AUC). In contrast to bacterial growth curves, there is typically no death phase in PMs, as the reduced tetrazolium dye is insoluble.

Software

Proprietary and commercially available software is available that provides a solution for storage, retrieval, and analysis of high throughput phenotype data. A powerful

free and open source software Free and open-source software (FOSS) is a term used to refer to groups of software consisting of both free software and open-source software where anyone is freely licensed to use, copy, study, and change the software in any way, and the source ...

is the "opm" package based on R. "opm" contains tools for analyzing PM data including management, visualization and statistical analysis of PM data, covering curve-parameter estimation, dedicated and customizable plots, metadata management, statistical comparison with

genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...

and

pathway Pathway or pathways may refer to: Entertainment * ''The Pathway'' (novel), a 1914 work by Gertrude Page *''The Pathway'', a 2001 album by Officium Triste * ''Pathway'' (album), by the Flaming Stars * ''Pathways'' (album) (2010), by the Dave Hol ...

annotations, automatic generation of taxonomic reports, data

discretization In applied mathematics, discretization is the process of transferring continuous functions, models, variables, and equations into discrete counterparts. This process is usually carried out as a first step toward making them suitable for numeri ...

for

phylogenetic In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...

software and export in the

YAML YAML ( and ) (''see '') is a human-readable data-serialization language. It is commonly used for configuration files and in applications where data is being stored or transmitted. YAML targets many of the same communications applications as Ext ...

markup language. In conjunction with other R packages it was used to apply boosting to re-analyse autism PM data and detect more determining factors. The "opm" package has been developed and is maintained at the

Deutsche Sammlung von Mikroorganismen und Zellkulturen The Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH (German: ''Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH''), located in Braunschweig, is a research infrastructure in th ...

. Another

developed to analyze Phenotype Microarray data is "DuctApe", a

Unix Unix (; trademarked as UNIX) is a family of multitasking, multiuser computer operating systems that derive from the original AT&T Unix, whose development started in 1969 at the Bell Labs research center by Ken Thompson, Dennis Ritchie, a ...

command-line tool that also correlates

genomic Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...

data. Other software tools are PheMaDB, which provides a solution for storage, retrieval, and analysis of high throughput phenotype data, and the PMViewer software which focuses on graphical display but does not enable further statistical analysis. The latter is not publicly available.

References

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External links

PheMaDB website
Microbiology Physiology Phenomics