Applied Spectral Imaging - Bringing the Details to Light

Allele: An alternative form of a given gene that occupies a corresponding position on each of our two chromosomes, one of which was inherited from each parent.

Amino Acid: Any of the 20 subunits that are the basic building blocks of proteins. The sequence of amino acids in a protein and, hence, the function of a protein are determined by the genetic code.

Base pair: The basic units of DNA, base pairs are chemical structures made up of the chemicals adenine, thymine, guanine and cytosine, which are designated by the letters A, T, G and C, respectively. Adenine always pairs with thymine and guanine always pairs with cytosine, creating the pairs or nucleotides in which genetic information is found. In RNA, uracil (U) substitutes for thymine.

Bioassay: Any procedure or test used to determine the nature, activity, location or retention of analytes in the body or system by direct (in vivo) measurement or by in vitro analysis of material excreted or otherwise removed from the body or system.

Bioinformatics: The science that uses advanced computing techniques for management and analysis of biological data. Bioinformatics is particularly important as an adjunct to genomic research, which generates a large amount of complex data, involving billions of individual DNA building blocks, and tens of thousands of genes.

Cell: The smallest structural unit of living organisms that is able to grow and reproduce independently. Basic unit of any living organism. It is a small, watery compartment filled with chemicals and a complete copy of the organism's genome.

Cell-based Assays: Any assay in which cells are used in conjunction with a test compound(s) or analyte(s). Cell-based assays are becoming increasingly important in high through-put screening (HTS). These assays allow for the ability to track the behavior of individual cells over time, and permit data gathering on functional behavior not available in any other kind of assay.

Chromosome: Composed of a long coiled strand of DNA covered with protein. Each individual has 23 pairs of human chromosomes and, therefore, a total of 46 chromosomes.

Coding region: The part of a gene that specifies the structure of a protein.

Codon: A sequence of three nucleotide bases that specifies an amino acid or represents a signal to stop or start a function.

Cytokines: A vast array of relatively low molecular weight, pharmacologically active proteins that are secreted by one cell for the purpose of altering either its own functions (autocrine effect) or those of adjacent cells (paracrine effect). Examples included the interleukins, TNF-a, etc.

Deconvolution: A mathematical technique for solutions of functions whose input includes their output; used to solve for the image elements in Applied Spectral Imaging's multiplexing technologies.

DNA (deoxyribonucleic acid): A double stranded molecule, called a double helix, which contains genetic instructions in the form of genes. The helix consists of a sugar-phosphate backbone with chemical bases that extend from the backbone. There are four different bases in DNA: adenine (A), thymine (T), guanine (G) and cytosine (C). The bases on one strand can only pair with a specific base on the other strand. A always pairs with T and G always pairs with C.

Evolution: In biological terms, a change in the genetic composition of a population over time.

Evolutionary Distance: In phylogenetic trees, the sum of the physical distance on a tree separating organisms. This distance is inversely proportional to evolutionary relatedness.

Exons: Segments of a gene on genomic DNA that contain the instructions for making a protein.

Gene: A unit of heredity that occupies a particular position on the DNA molecule in a chromosome; a segment of DNA containing all of the information necessary to make proteins.

Genetic Code: The sequence of nucleotides, coded in triplets (codons) along the messenger RNA (mRNA) molecule that determines the sequence of amino acids in a protein. The DNA sequence of a gene can be used to predict the mRNA sequence, and the genetic code can in turn be used to predict the amino acid sequence of a protein.

Genetic Map: The relative location of genes on a linear map of the DNA that is present in a chromosome.

Genetic Marker: Genomic information that is defined by measuring some inherited trait of an organism. The position of this genomic information can be mapped to a specific region on a chromosome by following the pattern of inheritance of this trait versus that of other inherited traits.

Genetic Testing: The analysis of an individual's genetic material. Among the purposes of genetic testing could be to gather information on an individual's genetic predisposition to particular health condition, or to confirm a diagnosis of genetic disease.

Genetics: The study of heredity: how biological information is transferred from one generation to the next as well as how that information is expressed within an organism.

Genome: The total genetic content of an organism, comprising genes and all other DNA sequences. Only about 4-5% of the human genome is estimated to constitute gene information. The function of the remaining DNA is unclear, but some of it is likely to have a role in maintaining the stability of the genome.

Genomic DNA: The basic chromosome set consisting of a species-specific number of linkage groups and the genes contained therein.

Genomics: The comprehensive analysis of all the genes of an organism.

Genotype: The genomic composition or specific sequence of nucleotides of an organism that is responsible for causing a specific trait or phenotype.

Haplotype: The nucleotides present at all of the known polymorphic sites in a gene; also a set of closely linked genes that are inherited together.

Human Genome Project: An ongoing, global research effort aimed at mapping and decoding the complete human genome.

Immunoassay: A process that measures and identifies a specific biological substance such as an antigen.

Inheritance: The passing on of genetic material from parents to offspring.

Informatics: Storing, manipulating, analyzing and visualizing information on a computer.

In silico: A process that is completed entirely by the use of a computer.

In vitro: Literally, "in glass." Performed in a test tube or other laboratory apparatus.

In vivo: In the living organism.

Interferometry: The branch of science devoted to the study and measurement of the interaction of waves, such as electromagnetic waves and acoustic waves. In the case of ASIs platform technology, interferometric techniques are to measure the intensity of light within a given sample. Many of these measurements together produce an interferogram that is then converted to a spectrum using Fourier Fast Transformation (FFT) algorithms.

Intron: The DNA base sequences that interrupt the protein-coding sequences of a gene on genomic DNA. These sequences are transcribed into RNA and are cut out of the messenger RNA (mRNA) before it is translated into a protein molecule.

Kinase: An enzyme that can transfer a phosphate from a high-energy phosphate such as ATP, to an organic molecule.

Linkage: The proximity of two or more genes on a chromosome. The closer together the genes are, the greater the probability that they will be inherited together or show linkage. Linkage Disequilibrium: A measure of the degree of association between two alleles in a population. Measures of linkage disequilibrium quantify how frequently two alleles are found on the same chromosome in a certain population.

Linkage Disequilibrium: A measure of the degree of association between two alleles in a population. Measures of linkage disequilibrium quantify how frequently two alleles are found on the same chromosome in a certain population.

Linkage Map: A map showing the relative positions of known genes on the chromosome. The distance between genes is measured in centimorgans (cM).

Linked Genes (linked markers): Genes and/or markers that are so closely associated on a chromosome that the allelic forms found on a chromosome are inherited together by a progeny at least 80% or more of the time.

Locus: The position of a gene on a chromosome.

Messenger RNA (mRNA): RNA that serves as a template for protein synthesis.

Microarray: An assay in which large numbers of 'test experiments' can be conducted on a single spot (in the case of ASIs multiplexing platform). Arrays are often manufactured on glass slides with a high density of test spots used to increase throughput and parallel processing of samples.

Microtiter Plate: A plate, often made of polystyrene, containing sample wells that is used for conducting assay testing. While plate size is generally fixed, well number (such as 96 and 384) may vary depending on assay needs.

Multiplexing: The ability to separate, identify, and quantitate multiple dyes/events in a single geographical location be it on a microarray, microtiter plater, cellular preparation (live or fixed), or any fixed assay platform.

Mutation: A permanent structural alteration in DNA that can be transmitted from one generation to the next. Changes in DNA either have no effect or cause harm. Occasionally a mutation can improve an organism's chance of surviving and passing the beneficial change on to its descendants.

Nucleotide: A subunit or base of DNA or RNA made up of adenine (A), guanine (G), thymine (T), or cytosine (C) for DNA; A, G, uracil (U), or C for RNA, along with a phosphate molecule, and a sugar molecule (deoxyribose in DNA and ribose in RNA). Thousands of nucleotides are linked together to form a DNA or RNA molecule.

Phenotype: A set of observable physical characteristics of an individual organism. A single characteristic can be referred to as a "trait," although a single trait is sometimes also called a phenotype. For example, blond hair could be called a trait or a phenotype, as could obesity. A phenotype can be the result of many factors, including an individual's genotype, environment, and lifestyle, and the interactions among these factors. The observed manifestation of a genotype, a phenotype may be expressed physically, biochemically, or physiologically.

Polymerase Chain Reaction (PCR): A method for creating millions of copies of a particular segment of DNA. If a scientist needs to detect the presence of a very small amount of a particular DNA sequence, PCR can be used to amplify the amount of that sequence until there are enough copies available to be detected.

Polymorphism: Differences in DNA sequences that occur naturally in a population. Single nucleotide substitutions, insertions and deletions of nucleotides and repetitive sequences (microsatellites) are all examples of polymorphism. The position at which such a sequence difference is found is a polymorphic site. A single nucleotide substitution is called a single nucleotide polymorphism or a SNP.

Population Genomics: The convergence of high-throughput analysis of genomic variation with population genetics to address the genomic basis of clinical variation.

Pharmacogenetics: The study of genetic factors that influence an organism's reaction to a drug. These genes include those that encode drug metabolizing enzymes, drug receptors and drug transporters.

Pharmacogenomics: The identification and analysis of genomic variations that will impact the efficacy of drugs or reveal different targets.

Phylogeny: The evolutionary history of a particular taxonomic group.

Protein: A large molecule composed of one or more chains of amino acids in a specific order; the order is determined by the base sequence of nucleotides in the gene coding for the protein. Proteins are required for the structure, function, and regulation of the body's cells, tissues, and organs, and each protein has unique functions. Examples are hormones, enzymes, and antibodies.

Proteomics: Proteomics has many definitions depending on the level of analysis. One definition of proteomics is the quantification of all proteins expressed at any individual time in a cell. Functional proteomics may be defined as the determination of the function of all the proteins encoded by an organism's entire genome. Structural proteomics is the determination of the structures of proteins, which may have multiple functions that can only be identified in the context of their interactions with other proteins, DNAs, small molecules, cofactors, etc.

RNA (ribonucleic acid): A single-stranded nucleic acid containing the bases adenine (A), cytosine (C), guanine (G) and uracil (U) and having an important role in protein synthesis and other chemical activities of the cell. There are several classes of RNA molecules, including messenger RNA, transfer RNA, ribosomal RNA, and other small RNAs, each serving a different function.

Single-to-noise Ratio: Often written S/N or SNR, is a measure of signal strength relative to background noise.

Single Nucleotide Polymorphism (SNP): Polymorphisms are differences in the genomic DNA sequences that naturally occur in a population. A single nucleotide substitution is called a single nucleotide polymorphism or a SNP.

SNP Map: A collection of SNPs that can be superimposed over the existing genome map, creating greater detail, and facilitating further genetic studies. (SNP consortium)

Spectral Imaging: The combination of spectrometry and CCD-imaging. CCD-imaging produces a finely detailed monochrome image of an object. Spectrometry measures the spectrum of selected areas on the object and then displays each spectrum as a separate graph. When the two technologies are combined, there is no separation between the image and the spectral information. The image itself contains the spectral information for each point in the image.

Spectrum: the complete range of the wavelengths of electromagnetic radiation, beginning with the longest radio waves (including those in the audio range) and extending through visible light (a very small part of the spectrum) all the way to the extremely short gamma rays that are a product of radioactive atoms. The visible spectrum resides between 400 Ð 700 nm.

Transition: A mutation from G to A or A to G (purine to purine) or C to T or T to C (pyrimidine to pyrimidine). In coding DNA, transitions are more likely to conserve the sequence of the resulting protein molecule.

Transversion: A mutation between A to C or C to A, G to T or T to G, A to T or T to A, G to C or C to G (purine to pyrimidine or pyrimidine to purine).

Waveform: The representation of a signal as a plot of amplitude versus time.

Wavelength: The distance between identical points in the adjacent cycles of a waveform signal propogated in space.

Contact:
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